diff options
Diffstat (limited to 'silx/io')
-rw-r--r-- | silx/io/__init__.py | 9 | ||||
-rw-r--r-- | silx/io/commonh5.py | 53 | ||||
-rw-r--r-- | silx/io/configdict.py | 8 | ||||
-rw-r--r-- | silx/io/convert.py | 81 | ||||
-rw-r--r-- | silx/io/dictdump.py | 27 | ||||
-rw-r--r-- | silx/io/fabioh5.py | 336 | ||||
-rw-r--r-- | silx/io/nxdata.py | 669 | ||||
-rw-r--r-- | silx/io/specfile.c | 12792 | ||||
-rw-r--r-- | silx/io/specfile.pyx | 18 | ||||
-rw-r--r-- | silx/io/specfile/src/locale_management.c | 24 | ||||
-rw-r--r-- | silx/io/specfilewrapper.py | 4 | ||||
-rw-r--r-- | silx/io/spech5.py | 155 | ||||
-rw-r--r-- | silx/io/test/__init__.py | 4 | ||||
-rw-r--r-- | silx/io/test/test_dictdump.py | 25 | ||||
-rw-r--r-- | silx/io/test/test_fabioh5.py | 181 | ||||
-rw-r--r-- | silx/io/test/test_nxdata.py | 271 | ||||
-rw-r--r-- | silx/io/test/test_specfile.py | 32 | ||||
-rw-r--r-- | silx/io/test/test_specfilewrapper.py | 17 | ||||
-rw-r--r-- | silx/io/test/test_spech5.py | 72 | ||||
-rw-r--r-- | silx/io/test/test_spectoh5.py | 23 | ||||
-rw-r--r-- | silx/io/test/test_url.py | 209 | ||||
-rw-r--r-- | silx/io/test/test_utils.py | 221 | ||||
-rw-r--r-- | silx/io/url.py | 366 | ||||
-rw-r--r-- | silx/io/utils.py | 419 |
24 files changed, 7567 insertions, 8449 deletions
diff --git a/silx/io/__init__.py b/silx/io/__init__.py index 96f6708..5e736b5 100644 --- a/silx/io/__init__.py +++ b/silx/io/__init__.py @@ -26,7 +26,7 @@ __authors__ = ["P. Knobel"] __license__ = "MIT" -__date__ = "15/05/2017" +__date__ = "11/12/2017" from .utils import open # pylint:disable=redefined-builtin @@ -36,6 +36,11 @@ from .utils import is_dataset from .utils import is_file from .utils import is_group from .utils import is_softlink +from .utils import supported_extensions +from .utils import get_data # avoid to import open with "import *" -__all__ = ["save1D", "is_dataset", "is_file", "is_group", "is_softlink"] +__all = locals().keys() +__all = filter(lambda x: not x.startswith("_"), __all) +__all = filter(lambda x: x != "open", __all) +__all__ = list(__all) diff --git a/silx/io/commonh5.py b/silx/io/commonh5.py index 02c4181..4fbcd08 100644 --- a/silx/io/commonh5.py +++ b/silx/io/commonh5.py @@ -1,6 +1,6 @@ # coding: utf-8 # /*########################################################################## -# Copyright (C) 2016-2017 European Synchrotron Radiation Facility +# Copyright (C) 2016-2018 European Synchrotron Radiation Facility # # Permission is hereby granted, free of charge, to any person obtaining a copy # of this software and associated documentation files (the "Software"), to deal @@ -32,12 +32,13 @@ import collections import h5py import numpy from silx.third_party import six +import weakref from .utils import is_dataset __authors__ = ["V. Valls", "P. Knobel"] __license__ = "MIT" -__date__ = "02/10/2017" +__date__ = "11/10/2017" class _MappingProxyType(collections.MutableMapping): @@ -90,7 +91,7 @@ class Node(object): """ def __init__(self, name, parent=None, attrs=None): - self.__parent = parent + self._set_parent(parent) self.__basename = name self.__attrs = {} if attrs is not None: @@ -114,7 +115,25 @@ class Node(object): :rtype: Node """ - return self.__parent + if self.__parent is None: + parent = None + else: + parent = self.__parent() + if parent is None: + self.__parent = None + return parent + + def _set_parent(self, parent): + """Set the parent of this node. + + It do not update the parent object. + + :param Node parent: New parent for this node + """ + if parent is not None: + self.__parent = weakref.ref(parent) + else: + self.__parent = None @property def file(self): @@ -123,22 +142,13 @@ class Node(object): :rtype: Node """ node = self - while node.__parent is not None: - node = node.__parent + while node.parent is not None: + node = node.parent if isinstance(node, File): return node else: return None - def _set_parent(self, parent): - """Set the parent of this node. - - It do not update the parent object. - - :param Node parent: New parent for this node - """ - self.__parent = parent - @property def attrs(self): """Returns HDF5 attributes of this node. @@ -154,11 +164,12 @@ class Node(object): def name(self): """Returns the HDF5 name of this node. """ - if self.__parent is None: + parent = self.parent + if parent is None: return "/" - if self.__parent.name == "/": + if parent.name == "/": return "/" + self.basename - return self.__parent.name + "/" + self.basename + return parent.name + "/" + self.basename @property def basename(self): @@ -709,7 +720,7 @@ class Group(Node): def __getitem__(self, name): """Return a child from his name. - :param name str: name of a member or a path throug members using '/' + :param str name: name of a member or a path throug members using '/' separator. A '/' as a prefix access to the root item of the tree. :rtype: Node """ @@ -806,7 +817,7 @@ class Group(Node): See the documentation for `h5py.Group.visit` for more help. :param func: Callable (function, method or callable object) - :type func: function + :type func: callable """ origin_name = self.name return self._visit(func, origin_name, visit_links) @@ -816,7 +827,7 @@ class Group(Node): See the documentation for `h5py.Group.visititems` for more help. :param func: Callable (function, method or callable object) - :type func: function + :type func: callable :param bool visit_links: If *False*, ignore links. If *True*, call `func(name)` for links and recurse into target groups. """ diff --git a/silx/io/configdict.py b/silx/io/configdict.py index 21e24b7..2ba9755 100644 --- a/silx/io/configdict.py +++ b/silx/io/configdict.py @@ -1,5 +1,5 @@ # /*########################################################################## -# Copyright (C) 2004-2016 European Synchrotron Radiation Facility +# Copyright (C) 2004-2018 European Synchrotron Radiation Facility # # This file is part of the PyMca X-ray Fluorescence Toolkit developed at # the ESRF by the Software group. @@ -92,7 +92,7 @@ from collections import OrderedDict import numpy import re import sys -if sys.version < '3.0': +if sys.version_info < (3, ): import ConfigParser as configparser else: import configparser @@ -382,7 +382,7 @@ class ConfigDict(OrderedDict): dictionary :param sections: If not ``None``, add only the content of the specified sections - :type sections: list + :type sections: List """ filelist = self.__tolist(filelist) sections = self.__tolist(sections) @@ -475,7 +475,7 @@ class ConfigDict(OrderedDict): # Escape commas sstr = sstr.replace(",", "\,") - if sys.version > '3.0': + if sys.version_info >= (3, ): # Escape % characters except in "%%" and "%(" sstr = re.sub(r'%([^%\(])', r'%%\1', sstr) diff --git a/silx/io/convert.py b/silx/io/convert.py index 41f1e36..a2639e6 100644 --- a/silx/io/convert.py +++ b/silx/io/convert.py @@ -1,6 +1,6 @@ # coding: utf-8 # /*########################################################################## -# Copyright (C) 2016-2017 European Synchrotron Radiation Facility +# Copyright (C) 2016-2018 European Synchrotron Radiation Facility # # Permission is hereby granted, free of charge, to any person obtaining a copy # of this software and associated documentation files (the "Software"), to deal @@ -28,39 +28,39 @@ supported formats. Read the documentation of :mod:`silx.io.spech5` and :mod:`silx.io.fabioh5` for information on the structure of the output HDF5 files. -Strings are written to the HDF5 datasets as fixed-length ASCII (NumPy *S* type). -This is done in order to produce files that have maximum compatibility with -other HDF5 libraries, as recommended in the -`h5py documentation <http://docs.h5py.org/en/latest/strings.html#how-to-store-text-strings>`_. +Text strings are written to the HDF5 datasets as variable-length utf-8. -If you read the files back with *h5py* in Python 3, you will recover strings -as bytes, which you should decode to transform them into python strings:: +.. warning:: - >>> import h5py - >>> f = h5py.File("myfile.h5") - >>> f["/1.1/instrument/specfile/scan_header"][0] - b'#S 94 ascan del -0.5 0.5 20 1' - >>> f["/1.1/instrument/specfile/scan_header"][0].decode() - '#S 94 ascan del -0.5 0.5 20 1' + The output format for text strings changed in silx version 0.7.0. + Prior to that, text was output as fixed-length ASCII. + + To be on the safe side, when reading back a HDF5 file written with an + older version of silx, you can test for the presence of a *decode* + attribute. To ensure that you always work with unicode text:: + + >>> import h5py + >>> h5f = h5py.File("my_scans.h5", "r") + >>> title = h5f["/68.1/title"] + >>> if hasattr(title, "decode"): + ... title = title.decode() -Arrays of strings, such as file and scan headers, are stored as fixed-length -strings. The length of all strings in an array is equal to the length of the -longest string. Shorter strings are right-padded with blank spaces. .. note:: This module has a dependency on the `h5py <http://www.h5py.org/>`_ library, which is not a mandatory dependency for `silx`. You might need to install it if you don't already have it. """ -import numpy import logging +import numpy import silx.io from silx.io import is_dataset, is_group, is_softlink +from silx.third_party import six __authors__ = ["P. Knobel"] __license__ = "MIT" -__date__ = "14/09/2017" +__date__ = "12/02/2018" _logger = logging.getLogger(__name__) @@ -92,7 +92,7 @@ def _create_link(h5f, link_name, target_name, target_name) del h5f[link_name] else: - _logger.warn(link_name + " already exist. Can't create link to " + + _logger.warn(link_name + " already exist. Cannot create link to " + target_name) return None @@ -104,6 +104,23 @@ def _create_link(h5f, link_name, target_name, raise ValueError("link_type must be 'hard' or 'soft'") +def _attr_utf8(attr_value): + """If attr_value is bytes, make sure we output utf-8 + + :param attr_value: String (possibly bytes if PY2) + :return: Attr ready to be written by h5py as utf8 + """ + if isinstance(attr_value, six.binary_type) or \ + isinstance(attr_value, six.text_type): + out_attr_value = numpy.array( + attr_value, + dtype=h5py.special_dtype(vlen=six.text_type)) + else: + out_attr_value = attr_value + + return out_attr_value + + class Hdf5Writer(object): """Converter class to write the content of a data file to a HDF5 file. """ @@ -168,7 +185,7 @@ class Hdf5Writer(object): for key in infile.attrs: if self.overwrite_data or key not in root_grp.attrs: root_grp.attrs.create(key, - numpy.string_(infile.attrs[key])) + _attr_utf8(infile.attrs[key])) # Handle links at the end, when their targets are created for link_name, target_name in self._links: @@ -208,10 +225,11 @@ class Hdf5Writer(object): # add HDF5 attributes for key in obj.attrs: if self.overwrite_data or key not in ds.attrs: - ds.attrs.create(key, numpy.string_(obj.attrs[key])) + ds.attrs.create(key, + _attr_utf8(obj.attrs[key])) if not self.overwrite_data and member_initially_exists: - _logger.warn("Ignoring existing dataset: " + h5_name) + _logger.warn("Not overwriting existing dataset: " + h5_name) elif is_group(obj): if h5_name not in self._h5f: @@ -223,7 +241,14 @@ class Hdf5Writer(object): # add HDF5 attributes for key in obj.attrs: if self.overwrite_data or key not in grp.attrs: - grp.attrs.create(key, numpy.string_(obj.attrs[key])) + grp.attrs.create(key, + _attr_utf8(obj.attrs[key])) + + +def _is_commonh5_group(grp): + """Return True if grp is a commonh5 group. + (h5py.Group objects are not commonh5 groups)""" + return is_group(grp) and not isinstance(grp, h5py.Group) def write_to_h5(infile, h5file, h5path='/', mode="a", @@ -232,7 +257,7 @@ def write_to_h5(infile, h5file, h5path='/', mode="a", """Write content of a h5py-like object into a HDF5 file. :param infile: Path of input file, or :class:`commonh5.File` object - or :class:`commonh5.Group` object + or :class:`commonh5.Group` object. :param h5file: Path of output HDF5 file or HDF5 file handle (`h5py.File` object) :param str h5path: Target path in HDF5 file in which scan groups are created. @@ -264,15 +289,23 @@ def write_to_h5(infile, h5file, h5path='/', mode="a", # both infile and h5file can be either file handle or a file name: 4 cases if not isinstance(h5file, h5py.File) and not is_group(infile): with silx.io.open(infile) as h5pylike: + if not _is_commonh5_group(h5pylike): + raise IOError("Cannot convert HDF5 file %s to HDF5" % infile) with h5py.File(h5file, mode) as h5f: writer.write(h5pylike, h5f) elif isinstance(h5file, h5py.File) and not is_group(infile): with silx.io.open(infile) as h5pylike: + if not _is_commonh5_group(h5pylike): + raise IOError("Cannot convert HDF5 file %s to HDF5" % infile) writer.write(h5pylike, h5file) elif is_group(infile) and not isinstance(h5file, h5py.File): + if not _is_commonh5_group(infile): + raise IOError("Cannot convert HDF5 file %s to HDF5" % infile.file.name) with h5py.File(h5file, mode) as h5f: writer.write(infile, h5f) else: + if not _is_commonh5_group(infile): + raise IOError("Cannot convert HDF5 file %s to HDF5" % infile.file.name) writer.write(infile, h5file) diff --git a/silx/io/dictdump.py b/silx/io/dictdump.py index 1860b7f..1857cdb 100644 --- a/silx/io/dictdump.py +++ b/silx/io/dictdump.py @@ -1,6 +1,6 @@ # coding: utf-8 # /*########################################################################## -# Copyright (C) 2016-2017 European Synchrotron Radiation Facility +# Copyright (C) 2016-2018 European Synchrotron Radiation Facility # # Permission is hereby granted, free of charge, to any person obtaining a copy # of this software and associated documentation files (the "Software"), to deal @@ -225,6 +225,13 @@ def dicttoh5(treedict, h5file, h5path='/', elif treedict[key] is None or (isinstance(treedict[key], dict) and not len(treedict[key])): + if (h5path + key) in h5f: + if overwrite_data is True: + del h5f[h5path + key] + else: + logger.warning('key (%s) already exists. ' + 'Not overwriting.' % (h5path + key)) + continue # Create empty group h5f.create_group(h5path + key) @@ -232,9 +239,25 @@ def dicttoh5(treedict, h5file, h5path='/', ds = _prepare_hdf5_dataset(treedict[key]) # can't apply filters on scalars (datasets with shape == () ) if ds.shape == () or create_dataset_args is None: + if h5path + key in h5f: + if overwrite_data is True: + del h5f[h5path + key] + else: + logger.warning('key (%s) already exists. ' + 'Not overwriting.' % (h5path + key)) + continue + h5f.create_dataset(h5path + key, data=ds) else: + if h5path + key in h5f: + if overwrite_data is True: + del h5f[h5path + key] + else: + logger.warning('key (%s) already exists. ' + 'Not overwriting.' % (h5path + key)) + continue + h5f.create_dataset(h5path + key, data=ds, **create_dataset_args) @@ -283,7 +306,7 @@ def h5todict(h5file, path="/", exclude_names=None): fabioh5 file. :param str path: Name of HDF5 group to use as dictionary root level, to read only a sub-group in the file - :param list[str] exclude_names: Groups and datasets whose name contains + :param List[str] exclude_names: Groups and datasets whose name contains a string in this list will be ignored. Default is None (ignore nothing) :return: Nested dictionary """ diff --git a/silx/io/fabioh5.py b/silx/io/fabioh5.py index 2cee032..95eef23 100644 --- a/silx/io/fabioh5.py +++ b/silx/io/fabioh5.py @@ -1,6 +1,6 @@ # coding: utf-8 # /*########################################################################## -# Copyright (C) 2016-2017 European Synchrotron Radiation Facility +# Copyright (C) 2016-2018 European Synchrotron Radiation Facility # # Permission is hereby granted, free of charge, to any person obtaining a copy # of this software and associated documentation files (the "Software"), to deal @@ -36,8 +36,9 @@ import collections import datetime import logging import numbers +import os -import fabio +import fabio.file_series import numpy from . import commonh5 @@ -53,15 +54,60 @@ except ImportError as e: _logger = logging.getLogger(__name__) +_fabio_extensions = set([]) + + +def supported_extensions(): + """Returns all extensions supported by fabio. + + :returns: A set containing extensions like "*.edf". + :rtype: Set[str] + """ + global _fabio_extensions + if len(_fabio_extensions) > 0: + return _fabio_extensions + + formats = fabio.fabioformats.get_classes(reader=True) + all_extensions = set([]) + + for reader in formats: + if not hasattr(reader, "DEFAULT_EXTENSIONS"): + continue + + ext = reader.DEFAULT_EXTENSIONS + ext = ["*.%s" % e for e in ext] + all_extensions.update(ext) + + _fabio_extensions = set(all_extensions) + return _fabio_extensions + + +class _FileSeries(fabio.file_series.file_series): + """ + .. note:: Overwrite a function to fix an issue in fabio. + """ + def jump(self, num): + """ + Goto a position in sequence + """ + assert num < len(self) and num >= 0, "num out of range" + self._current = num + return self[self._current] + + class FrameData(commonh5.LazyLoadableDataset): """Expose a cube of image from a Fabio file using `FabioReader` as cache.""" def __init__(self, name, fabio_reader, parent=None): - attrs = {"interpretation": "image"} + if fabio_reader.is_spectrum(): + attrs = {"interpretation": "spectrum"} + else: + attrs = {"interpretation": "image"} commonh5.LazyLoadableDataset.__init__(self, name, parent, attrs=attrs) self.__fabio_reader = fabio_reader + def _create_data(self): return self.__fabio_reader.get_data() @@ -69,20 +115,17 @@ class FrameData(commonh5.LazyLoadableDataset): class RawHeaderData(commonh5.LazyLoadableDataset): """Lazy loadable raw header""" - def __init__(self, name, fabio_file, parent=None): + def __init__(self, name, fabio_reader, parent=None): commonh5.LazyLoadableDataset.__init__(self, name, parent) - self.__fabio_file = fabio_file + self.__fabio_reader = fabio_reader def _create_data(self): """Initialize hold data by merging all headers of each frames. """ headers = [] types = set([]) - for frame in range(self.__fabio_file.nframes): - if self.__fabio_file.nframes == 1: - header = self.__fabio_file.header - else: - header = self.__fabio_file.getframe(frame).header + for fabio_frame in self.__fabio_reader.iter_frames(): + header = fabio_frame.header data = [] for key, value in header.items(): @@ -239,19 +282,100 @@ class FabioReader(object): COUNTER = 1 POSITIONER = 2 - def __init__(self, fabio_file): - self.__fabio_file = fabio_file + def __init__(self, file_name=None, fabio_image=None, file_series=None): + """ + Constructor + + :param str file_name: File name of the image file to read + :param fabio.fabioimage.FabioImage fabio_image: An already openned + :class:`fabio.fabioimage.FabioImage` instance. + :param Union[list[str],fabio.file_series.file_series] file_series: An + list of file name or a :class:`fabio.file_series.file_series` + instance + """ + self.__at_least_32bits = False + self.__signed_type = False + + self.__load(file_name, fabio_image, file_series) self.__counters = {} self.__positioners = {} self.__measurements = {} self.__key_filters = set([]) self.__data = None - self.__frame_count = self.__fabio_file.nframes - self._read(self.__fabio_file) + self.__frame_count = self.frame_count() + self._read() + + def __load(self, file_name=None, fabio_image=None, file_series=None): + if file_name is not None and fabio_image: + raise TypeError("Parameters file_name and fabio_image are mutually exclusive.") + if file_name is not None and fabio_image: + raise TypeError("Parameters fabio_image and file_series are mutually exclusive.") + + self.__must_be_closed = False + + if file_name is not None: + self.__fabio_file = fabio.open(file_name) + self.__must_be_closed = True + elif fabio_image is not None: + if isinstance(fabio_image, fabio.fabioimage.FabioImage): + self.__fabio_file = fabio_image + else: + raise TypeError("FabioImage expected but %s found.", fabio_image.__class__) + elif file_series is not None: + if isinstance(file_series, list): + self.__fabio_file = _FileSeries(file_series) + elif isinstance(file_series, fabio.file_series.file_series): + self.__fabio_file = file_series + else: + raise TypeError("file_series or list expected but %s found.", file_series.__class__) + + def close(self): + """Close the object, and free up associated resources. + + The associated FabioImage is closed only if the object was created from + a filename by this class itself. + + After calling this method, attempts to use the object (and children) + may fail. + """ + if self.__must_be_closed: + # It looks like there is no close on FabioImage + # self.__fabio_image.close() + pass + self.__fabio_image = None def fabio_file(self): return self.__fabio_file + def frame_count(self): + """Returns the number of frames available.""" + if isinstance(self.__fabio_file, fabio.file_series.file_series): + return len(self.__fabio_file) + elif isinstance(self.__fabio_file, fabio.fabioimage.FabioImage): + return self.__fabio_file.nframes + else: + raise TypeError("Unsupported type %s", self.__fabio_file.__class__) + + def iter_frames(self): + """Iter all the available frames. + + A frame provides at least `data` and `header` attributes. + """ + if isinstance(self.__fabio_file, fabio.file_series.file_series): + for file_number in range(len(self.__fabio_file)): + with self.__fabio_file.jump_image(file_number) as fabio_image: + # return the first frame only + assert(fabio_image.nframes == 1) + yield fabio_image + elif isinstance(self.__fabio_file, fabio.fabioimage.FabioImage): + for frame_count in range(self.__fabio_file.nframes): + if self.__fabio_file.nframes == 1: + yield self.__fabio_file + else: + yield self.__fabio_file.getframe(frame_count) + else: + raise TypeError("Unsupported type %s", self.__fabio_file.__class__) + def _create_data(self): """Initialize hold data by merging all frames into a single cube. @@ -261,12 +385,8 @@ class FabioReader(object): The computation is cached into the class, and only done ones. """ images = [] - for frame in range(self.__fabio_file.nframes): - if self.__fabio_file.nframes == 1: - image = self.__fabio_file.data - else: - image = self.__fabio_file.getframe(frame).data - images.append(image) + for fabio_frame in self.iter_frames(): + images.append(fabio_frame.data) # returns the data without extra dim in case of single frame if len(images) == 1: @@ -329,8 +449,15 @@ class FabioReader(object): """ value = self.__get_dict(kind)[name] if not isinstance(value, numpy.ndarray): + if kind in [self.COUNTER, self.POSITIONER]: + # Force normalization for counters and positioners + old = self._set_vector_normalization(at_least_32bits=True, signed_type=True) + else: + old = None value = self._convert_metadata_vector(value) self.__get_dict(kind)[name] = value + if old is not None: + self._set_vector_normalization(*old) return value def _set_counter_value(self, frame_id, name, value): @@ -351,22 +478,25 @@ class FabioReader(object): self.__measurements[name] = [None] * self.__frame_count self.__measurements[name][frame_id] = value - def _read(self, fabio_file): - """Read all metadata from the fabio file and store it into this - object.""" - + def _enable_key_filters(self, fabio_file): self.__key_filters.clear() if hasattr(fabio_file, "RESERVED_HEADER_KEYS"): # Provided in fabio 0.5 for key in fabio_file.RESERVED_HEADER_KEYS: self.__key_filters.add(key.lower()) - for frame in range(fabio_file.nframes): - if fabio_file.nframes == 1: - header = fabio_file.header - else: - header = fabio_file.getframe(frame).header - self._read_frame(frame, header) + def _read(self): + """Read all metadata from the fabio file and store it into this + object.""" + + file_series = isinstance(self.__fabio_file, fabio.file_series.file_series) + if not file_series: + self._enable_key_filters(self.__fabio_file) + + for frame_id, fabio_frame in enumerate(self.iter_frames()): + if file_series: + self._enable_key_filters(fabio_frame) + self._read_frame(frame_id, fabio_frame.header) def _is_filtered_key(self, key): """ @@ -390,6 +520,29 @@ class FabioReader(object): """Read a key from the metadata and cache it into this object.""" self._set_measurement_value(frame_id, name, value) + def _set_vector_normalization(self, at_least_32bits, signed_type): + previous = self.__at_least_32bits, self.__signed_type + self.__at_least_32bits = at_least_32bits + self.__signed_type = signed_type + return previous + + def _normalize_vector_type(self, dtype): + """Normalize the """ + if self.__at_least_32bits: + if numpy.issubdtype(dtype, numpy.signedinteger): + dtype = numpy.result_type(dtype, numpy.uint32) + if numpy.issubdtype(dtype, numpy.unsignedinteger): + dtype = numpy.result_type(dtype, numpy.uint32) + elif numpy.issubdtype(dtype, numpy.floating): + dtype = numpy.result_type(dtype, numpy.float32) + elif numpy.issubdtype(dtype, numpy.complexfloating): + dtype = numpy.result_type(dtype, numpy.complex64) + if self.__signed_type: + if numpy.issubdtype(dtype, numpy.unsignedinteger): + signed = numpy.dtype("%s%i" % ('i', dtype.itemsize)) + dtype = numpy.result_type(dtype, signed) + return dtype + def _convert_metadata_vector(self, values): """Convert a list of numpy data into a numpy array with the better fitting type.""" @@ -420,6 +573,8 @@ class FabioReader(object): else: result = converted + result_type = self._normalize_vector_type(result_type) + if has_none: # Fix missing data according to the array type if result_type.kind == "S": @@ -550,6 +705,14 @@ class FabioReader(object): """ return False + def is_spectrum(self): + """Returns true if the data should be interpreted as + MCA data. + + :rtype: bool + """ + return False + class EdfFabioReader(FabioReader): """Class which read and cache data and metadata from a fabio image. @@ -558,8 +721,8 @@ class EdfFabioReader(FabioReader): motor_mne are parsed using a special way. """ - def __init__(self, fabio_file): - FabioReader.__init__(self, fabio_file) + def __init__(self, file_name=None, fabio_image=None, file_series=None): + FabioReader.__init__(self, file_name, fabio_image, file_series) self.__unit_cell_abc = None self.__unit_cell_alphabetagamma = None self.__ub_matrix = None @@ -622,17 +785,26 @@ class EdfFabioReader(FabioReader): else: raise Exception("State unexpected (base_key: %s)" % base_key) + def _get_first_header(self): + """ + ..note:: This function can be cached + """ + fabio_file = self.fabio_file() + if isinstance(fabio_file, fabio.file_series.file_series): + return fabio_file.jump_image(0).header + return fabio_file.header + def has_ub_matrix(self): """Returns true if a UB matrix is available. :rtype: bool """ - header = self.fabio_file().header + header = self._get_first_header() expected_keys = set(["UB_mne", "UB_pos", "sample_mne", "sample_pos"]) return expected_keys.issubset(header) def parse_ub_matrix(self): - header = self.fabio_file().header + header = self._get_first_header() ub_data = self._get_mnemonic_key("UB", header) s_data = self._get_mnemonic_key("sample", header) if len(ub_data) > 9: @@ -685,31 +857,52 @@ class EdfFabioReader(FabioReader): self.parse_ub_matrix() return self.__ub_matrix + def is_spectrum(self): + """Returns true if the data should be interpreted as + MCA data. + EDF files or file series, with two or more header names starting with + "MCA", should be interpreted as MCA data. + + :rtype: bool + """ + count = 0 + for key in self._get_first_header(): + if key.lower().startswith("mca"): + count += 1 + if count >= 2: + return True + return False + class File(commonh5.File): """Class which handle a fabio image as a mimick of a h5py.File. """ - def __init__(self, file_name=None, fabio_image=None): - self.__must_be_closed = False - if file_name is not None and fabio_image is not None: - raise TypeError("Parameters file_name and fabio_image are mutually exclusive.") - if file_name is not None: - self.__fabio_image = fabio.open(file_name) - self.__must_be_closed = True - elif fabio_image is not None: - self.__fabio_image = fabio_image - file_name = self.__fabio_image.filename + def __init__(self, file_name=None, fabio_image=None, file_series=None): + """ + Constructor + + :param str file_name: File name of the image file to read + :param fabio.fabioimage.FabioImage fabio_image: An already openned + :class:`fabio.fabioimage.FabioImage` instance. + :param Union[list[str],fabio.file_series.file_series] file_series: An + list of file name or a :class:`fabio.file_series.file_series` + instance + """ + self.__fabio_reader = self.create_fabio_reader(file_name, fabio_image, file_series) + if fabio_image is not None: + file_name = fabio_image.filename + attrs = {"NX_class": "NXroot", "file_time": datetime.datetime.now().isoformat(), - "file_name": file_name, "creator": "silx %s" % silx_version} + if file_name is not None: + attrs["file_name"] = file_name commonh5.File.__init__(self, name=file_name, attrs=attrs) - self.__fabio_reader = self.create_fabio_reader(self.__fabio_image) - scan = self.create_scan_group(self.__fabio_image, self.__fabio_reader) + scan = self.create_scan_group(self.__fabio_reader) self.add_node(scan) - def create_scan_group(self, fabio_image, fabio_reader): + def create_scan_group(self, fabio_reader): """Factory to create the scan group. :param FabioImage fabio_image: A Fabio image @@ -722,7 +915,7 @@ class File(commonh5.File): measurement = MeasurementGroup("measurement", fabio_reader, attrs={"NX_class": "NXcollection"}) file_ = commonh5.Group("file", attrs={"NX_class": "NXcollection"}) positioners = MetadataGroup("positioners", fabio_reader, FabioReader.POSITIONER, attrs={"NX_class": "NXpositioner"}) - raw_header = RawHeaderData("scan_header", fabio_image, self) + raw_header = RawHeaderData("scan_header", fabio_reader, self) detector = DetectorGroup("detector_0", fabio_reader) scan.add_node(instrument) @@ -738,26 +931,43 @@ class File(commonh5.File): return scan - def create_fabio_reader(self, fabio_file): + def create_fabio_reader(self, file_name, fabio_image, file_series): """Factory to create fabio reader. :rtype: FabioReader""" - if isinstance(fabio_file, fabio.edfimage.EdfImage): - metadata = EdfFabioReader(fabio_file) + use_edf_reader = False + first_file_name = None + first_image = None + + if isinstance(file_series, list): + first_file_name = file_series[0] + elif isinstance(file_series, fabio.file_series.file_series): + first_image = file_series.first_image() + elif fabio_image is not None: + first_image = fabio_image + else: + first_file_name = file_name + + if first_file_name is not None: + _, ext = os.path.splitext(first_file_name) + ext = ext[1:] + use_edf_reader = ext in fabio.edfimage.EdfImage.DEFAULT_EXTENSIONS + elif first_image is not None: + use_edf_reader = isinstance(first_image, fabio.edfimage.EdfImage) + else: + assert(False) + + if use_edf_reader: + reader = EdfFabioReader(file_name, fabio_image, file_series) else: - metadata = FabioReader(fabio_file) - return metadata + reader = FabioReader(file_name, fabio_image, file_series) + return reader def close(self): """Close the object, and free up associated resources. - The associated FabioImage is closed anyway the object was created from - a filename or from a FabioImage. - - After calling this method, attempts to use the object may fail. + After calling this method, attempts to use the object (and children) + may fail. """ - if self.__must_be_closed: - # It looks like there is no close on FabioImage - # self.__fabio_image.close() - pass - self.__fabio_image = None + self.__fabio_reader.close() + self.__fabio_reader = None diff --git a/silx/io/nxdata.py b/silx/io/nxdata.py index 977721f..cc153b0 100644 --- a/silx/io/nxdata.py +++ b/silx/io/nxdata.py @@ -1,7 +1,7 @@ # coding: utf-8 # /*########################################################################## # -# Copyright (c) 2017 European Synchrotron Radiation Facility +# Copyright (c) 2017-2018 European Synchrotron Radiation Facility # # Permission is hereby granted, free of charge, to any person obtaining a copy # of this software and associated documentation files (the "Software"), to deal @@ -29,30 +29,47 @@ See http://download.nexusformat.org/sphinx/classes/base_classes/NXdata.html """ import logging +import os +import os.path import numpy -from .utils import is_dataset, is_group +from .utils import is_dataset, is_group, is_file from silx.third_party import six +try: + import h5py +except ImportError: + h5py = None + +__authors__ = ["P. Knobel"] +__license__ = "MIT" +__date__ = "12/02/2018" + _logger = logging.getLogger(__name__) _INTERPDIM = {"scalar": 0, "spectrum": 1, "image": 2, - # "rgba-image": 3, "hsla-image": 3, "cmyk-image": 3, # TODO + "rgba-image": 3, # "hsla-image": 3, "cmyk-image": 3, # TODO "vertex": 1} # 3D scatter: 1D signal + 3 axes (x, y, z) of same legth """Number of signal dimensions associated to each possible @interpretation attribute. """ -def _nxdata_warning(msg): +def _nxdata_warning(msg, group_name=""): """Log a warning message prefixed with *"NXdata warning: "* :param str msg: Warning message + :param str group_name: Name of NXdata group this warning relates to """ - _logger.warning("NXdata warning: " + msg) + warning_prefix = "NXdata warning" + if group_name: + warning_prefix += " (group %s): " % group_name + else: + warning_prefix += ": " + _logger.warning(warning_prefix + msg) def get_attr_as_string(item, attr_name, default=None): @@ -64,16 +81,26 @@ def get_attr_as_string(item, attr_name, default=None): :param item: Group or dataset :param attr_name: Attribute name + :param default: Value to be returned if attribute is not found. :return: item.attrs[attr_name] """ attr = item.attrs.get(attr_name, default) if six.PY2: - return attr + if isinstance(attr, six.text_type): + # unicode + return attr.encode("utf-8") + else: + return attr if six.PY3: if hasattr(attr, "decode"): # byte-string return attr.decode("utf-8") - elif isinstance(attr, numpy.ndarray) and hasattr(attr[0], "decode"): + elif isinstance(attr, numpy.ndarray) and not attr.shape and\ + hasattr(attr[()], "decode"): + # byte string as ndarray scalar + return attr[()].decode("utf-8") + elif isinstance(attr, numpy.ndarray) and len(attr.shape) and\ + hasattr(attr[0], "decode"): # array of byte-strings return [element.decode("utf-8") for element in attr] else: @@ -92,7 +119,7 @@ def is_valid_nxdata(group): # noqa :param group: h5py-like group :return: True if this NXdata group is valid. - :raise: TypeError if group is not a h5py group, a spech5 group, + :raise TypeError: if group is not a h5py group, a spech5 group, or a fabioh5 group """ if not is_group(group): @@ -100,28 +127,60 @@ def is_valid_nxdata(group): # noqa if get_attr_as_string(group, "NX_class") != "NXdata": return False if "signal" not in group.attrs: - _logger.warning("NXdata group does not define a signal attr.") - return False + _logger.info("NXdata group %s does not define a signal attr. " + "Testing legacy specification.", group.name) + signal_name = None + for key in group: + if "signal" in group[key].attrs: + signal_name = key + signal_attr = group[key].attrs["signal"] + if signal_attr in [1, b"1", u"1"]: + # This is the main (default) signal + break + if signal_name is None: + _nxdata_warning("No @signal attribute on the NXdata group, " + "and no dataset with a @signal=1 attr found", + group.name) + return False + else: + signal_name = get_attr_as_string(group, "signal") - signal_name = get_attr_as_string(group, "signal") if signal_name not in group or not is_dataset(group[signal_name]): - _logger.warning( - "Cannot find signal dataset '%s' in NXdata group" % signal_name) + _nxdata_warning( + "Cannot find signal dataset '%s'" % signal_name, + group.name) return False + auxiliary_signals_names = get_attr_as_string(group, "auxiliary_signals", + default=[]) + if isinstance(auxiliary_signals_names, (six.text_type, six.binary_type)): + auxiliary_signals_names = [auxiliary_signals_names] + for asn in auxiliary_signals_names: + if asn not in group or not is_dataset(group[asn]): + _nxdata_warning( + "Cannot find auxiliary signal dataset '%s'" % asn, + group.name) + return False + if group[signal_name].shape != group[asn].shape: + _nxdata_warning("Auxiliary signal dataset '%s' does not" % asn + + " have the same shape as the main signal.", + group.name) + return False + ndim = len(group[signal_name].shape) if "axes" in group.attrs: axes_names = get_attr_as_string(group, "axes") - if isinstance(axes_names, str): + if isinstance(axes_names, (six.text_type, six.binary_type)): axes_names = [axes_names] if 1 < ndim < len(axes_names): - # ndim = 1 and several axes could be a scatter + # ndim = 1 with several axes could be a scatter _nxdata_warning( "More @axes defined than there are " + "signal dimensions: " + - "%d axes, %d dimensions." % (len(axes_names), ndim)) + "%d axes, %d dimensions." % (len(axes_names), ndim), + group.name) return False # case of less axes than dimensions: number of axes must match @@ -132,18 +191,33 @@ def is_valid_nxdata(group): # noqa interpretation = get_attr_as_string(group, "interpretation") if interpretation is None: _nxdata_warning("No @interpretation and not enough" + - " @axes defined.") + " @axes defined.", group.name) return False if interpretation not in _INTERPDIM: _nxdata_warning("Unrecognized @interpretation=" + interpretation + - " for data with wrong number of defined @axes.") + " for data with wrong number of defined @axes.", + group.name) return False + if interpretation == "rgba-image": + if ndim != 3 or group[signal_name].shape[-1] not in [3, 4]: + _nxdata_warning( + "Inconsistent RGBA Image. Expected 3 dimensions with " + + "last one of length 3 or 4. Got ndim=%d " % ndim + + "with last dimension of length %d." % group[signal_name].shape[-1], + group.name) + return False + if len(axes_names) != 2: + _nxdata_warning( + "Inconsistent number of axes for RGBA Image. Expected " + "3, but got %d." % ndim, group.name) + return False - if len(axes_names) != _INTERPDIM[interpretation]: + elif len(axes_names) != _INTERPDIM[interpretation]: _nxdata_warning( "%d-D signal with @interpretation=%s " % (ndim, interpretation) + - "must define %d or %d axes." % (ndim, _INTERPDIM[interpretation])) + "must define %d or %d axes." % (ndim, _INTERPDIM[interpretation]), + group.name) return False # Test consistency of @uncertainties @@ -155,7 +229,7 @@ def is_valid_nxdata(group): # noqa if uncertainties_names is not None: if len(uncertainties_names) != len(axes_names): _nxdata_warning("@uncertainties does not define the same " + - "number of fields than @axes") + "number of fields than @axes", group.name) return False # Test individual axes @@ -165,10 +239,12 @@ def is_valid_nxdata(group): # noqa signal_size *= dim polynomial_axes_names = [] for i, axis_name in enumerate(axes_names): + if axis_name == ".": continue if axis_name not in group or not is_dataset(group[axis_name]): - _nxdata_warning("Could not find axis dataset '%s'" % axis_name) + _nxdata_warning("Could not find axis dataset '%s'" % axis_name, + group.name) return False axis_size = 1 @@ -180,7 +256,8 @@ def is_valid_nxdata(group): # noqa # size is exactly the signal's size (weird n-d scatter) if axis_size != signal_size: _nxdata_warning("Axis %s is not a 1D dataset" % axis_name + - " and its shape does not match the signal's shape") + " and its shape does not match the signal's shape", + group.name) return False axis_len = axis_size else: @@ -195,7 +272,7 @@ def is_valid_nxdata(group): # noqa "Axis %s number of elements does not " % axis_name + "correspond to the length of any signal dimension," " it does not appear to be a constant or a linear calibration," + - " and this does not seem to be a scatter plot.") + " and this does not seem to be a scatter plot.", group.name) return False elif axis_len in (1, 2): polynomial_axes_names.append(axis_name) @@ -205,7 +282,8 @@ def is_valid_nxdata(group): # noqa _nxdata_warning( "Axis %s number of elements is equal " % axis_name + "to the length of the signal, but this does not seem" + - " to be a scatter (other axes have different sizes)") + " to be a scatter (other axes have different sizes)", + group.name) return False # Test individual uncertainties @@ -216,14 +294,15 @@ def is_valid_nxdata(group): # noqa if group[errors_name].shape != group[axis_name].shape: _nxdata_warning( "Errors '%s' does not have the same " % errors_name + - "dimensions as axis '%s'." % axis_name) + "dimensions as axis '%s'." % axis_name, group.name) return False # test dimensions of errors associated with signal if "errors" in group and is_dataset(group["errors"]): if group["errors"].shape != group[signal_name].shape: _nxdata_warning("Dataset containing standard deviations must " + - "have the same dimensions as the signal.") + "have the same dimensions as the signal.", + group.name) return False return True @@ -245,10 +324,19 @@ class NXdata(object): """h5py-like group object compliant with NeXus NXdata specification. """ - self.signal = self.group[get_attr_as_string(self.group, "signal")] - """Signal dataset in this NXdata group. + self.signal = self.group[self.signal_dataset_name] + """Main signal dataset in this NXdata group. + + In case more than one signal is present in this group, + the other ones can be found in :attr:`auxiliary_signals`. """ + self.signal_name = get_attr_as_string(self.signal, "long_name") + """Signal long name, as specified in the @long_name attribute of the + signal dataset. If not specified, the dataset name is used.""" + if self.signal_name is None: + self.signal_name = self.signal_dataset_name + # ndim will be available in very recent h5py versions only self.signal_ndim = getattr(self.signal, "ndim", len(self.signal.shape)) @@ -276,6 +364,86 @@ class NXdata(object): self.signal_is_1d = self.signal_is_1d and len(self.axes) <= 1 # excludes n-D scatters @property + def signal_dataset_name(self): + """Name of the main signal dataset.""" + signal_dataset_name = get_attr_as_string(self.group, "signal") + if signal_dataset_name is None: + # find a dataset with @signal == 1 + for dsname in self.group: + signal_attr = self.group[dsname].attrs.get("signal") + if signal_attr in [1, b"1", u"1"]: + # This is the main (default) signal + signal_dataset_name = dsname + break + assert signal_dataset_name is not None + return signal_dataset_name + + @property + def auxiliary_signals_dataset_names(self): + """Sorted list of names of the auxiliary signals datasets. + + These are the names provided by the *@auxiliary_signals* attribute + on the NXdata group. + + In case the NXdata group does not specify a *@signal* attribute + but has a dataset with an attribute *@signal=1*, + we look for datasets with attributes *@signal=2, @signal=3...* + (deprecated NXdata specification).""" + signal_dataset_name = get_attr_as_string(self.group, "signal") + if signal_dataset_name is not None: + auxiliary_signals_names = get_attr_as_string(self.group, "auxiliary_signals") + if auxiliary_signals_names is not None: + if not isinstance(auxiliary_signals_names, + (tuple, list, numpy.ndarray)): + # tolerate a single string, but coerce into a list + return [auxiliary_signals_names] + return list(auxiliary_signals_names) + return [] + + # try old spec, @signal=1 (2, 3...) on dataset + numbered_names = [] + for dsname in self.group: + if dsname == self.signal_dataset_name: + # main signal, not auxiliary + continue + ds = self.group[dsname] + signal_attr = ds.attrs.get("signal") + if signal_attr is not None and not is_dataset(ds): + _logger.warning("Item %s with @signal=%s is not a dataset (%s)", + dsname, signal_attr, type(ds)) + continue + if signal_attr is not None: + try: + signal_number = int(signal_attr) + except (ValueError, TypeError): + _logger.warning("Could not parse attr @signal=%s on " + "dataset %s as an int", + signal_attr, dsname) + continue + numbered_names.append((signal_number, dsname)) + return [a[1] for a in sorted(numbered_names)] + + @property + def auxiliary_signals_names(self): + """List of names of the auxiliary signals. + + Similar to :attr:`auxiliary_signals_dataset_names`, but the @long_name + is used when this attribute is present, instead of the dataset name. + """ + signal_names = [] + for asdn in self.auxiliary_signals_dataset_names: + if "long_name" in self.group[asdn].attrs: + signal_names.append(self.group[asdn].attrs["long_name"]) + else: + signal_names.append(asdn) + return signal_names + + @property + def auxiliary_signals(self): + """List of all auxiliary signal datasets.""" + return [self.group[dsname] for dsname in self.auxiliary_signals_dataset_names] + + @property def interpretation(self): """*@interpretation* attribute associated with the *signal* dataset of the NXdata group. ``None`` if no interpretation @@ -300,7 +468,7 @@ class NXdata(object): interpretation is returned anyway. """ allowed_interpretations = [None, "scalar", "spectrum", "image", - # "rgba-image", "hsla-image", "cmyk-image" # TODO + "rgba-image", # "hsla-image", "cmyk-image" "vertex"] interpretation = get_attr_as_string(self.signal, "interpretation") @@ -317,20 +485,19 @@ class NXdata(object): """List of the axes datasets. The list typically has as many elements as there are dimensions in the - signal dataset, the exception being scatter plots which typically - use a 1D signal and several 1D axes of the same size. + signal dataset, the exception being scatter plots which use a 1D + signal and multiple 1D axes of the same size. If an axis dataset applies to several dimensions of the signal, it will be repeated in the list. - If a dimension of the signal has no dimension scale (i.e. there is a - "." in that position in the *@axes* array), `None` is inserted in the - output list in its position. + If a dimension of the signal has no dimension scale, `None` is + inserted in its position in the list. .. note:: - In theory, the *@axes* attribute defines as many entries as there - are dimensions in the signal. In such a case, there is no ambiguity. + The *@axes* attribute should define as many entries as there + are dimensions in the signal, to avoid any ambiguity. If this is not the case, this implementation relies on the existence of an *@interpretation* (*spectrum* or *image*) attribute in the *signal* dataset. @@ -339,47 +506,20 @@ class NXdata(object): If an axis dataset defines attributes @first_good or @last_good, the output will be a numpy array resulting from slicing that - axis to keep only the good index range: axis[first_good:last_good + 1] + axis (*axis[first_good:last_good + 1]*). - :rtype: list[Dataset or 1D array or None] + :rtype: List[Dataset or 1D array or None] """ if self._axes is not None: # use cache return self._axes - ndims = len(self.signal.shape) - axes_names = get_attr_as_string(self.group, "axes") - interpretation = self.interpretation - - if axes_names is None: - self._axes = [None for _i in range(ndims)] - return self._axes - - if isinstance(axes_names, str): - axes_names = [axes_names] + axes = [] + for axis_name in self.axes_dataset_names: + if axis_name is None: + axes.append(None) + else: + axes.append(self.group[axis_name]) - if len(axes_names) == ndims: - # axes is a list of strings, one axis per dim is explicitly defined - axes = [None] * ndims - for i, axis_n in enumerate(axes_names): - if axis_n != ".": - axes[i] = self.group[axis_n] - elif interpretation is not None: - # case of @interpretation attribute defined: we expect 1, 2 or 3 axes - # corresponding to the 1, 2, or 3 last dimensions of the signal - assert len(axes_names) == _INTERPDIM[interpretation] - axes = [None] * (ndims - _INTERPDIM[interpretation]) - for axis_n in axes_names: - if axis_n != ".": - axes.append(self.group[axis_n]) - else: - axes.append(None) - else: # scatter - axes = [] - for axis_n in axes_names: - if axis_n != ".": - axes.append(self.group[axis_n]) - else: - axes.append(None) # keep only good range of axis data for i, axis in enumerate(axes): if axis is None: @@ -395,7 +535,8 @@ class NXdata(object): @property def axes_dataset_names(self): - """ + """List of axes dataset names. + If an axis dataset applies to several dimensions of the signal, its name will be repeated in the list. @@ -403,15 +544,46 @@ class NXdata(object): "." in that position in the *@axes* array), `None` is inserted in the output list in its position. """ + numbered_names = [] # used in case of @axis=0 (old spec) axes_dataset_names = get_attr_as_string(self.group, "axes") if axes_dataset_names is None: - axes_dataset_names = get_attr_as_string(self.group, "axes") + # try @axes on signal dataset (older NXdata specification) + axes_dataset_names = get_attr_as_string(self.signal, "axes") + if axes_dataset_names is not None: + # we expect a comma separated string + if hasattr(axes_dataset_names, "split"): + axes_dataset_names = axes_dataset_names.split(":") + else: + # try @axis on the individual datasets (oldest NXdata specification) + for dsname in self.group: + if not is_dataset(self.group[dsname]): + continue + axis_attr = self.group[dsname].attrs.get("axis") + if axis_attr is not None: + try: + axis_num = int(axis_attr) + except (ValueError, TypeError): + _logger.warning("Could not interpret attr @axis as" + "int on dataset %s", dsname) + continue + numbered_names.append((axis_num, dsname)) ndims = len(self.signal.shape) if axes_dataset_names is None: - return [None] * ndims + if numbered_names: + axes_dataset_names = [] + numbers = [a[0] for a in numbered_names] + names = [a[1] for a in numbered_names] + for i in range(ndims): + if i in numbers: + axes_dataset_names.append(names[numbers.index(i)]) + else: + axes_dataset_names.append(None) + return axes_dataset_names + else: + return [None] * ndims - if isinstance(axes_dataset_names, str): + if isinstance(axes_dataset_names, (six.text_type, six.binary_type)): axes_dataset_names = [axes_dataset_names] for i, axis_name in enumerate(axes_dataset_names): @@ -422,17 +594,48 @@ class NXdata(object): if len(axes_dataset_names) != ndims: if self.is_scatter and ndims == 1: + # case of a 1D signal with arbitrary number of axes return list(axes_dataset_names) - # @axes may only define 1 or 2 axes if @interpretation=spectrum/image. - # Use the existing names for the last few dims, and prepend with Nones. - assert len(axes_dataset_names) == _INTERPDIM[self.interpretation] - all_dimensions_names = [None] * (ndims - _INTERPDIM[self.interpretation]) - for axis_name in axes_dataset_names: - all_dimensions_names.append(axis_name) + if self.interpretation != "rgba-image": + # @axes may only define 1 or 2 axes if @interpretation=spectrum/image. + # Use the existing names for the last few dims, and prepend with Nones. + assert len(axes_dataset_names) == _INTERPDIM[self.interpretation] + all_dimensions_names = [None] * (ndims - _INTERPDIM[self.interpretation]) + for axis_name in axes_dataset_names: + all_dimensions_names.append(axis_name) + else: + # 2 axes applying to the first two dimensions. + # The 3rd signal dimension is expected to contain 3(4) RGB(A) values. + assert len(axes_dataset_names) == 2 + all_dimensions_names = [axn for axn in axes_dataset_names] + all_dimensions_names.append(None) return all_dimensions_names return list(axes_dataset_names) + @property + def title(self): + """Plot title. If not found, returns an empty string. + + This attribute does not appear in the NXdata specification, but it is + implemented in *nexpy* as a dataset named "title" inside the NXdata + group. This dataset is expected to contain text. + + Because the *nexpy* approach could cause a conflict if the signal + dataset or an axis dataset happened to be called "title", we also + support providing the title as an attribute of the NXdata group. + """ + title = self.group.get("title") + data_dataset_names = [self.signal_name] + self.axes_dataset_names + if (title is not None and is_dataset(title) and + "title" not in data_dataset_names): + return str(title[()]) + + title = self.group.attrs.get("title") + if title is None: + return "" + return str(title) + def get_axis_errors(self, axis_name): """Return errors (uncertainties) associated with an axis. @@ -442,7 +645,7 @@ class NXdata(object): :param str axis_name: Name of axis dataset. This dataset **must exist**. :return: Dataset with axis errors, or None - :raise: KeyError if this group does not contain a dataset named axis_name + :raise KeyError: if this group does not contain a dataset named axis_name """ # ensure axis_name is decoded, before comparing it with decoded attributes if hasattr(axis_name, "decode"): @@ -541,3 +744,303 @@ class NXdata(object): def is_unsupported_scatter(self): """True if this is a scatter with a signal and more than 2 axes.""" return self.is_scatter and len(self.axes) > 2 + + @property + def is_curve(self): + """This property is True if the signal is 1D or :attr:`interpretation` is + *"spectrum"*, and there is at most one axis with a consistent length. + """ + if self.signal_is_0d or self.interpretation not in [None, "spectrum"]: + return False + # the axis, if any, must be of the same length as the last dimension + # of the signal, or of length 2 (a + b *x scale) + if self.axes[-1] is not None and len(self.axes[-1]) not in [ + self.signal.shape[-1], 2]: + return False + if self.interpretation is None: + # We no longer test whether x values are monotonic + # (in the past, in that case, we used to consider it a scatter) + return self.signal_is_1d + # everything looks good + return True + + @property + def is_image(self): + """True if the signal is 2D, or 3D with last dimension of length 3 or 4 + and interpretation *rgba-image*, or >2D with interpretation *image*. + The axes (if any) length must also be consistent with the signal shape. + """ + if self.interpretation in ["scalar", "spectrum", "scaler"]: + return False + if self.signal_is_0d or self.signal_is_1d: + return False + if not self.signal_is_2d and \ + self.interpretation not in ["image", "rgba-image"]: + return False + if self.signal_is_3d and self.interpretation == "rgba-image": + if self.signal.shape[-1] not in [3, 4]: + return False + img_axes = self.axes[0:2] + img_shape = self.signal.shape[0:2] + else: + img_axes = self.axes[-2:] + img_shape = self.signal.shape[-2:] + for i, axis in enumerate(img_axes): + if axis is not None and len(axis) not in [img_shape[i], 2]: + return False + + return True + + @property + def is_stack(self): + """True in the signal is at least 3D and interpretation is not + "scalar", "spectrum", "image" or "rgba-image". + The axes length must also be consistent with the last 3 dimensions + of the signal. + """ + if self.signal_ndim < 3 or self.interpretation in [ + "scalar", "scaler", "spectrum", "image", "rgba-image"]: + return False + stack_shape = self.signal.shape[-3:] + for i, axis in enumerate(self.axes[-3:]): + if axis is not None and len(axis) not in [stack_shape[i], 2]: + return False + return True + + +def is_NXentry_with_default_NXdata(group): + """Return True if group is a valid NXentry defining a valid default + NXdata.""" + if not is_group(group): + return False + + if get_attr_as_string(group, "NX_class") != "NXentry": + return False + + default_nxdata_name = group.attrs.get("default") + if default_nxdata_name is None or default_nxdata_name not in group: + return False + + default_nxdata_group = group.get(default_nxdata_name) + + if not is_group(default_nxdata_group): + return False + + return is_valid_nxdata(default_nxdata_group) + + +def is_NXroot_with_default_NXdata(group): + """Return True if group is a valid NXroot defining a default NXentry + defining a valid default NXdata.""" + if not is_group(group): + return False + + # A NXroot is supposed to be at the root of a data file, and @NX_class + # is therefore optional. We accept groups that are not located at the root + # if they have @NX_class=NXroot (use case: several nexus files archived + # in a single HDF5 file) + if get_attr_as_string(group, "NX_class") != "NXroot" and not is_file(group): + return False + + default_nxentry_name = group.attrs.get("default") + if default_nxentry_name is None or default_nxentry_name not in group: + return False + + default_nxentry_group = group.get(default_nxentry_name) + return is_NXentry_with_default_NXdata(default_nxentry_group) + + +def get_default(group): + """Return a :class:`NXdata` object corresponding to the default NXdata group + in the group specified as parameter. + + This function can find the NXdata if the group is already a NXdata, or + if it is a NXentry defining a default NXdata, or if it is a NXroot + defining such a default valid NXentry. + + Return None if no valid NXdata could be found. + + :param group: h5py-like group following the Nexus specification + (NXdata, NXentry or NXroot). + :return: :class:`NXdata` object or None + :raise TypeError: if group is not a h5py-like group + """ + if not is_group(group): + raise TypeError("Provided parameter is not a h5py-like group") + + if is_NXroot_with_default_NXdata(group): + default_entry = group[group.attrs["default"]] + default_data = default_entry[default_entry.attrs["default"]] + elif is_NXentry_with_default_NXdata(group): + default_data = group[group.attrs["default"]] + elif is_valid_nxdata(group): + default_data = group + else: + return None + + return NXdata(default_data) + + +def _str_to_utf8(text): + return numpy.array(text, dtype=h5py.special_dtype(vlen=six.text_type)) + + +def save_NXdata(filename, signal, axes=None, + signal_name="data", axes_names=None, + signal_long_name=None, axes_long_names=None, + signal_errors=None, axes_errors=None, + title=None, interpretation=None, + nxentry_name="entry", nxdata_name=None): + """Write data to an NXdata group. + + .. note:: + + No consistency checks are made regarding the dimensionality of the + signal and number of axes. The user is responsible for providing + meaningful data, that can be interpreted by visualization software. + + :param str filename: Path to output file. If the file does not + exists, it is created. + :param numpy.ndarray signal: Signal array. + :param List[numpy.ndarray] axes: List of axes arrays. + :param str signal_name: Name of signal dataset, in output file + :param List[str] axes_names: List of dataset names for axes, in + output file + :param str signal_long_name: *@long_name* attribute for signal, or None. + :param axes_long_names: None, or list of long names + for axes + :type axes_long_names: List[str, None] + :param numpy.ndarray signal_errors: Array of errors associated with the + signal + :param axes_errors: List of arrays of errors + associated with each axis + :type axes_errors: List[numpy.ndarray, None] + :param str title: Graph title (saved as a "title" dataset) or None. + :param str interpretation: *@interpretation* attribute ("spectrum", + "image", "rgba-image" or None). This is only needed in cases of + ambiguous dimensionality, e.g. a 3D array which represents a RGBA + image rather than a stack. + :param str nxentry_name: Name of group in which the NXdata group + is created. By default, "/entry" is used. + + .. note:: + + The Nexus format specification requires for NXdata groups + be part of a NXentry group. + The specified group should have attribute *@NX_class=NXentry*, in + order for the created file to be nexus compliant. + :param str nxdata_name: Name of NXdata group. If omitted (None), the + function creates a new group using the first available name ("data0", + or "data1"...). + Overwriting an existing group (or dataset) is not supported, you must + delete it yourself prior to calling this function if this is what you + want. + :return: True if save was successful, else False. + """ + if h5py is None: + raise ImportError("h5py could not be imported, but is required by " + "save_NXdata function") + + if axes_names is not None: + assert axes is not None, "Axes names defined, but missing axes arrays" + assert len(axes) == len(axes_names), \ + "Mismatch between number of axes and axes_names" + + if axes is not None and axes_names is None: + axes_names = [] + for i, axis in enumerate(axes): + axes_names.append("dim%d" % i if axis is not None else ".") + if axes is None: + axes = [] + + # Open file in + if os.path.exists(filename): + errmsg = "Cannot write/append to existing path %s" + if not os.path.isfile(filename): + errmsg += " (not a file)" + _logger.error(errmsg, filename) + return False + if not os.access(filename, os.W_OK): + errmsg += " (no permission to write)" + _logger.error(errmsg, filename) + return False + mode = "r+" + else: + mode = "w-" + + with h5py.File(filename, mode=mode) as h5f: + # get or create entry + if nxentry_name is not None: + entry = h5f.require_group(nxentry_name) + if "default" not in h5f.attrs: + # set this entry as default + h5f.attrs["default"] = _str_to_utf8(nxentry_name) + if "NX_class" not in entry.attrs: + entry.attrs["NX_class"] = u"NXentry" + else: + # write NXdata into the root of the file (invalid nexus!) + entry = h5f + + # Create NXdata group + if nxdata_name is not None: + if nxdata_name in entry: + _logger.error("Cannot assign an NXdata group to an existing" + " group or dataset") + return False + else: + # no name specified, take one that is available + nxdata_name = "data0" + i = 1 + while nxdata_name in entry: + _logger.info("%s item already exists in NXentry group," + + " trying %s", nxdata_name, "data%d" % i) + nxdata_name = "data%d" % i + i += 1 + + data_group = entry.create_group(nxdata_name) + data_group.attrs["NX_class"] = u"NXdata" + data_group.attrs["signal"] = _str_to_utf8(signal_name) + if axes: + data_group.attrs["axes"] = _str_to_utf8(axes_names) + if title: + # not in NXdata spec, but implemented by nexpy + data_group["title"] = title + # better way imho + data_group.attrs["title"] = _str_to_utf8(title) + + signal_dataset = data_group.create_dataset(signal_name, + data=signal) + if signal_long_name: + signal_dataset.attrs["long_name"] = _str_to_utf8(signal_long_name) + if interpretation: + signal_dataset.attrs["interpretation"] = _str_to_utf8(interpretation) + + for i, axis_array in enumerate(axes): + if axis_array is None: + assert axes_names[i] in [".", None], \ + "Axis name defined for dim %d but no axis array" % i + continue + axis_dataset = data_group.create_dataset(axes_names[i], + data=axis_array) + if axes_long_names is not None: + axis_dataset.attrs["long_name"] = _str_to_utf8(axes_long_names[i]) + + if signal_errors is not None: + data_group.create_dataset("errors", + data=signal_errors) + + if axes_errors is not None: + assert isinstance(axes_errors, (list, tuple)), \ + "axes_errors must be a list or a tuple of ndarray or None" + assert len(axes_errors) == len(axes_names), \ + "Mismatch between number of axes_errors and axes_names" + for i, axis_errors in enumerate(axes_errors): + if axis_errors is not None: + dsname = axes_names[i] + "_errors" + data_group.create_dataset(dsname, + data=axis_errors) + if "default" not in entry.attrs: + # set this NXdata as default + entry.attrs["default"] = nxdata_name + + return True diff --git a/silx/io/specfile.c b/silx/io/specfile.c index e244f3d..a95282a 100644 --- a/silx/io/specfile.c +++ b/silx/io/specfile.c @@ -1,40 +1,28 @@ -/* Generated by Cython 0.25.2 */ - -/* BEGIN: Cython Metadata -{ - "distutils": { - "define_macros": [ - [ - "SPECFILE_POSIX", - null - ] - ], - "depends": [ - "/usr/lib/python2.7/dist-packages/numpy/core/include/numpy/arrayobject.h", - "/usr/lib/python2.7/dist-packages/numpy/core/include/numpy/ufuncobject.h", - "silx/io/specfile/include/SpecFileCython.h" - ], - "include_dirs": [ - "silx/io/specfile/include", - "/usr/lib/python2.7/dist-packages/numpy/core/include" - ], - "language": "c" - }, - "module_name": "silx.io.specfile" -} -END: Cython Metadata */ +/* Generated by Cython 0.21.1 */ #define PY_SSIZE_T_CLEAN +#ifndef CYTHON_USE_PYLONG_INTERNALS +#ifdef PYLONG_BITS_IN_DIGIT +#define CYTHON_USE_PYLONG_INTERNALS 0 +#else +#include "pyconfig.h" +#ifdef PYLONG_BITS_IN_DIGIT +#define CYTHON_USE_PYLONG_INTERNALS 1 +#else +#define CYTHON_USE_PYLONG_INTERNALS 0 +#endif +#endif +#endif #include "Python.h" #ifndef Py_PYTHON_H #error Python headers needed to compile C extensions, please install development version of Python. #elif PY_VERSION_HEX < 0x02060000 || (0x03000000 <= PY_VERSION_HEX && PY_VERSION_HEX < 0x03020000) #error Cython requires Python 2.6+ or Python 3.2+. #else -#define CYTHON_ABI "0_25_2" +#define CYTHON_ABI "0_21_1" #include <stddef.h> #ifndef offsetof - #define offsetof(type, member) ( (size_t) & ((type*)0) -> member ) +#define offsetof(type, member) ( (size_t) & ((type*)0) -> member ) #endif #if !defined(WIN32) && !defined(MS_WINDOWS) #ifndef __stdcall @@ -53,11 +41,6 @@ END: Cython Metadata */ #ifndef DL_EXPORT #define DL_EXPORT(t) t #endif -#ifndef HAVE_LONG_LONG - #if PY_VERSION_HEX >= 0x03030000 || (PY_MAJOR_VERSION == 2 && PY_VERSION_HEX >= 0x02070000) - #define HAVE_LONG_LONG - #endif -#endif #ifndef PY_LONG_LONG #define PY_LONG_LONG LONG_LONG #endif @@ -65,214 +48,63 @@ END: Cython Metadata */ #define Py_HUGE_VAL HUGE_VAL #endif #ifdef PYPY_VERSION - #define CYTHON_COMPILING_IN_PYPY 1 - #define CYTHON_COMPILING_IN_PYSTON 0 - #define CYTHON_COMPILING_IN_CPYTHON 0 - #undef CYTHON_USE_TYPE_SLOTS - #define CYTHON_USE_TYPE_SLOTS 0 - #undef CYTHON_USE_ASYNC_SLOTS - #define CYTHON_USE_ASYNC_SLOTS 0 - #undef CYTHON_USE_PYLIST_INTERNALS - #define CYTHON_USE_PYLIST_INTERNALS 0 - #undef CYTHON_USE_UNICODE_INTERNALS - #define CYTHON_USE_UNICODE_INTERNALS 0 - #undef CYTHON_USE_UNICODE_WRITER - #define CYTHON_USE_UNICODE_WRITER 0 - #undef CYTHON_USE_PYLONG_INTERNALS - #define CYTHON_USE_PYLONG_INTERNALS 0 - #undef CYTHON_AVOID_BORROWED_REFS - #define CYTHON_AVOID_BORROWED_REFS 1 - #undef CYTHON_ASSUME_SAFE_MACROS - #define CYTHON_ASSUME_SAFE_MACROS 0 - #undef CYTHON_UNPACK_METHODS - #define CYTHON_UNPACK_METHODS 0 - #undef CYTHON_FAST_THREAD_STATE - #define CYTHON_FAST_THREAD_STATE 0 - #undef CYTHON_FAST_PYCALL - #define CYTHON_FAST_PYCALL 0 -#elif defined(PYSTON_VERSION) - #define CYTHON_COMPILING_IN_PYPY 0 - #define CYTHON_COMPILING_IN_PYSTON 1 - #define CYTHON_COMPILING_IN_CPYTHON 0 - #ifndef CYTHON_USE_TYPE_SLOTS - #define CYTHON_USE_TYPE_SLOTS 1 - #endif - #undef CYTHON_USE_ASYNC_SLOTS - #define CYTHON_USE_ASYNC_SLOTS 0 - #undef CYTHON_USE_PYLIST_INTERNALS - #define CYTHON_USE_PYLIST_INTERNALS 0 - #ifndef CYTHON_USE_UNICODE_INTERNALS - #define CYTHON_USE_UNICODE_INTERNALS 1 - #endif - #undef CYTHON_USE_UNICODE_WRITER - #define CYTHON_USE_UNICODE_WRITER 0 - #undef CYTHON_USE_PYLONG_INTERNALS - #define CYTHON_USE_PYLONG_INTERNALS 0 - #ifndef CYTHON_AVOID_BORROWED_REFS - #define CYTHON_AVOID_BORROWED_REFS 0 - #endif - #ifndef CYTHON_ASSUME_SAFE_MACROS - #define CYTHON_ASSUME_SAFE_MACROS 1 - #endif - #ifndef CYTHON_UNPACK_METHODS - #define CYTHON_UNPACK_METHODS 1 - #endif - #undef CYTHON_FAST_THREAD_STATE - #define CYTHON_FAST_THREAD_STATE 0 - #undef CYTHON_FAST_PYCALL - #define CYTHON_FAST_PYCALL 0 +#define CYTHON_COMPILING_IN_PYPY 1 +#define CYTHON_COMPILING_IN_CPYTHON 0 #else - #define CYTHON_COMPILING_IN_PYPY 0 - #define CYTHON_COMPILING_IN_PYSTON 0 - #define CYTHON_COMPILING_IN_CPYTHON 1 - #ifndef CYTHON_USE_TYPE_SLOTS - #define CYTHON_USE_TYPE_SLOTS 1 - #endif - #if PY_MAJOR_VERSION < 3 - #undef CYTHON_USE_ASYNC_SLOTS - #define CYTHON_USE_ASYNC_SLOTS 0 - #elif !defined(CYTHON_USE_ASYNC_SLOTS) - #define CYTHON_USE_ASYNC_SLOTS 1 - #endif - #if PY_VERSION_HEX < 0x02070000 - #undef CYTHON_USE_PYLONG_INTERNALS - #define CYTHON_USE_PYLONG_INTERNALS 0 - #elif !defined(CYTHON_USE_PYLONG_INTERNALS) - #define CYTHON_USE_PYLONG_INTERNALS 1 - #endif - #ifndef CYTHON_USE_PYLIST_INTERNALS - #define CYTHON_USE_PYLIST_INTERNALS 1 - #endif - #ifndef CYTHON_USE_UNICODE_INTERNALS - #define CYTHON_USE_UNICODE_INTERNALS 1 - #endif - #if PY_VERSION_HEX < 0x030300F0 - #undef CYTHON_USE_UNICODE_WRITER - #define CYTHON_USE_UNICODE_WRITER 0 - #elif !defined(CYTHON_USE_UNICODE_WRITER) - #define CYTHON_USE_UNICODE_WRITER 1 - #endif - #ifndef CYTHON_AVOID_BORROWED_REFS - #define CYTHON_AVOID_BORROWED_REFS 0 - #endif - #ifndef CYTHON_ASSUME_SAFE_MACROS - #define CYTHON_ASSUME_SAFE_MACROS 1 - #endif - #ifndef CYTHON_UNPACK_METHODS - #define CYTHON_UNPACK_METHODS 1 - #endif - #ifndef CYTHON_FAST_THREAD_STATE - #define CYTHON_FAST_THREAD_STATE 1 - #endif - #ifndef CYTHON_FAST_PYCALL - #define CYTHON_FAST_PYCALL 1 - #endif +#define CYTHON_COMPILING_IN_PYPY 0 +#define CYTHON_COMPILING_IN_CPYTHON 1 #endif -#if !defined(CYTHON_FAST_PYCCALL) -#define CYTHON_FAST_PYCCALL (CYTHON_FAST_PYCALL && PY_VERSION_HEX >= 0x030600B1) -#endif -#if CYTHON_USE_PYLONG_INTERNALS - #include "longintrepr.h" - #undef SHIFT - #undef BASE - #undef MASK -#endif -#if CYTHON_COMPILING_IN_PYPY && PY_VERSION_HEX < 0x02070600 && !defined(Py_OptimizeFlag) - #define Py_OptimizeFlag 0 +#if CYTHON_COMPILING_IN_PYPY && PY_VERSION_HEX < 0x02070600 +#define Py_OptimizeFlag 0 #endif #define __PYX_BUILD_PY_SSIZE_T "n" #define CYTHON_FORMAT_SSIZE_T "z" #if PY_MAJOR_VERSION < 3 #define __Pyx_BUILTIN_MODULE_NAME "__builtin__" - #define __Pyx_PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos)\ + #define __Pyx_PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) \ PyCode_New(a+k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) #define __Pyx_DefaultClassType PyClass_Type #else #define __Pyx_BUILTIN_MODULE_NAME "builtins" - #define __Pyx_PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos)\ + #define __Pyx_PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) \ PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) #define __Pyx_DefaultClassType PyType_Type #endif -#ifndef Py_TPFLAGS_CHECKTYPES +#if PY_MAJOR_VERSION >= 3 #define Py_TPFLAGS_CHECKTYPES 0 -#endif -#ifndef Py_TPFLAGS_HAVE_INDEX #define Py_TPFLAGS_HAVE_INDEX 0 -#endif -#ifndef Py_TPFLAGS_HAVE_NEWBUFFER #define Py_TPFLAGS_HAVE_NEWBUFFER 0 #endif -#ifndef Py_TPFLAGS_HAVE_FINALIZE +#if PY_VERSION_HEX < 0x030400a1 && !defined(Py_TPFLAGS_HAVE_FINALIZE) #define Py_TPFLAGS_HAVE_FINALIZE 0 #endif -#ifndef METH_FASTCALL - #define METH_FASTCALL 0x80 - typedef PyObject *(*__Pyx_PyCFunctionFast) (PyObject *self, PyObject **args, - Py_ssize_t nargs, PyObject *kwnames); -#else - #define __Pyx_PyCFunctionFast _PyCFunctionFast -#endif -#if CYTHON_FAST_PYCCALL -#define __Pyx_PyFastCFunction_Check(func)\ - ((PyCFunction_Check(func) && (METH_FASTCALL == (PyCFunction_GET_FLAGS(func) & ~(METH_CLASS | METH_STATIC | METH_COEXIST))))) -#else -#define __Pyx_PyFastCFunction_Check(func) 0 -#endif #if PY_VERSION_HEX > 0x03030000 && defined(PyUnicode_KIND) #define CYTHON_PEP393_ENABLED 1 - #define __Pyx_PyUnicode_READY(op) (likely(PyUnicode_IS_READY(op)) ?\ + #define __Pyx_PyUnicode_READY(op) (likely(PyUnicode_IS_READY(op)) ? \ 0 : _PyUnicode_Ready((PyObject *)(op))) #define __Pyx_PyUnicode_GET_LENGTH(u) PyUnicode_GET_LENGTH(u) #define __Pyx_PyUnicode_READ_CHAR(u, i) PyUnicode_READ_CHAR(u, i) - #define __Pyx_PyUnicode_MAX_CHAR_VALUE(u) PyUnicode_MAX_CHAR_VALUE(u) #define __Pyx_PyUnicode_KIND(u) PyUnicode_KIND(u) #define __Pyx_PyUnicode_DATA(u) PyUnicode_DATA(u) #define __Pyx_PyUnicode_READ(k, d, i) PyUnicode_READ(k, d, i) - #define __Pyx_PyUnicode_WRITE(k, d, i, ch) PyUnicode_WRITE(k, d, i, ch) - #define __Pyx_PyUnicode_IS_TRUE(u) (0 != (likely(PyUnicode_IS_READY(u)) ? PyUnicode_GET_LENGTH(u) : PyUnicode_GET_SIZE(u))) #else #define CYTHON_PEP393_ENABLED 0 - #define PyUnicode_1BYTE_KIND 1 - #define PyUnicode_2BYTE_KIND 2 - #define PyUnicode_4BYTE_KIND 4 #define __Pyx_PyUnicode_READY(op) (0) #define __Pyx_PyUnicode_GET_LENGTH(u) PyUnicode_GET_SIZE(u) #define __Pyx_PyUnicode_READ_CHAR(u, i) ((Py_UCS4)(PyUnicode_AS_UNICODE(u)[i])) - #define __Pyx_PyUnicode_MAX_CHAR_VALUE(u) ((sizeof(Py_UNICODE) == 2) ? 65535 : 1114111) #define __Pyx_PyUnicode_KIND(u) (sizeof(Py_UNICODE)) #define __Pyx_PyUnicode_DATA(u) ((void*)PyUnicode_AS_UNICODE(u)) #define __Pyx_PyUnicode_READ(k, d, i) ((void)(k), (Py_UCS4)(((Py_UNICODE*)d)[i])) - #define __Pyx_PyUnicode_WRITE(k, d, i, ch) (((void)(k)), ((Py_UNICODE*)d)[i] = ch) - #define __Pyx_PyUnicode_IS_TRUE(u) (0 != PyUnicode_GET_SIZE(u)) #endif #if CYTHON_COMPILING_IN_PYPY #define __Pyx_PyUnicode_Concat(a, b) PyNumber_Add(a, b) #define __Pyx_PyUnicode_ConcatSafe(a, b) PyNumber_Add(a, b) + #define __Pyx_PyFrozenSet_Size(s) PyObject_Size(s) #else #define __Pyx_PyUnicode_Concat(a, b) PyUnicode_Concat(a, b) - #define __Pyx_PyUnicode_ConcatSafe(a, b) ((unlikely((a) == Py_None) || unlikely((b) == Py_None)) ?\ + #define __Pyx_PyUnicode_ConcatSafe(a, b) ((unlikely((a) == Py_None) || unlikely((b) == Py_None)) ? \ PyNumber_Add(a, b) : __Pyx_PyUnicode_Concat(a, b)) -#endif -#if CYTHON_COMPILING_IN_PYPY && !defined(PyUnicode_Contains) - #define PyUnicode_Contains(u, s) PySequence_Contains(u, s) -#endif -#if CYTHON_COMPILING_IN_PYPY && !defined(PyByteArray_Check) - #define PyByteArray_Check(obj) PyObject_TypeCheck(obj, &PyByteArray_Type) -#endif -#if CYTHON_COMPILING_IN_PYPY && !defined(PyObject_Format) - #define PyObject_Format(obj, fmt) PyObject_CallMethod(obj, "__format__", "O", fmt) -#endif -#if CYTHON_COMPILING_IN_PYPY && !defined(PyObject_Malloc) - #define PyObject_Malloc(s) PyMem_Malloc(s) - #define PyObject_Free(p) PyMem_Free(p) - #define PyObject_Realloc(p) PyMem_Realloc(p) -#endif -#if CYTHON_COMPILING_IN_PYSTON - #define __Pyx_PyCode_HasFreeVars(co) PyCode_HasFreeVars(co) - #define __Pyx_PyFrame_SetLineNumber(frame, lineno) PyFrame_SetLineNumber(frame, lineno) -#else - #define __Pyx_PyCode_HasFreeVars(co) (PyCode_GetNumFree(co) > 0) - #define __Pyx_PyFrame_SetLineNumber(frame, lineno) (frame)->f_lineno = (lineno) + #define __Pyx_PyFrozenSet_Size(s) PySet_Size(s) #endif #define __Pyx_PyString_FormatSafe(a, b) ((unlikely((a) == Py_None)) ? PyNumber_Remainder(a, b) : __Pyx_PyString_Format(a, b)) #define __Pyx_PyUnicode_FormatSafe(a, b) ((unlikely((a) == Py_None)) ? PyNumber_Remainder(a, b) : PyUnicode_Format(a, b)) @@ -281,9 +113,6 @@ END: Cython Metadata */ #else #define __Pyx_PyString_Format(a, b) PyString_Format(a, b) #endif -#if PY_MAJOR_VERSION < 3 && !defined(PyObject_ASCII) - #define PyObject_ASCII(o) PyObject_Repr(o) -#endif #if PY_MAJOR_VERSION >= 3 #define PyBaseString_Type PyUnicode_Type #define PyStringObject PyUnicodeObject @@ -302,7 +131,6 @@ END: Cython Metadata */ #define PySet_CheckExact(obj) (Py_TYPE(obj) == &PySet_Type) #endif #define __Pyx_TypeCheck(obj, type) PyObject_TypeCheck(obj, (PyTypeObject *)type) -#define __Pyx_PyException_Check(obj) __Pyx_TypeCheck(obj, PyExc_Exception) #if PY_MAJOR_VERSION >= 3 #define PyIntObject PyLongObject #define PyInt_Type PyLong_Type @@ -341,20 +169,16 @@ END: Cython Metadata */ #else #define __Pyx_PyMethod_New(func, self, klass) PyMethod_New(func, self, klass) #endif -#if CYTHON_USE_ASYNC_SLOTS - #if PY_VERSION_HEX >= 0x030500B1 - #define __Pyx_PyAsyncMethodsStruct PyAsyncMethods - #define __Pyx_PyType_AsAsync(obj) (Py_TYPE(obj)->tp_as_async) +#ifndef CYTHON_INLINE + #if defined(__GNUC__) + #define CYTHON_INLINE __inline__ + #elif defined(_MSC_VER) + #define CYTHON_INLINE __inline + #elif defined (__STDC_VERSION__) && __STDC_VERSION__ >= 199901L + #define CYTHON_INLINE inline #else - typedef struct { - unaryfunc am_await; - unaryfunc am_aiter; - unaryfunc am_anext; - } __Pyx_PyAsyncMethodsStruct; - #define __Pyx_PyType_AsAsync(obj) ((__Pyx_PyAsyncMethodsStruct*) (Py_TYPE(obj)->tp_reserved)) + #define CYTHON_INLINE #endif -#else - #define __Pyx_PyType_AsAsync(obj) NULL #endif #ifndef CYTHON_RESTRICT #if defined(__GNUC__) @@ -367,74 +191,26 @@ END: Cython Metadata */ #define CYTHON_RESTRICT #endif #endif -#ifndef CYTHON_UNUSED -# if defined(__GNUC__) -# if !(defined(__cplusplus)) || (__GNUC__ > 3 || (__GNUC__ == 3 && __GNUC_MINOR__ >= 4)) -# define CYTHON_UNUSED __attribute__ ((__unused__)) -# else -# define CYTHON_UNUSED -# endif -# elif defined(__ICC) || (defined(__INTEL_COMPILER) && !defined(_MSC_VER)) -# define CYTHON_UNUSED __attribute__ ((__unused__)) -# else -# define CYTHON_UNUSED -# endif -#endif -#ifndef CYTHON_MAYBE_UNUSED_VAR -# if defined(__cplusplus) - template<class T> void CYTHON_MAYBE_UNUSED_VAR( const T& ) { } -# else -# define CYTHON_MAYBE_UNUSED_VAR(x) (void)(x) -# endif -#endif -#ifndef CYTHON_NCP_UNUSED -# if CYTHON_COMPILING_IN_CPYTHON -# define CYTHON_NCP_UNUSED -# else -# define CYTHON_NCP_UNUSED CYTHON_UNUSED -# endif -#endif -#define __Pyx_void_to_None(void_result) ((void)(void_result), Py_INCREF(Py_None), Py_None) - -#ifndef CYTHON_INLINE - #if defined(__clang__) - #define CYTHON_INLINE __inline__ __attribute__ ((__unused__)) - #elif defined(__GNUC__) - #define CYTHON_INLINE __inline__ - #elif defined(_MSC_VER) - #define CYTHON_INLINE __inline - #elif defined (__STDC_VERSION__) && __STDC_VERSION__ >= 199901L - #define CYTHON_INLINE inline - #else - #define CYTHON_INLINE - #endif -#endif - -#if defined(WIN32) || defined(MS_WINDOWS) - #define _USE_MATH_DEFINES -#endif -#include <math.h> #ifdef NAN #define __PYX_NAN() ((float) NAN) #else static CYTHON_INLINE float __PYX_NAN() { + /* Initialize NaN. The sign is irrelevant, an exponent with all bits 1 and + a nonzero mantissa means NaN. If the first bit in the mantissa is 1, it is + a quiet NaN. */ float value; memset(&value, 0xFF, sizeof(value)); return value; } #endif -#if defined(__CYGWIN__) && defined(_LDBL_EQ_DBL) -#define __Pyx_truncl trunc -#else -#define __Pyx_truncl truncl +#ifdef __cplusplus +template<typename T> +void __Pyx_call_destructor(T* x) { + x->~T(); +} #endif -#define __PYX_ERR(f_index, lineno, Ln_error) \ -{ \ - __pyx_filename = __pyx_f[f_index]; __pyx_lineno = lineno; __pyx_clineno = __LINE__; goto Ln_error; \ -} - #if PY_MAJOR_VERSION >= 3 #define __Pyx_PyNumber_Divide(x,y) PyNumber_TrueDivide(x,y) #define __Pyx_PyNumber_InPlaceDivide(x,y) PyNumber_InPlaceTrueDivide(x,y) @@ -451,11 +227,15 @@ static CYTHON_INLINE float __PYX_NAN() { #endif #endif +#if defined(WIN32) || defined(MS_WINDOWS) +#define _USE_MATH_DEFINES +#endif +#include <math.h> #define __PYX_HAVE__silx__io__specfile #define __PYX_HAVE_API__silx__io__specfile -#include <string.h> -#include <stdio.h> -#include <stdlib.h> +#include "string.h" +#include "stdio.h" +#include "stdlib.h" #include "numpy/arrayobject.h" #include "numpy/ufuncobject.h" #include "SpecFileCython.h" @@ -467,7 +247,20 @@ static CYTHON_INLINE float __PYX_NAN() { #define CYTHON_WITHOUT_ASSERTIONS #endif -typedef struct {PyObject **p; const char *s; const Py_ssize_t n; const char* encoding; +#ifndef CYTHON_UNUSED +# if defined(__GNUC__) +# if !(defined(__cplusplus)) || (__GNUC__ > 3 || (__GNUC__ == 3 && __GNUC_MINOR__ >= 4)) +# define CYTHON_UNUSED __attribute__ ((__unused__)) +# else +# define CYTHON_UNUSED +# endif +# elif defined(__ICC) || (defined(__INTEL_COMPILER) && !defined(_MSC_VER)) +# define CYTHON_UNUSED __attribute__ ((__unused__)) +# else +# define CYTHON_UNUSED +# endif +#endif +typedef struct {PyObject **p; char *s; const Py_ssize_t n; const char* encoding; const char is_unicode; const char is_str; const char intern; } __Pyx_StringTabEntry; #define __PYX_DEFAULT_STRING_ENCODING_IS_ASCII 0 @@ -475,34 +268,16 @@ typedef struct {PyObject **p; const char *s; const Py_ssize_t n; const char* enc #define __PYX_DEFAULT_STRING_ENCODING "" #define __Pyx_PyObject_FromString __Pyx_PyBytes_FromString #define __Pyx_PyObject_FromStringAndSize __Pyx_PyBytes_FromStringAndSize -#define __Pyx_uchar_cast(c) ((unsigned char)c) -#define __Pyx_long_cast(x) ((long)x) -#define __Pyx_fits_Py_ssize_t(v, type, is_signed) (\ - (sizeof(type) < sizeof(Py_ssize_t)) ||\ - (sizeof(type) > sizeof(Py_ssize_t) &&\ - likely(v < (type)PY_SSIZE_T_MAX ||\ - v == (type)PY_SSIZE_T_MAX) &&\ - (!is_signed || likely(v > (type)PY_SSIZE_T_MIN ||\ - v == (type)PY_SSIZE_T_MIN))) ||\ - (sizeof(type) == sizeof(Py_ssize_t) &&\ - (is_signed || likely(v < (type)PY_SSIZE_T_MAX ||\ +#define __Pyx_fits_Py_ssize_t(v, type, is_signed) ( \ + (sizeof(type) < sizeof(Py_ssize_t)) || \ + (sizeof(type) > sizeof(Py_ssize_t) && \ + likely(v < (type)PY_SSIZE_T_MAX || \ + v == (type)PY_SSIZE_T_MAX) && \ + (!is_signed || likely(v > (type)PY_SSIZE_T_MIN || \ + v == (type)PY_SSIZE_T_MIN))) || \ + (sizeof(type) == sizeof(Py_ssize_t) && \ + (is_signed || likely(v < (type)PY_SSIZE_T_MAX || \ v == (type)PY_SSIZE_T_MAX))) ) -#if defined (__cplusplus) && __cplusplus >= 201103L - #include <cstdlib> - #define __Pyx_sst_abs(value) std::abs(value) -#elif SIZEOF_INT >= SIZEOF_SIZE_T - #define __Pyx_sst_abs(value) abs(value) -#elif SIZEOF_LONG >= SIZEOF_SIZE_T - #define __Pyx_sst_abs(value) labs(value) -#elif defined (_MSC_VER) && defined (_M_X64) - #define __Pyx_sst_abs(value) _abs64(value) -#elif defined (__STDC_VERSION__) && __STDC_VERSION__ >= 199901L - #define __Pyx_sst_abs(value) llabs(value) -#elif defined (__GNUC__) - #define __Pyx_sst_abs(value) __builtin_llabs(value) -#else - #define __Pyx_sst_abs(value) ((value<0) ? -value : value) -#endif static CYTHON_INLINE char* __Pyx_PyObject_AsString(PyObject*); static CYTHON_INLINE char* __Pyx_PyObject_AsStringAndSize(PyObject*, Py_ssize_t* length); #define __Pyx_PyByteArray_FromString(s) PyByteArray_FromStringAndSize((const char*)s, strlen((const char*)s)) @@ -519,11 +294,11 @@ static CYTHON_INLINE PyObject* __Pyx_PyUnicode_FromString(const char*); #endif #define __Pyx_PyObject_AsSString(s) ((signed char*) __Pyx_PyObject_AsString(s)) #define __Pyx_PyObject_AsUString(s) ((unsigned char*) __Pyx_PyObject_AsString(s)) -#define __Pyx_PyObject_FromCString(s) __Pyx_PyObject_FromString((const char*)s) -#define __Pyx_PyBytes_FromCString(s) __Pyx_PyBytes_FromString((const char*)s) -#define __Pyx_PyByteArray_FromCString(s) __Pyx_PyByteArray_FromString((const char*)s) -#define __Pyx_PyStr_FromCString(s) __Pyx_PyStr_FromString((const char*)s) -#define __Pyx_PyUnicode_FromCString(s) __Pyx_PyUnicode_FromString((const char*)s) +#define __Pyx_PyObject_FromUString(s) __Pyx_PyObject_FromString((const char*)s) +#define __Pyx_PyBytes_FromUString(s) __Pyx_PyBytes_FromString((const char*)s) +#define __Pyx_PyByteArray_FromUString(s) __Pyx_PyByteArray_FromString((const char*)s) +#define __Pyx_PyStr_FromUString(s) __Pyx_PyStr_FromString((const char*)s) +#define __Pyx_PyUnicode_FromUString(s) __Pyx_PyUnicode_FromString((const char*)s) #if PY_MAJOR_VERSION < 3 static CYTHON_INLINE size_t __Pyx_Py_UNICODE_strlen(const Py_UNICODE *u) { @@ -537,25 +312,18 @@ static CYTHON_INLINE size_t __Pyx_Py_UNICODE_strlen(const Py_UNICODE *u) #define __Pyx_PyUnicode_FromUnicode(u) PyUnicode_FromUnicode(u, __Pyx_Py_UNICODE_strlen(u)) #define __Pyx_PyUnicode_FromUnicodeAndLength PyUnicode_FromUnicode #define __Pyx_PyUnicode_AsUnicode PyUnicode_AsUnicode -#define __Pyx_NewRef(obj) (Py_INCREF(obj), obj) -#define __Pyx_Owned_Py_None(b) __Pyx_NewRef(Py_None) -#define __Pyx_PyBool_FromLong(b) ((b) ? __Pyx_NewRef(Py_True) : __Pyx_NewRef(Py_False)) +#define __Pyx_Owned_Py_None(b) (Py_INCREF(Py_None), Py_None) +#define __Pyx_PyBool_FromLong(b) ((b) ? (Py_INCREF(Py_True), Py_True) : (Py_INCREF(Py_False), Py_False)) static CYTHON_INLINE int __Pyx_PyObject_IsTrue(PyObject*); -static CYTHON_INLINE PyObject* __Pyx_PyNumber_IntOrLong(PyObject* x); +static CYTHON_INLINE PyObject* __Pyx_PyNumber_Int(PyObject* x); static CYTHON_INLINE Py_ssize_t __Pyx_PyIndex_AsSsize_t(PyObject*); static CYTHON_INLINE PyObject * __Pyx_PyInt_FromSize_t(size_t); -#if CYTHON_ASSUME_SAFE_MACROS +#if CYTHON_COMPILING_IN_CPYTHON #define __pyx_PyFloat_AsDouble(x) (PyFloat_CheckExact(x) ? PyFloat_AS_DOUBLE(x) : PyFloat_AsDouble(x)) #else #define __pyx_PyFloat_AsDouble(x) PyFloat_AsDouble(x) #endif #define __pyx_PyFloat_AsFloat(x) ((float) __pyx_PyFloat_AsDouble(x)) -#if PY_MAJOR_VERSION >= 3 -#define __Pyx_PyNumber_Int(x) (PyLong_CheckExact(x) ? __Pyx_NewRef(x) : PyNumber_Long(x)) -#else -#define __Pyx_PyNumber_Int(x) (PyInt_CheckExact(x) ? __Pyx_NewRef(x) : PyNumber_Int(x)) -#endif -#define __Pyx_PyNumber_Float(x) (PyFloat_CheckExact(x) ? __Pyx_NewRef(x) : PyNumber_Float(x)) #if PY_MAJOR_VERSION < 3 && __PYX_DEFAULT_STRING_ENCODING_IS_ASCII static int __Pyx_sys_getdefaultencoding_not_ascii; static int __Pyx_init_sys_getdefaultencoding_params(void) { @@ -566,7 +334,7 @@ static int __Pyx_init_sys_getdefaultencoding_params(void) { const char* default_encoding_c; sys = PyImport_ImportModule("sys"); if (!sys) goto bad; - default_encoding = PyObject_CallMethod(sys, (char*) "getdefaultencoding", NULL); + default_encoding = PyObject_CallMethod(sys, (char*) (const char*) "getdefaultencoding", NULL); Py_DECREF(sys); if (!default_encoding) goto bad; default_encoding_c = PyBytes_AsString(default_encoding); @@ -646,13 +414,11 @@ static PyObject *__pyx_d; static PyObject *__pyx_b; static PyObject *__pyx_empty_tuple; static PyObject *__pyx_empty_bytes; -static PyObject *__pyx_empty_unicode; static int __pyx_lineno; static int __pyx_clineno = 0; static const char * __pyx_cfilenm= __FILE__; static const char *__pyx_filename; -/* Header.proto */ #if !defined(CYTHON_CCOMPLEX) #if defined(__cplusplus) #define CYTHON_CCOMPLEX 1 @@ -681,7 +447,7 @@ static const char *__pyx_f[] = { "type.pxd", }; -/* "../../../../../usr/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":725 +/* "../../../../usr/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":723 * # in Cython to enable them only on the right systems. * * ctypedef npy_int8 int8_t # <<<<<<<<<<<<<< @@ -690,7 +456,7 @@ static const char *__pyx_f[] = { */ typedef npy_int8 __pyx_t_5numpy_int8_t; -/* "../../../../../usr/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":726 +/* "../../../../usr/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":724 * * ctypedef npy_int8 int8_t * ctypedef npy_int16 int16_t # <<<<<<<<<<<<<< @@ -699,7 +465,7 @@ typedef npy_int8 __pyx_t_5numpy_int8_t; */ typedef npy_int16 __pyx_t_5numpy_int16_t; -/* "../../../../../usr/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":727 +/* "../../../../usr/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":725 * ctypedef npy_int8 int8_t * ctypedef npy_int16 int16_t * ctypedef npy_int32 int32_t # <<<<<<<<<<<<<< @@ -708,7 +474,7 @@ typedef npy_int16 __pyx_t_5numpy_int16_t; */ typedef npy_int32 __pyx_t_5numpy_int32_t; -/* "../../../../../usr/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":728 +/* "../../../../usr/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":726 * ctypedef npy_int16 int16_t * ctypedef npy_int32 int32_t * ctypedef npy_int64 int64_t # <<<<<<<<<<<<<< @@ -717,7 +483,7 @@ typedef npy_int32 __pyx_t_5numpy_int32_t; */ typedef npy_int64 __pyx_t_5numpy_int64_t; -/* "../../../../../usr/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":732 +/* "../../../../usr/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":730 * #ctypedef npy_int128 int128_t * * ctypedef npy_uint8 uint8_t # <<<<<<<<<<<<<< @@ -726,7 +492,7 @@ typedef npy_int64 __pyx_t_5numpy_int64_t; */ typedef npy_uint8 __pyx_t_5numpy_uint8_t; -/* "../../../../../usr/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":733 +/* "../../../../usr/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":731 * * ctypedef npy_uint8 uint8_t * ctypedef npy_uint16 uint16_t # <<<<<<<<<<<<<< @@ -735,7 +501,7 @@ typedef npy_uint8 __pyx_t_5numpy_uint8_t; */ typedef npy_uint16 __pyx_t_5numpy_uint16_t; -/* "../../../../../usr/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":734 +/* "../../../../usr/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":732 * ctypedef npy_uint8 uint8_t * ctypedef npy_uint16 uint16_t * ctypedef npy_uint32 uint32_t # <<<<<<<<<<<<<< @@ -744,7 +510,7 @@ typedef npy_uint16 __pyx_t_5numpy_uint16_t; */ typedef npy_uint32 __pyx_t_5numpy_uint32_t; -/* "../../../../../usr/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":735 +/* "../../../../usr/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":733 * ctypedef npy_uint16 uint16_t * ctypedef npy_uint32 uint32_t * ctypedef npy_uint64 uint64_t # <<<<<<<<<<<<<< @@ -753,7 +519,7 @@ typedef npy_uint32 __pyx_t_5numpy_uint32_t; */ typedef npy_uint64 __pyx_t_5numpy_uint64_t; -/* "../../../../../usr/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":739 +/* "../../../../usr/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":737 * #ctypedef npy_uint128 uint128_t * * ctypedef npy_float32 float32_t # <<<<<<<<<<<<<< @@ -762,7 +528,7 @@ typedef npy_uint64 __pyx_t_5numpy_uint64_t; */ typedef npy_float32 __pyx_t_5numpy_float32_t; -/* "../../../../../usr/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":740 +/* "../../../../usr/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":738 * * ctypedef npy_float32 float32_t * ctypedef npy_float64 float64_t # <<<<<<<<<<<<<< @@ -771,7 +537,7 @@ typedef npy_float32 __pyx_t_5numpy_float32_t; */ typedef npy_float64 __pyx_t_5numpy_float64_t; -/* "../../../../../usr/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":749 +/* "../../../../usr/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":747 * # The int types are mapped a bit surprising -- * # numpy.int corresponds to 'l' and numpy.long to 'q' * ctypedef npy_long int_t # <<<<<<<<<<<<<< @@ -780,7 +546,7 @@ typedef npy_float64 __pyx_t_5numpy_float64_t; */ typedef npy_long __pyx_t_5numpy_int_t; -/* "../../../../../usr/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":750 +/* "../../../../usr/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":748 * # numpy.int corresponds to 'l' and numpy.long to 'q' * ctypedef npy_long int_t * ctypedef npy_longlong long_t # <<<<<<<<<<<<<< @@ -789,7 +555,7 @@ typedef npy_long __pyx_t_5numpy_int_t; */ typedef npy_longlong __pyx_t_5numpy_long_t; -/* "../../../../../usr/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":751 +/* "../../../../usr/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":749 * ctypedef npy_long int_t * ctypedef npy_longlong long_t * ctypedef npy_longlong longlong_t # <<<<<<<<<<<<<< @@ -798,7 +564,7 @@ typedef npy_longlong __pyx_t_5numpy_long_t; */ typedef npy_longlong __pyx_t_5numpy_longlong_t; -/* "../../../../../usr/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":753 +/* "../../../../usr/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":751 * ctypedef npy_longlong longlong_t * * ctypedef npy_ulong uint_t # <<<<<<<<<<<<<< @@ -807,7 +573,7 @@ typedef npy_longlong __pyx_t_5numpy_longlong_t; */ typedef npy_ulong __pyx_t_5numpy_uint_t; -/* "../../../../../usr/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":754 +/* "../../../../usr/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":752 * * ctypedef npy_ulong uint_t * ctypedef npy_ulonglong ulong_t # <<<<<<<<<<<<<< @@ -816,7 +582,7 @@ typedef npy_ulong __pyx_t_5numpy_uint_t; */ typedef npy_ulonglong __pyx_t_5numpy_ulong_t; -/* "../../../../../usr/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":755 +/* "../../../../usr/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":753 * ctypedef npy_ulong uint_t * ctypedef npy_ulonglong ulong_t * ctypedef npy_ulonglong ulonglong_t # <<<<<<<<<<<<<< @@ -825,7 +591,7 @@ typedef npy_ulonglong __pyx_t_5numpy_ulong_t; */ typedef npy_ulonglong __pyx_t_5numpy_ulonglong_t; -/* "../../../../../usr/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":757 +/* "../../../../usr/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":755 * ctypedef npy_ulonglong ulonglong_t * * ctypedef npy_intp intp_t # <<<<<<<<<<<<<< @@ -834,7 +600,7 @@ typedef npy_ulonglong __pyx_t_5numpy_ulonglong_t; */ typedef npy_intp __pyx_t_5numpy_intp_t; -/* "../../../../../usr/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":758 +/* "../../../../usr/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":756 * * ctypedef npy_intp intp_t * ctypedef npy_uintp uintp_t # <<<<<<<<<<<<<< @@ -843,7 +609,7 @@ typedef npy_intp __pyx_t_5numpy_intp_t; */ typedef npy_uintp __pyx_t_5numpy_uintp_t; -/* "../../../../../usr/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":760 +/* "../../../../usr/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":758 * ctypedef npy_uintp uintp_t * * ctypedef npy_double float_t # <<<<<<<<<<<<<< @@ -852,7 +618,7 @@ typedef npy_uintp __pyx_t_5numpy_uintp_t; */ typedef npy_double __pyx_t_5numpy_float_t; -/* "../../../../../usr/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":761 +/* "../../../../usr/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":759 * * ctypedef npy_double float_t * ctypedef npy_double double_t # <<<<<<<<<<<<<< @@ -861,7 +627,7 @@ typedef npy_double __pyx_t_5numpy_float_t; */ typedef npy_double __pyx_t_5numpy_double_t; -/* "../../../../../usr/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":762 +/* "../../../../usr/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":760 * ctypedef npy_double float_t * ctypedef npy_double double_t * ctypedef npy_longdouble longdouble_t # <<<<<<<<<<<<<< @@ -869,7 +635,6 @@ typedef npy_double __pyx_t_5numpy_double_t; * ctypedef npy_cfloat cfloat_t */ typedef npy_longdouble __pyx_t_5numpy_longdouble_t; -/* Declarations.proto */ #if CYTHON_CCOMPLEX #ifdef __cplusplus typedef ::std::complex< float > __pyx_t_float_complex; @@ -879,9 +644,7 @@ typedef npy_longdouble __pyx_t_5numpy_longdouble_t; #else typedef struct { float real, imag; } __pyx_t_float_complex; #endif -static CYTHON_INLINE __pyx_t_float_complex __pyx_t_float_complex_from_parts(float, float); -/* Declarations.proto */ #if CYTHON_CCOMPLEX #ifdef __cplusplus typedef ::std::complex< double > __pyx_t_double_complex; @@ -891,7 +654,6 @@ static CYTHON_INLINE __pyx_t_float_complex __pyx_t_float_complex_from_parts(floa #else typedef struct { double real, imag; } __pyx_t_double_complex; #endif -static CYTHON_INLINE __pyx_t_double_complex __pyx_t_double_complex_from_parts(double, double); /*--- Type declarations ---*/ @@ -899,7 +661,7 @@ struct __pyx_obj_4silx_2io_8specfile_SpecFile; struct __pyx_obj_4silx_2io_8specfile___pyx_scope_struct____iter__; struct __pyx_obj_4silx_2io_8specfile___pyx_scope_struct_1___iter__; -/* "../../../../../usr/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":764 +/* "../../../../usr/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":762 * ctypedef npy_longdouble longdouble_t * * ctypedef npy_cfloat cfloat_t # <<<<<<<<<<<<<< @@ -908,7 +670,7 @@ struct __pyx_obj_4silx_2io_8specfile___pyx_scope_struct_1___iter__; */ typedef npy_cfloat __pyx_t_5numpy_cfloat_t; -/* "../../../../../usr/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":765 +/* "../../../../usr/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":763 * * ctypedef npy_cfloat cfloat_t * ctypedef npy_cdouble cdouble_t # <<<<<<<<<<<<<< @@ -917,7 +679,7 @@ typedef npy_cfloat __pyx_t_5numpy_cfloat_t; */ typedef npy_cdouble __pyx_t_5numpy_cdouble_t; -/* "../../../../../usr/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":766 +/* "../../../../usr/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":764 * ctypedef npy_cfloat cfloat_t * ctypedef npy_cdouble cdouble_t * ctypedef npy_clongdouble clongdouble_t # <<<<<<<<<<<<<< @@ -926,7 +688,7 @@ typedef npy_cdouble __pyx_t_5numpy_cdouble_t; */ typedef npy_clongdouble __pyx_t_5numpy_clongdouble_t; -/* "../../../../../usr/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":768 +/* "../../../../usr/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":766 * ctypedef npy_clongdouble clongdouble_t * * ctypedef npy_cdouble complex_t # <<<<<<<<<<<<<< @@ -944,7 +706,7 @@ typedef npy_cdouble __pyx_t_5numpy_complex_t; */ typedef struct _SpecFile __pyx_t_4silx_2io_16specfile_wrapper_SpecFileHandle; -/* "silx/io/specfile.pyx":644 +/* "silx/io/specfile.pyx":643 * * * cdef class SpecFile(object): # <<<<<<<<<<<<<< @@ -974,7 +736,7 @@ struct __pyx_obj_4silx_2io_8specfile___pyx_scope_struct____iter__ { }; -/* "silx/io/specfile.pyx":694 +/* "silx/io/specfile.pyx":698 * return specfile_wrapper.SfScanNo(self.handle) * * def __iter__(self): # <<<<<<<<<<<<<< @@ -989,9 +751,6 @@ struct __pyx_obj_4silx_2io_8specfile___pyx_scope_struct_1___iter__ { Py_ssize_t __pyx_t_1; }; - -/* --- Runtime support code (head) --- */ -/* Refnanny.proto */ #ifndef CYTHON_REFNANNY #define CYTHON_REFNANNY 0 #endif @@ -1008,19 +767,19 @@ struct __pyx_obj_4silx_2io_8specfile___pyx_scope_struct_1___iter__ { static __Pyx_RefNannyAPIStruct *__Pyx_RefNannyImportAPI(const char *modname); #define __Pyx_RefNannyDeclarations void *__pyx_refnanny = NULL; #ifdef WITH_THREAD - #define __Pyx_RefNannySetupContext(name, acquire_gil)\ - if (acquire_gil) {\ - PyGILState_STATE __pyx_gilstate_save = PyGILState_Ensure();\ - __pyx_refnanny = __Pyx_RefNanny->SetupContext((name), __LINE__, __FILE__);\ - PyGILState_Release(__pyx_gilstate_save);\ - } else {\ - __pyx_refnanny = __Pyx_RefNanny->SetupContext((name), __LINE__, __FILE__);\ + #define __Pyx_RefNannySetupContext(name, acquire_gil) \ + if (acquire_gil) { \ + PyGILState_STATE __pyx_gilstate_save = PyGILState_Ensure(); \ + __pyx_refnanny = __Pyx_RefNanny->SetupContext((name), __LINE__, __FILE__); \ + PyGILState_Release(__pyx_gilstate_save); \ + } else { \ + __pyx_refnanny = __Pyx_RefNanny->SetupContext((name), __LINE__, __FILE__); \ } #else - #define __Pyx_RefNannySetupContext(name, acquire_gil)\ + #define __Pyx_RefNannySetupContext(name, acquire_gil) \ __pyx_refnanny = __Pyx_RefNanny->SetupContext((name), __LINE__, __FILE__) #endif - #define __Pyx_RefNannyFinishContext()\ + #define __Pyx_RefNannyFinishContext() \ __Pyx_RefNanny->FinishContext(&__pyx_refnanny) #define __Pyx_INCREF(r) __Pyx_RefNanny->INCREF(__pyx_refnanny, (PyObject *)(r), __LINE__) #define __Pyx_DECREF(r) __Pyx_RefNanny->DECREF(__pyx_refnanny, (PyObject *)(r), __LINE__) @@ -1043,19 +802,18 @@ struct __pyx_obj_4silx_2io_8specfile___pyx_scope_struct_1___iter__ { #define __Pyx_XGOTREF(r) #define __Pyx_XGIVEREF(r) #endif -#define __Pyx_XDECREF_SET(r, v) do {\ - PyObject *tmp = (PyObject *) r;\ - r = v; __Pyx_XDECREF(tmp);\ +#define __Pyx_XDECREF_SET(r, v) do { \ + PyObject *tmp = (PyObject *) r; \ + r = v; __Pyx_XDECREF(tmp); \ } while (0) -#define __Pyx_DECREF_SET(r, v) do {\ - PyObject *tmp = (PyObject *) r;\ - r = v; __Pyx_DECREF(tmp);\ +#define __Pyx_DECREF_SET(r, v) do { \ + PyObject *tmp = (PyObject *) r; \ + r = v; __Pyx_DECREF(tmp); \ } while (0) #define __Pyx_CLEAR(r) do { PyObject* tmp = ((PyObject*)(r)); r = NULL; __Pyx_DECREF(tmp);} while(0) #define __Pyx_XCLEAR(r) do { if((r) != NULL) {PyObject* tmp = ((PyObject*)(r)); r = NULL; __Pyx_DECREF(tmp);}} while(0) -/* PyObjectGetAttrStr.proto */ -#if CYTHON_USE_TYPE_SLOTS +#if CYTHON_COMPILING_IN_CPYTHON static CYTHON_INLINE PyObject* __Pyx_PyObject_GetAttrStr(PyObject* obj, PyObject* attr_name) { PyTypeObject* tp = Py_TYPE(obj); if (likely(tp->tp_getattro)) @@ -1070,23 +828,18 @@ static CYTHON_INLINE PyObject* __Pyx_PyObject_GetAttrStr(PyObject* obj, PyObject #define __Pyx_PyObject_GetAttrStr(o,n) PyObject_GetAttr(o,n) #endif -/* GetBuiltinName.proto */ static PyObject *__Pyx_GetBuiltinName(PyObject *name); -/* RaiseArgTupleInvalid.proto */ static void __Pyx_RaiseArgtupleInvalid(const char* func_name, int exact, Py_ssize_t num_min, Py_ssize_t num_max, Py_ssize_t num_found); -/* RaiseDoubleKeywords.proto */ static void __Pyx_RaiseDoubleKeywordsError(const char* func_name, PyObject* kw_name); -/* ParseKeywords.proto */ -static int __Pyx_ParseOptionalKeywords(PyObject *kwds, PyObject **argnames[],\ - PyObject *kwds2, PyObject *values[], Py_ssize_t num_pos_args,\ +static int __Pyx_ParseOptionalKeywords(PyObject *kwds, PyObject **argnames[], \ + PyObject *kwds2, PyObject *values[], Py_ssize_t num_pos_args, \ const char* function_name); -/* PyObjectSetAttrStr.proto */ -#if CYTHON_USE_TYPE_SLOTS +#if CYTHON_COMPILING_IN_CPYTHON #define __Pyx_PyObject_DelAttrStr(o,n) __Pyx_PyObject_SetAttrStr(o,n,NULL) static CYTHON_INLINE int __Pyx_PyObject_SetAttrStr(PyObject* obj, PyObject* attr_name, PyObject* value) { PyTypeObject* tp = Py_TYPE(obj); @@ -1103,54 +856,30 @@ static CYTHON_INLINE int __Pyx_PyObject_SetAttrStr(PyObject* obj, PyObject* attr #define __Pyx_PyObject_SetAttrStr(o,n,v) PyObject_SetAttr(o,n,v) #endif -/* PyCFunctionFastCall.proto */ -#if CYTHON_FAST_PYCCALL -static CYTHON_INLINE PyObject *__Pyx_PyCFunction_FastCall(PyObject *func, PyObject **args, Py_ssize_t nargs); -#else -#define __Pyx_PyCFunction_FastCall(func, args, nargs) (assert(0), NULL) -#endif - -/* PyFunctionFastCall.proto */ -#if CYTHON_FAST_PYCALL -#define __Pyx_PyFunction_FastCall(func, args, nargs)\ - __Pyx_PyFunction_FastCallDict((func), (args), (nargs), NULL) -#if 1 || PY_VERSION_HEX < 0x030600B1 -static PyObject *__Pyx_PyFunction_FastCallDict(PyObject *func, PyObject **args, int nargs, PyObject *kwargs); -#else -#define __Pyx_PyFunction_FastCallDict(func, args, nargs, kwargs) _PyFunction_FastCallDict(func, args, nargs, kwargs) -#endif -#endif - -/* PyObjectCall.proto */ #if CYTHON_COMPILING_IN_CPYTHON static CYTHON_INLINE PyObject* __Pyx_PyObject_Call(PyObject *func, PyObject *arg, PyObject *kw); #else #define __Pyx_PyObject_Call(func, arg, kw) PyObject_Call(func, arg, kw) #endif -/* PyObjectCallMethO.proto */ #if CYTHON_COMPILING_IN_CPYTHON static CYTHON_INLINE PyObject* __Pyx_PyObject_CallMethO(PyObject *func, PyObject *arg); #endif -/* PyObjectCallOneArg.proto */ static CYTHON_INLINE PyObject* __Pyx_PyObject_CallOneArg(PyObject *func, PyObject *arg); -/* PyObjectCallNoArg.proto */ #if CYTHON_COMPILING_IN_CPYTHON static CYTHON_INLINE PyObject* __Pyx_PyObject_CallNoArg(PyObject *func); #else #define __Pyx_PyObject_CallNoArg(func) __Pyx_PyObject_Call(func, __pyx_empty_tuple, NULL) #endif -/* PySequenceContains.proto */ -static CYTHON_INLINE int __Pyx_PySequence_ContainsTF(PyObject* item, PyObject* seq, int eq) { +static CYTHON_INLINE int __Pyx_PySequence_Contains(PyObject* item, PyObject* seq, int eq) { int result = PySequence_Contains(seq, item); return unlikely(result < 0) ? result : (result == (eq == Py_EQ)); } -/* ListCompAppend.proto */ -#if CYTHON_USE_PYLIST_INTERNALS && CYTHON_ASSUME_SAFE_MACROS +#if CYTHON_COMPILING_IN_CPYTHON static CYTHON_INLINE int __Pyx_ListComp_Append(PyObject* list, PyObject* x) { PyListObject* L = (PyListObject*) list; Py_ssize_t len = Py_SIZE(list); @@ -1166,20 +895,15 @@ static CYTHON_INLINE int __Pyx_ListComp_Append(PyObject* list, PyObject* x) { #define __Pyx_ListComp_Append(L,x) PyList_Append(L,x) #endif -/* RaiseTooManyValuesToUnpack.proto */ static CYTHON_INLINE void __Pyx_RaiseTooManyValuesError(Py_ssize_t expected); -/* RaiseNeedMoreValuesToUnpack.proto */ static CYTHON_INLINE void __Pyx_RaiseNeedMoreValuesError(Py_ssize_t index); -/* IterFinish.proto */ static CYTHON_INLINE int __Pyx_IterFinish(void); -/* UnpackItemEndCheck.proto */ static int __Pyx_IternextUnpackEndCheck(PyObject *retval, Py_ssize_t expected); -/* ListAppend.proto */ -#if CYTHON_USE_PYLIST_INTERNALS && CYTHON_ASSUME_SAFE_MACROS +#if CYTHON_COMPILING_IN_CPYTHON static CYTHON_INLINE int __Pyx_PyList_Append(PyObject* list, PyObject* x) { PyListObject* L = (PyListObject*) list; Py_ssize_t len = Py_SIZE(list); @@ -1195,35 +919,24 @@ static CYTHON_INLINE int __Pyx_PyList_Append(PyObject* list, PyObject* x) { #define __Pyx_PyList_Append(L,x) PyList_Append(L,x) #endif -/* PyObjectCallMethod1.proto */ static PyObject* __Pyx_PyObject_CallMethod1(PyObject* obj, PyObject* method_name, PyObject* arg); -/* append.proto */ static CYTHON_INLINE int __Pyx_PyObject_Append(PyObject* L, PyObject* x); -/* PyIntBinop.proto */ -#if !CYTHON_COMPILING_IN_PYPY -static PyObject* __Pyx_PyInt_AddObjC(PyObject *op1, PyObject *op2, long intval, int inplace); -#else -#define __Pyx_PyInt_AddObjC(op1, op2, intval, inplace)\ - (inplace ? PyNumber_InPlaceAdd(op1, op2) : PyNumber_Add(op1, op2)) -#endif - -/* GetItemInt.proto */ -#define __Pyx_GetItemInt(o, i, type, is_signed, to_py_func, is_list, wraparound, boundscheck)\ - (__Pyx_fits_Py_ssize_t(i, type, is_signed) ?\ - __Pyx_GetItemInt_Fast(o, (Py_ssize_t)i, is_list, wraparound, boundscheck) :\ - (is_list ? (PyErr_SetString(PyExc_IndexError, "list index out of range"), (PyObject*)NULL) :\ +#define __Pyx_GetItemInt(o, i, type, is_signed, to_py_func, is_list, wraparound, boundscheck) \ + (__Pyx_fits_Py_ssize_t(i, type, is_signed) ? \ + __Pyx_GetItemInt_Fast(o, (Py_ssize_t)i, is_list, wraparound, boundscheck) : \ + (is_list ? (PyErr_SetString(PyExc_IndexError, "list index out of range"), (PyObject*)NULL) : \ __Pyx_GetItemInt_Generic(o, to_py_func(i)))) -#define __Pyx_GetItemInt_List(o, i, type, is_signed, to_py_func, is_list, wraparound, boundscheck)\ - (__Pyx_fits_Py_ssize_t(i, type, is_signed) ?\ - __Pyx_GetItemInt_List_Fast(o, (Py_ssize_t)i, wraparound, boundscheck) :\ +#define __Pyx_GetItemInt_List(o, i, type, is_signed, to_py_func, is_list, wraparound, boundscheck) \ + (__Pyx_fits_Py_ssize_t(i, type, is_signed) ? \ + __Pyx_GetItemInt_List_Fast(o, (Py_ssize_t)i, wraparound, boundscheck) : \ (PyErr_SetString(PyExc_IndexError, "list index out of range"), (PyObject*)NULL)) static CYTHON_INLINE PyObject *__Pyx_GetItemInt_List_Fast(PyObject *o, Py_ssize_t i, int wraparound, int boundscheck); -#define __Pyx_GetItemInt_Tuple(o, i, type, is_signed, to_py_func, is_list, wraparound, boundscheck)\ - (__Pyx_fits_Py_ssize_t(i, type, is_signed) ?\ - __Pyx_GetItemInt_Tuple_Fast(o, (Py_ssize_t)i, wraparound, boundscheck) :\ +#define __Pyx_GetItemInt_Tuple(o, i, type, is_signed, to_py_func, is_list, wraparound, boundscheck) \ + (__Pyx_fits_Py_ssize_t(i, type, is_signed) ? \ + __Pyx_GetItemInt_Tuple_Fast(o, (Py_ssize_t)i, wraparound, boundscheck) : \ (PyErr_SetString(PyExc_IndexError, "tuple index out of range"), (PyObject*)NULL)) static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Tuple_Fast(PyObject *o, Py_ssize_t i, int wraparound, int boundscheck); @@ -1231,77 +944,49 @@ static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Generic(PyObject *o, PyObject* j static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Fast(PyObject *o, Py_ssize_t i, int is_list, int wraparound, int boundscheck); -/* PyIntBinop.proto */ -#if !CYTHON_COMPILING_IN_PYPY -static PyObject* __Pyx_PyInt_SubtractObjC(PyObject *op1, PyObject *op2, long intval, int inplace); -#else -#define __Pyx_PyInt_SubtractObjC(op1, op2, intval, inplace)\ - (inplace ? PyNumber_InPlaceSubtract(op1, op2) : PyNumber_Subtract(op1, op2)) -#endif +static CYTHON_INLINE void __Pyx_ErrRestore(PyObject *type, PyObject *value, PyObject *tb); +static CYTHON_INLINE void __Pyx_ErrFetch(PyObject **type, PyObject **value, PyObject **tb); -/* PyThreadStateGet.proto */ -#if CYTHON_FAST_THREAD_STATE -#define __Pyx_PyThreadState_declare PyThreadState *__pyx_tstate; -#define __Pyx_PyThreadState_assign __pyx_tstate = PyThreadState_GET(); -#else -#define __Pyx_PyThreadState_declare -#define __Pyx_PyThreadState_assign -#endif +static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb, PyObject *cause); -/* PyErrFetchRestore.proto */ -#if CYTHON_FAST_THREAD_STATE -#define __Pyx_ErrRestoreWithState(type, value, tb) __Pyx_ErrRestoreInState(PyThreadState_GET(), type, value, tb) -#define __Pyx_ErrFetchWithState(type, value, tb) __Pyx_ErrFetchInState(PyThreadState_GET(), type, value, tb) -#define __Pyx_ErrRestore(type, value, tb) __Pyx_ErrRestoreInState(__pyx_tstate, type, value, tb) -#define __Pyx_ErrFetch(type, value, tb) __Pyx_ErrFetchInState(__pyx_tstate, type, value, tb) -static CYTHON_INLINE void __Pyx_ErrRestoreInState(PyThreadState *tstate, PyObject *type, PyObject *value, PyObject *tb); -static CYTHON_INLINE void __Pyx_ErrFetchInState(PyThreadState *tstate, PyObject **type, PyObject **value, PyObject **tb); -#else -#define __Pyx_ErrRestoreWithState(type, value, tb) PyErr_Restore(type, value, tb) -#define __Pyx_ErrFetchWithState(type, value, tb) PyErr_Fetch(type, value, tb) -#define __Pyx_ErrRestore(type, value, tb) PyErr_Restore(type, value, tb) -#define __Pyx_ErrFetch(type, value, tb) PyErr_Fetch(type, value, tb) -#endif +static CYTHON_INLINE void __Pyx_ExceptionSave(PyObject **type, PyObject **value, PyObject **tb); +static void __Pyx_ExceptionReset(PyObject *type, PyObject *value, PyObject *tb); -/* RaiseException.proto */ -static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb, PyObject *cause); +static int __Pyx_GetException(PyObject **type, PyObject **value, PyObject **tb); -/* SaveResetException.proto */ -#if CYTHON_FAST_THREAD_STATE -#define __Pyx_ExceptionSave(type, value, tb) __Pyx__ExceptionSave(__pyx_tstate, type, value, tb) -static CYTHON_INLINE void __Pyx__ExceptionSave(PyThreadState *tstate, PyObject **type, PyObject **value, PyObject **tb); -#define __Pyx_ExceptionReset(type, value, tb) __Pyx__ExceptionReset(__pyx_tstate, type, value, tb) -static CYTHON_INLINE void __Pyx__ExceptionReset(PyThreadState *tstate, PyObject *type, PyObject *value, PyObject *tb); -#else -#define __Pyx_ExceptionSave(type, value, tb) PyErr_GetExcInfo(type, value, tb) -#define __Pyx_ExceptionReset(type, value, tb) PyErr_SetExcInfo(type, value, tb) -#endif +static CYTHON_INLINE PyObject *__Pyx_GetModuleGlobalName(PyObject *name); -/* PyErrExceptionMatches.proto */ -#if CYTHON_FAST_THREAD_STATE -#define __Pyx_PyErr_ExceptionMatches(err) __Pyx_PyErr_ExceptionMatchesInState(__pyx_tstate, err) -static CYTHON_INLINE int __Pyx_PyErr_ExceptionMatchesInState(PyThreadState* tstate, PyObject* err); -#else -#define __Pyx_PyErr_ExceptionMatches(err) PyErr_ExceptionMatches(err) +#if CYTHON_COMPILING_IN_CPYTHON && PY_VERSION_HEX >= 0x02070000 +static CYTHON_INLINE PyObject* __Pyx_PyObject_LookupSpecial(PyObject* obj, PyObject* attr_name) { + PyObject *res; + PyTypeObject *tp = Py_TYPE(obj); +#if PY_MAJOR_VERSION < 3 + if (unlikely(PyInstance_Check(obj))) + return __Pyx_PyObject_GetAttrStr(obj, attr_name); #endif - -/* GetException.proto */ -#if CYTHON_FAST_THREAD_STATE -#define __Pyx_GetException(type, value, tb) __Pyx__GetException(__pyx_tstate, type, value, tb) -static int __Pyx__GetException(PyThreadState *tstate, PyObject **type, PyObject **value, PyObject **tb); + res = _PyType_Lookup(tp, attr_name); + if (likely(res)) { + descrgetfunc f = Py_TYPE(res)->tp_descr_get; + if (!f) { + Py_INCREF(res); + } else { + res = f(res, obj, (PyObject *)tp); + } + } else { + PyErr_SetObject(PyExc_AttributeError, attr_name); + } + return res; +} #else -static int __Pyx_GetException(PyObject **type, PyObject **value, PyObject **tb); +#define __Pyx_PyObject_LookupSpecial(o,n) __Pyx_PyObject_GetAttrStr(o,n) #endif -/* GetModuleGlobalName.proto */ -static CYTHON_INLINE PyObject *__Pyx_GetModuleGlobalName(PyObject *name); +static CYTHON_INLINE void __Pyx_RaiseUnboundLocalError(const char *varname); -/* WriteUnraisableException.proto */ static void __Pyx_WriteUnraisable(const char *name, int clineno, int lineno, const char *filename, - int full_traceback, int nogil); + int full_traceback); -/* StringJoin.proto */ #if PY_MAJOR_VERSION < 3 #define __Pyx_PyString_Join __Pyx_PyBytes_Join #define __Pyx_PyBaseString_Join(s, v) (PyUnicode_CheckExact(s) ? PyUnicode_Join(s, v) : __Pyx_PyBytes_Join(s, v)) @@ -1319,14 +1004,12 @@ static void __Pyx_WriteUnraisable(const char *name, int clineno, static CYTHON_INLINE PyObject* __Pyx_PyBytes_Join(PyObject* sep, PyObject* values); #endif -/* PyDictContains.proto */ -static CYTHON_INLINE int __Pyx_PyDict_ContainsTF(PyObject* item, PyObject* dict, int eq) { +static CYTHON_INLINE int __Pyx_PyDict_Contains(PyObject* item, PyObject* dict, int eq) { int result = PyDict_Contains(dict, item); return unlikely(result < 0) ? result : (result == (eq == Py_EQ)); } -/* DictGetItem.proto */ -#if PY_MAJOR_VERSION >= 3 && !CYTHON_COMPILING_IN_PYPY +#if PY_MAJOR_VERSION >= 3 static PyObject *__Pyx_PyDict_GetItem(PyObject *d, PyObject* key) { PyObject *value; value = PyDict_GetItemWithError(d, key); @@ -1346,13 +1029,11 @@ static PyObject *__Pyx_PyDict_GetItem(PyObject *d, PyObject* key) { #define __Pyx_PyDict_GetItem(d, key) PyObject_GetItem(d, key) #endif -/* decode_c_bytes.proto */ static CYTHON_INLINE PyObject* __Pyx_decode_c_bytes( const char* cstring, Py_ssize_t length, Py_ssize_t start, Py_ssize_t stop, const char* encoding, const char* errors, PyObject* (*decode_func)(const char *s, Py_ssize_t size, const char *errors)); -/* decode_bytes.proto */ static CYTHON_INLINE PyObject* __Pyx_decode_bytes( PyObject* string, Py_ssize_t start, Py_ssize_t stop, const char* encoding, const char* errors, @@ -1362,67 +1043,47 @@ static CYTHON_INLINE PyObject* __Pyx_decode_bytes( start, stop, encoding, errors, decode_func); } -/* PyIntBinop.proto */ -#if !CYTHON_COMPILING_IN_PYPY -static PyObject* __Pyx_PyInt_EqObjC(PyObject *op1, PyObject *op2, long intval, int inplace); -#else -#define __Pyx_PyInt_EqObjC(op1, op2, intval, inplace)\ - PyObject_RichCompare(op1, op2, Py_EQ) - #endif - -/* ExtTypeTest.proto */ static CYTHON_INLINE int __Pyx_TypeTest(PyObject *obj, PyTypeObject *type); -/* SetItemInt.proto */ -#define __Pyx_SetItemInt(o, i, v, type, is_signed, to_py_func, is_list, wraparound, boundscheck)\ - (__Pyx_fits_Py_ssize_t(i, type, is_signed) ?\ - __Pyx_SetItemInt_Fast(o, (Py_ssize_t)i, v, is_list, wraparound, boundscheck) :\ - (is_list ? (PyErr_SetString(PyExc_IndexError, "list assignment index out of range"), -1) :\ +#define __Pyx_SetItemInt(o, i, v, type, is_signed, to_py_func, is_list, wraparound, boundscheck) \ + (__Pyx_fits_Py_ssize_t(i, type, is_signed) ? \ + __Pyx_SetItemInt_Fast(o, (Py_ssize_t)i, v, is_list, wraparound, boundscheck) : \ + (is_list ? (PyErr_SetString(PyExc_IndexError, "list assignment index out of range"), -1) : \ __Pyx_SetItemInt_Generic(o, to_py_func(i), v))) static CYTHON_INLINE int __Pyx_SetItemInt_Generic(PyObject *o, PyObject *j, PyObject *v); static CYTHON_INLINE int __Pyx_SetItemInt_Fast(PyObject *o, Py_ssize_t i, PyObject *v, int is_list, int wraparound, int boundscheck); -/* IncludeStringH.proto */ #include <string.h> -/* decode_c_string.proto */ static CYTHON_INLINE PyObject* __Pyx_decode_c_string( const char* cstring, Py_ssize_t start, Py_ssize_t stop, const char* encoding, const char* errors, PyObject* (*decode_func)(const char *s, Py_ssize_t size, const char *errors)); -/* RaiseNoneIterError.proto */ static CYTHON_INLINE void __Pyx_RaiseNoneNotIterableError(void); -/* Import.proto */ -static PyObject *__Pyx_Import(PyObject *name, PyObject *from_list, int level); - -/* CalculateMetaclass.proto */ static PyObject *__Pyx_CalculateMetaclass(PyTypeObject *metaclass, PyObject *bases); -/* Py3ClassCreate.proto */ static PyObject *__Pyx_Py3MetaclassPrepare(PyObject *metaclass, PyObject *bases, PyObject *name, PyObject *qualname, PyObject *mkw, PyObject *modname, PyObject *doc); static PyObject *__Pyx_Py3ClassCreate(PyObject *metaclass, PyObject *name, PyObject *bases, PyObject *dict, PyObject *mkw, int calculate_metaclass, int allow_py2_metaclass); -/* FetchCommonType.proto */ static PyTypeObject* __Pyx_FetchCommonType(PyTypeObject* type); -/* CythonFunction.proto */ #define __Pyx_CyFunction_USED 1 #include <structmember.h> #define __Pyx_CYFUNCTION_STATICMETHOD 0x01 #define __Pyx_CYFUNCTION_CLASSMETHOD 0x02 #define __Pyx_CYFUNCTION_CCLASS 0x04 -#define __Pyx_CyFunction_GetClosure(f)\ +#define __Pyx_CyFunction_GetClosure(f) \ (((__pyx_CyFunctionObject *) (f))->func_closure) -#define __Pyx_CyFunction_GetClassObj(f)\ +#define __Pyx_CyFunction_GetClassObj(f) \ (((__pyx_CyFunctionObject *) (f))->func_classobj) -#define __Pyx_CyFunction_Defaults(type, f)\ +#define __Pyx_CyFunction_Defaults(type, f) \ ((type *)(((__pyx_CyFunctionObject *) (f))->defaults)) -#define __Pyx_CyFunction_SetDefaultsGetter(f, g)\ +#define __Pyx_CyFunction_SetDefaultsGetter(f, g) \ ((__pyx_CyFunctionObject *) (f))->defaults_getter = (g) typedef struct { PyCFunctionObject func; @@ -1446,7 +1107,7 @@ typedef struct { PyObject *func_annotations; } __pyx_CyFunctionObject; static PyTypeObject *__pyx_CyFunctionType = 0; -#define __Pyx_CyFunction_NewEx(ml, flags, qualname, self, module, globals, code)\ +#define __Pyx_CyFunction_NewEx(ml, flags, qualname, self, module, globals, code) \ __Pyx_CyFunction_New(__pyx_CyFunctionType, ml, flags, qualname, self, module, globals, code) static PyObject *__Pyx_CyFunction_New(PyTypeObject *, PyMethodDef *ml, int flags, PyObject* qualname, @@ -1462,12 +1123,11 @@ static CYTHON_INLINE void __Pyx_CyFunction_SetDefaultsKwDict(PyObject *m, PyObject *dict); static CYTHON_INLINE void __Pyx_CyFunction_SetAnnotationsDict(PyObject *m, PyObject *dict); -static int __pyx_CyFunction_init(void); +static int __Pyx_CyFunction_init(void); -/* CodeObjectCache.proto */ typedef struct { - PyCodeObject* code_object; int code_line; + PyCodeObject* code_object; } __Pyx_CodeObjectCacheEntry; struct __Pyx_CodeObjectCache { int count; @@ -1479,17 +1139,19 @@ static int __pyx_bisect_code_objects(__Pyx_CodeObjectCacheEntry* entries, int co static PyCodeObject *__pyx_find_code_object(int code_line); static void __pyx_insert_code_object(int code_line, PyCodeObject* code_object); -/* AddTraceback.proto */ static void __Pyx_AddTraceback(const char *funcname, int c_line, int py_line, const char *filename); -/* CIntToPy.proto */ +static PyObject *__Pyx_Import(PyObject *name, PyObject *from_list, int level); + static CYTHON_INLINE PyObject* __Pyx_PyInt_From_long(long value); -/* CIntToPy.proto */ +static CYTHON_INLINE int __Pyx_PyInt_As_int(PyObject *); + static CYTHON_INLINE PyObject* __Pyx_PyInt_From_int(int value); -/* RealImag.proto */ +static CYTHON_INLINE long __Pyx_PyInt_As_long(PyObject *); + #if CYTHON_CCOMPLEX #ifdef __cplusplus #define __Pyx_CREAL(z) ((z).real()) @@ -1502,8 +1164,7 @@ static CYTHON_INLINE PyObject* __Pyx_PyInt_From_int(int value); #define __Pyx_CREAL(z) ((z).real) #define __Pyx_CIMAG(z) ((z).imag) #endif -#if defined(__cplusplus) && CYTHON_CCOMPLEX\ - && (defined(_WIN32) || defined(__clang__) || (defined(__GNUC__) && (__GNUC__ >= 5 || __GNUC__ == 4 && __GNUC_MINOR__ >= 4 )) || __cplusplus >= 201103) +#if (defined(_WIN32) || defined(__clang__)) && defined(__cplusplus) && CYTHON_CCOMPLEX #define __Pyx_SET_CREAL(z,x) ((z).real(x)) #define __Pyx_SET_CIMAG(z,y) ((z).imag(y)) #else @@ -1511,104 +1172,93 @@ static CYTHON_INLINE PyObject* __Pyx_PyInt_From_int(int value); #define __Pyx_SET_CIMAG(z,y) __Pyx_CIMAG(z) = (y) #endif -/* Arithmetic.proto */ +static CYTHON_INLINE __pyx_t_float_complex __pyx_t_float_complex_from_parts(float, float); + #if CYTHON_CCOMPLEX - #define __Pyx_c_eq_float(a, b) ((a)==(b)) - #define __Pyx_c_sum_float(a, b) ((a)+(b)) - #define __Pyx_c_diff_float(a, b) ((a)-(b)) - #define __Pyx_c_prod_float(a, b) ((a)*(b)) - #define __Pyx_c_quot_float(a, b) ((a)/(b)) - #define __Pyx_c_neg_float(a) (-(a)) + #define __Pyx_c_eqf(a, b) ((a)==(b)) + #define __Pyx_c_sumf(a, b) ((a)+(b)) + #define __Pyx_c_difff(a, b) ((a)-(b)) + #define __Pyx_c_prodf(a, b) ((a)*(b)) + #define __Pyx_c_quotf(a, b) ((a)/(b)) + #define __Pyx_c_negf(a) (-(a)) #ifdef __cplusplus - #define __Pyx_c_is_zero_float(z) ((z)==(float)0) - #define __Pyx_c_conj_float(z) (::std::conj(z)) + #define __Pyx_c_is_zerof(z) ((z)==(float)0) + #define __Pyx_c_conjf(z) (::std::conj(z)) #if 1 - #define __Pyx_c_abs_float(z) (::std::abs(z)) - #define __Pyx_c_pow_float(a, b) (::std::pow(a, b)) + #define __Pyx_c_absf(z) (::std::abs(z)) + #define __Pyx_c_powf(a, b) (::std::pow(a, b)) #endif #else - #define __Pyx_c_is_zero_float(z) ((z)==0) - #define __Pyx_c_conj_float(z) (conjf(z)) + #define __Pyx_c_is_zerof(z) ((z)==0) + #define __Pyx_c_conjf(z) (conjf(z)) #if 1 - #define __Pyx_c_abs_float(z) (cabsf(z)) - #define __Pyx_c_pow_float(a, b) (cpowf(a, b)) + #define __Pyx_c_absf(z) (cabsf(z)) + #define __Pyx_c_powf(a, b) (cpowf(a, b)) #endif #endif #else - static CYTHON_INLINE int __Pyx_c_eq_float(__pyx_t_float_complex, __pyx_t_float_complex); - static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_sum_float(__pyx_t_float_complex, __pyx_t_float_complex); - static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_diff_float(__pyx_t_float_complex, __pyx_t_float_complex); - static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_prod_float(__pyx_t_float_complex, __pyx_t_float_complex); - static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_quot_float(__pyx_t_float_complex, __pyx_t_float_complex); - static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_neg_float(__pyx_t_float_complex); - static CYTHON_INLINE int __Pyx_c_is_zero_float(__pyx_t_float_complex); - static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_conj_float(__pyx_t_float_complex); + static CYTHON_INLINE int __Pyx_c_eqf(__pyx_t_float_complex, __pyx_t_float_complex); + static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_sumf(__pyx_t_float_complex, __pyx_t_float_complex); + static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_difff(__pyx_t_float_complex, __pyx_t_float_complex); + static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_prodf(__pyx_t_float_complex, __pyx_t_float_complex); + static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_quotf(__pyx_t_float_complex, __pyx_t_float_complex); + static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_negf(__pyx_t_float_complex); + static CYTHON_INLINE int __Pyx_c_is_zerof(__pyx_t_float_complex); + static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_conjf(__pyx_t_float_complex); #if 1 - static CYTHON_INLINE float __Pyx_c_abs_float(__pyx_t_float_complex); - static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_pow_float(__pyx_t_float_complex, __pyx_t_float_complex); + static CYTHON_INLINE float __Pyx_c_absf(__pyx_t_float_complex); + static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_powf(__pyx_t_float_complex, __pyx_t_float_complex); #endif #endif -/* Arithmetic.proto */ +static CYTHON_INLINE __pyx_t_double_complex __pyx_t_double_complex_from_parts(double, double); + #if CYTHON_CCOMPLEX - #define __Pyx_c_eq_double(a, b) ((a)==(b)) - #define __Pyx_c_sum_double(a, b) ((a)+(b)) - #define __Pyx_c_diff_double(a, b) ((a)-(b)) - #define __Pyx_c_prod_double(a, b) ((a)*(b)) - #define __Pyx_c_quot_double(a, b) ((a)/(b)) - #define __Pyx_c_neg_double(a) (-(a)) + #define __Pyx_c_eq(a, b) ((a)==(b)) + #define __Pyx_c_sum(a, b) ((a)+(b)) + #define __Pyx_c_diff(a, b) ((a)-(b)) + #define __Pyx_c_prod(a, b) ((a)*(b)) + #define __Pyx_c_quot(a, b) ((a)/(b)) + #define __Pyx_c_neg(a) (-(a)) #ifdef __cplusplus - #define __Pyx_c_is_zero_double(z) ((z)==(double)0) - #define __Pyx_c_conj_double(z) (::std::conj(z)) + #define __Pyx_c_is_zero(z) ((z)==(double)0) + #define __Pyx_c_conj(z) (::std::conj(z)) #if 1 - #define __Pyx_c_abs_double(z) (::std::abs(z)) - #define __Pyx_c_pow_double(a, b) (::std::pow(a, b)) + #define __Pyx_c_abs(z) (::std::abs(z)) + #define __Pyx_c_pow(a, b) (::std::pow(a, b)) #endif #else - #define __Pyx_c_is_zero_double(z) ((z)==0) - #define __Pyx_c_conj_double(z) (conj(z)) + #define __Pyx_c_is_zero(z) ((z)==0) + #define __Pyx_c_conj(z) (conj(z)) #if 1 - #define __Pyx_c_abs_double(z) (cabs(z)) - #define __Pyx_c_pow_double(a, b) (cpow(a, b)) + #define __Pyx_c_abs(z) (cabs(z)) + #define __Pyx_c_pow(a, b) (cpow(a, b)) #endif #endif #else - static CYTHON_INLINE int __Pyx_c_eq_double(__pyx_t_double_complex, __pyx_t_double_complex); - static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_sum_double(__pyx_t_double_complex, __pyx_t_double_complex); - static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_diff_double(__pyx_t_double_complex, __pyx_t_double_complex); - static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_prod_double(__pyx_t_double_complex, __pyx_t_double_complex); - static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_quot_double(__pyx_t_double_complex, __pyx_t_double_complex); - static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_neg_double(__pyx_t_double_complex); - static CYTHON_INLINE int __Pyx_c_is_zero_double(__pyx_t_double_complex); - static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_conj_double(__pyx_t_double_complex); + static CYTHON_INLINE int __Pyx_c_eq(__pyx_t_double_complex, __pyx_t_double_complex); + static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_sum(__pyx_t_double_complex, __pyx_t_double_complex); + static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_diff(__pyx_t_double_complex, __pyx_t_double_complex); + static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_prod(__pyx_t_double_complex, __pyx_t_double_complex); + static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_quot(__pyx_t_double_complex, __pyx_t_double_complex); + static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_neg(__pyx_t_double_complex); + static CYTHON_INLINE int __Pyx_c_is_zero(__pyx_t_double_complex); + static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_conj(__pyx_t_double_complex); #if 1 - static CYTHON_INLINE double __Pyx_c_abs_double(__pyx_t_double_complex); - static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_pow_double(__pyx_t_double_complex, __pyx_t_double_complex); + static CYTHON_INLINE double __Pyx_c_abs(__pyx_t_double_complex); + static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_pow(__pyx_t_double_complex, __pyx_t_double_complex); #endif #endif -/* CIntToPy.proto */ -static CYTHON_INLINE PyObject* __Pyx_PyInt_From_enum__NPY_TYPES(enum NPY_TYPES value); - -/* CIntFromPy.proto */ -static CYTHON_INLINE int __Pyx_PyInt_As_int(PyObject *); - -/* CIntFromPy.proto */ -static CYTHON_INLINE long __Pyx_PyInt_As_long(PyObject *); - -/* SwapException.proto */ -#if CYTHON_FAST_THREAD_STATE -#define __Pyx_ExceptionSwap(type, value, tb) __Pyx__ExceptionSwap(__pyx_tstate, type, value, tb) -static CYTHON_INLINE void __Pyx__ExceptionSwap(PyThreadState *tstate, PyObject **type, PyObject **value, PyObject **tb); -#else static CYTHON_INLINE void __Pyx_ExceptionSwap(PyObject **type, PyObject **value, PyObject **tb); -#endif -/* CoroutineBase.proto */ -typedef PyObject *(*__pyx_coroutine_body_t)(PyObject *, PyObject *); +#define __Pyx_Generator_USED +#include <structmember.h> +#include <frameobject.h> +typedef PyObject *(*__pyx_generator_body_t)(PyObject *, PyObject *); typedef struct { PyObject_HEAD - __pyx_coroutine_body_t body; + __pyx_generator_body_t body; PyObject *closure; PyObject *exc_type; PyObject *exc_value; @@ -1618,39 +1268,21 @@ typedef struct { PyObject *yieldfrom; PyObject *gi_name; PyObject *gi_qualname; - PyObject *gi_modulename; int resume_label; char is_running; -} __pyx_CoroutineObject; -static __pyx_CoroutineObject *__Pyx__Coroutine_New( - PyTypeObject *type, __pyx_coroutine_body_t body, PyObject *closure, - PyObject *name, PyObject *qualname, PyObject *module_name); -static int __Pyx_Coroutine_clear(PyObject *self); +} __pyx_GeneratorObject; +static __pyx_GeneratorObject *__Pyx_Generator_New(__pyx_generator_body_t body, + PyObject *closure, PyObject *name, PyObject *qualname); +static int __pyx_Generator_init(void); +static int __Pyx_Generator_clear(PyObject* self); #if 1 || PY_VERSION_HEX < 0x030300B0 static int __Pyx_PyGen_FetchStopIterationValue(PyObject **pvalue); #else #define __Pyx_PyGen_FetchStopIterationValue(pvalue) PyGen_FetchStopIterationValue(pvalue) #endif -/* PatchModuleWithCoroutine.proto */ -static PyObject* __Pyx_Coroutine_patch_module(PyObject* module, const char* py_code); - -/* PatchGeneratorABC.proto */ -static int __Pyx_patch_abc(void); - -/* Generator.proto */ -#define __Pyx_Generator_USED -static PyTypeObject *__pyx_GeneratorType = 0; -#define __Pyx_Generator_CheckExact(obj) (Py_TYPE(obj) == __pyx_GeneratorType) -#define __Pyx_Generator_New(body, closure, name, qualname, module_name)\ - __Pyx__Coroutine_New(__pyx_GeneratorType, body, closure, name, qualname, module_name) -static PyObject *__Pyx_Generator_Next(PyObject *self); -static int __pyx_Generator_init(void); - -/* CheckBinaryVersion.proto */ static int __Pyx_check_binary_version(void); -/* PyIdentifierFromString.proto */ #if !defined(__Pyx_PyIdentifier_FromString) #if PY_MAJOR_VERSION < 3 #define __Pyx_PyIdentifier_FromString(s) PyString_FromString(s) @@ -1659,33 +1291,28 @@ static int __Pyx_check_binary_version(void); #endif #endif -/* ModuleImport.proto */ static PyObject *__Pyx_ImportModule(const char *name); -/* TypeImport.proto */ static PyTypeObject *__Pyx_ImportType(const char *module_name, const char *class_name, size_t size, int strict); -/* InitStrings.proto */ static int __Pyx_InitStrings(__Pyx_StringTabEntry *t); /* Module declarations from 'cpython.buffer' */ +/* Module declarations from 'cpython.ref' */ + /* Module declarations from 'libc.string' */ /* Module declarations from 'libc.stdio' */ +/* Module declarations from 'cpython.object' */ + /* Module declarations from '__builtin__' */ /* Module declarations from 'cpython.type' */ static PyTypeObject *__pyx_ptype_7cpython_4type_type = 0; -/* Module declarations from 'cpython' */ - -/* Module declarations from 'cpython.object' */ - -/* Module declarations from 'cpython.ref' */ - /* Module declarations from 'libc.stdlib' */ /* Module declarations from 'numpy' */ @@ -1697,7 +1324,6 @@ static PyTypeObject *__pyx_ptype_5numpy_broadcast = 0; static PyTypeObject *__pyx_ptype_5numpy_ndarray = 0; static PyTypeObject *__pyx_ptype_5numpy_ufunc = 0; static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *, char *, char *, int *); /*proto*/ -static CYTHON_INLINE int __pyx_f_5numpy_import_array(void); /*proto*/ /* Module declarations from 'cython' */ @@ -1711,6 +1337,7 @@ static PyTypeObject *__pyx_ptype_4silx_2io_8specfile___pyx_scope_struct_1___iter int __pyx_module_is_main_silx__io__specfile = 0; /* Implementation of 'silx.io.specfile' */ +static PyObject *__pyx_builtin_Exception; static PyObject *__pyx_builtin_MemoryError; static PyObject *__pyx_builtin_IOError; static PyObject *__pyx_builtin_KeyError; @@ -1725,256 +1352,337 @@ static PyObject *__pyx_builtin_enumerate; static PyObject *__pyx_builtin_ValueError; static PyObject *__pyx_builtin_AttributeError; static PyObject *__pyx_builtin_RuntimeError; -static PyObject *__pyx_builtin_ImportError; -static const char __pyx_k_[] = "\n"; -static const char __pyx_k_2[] = " {2,}"; -static const char __pyx_k_3[] = "3"; -static const char __pyx_k_F[] = "#F "; -static const char __pyx_k_L[] = "L"; -static const char __pyx_k_S[] = "#S "; -static const char __pyx_k_f[] = "f"; -static const char __pyx_k_i[] = "i"; -static const char __pyx_k_w[] = "#(\\w+) *(.*)"; -static const char __pyx_k__7[] = "#"; -static const char __pyx_k_os[] = "os"; -static const char __pyx_k_re[] = "re"; -static const char __pyx_k_MCA[] = "MCA"; -static const char __pyx_k_MIT[] = "MIT"; -static const char __pyx_k__14[] = " "; -static const char __pyx_k__25[] = "."; -static const char __pyx_k__27[] = "', '"; -static const char __pyx_k__28[] = "'"; -static const char __pyx_k_d_d[] = "%d.%d"; -static const char __pyx_k_doc[] = "__doc__"; -static const char __pyx_k_key[] = "key"; -static const char __pyx_k_len[] = "__len__"; -static const char __pyx_k_map[] = "map"; -static const char __pyx_k_mca[] = "_mca"; -static const char __pyx_k_msg[] = "msg"; -static const char __pyx_k_ret[] = "ret"; -static const char __pyx_k_sub[] = "sub"; -static const char __pyx_k_sys[] = "sys"; -static const char __pyx_k_w_2[] = "#@(\\w+) *(.*)"; -static const char __pyx_k_Scan[] = "Scan"; -static const char __pyx_k_args[] = "args"; -static const char __pyx_k_data[] = "_data"; -static const char __pyx_k_date[] = "__date__"; -static const char __pyx_k_hkey[] = "hkey"; -static const char __pyx_k_init[] = "__init__"; -static const char __pyx_k_iter[] = "__iter__"; -static const char __pyx_k_join[] = "join"; -static const char __pyx_k_keys[] = "keys"; -static const char __pyx_k_line[] = "line"; -static const char __pyx_k_list[] = "_list"; -static const char __pyx_k_main[] = "__main__"; -static const char __pyx_k_name[] = "name"; -static const char __pyx_k_open[] = "open"; -static const char __pyx_k_path[] = "path"; -static const char __pyx_k_scan[] = "scan"; -static const char __pyx_k_self[] = "self"; -static const char __pyx_k_send[] = "send"; -static const char __pyx_k_stop[] = "stop"; -static const char __pyx_k_test[] = "__test__"; -static const char __pyx_k_CALIB[] = "CALIB"; -static const char __pyx_k_CHANN[] = "CHANN"; -static const char __pyx_k_ascii[] = "ascii"; -static const char __pyx_k_close[] = "close"; -static const char __pyx_k_dtype[] = "dtype"; -static const char __pyx_k_empty[] = "empty"; -static const char __pyx_k_group[] = "group"; -static const char __pyx_k_index[] = "index"; -static const char __pyx_k_label[] = "label"; -static const char __pyx_k_match[] = "match"; -static const char __pyx_k_mca_2[] = "mca"; -static const char __pyx_k_numpy[] = "numpy"; -static const char __pyx_k_order[] = "order"; -static const char __pyx_k_range[] = "range"; -static const char __pyx_k_shape[] = "shape"; -static const char __pyx_k_split[] = "split"; -static const char __pyx_k_start[] = "start"; -static const char __pyx_k_strip[] = "strip"; -static const char __pyx_k_throw[] = "throw"; -static const char __pyx_k_value[] = "value"; -static const char __pyx_k_ERRORS[] = "ERRORS"; -static const char __pyx_k_append[] = "append"; -static const char __pyx_k_data_2[] = "data"; -static const char __pyx_k_decode[] = "decode"; -static const char __pyx_k_double[] = "double"; -static const char __pyx_k_encode[] = "encode"; -static const char __pyx_k_header[] = "_header"; -static const char __pyx_k_hvalue[] = "hvalue"; -static const char __pyx_k_import[] = "__import__"; -static const char __pyx_k_isfile[] = "isfile"; -static const char __pyx_k_labels[] = "_labels"; -static const char __pyx_k_length[] = "length"; -static const char __pyx_k_logger[] = "_logger"; -static const char __pyx_k_lstrip[] = "lstrip"; -static const char __pyx_k_module[] = "__module__"; -static const char __pyx_k_name_2[] = "__name__"; -static const char __pyx_k_number[] = "number"; -static const char __pyx_k_object[] = "object"; -static const char __pyx_k_record[] = "record"; -static const char __pyx_k_scan_2[] = "_scan"; -static const char __pyx_k_search[] = "search"; -static const char __pyx_k_string[] = "string_"; -static const char __pyx_k_IOError[] = "IOError"; -static const char __pyx_k_SfError[] = "SfError"; -static const char __pyx_k_authors[] = "__authors__"; -static const char __pyx_k_get_mca[] = "get_mca"; -static const char __pyx_k_getitem[] = "__getitem__"; -static const char __pyx_k_index_2[] = "_index"; -static const char __pyx_k_license[] = "__license__"; -static const char __pyx_k_logging[] = "logging"; -static const char __pyx_k_order_2[] = "_order"; -static const char __pyx_k_os_path[] = "os.path"; -static const char __pyx_k_prepare[] = "__prepare__"; -static const char __pyx_k_version[] = "version"; -static const char __pyx_k_warning[] = "warning"; -static const char __pyx_k_KeyError[] = "KeyError"; -static const char __pyx_k_L_header[] = "L_header"; -static const char __pyx_k_P_Knobel[] = "P. Knobel"; -static const char __pyx_k_Scan_mca[] = "Scan.mca"; -static const char __pyx_k_channels[] = "channels"; -static const char __pyx_k_filename[] = "filename"; -static const char __pyx_k_header_2[] = "header"; -static const char __pyx_k_labels_2[] = "labels"; -static const char __pyx_k_number_2[] = "_number"; -static const char __pyx_k_property[] = "property"; -static const char __pyx_k_qualname[] = "__qualname__"; -static const char __pyx_k_specfile[] = "_specfile"; -static const char __pyx_k_MCA___len[] = "MCA.__len__"; -static const char __pyx_k_Scan_data[] = "Scan.data"; -static const char __pyx_k_TypeError[] = "TypeError"; -static const char __pyx_k_data_line[] = "data_line"; -static const char __pyx_k_enumerate[] = "enumerate"; -static const char __pyx_k_getLogger[] = "getLogger"; -static const char __pyx_k_increment[] = "increment"; -static const char __pyx_k_match_mca[] = "match_mca"; -static const char __pyx_k_mca_index[] = "mca_index"; -static const char __pyx_k_metaclass[] = "__metaclass__"; -static const char __pyx_k_transpose[] = "transpose"; -static const char __pyx_k_11_08_2017[] = "11/08/2017"; -static const char __pyx_k_IndexError[] = "IndexError"; -static const char __pyx_k_MCA___init[] = "MCA.__init__"; -static const char __pyx_k_MCA___iter[] = "MCA.__iter__"; -static const char __pyx_k_Scan_index[] = "Scan.index"; -static const char __pyx_k_Scan_order[] = "Scan.order"; -static const char __pyx_k_Valid_keys[] = "\nValid keys: '"; -static const char __pyx_k_ValueError[] = "ValueError"; -static const char __pyx_k_calib_line[] = "calib_line"; -static const char __pyx_k_chann_line[] = "chann_line"; -static const char __pyx_k_dictionary[] = "dictionary"; -static const char __pyx_k_line_index[] = "line_index"; -static const char __pyx_k_scan_index[] = "scan_index"; -static const char __pyx_k_scan_order[] = "scan_order"; -static const char __pyx_k_specfile_2[] = "specfile"; -static const char __pyx_k_startswith[] = "startswith"; -static const char __pyx_k_ImportError[] = "ImportError"; -static const char __pyx_k_MemoryError[] = "MemoryError"; -static const char __pyx_k_Scan___init[] = "Scan.__init__"; -static const char __pyx_k_Scan_header[] = "Scan.header"; -static const char __pyx_k_Scan_labels[] = "Scan.labels"; -static const char __pyx_k_Scan_number[] = "Scan.number"; -static const char __pyx_k_calib_lines[] = "calib_lines"; -static const char __pyx_k_calibration[] = "calibration"; -static const char __pyx_k_chann_lines[] = "chann_lines"; -static const char __pyx_k_file_header[] = "file_header"; -static const char __pyx_k_is_specfile[] = "is_specfile"; -static const char __pyx_k_motor_names[] = "motor_names"; -static const char __pyx_k_scan_header[] = "scan_header"; -static const char __pyx_k_scan_number[] = "scan_number"; -static const char __pyx_k_RuntimeError[] = "RuntimeError"; -static const char __pyx_k_SfNoMcaError[] = "SfNoMcaError"; -static const char __pyx_k_handle_error[] = "_handle_error"; -static const char __pyx_k_version_info[] = "version_info"; -static const char __pyx_k_MCA___getitem[] = "MCA.__getitem__"; -static const char __pyx_k_SfErrFileOpen[] = "SfErrFileOpen"; -static const char __pyx_k_SfErrFileRead[] = "SfErrFileRead"; -static const char __pyx_k_motor_names_2[] = "_motor_names"; -static const char __pyx_k_number_of_mca[] = "number_of_mca"; -static const char __pyx_k_AttributeError[] = "AttributeError"; -static const char __pyx_k_Scan_data_line[] = "Scan.data_line"; -static const char __pyx_k_SfErrFileClose[] = "SfErrFileClose"; -static const char __pyx_k_SfErrFileWrite[] = "SfErrFileWrite"; -static const char __pyx_k_SfErrLineEmpty[] = "SfErrLineEmpty"; -static const char __pyx_k_parse_channels[] = "_parse_channels"; -static const char __pyx_k_SpecFile___iter[] = "SpecFile.__iter__"; -static const char __pyx_k_mca_header_dict[] = "mca_header_dict"; -static const char __pyx_k_motor_positions[] = "motor_positions"; -static const char __pyx_k_SF_ERR_FILE_OPEN[] = "SF_ERR_FILE_OPEN"; -static const char __pyx_k_SF_ERR_NO_ERRORS[] = "SF_ERR_NO_ERRORS"; -static const char __pyx_k_Scan_file_header[] = "Scan.file_header"; -static const char __pyx_k_Scan_motor_names[] = "Scan.motor_names"; -static const char __pyx_k_Scan_scan_header[] = "Scan.scan_header"; -static const char __pyx_k_SfErrColNotFound[] = "SfErrColNotFound"; -static const char __pyx_k_SfErrMcaNotFound[] = "SfErrMcaNotFound"; -static const char __pyx_k_SfErrMemoryAlloc[] = "SfErrMemoryAlloc"; -static const char __pyx_k_all_calib_values[] = "all_calib_values"; -static const char __pyx_k_all_chann_values[] = "all_chann_values"; -static const char __pyx_k_file_header_dict[] = "_file_header_dict"; -static const char __pyx_k_get_error_string[] = "_get_error_string"; -static const char __pyx_k_scan_header_dict[] = "_scan_header_dict"; -static const char __pyx_k_silx_io_specfile[] = "silx.io.specfile"; -static const char __pyx_k_SfErrLineNotFound[] = "SfErrLineNotFound"; -static const char __pyx_k_SfErrScanNotFound[] = "SfErrScanNotFound"; -static const char __pyx_k_SfErrUserNotFound[] = "SfErrUserNotFound"; -static const char __pyx_k_file_header_lines[] = "_file_header_lines"; -static const char __pyx_k_mca_header_dict_2[] = "_mca_header_dict"; -static const char __pyx_k_motor_positions_2[] = "_motor_positions"; -static const char __pyx_k_parse_calibration[] = "_parse_calibration"; -static const char __pyx_k_scan_header_lines[] = "_scan_header_lines"; -static const char __pyx_k_SfErrLabelNotFound[] = "SfErrLabelNotFound"; -static const char __pyx_k_SfErrMotorNotFound[] = "SfErrMotorNotFound"; -static const char __pyx_k_SfNoMca_returned_1[] = "(SfNoMca returned -1)"; -static const char __pyx_k_add_or_concatenate[] = "_add_or_concatenate"; -static const char __pyx_k_file_header_dict_2[] = "file_header_dict"; -static const char __pyx_k_scan_header_dict_2[] = "scan_header_dict"; -static const char __pyx_k_MCA__parse_channels[] = "MCA._parse_channels"; -static const char __pyx_k_SfErrHeaderNotFound[] = "SfErrHeaderNotFound"; -static const char __pyx_k_data_column_by_name[] = "data_column_by_name"; -static const char __pyx_k_string_to_char_star[] = "_string_to_char_star"; -static const char __pyx_k_Scan_mca_header_dict[] = "Scan.mca_header_dict"; -static const char __pyx_k_Scan_motor_positions[] = "Scan.motor_positions"; -static const char __pyx_k_record_exists_in_hdr[] = "record_exists_in_hdr"; -static const char __pyx_k_SF_ERR_SCAN_NOT_FOUND[] = "SF_ERR_SCAN_NOT_FOUND"; -static const char __pyx_k_Scan_file_header_dict[] = "Scan.file_header_dict"; -static const char __pyx_k_Scan_scan_header_dict[] = "Scan.scan_header_dict"; -static const char __pyx_k_SfErrPositionNotFound[] = "SfErrPositionNotFound"; -static const char __pyx_k_one_line_calib_values[] = "one_line_calib_values"; -static const char __pyx_k_one_line_chann_values[] = "one_line_chann_values"; -static const char __pyx_k_MCA__parse_calibration[] = "MCA._parse_calibration"; -static const char __pyx_k_motor_position_by_name[] = "motor_position_by_name"; -static const char __pyx_k_Scan_data_column_by_name[] = "Scan.data_column_by_name"; -static const char __pyx_k_Scan_record_exists_in_hdr[] = "Scan.record_exists_in_hdr"; -static const char __pyx_k_Scan_motor_position_by_name[] = "Scan.motor_position_by_name"; -static const char __pyx_k_ndarray_is_not_C_contiguous[] = "ndarray is not C contiguous"; -static const char __pyx_k_Error_while_closing_SpecFile[] = "Error while closing SpecFile"; -static const char __pyx_k_number_and_M_the_order_eg_2_3[] = " number and M the order (eg '2.3')."; -static const char __pyx_k_MCA_index_must_be_in_range_0_d[] = "MCA index must be in range 0-%d"; -static const char __pyx_k_param_specfile_Parent_SpecFile[] = "\n\n :param specfile: Parent SpecFile from which this scan is extracted.\n :type specfile: :class:`SpecFile`\n :param scan_index: Unique index defining the scan in the SpecFile\n :type scan_index: int\n\n Interface to access a SpecFile scan\n\n A scan is a block of descriptive header lines followed by a 2D data array.\n\n Following three ways of accessing a scan are equivalent::\n\n sf = SpecFile(\"/path/to/specfile.dat\")\n\n # Explicit class instantiation\n scan2 = Scan(sf, scan_index=2)\n\n # 0-based index on a SpecFile object\n scan2 = sf[2]\n\n # Using a \"n.m\" key (scan number starting with 1, scan order)\n scan2 = sf[\"3.1\"]\n "; -static const char __pyx_k_Base_exception_inherited_by_all[] = "Base exception inherited by all exceptions raised when a\n C function from the legacy SpecFile library returns an error\n code.\n "; -static const char __pyx_k_Scan_index_must_be_in_range_0_d[] = "Scan index must be in range 0-%d"; -static const char __pyx_k_The_scan_identification_key_can[] = "The scan identification key can be an integer representing "; -static const char __pyx_k_This_module_is_a_cython_binding[] = "\nThis module is a cython binding to wrap the C SpecFile library, to access\nSpecFile data within a python program.\n\nDocumentation for the original C library SpecFile can be found on the ESRF\nwebsite:\n`The manual for the SpecFile Library <http://www.esrf.eu/files/live/sites/www/files/Instrumentation/software/beamline-control/BLISS/documentation/SpecFileManual.pdf>`_\n\nExamples\n========\n\nStart by importing :class:`SpecFile` and instantiate it:\n\n.. code-block:: python\n\n from silx.io.specfile import SpecFile\n\n sf = SpecFile(\"test.dat\")\n\nA :class:`SpecFile` instance can be accessed like a dictionary to obtain a\n:class:`Scan` instance.\n\nIf the key is a string representing two values\nseparated by a dot (e.g. ``\"1.2\"``), they will be treated as the scan number\n(``#S`` header line) and the scan order::\n\n # get second occurrence of scan \"#S 1\"\n myscan = sf[\"1.2\"]\n\n # access scan data as a numpy array\n nlines, ncolumns = myscan.data.shape\n\nIf the key is an integer, it will be treated as a 0-based index::\n\n first_scan = sf[0]\n second_scan = sf[1]\n\nIt is also possible to browse through all scans using :class:`SpecFile` as\nan iterator::\n\n for scan in sf:\n print(scan.scan_header_dict['S'])\n\nMCA spectra can be selectively loaded using an instance of :class:`MCA`\nprovided by :class:`Scan`::\n\n # Only one MCA spectrum is loaded in memory\n second_mca = first_scan.mca[1]\n\n # Iterating trough all MCA spectra in a scan:\n for mca_data in first_scan.mca:\n print(sum(mca_data))\n\nClasses\n=======\n\n- :class:`SpecFile`\n- :class:`Scan`\n- :class:`MCA`\n\nExceptions\n==========\n\n- :class:`SfError`\n- :class:`SfErrMemoryAlloc`\n- :class:`SfErrFileOpen`\n- :class:`SfErrFileClose`\n- :class:`SfErrFileRead`\n- :class:`SfErrFileWrite`\n- :class:`SfErrLineNotFound`\n- :class:`SfErrScanNotFound`\n- :class:`SfErrHeaderNotFound`\n- :class:`SfErrLabelNotFound`\n- :class:`SfErrMotorNotFound`""\n- :class:`SfErrPositionNotFound`\n- :class:`SfErrLineEmpty`\n- :class:`SfErrUserNotFound`\n- :class:`SfErrColNotFound`\n- :class:`SfErrMcaNotFound`\n\n"; -static const char __pyx_k_numpy_core_multiarray_failed_to[] = "numpy.core.multiarray failed to import"; -static const char __pyx_k_param_scan_Parent_Scan_instance[] = "\n\n :param scan: Parent Scan instance\n :type scan: :class:`Scan`\n\n :var calibration: MCA calibration :math:`(a, b, c)` (as in\n :math:`a + b x + c x\302\262`) from ``#@CALIB`` scan header.\n :type calibration: list of 3 floats, default ``[0., 1., 0.]``\n :var channels: MCA channels list from ``#@CHANN`` scan header.\n In the absence of a ``#@CHANN`` header, this attribute is a list\n ``[0, \342\200\246, N-1]`` where ``N`` is the length of the first spectrum.\n In the absence of MCA spectra, this attribute defaults to ``None``.\n :type channels: list of int\n\n This class provides access to Multi-Channel Analysis data. A :class:`MCA`\n instance can be indexed to access 1D numpy arrays representing single\n MCA\302\240spectra.\n\n To create a :class:`MCA` instance, you must provide a parent :class:`Scan`\n instance, which in turn will provide a reference to the original\n :class:`SpecFile` instance::\n\n sf = SpecFile(\"/path/to/specfile.dat\")\n scan2 = Scan(sf, scan_index=2)\n mcas_in_scan2 = MCA(scan2)\n for i in len(mcas_in_scan2):\n mca_data = mcas_in_scan2[i]\n ... # do some something with mca_data (1D numpy array)\n\n A more pythonic way to do the same work, without having to explicitly\n instantiate ``scan`` and ``mcas_in_scan``, would be::\n\n sf = SpecFile(\"specfilename.dat\")\n # scan2 from previous example can be referred to as sf[2]\n # mcas_in_scan2 from previous example can be referred to as scan2.mca\n for mca_data in sf[2].mca:\n ... # do some something with mca_data (1D numpy array)\n\n "; -static const char __pyx_k_unknown_dtype_code_in_numpy_pxd[] = "unknown dtype code in numpy.pxd (%d)"; -static const char __pyx_k_users_kieffer_workspace_400_rel[] = "/users/kieffer/workspace-400/release/silx/silx/io/specfile.pyx"; -static const char __pyx_k_Cannot_get_data_column_s_in_scan[] = "Cannot get data column %s in scan %d.%d"; -static const char __pyx_k_Custom_exception_raised_when_SfN[] = "Custom exception raised when ``SfNoMca()`` returns ``-1``\n "; -static const char __pyx_k_Failed_to_retrieve_number_of_MCA[] = "Failed to retrieve number of MCA "; -static const char __pyx_k_Format_string_allocated_too_shor[] = "Format string allocated too short, see comment in numpy.pxd"; -static const char __pyx_k_MCA_calibration_line_CALIB_not_f[] = "MCA calibration line (@CALIB) not found"; -static const char __pyx_k_MCA_index_should_be_an_integer_s[] = "MCA index should be an integer (%s provided)"; -static const char __pyx_k_No_MCA_spectrum_found_in_this_sc[] = "No MCA spectrum found in this scan"; -static const char __pyx_k_Non_native_byte_order_not_suppor[] = "Non-native byte order not supported"; -static const char __pyx_k_Parameter_value_must_be_a_string[] = "Parameter value must be a string."; -static const char __pyx_k_Unable_to_parse_file_header_line[] = "Unable to parse file header line "; -static const char __pyx_k_Unable_to_parse_scan_header_line[] = "Unable to parse scan header line "; -static const char __pyx_k_ndarray_is_not_Fortran_contiguou[] = "ndarray is not Fortran contiguous"; -static const char __pyx_k_numpy_core_umath_failed_to_impor[] = "numpy.core.umath failed to import"; -static const char __pyx_k_the_unique_scan_index_or_a_strin[] = "the unique scan index or a string 'N.M' with N being the scan"; -static const char __pyx_k_Format_string_allocated_too_shor_2[] = "Format string allocated too short."; +static PyObject *__pyx_pf_4silx_2io_8specfile_3MCA___init__(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_scan); /* proto */ +static PyObject *__pyx_pf_4silx_2io_8specfile_3MCA_2_parse_channels(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self); /* proto */ +static PyObject *__pyx_pf_4silx_2io_8specfile_3MCA_4_parse_calibration(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self); /* proto */ +static PyObject *__pyx_pf_4silx_2io_8specfile_3MCA_6__len__(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self); /* proto */ +static PyObject *__pyx_pf_4silx_2io_8specfile_3MCA_8__getitem__(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_key); /* proto */ +static PyObject *__pyx_pf_4silx_2io_8specfile_3MCA_10__iter__(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self); /* proto */ +static PyObject *__pyx_pf_4silx_2io_8specfile__add_or_concatenate(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_dictionary, PyObject *__pyx_v_key, PyObject *__pyx_v_value); /* proto */ +static PyObject *__pyx_pf_4silx_2io_8specfile_4Scan___init__(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_specfile, PyObject *__pyx_v_scan_index); /* proto */ +static PyObject *__pyx_pf_4silx_2io_8specfile_4Scan_2index(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self); /* proto */ +static PyObject *__pyx_pf_4silx_2io_8specfile_4Scan_4number(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self); /* proto */ +static PyObject *__pyx_pf_4silx_2io_8specfile_4Scan_6order(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self); /* proto */ +static PyObject *__pyx_pf_4silx_2io_8specfile_4Scan_8header(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self); /* proto */ +static PyObject *__pyx_pf_4silx_2io_8specfile_4Scan_10scan_header(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self); /* proto */ +static PyObject *__pyx_pf_4silx_2io_8specfile_4Scan_12file_header(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self); /* proto */ +static PyObject *__pyx_pf_4silx_2io_8specfile_4Scan_14scan_header_dict(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self); /* proto */ +static PyObject *__pyx_pf_4silx_2io_8specfile_4Scan_16mca_header_dict(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self); /* proto */ +static PyObject *__pyx_pf_4silx_2io_8specfile_4Scan_18file_header_dict(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self); /* proto */ +static PyObject *__pyx_pf_4silx_2io_8specfile_4Scan_20labels(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self); /* proto */ +static PyObject *__pyx_pf_4silx_2io_8specfile_4Scan_22data(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self); /* proto */ +static PyObject *__pyx_pf_4silx_2io_8specfile_4Scan_24mca(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self); /* proto */ +static PyObject *__pyx_pf_4silx_2io_8specfile_4Scan_26motor_names(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self); /* proto */ +static PyObject *__pyx_pf_4silx_2io_8specfile_4Scan_28motor_positions(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self); /* proto */ +static PyObject *__pyx_pf_4silx_2io_8specfile_4Scan_30record_exists_in_hdr(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_record); /* proto */ +static PyObject *__pyx_pf_4silx_2io_8specfile_4Scan_32data_line(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_line_index); /* proto */ +static PyObject *__pyx_pf_4silx_2io_8specfile_4Scan_34data_column_by_name(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_label); /* proto */ +static PyObject *__pyx_pf_4silx_2io_8specfile_4Scan_36motor_position_by_name(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_name); /* proto */ +static PyObject *__pyx_pf_4silx_2io_8specfile_2_string_to_char_star(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_string_); /* proto */ +static PyObject *__pyx_pf_4silx_2io_8specfile_4is_specfile(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_filename); /* proto */ +static int __pyx_pf_4silx_2io_8specfile_8SpecFile___cinit__(struct __pyx_obj_4silx_2io_8specfile_SpecFile *__pyx_v_self, PyObject *__pyx_v_filename); /* proto */ +static int __pyx_pf_4silx_2io_8specfile_8SpecFile_2__init__(struct __pyx_obj_4silx_2io_8specfile_SpecFile *__pyx_v_self, PyObject *__pyx_v_filename); /* proto */ +static void __pyx_pf_4silx_2io_8specfile_8SpecFile_4__dealloc__(struct __pyx_obj_4silx_2io_8specfile_SpecFile *__pyx_v_self); /* proto */ +static PyObject *__pyx_pf_4silx_2io_8specfile_8SpecFile_6close(struct __pyx_obj_4silx_2io_8specfile_SpecFile *__pyx_v_self); /* proto */ +static Py_ssize_t __pyx_pf_4silx_2io_8specfile_8SpecFile_8__len__(struct __pyx_obj_4silx_2io_8specfile_SpecFile *__pyx_v_self); /* proto */ +static PyObject *__pyx_pf_4silx_2io_8specfile_8SpecFile_10__iter__(struct __pyx_obj_4silx_2io_8specfile_SpecFile *__pyx_v_self); /* proto */ +static PyObject *__pyx_pf_4silx_2io_8specfile_8SpecFile_13__getitem__(struct __pyx_obj_4silx_2io_8specfile_SpecFile *__pyx_v_self, PyObject *__pyx_v_key); /* proto */ +static PyObject *__pyx_pf_4silx_2io_8specfile_8SpecFile_15keys(struct __pyx_obj_4silx_2io_8specfile_SpecFile *__pyx_v_self); /* proto */ +static int __pyx_pf_4silx_2io_8specfile_8SpecFile_17__contains__(struct __pyx_obj_4silx_2io_8specfile_SpecFile *__pyx_v_self, PyObject *__pyx_v_key); /* proto */ +static PyObject *__pyx_pf_4silx_2io_8specfile_8SpecFile_19_get_error_string(CYTHON_UNUSED struct __pyx_obj_4silx_2io_8specfile_SpecFile *__pyx_v_self, PyObject *__pyx_v_error_code); /* proto */ +static PyObject *__pyx_pf_4silx_2io_8specfile_8SpecFile_21_handle_error(struct __pyx_obj_4silx_2io_8specfile_SpecFile *__pyx_v_self, PyObject *__pyx_v_error_code); /* proto */ +static PyObject *__pyx_pf_4silx_2io_8specfile_8SpecFile_23index(struct __pyx_obj_4silx_2io_8specfile_SpecFile *__pyx_v_self, PyObject *__pyx_v_scan_number, PyObject *__pyx_v_scan_order); /* proto */ +static PyObject *__pyx_pf_4silx_2io_8specfile_8SpecFile_25number(struct __pyx_obj_4silx_2io_8specfile_SpecFile *__pyx_v_self, PyObject *__pyx_v_scan_index); /* proto */ +static PyObject *__pyx_pf_4silx_2io_8specfile_8SpecFile_27order(struct __pyx_obj_4silx_2io_8specfile_SpecFile *__pyx_v_self, PyObject *__pyx_v_scan_index); /* proto */ +static PyObject *__pyx_pf_4silx_2io_8specfile_8SpecFile_29_list(struct __pyx_obj_4silx_2io_8specfile_SpecFile *__pyx_v_self); /* proto */ +static PyObject *__pyx_pf_4silx_2io_8specfile_8SpecFile_31list(struct __pyx_obj_4silx_2io_8specfile_SpecFile *__pyx_v_self); /* proto */ +static PyObject *__pyx_pf_4silx_2io_8specfile_8SpecFile_33data(struct __pyx_obj_4silx_2io_8specfile_SpecFile *__pyx_v_self, PyObject *__pyx_v_scan_index); /* proto */ +static PyObject *__pyx_pf_4silx_2io_8specfile_8SpecFile_35data_column_by_name(struct __pyx_obj_4silx_2io_8specfile_SpecFile *__pyx_v_self, PyObject *__pyx_v_scan_index, PyObject *__pyx_v_label); /* proto */ +static PyObject *__pyx_pf_4silx_2io_8specfile_8SpecFile_37scan_header(struct __pyx_obj_4silx_2io_8specfile_SpecFile *__pyx_v_self, PyObject *__pyx_v_scan_index); /* proto */ +static PyObject *__pyx_pf_4silx_2io_8specfile_8SpecFile_39file_header(struct __pyx_obj_4silx_2io_8specfile_SpecFile *__pyx_v_self, PyObject *__pyx_v_scan_index); /* proto */ +static PyObject *__pyx_pf_4silx_2io_8specfile_8SpecFile_41columns(struct __pyx_obj_4silx_2io_8specfile_SpecFile *__pyx_v_self, PyObject *__pyx_v_scan_index); /* proto */ +static PyObject *__pyx_pf_4silx_2io_8specfile_8SpecFile_43command(struct __pyx_obj_4silx_2io_8specfile_SpecFile *__pyx_v_self, PyObject *__pyx_v_scan_index); /* proto */ +static PyObject *__pyx_pf_4silx_2io_8specfile_8SpecFile_45date(struct __pyx_obj_4silx_2io_8specfile_SpecFile *__pyx_v_self, PyObject *__pyx_v_scan_index); /* proto */ +static PyObject *__pyx_pf_4silx_2io_8specfile_8SpecFile_47labels(struct __pyx_obj_4silx_2io_8specfile_SpecFile *__pyx_v_self, PyObject *__pyx_v_scan_index); /* proto */ +static PyObject *__pyx_pf_4silx_2io_8specfile_8SpecFile_49motor_names(struct __pyx_obj_4silx_2io_8specfile_SpecFile *__pyx_v_self, PyObject *__pyx_v_scan_index); /* proto */ +static PyObject *__pyx_pf_4silx_2io_8specfile_8SpecFile_51motor_positions(struct __pyx_obj_4silx_2io_8specfile_SpecFile *__pyx_v_self, PyObject *__pyx_v_scan_index); /* proto */ +static PyObject *__pyx_pf_4silx_2io_8specfile_8SpecFile_53motor_position_by_name(struct __pyx_obj_4silx_2io_8specfile_SpecFile *__pyx_v_self, PyObject *__pyx_v_scan_index, PyObject *__pyx_v_name); /* proto */ +static PyObject *__pyx_pf_4silx_2io_8specfile_8SpecFile_55number_of_mca(struct __pyx_obj_4silx_2io_8specfile_SpecFile *__pyx_v_self, PyObject *__pyx_v_scan_index); /* proto */ +static PyObject *__pyx_pf_4silx_2io_8specfile_8SpecFile_57mca_calibration(struct __pyx_obj_4silx_2io_8specfile_SpecFile *__pyx_v_self, PyObject *__pyx_v_scan_index); /* proto */ +static PyObject *__pyx_pf_4silx_2io_8specfile_8SpecFile_59get_mca(struct __pyx_obj_4silx_2io_8specfile_SpecFile *__pyx_v_self, PyObject *__pyx_v_scan_index, PyObject *__pyx_v_mca_index); /* proto */ +static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, Py_buffer *__pyx_v_info, int __pyx_v_flags); /* proto */ +static void __pyx_pf_5numpy_7ndarray_2__releasebuffer__(PyArrayObject *__pyx_v_self, Py_buffer *__pyx_v_info); /* proto */ +static PyObject *__pyx_tp_new_4silx_2io_8specfile_SpecFile(PyTypeObject *t, PyObject *a, PyObject *k); /*proto*/ +static PyObject *__pyx_tp_new_4silx_2io_8specfile___pyx_scope_struct____iter__(PyTypeObject *t, PyObject *a, PyObject *k); /*proto*/ +static PyObject *__pyx_tp_new_4silx_2io_8specfile___pyx_scope_struct_1___iter__(PyTypeObject *t, PyObject *a, PyObject *k); /*proto*/ +static char __pyx_k_[] = "\n"; +static char __pyx_k_2[] = " {2,}"; +static char __pyx_k_3[] = "3"; +static char __pyx_k_B[] = "B"; +static char __pyx_k_F[] = "#F "; +static char __pyx_k_H[] = "H"; +static char __pyx_k_I[] = "I"; +static char __pyx_k_L[] = "L"; +static char __pyx_k_O[] = "O"; +static char __pyx_k_Q[] = "Q"; +static char __pyx_k_S[] = "#S "; +static char __pyx_k_b[] = "b"; +static char __pyx_k_d[] = "d"; +static char __pyx_k_f[] = "f"; +static char __pyx_k_g[] = "g"; +static char __pyx_k_h[] = "h"; +static char __pyx_k_i[] = "i"; +static char __pyx_k_l[] = "l"; +static char __pyx_k_q[] = "q"; +static char __pyx_k_w[] = "#(\\w+) *(.*)"; +static char __pyx_k_Zd[] = "Zd"; +static char __pyx_k_Zf[] = "Zf"; +static char __pyx_k_Zg[] = "Zg"; +static char __pyx_k__7[] = "#"; +static char __pyx_k_os[] = "os"; +static char __pyx_k_rb[] = "rb"; +static char __pyx_k_re[] = "re"; +static char __pyx_k_MCA[] = "MCA"; +static char __pyx_k_MIT[] = "MIT"; +static char __pyx_k__14[] = " "; +static char __pyx_k__28[] = "."; +static char __pyx_k__30[] = "', '"; +static char __pyx_k__31[] = "'"; +static char __pyx_k__32[] = ""; +static char __pyx_k_d_d[] = "%d.%d"; +static char __pyx_k_doc[] = "__doc__"; +static char __pyx_k_key[] = "key"; +static char __pyx_k_len[] = "__len__"; +static char __pyx_k_map[] = "map"; +static char __pyx_k_mca[] = "_mca"; +static char __pyx_k_msg[] = "msg"; +static char __pyx_k_ret[] = "ret"; +static char __pyx_k_sub[] = "sub"; +static char __pyx_k_sys[] = "sys"; +static char __pyx_k_w_2[] = "#@(\\w+) *(.*)"; +static char __pyx_k_Scan[] = "Scan"; +static char __pyx_k_args[] = "args"; +static char __pyx_k_data[] = "_data"; +static char __pyx_k_date[] = "__date__"; +static char __pyx_k_exit[] = "__exit__"; +static char __pyx_k_hkey[] = "hkey"; +static char __pyx_k_init[] = "__init__"; +static char __pyx_k_iter[] = "__iter__"; +static char __pyx_k_join[] = "join"; +static char __pyx_k_keys[] = "keys"; +static char __pyx_k_line[] = "line"; +static char __pyx_k_list[] = "_list"; +static char __pyx_k_main[] = "__main__"; +static char __pyx_k_name[] = "name"; +static char __pyx_k_open[] = "open"; +static char __pyx_k_path[] = "path"; +static char __pyx_k_read[] = "read"; +static char __pyx_k_scan[] = "scan"; +static char __pyx_k_self[] = "self"; +static char __pyx_k_send[] = "send"; +static char __pyx_k_stop[] = "stop"; +static char __pyx_k_test[] = "__test__"; +static char __pyx_k_CALIB[] = "CALIB"; +static char __pyx_k_CHANN[] = "CHANN"; +static char __pyx_k_ascii[] = "ascii"; +static char __pyx_k_chunk[] = "chunk"; +static char __pyx_k_close[] = "close"; +static char __pyx_k_dtype[] = "dtype"; +static char __pyx_k_empty[] = "empty"; +static char __pyx_k_enter[] = "__enter__"; +static char __pyx_k_group[] = "group"; +static char __pyx_k_index[] = "index"; +static char __pyx_k_label[] = "label"; +static char __pyx_k_match[] = "match"; +static char __pyx_k_mca_2[] = "mca"; +static char __pyx_k_numpy[] = "numpy"; +static char __pyx_k_order[] = "order"; +static char __pyx_k_range[] = "range"; +static char __pyx_k_shape[] = "shape"; +static char __pyx_k_split[] = "split"; +static char __pyx_k_start[] = "start"; +static char __pyx_k_strip[] = "strip"; +static char __pyx_k_throw[] = "throw"; +static char __pyx_k_value[] = "value"; +static char __pyx_k_ERRORS[] = "ERRORS"; +static char __pyx_k_append[] = "append"; +static char __pyx_k_data_2[] = "data"; +static char __pyx_k_decode[] = "decode"; +static char __pyx_k_double[] = "double"; +static char __pyx_k_encode[] = "encode"; +static char __pyx_k_header[] = "_header"; +static char __pyx_k_hvalue[] = "hvalue"; +static char __pyx_k_import[] = "__import__"; +static char __pyx_k_isfile[] = "isfile"; +static char __pyx_k_labels[] = "_labels"; +static char __pyx_k_length[] = "length"; +static char __pyx_k_logger[] = "_logger"; +static char __pyx_k_lstrip[] = "lstrip"; +static char __pyx_k_module[] = "__module__"; +static char __pyx_k_name_2[] = "__name__"; +static char __pyx_k_number[] = "number"; +static char __pyx_k_object[] = "object"; +static char __pyx_k_record[] = "record"; +static char __pyx_k_scan_2[] = "_scan"; +static char __pyx_k_search[] = "search"; +static char __pyx_k_string[] = "string_"; +static char __pyx_k_IOError[] = "IOError"; +static char __pyx_k_SfError[] = "SfError"; +static char __pyx_k_authors[] = "__authors__"; +static char __pyx_k_get_mca[] = "get_mca"; +static char __pyx_k_getitem[] = "__getitem__"; +static char __pyx_k_index_2[] = "_index"; +static char __pyx_k_license[] = "__license__"; +static char __pyx_k_logging[] = "logging"; +static char __pyx_k_order_2[] = "_order"; +static char __pyx_k_os_path[] = "os.path"; +static char __pyx_k_prepare[] = "__prepare__"; +static char __pyx_k_version[] = "version"; +static char __pyx_k_warning[] = "warning"; +static char __pyx_k_KeyError[] = "KeyError"; +static char __pyx_k_L_header[] = "L_header"; +static char __pyx_k_P_Knobel[] = "P. Knobel"; +static char __pyx_k_Scan_mca[] = "Scan.mca"; +static char __pyx_k_channels[] = "channels"; +static char __pyx_k_filename[] = "filename"; +static char __pyx_k_header_2[] = "header"; +static char __pyx_k_labels_2[] = "labels"; +static char __pyx_k_number_2[] = "_number"; +static char __pyx_k_property[] = "property"; +static char __pyx_k_qualname[] = "__qualname__"; +static char __pyx_k_specfile[] = "_specfile"; +static char __pyx_k_Exception[] = "Exception"; +static char __pyx_k_MCA___len[] = "MCA.__len__"; +static char __pyx_k_Scan_data[] = "Scan.data"; +static char __pyx_k_TypeError[] = "TypeError"; +static char __pyx_k_data_line[] = "data_line"; +static char __pyx_k_enumerate[] = "enumerate"; +static char __pyx_k_getLogger[] = "getLogger"; +static char __pyx_k_increment[] = "increment"; +static char __pyx_k_match_mca[] = "match_mca"; +static char __pyx_k_mca_index[] = "mca_index"; +static char __pyx_k_metaclass[] = "__metaclass__"; +static char __pyx_k_transpose[] = "transpose"; +static char __pyx_k_11_08_2017[] = "11/08/2017"; +static char __pyx_k_IndexError[] = "IndexError"; +static char __pyx_k_MCA___init[] = "MCA.__init__"; +static char __pyx_k_MCA___iter[] = "MCA.__iter__"; +static char __pyx_k_Scan_index[] = "Scan.index"; +static char __pyx_k_Scan_order[] = "Scan.order"; +static char __pyx_k_Valid_keys[] = "\nValid keys: '"; +static char __pyx_k_ValueError[] = "ValueError"; +static char __pyx_k_calib_line[] = "calib_line"; +static char __pyx_k_chann_line[] = "chann_line"; +static char __pyx_k_dictionary[] = "dictionary"; +static char __pyx_k_line_index[] = "line_index"; +static char __pyx_k_scan_index[] = "scan_index"; +static char __pyx_k_scan_order[] = "scan_order"; +static char __pyx_k_specfile_2[] = "specfile"; +static char __pyx_k_startswith[] = "startswith"; +static char __pyx_k_MemoryError[] = "MemoryError"; +static char __pyx_k_Scan___init[] = "Scan.__init__"; +static char __pyx_k_Scan_header[] = "Scan.header"; +static char __pyx_k_Scan_labels[] = "Scan.labels"; +static char __pyx_k_Scan_number[] = "Scan.number"; +static char __pyx_k_calib_lines[] = "calib_lines"; +static char __pyx_k_calibration[] = "calibration"; +static char __pyx_k_chann_lines[] = "chann_lines"; +static char __pyx_k_file_header[] = "file_header"; +static char __pyx_k_is_specfile[] = "is_specfile"; +static char __pyx_k_motor_names[] = "motor_names"; +static char __pyx_k_scan_header[] = "scan_header"; +static char __pyx_k_scan_number[] = "scan_number"; +static char __pyx_k_RuntimeError[] = "RuntimeError"; +static char __pyx_k_SfNoMcaError[] = "SfNoMcaError"; +static char __pyx_k_handle_error[] = "_handle_error"; +static char __pyx_k_version_info[] = "version_info"; +static char __pyx_k_MCA___getitem[] = "MCA.__getitem__"; +static char __pyx_k_SfErrFileOpen[] = "SfErrFileOpen"; +static char __pyx_k_SfErrFileRead[] = "SfErrFileRead"; +static char __pyx_k_motor_names_2[] = "_motor_names"; +static char __pyx_k_number_of_mca[] = "number_of_mca"; +static char __pyx_k_AttributeError[] = "AttributeError"; +static char __pyx_k_Scan_data_line[] = "Scan.data_line"; +static char __pyx_k_SfErrFileClose[] = "SfErrFileClose"; +static char __pyx_k_SfErrFileWrite[] = "SfErrFileWrite"; +static char __pyx_k_SfErrLineEmpty[] = "SfErrLineEmpty"; +static char __pyx_k_parse_channels[] = "_parse_channels"; +static char __pyx_k_SpecFile___iter[] = "SpecFile.__iter__"; +static char __pyx_k_mca_header_dict[] = "mca_header_dict"; +static char __pyx_k_motor_positions[] = "motor_positions"; +static char __pyx_k_SF_ERR_FILE_OPEN[] = "SF_ERR_FILE_OPEN"; +static char __pyx_k_SF_ERR_NO_ERRORS[] = "SF_ERR_NO_ERRORS"; +static char __pyx_k_Scan_file_header[] = "Scan.file_header"; +static char __pyx_k_Scan_motor_names[] = "Scan.motor_names"; +static char __pyx_k_Scan_scan_header[] = "Scan.scan_header"; +static char __pyx_k_SfErrColNotFound[] = "SfErrColNotFound"; +static char __pyx_k_SfErrMcaNotFound[] = "SfErrMcaNotFound"; +static char __pyx_k_SfErrMemoryAlloc[] = "SfErrMemoryAlloc"; +static char __pyx_k_all_calib_values[] = "all_calib_values"; +static char __pyx_k_all_chann_values[] = "all_chann_values"; +static char __pyx_k_file_header_dict[] = "_file_header_dict"; +static char __pyx_k_get_error_string[] = "_get_error_string"; +static char __pyx_k_scan_header_dict[] = "_scan_header_dict"; +static char __pyx_k_silx_io_specfile[] = "silx.io.specfile"; +static char __pyx_k_SfErrLineNotFound[] = "SfErrLineNotFound"; +static char __pyx_k_SfErrScanNotFound[] = "SfErrScanNotFound"; +static char __pyx_k_SfErrUserNotFound[] = "SfErrUserNotFound"; +static char __pyx_k_file_header_lines[] = "_file_header_lines"; +static char __pyx_k_mca_header_dict_2[] = "_mca_header_dict"; +static char __pyx_k_motor_positions_2[] = "_motor_positions"; +static char __pyx_k_parse_calibration[] = "_parse_calibration"; +static char __pyx_k_scan_header_lines[] = "_scan_header_lines"; +static char __pyx_k_SfErrLabelNotFound[] = "SfErrLabelNotFound"; +static char __pyx_k_SfErrMotorNotFound[] = "SfErrMotorNotFound"; +static char __pyx_k_SfNoMca_returned_1[] = "(SfNoMca returned -1)"; +static char __pyx_k_add_or_concatenate[] = "_add_or_concatenate"; +static char __pyx_k_file_header_dict_2[] = "file_header_dict"; +static char __pyx_k_scan_header_dict_2[] = "scan_header_dict"; +static char __pyx_k_MCA__parse_channels[] = "MCA._parse_channels"; +static char __pyx_k_SfErrHeaderNotFound[] = "SfErrHeaderNotFound"; +static char __pyx_k_data_column_by_name[] = "data_column_by_name"; +static char __pyx_k_string_to_char_star[] = "_string_to_char_star"; +static char __pyx_k_Scan_mca_header_dict[] = "Scan.mca_header_dict"; +static char __pyx_k_Scan_motor_positions[] = "Scan.motor_positions"; +static char __pyx_k_record_exists_in_hdr[] = "record_exists_in_hdr"; +static char __pyx_k_SF_ERR_SCAN_NOT_FOUND[] = "SF_ERR_SCAN_NOT_FOUND"; +static char __pyx_k_Scan_file_header_dict[] = "Scan.file_header_dict"; +static char __pyx_k_Scan_scan_header_dict[] = "Scan.scan_header_dict"; +static char __pyx_k_SfErrPositionNotFound[] = "SfErrPositionNotFound"; +static char __pyx_k_one_line_calib_values[] = "one_line_calib_values"; +static char __pyx_k_one_line_chann_values[] = "one_line_chann_values"; +static char __pyx_k_MCA__parse_calibration[] = "MCA._parse_calibration"; +static char __pyx_k_motor_position_by_name[] = "motor_position_by_name"; +static char __pyx_k_Scan_data_column_by_name[] = "Scan.data_column_by_name"; +static char __pyx_k_Scan_record_exists_in_hdr[] = "Scan.record_exists_in_hdr"; +static char __pyx_k_Scan_motor_position_by_name[] = "Scan.motor_position_by_name"; +static char __pyx_k_ndarray_is_not_C_contiguous[] = "ndarray is not C contiguous"; +static char __pyx_k_Error_while_closing_SpecFile[] = "Error while closing SpecFile"; +static char __pyx_k_number_and_M_the_order_eg_2_3[] = " number and M the order (eg '2.3')."; +static char __pyx_k_MCA_index_must_be_in_range_0_d[] = "MCA index must be in range 0-%d"; +static char __pyx_k_param_specfile_Parent_SpecFile[] = "\n\n :param specfile: Parent SpecFile from which this scan is extracted.\n :type specfile: :class:`SpecFile`\n :param scan_index: Unique index defining the scan in the SpecFile\n :type scan_index: int\n\n Interface to access a SpecFile scan\n\n A scan is a block of descriptive header lines followed by a 2D data array.\n\n Following three ways of accessing a scan are equivalent::\n\n sf = SpecFile(\"/path/to/specfile.dat\")\n\n # Explicit class instantiation\n scan2 = Scan(sf, scan_index=2)\n\n # 0-based index on a SpecFile object\n scan2 = sf[2]\n\n # Using a \"n.m\" key (scan number starting with 1, scan order)\n scan2 = sf[\"3.1\"]\n "; +static char __pyx_k_Base_exception_inherited_by_all[] = "Base exception inherited by all exceptions raised when a\n C function from the legacy SpecFile library returns an error\n code.\n "; +static char __pyx_k_Scan_index_must_be_in_range_0_d[] = "Scan index must be in range 0-%d"; +static char __pyx_k_The_scan_identification_key_can[] = "The scan identification key can be an integer representing "; +static char __pyx_k_This_module_is_a_cython_binding[] = "\nThis module is a cython binding to wrap the C SpecFile library, to access\nSpecFile data within a python program.\n\nDocumentation for the original C library SpecFile can be found on the ESRF\nwebsite:\n`The manual for the SpecFile Library <http://www.esrf.eu/files/live/sites/www/files/Instrumentation/software/beamline-control/BLISS/documentation/SpecFileManual.pdf>`_\n\nExamples\n========\n\nStart by importing :class:`SpecFile` and instantiate it:\n\n.. code-block:: python\n\n from silx.io.specfile import SpecFile\n\n sf = SpecFile(\"test.dat\")\n\nA :class:`SpecFile` instance can be accessed like a dictionary to obtain a\n:class:`Scan` instance.\n\nIf the key is a string representing two values\nseparated by a dot (e.g. ``\"1.2\"``), they will be treated as the scan number\n(``#S`` header line) and the scan order::\n\n # get second occurrence of scan \"#S 1\"\n myscan = sf[\"1.2\"]\n\n # access scan data as a numpy array\n nlines, ncolumns = myscan.data.shape\n\nIf the key is an integer, it will be treated as a 0-based index::\n\n first_scan = sf[0]\n second_scan = sf[1]\n\nIt is also possible to browse through all scans using :class:`SpecFile` as\nan iterator::\n\n for scan in sf:\n print(scan.scan_header_dict['S'])\n\nMCA spectra can be selectively loaded using an instance of :class:`MCA`\nprovided by :class:`Scan`::\n\n # Only one MCA spectrum is loaded in memory\n second_mca = first_scan.mca[1]\n\n # Iterating trough all MCA spectra in a scan:\n for mca_data in first_scan.mca:\n print(sum(mca_data))\n\nClasses\n=======\n\n- :class:`SpecFile`\n- :class:`Scan`\n- :class:`MCA`\n\nExceptions\n==========\n\n- :class:`SfError`\n- :class:`SfErrMemoryAlloc`\n- :class:`SfErrFileOpen`\n- :class:`SfErrFileClose`\n- :class:`SfErrFileRead`\n- :class:`SfErrFileWrite`\n- :class:`SfErrLineNotFound`\n- :class:`SfErrScanNotFound`\n- :class:`SfErrHeaderNotFound`\n- :class:`SfErrLabelNotFound`\n- :class:`SfErrMotorNotFound`""\n- :class:`SfErrPositionNotFound`\n- :class:`SfErrLineEmpty`\n- :class:`SfErrUserNotFound`\n- :class:`SfErrColNotFound`\n- :class:`SfErrMcaNotFound`\n\n"; +static char __pyx_k_param_scan_Parent_Scan_instance[] = "\n\n :param scan: Parent Scan instance\n :type scan: :class:`Scan`\n\n :var calibration: MCA calibration :math:`(a, b, c)` (as in\n :math:`a + b x + c x\302\262`) from ``#@CALIB`` scan header.\n :type calibration: list of 3 floats, default ``[0., 1., 0.]``\n :var channels: MCA channels list from ``#@CHANN`` scan header.\n In the absence of a ``#@CHANN`` header, this attribute is a list\n ``[0, \342\200\246, N-1]`` where ``N`` is the length of the first spectrum.\n In the absence of MCA spectra, this attribute defaults to ``None``.\n :type channels: list of int\n\n This class provides access to Multi-Channel Analysis data. A :class:`MCA`\n instance can be indexed to access 1D numpy arrays representing single\n MCA\302\240spectra.\n\n To create a :class:`MCA` instance, you must provide a parent :class:`Scan`\n instance, which in turn will provide a reference to the original\n :class:`SpecFile` instance::\n\n sf = SpecFile(\"/path/to/specfile.dat\")\n scan2 = Scan(sf, scan_index=2)\n mcas_in_scan2 = MCA(scan2)\n for i in len(mcas_in_scan2):\n mca_data = mcas_in_scan2[i]\n ... # do some something with mca_data (1D numpy array)\n\n A more pythonic way to do the same work, without having to explicitly\n instantiate ``scan`` and ``mcas_in_scan``, would be::\n\n sf = SpecFile(\"specfilename.dat\")\n # scan2 from previous example can be referred to as sf[2]\n # mcas_in_scan2 from previous example can be referred to as scan2.mca\n for mca_data in sf[2].mca:\n ... # do some something with mca_data (1D numpy array)\n\n "; +static char __pyx_k_unknown_dtype_code_in_numpy_pxd[] = "unknown dtype code in numpy.pxd (%d)"; +static char __pyx_k_users_knobel_git_silx_silx_io_s[] = "/users/knobel/git/silx/silx/io/specfile.pyx"; +static char __pyx_k_Cannot_get_data_column_s_in_scan[] = "Cannot get data column %s in scan %d.%d"; +static char __pyx_k_Custom_exception_raised_when_SfN[] = "Custom exception raised when ``SfNoMca()`` returns ``-1``\n "; +static char __pyx_k_Failed_to_retrieve_number_of_MCA[] = "Failed to retrieve number of MCA "; +static char __pyx_k_Format_string_allocated_too_shor[] = "Format string allocated too short, see comment in numpy.pxd"; +static char __pyx_k_MCA_calibration_line_CALIB_not_f[] = "MCA calibration line (@CALIB) not found"; +static char __pyx_k_MCA_index_should_be_an_integer_s[] = "MCA index should be an integer (%s provided)"; +static char __pyx_k_No_MCA_spectrum_found_in_this_sc[] = "No MCA spectrum found in this scan"; +static char __pyx_k_Non_native_byte_order_not_suppor[] = "Non-native byte order not supported"; +static char __pyx_k_Parameter_value_must_be_a_string[] = "Parameter value must be a string."; +static char __pyx_k_Unable_to_parse_file_header_line[] = "Unable to parse file header line "; +static char __pyx_k_Unable_to_parse_scan_header_line[] = "Unable to parse scan header line "; +static char __pyx_k_ndarray_is_not_Fortran_contiguou[] = "ndarray is not Fortran contiguous"; +static char __pyx_k_the_unique_scan_index_or_a_strin[] = "the unique scan index or a string 'N.M' with N being the scan"; +static char __pyx_k_Format_string_allocated_too_shor_2[] = "Format string allocated too short."; +static PyObject *__pyx_kp_b_; static PyObject *__pyx_kp_s_; static PyObject *__pyx_kp_s_11_08_2017; static PyObject *__pyx_kp_s_2; @@ -1987,12 +1695,12 @@ static PyObject *__pyx_kp_s_Cannot_get_data_column_s_in_scan; static PyObject *__pyx_kp_s_Custom_exception_raised_when_SfN; static PyObject *__pyx_n_s_ERRORS; static PyObject *__pyx_kp_s_Error_while_closing_SpecFile; -static PyObject *__pyx_kp_s_F; +static PyObject *__pyx_n_s_Exception; +static PyObject *__pyx_kp_b_F; static PyObject *__pyx_kp_s_Failed_to_retrieve_number_of_MCA; static PyObject *__pyx_kp_u_Format_string_allocated_too_shor; static PyObject *__pyx_kp_u_Format_string_allocated_too_shor_2; static PyObject *__pyx_n_s_IOError; -static PyObject *__pyx_n_s_ImportError; static PyObject *__pyx_n_s_IndexError; static PyObject *__pyx_n_s_KeyError; static PyObject *__pyx_n_s_L; @@ -2014,7 +1722,7 @@ static PyObject *__pyx_kp_u_Non_native_byte_order_not_suppor; static PyObject *__pyx_kp_s_P_Knobel; static PyObject *__pyx_kp_s_Parameter_value_must_be_a_string; static PyObject *__pyx_n_s_RuntimeError; -static PyObject *__pyx_kp_s_S; +static PyObject *__pyx_kp_b_S; static PyObject *__pyx_n_s_SF_ERR_FILE_OPEN; static PyObject *__pyx_n_s_SF_ERR_NO_ERRORS; static PyObject *__pyx_n_s_SF_ERR_SCAN_NOT_FOUND; @@ -2065,9 +1773,9 @@ static PyObject *__pyx_kp_s_Unable_to_parse_scan_header_line; static PyObject *__pyx_kp_s_Valid_keys; static PyObject *__pyx_n_s_ValueError; static PyObject *__pyx_kp_s__14; -static PyObject *__pyx_kp_s__25; -static PyObject *__pyx_kp_s__27; static PyObject *__pyx_kp_s__28; +static PyObject *__pyx_kp_s__30; +static PyObject *__pyx_kp_s__31; static PyObject *__pyx_kp_s__7; static PyObject *__pyx_n_s_add_or_concatenate; static PyObject *__pyx_n_s_all_calib_values; @@ -2082,6 +1790,7 @@ static PyObject *__pyx_n_s_calibration; static PyObject *__pyx_n_s_chann_line; static PyObject *__pyx_n_s_chann_lines; static PyObject *__pyx_n_s_channels; +static PyObject *__pyx_n_s_chunk; static PyObject *__pyx_n_s_close; static PyObject *__pyx_kp_u_d_d; static PyObject *__pyx_n_s_data; @@ -2096,7 +1805,9 @@ static PyObject *__pyx_n_s_double; static PyObject *__pyx_n_s_dtype; static PyObject *__pyx_n_s_empty; static PyObject *__pyx_n_s_encode; +static PyObject *__pyx_n_s_enter; static PyObject *__pyx_n_s_enumerate; +static PyObject *__pyx_n_s_exit; static PyObject *__pyx_n_s_f; static PyObject *__pyx_n_s_file_header; static PyObject *__pyx_n_s_file_header_dict; @@ -2163,8 +1874,6 @@ static PyObject *__pyx_n_s_number_2; static PyObject *__pyx_kp_s_number_and_M_the_order_eg_2_3; static PyObject *__pyx_n_s_number_of_mca; static PyObject *__pyx_n_s_numpy; -static PyObject *__pyx_kp_s_numpy_core_multiarray_failed_to; -static PyObject *__pyx_kp_s_numpy_core_umath_failed_to_impor; static PyObject *__pyx_n_s_object; static PyObject *__pyx_n_s_one_line_calib_values; static PyObject *__pyx_n_s_one_line_chann_values; @@ -2182,7 +1891,9 @@ static PyObject *__pyx_n_s_prepare; static PyObject *__pyx_n_s_property; static PyObject *__pyx_n_s_qualname; static PyObject *__pyx_n_s_range; +static PyObject *__pyx_n_s_rb; static PyObject *__pyx_n_s_re; +static PyObject *__pyx_n_s_read; static PyObject *__pyx_n_s_record; static PyObject *__pyx_n_s_record_exists_in_hdr; static PyObject *__pyx_n_s_ret; @@ -2216,75 +1927,13 @@ static PyObject *__pyx_kp_s_the_unique_scan_index_or_a_strin; static PyObject *__pyx_n_s_throw; static PyObject *__pyx_n_s_transpose; static PyObject *__pyx_kp_u_unknown_dtype_code_in_numpy_pxd; -static PyObject *__pyx_kp_s_users_kieffer_workspace_400_rel; +static PyObject *__pyx_kp_s_users_knobel_git_silx_silx_io_s; static PyObject *__pyx_n_s_value; static PyObject *__pyx_n_s_version; static PyObject *__pyx_n_s_version_info; static PyObject *__pyx_kp_s_w; static PyObject *__pyx_kp_s_w_2; static PyObject *__pyx_n_s_warning; -static PyObject *__pyx_pf_4silx_2io_8specfile_3MCA___init__(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_scan); /* proto */ -static PyObject *__pyx_pf_4silx_2io_8specfile_3MCA_2_parse_channels(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self); /* proto */ -static PyObject *__pyx_pf_4silx_2io_8specfile_3MCA_4_parse_calibration(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self); /* proto */ -static PyObject *__pyx_pf_4silx_2io_8specfile_3MCA_6__len__(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self); /* proto */ -static PyObject *__pyx_pf_4silx_2io_8specfile_3MCA_8__getitem__(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_key); /* proto */ -static PyObject *__pyx_pf_4silx_2io_8specfile_3MCA_10__iter__(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self); /* proto */ -static PyObject *__pyx_pf_4silx_2io_8specfile__add_or_concatenate(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_dictionary, PyObject *__pyx_v_key, PyObject *__pyx_v_value); /* proto */ -static PyObject *__pyx_pf_4silx_2io_8specfile_4Scan___init__(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_specfile, PyObject *__pyx_v_scan_index); /* proto */ -static PyObject *__pyx_pf_4silx_2io_8specfile_4Scan_2index(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self); /* proto */ -static PyObject *__pyx_pf_4silx_2io_8specfile_4Scan_4number(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self); /* proto */ -static PyObject *__pyx_pf_4silx_2io_8specfile_4Scan_6order(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self); /* proto */ -static PyObject *__pyx_pf_4silx_2io_8specfile_4Scan_8header(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self); /* proto */ -static PyObject *__pyx_pf_4silx_2io_8specfile_4Scan_10scan_header(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self); /* proto */ -static PyObject *__pyx_pf_4silx_2io_8specfile_4Scan_12file_header(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self); /* proto */ -static PyObject *__pyx_pf_4silx_2io_8specfile_4Scan_14scan_header_dict(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self); /* proto */ -static PyObject *__pyx_pf_4silx_2io_8specfile_4Scan_16mca_header_dict(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self); /* proto */ -static PyObject *__pyx_pf_4silx_2io_8specfile_4Scan_18file_header_dict(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self); /* proto */ -static PyObject *__pyx_pf_4silx_2io_8specfile_4Scan_20labels(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self); /* proto */ -static PyObject *__pyx_pf_4silx_2io_8specfile_4Scan_22data(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self); /* proto */ -static PyObject *__pyx_pf_4silx_2io_8specfile_4Scan_24mca(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self); /* proto */ -static PyObject *__pyx_pf_4silx_2io_8specfile_4Scan_26motor_names(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self); /* proto */ -static PyObject *__pyx_pf_4silx_2io_8specfile_4Scan_28motor_positions(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self); /* proto */ -static PyObject *__pyx_pf_4silx_2io_8specfile_4Scan_30record_exists_in_hdr(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_record); /* proto */ -static PyObject *__pyx_pf_4silx_2io_8specfile_4Scan_32data_line(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_line_index); /* proto */ -static PyObject *__pyx_pf_4silx_2io_8specfile_4Scan_34data_column_by_name(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_label); /* proto */ -static PyObject *__pyx_pf_4silx_2io_8specfile_4Scan_36motor_position_by_name(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_self, PyObject *__pyx_v_name); /* proto */ -static PyObject *__pyx_pf_4silx_2io_8specfile_2_string_to_char_star(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_string_); /* proto */ -static PyObject *__pyx_pf_4silx_2io_8specfile_4is_specfile(CYTHON_UNUSED PyObject *__pyx_self, PyObject *__pyx_v_filename); /* proto */ -static int __pyx_pf_4silx_2io_8specfile_8SpecFile___cinit__(struct __pyx_obj_4silx_2io_8specfile_SpecFile *__pyx_v_self, PyObject *__pyx_v_filename); /* proto */ -static int __pyx_pf_4silx_2io_8specfile_8SpecFile_2__init__(struct __pyx_obj_4silx_2io_8specfile_SpecFile *__pyx_v_self, PyObject *__pyx_v_filename); /* proto */ -static void __pyx_pf_4silx_2io_8specfile_8SpecFile_4__dealloc__(struct __pyx_obj_4silx_2io_8specfile_SpecFile *__pyx_v_self); /* proto */ -static Py_ssize_t __pyx_pf_4silx_2io_8specfile_8SpecFile_6__len__(struct __pyx_obj_4silx_2io_8specfile_SpecFile *__pyx_v_self); /* proto */ -static PyObject *__pyx_pf_4silx_2io_8specfile_8SpecFile_8__iter__(struct __pyx_obj_4silx_2io_8specfile_SpecFile *__pyx_v_self); /* proto */ -static PyObject *__pyx_pf_4silx_2io_8specfile_8SpecFile_11__getitem__(struct __pyx_obj_4silx_2io_8specfile_SpecFile *__pyx_v_self, PyObject *__pyx_v_key); /* proto */ -static PyObject *__pyx_pf_4silx_2io_8specfile_8SpecFile_13keys(struct __pyx_obj_4silx_2io_8specfile_SpecFile *__pyx_v_self); /* proto */ -static int __pyx_pf_4silx_2io_8specfile_8SpecFile_15__contains__(struct __pyx_obj_4silx_2io_8specfile_SpecFile *__pyx_v_self, PyObject *__pyx_v_key); /* proto */ -static PyObject *__pyx_pf_4silx_2io_8specfile_8SpecFile_17_get_error_string(CYTHON_UNUSED struct __pyx_obj_4silx_2io_8specfile_SpecFile *__pyx_v_self, PyObject *__pyx_v_error_code); /* proto */ -static PyObject *__pyx_pf_4silx_2io_8specfile_8SpecFile_19_handle_error(struct __pyx_obj_4silx_2io_8specfile_SpecFile *__pyx_v_self, PyObject *__pyx_v_error_code); /* proto */ -static PyObject *__pyx_pf_4silx_2io_8specfile_8SpecFile_21index(struct __pyx_obj_4silx_2io_8specfile_SpecFile *__pyx_v_self, PyObject *__pyx_v_scan_number, PyObject *__pyx_v_scan_order); /* proto */ -static PyObject *__pyx_pf_4silx_2io_8specfile_8SpecFile_23number(struct __pyx_obj_4silx_2io_8specfile_SpecFile *__pyx_v_self, PyObject *__pyx_v_scan_index); /* proto */ -static PyObject *__pyx_pf_4silx_2io_8specfile_8SpecFile_25order(struct __pyx_obj_4silx_2io_8specfile_SpecFile *__pyx_v_self, PyObject *__pyx_v_scan_index); /* proto */ -static PyObject *__pyx_pf_4silx_2io_8specfile_8SpecFile_27_list(struct __pyx_obj_4silx_2io_8specfile_SpecFile *__pyx_v_self); /* proto */ -static PyObject *__pyx_pf_4silx_2io_8specfile_8SpecFile_29list(struct __pyx_obj_4silx_2io_8specfile_SpecFile *__pyx_v_self); /* proto */ -static PyObject *__pyx_pf_4silx_2io_8specfile_8SpecFile_31data(struct __pyx_obj_4silx_2io_8specfile_SpecFile *__pyx_v_self, PyObject *__pyx_v_scan_index); /* proto */ -static PyObject *__pyx_pf_4silx_2io_8specfile_8SpecFile_33data_column_by_name(struct __pyx_obj_4silx_2io_8specfile_SpecFile *__pyx_v_self, PyObject *__pyx_v_scan_index, PyObject *__pyx_v_label); /* proto */ -static PyObject *__pyx_pf_4silx_2io_8specfile_8SpecFile_35scan_header(struct __pyx_obj_4silx_2io_8specfile_SpecFile *__pyx_v_self, PyObject *__pyx_v_scan_index); /* proto */ -static PyObject *__pyx_pf_4silx_2io_8specfile_8SpecFile_37file_header(struct __pyx_obj_4silx_2io_8specfile_SpecFile *__pyx_v_self, PyObject *__pyx_v_scan_index); /* proto */ -static PyObject *__pyx_pf_4silx_2io_8specfile_8SpecFile_39columns(struct __pyx_obj_4silx_2io_8specfile_SpecFile *__pyx_v_self, PyObject *__pyx_v_scan_index); /* proto */ -static PyObject *__pyx_pf_4silx_2io_8specfile_8SpecFile_41command(struct __pyx_obj_4silx_2io_8specfile_SpecFile *__pyx_v_self, PyObject *__pyx_v_scan_index); /* proto */ -static PyObject *__pyx_pf_4silx_2io_8specfile_8SpecFile_43date(struct __pyx_obj_4silx_2io_8specfile_SpecFile *__pyx_v_self, PyObject *__pyx_v_scan_index); /* proto */ -static PyObject *__pyx_pf_4silx_2io_8specfile_8SpecFile_45labels(struct __pyx_obj_4silx_2io_8specfile_SpecFile *__pyx_v_self, PyObject *__pyx_v_scan_index); /* proto */ -static PyObject *__pyx_pf_4silx_2io_8specfile_8SpecFile_47motor_names(struct __pyx_obj_4silx_2io_8specfile_SpecFile *__pyx_v_self, PyObject *__pyx_v_scan_index); /* proto */ -static PyObject *__pyx_pf_4silx_2io_8specfile_8SpecFile_49motor_positions(struct __pyx_obj_4silx_2io_8specfile_SpecFile *__pyx_v_self, PyObject *__pyx_v_scan_index); /* proto */ -static PyObject *__pyx_pf_4silx_2io_8specfile_8SpecFile_51motor_position_by_name(struct __pyx_obj_4silx_2io_8specfile_SpecFile *__pyx_v_self, PyObject *__pyx_v_scan_index, PyObject *__pyx_v_name); /* proto */ -static PyObject *__pyx_pf_4silx_2io_8specfile_8SpecFile_53number_of_mca(struct __pyx_obj_4silx_2io_8specfile_SpecFile *__pyx_v_self, PyObject *__pyx_v_scan_index); /* proto */ -static PyObject *__pyx_pf_4silx_2io_8specfile_8SpecFile_55mca_calibration(struct __pyx_obj_4silx_2io_8specfile_SpecFile *__pyx_v_self, PyObject *__pyx_v_scan_index); /* proto */ -static PyObject *__pyx_pf_4silx_2io_8specfile_8SpecFile_57get_mca(struct __pyx_obj_4silx_2io_8specfile_SpecFile *__pyx_v_self, PyObject *__pyx_v_scan_index, PyObject *__pyx_v_mca_index); /* proto */ -static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, Py_buffer *__pyx_v_info, int __pyx_v_flags); /* proto */ -static void __pyx_pf_5numpy_7ndarray_2__releasebuffer__(PyArrayObject *__pyx_v_self, Py_buffer *__pyx_v_info); /* proto */ -static PyObject *__pyx_tp_new_4silx_2io_8specfile_SpecFile(PyTypeObject *t, PyObject *a, PyObject *k); /*proto*/ -static PyObject *__pyx_tp_new_4silx_2io_8specfile___pyx_scope_struct____iter__(PyTypeObject *t, PyObject *a, PyObject *k); /*proto*/ -static PyObject *__pyx_tp_new_4silx_2io_8specfile___pyx_scope_struct_1___iter__(PyTypeObject *t, PyObject *a, PyObject *k); /*proto*/ static PyObject *__pyx_float_0_; static PyObject *__pyx_float_1_; static PyObject *__pyx_int_0; @@ -2303,6 +1952,7 @@ static PyObject *__pyx_int_12; static PyObject *__pyx_int_13; static PyObject *__pyx_int_14; static PyObject *__pyx_int_15; +static PyObject *__pyx_int_2500; static PyObject *__pyx_int_neg_1; static PyObject *__pyx_tuple__2; static PyObject *__pyx_tuple__3; @@ -2325,11 +1975,10 @@ static PyObject *__pyx_tuple__21; static PyObject *__pyx_tuple__22; static PyObject *__pyx_tuple__23; static PyObject *__pyx_tuple__24; +static PyObject *__pyx_tuple__25; static PyObject *__pyx_tuple__26; +static PyObject *__pyx_tuple__27; static PyObject *__pyx_tuple__29; -static PyObject *__pyx_tuple__30; -static PyObject *__pyx_tuple__31; -static PyObject *__pyx_tuple__32; static PyObject *__pyx_tuple__33; static PyObject *__pyx_tuple__34; static PyObject *__pyx_tuple__35; @@ -2337,61 +1986,62 @@ static PyObject *__pyx_tuple__36; static PyObject *__pyx_tuple__37; static PyObject *__pyx_tuple__38; static PyObject *__pyx_tuple__39; -static PyObject *__pyx_tuple__41; -static PyObject *__pyx_tuple__43; -static PyObject *__pyx_tuple__45; -static PyObject *__pyx_tuple__47; -static PyObject *__pyx_tuple__49; -static PyObject *__pyx_tuple__51; -static PyObject *__pyx_tuple__53; -static PyObject *__pyx_tuple__55; -static PyObject *__pyx_tuple__57; -static PyObject *__pyx_tuple__59; -static PyObject *__pyx_tuple__61; -static PyObject *__pyx_tuple__63; -static PyObject *__pyx_tuple__65; -static PyObject *__pyx_tuple__67; -static PyObject *__pyx_tuple__69; -static PyObject *__pyx_tuple__71; -static PyObject *__pyx_tuple__73; -static PyObject *__pyx_tuple__75; -static PyObject *__pyx_tuple__77; -static PyObject *__pyx_tuple__79; -static PyObject *__pyx_tuple__81; -static PyObject *__pyx_tuple__83; -static PyObject *__pyx_tuple__85; -static PyObject *__pyx_tuple__87; -static PyObject *__pyx_tuple__89; -static PyObject *__pyx_tuple__91; -static PyObject *__pyx_tuple__93; -static PyObject *__pyx_codeobj__40; -static PyObject *__pyx_codeobj__42; -static PyObject *__pyx_codeobj__44; -static PyObject *__pyx_codeobj__46; -static PyObject *__pyx_codeobj__48; -static PyObject *__pyx_codeobj__50; -static PyObject *__pyx_codeobj__52; -static PyObject *__pyx_codeobj__54; -static PyObject *__pyx_codeobj__56; -static PyObject *__pyx_codeobj__58; -static PyObject *__pyx_codeobj__60; -static PyObject *__pyx_codeobj__62; -static PyObject *__pyx_codeobj__64; -static PyObject *__pyx_codeobj__66; -static PyObject *__pyx_codeobj__68; -static PyObject *__pyx_codeobj__70; -static PyObject *__pyx_codeobj__72; -static PyObject *__pyx_codeobj__74; -static PyObject *__pyx_codeobj__76; -static PyObject *__pyx_codeobj__78; -static PyObject *__pyx_codeobj__80; -static PyObject *__pyx_codeobj__82; -static PyObject *__pyx_codeobj__84; -static PyObject *__pyx_codeobj__86; -static PyObject *__pyx_codeobj__88; -static PyObject *__pyx_codeobj__90; -static PyObject *__pyx_codeobj__92; -static PyObject *__pyx_codeobj__94; +static PyObject *__pyx_tuple__40; +static PyObject *__pyx_tuple__42; +static PyObject *__pyx_tuple__44; +static PyObject *__pyx_tuple__46; +static PyObject *__pyx_tuple__48; +static PyObject *__pyx_tuple__50; +static PyObject *__pyx_tuple__52; +static PyObject *__pyx_tuple__54; +static PyObject *__pyx_tuple__56; +static PyObject *__pyx_tuple__58; +static PyObject *__pyx_tuple__60; +static PyObject *__pyx_tuple__62; +static PyObject *__pyx_tuple__64; +static PyObject *__pyx_tuple__66; +static PyObject *__pyx_tuple__68; +static PyObject *__pyx_tuple__70; +static PyObject *__pyx_tuple__72; +static PyObject *__pyx_tuple__74; +static PyObject *__pyx_tuple__76; +static PyObject *__pyx_tuple__78; +static PyObject *__pyx_tuple__80; +static PyObject *__pyx_tuple__82; +static PyObject *__pyx_tuple__84; +static PyObject *__pyx_tuple__86; +static PyObject *__pyx_tuple__88; +static PyObject *__pyx_tuple__90; +static PyObject *__pyx_tuple__92; +static PyObject *__pyx_tuple__94; +static PyObject *__pyx_codeobj__41; +static PyObject *__pyx_codeobj__43; +static PyObject *__pyx_codeobj__45; +static PyObject *__pyx_codeobj__47; +static PyObject *__pyx_codeobj__49; +static PyObject *__pyx_codeobj__51; +static PyObject *__pyx_codeobj__53; +static PyObject *__pyx_codeobj__55; +static PyObject *__pyx_codeobj__57; +static PyObject *__pyx_codeobj__59; +static PyObject *__pyx_codeobj__61; +static PyObject *__pyx_codeobj__63; +static PyObject *__pyx_codeobj__65; +static PyObject *__pyx_codeobj__67; +static PyObject *__pyx_codeobj__69; +static PyObject *__pyx_codeobj__71; +static PyObject *__pyx_codeobj__73; +static PyObject *__pyx_codeobj__75; +static PyObject *__pyx_codeobj__77; +static PyObject *__pyx_codeobj__79; +static PyObject *__pyx_codeobj__81; +static PyObject *__pyx_codeobj__83; +static PyObject *__pyx_codeobj__85; +static PyObject *__pyx_codeobj__87; +static PyObject *__pyx_codeobj__89; +static PyObject *__pyx_codeobj__91; +static PyObject *__pyx_codeobj__93; +static PyObject *__pyx_codeobj__95; /* "silx/io/specfile.pyx":233 * @@ -2408,6 +2058,9 @@ static PyMethodDef __pyx_mdef_4silx_2io_8specfile_3MCA_1__init__ = {"__init__", static PyObject *__pyx_pw_4silx_2io_8specfile_3MCA_1__init__(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds) { PyObject *__pyx_v_self = 0; PyObject *__pyx_v_scan = 0; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; PyObject *__pyx_r = 0; __Pyx_RefNannyDeclarations __Pyx_RefNannySetupContext("__init__ (wrapper)", 0); @@ -2431,11 +2084,11 @@ static PyObject *__pyx_pw_4silx_2io_8specfile_3MCA_1__init__(PyObject *__pyx_sel case 1: if (likely((values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s_scan)) != 0)) kw_args--; else { - __Pyx_RaiseArgtupleInvalid("__init__", 1, 2, 2, 1); __PYX_ERR(0, 233, __pyx_L3_error) + __Pyx_RaiseArgtupleInvalid("__init__", 1, 2, 2, 1); {__pyx_filename = __pyx_f[0]; __pyx_lineno = 233; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } } if (unlikely(kw_args > 0)) { - if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "__init__") < 0)) __PYX_ERR(0, 233, __pyx_L3_error) + if (unlikely(__Pyx_ParseOptionalKeywords(__pyx_kwds, __pyx_pyargnames, 0, values, pos_args, "__init__") < 0)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 233; __pyx_clineno = __LINE__; goto __pyx_L3_error;} } } else if (PyTuple_GET_SIZE(__pyx_args) != 2) { goto __pyx_L5_argtuple_error; @@ -2448,7 +2101,7 @@ static PyObject *__pyx_pw_4silx_2io_8specfile_3MCA_1__init__(PyObject *__pyx_sel } goto __pyx_L4_argument_unpacking_done; __pyx_L5_argtuple_error:; - __Pyx_RaiseArgtupleInvalid("__init__", 1, 2, 2, PyTuple_GET_SIZE(__pyx_args)); __PYX_ERR(0, 233, __pyx_L3_error) + __Pyx_RaiseArgtupleInvalid("__init__", 1, 2, 2, PyTuple_GET_SIZE(__pyx_args)); 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__pyx_t_3 = NULL; + PyTuple_SET_ITEM(__pyx_t_5, 0+1, __pyx_t_4); + __Pyx_GIVEREF(__pyx_t_4); + __pyx_t_4 = 0; + __pyx_t_1 = __Pyx_PyObject_Call(__pyx_t_2, __pyx_t_5, NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 284; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_1); + __Pyx_DECREF(__pyx_t_5); __pyx_t_5 = 0; } __Pyx_DECREF(__pyx_t_2); __pyx_t_2 = 0; __pyx_r = __pyx_t_1; @@ -3461,6 +3092,9 @@ static PyMethodDef __pyx_mdef_4silx_2io_8specfile_3MCA_9__getitem__ = {"__getite static PyObject *__pyx_pw_4silx_2io_8specfile_3MCA_9__getitem__(PyObject *__pyx_self, PyObject *__pyx_args, PyObject *__pyx_kwds) { PyObject *__pyx_v_self = 0; PyObject *__pyx_v_key = 0; + int __pyx_lineno = 0; + const char *__pyx_filename = NULL; + int __pyx_clineno = 0; PyObject *__pyx_r = 0; __Pyx_RefNannyDeclarations __Pyx_RefNannySetupContext("__getitem__ (wrapper)", 0); @@ -3484,11 +3118,11 @@ static PyObject *__pyx_pw_4silx_2io_8specfile_3MCA_9__getitem__(PyObject *__pyx_ case 1: if (likely((values[1] = PyDict_GetItem(__pyx_kwds, __pyx_n_s_key)) != 0)) kw_args--; 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__pyx_lineno = 321; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_9); + if (__pyx_t_7) { + PyTuple_SET_ITEM(__pyx_t_9, 0, __pyx_t_7); __Pyx_GIVEREF(__pyx_t_7); __pyx_t_7 = NULL; } + PyTuple_SET_ITEM(__pyx_t_9, 0+__pyx_t_8, __pyx_t_6); + __Pyx_GIVEREF(__pyx_t_6); + PyTuple_SET_ITEM(__pyx_t_9, 1+__pyx_t_8, __pyx_t_5); + __Pyx_GIVEREF(__pyx_t_5); + __pyx_t_6 = 0; + __pyx_t_5 = 0; + __pyx_t_3 = __Pyx_PyObject_Call(__pyx_t_4, __pyx_t_9, NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 321; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __Pyx_GOTREF(__pyx_t_3); + __Pyx_DECREF(__pyx_t_9); __pyx_t_9 = 0; __Pyx_DECREF(__pyx_t_4); __pyx_t_4 = 0; __pyx_r = __pyx_t_3; __pyx_t_3 = 0; @@ -4028,9 +3580,8 @@ static PyObject *__pyx_gb_4silx_2io_8specfile_3MCA_12generator(__pyx_CoroutineOb __pyx_L6_resume_from_yield:; __pyx_t_1 = __pyx_cur_scope->__pyx_t_0; __pyx_t_2 = __pyx_cur_scope->__pyx_t_1; - if (unlikely(!__pyx_sent_value)) __PYX_ERR(0, 321, __pyx_L1_error) + if (unlikely(!__pyx_sent_value)) {__pyx_filename = __pyx_f[0]; 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#if CYTHON_COMPILING_IN_CPYTHON -struct wrapperbase __pyx_wrapperbase_4silx_2io_8specfile_8SpecFile_11__getitem__; +struct wrapperbase __pyx_wrapperbase_4silx_2io_8specfile_8SpecFile_13__getitem__; #endif -static PyObject *__pyx_pw_4silx_2io_8specfile_8SpecFile_12__getitem__(PyObject *__pyx_v_self, PyObject *__pyx_v_key) { +static PyObject *__pyx_pw_4silx_2io_8specfile_8SpecFile_14__getitem__(PyObject *__pyx_v_self, PyObject *__pyx_v_key) { PyObject *__pyx_r = 0; __Pyx_RefNannyDeclarations __Pyx_RefNannySetupContext("__getitem__ (wrapper)", 0); - __pyx_r = __pyx_pf_4silx_2io_8specfile_8SpecFile_11__getitem__(((struct __pyx_obj_4silx_2io_8specfile_SpecFile *)__pyx_v_self), ((PyObject *)__pyx_v_key)); + __pyx_r = __pyx_pf_4silx_2io_8specfile_8SpecFile_13__getitem__(((struct __pyx_obj_4silx_2io_8specfile_SpecFile *)__pyx_v_self), ((PyObject *)__pyx_v_key)); /* function exit code */ __Pyx_RefNannyFinishContext(); return __pyx_r; } -static PyObject *__pyx_pf_4silx_2io_8specfile_8SpecFile_11__getitem__(struct __pyx_obj_4silx_2io_8specfile_SpecFile *__pyx_v_self, PyObject *__pyx_v_key) { +static PyObject *__pyx_pf_4silx_2io_8specfile_8SpecFile_13__getitem__(struct __pyx_obj_4silx_2io_8specfile_SpecFile *__pyx_v_self, PyObject *__pyx_v_key) { PyObject *__pyx_v_msg = NULL; 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/* "silx/io/specfile.pyx":1229 + /* "silx/io/specfile.pyx":1233 * * # error code updating isn't implemented in SfMcaCalib * if mca_calib_error: # <<<<<<<<<<<<<< @@ -14885,41 +13490,33 @@ static PyObject *__pyx_pf_4silx_2io_8specfile_8SpecFile_55mca_calibration(struct __pyx_t_4 = (__pyx_v_mca_calib_error != 0); if (__pyx_t_4) { - /* "silx/io/specfile.pyx":1230 + /* "silx/io/specfile.pyx":1234 * # error code updating isn't implemented in SfMcaCalib * if mca_calib_error: * raise KeyError("MCA calibration line (@CALIB) not found") # <<<<<<<<<<<<<< * * mca_calib_list = [] */ - __pyx_t_1 = __Pyx_PyObject_Call(__pyx_builtin_KeyError, __pyx_tuple__29, NULL); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 1230, __pyx_L1_error) + __pyx_t_1 = __Pyx_PyObject_Call(__pyx_builtin_KeyError, __pyx_tuple__33, NULL); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1234; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); __Pyx_Raise(__pyx_t_1, 0, 0, 0); __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; - 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/* "silx/io/specfile.pyx":1234 + /* "silx/io/specfile.pyx":1238 * mca_calib_list = [] * for i in range(3): * mca_calib_list.append(mca_calib[i]) # <<<<<<<<<<<<<< * * free(mca_calib) */ - __pyx_t_1 = PyFloat_FromDouble((__pyx_v_mca_calib[__pyx_v_i])); if (unlikely(!__pyx_t_1)) __PYX_ERR(0, 1234, __pyx_L1_error) + __pyx_t_1 = PyFloat_FromDouble((__pyx_v_mca_calib[__pyx_v_i])); if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1238; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); - __pyx_t_5 = __Pyx_PyList_Append(__pyx_v_mca_calib_list, __pyx_t_1); if (unlikely(__pyx_t_5 == -1)) __PYX_ERR(0, 1234, __pyx_L1_error) + __pyx_t_5 = __Pyx_PyList_Append(__pyx_v_mca_calib_list, __pyx_t_1); if (unlikely(__pyx_t_5 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1238; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; } - /* "silx/io/specfile.pyx":1236 + /* "silx/io/specfile.pyx":1240 * mca_calib_list.append(mca_calib[i]) * * free(mca_calib) # <<<<<<<<<<<<<< @@ -14951,7 +13548,7 @@ static PyObject *__pyx_pf_4silx_2io_8specfile_8SpecFile_55mca_calibration(struct */ free(__pyx_v_mca_calib); - 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/* "../../../../../usr/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":230 + /* "../../../../usr/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":227 * # This is allocated as one block, strides first. * info.strides = <Py_ssize_t*>stdlib.malloc(sizeof(Py_ssize_t) * <size_t>ndim * 2) * info.shape = info.strides + ndim # <<<<<<<<<<<<<< @@ -15583,7 +14129,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ __pyx_v_info->shape = (__pyx_v_info->strides + __pyx_v_ndim); - /* "../../../../../usr/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":231 + /* "../../../../usr/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":228 * info.strides = <Py_ssize_t*>stdlib.malloc(sizeof(Py_ssize_t) * <size_t>ndim * 2) * info.shape = info.strides + ndim * for i in range(ndim): # <<<<<<<<<<<<<< @@ -15594,7 +14140,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P for (__pyx_t_5 = 0; __pyx_t_5 < __pyx_t_4; __pyx_t_5+=1) { __pyx_v_i = __pyx_t_5; - /* "../../../../../usr/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":232 + /* "../../../../usr/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":229 * info.shape = info.strides + ndim * for i in range(ndim): * info.strides[i] = PyArray_STRIDES(self)[i] # <<<<<<<<<<<<<< @@ -15603,7 +14149,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ (__pyx_v_info->strides[__pyx_v_i]) = (PyArray_STRIDES(__pyx_v_self)[__pyx_v_i]); - /* "../../../../../usr/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":233 + /* "../../../../usr/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":230 * for i in range(ndim): * info.strides[i] = PyArray_STRIDES(self)[i] * info.shape[i] = PyArray_DIMS(self)[i] # <<<<<<<<<<<<<< @@ -15612,28 +14158,20 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ (__pyx_v_info->shape[__pyx_v_i]) = (PyArray_DIMS(__pyx_v_self)[__pyx_v_i]); } - - /* "../../../../../usr/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":226 - * info.buf = PyArray_DATA(self) - * info.ndim = ndim - * if copy_shape: # <<<<<<<<<<<<<< - * # Allocate new buffer for strides and shape info. - * # This is allocated as one block, strides first. - */ goto __pyx_L11; } + /*else*/ { - /* "../../../../../usr/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":235 + /* "../../../../usr/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":232 * info.shape[i] = PyArray_DIMS(self)[i] * else: * info.strides = <Py_ssize_t*>PyArray_STRIDES(self) # <<<<<<<<<<<<<< * info.shape = <Py_ssize_t*>PyArray_DIMS(self) * info.suboffsets = NULL */ - /*else*/ { __pyx_v_info->strides = ((Py_ssize_t *)PyArray_STRIDES(__pyx_v_self)); - /* "../../../../../usr/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":236 + /* "../../../../usr/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":233 * else: * info.strides = <Py_ssize_t*>PyArray_STRIDES(self) * info.shape = <Py_ssize_t*>PyArray_DIMS(self) # <<<<<<<<<<<<<< @@ -15644,7 +14182,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P } __pyx_L11:; - /* "../../../../../usr/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":237 + /* "../../../../usr/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":234 * info.strides = <Py_ssize_t*>PyArray_STRIDES(self) * info.shape = <Py_ssize_t*>PyArray_DIMS(self) * info.suboffsets = NULL # <<<<<<<<<<<<<< @@ -15653,7 +14191,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ __pyx_v_info->suboffsets = NULL; - /* "../../../../../usr/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":238 + /* "../../../../usr/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":235 * info.shape = <Py_ssize_t*>PyArray_DIMS(self) * info.suboffsets = NULL * info.itemsize = PyArray_ITEMSIZE(self) # <<<<<<<<<<<<<< @@ -15662,7 +14200,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ __pyx_v_info->itemsize = PyArray_ITEMSIZE(__pyx_v_self); - /* "../../../../../usr/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":239 + /* "../../../../usr/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":236 * info.suboffsets = NULL * info.itemsize = PyArray_ITEMSIZE(self) * info.readonly = not PyArray_ISWRITEABLE(self) # <<<<<<<<<<<<<< @@ -15671,28 +14209,28 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ __pyx_v_info->readonly = (!(PyArray_ISWRITEABLE(__pyx_v_self) != 0)); - /* "../../../../../usr/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":242 + /* "../../../../usr/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":239 * * cdef int t * cdef char* f = NULL # <<<<<<<<<<<<<< * cdef dtype descr = self.descr - * cdef int offset + * cdef list stack */ __pyx_v_f = NULL; - /* "../../../../../usr/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":243 + /* "../../../../usr/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":240 * cdef int t * cdef char* f = NULL * cdef dtype descr = self.descr # <<<<<<<<<<<<<< + * cdef list stack * cdef int offset - * */ __pyx_t_3 = ((PyObject *)__pyx_v_self->descr); __Pyx_INCREF(__pyx_t_3); __pyx_v_descr = ((PyArray_Descr *)__pyx_t_3); __pyx_t_3 = 0; - /* "../../../../../usr/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":246 + /* "../../../../usr/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":244 * cdef int offset * * cdef bint hasfields = PyDataType_HASFIELDS(descr) # <<<<<<<<<<<<<< @@ -15701,7 +14239,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P */ __pyx_v_hasfields = PyDataType_HASFIELDS(__pyx_v_descr); - /* "../../../../../usr/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":248 + /* "../../../../usr/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":246 * cdef bint hasfields = PyDataType_HASFIELDS(descr) * * if not hasfields and not copy_shape: # <<<<<<<<<<<<<< @@ -15719,7 +14257,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_L15_bool_binop_done:; if (__pyx_t_1) { - /* "../../../../../usr/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":250 + /* "../../../../usr/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":248 * if not hasfields and not copy_shape: * # do not call releasebuffer * info.obj = None # <<<<<<<<<<<<<< @@ -15731,25 +14269,17 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __Pyx_GOTREF(__pyx_v_info->obj); __Pyx_DECREF(__pyx_v_info->obj); __pyx_v_info->obj = Py_None; - - /* "../../../../../usr/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":248 - * cdef bint hasfields = PyDataType_HASFIELDS(descr) - * - * if not hasfields and not copy_shape: # <<<<<<<<<<<<<< - * # do not call releasebuffer - * info.obj = None - */ goto __pyx_L14; } + /*else*/ { - /* "../../../../../usr/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":253 + /* "../../../../usr/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":251 * else: * # need to call releasebuffer * info.obj = self # <<<<<<<<<<<<<< * * if not hasfields: */ - /*else*/ { __Pyx_INCREF(((PyObject *)__pyx_v_self)); __Pyx_GIVEREF(((PyObject *)__pyx_v_self)); __Pyx_GOTREF(__pyx_v_info->obj); @@ -15758,7 +14288,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P } __pyx_L14:; - /* "../../../../../usr/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":255 + /* "../../../../usr/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":253 * info.obj = self * * if not hasfields: # <<<<<<<<<<<<<< @@ -15768,7 +14298,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_t_1 = ((!(__pyx_v_hasfields != 0)) != 0); if (__pyx_t_1) { - /* "../../../../../usr/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":256 + /* "../../../../usr/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":254 * * if not hasfields: * t = descr.type_num # <<<<<<<<<<<<<< @@ -15778,7 +14308,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_t_4 = __pyx_v_descr->type_num; __pyx_v_t = __pyx_t_4; - /* "../../../../../usr/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":257 + /* "../../../../usr/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":255 * if not hasfields: * t = descr.type_num * if ((descr.byteorder == c'>' and little_endian) or # <<<<<<<<<<<<<< @@ -15798,7 +14328,7 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P } __pyx_L20_next_or:; - /* "../../../../../usr/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":258 + /* "../../../../usr/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":256 * t = descr.type_num * if ((descr.byteorder == c'>' and little_endian) or * (descr.byteorder == c'<' and not little_endian)): # <<<<<<<<<<<<<< @@ -15814,51 +14344,43 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P __pyx_t_2 = ((!(__pyx_v_little_endian != 0)) != 0); __pyx_t_1 = __pyx_t_2; __pyx_L19_bool_binop_done:; - - /* "../../../../../usr/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":257 - * if not hasfields: - * t = descr.type_num - * if ((descr.byteorder == c'>' and little_endian) or # <<<<<<<<<<<<<< - * (descr.byteorder == c'<' and not little_endian)): - * raise ValueError(u"Non-native byte order not supported") - */ if (__pyx_t_1) { - /* "../../../../../usr/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":259 + /* "../../../../usr/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":257 * if ((descr.byteorder == c'>' and little_endian) or * (descr.byteorder == c'<' and not little_endian)): * raise ValueError(u"Non-native byte order not supported") # <<<<<<<<<<<<<< * if t == NPY_BYTE: f = "b" * elif t == NPY_UBYTE: f = "B" */ - __pyx_t_3 = __Pyx_PyObject_Call(__pyx_builtin_ValueError, __pyx_tuple__32, NULL); if (unlikely(!__pyx_t_3)) __PYX_ERR(1, 259, __pyx_L1_error) + __pyx_t_3 = __Pyx_PyObject_Call(__pyx_builtin_ValueError, __pyx_tuple__36, NULL); if (unlikely(!__pyx_t_3)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 257; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_3); __Pyx_Raise(__pyx_t_3, 0, 0, 0); __Pyx_DECREF(__pyx_t_3); __pyx_t_3 = 0; - __PYX_ERR(1, 259, __pyx_L1_error) + {__pyx_filename = __pyx_f[1]; __pyx_lineno = 257; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + } - /* "../../../../../usr/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":257 - * if not hasfields: - * t = descr.type_num - * if ((descr.byteorder == c'>' and little_endian) or # <<<<<<<<<<<<<< - * (descr.byteorder == c'<' and not little_endian)): - * raise ValueError(u"Non-native byte order not supported") + /* "../../../../usr/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":274 + * elif t == NPY_CDOUBLE: f = "Zd" + * elif t == NPY_CLONGDOUBLE: f = "Zg" + * elif t == NPY_OBJECT: f = "O" # <<<<<<<<<<<<<< + * else: + * raise ValueError(u"unknown dtype code in numpy.pxd (%d)" % t) */ - } + switch (__pyx_v_t) { - /* "../../../../../usr/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":260 + /* "../../../../usr/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":258 * (descr.byteorder == c'<' and not little_endian)): * raise ValueError(u"Non-native byte order not supported") * if t == NPY_BYTE: f = "b" # <<<<<<<<<<<<<< * elif t == NPY_UBYTE: f = "B" * elif t == NPY_SHORT: f = "h" */ - switch (__pyx_v_t) { case NPY_BYTE: - __pyx_v_f = ((char *)"b"); + __pyx_v_f = __pyx_k_b; break; - /* "../../../../../usr/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":261 + /* "../../../../usr/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":259 * raise ValueError(u"Non-native byte order not supported") * if t == NPY_BYTE: f = "b" * elif t == NPY_UBYTE: f = "B" # <<<<<<<<<<<<<< @@ -15866,10 +14388,10 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P * elif t == NPY_USHORT: f = "H" */ case NPY_UBYTE: - __pyx_v_f = ((char *)"B"); + __pyx_v_f = __pyx_k_B; break; - /* "../../../../../usr/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":262 + /* "../../../../usr/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":260 * if t == NPY_BYTE: f = "b" * elif t == NPY_UBYTE: f = "B" * elif t == NPY_SHORT: f = "h" # <<<<<<<<<<<<<< @@ -15877,10 +14399,10 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P * elif t == NPY_INT: f = "i" */ case NPY_SHORT: - __pyx_v_f = ((char *)"h"); + __pyx_v_f = __pyx_k_h; break; - /* "../../../../../usr/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":263 + /* "../../../../usr/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":261 * elif t == NPY_UBYTE: f = "B" * elif t == NPY_SHORT: f = "h" * elif t == NPY_USHORT: f = "H" # <<<<<<<<<<<<<< @@ -15888,10 +14410,10 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P * elif t == NPY_UINT: f = "I" */ case NPY_USHORT: - __pyx_v_f = ((char *)"H"); + __pyx_v_f = __pyx_k_H; break; - /* "../../../../../usr/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":264 + /* "../../../../usr/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":262 * elif t == NPY_SHORT: f = "h" * elif t == NPY_USHORT: f = "H" * elif t == NPY_INT: f = "i" # <<<<<<<<<<<<<< @@ -15899,10 +14421,10 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P * elif t == NPY_LONG: f = "l" */ case NPY_INT: - __pyx_v_f = ((char *)"i"); + __pyx_v_f = __pyx_k_i; break; - /* "../../../../../usr/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":265 + /* "../../../../usr/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":263 * elif t == NPY_USHORT: f = "H" * elif t == NPY_INT: f = "i" * elif t == NPY_UINT: f = "I" # <<<<<<<<<<<<<< @@ -15910,10 +14432,10 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P * elif t == NPY_ULONG: f = "L" */ case NPY_UINT: - __pyx_v_f = ((char *)"I"); + __pyx_v_f = __pyx_k_I; break; - /* "../../../../../usr/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":266 + /* "../../../../usr/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":264 * elif t == NPY_INT: f = "i" * elif t == NPY_UINT: f = "I" * elif t == NPY_LONG: f = "l" # <<<<<<<<<<<<<< @@ -15921,10 +14443,10 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P * elif t == NPY_LONGLONG: f = "q" */ case NPY_LONG: - __pyx_v_f = ((char *)"l"); + __pyx_v_f = __pyx_k_l; break; - /* "../../../../../usr/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":267 + /* "../../../../usr/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":265 * elif t == NPY_UINT: f = "I" * elif t == NPY_LONG: f = "l" * elif t == NPY_ULONG: f = "L" # <<<<<<<<<<<<<< @@ -15932,10 +14454,10 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P * elif t == NPY_ULONGLONG: f = "Q" */ case NPY_ULONG: - __pyx_v_f = ((char *)"L"); + __pyx_v_f = __pyx_k_L; break; - /* "../../../../../usr/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":268 + /* "../../../../usr/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":266 * elif t == NPY_LONG: f = "l" * elif t == NPY_ULONG: f = "L" * elif t == NPY_LONGLONG: f = "q" # <<<<<<<<<<<<<< @@ -15943,10 +14465,10 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P * elif t == NPY_FLOAT: f = "f" */ case NPY_LONGLONG: - __pyx_v_f = ((char *)"q"); + __pyx_v_f = __pyx_k_q; break; - /* "../../../../../usr/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":269 + /* "../../../../usr/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":267 * elif t == NPY_ULONG: f = "L" * elif t == NPY_LONGLONG: f = "q" * elif t == NPY_ULONGLONG: f = "Q" # <<<<<<<<<<<<<< @@ -15954,10 +14476,10 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P * elif t == NPY_DOUBLE: f = "d" */ case NPY_ULONGLONG: - __pyx_v_f = ((char *)"Q"); + __pyx_v_f = __pyx_k_Q; break; - /* "../../../../../usr/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":270 + /* "../../../../usr/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":268 * elif t == NPY_LONGLONG: f = "q" * elif t == NPY_ULONGLONG: f = "Q" * elif t == NPY_FLOAT: f = "f" # <<<<<<<<<<<<<< @@ -15965,10 +14487,10 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P * elif t == NPY_LONGDOUBLE: f = "g" */ case NPY_FLOAT: - __pyx_v_f = ((char *)"f"); + __pyx_v_f = __pyx_k_f; break; - /* "../../../../../usr/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":271 + /* "../../../../usr/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":269 * elif t == NPY_ULONGLONG: f = "Q" * elif t == NPY_FLOAT: f = "f" * elif t == NPY_DOUBLE: f = "d" # <<<<<<<<<<<<<< @@ -15976,10 +14498,10 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P * elif t == NPY_CFLOAT: f = "Zf" */ case NPY_DOUBLE: - __pyx_v_f = ((char *)"d"); + __pyx_v_f = __pyx_k_d; break; - /* "../../../../../usr/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":272 + /* "../../../../usr/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":270 * elif t == NPY_FLOAT: f = "f" * elif t == NPY_DOUBLE: f = "d" * elif t == NPY_LONGDOUBLE: f = "g" # <<<<<<<<<<<<<< @@ -15987,10 +14509,10 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P * elif t == NPY_CDOUBLE: f = "Zd" */ case NPY_LONGDOUBLE: - __pyx_v_f = ((char *)"g"); + __pyx_v_f = __pyx_k_g; break; - /* "../../../../../usr/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":273 + /* "../../../../usr/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":271 * elif t == NPY_DOUBLE: f = "d" * elif t == NPY_LONGDOUBLE: f = "g" * elif t == NPY_CFLOAT: f = "Zf" # <<<<<<<<<<<<<< @@ -15998,10 +14520,10 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P * elif t == NPY_CLONGDOUBLE: f = "Zg" */ case NPY_CFLOAT: - __pyx_v_f = ((char *)"Zf"); + __pyx_v_f = __pyx_k_Zf; break; - /* "../../../../../usr/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":274 + /* "../../../../usr/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":272 * elif t == NPY_LONGDOUBLE: f = "g" * elif t == NPY_CFLOAT: f = "Zf" * elif t == NPY_CDOUBLE: f = "Zd" # <<<<<<<<<<<<<< @@ -16009,10 +14531,10 @@ static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, P * elif t == NPY_OBJECT: f = "O" */ case NPY_CDOUBLE: - 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{"keys", (PyCFunction)__pyx_pw_4silx_2io_8specfile_8SpecFile_14keys, METH_NOARGS, __pyx_doc_4silx_2io_8specfile_8SpecFile_13keys}, - {"_get_error_string", (PyCFunction)__pyx_pw_4silx_2io_8specfile_8SpecFile_18_get_error_string, METH_O, __pyx_doc_4silx_2io_8specfile_8SpecFile_17_get_error_string}, - {"_handle_error", (PyCFunction)__pyx_pw_4silx_2io_8specfile_8SpecFile_20_handle_error, METH_O, __pyx_doc_4silx_2io_8specfile_8SpecFile_19_handle_error}, - {"index", (PyCFunction)__pyx_pw_4silx_2io_8specfile_8SpecFile_22index, METH_VARARGS|METH_KEYWORDS, __pyx_doc_4silx_2io_8specfile_8SpecFile_21index}, - {"number", (PyCFunction)__pyx_pw_4silx_2io_8specfile_8SpecFile_24number, METH_O, __pyx_doc_4silx_2io_8specfile_8SpecFile_23number}, - {"order", (PyCFunction)__pyx_pw_4silx_2io_8specfile_8SpecFile_26order, METH_O, __pyx_doc_4silx_2io_8specfile_8SpecFile_25order}, - {"_list", (PyCFunction)__pyx_pw_4silx_2io_8specfile_8SpecFile_28_list, METH_NOARGS, __pyx_doc_4silx_2io_8specfile_8SpecFile_27_list}, - {"list", (PyCFunction)__pyx_pw_4silx_2io_8specfile_8SpecFile_30list, METH_NOARGS, __pyx_doc_4silx_2io_8specfile_8SpecFile_29list}, - {"data", (PyCFunction)__pyx_pw_4silx_2io_8specfile_8SpecFile_32data, METH_O, __pyx_doc_4silx_2io_8specfile_8SpecFile_31data}, - {"data_column_by_name", (PyCFunction)__pyx_pw_4silx_2io_8specfile_8SpecFile_34data_column_by_name, METH_VARARGS|METH_KEYWORDS, __pyx_doc_4silx_2io_8specfile_8SpecFile_33data_column_by_name}, - {"scan_header", (PyCFunction)__pyx_pw_4silx_2io_8specfile_8SpecFile_36scan_header, METH_O, __pyx_doc_4silx_2io_8specfile_8SpecFile_35scan_header}, - {"file_header", (PyCFunction)__pyx_pw_4silx_2io_8specfile_8SpecFile_38file_header, METH_VARARGS|METH_KEYWORDS, __pyx_doc_4silx_2io_8specfile_8SpecFile_37file_header}, - {"columns", (PyCFunction)__pyx_pw_4silx_2io_8specfile_8SpecFile_40columns, METH_O, __pyx_doc_4silx_2io_8specfile_8SpecFile_39columns}, - {"command", (PyCFunction)__pyx_pw_4silx_2io_8specfile_8SpecFile_42command, METH_O, __pyx_doc_4silx_2io_8specfile_8SpecFile_41command}, - {"date", (PyCFunction)__pyx_pw_4silx_2io_8specfile_8SpecFile_44date, METH_VARARGS|METH_KEYWORDS, __pyx_doc_4silx_2io_8specfile_8SpecFile_43date}, - {"labels", (PyCFunction)__pyx_pw_4silx_2io_8specfile_8SpecFile_46labels, METH_O, __pyx_doc_4silx_2io_8specfile_8SpecFile_45labels}, - {"motor_names", (PyCFunction)__pyx_pw_4silx_2io_8specfile_8SpecFile_48motor_names, METH_VARARGS|METH_KEYWORDS, __pyx_doc_4silx_2io_8specfile_8SpecFile_47motor_names}, - {"motor_positions", (PyCFunction)__pyx_pw_4silx_2io_8specfile_8SpecFile_50motor_positions, METH_O, __pyx_doc_4silx_2io_8specfile_8SpecFile_49motor_positions}, - {"motor_position_by_name", (PyCFunction)__pyx_pw_4silx_2io_8specfile_8SpecFile_52motor_position_by_name, METH_VARARGS|METH_KEYWORDS, __pyx_doc_4silx_2io_8specfile_8SpecFile_51motor_position_by_name}, - {"number_of_mca", (PyCFunction)__pyx_pw_4silx_2io_8specfile_8SpecFile_54number_of_mca, METH_O, __pyx_doc_4silx_2io_8specfile_8SpecFile_53number_of_mca}, - {"mca_calibration", (PyCFunction)__pyx_pw_4silx_2io_8specfile_8SpecFile_56mca_calibration, METH_O, __pyx_doc_4silx_2io_8specfile_8SpecFile_55mca_calibration}, - {"get_mca", (PyCFunction)__pyx_pw_4silx_2io_8specfile_8SpecFile_58get_mca, METH_VARARGS|METH_KEYWORDS, __pyx_doc_4silx_2io_8specfile_8SpecFile_57get_mca}, + {"close", (PyCFunction)__pyx_pw_4silx_2io_8specfile_8SpecFile_7close, METH_NOARGS, __pyx_doc_4silx_2io_8specfile_8SpecFile_6close}, + {"keys", (PyCFunction)__pyx_pw_4silx_2io_8specfile_8SpecFile_16keys, METH_NOARGS, __pyx_doc_4silx_2io_8specfile_8SpecFile_15keys}, + {"_get_error_string", (PyCFunction)__pyx_pw_4silx_2io_8specfile_8SpecFile_20_get_error_string, METH_O, __pyx_doc_4silx_2io_8specfile_8SpecFile_19_get_error_string}, + {"_handle_error", (PyCFunction)__pyx_pw_4silx_2io_8specfile_8SpecFile_22_handle_error, METH_O, __pyx_doc_4silx_2io_8specfile_8SpecFile_21_handle_error}, + {"index", (PyCFunction)__pyx_pw_4silx_2io_8specfile_8SpecFile_24index, METH_VARARGS|METH_KEYWORDS, __pyx_doc_4silx_2io_8specfile_8SpecFile_23index}, + {"number", (PyCFunction)__pyx_pw_4silx_2io_8specfile_8SpecFile_26number, METH_O, __pyx_doc_4silx_2io_8specfile_8SpecFile_25number}, + {"order", (PyCFunction)__pyx_pw_4silx_2io_8specfile_8SpecFile_28order, METH_O, __pyx_doc_4silx_2io_8specfile_8SpecFile_27order}, + {"_list", (PyCFunction)__pyx_pw_4silx_2io_8specfile_8SpecFile_30_list, METH_NOARGS, __pyx_doc_4silx_2io_8specfile_8SpecFile_29_list}, + {"list", (PyCFunction)__pyx_pw_4silx_2io_8specfile_8SpecFile_32list, METH_NOARGS, __pyx_doc_4silx_2io_8specfile_8SpecFile_31list}, + {"data", (PyCFunction)__pyx_pw_4silx_2io_8specfile_8SpecFile_34data, METH_O, __pyx_doc_4silx_2io_8specfile_8SpecFile_33data}, + {"data_column_by_name", (PyCFunction)__pyx_pw_4silx_2io_8specfile_8SpecFile_36data_column_by_name, METH_VARARGS|METH_KEYWORDS, __pyx_doc_4silx_2io_8specfile_8SpecFile_35data_column_by_name}, + {"scan_header", (PyCFunction)__pyx_pw_4silx_2io_8specfile_8SpecFile_38scan_header, METH_O, __pyx_doc_4silx_2io_8specfile_8SpecFile_37scan_header}, + {"file_header", (PyCFunction)__pyx_pw_4silx_2io_8specfile_8SpecFile_40file_header, METH_VARARGS|METH_KEYWORDS, __pyx_doc_4silx_2io_8specfile_8SpecFile_39file_header}, + {"columns", (PyCFunction)__pyx_pw_4silx_2io_8specfile_8SpecFile_42columns, METH_O, __pyx_doc_4silx_2io_8specfile_8SpecFile_41columns}, + {"command", (PyCFunction)__pyx_pw_4silx_2io_8specfile_8SpecFile_44command, METH_O, __pyx_doc_4silx_2io_8specfile_8SpecFile_43command}, + {"date", (PyCFunction)__pyx_pw_4silx_2io_8specfile_8SpecFile_46date, METH_VARARGS|METH_KEYWORDS, __pyx_doc_4silx_2io_8specfile_8SpecFile_45date}, + {"labels", (PyCFunction)__pyx_pw_4silx_2io_8specfile_8SpecFile_48labels, METH_O, __pyx_doc_4silx_2io_8specfile_8SpecFile_47labels}, + {"motor_names", (PyCFunction)__pyx_pw_4silx_2io_8specfile_8SpecFile_50motor_names, METH_VARARGS|METH_KEYWORDS, __pyx_doc_4silx_2io_8specfile_8SpecFile_49motor_names}, + {"motor_positions", (PyCFunction)__pyx_pw_4silx_2io_8specfile_8SpecFile_52motor_positions, METH_O, __pyx_doc_4silx_2io_8specfile_8SpecFile_51motor_positions}, + {"motor_position_by_name", (PyCFunction)__pyx_pw_4silx_2io_8specfile_8SpecFile_54motor_position_by_name, METH_VARARGS|METH_KEYWORDS, __pyx_doc_4silx_2io_8specfile_8SpecFile_53motor_position_by_name}, + {"number_of_mca", (PyCFunction)__pyx_pw_4silx_2io_8specfile_8SpecFile_56number_of_mca, METH_O, __pyx_doc_4silx_2io_8specfile_8SpecFile_55number_of_mca}, + {"mca_calibration", (PyCFunction)__pyx_pw_4silx_2io_8specfile_8SpecFile_58mca_calibration, METH_O, __pyx_doc_4silx_2io_8specfile_8SpecFile_57mca_calibration}, + {"get_mca", (PyCFunction)__pyx_pw_4silx_2io_8specfile_8SpecFile_60get_mca, METH_VARARGS|METH_KEYWORDS, __pyx_doc_4silx_2io_8specfile_8SpecFile_59get_mca}, {0, 0, 0, 0} }; static PySequenceMethods __pyx_tp_as_sequence_SpecFile = { - __pyx_pw_4silx_2io_8specfile_8SpecFile_7__len__, /*sq_length*/ + __pyx_pw_4silx_2io_8specfile_8SpecFile_9__len__, /*sq_length*/ 0, /*sq_concat*/ 0, /*sq_repeat*/ __pyx_sq_item_4silx_2io_8specfile_SpecFile, /*sq_item*/ 0, /*sq_slice*/ 0, /*sq_ass_item*/ 0, /*sq_ass_slice*/ - __pyx_pw_4silx_2io_8specfile_8SpecFile_16__contains__, /*sq_contains*/ + __pyx_pw_4silx_2io_8specfile_8SpecFile_18__contains__, /*sq_contains*/ 0, /*sq_inplace_concat*/ 0, /*sq_inplace_repeat*/ }; static PyMappingMethods __pyx_tp_as_mapping_SpecFile = { - __pyx_pw_4silx_2io_8specfile_8SpecFile_7__len__, /*mp_length*/ - __pyx_pw_4silx_2io_8specfile_8SpecFile_12__getitem__, /*mp_subscript*/ + __pyx_pw_4silx_2io_8specfile_8SpecFile_9__len__, /*mp_length*/ + __pyx_pw_4silx_2io_8specfile_8SpecFile_14__getitem__, /*mp_subscript*/ 0, /*mp_ass_subscript*/ }; @@ -17911,9 +15978,8 @@ static PyTypeObject __pyx_type_4silx_2io_8specfile_SpecFile = { 0, /*tp_setattr*/ #if PY_MAJOR_VERSION < 3 0, /*tp_compare*/ - #endif - #if PY_MAJOR_VERSION >= 3 - 0, /*tp_as_async*/ + #else + 0, /*reserved*/ #endif 0, /*tp_repr*/ 0, /*tp_as_number*/ @@ -17931,7 +15997,7 @@ static PyTypeObject __pyx_type_4silx_2io_8specfile_SpecFile = { 0, /*tp_clear*/ 0, /*tp_richcompare*/ 0, /*tp_weaklistoffset*/ - __pyx_pw_4silx_2io_8specfile_8SpecFile_9__iter__, /*tp_iter*/ + __pyx_pw_4silx_2io_8specfile_8SpecFile_11__iter__, /*tp_iter*/ 0, /*tp_iternext*/ __pyx_methods_4silx_2io_8specfile_SpecFile, /*tp_methods*/ 0, /*tp_members*/ @@ -18015,9 +16081,8 @@ static PyTypeObject __pyx_type_4silx_2io_8specfile___pyx_scope_struct____iter__ 0, /*tp_setattr*/ #if PY_MAJOR_VERSION < 3 0, /*tp_compare*/ - #endif - #if PY_MAJOR_VERSION >= 3 - 0, /*tp_as_async*/ + #else + 0, /*reserved*/ #endif 0, /*tp_repr*/ 0, /*tp_as_number*/ @@ -18119,9 +16184,8 @@ static PyTypeObject __pyx_type_4silx_2io_8specfile___pyx_scope_struct_1___iter__ 0, /*tp_setattr*/ #if PY_MAJOR_VERSION < 3 0, /*tp_compare*/ - #endif - #if PY_MAJOR_VERSION >= 3 - 0, /*tp_as_async*/ + #else + 0, /*reserved*/ #endif 0, /*tp_repr*/ 0, /*tp_as_number*/ @@ -18189,6 +16253,7 @@ static struct PyModuleDef __pyx_moduledef = { #endif static __Pyx_StringTabEntry __pyx_string_tab[] = { + {&__pyx_kp_b_, __pyx_k_, sizeof(__pyx_k_), 0, 0, 0, 0}, {&__pyx_kp_s_, __pyx_k_, sizeof(__pyx_k_), 0, 0, 1, 0}, {&__pyx_kp_s_11_08_2017, __pyx_k_11_08_2017, sizeof(__pyx_k_11_08_2017), 0, 0, 1, 0}, {&__pyx_kp_s_2, __pyx_k_2, sizeof(__pyx_k_2), 0, 0, 1, 0}, @@ -18201,12 +16266,12 @@ static __Pyx_StringTabEntry __pyx_string_tab[] = { {&__pyx_kp_s_Custom_exception_raised_when_SfN, __pyx_k_Custom_exception_raised_when_SfN, sizeof(__pyx_k_Custom_exception_raised_when_SfN), 0, 0, 1, 0}, {&__pyx_n_s_ERRORS, __pyx_k_ERRORS, sizeof(__pyx_k_ERRORS), 0, 0, 1, 1}, {&__pyx_kp_s_Error_while_closing_SpecFile, __pyx_k_Error_while_closing_SpecFile, sizeof(__pyx_k_Error_while_closing_SpecFile), 0, 0, 1, 0}, - {&__pyx_kp_s_F, __pyx_k_F, sizeof(__pyx_k_F), 0, 0, 1, 0}, + {&__pyx_n_s_Exception, __pyx_k_Exception, sizeof(__pyx_k_Exception), 0, 0, 1, 1}, + {&__pyx_kp_b_F, __pyx_k_F, sizeof(__pyx_k_F), 0, 0, 0, 0}, {&__pyx_kp_s_Failed_to_retrieve_number_of_MCA, __pyx_k_Failed_to_retrieve_number_of_MCA, sizeof(__pyx_k_Failed_to_retrieve_number_of_MCA), 0, 0, 1, 0}, {&__pyx_kp_u_Format_string_allocated_too_shor, __pyx_k_Format_string_allocated_too_shor, sizeof(__pyx_k_Format_string_allocated_too_shor), 0, 1, 0, 0}, {&__pyx_kp_u_Format_string_allocated_too_shor_2, __pyx_k_Format_string_allocated_too_shor_2, sizeof(__pyx_k_Format_string_allocated_too_shor_2), 0, 1, 0, 0}, {&__pyx_n_s_IOError, __pyx_k_IOError, sizeof(__pyx_k_IOError), 0, 0, 1, 1}, - {&__pyx_n_s_ImportError, __pyx_k_ImportError, sizeof(__pyx_k_ImportError), 0, 0, 1, 1}, {&__pyx_n_s_IndexError, __pyx_k_IndexError, sizeof(__pyx_k_IndexError), 0, 0, 1, 1}, {&__pyx_n_s_KeyError, __pyx_k_KeyError, sizeof(__pyx_k_KeyError), 0, 0, 1, 1}, {&__pyx_n_s_L, __pyx_k_L, sizeof(__pyx_k_L), 0, 0, 1, 1}, @@ -18228,7 +16293,7 @@ static __Pyx_StringTabEntry __pyx_string_tab[] = { {&__pyx_kp_s_P_Knobel, __pyx_k_P_Knobel, sizeof(__pyx_k_P_Knobel), 0, 0, 1, 0}, {&__pyx_kp_s_Parameter_value_must_be_a_string, __pyx_k_Parameter_value_must_be_a_string, sizeof(__pyx_k_Parameter_value_must_be_a_string), 0, 0, 1, 0}, {&__pyx_n_s_RuntimeError, __pyx_k_RuntimeError, sizeof(__pyx_k_RuntimeError), 0, 0, 1, 1}, - {&__pyx_kp_s_S, __pyx_k_S, sizeof(__pyx_k_S), 0, 0, 1, 0}, + {&__pyx_kp_b_S, __pyx_k_S, sizeof(__pyx_k_S), 0, 0, 0, 0}, {&__pyx_n_s_SF_ERR_FILE_OPEN, __pyx_k_SF_ERR_FILE_OPEN, sizeof(__pyx_k_SF_ERR_FILE_OPEN), 0, 0, 1, 1}, {&__pyx_n_s_SF_ERR_NO_ERRORS, __pyx_k_SF_ERR_NO_ERRORS, sizeof(__pyx_k_SF_ERR_NO_ERRORS), 0, 0, 1, 1}, {&__pyx_n_s_SF_ERR_SCAN_NOT_FOUND, __pyx_k_SF_ERR_SCAN_NOT_FOUND, sizeof(__pyx_k_SF_ERR_SCAN_NOT_FOUND), 0, 0, 1, 1}, @@ -18279,9 +16344,9 @@ static __Pyx_StringTabEntry __pyx_string_tab[] = { {&__pyx_kp_s_Valid_keys, __pyx_k_Valid_keys, sizeof(__pyx_k_Valid_keys), 0, 0, 1, 0}, {&__pyx_n_s_ValueError, __pyx_k_ValueError, sizeof(__pyx_k_ValueError), 0, 0, 1, 1}, {&__pyx_kp_s__14, __pyx_k__14, sizeof(__pyx_k__14), 0, 0, 1, 0}, - {&__pyx_kp_s__25, __pyx_k__25, sizeof(__pyx_k__25), 0, 0, 1, 0}, - {&__pyx_kp_s__27, __pyx_k__27, sizeof(__pyx_k__27), 0, 0, 1, 0}, {&__pyx_kp_s__28, __pyx_k__28, sizeof(__pyx_k__28), 0, 0, 1, 0}, + {&__pyx_kp_s__30, __pyx_k__30, sizeof(__pyx_k__30), 0, 0, 1, 0}, + {&__pyx_kp_s__31, __pyx_k__31, sizeof(__pyx_k__31), 0, 0, 1, 0}, {&__pyx_kp_s__7, __pyx_k__7, sizeof(__pyx_k__7), 0, 0, 1, 0}, {&__pyx_n_s_add_or_concatenate, __pyx_k_add_or_concatenate, sizeof(__pyx_k_add_or_concatenate), 0, 0, 1, 1}, {&__pyx_n_s_all_calib_values, __pyx_k_all_calib_values, sizeof(__pyx_k_all_calib_values), 0, 0, 1, 1}, @@ -18296,6 +16361,7 @@ static __Pyx_StringTabEntry __pyx_string_tab[] = { {&__pyx_n_s_chann_line, __pyx_k_chann_line, sizeof(__pyx_k_chann_line), 0, 0, 1, 1}, {&__pyx_n_s_chann_lines, __pyx_k_chann_lines, sizeof(__pyx_k_chann_lines), 0, 0, 1, 1}, {&__pyx_n_s_channels, __pyx_k_channels, sizeof(__pyx_k_channels), 0, 0, 1, 1}, + {&__pyx_n_s_chunk, __pyx_k_chunk, sizeof(__pyx_k_chunk), 0, 0, 1, 1}, {&__pyx_n_s_close, __pyx_k_close, sizeof(__pyx_k_close), 0, 0, 1, 1}, {&__pyx_kp_u_d_d, __pyx_k_d_d, sizeof(__pyx_k_d_d), 0, 1, 0, 0}, {&__pyx_n_s_data, __pyx_k_data, sizeof(__pyx_k_data), 0, 0, 1, 1}, @@ -18310,7 +16376,9 @@ static __Pyx_StringTabEntry __pyx_string_tab[] = { {&__pyx_n_s_dtype, __pyx_k_dtype, sizeof(__pyx_k_dtype), 0, 0, 1, 1}, {&__pyx_n_s_empty, __pyx_k_empty, sizeof(__pyx_k_empty), 0, 0, 1, 1}, {&__pyx_n_s_encode, __pyx_k_encode, sizeof(__pyx_k_encode), 0, 0, 1, 1}, + {&__pyx_n_s_enter, __pyx_k_enter, sizeof(__pyx_k_enter), 0, 0, 1, 1}, {&__pyx_n_s_enumerate, __pyx_k_enumerate, sizeof(__pyx_k_enumerate), 0, 0, 1, 1}, + {&__pyx_n_s_exit, __pyx_k_exit, sizeof(__pyx_k_exit), 0, 0, 1, 1}, {&__pyx_n_s_f, __pyx_k_f, sizeof(__pyx_k_f), 0, 0, 1, 1}, {&__pyx_n_s_file_header, __pyx_k_file_header, sizeof(__pyx_k_file_header), 0, 0, 1, 1}, {&__pyx_n_s_file_header_dict, __pyx_k_file_header_dict, sizeof(__pyx_k_file_header_dict), 0, 0, 1, 1}, @@ -18377,8 +16445,6 @@ static __Pyx_StringTabEntry __pyx_string_tab[] = { {&__pyx_kp_s_number_and_M_the_order_eg_2_3, __pyx_k_number_and_M_the_order_eg_2_3, sizeof(__pyx_k_number_and_M_the_order_eg_2_3), 0, 0, 1, 0}, {&__pyx_n_s_number_of_mca, __pyx_k_number_of_mca, sizeof(__pyx_k_number_of_mca), 0, 0, 1, 1}, {&__pyx_n_s_numpy, __pyx_k_numpy, sizeof(__pyx_k_numpy), 0, 0, 1, 1}, - {&__pyx_kp_s_numpy_core_multiarray_failed_to, __pyx_k_numpy_core_multiarray_failed_to, sizeof(__pyx_k_numpy_core_multiarray_failed_to), 0, 0, 1, 0}, - {&__pyx_kp_s_numpy_core_umath_failed_to_impor, __pyx_k_numpy_core_umath_failed_to_impor, sizeof(__pyx_k_numpy_core_umath_failed_to_impor), 0, 0, 1, 0}, {&__pyx_n_s_object, __pyx_k_object, sizeof(__pyx_k_object), 0, 0, 1, 1}, {&__pyx_n_s_one_line_calib_values, __pyx_k_one_line_calib_values, sizeof(__pyx_k_one_line_calib_values), 0, 0, 1, 1}, {&__pyx_n_s_one_line_chann_values, __pyx_k_one_line_chann_values, sizeof(__pyx_k_one_line_chann_values), 0, 0, 1, 1}, @@ -18396,7 +16462,9 @@ static __Pyx_StringTabEntry __pyx_string_tab[] = { {&__pyx_n_s_property, __pyx_k_property, sizeof(__pyx_k_property), 0, 0, 1, 1}, {&__pyx_n_s_qualname, __pyx_k_qualname, sizeof(__pyx_k_qualname), 0, 0, 1, 1}, {&__pyx_n_s_range, __pyx_k_range, sizeof(__pyx_k_range), 0, 0, 1, 1}, + {&__pyx_n_s_rb, __pyx_k_rb, sizeof(__pyx_k_rb), 0, 0, 1, 1}, {&__pyx_n_s_re, __pyx_k_re, sizeof(__pyx_k_re), 0, 0, 1, 1}, + {&__pyx_n_s_read, __pyx_k_read, sizeof(__pyx_k_read), 0, 0, 1, 1}, {&__pyx_n_s_record, __pyx_k_record, sizeof(__pyx_k_record), 0, 0, 1, 1}, {&__pyx_n_s_record_exists_in_hdr, __pyx_k_record_exists_in_hdr, sizeof(__pyx_k_record_exists_in_hdr), 0, 0, 1, 1}, {&__pyx_n_s_ret, __pyx_k_ret, sizeof(__pyx_k_ret), 0, 0, 1, 1}, @@ -18430,7 +16498,7 @@ static __Pyx_StringTabEntry __pyx_string_tab[] = { {&__pyx_n_s_throw, __pyx_k_throw, sizeof(__pyx_k_throw), 0, 0, 1, 1}, {&__pyx_n_s_transpose, __pyx_k_transpose, sizeof(__pyx_k_transpose), 0, 0, 1, 1}, {&__pyx_kp_u_unknown_dtype_code_in_numpy_pxd, __pyx_k_unknown_dtype_code_in_numpy_pxd, sizeof(__pyx_k_unknown_dtype_code_in_numpy_pxd), 0, 1, 0, 0}, - {&__pyx_kp_s_users_kieffer_workspace_400_rel, __pyx_k_users_kieffer_workspace_400_rel, sizeof(__pyx_k_users_kieffer_workspace_400_rel), 0, 0, 1, 0}, + {&__pyx_kp_s_users_knobel_git_silx_silx_io_s, __pyx_k_users_knobel_git_silx_silx_io_s, sizeof(__pyx_k_users_knobel_git_silx_silx_io_s), 0, 0, 1, 0}, {&__pyx_n_s_value, __pyx_k_value, sizeof(__pyx_k_value), 0, 0, 1, 1}, {&__pyx_n_s_version, __pyx_k_version, sizeof(__pyx_k_version), 0, 0, 1, 1}, {&__pyx_n_s_version_info, __pyx_k_version_info, sizeof(__pyx_k_version_info), 0, 0, 1, 1}, @@ -18440,21 +16508,21 @@ static __Pyx_StringTabEntry __pyx_string_tab[] = { {0, 0, 0, 0, 0, 0, 0} }; static int __Pyx_InitCachedBuiltins(void) { - __pyx_builtin_MemoryError = __Pyx_GetBuiltinName(__pyx_n_s_MemoryError); if (!__pyx_builtin_MemoryError) __PYX_ERR(0, 151, __pyx_L1_error) - __pyx_builtin_IOError = __Pyx_GetBuiltinName(__pyx_n_s_IOError); if (!__pyx_builtin_IOError) __PYX_ERR(0, 152, __pyx_L1_error) - __pyx_builtin_KeyError = __Pyx_GetBuiltinName(__pyx_n_s_KeyError); if (!__pyx_builtin_KeyError) __PYX_ERR(0, 156, __pyx_L1_error) - __pyx_builtin_IndexError = __Pyx_GetBuiltinName(__pyx_n_s_IndexError); if (!__pyx_builtin_IndexError) __PYX_ERR(0, 157, __pyx_L1_error) - __pyx_builtin_object = __Pyx_GetBuiltinName(__pyx_n_s_object); if (!__pyx_builtin_object) __PYX_ERR(0, 193, __pyx_L1_error) - __pyx_builtin_property = __Pyx_GetBuiltinName(__pyx_n_s_property); if (!__pyx_builtin_property) __PYX_ERR(0, 422, __pyx_L1_error) - __pyx_builtin_map = __Pyx_GetBuiltinName(__pyx_n_s_map); if (!__pyx_builtin_map) __PYX_ERR(0, 258, __pyx_L1_error) - __pyx_builtin_range = __Pyx_GetBuiltinName(__pyx_n_s_range); if (!__pyx_builtin_range) __PYX_ERR(0, 259, __pyx_L1_error) - __pyx_builtin_TypeError = __Pyx_GetBuiltinName(__pyx_n_s_TypeError); if (!__pyx_builtin_TypeError) __PYX_ERR(0, 304, __pyx_L1_error) - __pyx_builtin_open = __Pyx_GetBuiltinName(__pyx_n_s_open); if (!__pyx_builtin_open) __PYX_ERR(0, 633, __pyx_L1_error) - __pyx_builtin_enumerate = __Pyx_GetBuiltinName(__pyx_n_s_enumerate); if (!__pyx_builtin_enumerate) __PYX_ERR(0, 634, __pyx_L1_error) - __pyx_builtin_ValueError = __Pyx_GetBuiltinName(__pyx_n_s_ValueError); if (!__pyx_builtin_ValueError) __PYX_ERR(0, 732, __pyx_L1_error) - __pyx_builtin_AttributeError = __Pyx_GetBuiltinName(__pyx_n_s_AttributeError); if (!__pyx_builtin_AttributeError) __PYX_ERR(0, 736, __pyx_L1_error) - __pyx_builtin_RuntimeError = __Pyx_GetBuiltinName(__pyx_n_s_RuntimeError); if (!__pyx_builtin_RuntimeError) __PYX_ERR(1, 799, __pyx_L1_error) - __pyx_builtin_ImportError = __Pyx_GetBuiltinName(__pyx_n_s_ImportError); if (!__pyx_builtin_ImportError) __PYX_ERR(1, 989, __pyx_L1_error) + __pyx_builtin_Exception = __Pyx_GetBuiltinName(__pyx_n_s_Exception); if (!__pyx_builtin_Exception) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 144; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_builtin_MemoryError = __Pyx_GetBuiltinName(__pyx_n_s_MemoryError); if (!__pyx_builtin_MemoryError) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 151; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_builtin_IOError = __Pyx_GetBuiltinName(__pyx_n_s_IOError); if (!__pyx_builtin_IOError) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 152; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_builtin_KeyError = __Pyx_GetBuiltinName(__pyx_n_s_KeyError); if (!__pyx_builtin_KeyError) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 156; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_builtin_IndexError = __Pyx_GetBuiltinName(__pyx_n_s_IndexError); if (!__pyx_builtin_IndexError) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 157; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_builtin_object = __Pyx_GetBuiltinName(__pyx_n_s_object); if (!__pyx_builtin_object) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 193; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_builtin_property = __Pyx_GetBuiltinName(__pyx_n_s_property); if (!__pyx_builtin_property) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 422; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_builtin_map = __Pyx_GetBuiltinName(__pyx_n_s_map); if (!__pyx_builtin_map) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 258; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_builtin_range = __Pyx_GetBuiltinName(__pyx_n_s_range); if (!__pyx_builtin_range) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 259; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_builtin_TypeError = __Pyx_GetBuiltinName(__pyx_n_s_TypeError); if (!__pyx_builtin_TypeError) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 304; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_builtin_open = __Pyx_GetBuiltinName(__pyx_n_s_open); if (!__pyx_builtin_open) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 633; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_builtin_enumerate = __Pyx_GetBuiltinName(__pyx_n_s_enumerate); if (!__pyx_builtin_enumerate) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 635; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_builtin_ValueError = __Pyx_GetBuiltinName(__pyx_n_s_ValueError); if (!__pyx_builtin_ValueError) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 736; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_builtin_AttributeError = __Pyx_GetBuiltinName(__pyx_n_s_AttributeError); if (!__pyx_builtin_AttributeError) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 740; __pyx_clineno = __LINE__; goto __pyx_L1_error;} + __pyx_builtin_RuntimeError = __Pyx_GetBuiltinName(__pyx_n_s_RuntimeError); if (!__pyx_builtin_RuntimeError) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 799; __pyx_clineno = __LINE__; goto __pyx_L1_error;} return 0; __pyx_L1_error:; return -1; @@ -18471,7 +16539,7 @@ static int __Pyx_InitCachedConstants(void) { * all_chann_values = [chann_line.split() for chann_line in chann_lines] * for one_line_chann_values in all_chann_values: */ - __pyx_tuple__2 = PyTuple_Pack(1, __pyx_kp_s_); if (unlikely(!__pyx_tuple__2)) __PYX_ERR(0, 255, __pyx_L1_error) + __pyx_tuple__2 = PyTuple_Pack(1, __pyx_kp_s_); if (unlikely(!__pyx_tuple__2)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 255; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_tuple__2); __Pyx_GIVEREF(__pyx_tuple__2); @@ -18482,7 +16550,7 @@ static int __Pyx_InitCachedConstants(void) { * all_calib_values = [calib_line.split() for calib_line in calib_lines] * for one_line_calib_values in all_calib_values: */ - __pyx_tuple__3 = PyTuple_Pack(1, __pyx_kp_s_); if (unlikely(!__pyx_tuple__3)) __PYX_ERR(0, 270, __pyx_L1_error) + __pyx_tuple__3 = PyTuple_Pack(1, __pyx_kp_s_); if (unlikely(!__pyx_tuple__3)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 270; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_tuple__3); __Pyx_GIVEREF(__pyx_tuple__3); @@ -18493,7 +16561,7 @@ static int __Pyx_InitCachedConstants(void) { * * if isinstance(key, (int, long)): */ - __pyx_tuple__4 = PyTuple_Pack(1, __pyx_kp_s_No_MCA_spectrum_found_in_this_sc); if (unlikely(!__pyx_tuple__4)) __PYX_ERR(0, 296, __pyx_L1_error) + __pyx_tuple__4 = PyTuple_Pack(1, __pyx_kp_s_No_MCA_spectrum_found_in_this_sc); if (unlikely(!__pyx_tuple__4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 296; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_tuple__4); __Pyx_GIVEREF(__pyx_tuple__4); @@ -18504,7 +16572,7 @@ static int __Pyx_InitCachedConstants(void) { * * */ - __pyx_tuple__5 = PyTuple_Pack(1, __pyx_kp_s_Parameter_value_must_be_a_string); if (unlikely(!__pyx_tuple__5)) __PYX_ERR(0, 334, __pyx_L1_error) + __pyx_tuple__5 = PyTuple_Pack(1, __pyx_kp_s_Parameter_value_must_be_a_string); if (unlikely(!__pyx_tuple__5)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 334; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_tuple__5); __Pyx_GIVEREF(__pyx_tuple__5); @@ -18515,10 +16583,10 @@ static int __Pyx_InitCachedConstants(void) { * hvalue = match.group(2).strip() * _add_or_concatenate(self._scan_header_dict, hkey, hvalue) */ - 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__pyx_tuple__10 = PyTuple_Pack(1, __pyx_int_1); if (unlikely(!__pyx_tuple__10)) __PYX_ERR(0, 386, __pyx_L1_error) + __pyx_tuple__10 = PyTuple_Pack(1, __pyx_int_1); if (unlikely(!__pyx_tuple__10)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 386; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_tuple__10); __Pyx_GIVEREF(__pyx_tuple__10); - __pyx_tuple__11 = PyTuple_Pack(1, __pyx_kp_s__7); if (unlikely(!__pyx_tuple__11)) __PYX_ERR(0, 386, __pyx_L1_error) + __pyx_tuple__11 = PyTuple_Pack(1, __pyx_kp_s__7); if (unlikely(!__pyx_tuple__11)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 386; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_tuple__11); __Pyx_GIVEREF(__pyx_tuple__11); @@ -18554,7 +16622,7 @@ static int __Pyx_InitCachedConstants(void) { * _add_or_concatenate(self._mca_header_dict, hkey, hvalue) * else: */ - __pyx_tuple__12 = PyTuple_Pack(1, __pyx_int_2); if (unlikely(!__pyx_tuple__12)) __PYX_ERR(0, 387, __pyx_L1_error) + __pyx_tuple__12 = PyTuple_Pack(1, __pyx_int_2); if (unlikely(!__pyx_tuple__12)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 387; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_tuple__12); __Pyx_GIVEREF(__pyx_tuple__12); @@ -18565,7 +16633,7 @@ static int __Pyx_InitCachedConstants(void) { * try: * self._labels = self._specfile.labels(self._index) */ - 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if (unlikely(!__pyx_t_1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_GOTREF(__pyx_t_1); - if (PyDict_SetItem(__pyx_d, __pyx_n_s_test, __pyx_t_1) < 0) __PYX_ERR(0, 1, __pyx_L1_error) + if (PyDict_SetItem(__pyx_d, __pyx_n_s_test, __pyx_t_1) < 0) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1; __pyx_clineno = __LINE__; goto __pyx_L1_error;} __Pyx_DECREF(__pyx_t_1); __pyx_t_1 = 0; - /* "../../../../../usr/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":997 - * raise ImportError("numpy.core.umath failed to import") + /* "../../../../usr/lib/python2.7/dist-packages/Cython/Includes/numpy/__init__.pxd":976 + * arr.base = baseptr * - * cdef inline int import_ufunc() except -1: # <<<<<<<<<<<<<< - * try: - * _import_umath() + * cdef inline object get_array_base(ndarray arr): # <<<<<<<<<<<<<< + * if arr.base is NULL: + * return None */ /*--- Wrapped vars code ---*/ @@ -20876,8 +18921,7 @@ PyMODINIT_FUNC PyInit_specfile(void) #endif } -/* --- Runtime support code --- */ -/* Refnanny */ +/* Runtime support code */ #if CYTHON_REFNANNY static __Pyx_RefNannyAPIStruct *__Pyx_RefNannyImportAPI(const char *modname) { PyObject *m = NULL, *p = NULL; @@ -20894,7 +18938,6 @@ end: } #endif -/* GetBuiltinName */ static PyObject *__Pyx_GetBuiltinName(PyObject *name) { PyObject* result = __Pyx_PyObject_GetAttrStr(__pyx_b, name); if (unlikely(!result)) { @@ -20908,7 +18951,6 @@ static PyObject *__Pyx_GetBuiltinName(PyObject *name) { return result; } -/* RaiseArgTupleInvalid */ static void __Pyx_RaiseArgtupleInvalid( const char* func_name, int exact, @@ -20934,7 +18976,6 @@ static void __Pyx_RaiseArgtupleInvalid( (num_expected == 1) ? "" : "s", num_found); } -/* RaiseDoubleKeywords */ static void __Pyx_RaiseDoubleKeywordsError( const char* func_name, PyObject* kw_name) @@ -20948,7 +18989,6 @@ static void __Pyx_RaiseDoubleKeywordsError( #endif } -/* ParseKeywords */ static int __Pyx_ParseOptionalKeywords( PyObject *kwds, PyObject **argnames[], @@ -21050,145 +19090,6 @@ bad: return -1; } -/* PyCFunctionFastCall */ -#if CYTHON_FAST_PYCCALL -static CYTHON_INLINE PyObject * __Pyx_PyCFunction_FastCall(PyObject *func_obj, PyObject **args, Py_ssize_t nargs) { - PyCFunctionObject *func = (PyCFunctionObject*)func_obj; - PyCFunction meth = PyCFunction_GET_FUNCTION(func); - PyObject *self = PyCFunction_GET_SELF(func); - assert(PyCFunction_Check(func)); - assert(METH_FASTCALL == (PyCFunction_GET_FLAGS(func) & ~(METH_CLASS | METH_STATIC | METH_COEXIST))); - assert(nargs >= 0); - assert(nargs == 0 || args != NULL); - /* _PyCFunction_FastCallDict() must not be called with an exception set, - because it may clear it (directly or indirectly) and so the - caller loses its exception */ - assert(!PyErr_Occurred()); - return (*((__Pyx_PyCFunctionFast)meth)) (self, args, nargs, NULL); -} -#endif // CYTHON_FAST_PYCCALL - -/* PyFunctionFastCall */ -#if CYTHON_FAST_PYCALL -#include "frameobject.h" -static PyObject* __Pyx_PyFunction_FastCallNoKw(PyCodeObject *co, PyObject **args, Py_ssize_t na, - PyObject *globals) { - PyFrameObject *f; - PyThreadState *tstate = PyThreadState_GET(); - PyObject **fastlocals; - Py_ssize_t i; - PyObject *result; - assert(globals != NULL); - /* XXX Perhaps we should create a specialized - PyFrame_New() that doesn't take locals, but does - take builtins without sanity checking them. - */ - assert(tstate != NULL); - f = PyFrame_New(tstate, co, globals, NULL); - if (f == NULL) { - return NULL; - } - fastlocals = f->f_localsplus; - for (i = 0; i < na; i++) { - Py_INCREF(*args); - fastlocals[i] = *args++; - } - result = PyEval_EvalFrameEx(f,0); - ++tstate->recursion_depth; - Py_DECREF(f); - --tstate->recursion_depth; - return result; -} -#if 1 || PY_VERSION_HEX < 0x030600B1 -static PyObject *__Pyx_PyFunction_FastCallDict(PyObject *func, PyObject **args, int nargs, PyObject *kwargs) { - PyCodeObject *co = (PyCodeObject *)PyFunction_GET_CODE(func); - PyObject *globals = PyFunction_GET_GLOBALS(func); - PyObject *argdefs = PyFunction_GET_DEFAULTS(func); - PyObject *closure; -#if PY_MAJOR_VERSION >= 3 - PyObject *kwdefs; -#endif - PyObject *kwtuple, **k; - PyObject **d; - Py_ssize_t nd; - Py_ssize_t nk; - PyObject *result; - assert(kwargs == NULL || PyDict_Check(kwargs)); - nk = kwargs ? PyDict_Size(kwargs) : 0; - if (Py_EnterRecursiveCall((char*)" while calling a Python object")) { - return NULL; - } - if ( -#if PY_MAJOR_VERSION >= 3 - co->co_kwonlyargcount == 0 && -#endif - likely(kwargs == NULL || nk == 0) && - co->co_flags == (CO_OPTIMIZED | CO_NEWLOCALS | CO_NOFREE)) { - if (argdefs == NULL && co->co_argcount == nargs) { - result = __Pyx_PyFunction_FastCallNoKw(co, args, nargs, globals); - goto done; - } - else if (nargs == 0 && argdefs != NULL - && co->co_argcount == Py_SIZE(argdefs)) { - /* function called with no arguments, but all parameters have - a default value: use default values as arguments .*/ - args = &PyTuple_GET_ITEM(argdefs, 0); - result =__Pyx_PyFunction_FastCallNoKw(co, args, Py_SIZE(argdefs), globals); - goto done; - } - } - if (kwargs != NULL) { - Py_ssize_t pos, i; - kwtuple = PyTuple_New(2 * nk); - if (kwtuple == NULL) { - result = NULL; - goto done; - } - k = &PyTuple_GET_ITEM(kwtuple, 0); - pos = i = 0; - while (PyDict_Next(kwargs, &pos, &k[i], &k[i+1])) { - Py_INCREF(k[i]); - Py_INCREF(k[i+1]); - i += 2; - } - nk = i / 2; - } - else { - kwtuple = NULL; - k = NULL; - } - closure = PyFunction_GET_CLOSURE(func); -#if PY_MAJOR_VERSION >= 3 - kwdefs = PyFunction_GET_KW_DEFAULTS(func); -#endif - if (argdefs != NULL) { - d = &PyTuple_GET_ITEM(argdefs, 0); - nd = Py_SIZE(argdefs); - } - else { - d = NULL; - nd = 0; - } -#if PY_MAJOR_VERSION >= 3 - result = PyEval_EvalCodeEx((PyObject*)co, globals, (PyObject *)NULL, - args, nargs, - k, (int)nk, - d, (int)nd, kwdefs, closure); -#else - result = PyEval_EvalCodeEx(co, globals, (PyObject *)NULL, - args, nargs, - k, (int)nk, - d, (int)nd, closure); -#endif - Py_XDECREF(kwtuple); -done: - Py_LeaveRecursiveCall(); - return result; -} -#endif // CPython < 3.6 -#endif // CYTHON_FAST_PYCALL - -/* PyObjectCall */ #if CYTHON_COMPILING_IN_CPYTHON static CYTHON_INLINE PyObject* __Pyx_PyObject_Call(PyObject *func, PyObject *arg, PyObject *kw) { PyObject *result; @@ -21208,7 +19109,6 @@ static CYTHON_INLINE PyObject* __Pyx_PyObject_Call(PyObject *func, PyObject *arg } #endif -/* PyObjectCallMethO */ #if CYTHON_COMPILING_IN_CPYTHON static CYTHON_INLINE PyObject* __Pyx_PyObject_CallMethO(PyObject *func, PyObject *arg) { PyObject *self, *result; @@ -21228,7 +19128,6 @@ static CYTHON_INLINE PyObject* __Pyx_PyObject_CallMethO(PyObject *func, PyObject } #endif -/* PyObjectCallOneArg */ #if CYTHON_COMPILING_IN_CPYTHON static PyObject* __Pyx__PyObject_CallOneArg(PyObject *func, PyObject *arg) { PyObject *result; @@ -21241,11 +19140,6 @@ static PyObject* __Pyx__PyObject_CallOneArg(PyObject *func, PyObject *arg) { return result; } static CYTHON_INLINE PyObject* __Pyx_PyObject_CallOneArg(PyObject *func, PyObject *arg) { -#if CYTHON_FAST_PYCALL - if (PyFunction_Check(func)) { - return __Pyx_PyFunction_FastCall(func, &arg, 1); - } -#endif #ifdef __Pyx_CyFunction_USED if (likely(PyCFunction_Check(func) || PyObject_TypeCheck(func, __pyx_CyFunctionType))) { #else @@ -21253,33 +19147,19 @@ static CYTHON_INLINE PyObject* __Pyx_PyObject_CallOneArg(PyObject *func, PyObjec #endif if (likely(PyCFunction_GET_FLAGS(func) & METH_O)) { return __Pyx_PyObject_CallMethO(func, arg); -#if CYTHON_FAST_PYCCALL - } else if (PyCFunction_GET_FLAGS(func) & METH_FASTCALL) { - return __Pyx_PyCFunction_FastCall(func, &arg, 1); -#endif } } return __Pyx__PyObject_CallOneArg(func, arg); } #else static CYTHON_INLINE PyObject* __Pyx_PyObject_CallOneArg(PyObject *func, PyObject *arg) { - PyObject *result; - PyObject *args = PyTuple_Pack(1, arg); - if (unlikely(!args)) return NULL; - result = __Pyx_PyObject_Call(func, args, NULL); - Py_DECREF(args); - return result; + PyObject* args = PyTuple_Pack(1, arg); + return (likely(args)) ? __Pyx_PyObject_Call(func, args, NULL) : NULL; } #endif -/* PyObjectCallNoArg */ - #if CYTHON_COMPILING_IN_CPYTHON +#if CYTHON_COMPILING_IN_CPYTHON static CYTHON_INLINE PyObject* __Pyx_PyObject_CallNoArg(PyObject *func) { -#if CYTHON_FAST_PYCALL - if (PyFunction_Check(func)) { - return __Pyx_PyFunction_FastCall(func, NULL, 0); - } -#endif #ifdef __Pyx_CyFunction_USED if (likely(PyCFunction_Check(func) || PyObject_TypeCheck(func, __pyx_CyFunctionType))) { #else @@ -21293,22 +19173,19 @@ static CYTHON_INLINE PyObject* __Pyx_PyObject_CallNoArg(PyObject *func) { } #endif -/* RaiseTooManyValuesToUnpack */ - static CYTHON_INLINE void __Pyx_RaiseTooManyValuesError(Py_ssize_t expected) { +static CYTHON_INLINE void __Pyx_RaiseTooManyValuesError(Py_ssize_t expected) { PyErr_Format(PyExc_ValueError, "too many values to unpack (expected %" CYTHON_FORMAT_SSIZE_T "d)", expected); } -/* RaiseNeedMoreValuesToUnpack */ - static CYTHON_INLINE void __Pyx_RaiseNeedMoreValuesError(Py_ssize_t index) { +static CYTHON_INLINE void __Pyx_RaiseNeedMoreValuesError(Py_ssize_t index) { PyErr_Format(PyExc_ValueError, "need more than %" CYTHON_FORMAT_SSIZE_T "d value%.1s to unpack", index, (index == 1) ? "" : "s"); } -/* IterFinish */ - static CYTHON_INLINE int __Pyx_IterFinish(void) { -#if CYTHON_FAST_THREAD_STATE +static CYTHON_INLINE int __Pyx_IterFinish(void) { +#if CYTHON_COMPILING_IN_CPYTHON PyThreadState *tstate = PyThreadState_GET(); PyObject* exc_type = tstate->curexc_type; if (unlikely(exc_type)) { @@ -21341,8 +19218,7 @@ static CYTHON_INLINE PyObject* __Pyx_PyObject_CallNoArg(PyObject *func) { #endif } -/* UnpackItemEndCheck */ - static int __Pyx_IternextUnpackEndCheck(PyObject *retval, Py_ssize_t expected) { +static int __Pyx_IternextUnpackEndCheck(PyObject *retval, Py_ssize_t expected) { if (unlikely(retval)) { Py_DECREF(retval); __Pyx_RaiseTooManyValuesError(expected); @@ -21353,33 +19229,18 @@ static CYTHON_INLINE PyObject* __Pyx_PyObject_CallNoArg(PyObject *func) { return 0; } -/* PyObjectCallMethod1 */ - static PyObject* __Pyx_PyObject_CallMethod1(PyObject* obj, PyObject* method_name, PyObject* arg) { +static PyObject* __Pyx_PyObject_CallMethod1(PyObject* obj, PyObject* method_name, PyObject* arg) { PyObject *method, *result = NULL; method = __Pyx_PyObject_GetAttrStr(obj, method_name); - if (unlikely(!method)) goto done; -#if CYTHON_UNPACK_METHODS + if (unlikely(!method)) goto bad; +#if CYTHON_COMPILING_IN_CPYTHON if (likely(PyMethod_Check(method))) { PyObject *self = PyMethod_GET_SELF(method); if (likely(self)) { PyObject *args; PyObject *function = PyMethod_GET_FUNCTION(method); - #if CYTHON_FAST_PYCALL - if (PyFunction_Check(function)) { - PyObject *args[2] = {self, arg}; - result = __Pyx_PyFunction_FastCall(function, args, 2); - goto done; - } - #endif - #if CYTHON_FAST_PYCCALL - if (__Pyx_PyFastCFunction_Check(function)) { - PyObject *args[2] = {self, arg}; - result = __Pyx_PyCFunction_FastCall(function, args, 2); - goto done; - } - #endif args = PyTuple_New(2); - if (unlikely(!args)) goto done; + if (unlikely(!args)) goto bad; Py_INCREF(self); PyTuple_SET_ITEM(args, 0, self); Py_INCREF(arg); @@ -21394,13 +19255,12 @@ static CYTHON_INLINE PyObject* __Pyx_PyObject_CallNoArg(PyObject *func) { } #endif result = __Pyx_PyObject_CallOneArg(method, arg); -done: +bad: Py_XDECREF(method); return result; } -/* append */ - static CYTHON_INLINE int __Pyx_PyObject_Append(PyObject* L, PyObject* x) { +static CYTHON_INLINE int __Pyx_PyObject_Append(PyObject* L, PyObject* x) { if (likely(PyList_CheckExact(L))) { if (unlikely(__Pyx_PyList_Append(L, x) < 0)) return -1; } else { @@ -21412,124 +19272,7 @@ done: return 0; } -/* PyIntBinop */ - #if !CYTHON_COMPILING_IN_PYPY -static PyObject* __Pyx_PyInt_AddObjC(PyObject *op1, PyObject *op2, CYTHON_UNUSED long intval, CYTHON_UNUSED int inplace) { - #if PY_MAJOR_VERSION < 3 - if (likely(PyInt_CheckExact(op1))) { - const long b = intval; - long x; - long a = PyInt_AS_LONG(op1); - x = (long)((unsigned long)a + b); - if (likely((x^a) >= 0 || (x^b) >= 0)) - return PyInt_FromLong(x); - return PyLong_Type.tp_as_number->nb_add(op1, op2); - } - #endif - #if CYTHON_USE_PYLONG_INTERNALS - if (likely(PyLong_CheckExact(op1))) { - const long b = intval; - long a, x; -#ifdef HAVE_LONG_LONG - const PY_LONG_LONG llb = intval; - PY_LONG_LONG lla, llx; -#endif - const digit* digits = ((PyLongObject*)op1)->ob_digit; - const Py_ssize_t size = Py_SIZE(op1); - if (likely(__Pyx_sst_abs(size) <= 1)) { - a = likely(size) ? digits[0] : 0; - if (size == -1) a = -a; - } else { - switch (size) { - case -2: - if (8 * sizeof(long) - 1 > 2 * PyLong_SHIFT) { - a = -(long) (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])); - break; -#ifdef HAVE_LONG_LONG - } else if (8 * sizeof(PY_LONG_LONG) - 1 > 2 * PyLong_SHIFT) { - lla = -(PY_LONG_LONG) (((((unsigned PY_LONG_LONG)digits[1]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[0])); - goto long_long; -#endif - } - case 2: - if (8 * sizeof(long) - 1 > 2 * PyLong_SHIFT) { - a = (long) (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])); - break; -#ifdef HAVE_LONG_LONG - } else if (8 * sizeof(PY_LONG_LONG) - 1 > 2 * PyLong_SHIFT) { - lla = (PY_LONG_LONG) (((((unsigned PY_LONG_LONG)digits[1]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[0])); - goto long_long; -#endif - } - case -3: - if (8 * sizeof(long) - 1 > 3 * PyLong_SHIFT) { - a = -(long) (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])); - break; -#ifdef HAVE_LONG_LONG - } else if (8 * sizeof(PY_LONG_LONG) - 1 > 3 * PyLong_SHIFT) { - lla = -(PY_LONG_LONG) (((((((unsigned PY_LONG_LONG)digits[2]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[1]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[0])); - goto long_long; -#endif - } - case 3: - if (8 * sizeof(long) - 1 > 3 * PyLong_SHIFT) { - a = (long) (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])); - break; -#ifdef HAVE_LONG_LONG - } else if (8 * sizeof(PY_LONG_LONG) - 1 > 3 * PyLong_SHIFT) { - lla = (PY_LONG_LONG) (((((((unsigned PY_LONG_LONG)digits[2]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[1]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[0])); - goto long_long; -#endif - } - case -4: - if (8 * sizeof(long) - 1 > 4 * PyLong_SHIFT) { - a = -(long) (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])); - break; -#ifdef HAVE_LONG_LONG - } else if (8 * sizeof(PY_LONG_LONG) - 1 > 4 * PyLong_SHIFT) { - lla = -(PY_LONG_LONG) (((((((((unsigned PY_LONG_LONG)digits[3]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[2]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[1]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[0])); - goto long_long; -#endif - } - case 4: - if (8 * sizeof(long) - 1 > 4 * PyLong_SHIFT) { - a = (long) (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])); - break; -#ifdef HAVE_LONG_LONG - } else if (8 * sizeof(PY_LONG_LONG) - 1 > 4 * PyLong_SHIFT) { - lla = (PY_LONG_LONG) (((((((((unsigned PY_LONG_LONG)digits[3]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[2]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[1]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[0])); - goto long_long; -#endif - } - default: return PyLong_Type.tp_as_number->nb_add(op1, op2); - } - } - x = a + b; - return PyLong_FromLong(x); -#ifdef HAVE_LONG_LONG - long_long: - llx = lla + llb; - return PyLong_FromLongLong(llx); -#endif - - - } - #endif - if (PyFloat_CheckExact(op1)) { - const long b = intval; - double a = PyFloat_AS_DOUBLE(op1); - double result; - PyFPE_START_PROTECT("add", return NULL) - result = ((double)a) + (double)b; - PyFPE_END_PROTECT(result) - return PyFloat_FromDouble(result); - } - return (inplace ? PyNumber_InPlaceAdd : PyNumber_Add)(op1, op2); -} -#endif - -/* GetItemInt */ - static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Generic(PyObject *o, PyObject* j) { +static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Generic(PyObject *o, PyObject* j) { PyObject *r; if (!j) return NULL; r = PyObject_GetItem(o, j); @@ -21537,9 +19280,8 @@ static PyObject* __Pyx_PyInt_AddObjC(PyObject *op1, PyObject *op2, CYTHON_UNUSED return r; } static CYTHON_INLINE PyObject *__Pyx_GetItemInt_List_Fast(PyObject *o, Py_ssize_t i, - CYTHON_NCP_UNUSED int wraparound, - CYTHON_NCP_UNUSED int boundscheck) { -#if CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS + int wraparound, int boundscheck) { +#if CYTHON_COMPILING_IN_CPYTHON if (wraparound & unlikely(i < 0)) i += PyList_GET_SIZE(o); if ((!boundscheck) || likely((0 <= i) & (i < PyList_GET_SIZE(o)))) { PyObject *r = PyList_GET_ITEM(o, i); @@ -21552,9 +19294,8 @@ static CYTHON_INLINE PyObject *__Pyx_GetItemInt_List_Fast(PyObject *o, Py_ssize_ #endif } static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Tuple_Fast(PyObject *o, Py_ssize_t i, - CYTHON_NCP_UNUSED int wraparound, - CYTHON_NCP_UNUSED int boundscheck) { -#if CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS + int wraparound, int boundscheck) { +#if CYTHON_COMPILING_IN_CPYTHON if (wraparound & unlikely(i < 0)) i += PyTuple_GET_SIZE(o); if ((!boundscheck) || likely((0 <= i) & (i < PyTuple_GET_SIZE(o)))) { PyObject *r = PyTuple_GET_ITEM(o, i); @@ -21566,10 +19307,9 @@ static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Tuple_Fast(PyObject *o, Py_ssize return PySequence_GetItem(o, i); #endif } -static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Fast(PyObject *o, Py_ssize_t i, int is_list, - CYTHON_NCP_UNUSED int wraparound, - CYTHON_NCP_UNUSED int boundscheck) { -#if CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS && CYTHON_USE_TYPE_SLOTS +static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Fast(PyObject *o, Py_ssize_t i, + int is_list, int wraparound, int boundscheck) { +#if CYTHON_COMPILING_IN_CPYTHON if (is_list || PyList_CheckExact(o)) { Py_ssize_t n = ((!wraparound) | likely(i >= 0)) ? i : i + PyList_GET_SIZE(o); if ((!boundscheck) || (likely((n >= 0) & (n < PyList_GET_SIZE(o))))) { @@ -21593,9 +19333,10 @@ static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Fast(PyObject *o, Py_ssize_t i, if (likely(l >= 0)) { i += l; } else { - if (!PyErr_ExceptionMatches(PyExc_OverflowError)) + if (PyErr_ExceptionMatches(PyExc_OverflowError)) + PyErr_Clear(); + else return NULL; - PyErr_Clear(); } } return m->sq_item(o, i); @@ -21609,126 +19350,10 @@ static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Fast(PyObject *o, Py_ssize_t i, return __Pyx_GetItemInt_Generic(o, PyInt_FromSsize_t(i)); } -/* PyIntBinop */ - #if !CYTHON_COMPILING_IN_PYPY -static PyObject* __Pyx_PyInt_SubtractObjC(PyObject *op1, PyObject *op2, CYTHON_UNUSED long intval, CYTHON_UNUSED int inplace) { - #if PY_MAJOR_VERSION < 3 - if (likely(PyInt_CheckExact(op1))) { - const long b = intval; - long x; - long a = PyInt_AS_LONG(op1); - x = (long)((unsigned long)a - b); - if (likely((x^a) >= 0 || (x^~b) >= 0)) - return PyInt_FromLong(x); - return PyLong_Type.tp_as_number->nb_subtract(op1, op2); - } - #endif - #if CYTHON_USE_PYLONG_INTERNALS - if (likely(PyLong_CheckExact(op1))) { - const long b = intval; - long a, x; -#ifdef HAVE_LONG_LONG - const PY_LONG_LONG llb = intval; - PY_LONG_LONG lla, llx; -#endif - const digit* digits = ((PyLongObject*)op1)->ob_digit; - const Py_ssize_t size = Py_SIZE(op1); - if (likely(__Pyx_sst_abs(size) <= 1)) { - a = likely(size) ? digits[0] : 0; - if (size == -1) a = -a; - } else { - switch (size) { - case -2: - if (8 * sizeof(long) - 1 > 2 * PyLong_SHIFT) { - a = -(long) (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])); - break; -#ifdef HAVE_LONG_LONG - } else if (8 * sizeof(PY_LONG_LONG) - 1 > 2 * PyLong_SHIFT) { - lla = -(PY_LONG_LONG) (((((unsigned PY_LONG_LONG)digits[1]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[0])); - goto long_long; -#endif - } - case 2: - if (8 * sizeof(long) - 1 > 2 * PyLong_SHIFT) { - a = (long) (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])); - break; -#ifdef HAVE_LONG_LONG - } else if (8 * sizeof(PY_LONG_LONG) - 1 > 2 * PyLong_SHIFT) { - lla = (PY_LONG_LONG) (((((unsigned PY_LONG_LONG)digits[1]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[0])); - goto long_long; -#endif - } - case -3: - if (8 * sizeof(long) - 1 > 3 * PyLong_SHIFT) { - a = -(long) (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])); - break; -#ifdef HAVE_LONG_LONG - } else if (8 * sizeof(PY_LONG_LONG) - 1 > 3 * PyLong_SHIFT) { - lla = -(PY_LONG_LONG) (((((((unsigned PY_LONG_LONG)digits[2]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[1]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[0])); - goto long_long; -#endif - } - case 3: - if (8 * sizeof(long) - 1 > 3 * PyLong_SHIFT) { - a = (long) (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])); - break; -#ifdef HAVE_LONG_LONG - } else if (8 * sizeof(PY_LONG_LONG) - 1 > 3 * PyLong_SHIFT) { - lla = (PY_LONG_LONG) (((((((unsigned PY_LONG_LONG)digits[2]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[1]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[0])); - goto long_long; -#endif - } - case -4: - if (8 * sizeof(long) - 1 > 4 * PyLong_SHIFT) { - a = -(long) (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])); - break; -#ifdef HAVE_LONG_LONG - } else if (8 * sizeof(PY_LONG_LONG) - 1 > 4 * PyLong_SHIFT) { - lla = -(PY_LONG_LONG) (((((((((unsigned PY_LONG_LONG)digits[3]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[2]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[1]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[0])); - goto long_long; -#endif - } - case 4: - if (8 * sizeof(long) - 1 > 4 * PyLong_SHIFT) { - a = (long) (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])); - break; -#ifdef HAVE_LONG_LONG - } else if (8 * sizeof(PY_LONG_LONG) - 1 > 4 * PyLong_SHIFT) { - lla = (PY_LONG_LONG) (((((((((unsigned PY_LONG_LONG)digits[3]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[2]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[1]) << PyLong_SHIFT) | (unsigned PY_LONG_LONG)digits[0])); - goto long_long; -#endif - } - default: return PyLong_Type.tp_as_number->nb_subtract(op1, op2); - } - } - x = a - b; - return PyLong_FromLong(x); -#ifdef HAVE_LONG_LONG - long_long: - llx = lla - llb; - return PyLong_FromLongLong(llx); -#endif - - - } - #endif - if (PyFloat_CheckExact(op1)) { - const long b = intval; - double a = PyFloat_AS_DOUBLE(op1); - double result; - PyFPE_START_PROTECT("subtract", return NULL) - result = ((double)a) - (double)b; - PyFPE_END_PROTECT(result) - return PyFloat_FromDouble(result); - } - return (inplace ? PyNumber_InPlaceSubtract : PyNumber_Subtract)(op1, op2); -} -#endif - -/* PyErrFetchRestore */ - #if CYTHON_FAST_THREAD_STATE -static CYTHON_INLINE void __Pyx_ErrRestoreInState(PyThreadState *tstate, PyObject *type, PyObject *value, PyObject *tb) { +static CYTHON_INLINE void __Pyx_ErrRestore(PyObject *type, PyObject *value, PyObject *tb) { +#if CYTHON_COMPILING_IN_CPYTHON PyObject *tmp_type, *tmp_value, *tmp_tb; + PyThreadState *tstate = PyThreadState_GET(); tmp_type = tstate->curexc_type; tmp_value = tstate->curexc_value; tmp_tb = tstate->curexc_traceback; @@ -21738,22 +19363,27 @@ static CYTHON_INLINE void __Pyx_ErrRestoreInState(PyThreadState *tstate, PyObjec Py_XDECREF(tmp_type); Py_XDECREF(tmp_value); Py_XDECREF(tmp_tb); +#else + PyErr_Restore(type, value, tb); +#endif } -static CYTHON_INLINE void __Pyx_ErrFetchInState(PyThreadState *tstate, PyObject **type, PyObject **value, PyObject **tb) { +static CYTHON_INLINE void __Pyx_ErrFetch(PyObject **type, PyObject **value, PyObject **tb) { +#if CYTHON_COMPILING_IN_CPYTHON + PyThreadState *tstate = PyThreadState_GET(); *type = tstate->curexc_type; *value = tstate->curexc_value; *tb = tstate->curexc_traceback; tstate->curexc_type = 0; tstate->curexc_value = 0; tstate->curexc_traceback = 0; -} +#else + PyErr_Fetch(type, value, tb); #endif +} -/* RaiseException */ - #if PY_MAJOR_VERSION < 3 +#if PY_MAJOR_VERSION < 3 static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb, CYTHON_UNUSED PyObject *cause) { - __Pyx_PyThreadState_declare Py_XINCREF(type); if (!value || value == Py_None) value = NULL; @@ -21792,7 +19422,6 @@ static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb, goto raise_error; } } - __Pyx_PyThreadState_assign __Pyx_ErrRestore(type, value, tb); return; raise_error: @@ -21826,13 +19455,10 @@ static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb, PyObject if (value && PyExceptionInstance_Check(value)) { instance_class = (PyObject*) Py_TYPE(value); if (instance_class != type) { - int is_subclass = PyObject_IsSubclass(instance_class, type); - if (!is_subclass) { - instance_class = NULL; - } else if (unlikely(is_subclass == -1)) { - goto bad; - } else { + if (PyObject_IsSubclass(instance_class, type)) { type = instance_class; + } else { + instance_class = NULL; } } } @@ -21892,7 +19518,7 @@ static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb, PyObject if (tb) { #if CYTHON_COMPILING_IN_PYPY PyObject *tmp_type, *tmp_value, *tmp_tb; - PyErr_Fetch(&tmp_type, &tmp_value, &tmp_tb); + PyErr_Fetch(tmp_type, tmp_value, tmp_tb); Py_INCREF(tb); PyErr_Restore(tmp_type, tmp_value, tb); Py_XDECREF(tmp_tb); @@ -21912,18 +19538,23 @@ bad: } #endif -/* SaveResetException */ - #if CYTHON_FAST_THREAD_STATE -static CYTHON_INLINE void __Pyx__ExceptionSave(PyThreadState *tstate, PyObject **type, PyObject **value, PyObject **tb) { +static CYTHON_INLINE void __Pyx_ExceptionSave(PyObject **type, PyObject **value, PyObject **tb) { +#if CYTHON_COMPILING_IN_CPYTHON + PyThreadState *tstate = PyThreadState_GET(); *type = tstate->exc_type; *value = tstate->exc_value; *tb = tstate->exc_traceback; Py_XINCREF(*type); Py_XINCREF(*value); Py_XINCREF(*tb); +#else + PyErr_GetExcInfo(type, value, tb); +#endif } -static CYTHON_INLINE void __Pyx__ExceptionReset(PyThreadState *tstate, PyObject *type, PyObject *value, PyObject *tb) { +static void __Pyx_ExceptionReset(PyObject *type, PyObject *value, PyObject *tb) { +#if CYTHON_COMPILING_IN_CPYTHON PyObject *tmp_type, *tmp_value, *tmp_tb; + PyThreadState *tstate = PyThreadState_GET(); tmp_type = tstate->exc_type; tmp_value = tstate->exc_value; tmp_tb = tstate->exc_traceback; @@ -21933,28 +19564,16 @@ static CYTHON_INLINE void __Pyx__ExceptionReset(PyThreadState *tstate, PyObject Py_XDECREF(tmp_type); Py_XDECREF(tmp_value); Py_XDECREF(tmp_tb); -} +#else + PyErr_SetExcInfo(type, value, tb); #endif - -/* PyErrExceptionMatches */ - #if CYTHON_FAST_THREAD_STATE -static CYTHON_INLINE int __Pyx_PyErr_ExceptionMatchesInState(PyThreadState* tstate, PyObject* err) { - PyObject *exc_type = tstate->curexc_type; - if (exc_type == err) return 1; - if (unlikely(!exc_type)) return 0; - return PyErr_GivenExceptionMatches(exc_type, err); } -#endif -/* GetException */ - #if CYTHON_FAST_THREAD_STATE -static int __Pyx__GetException(PyThreadState *tstate, PyObject **type, PyObject **value, PyObject **tb) { -#else static int __Pyx_GetException(PyObject **type, PyObject **value, PyObject **tb) { -#endif PyObject *local_type, *local_value, *local_tb; -#if CYTHON_FAST_THREAD_STATE +#if CYTHON_COMPILING_IN_CPYTHON PyObject *tmp_type, *tmp_value, *tmp_tb; + PyThreadState *tstate = PyThreadState_GET(); local_type = tstate->curexc_type; local_value = tstate->curexc_value; local_tb = tstate->curexc_traceback; @@ -21965,7 +19584,7 @@ static int __Pyx_GetException(PyObject **type, PyObject **value, PyObject **tb) PyErr_Fetch(&local_type, &local_value, &local_tb); #endif PyErr_NormalizeException(&local_type, &local_value, &local_tb); -#if CYTHON_FAST_THREAD_STATE +#if CYTHON_COMPILING_IN_CPYTHON if (unlikely(tstate->curexc_type)) #else if (unlikely(PyErr_Occurred())) @@ -21983,7 +19602,7 @@ static int __Pyx_GetException(PyObject **type, PyObject **value, PyObject **tb) *type = local_type; *value = local_value; *tb = local_tb; -#if CYTHON_FAST_THREAD_STATE +#if CYTHON_COMPILING_IN_CPYTHON tmp_type = tstate->exc_type; tmp_value = tstate->exc_value; tmp_tb = tstate->exc_traceback; @@ -22007,10 +19626,9 @@ bad: return -1; } -/* GetModuleGlobalName */ - static CYTHON_INLINE PyObject *__Pyx_GetModuleGlobalName(PyObject *name) { +static CYTHON_INLINE PyObject *__Pyx_GetModuleGlobalName(PyObject *name) { PyObject *result; -#if !CYTHON_AVOID_BORROWED_REFS +#if CYTHON_COMPILING_IN_CPYTHON result = PyDict_GetItem(__pyx_d, name); if (likely(result)) { Py_INCREF(result); @@ -22025,22 +19643,15 @@ bad: return result; } -/* WriteUnraisableException */ - static void __Pyx_WriteUnraisable(const char *name, CYTHON_UNUSED int clineno, +static CYTHON_INLINE void __Pyx_RaiseUnboundLocalError(const char *varname) { + PyErr_Format(PyExc_UnboundLocalError, "local variable '%s' referenced before assignment", varname); +} + +static void __Pyx_WriteUnraisable(const char *name, CYTHON_UNUSED int clineno, CYTHON_UNUSED int lineno, CYTHON_UNUSED const char *filename, - int full_traceback, CYTHON_UNUSED int nogil) { + int full_traceback) { PyObject *old_exc, *old_val, *old_tb; PyObject *ctx; - __Pyx_PyThreadState_declare -#ifdef WITH_THREAD - PyGILState_STATE state; - if (nogil) - state = PyGILState_Ensure(); -#ifdef _MSC_VER - else state = (PyGILState_STATE)-1; -#endif -#endif - __Pyx_PyThreadState_assign __Pyx_ErrFetch(&old_exc, &old_val, &old_tb); if (full_traceback) { Py_XINCREF(old_exc); @@ -22061,21 +19672,15 @@ bad: PyErr_WriteUnraisable(ctx); Py_DECREF(ctx); } -#ifdef WITH_THREAD - if (nogil) - PyGILState_Release(state); -#endif } -/* StringJoin */ - #if !CYTHON_COMPILING_IN_CPYTHON +#if !CYTHON_COMPILING_IN_CPYTHON static CYTHON_INLINE PyObject* __Pyx_PyBytes_Join(PyObject* sep, PyObject* values) { return PyObject_CallMethodObjArgs(sep, __pyx_n_s_join, values, NULL); } #endif -/* decode_c_bytes */ - static CYTHON_INLINE PyObject* __Pyx_decode_c_bytes( +static CYTHON_INLINE PyObject* __Pyx_decode_c_bytes( const char* cstring, Py_ssize_t length, Py_ssize_t start, Py_ssize_t stop, const char* encoding, const char* errors, PyObject* (*decode_func)(const char *s, Py_ssize_t size, const char *errors)) { @@ -22101,93 +19706,7 @@ static CYTHON_INLINE PyObject* __Pyx_PyBytes_Join(PyObject* sep, PyObject* value } } -/* PyIntBinop */ - #if !CYTHON_COMPILING_IN_PYPY -static PyObject* __Pyx_PyInt_EqObjC(PyObject *op1, PyObject *op2, CYTHON_UNUSED long intval, CYTHON_UNUSED int inplace) { - if (op1 == op2) { - Py_RETURN_TRUE; - } - #if PY_MAJOR_VERSION < 3 - if (likely(PyInt_CheckExact(op1))) { - const long b = intval; - long a = PyInt_AS_LONG(op1); - if (a == b) { - Py_RETURN_TRUE; - } else { - Py_RETURN_FALSE; - } - } - #endif - #if CYTHON_USE_PYLONG_INTERNALS - if (likely(PyLong_CheckExact(op1))) { - const long b = intval; - long a; - const digit* digits = ((PyLongObject*)op1)->ob_digit; - const Py_ssize_t size = Py_SIZE(op1); - if (likely(__Pyx_sst_abs(size) <= 1)) { - a = likely(size) ? digits[0] : 0; - if (size == -1) a = -a; - } else { - switch (size) { - case -2: - if (8 * sizeof(long) - 1 > 2 * PyLong_SHIFT) { - a = -(long) (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])); - break; - } - case 2: - if (8 * sizeof(long) - 1 > 2 * PyLong_SHIFT) { - a = (long) (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])); - break; - } - case -3: - if (8 * sizeof(long) - 1 > 3 * PyLong_SHIFT) { - a = -(long) (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])); - break; - } - case 3: - if (8 * sizeof(long) - 1 > 3 * PyLong_SHIFT) { - a = (long) (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])); - break; - } - case -4: - if (8 * sizeof(long) - 1 > 4 * PyLong_SHIFT) { - a = -(long) (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])); - break; - } - case 4: - if (8 * sizeof(long) - 1 > 4 * PyLong_SHIFT) { - a = (long) (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0])); - break; - } - #if PyLong_SHIFT < 30 && PyLong_SHIFT != 15 - default: return PyLong_Type.tp_richcompare(op1, op2, Py_EQ); - #else - default: Py_RETURN_FALSE; - #endif - } - } - if (a == b) { - Py_RETURN_TRUE; - } else { - Py_RETURN_FALSE; - } - } - #endif - if (PyFloat_CheckExact(op1)) { - const long b = intval; - double a = PyFloat_AS_DOUBLE(op1); - if ((double)a == (double)b) { - Py_RETURN_TRUE; - } else { - Py_RETURN_FALSE; - } - } - return PyObject_RichCompare(op1, op2, Py_EQ); -} -#endif - -/* ExtTypeTest */ - static CYTHON_INLINE int __Pyx_TypeTest(PyObject *obj, PyTypeObject *type) { +static CYTHON_INLINE int __Pyx_TypeTest(PyObject *obj, PyTypeObject *type) { if (unlikely(!type)) { PyErr_SetString(PyExc_SystemError, "Missing type object"); return 0; @@ -22199,17 +19718,16 @@ static PyObject* __Pyx_PyInt_EqObjC(PyObject *op1, PyObject *op2, CYTHON_UNUSED return 0; } -/* SetItemInt */ - static CYTHON_INLINE int __Pyx_SetItemInt_Generic(PyObject *o, PyObject *j, PyObject *v) { +static CYTHON_INLINE int __Pyx_SetItemInt_Generic(PyObject *o, PyObject *j, PyObject *v) { int r; if (!j) return -1; r = PyObject_SetItem(o, j, v); Py_DECREF(j); return r; } -static CYTHON_INLINE int __Pyx_SetItemInt_Fast(PyObject *o, Py_ssize_t i, PyObject *v, int is_list, - CYTHON_NCP_UNUSED int wraparound, CYTHON_NCP_UNUSED int boundscheck) { -#if CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS && CYTHON_USE_TYPE_SLOTS +static CYTHON_INLINE int __Pyx_SetItemInt_Fast(PyObject *o, Py_ssize_t i, PyObject *v, + int is_list, int wraparound, int boundscheck) { +#if CYTHON_COMPILING_IN_CPYTHON if (is_list || PyList_CheckExact(o)) { Py_ssize_t n = (!wraparound) ? i : ((likely(i >= 0)) ? i : i + PyList_GET_SIZE(o)); if ((!boundscheck) || likely((n >= 0) & (n < PyList_GET_SIZE(o)))) { @@ -22227,9 +19745,10 @@ static CYTHON_INLINE int __Pyx_SetItemInt_Fast(PyObject *o, Py_ssize_t i, PyObje if (likely(l >= 0)) { i += l; } else { - if (!PyErr_ExceptionMatches(PyExc_OverflowError)) + if (PyErr_ExceptionMatches(PyExc_OverflowError)) + PyErr_Clear(); + else return -1; - PyErr_Clear(); } } return m->sq_ass_item(o, i, v); @@ -22247,20 +19766,13 @@ static CYTHON_INLINE int __Pyx_SetItemInt_Fast(PyObject *o, Py_ssize_t i, PyObje return __Pyx_SetItemInt_Generic(o, PyInt_FromSsize_t(i), v); } -/* decode_c_string */ - static CYTHON_INLINE PyObject* __Pyx_decode_c_string( +static CYTHON_INLINE PyObject* __Pyx_decode_c_string( const char* cstring, Py_ssize_t start, Py_ssize_t stop, const char* encoding, const char* errors, PyObject* (*decode_func)(const char *s, Py_ssize_t size, const char *errors)) { Py_ssize_t length; if (unlikely((start < 0) | (stop < 0))) { - size_t slen = strlen(cstring); - if (unlikely(slen > (size_t) PY_SSIZE_T_MAX)) { - PyErr_SetString(PyExc_OverflowError, - "c-string too long to convert to Python"); - return NULL; - } - length = (Py_ssize_t) slen; + length = strlen(cstring); if (start < 0) { start += length; if (start < 0) @@ -22280,87 +19792,11 @@ static CYTHON_INLINE int __Pyx_SetItemInt_Fast(PyObject *o, Py_ssize_t i, PyObje } } -/* RaiseNoneIterError */ - static CYTHON_INLINE void __Pyx_RaiseNoneNotIterableError(void) { +static CYTHON_INLINE void __Pyx_RaiseNoneNotIterableError(void) { PyErr_SetString(PyExc_TypeError, "'NoneType' object is not iterable"); } -/* Import */ - static PyObject *__Pyx_Import(PyObject *name, PyObject *from_list, int level) { - PyObject *empty_list = 0; - PyObject *module = 0; - PyObject *global_dict = 0; - PyObject *empty_dict = 0; - PyObject *list; - #if PY_VERSION_HEX < 0x03030000 - PyObject *py_import; - py_import = __Pyx_PyObject_GetAttrStr(__pyx_b, __pyx_n_s_import); - if (!py_import) - goto bad; - #endif - if (from_list) - list = from_list; - else { - empty_list = PyList_New(0); - if (!empty_list) - goto bad; - list = empty_list; - } - global_dict = PyModule_GetDict(__pyx_m); - if (!global_dict) - goto bad; - empty_dict = PyDict_New(); - if (!empty_dict) - goto bad; - { - #if PY_MAJOR_VERSION >= 3 - if (level == -1) { - if (strchr(__Pyx_MODULE_NAME, '.')) { - #if PY_VERSION_HEX < 0x03030000 - PyObject *py_level = PyInt_FromLong(1); - if (!py_level) - goto bad; - module = PyObject_CallFunctionObjArgs(py_import, - name, global_dict, empty_dict, list, py_level, NULL); - Py_DECREF(py_level); - #else - module = PyImport_ImportModuleLevelObject( - name, global_dict, empty_dict, list, 1); - #endif - if (!module) { - if (!PyErr_ExceptionMatches(PyExc_ImportError)) - goto bad; - PyErr_Clear(); - } - } - level = 0; - } - #endif - if (!module) { - #if PY_VERSION_HEX < 0x03030000 - PyObject *py_level = PyInt_FromLong(level); - if (!py_level) - goto bad; - module = PyObject_CallFunctionObjArgs(py_import, - name, global_dict, empty_dict, list, py_level, NULL); - Py_DECREF(py_level); - #else - module = PyImport_ImportModuleLevelObject( - name, global_dict, empty_dict, list, level); - #endif - } - } -bad: - #if PY_VERSION_HEX < 0x03030000 - Py_XDECREF(py_import); - #endif - Py_XDECREF(empty_list); - Py_XDECREF(empty_dict); - return module; -} - -/* CalculateMetaclass */ - static PyObject *__Pyx_CalculateMetaclass(PyTypeObject *metaclass, PyObject *bases) { +static PyObject *__Pyx_CalculateMetaclass(PyTypeObject *metaclass, PyObject *bases) { Py_ssize_t i, nbases = PyTuple_GET_SIZE(bases); for (i=0; i < nbases; i++) { PyTypeObject *tmptype; @@ -22398,8 +19834,7 @@ bad: return (PyObject*) metaclass; } -/* Py3ClassCreate */ - static PyObject *__Pyx_Py3MetaclassPrepare(PyObject *metaclass, PyObject *bases, PyObject *name, +static PyObject *__Pyx_Py3MetaclassPrepare(PyObject *metaclass, PyObject *bases, PyObject *name, PyObject *qualname, PyObject *mkw, PyObject *modname, PyObject *doc) { PyObject *ns; if (metaclass) { @@ -22465,8 +19900,7 @@ static PyObject *__Pyx_Py3ClassCreate(PyObject *metaclass, PyObject *name, PyObj return result; } -/* FetchCommonType */ - static PyTypeObject* __Pyx_FetchCommonType(PyTypeObject* type) { +static PyTypeObject* __Pyx_FetchCommonType(PyTypeObject* type) { PyObject* fake_module; PyTypeObject* cached_type = NULL; fake_module = PyImport_AddModule((char*) "_cython_" CYTHON_ABI); @@ -22504,8 +19938,7 @@ bad: goto done; } -/* CythonFunction */ - static PyObject * +static PyObject * __Pyx_CyFunction_get_doc(__pyx_CyFunctionObject *op, CYTHON_UNUSED void *closure) { if (unlikely(op->func_doc == NULL)) { @@ -22658,25 +20091,15 @@ __Pyx_CyFunction_get_code(__pyx_CyFunctionObject *op) } static int __Pyx_CyFunction_init_defaults(__pyx_CyFunctionObject *op) { - int result = 0; PyObject *res = op->defaults_getter((PyObject *) op); if (unlikely(!res)) return -1; - #if CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS op->defaults_tuple = PyTuple_GET_ITEM(res, 0); Py_INCREF(op->defaults_tuple); op->defaults_kwdict = PyTuple_GET_ITEM(res, 1); Py_INCREF(op->defaults_kwdict); - #else - op->defaults_tuple = PySequence_ITEM(res, 0); - if (unlikely(!op->defaults_tuple)) result = -1; - else { - op->defaults_kwdict = PySequence_ITEM(res, 1); - if (unlikely(!op->defaults_kwdict)) result = -1; - } - #endif Py_DECREF(res); - return result; + return 0; } static int __Pyx_CyFunction_set_defaults(__pyx_CyFunctionObject *op, PyObject* value) { @@ -22786,6 +20209,9 @@ static PyGetSetDef __pyx_CyFunction_getsets[] = { {(char *) "__annotations__", (getter)__Pyx_CyFunction_get_annotations, (setter)__Pyx_CyFunction_set_annotations, 0, 0}, {0, 0, 0, 0, 0} }; +#ifndef PY_WRITE_RESTRICTED +#define PY_WRITE_RESTRICTED WRITE_RESTRICTED +#endif static PyMemberDef __pyx_CyFunction_members[] = { {(char *) "__module__", T_OBJECT, offsetof(__pyx_CyFunctionObject, func.m_module), PY_WRITE_RESTRICTED, 0}, {0, 0, 0, 0, 0} @@ -22860,7 +20286,7 @@ __Pyx_CyFunction_clear(__pyx_CyFunctionObject *m) int i; for (i = 0; i < m->defaults_pyobjects; i++) Py_XDECREF(pydefaults[i]); - PyObject_Free(m->defaults); + PyMem_Free(m->defaults); m->defaults = NULL; } return 0; @@ -22921,40 +20347,37 @@ __Pyx_CyFunction_repr(__pyx_CyFunctionObject *op) PyString_AsString(op->func_qualname), (void *)op); #endif } -static PyObject * __Pyx_CyFunction_CallMethod(PyObject *func, PyObject *self, PyObject *arg, PyObject *kw) { +#if CYTHON_COMPILING_IN_PYPY +static PyObject * __Pyx_CyFunction_Call(PyObject *func, PyObject *arg, PyObject *kw) { PyCFunctionObject* f = (PyCFunctionObject*)func; - PyCFunction meth = f->m_ml->ml_meth; + PyCFunction meth = PyCFunction_GET_FUNCTION(func); + PyObject *self = PyCFunction_GET_SELF(func); Py_ssize_t size; - switch (f->m_ml->ml_flags & (METH_VARARGS | METH_KEYWORDS | METH_NOARGS | METH_O)) { + switch (PyCFunction_GET_FLAGS(func) & ~(METH_CLASS | METH_STATIC | METH_COEXIST)) { case METH_VARARGS: - if (likely(kw == NULL || PyDict_Size(kw) == 0)) + if (likely(kw == NULL) || PyDict_Size(kw) == 0) return (*meth)(self, arg); break; case METH_VARARGS | METH_KEYWORDS: return (*(PyCFunctionWithKeywords)meth)(self, arg, kw); case METH_NOARGS: - if (likely(kw == NULL || PyDict_Size(kw) == 0)) { + if (likely(kw == NULL) || PyDict_Size(kw) == 0) { size = PyTuple_GET_SIZE(arg); - if (likely(size == 0)) + if (size == 0) return (*meth)(self, NULL); PyErr_Format(PyExc_TypeError, - "%.200s() takes no arguments (%" CYTHON_FORMAT_SSIZE_T "d given)", + "%.200s() takes no arguments (%zd given)", f->m_ml->ml_name, size); return NULL; } break; case METH_O: - if (likely(kw == NULL || PyDict_Size(kw) == 0)) { + if (likely(kw == NULL) || PyDict_Size(kw) == 0) { size = PyTuple_GET_SIZE(arg); - if (likely(size == 1)) { - PyObject *result, *arg0 = PySequence_ITEM(arg, 0); - if (unlikely(!arg0)) return NULL; - result = (*meth)(self, arg0); - Py_DECREF(arg0); - return result; - } + if (size == 1) + return (*meth)(self, PyTuple_GET_ITEM(arg, 0)); PyErr_Format(PyExc_TypeError, - "%.200s() takes exactly one argument (%" CYTHON_FORMAT_SSIZE_T "d given)", + "%.200s() takes exactly one argument (%zd given)", f->m_ml->ml_name, size); return NULL; } @@ -22969,32 +20392,11 @@ static PyObject * __Pyx_CyFunction_CallMethod(PyObject *func, PyObject *self, Py f->m_ml->ml_name); return NULL; } -static CYTHON_INLINE PyObject *__Pyx_CyFunction_Call(PyObject *func, PyObject *arg, PyObject *kw) { - return __Pyx_CyFunction_CallMethod(func, ((PyCFunctionObject*)func)->m_self, arg, kw); -} -static PyObject *__Pyx_CyFunction_CallAsMethod(PyObject *func, PyObject *args, PyObject *kw) { - PyObject *result; - __pyx_CyFunctionObject *cyfunc = (__pyx_CyFunctionObject *) func; - if ((cyfunc->flags & __Pyx_CYFUNCTION_CCLASS) && !(cyfunc->flags & __Pyx_CYFUNCTION_STATICMETHOD)) { - Py_ssize_t argc; - PyObject *new_args; - PyObject *self; - argc = PyTuple_GET_SIZE(args); - new_args = PyTuple_GetSlice(args, 1, argc); - if (unlikely(!new_args)) - return NULL; - self = PyTuple_GetItem(args, 0); - if (unlikely(!self)) { - Py_DECREF(new_args); - return NULL; - } - result = __Pyx_CyFunction_CallMethod(func, self, new_args, kw); - Py_DECREF(new_args); - } else { - result = __Pyx_CyFunction_Call(func, args, kw); - } - return result; +#else +static PyObject * __Pyx_CyFunction_Call(PyObject *func, PyObject *arg, PyObject *kw) { + return PyCFunction_Call(func, arg, kw); } +#endif static PyTypeObject __pyx_CyFunctionType_type = { PyVarObject_HEAD_INIT(0, 0) "cython_function_or_method", @@ -23014,7 +20416,7 @@ static PyTypeObject __pyx_CyFunctionType_type = { 0, 0, 0, - __Pyx_CyFunction_CallAsMethod, + __Pyx_CyFunction_Call, 0, 0, 0, @@ -23055,7 +20457,10 @@ static PyTypeObject __pyx_CyFunctionType_type = { 0, #endif }; -static int __pyx_CyFunction_init(void) { +static int __Pyx_CyFunction_init(void) { +#if !CYTHON_COMPILING_IN_PYPY + __pyx_CyFunctionType_type.tp_call = PyCFunction_Call; +#endif __pyx_CyFunctionType = __Pyx_FetchCommonType(&__pyx_CyFunctionType_type); if (__pyx_CyFunctionType == NULL) { return -1; @@ -23064,7 +20469,7 @@ static int __pyx_CyFunction_init(void) { } static CYTHON_INLINE void *__Pyx_CyFunction_InitDefaults(PyObject *func, size_t size, int pyobjects) { __pyx_CyFunctionObject *m = (__pyx_CyFunctionObject *) func; - m->defaults = PyObject_Malloc(size); + m->defaults = PyMem_Malloc(size); if (!m->defaults) return PyErr_NoMemory(); memset(m->defaults, 0, size); @@ -23087,14 +20492,13 @@ static CYTHON_INLINE void __Pyx_CyFunction_SetAnnotationsDict(PyObject *func, Py Py_INCREF(dict); } -/* CodeObjectCache */ - static int __pyx_bisect_code_objects(__Pyx_CodeObjectCacheEntry* entries, int count, int code_line) { +static int __pyx_bisect_code_objects(__Pyx_CodeObjectCacheEntry* entries, int count, int code_line) { int start = 0, mid = 0, end = count - 1; if (end >= 0 && code_line > entries[end].code_line) { return count; } while (start < end) { - mid = start + (end - start) / 2; + mid = (start + end) / 2; if (code_line < entries[mid].code_line) { end = mid; } else if (code_line > entries[mid].code_line) { @@ -23167,8 +20571,7 @@ static void __pyx_insert_code_object(int code_line, PyCodeObject* code_object) { Py_INCREF(code_object); } -/* AddTraceback */ - #include "compile.h" +#include "compile.h" #include "frameobject.h" #include "traceback.h" static PyCodeObject* __Pyx_CreateCodeObjectForTraceback( @@ -23241,34 +20644,102 @@ static void __Pyx_AddTraceback(const char *funcname, int c_line, 0 /*PyObject *locals*/ ); if (!py_frame) goto bad; - __Pyx_PyFrame_SetLineNumber(py_frame, py_line); + py_frame->f_lineno = py_line; PyTraceBack_Here(py_frame); bad: Py_XDECREF(py_code); Py_XDECREF(py_frame); } -/* CIntToPy */ - static CYTHON_INLINE PyObject* __Pyx_PyInt_From_long(long value) { - const long neg_one = (long) -1, const_zero = (long) 0; +static PyObject *__Pyx_Import(PyObject *name, PyObject *from_list, int level) { + PyObject *empty_list = 0; + PyObject *module = 0; + PyObject *global_dict = 0; + PyObject *empty_dict = 0; + PyObject *list; + #if PY_VERSION_HEX < 0x03030000 + PyObject *py_import; + py_import = __Pyx_PyObject_GetAttrStr(__pyx_b, __pyx_n_s_import); + if (!py_import) + goto bad; + #endif + if (from_list) + list = from_list; + else { + empty_list = PyList_New(0); + if (!empty_list) + goto bad; + list = empty_list; + } + global_dict = PyModule_GetDict(__pyx_m); + if (!global_dict) + goto bad; + empty_dict = PyDict_New(); + if (!empty_dict) + goto bad; + { + #if PY_MAJOR_VERSION >= 3 + if (level == -1) { + if (strchr(__Pyx_MODULE_NAME, '.')) { + #if PY_VERSION_HEX < 0x03030000 + PyObject *py_level = PyInt_FromLong(1); + if (!py_level) + goto bad; + module = PyObject_CallFunctionObjArgs(py_import, + name, global_dict, empty_dict, list, py_level, NULL); + Py_DECREF(py_level); + #else + module = PyImport_ImportModuleLevelObject( + name, global_dict, empty_dict, list, 1); + #endif + if (!module) { + if (!PyErr_ExceptionMatches(PyExc_ImportError)) + goto bad; + PyErr_Clear(); + } + } + level = 0; + } + #endif + if (!module) { + #if PY_VERSION_HEX < 0x03030000 + PyObject *py_level = PyInt_FromLong(level); + if (!py_level) + goto bad; + module = PyObject_CallFunctionObjArgs(py_import, + name, global_dict, empty_dict, list, py_level, NULL); + Py_DECREF(py_level); + #else + module = PyImport_ImportModuleLevelObject( + name, global_dict, empty_dict, list, level); + #endif + } + } +bad: + #if PY_VERSION_HEX < 0x03030000 + Py_XDECREF(py_import); + #endif + Py_XDECREF(empty_list); + Py_XDECREF(empty_dict); + return module; +} + +static CYTHON_INLINE PyObject* __Pyx_PyInt_From_long(long value) { + const long neg_one = (long) -1, const_zero = 0; const int is_unsigned = neg_one > const_zero; if (is_unsigned) { if (sizeof(long) < sizeof(long)) { return PyInt_FromLong((long) value); } else if (sizeof(long) <= sizeof(unsigned long)) { return PyLong_FromUnsignedLong((unsigned long) value); -#ifdef HAVE_LONG_LONG - } else if (sizeof(long) <= sizeof(unsigned PY_LONG_LONG)) { - return PyLong_FromUnsignedLongLong((unsigned PY_LONG_LONG) value); -#endif + } else if (sizeof(long) <= sizeof(unsigned long long)) { + return PyLong_FromUnsignedLongLong((unsigned long long) value); } } else { if (sizeof(long) <= sizeof(long)) { return PyInt_FromLong((long) value); -#ifdef HAVE_LONG_LONG - } else if (sizeof(long) <= sizeof(PY_LONG_LONG)) { - return PyLong_FromLongLong((PY_LONG_LONG) value); -#endif + } else if (sizeof(long) <= sizeof(long long)) { + return PyLong_FromLongLong((long long) value); } } { @@ -23279,49 +20750,138 @@ bad: } } -/* CIntFromPyVerify */ - #define __PYX_VERIFY_RETURN_INT(target_type, func_type, func_value)\ - __PYX__VERIFY_RETURN_INT(target_type, func_type, func_value, 0) -#define __PYX_VERIFY_RETURN_INT_EXC(target_type, func_type, func_value)\ - __PYX__VERIFY_RETURN_INT(target_type, func_type, func_value, 1) -#define __PYX__VERIFY_RETURN_INT(target_type, func_type, func_value, exc)\ - {\ - func_type value = func_value;\ - if (sizeof(target_type) < sizeof(func_type)) {\ - if (unlikely(value != (func_type) (target_type) value)) {\ - func_type zero = 0;\ - if (exc && unlikely(value == (func_type)-1 && PyErr_Occurred()))\ - return (target_type) -1;\ - if (is_unsigned && unlikely(value < zero))\ - goto raise_neg_overflow;\ - else\ - goto raise_overflow;\ - }\ - }\ - return (target_type) value;\ - } - -/* CIntToPy */ - static CYTHON_INLINE PyObject* __Pyx_PyInt_From_int(int value) { - const int neg_one = (int) -1, const_zero = (int) 0; +#define __PYX_VERIFY_RETURN_INT(target_type, func_type, func_value) \ + { \ + func_type value = func_value; \ + if (sizeof(target_type) < sizeof(func_type)) { \ + if (unlikely(value != (func_type) (target_type) value)) { \ + func_type zero = 0; \ + if (is_unsigned && unlikely(value < zero)) \ + goto raise_neg_overflow; \ + else \ + goto raise_overflow; \ + } \ + } \ + return (target_type) value; \ + } + +#if CYTHON_COMPILING_IN_CPYTHON && PY_MAJOR_VERSION >= 3 + #if CYTHON_USE_PYLONG_INTERNALS + #include "longintrepr.h" + #endif +#endif + +static CYTHON_INLINE int __Pyx_PyInt_As_int(PyObject *x) { + const int neg_one = (int) -1, const_zero = 0; + const int is_unsigned = neg_one > const_zero; +#if PY_MAJOR_VERSION < 3 + if (likely(PyInt_Check(x))) { + if (sizeof(int) < sizeof(long)) { + __PYX_VERIFY_RETURN_INT(int, long, PyInt_AS_LONG(x)) + } else { + long val = PyInt_AS_LONG(x); + if (is_unsigned && unlikely(val < 0)) { + goto raise_neg_overflow; + } + return (int) val; + } + } else +#endif + if (likely(PyLong_Check(x))) { + if (is_unsigned) { +#if CYTHON_COMPILING_IN_CPYTHON && PY_MAJOR_VERSION >= 3 + #if CYTHON_USE_PYLONG_INTERNALS + switch (Py_SIZE(x)) { + case 0: return 0; + case 1: __PYX_VERIFY_RETURN_INT(int, digit, ((PyLongObject*)x)->ob_digit[0]); + } + #endif +#endif + if (unlikely(Py_SIZE(x) < 0)) { + goto raise_neg_overflow; + } + if (sizeof(int) <= sizeof(unsigned long)) { + __PYX_VERIFY_RETURN_INT(int, unsigned long, PyLong_AsUnsignedLong(x)) + } else if (sizeof(int) <= sizeof(unsigned long long)) { + __PYX_VERIFY_RETURN_INT(int, unsigned long long, PyLong_AsUnsignedLongLong(x)) + } + } else { +#if CYTHON_COMPILING_IN_CPYTHON && PY_MAJOR_VERSION >= 3 + #if CYTHON_USE_PYLONG_INTERNALS + switch (Py_SIZE(x)) { + case 0: return 0; + case 1: __PYX_VERIFY_RETURN_INT(int, digit, +(((PyLongObject*)x)->ob_digit[0])); + case -1: __PYX_VERIFY_RETURN_INT(int, sdigit, -(sdigit) ((PyLongObject*)x)->ob_digit[0]); + } + #endif +#endif + if (sizeof(int) <= sizeof(long)) { + __PYX_VERIFY_RETURN_INT(int, long, PyLong_AsLong(x)) + } else if (sizeof(int) <= sizeof(long long)) { + __PYX_VERIFY_RETURN_INT(int, long long, PyLong_AsLongLong(x)) + } + } + { +#if CYTHON_COMPILING_IN_PYPY && !defined(_PyLong_AsByteArray) + PyErr_SetString(PyExc_RuntimeError, + "_PyLong_AsByteArray() not available in PyPy, cannot convert large numbers"); +#else + int val; + PyObject *v = __Pyx_PyNumber_Int(x); + #if PY_MAJOR_VERSION < 3 + if (likely(v) && !PyLong_Check(v)) { + PyObject *tmp = v; + v = PyNumber_Long(tmp); + Py_DECREF(tmp); + } + #endif + if (likely(v)) { + int one = 1; int is_little = (int)*(unsigned char *)&one; + unsigned char *bytes = (unsigned char *)&val; + int ret = _PyLong_AsByteArray((PyLongObject *)v, + bytes, sizeof(val), + is_little, !is_unsigned); + Py_DECREF(v); + if (likely(!ret)) + return val; + } +#endif + return (int) -1; + } + } else { + int val; + PyObject *tmp = __Pyx_PyNumber_Int(x); + if (!tmp) return (int) -1; + val = __Pyx_PyInt_As_int(tmp); + Py_DECREF(tmp); + return val; + } +raise_overflow: + PyErr_SetString(PyExc_OverflowError, + "value too large to convert to int"); + return (int) -1; +raise_neg_overflow: + PyErr_SetString(PyExc_OverflowError, + "can't convert negative value to int"); + return (int) -1; +} + +static CYTHON_INLINE PyObject* __Pyx_PyInt_From_int(int value) { + const int neg_one = (int) -1, const_zero = 0; const int is_unsigned = neg_one > const_zero; if (is_unsigned) { if (sizeof(int) < sizeof(long)) { return PyInt_FromLong((long) value); } else if (sizeof(int) <= sizeof(unsigned long)) { return PyLong_FromUnsignedLong((unsigned long) value); -#ifdef HAVE_LONG_LONG - } else if (sizeof(int) <= sizeof(unsigned PY_LONG_LONG)) { - return PyLong_FromUnsignedLongLong((unsigned PY_LONG_LONG) value); -#endif + } else if (sizeof(int) <= sizeof(unsigned long long)) { + return PyLong_FromUnsignedLongLong((unsigned long long) value); } } else { if (sizeof(int) <= sizeof(long)) { return PyInt_FromLong((long) value); -#ifdef HAVE_LONG_LONG - } else if (sizeof(int) <= sizeof(PY_LONG_LONG)) { - return PyLong_FromLongLong((PY_LONG_LONG) value); -#endif + } else if (sizeof(int) <= sizeof(long long)) { + return PyLong_FromLongLong((long long) value); } } { @@ -23332,8 +20892,102 @@ bad: } } -/* Declarations */ - #if CYTHON_CCOMPLEX +static CYTHON_INLINE long __Pyx_PyInt_As_long(PyObject *x) { + const long neg_one = (long) -1, const_zero = 0; + const int is_unsigned = neg_one > const_zero; +#if PY_MAJOR_VERSION < 3 + if (likely(PyInt_Check(x))) { + if (sizeof(long) < sizeof(long)) { + __PYX_VERIFY_RETURN_INT(long, long, PyInt_AS_LONG(x)) + } else { + long val = PyInt_AS_LONG(x); + if (is_unsigned && unlikely(val < 0)) { + goto raise_neg_overflow; + } + return (long) val; + } + } else +#endif + if (likely(PyLong_Check(x))) { + if (is_unsigned) { +#if CYTHON_COMPILING_IN_CPYTHON && PY_MAJOR_VERSION >= 3 + #if CYTHON_USE_PYLONG_INTERNALS + switch (Py_SIZE(x)) { + case 0: return 0; + case 1: __PYX_VERIFY_RETURN_INT(long, digit, ((PyLongObject*)x)->ob_digit[0]); + } + #endif +#endif + if (unlikely(Py_SIZE(x) < 0)) { + goto raise_neg_overflow; + } + if (sizeof(long) <= sizeof(unsigned long)) { + __PYX_VERIFY_RETURN_INT(long, unsigned long, PyLong_AsUnsignedLong(x)) + } else if (sizeof(long) <= sizeof(unsigned long long)) { + __PYX_VERIFY_RETURN_INT(long, unsigned long long, PyLong_AsUnsignedLongLong(x)) + } + } else { +#if CYTHON_COMPILING_IN_CPYTHON && PY_MAJOR_VERSION >= 3 + #if CYTHON_USE_PYLONG_INTERNALS + switch (Py_SIZE(x)) { + case 0: return 0; + case 1: __PYX_VERIFY_RETURN_INT(long, digit, +(((PyLongObject*)x)->ob_digit[0])); + case -1: __PYX_VERIFY_RETURN_INT(long, sdigit, -(sdigit) ((PyLongObject*)x)->ob_digit[0]); + } + #endif +#endif + if (sizeof(long) <= sizeof(long)) { + __PYX_VERIFY_RETURN_INT(long, long, PyLong_AsLong(x)) + } else if (sizeof(long) <= sizeof(long long)) { + __PYX_VERIFY_RETURN_INT(long, long long, PyLong_AsLongLong(x)) + } + } + { +#if CYTHON_COMPILING_IN_PYPY && !defined(_PyLong_AsByteArray) + PyErr_SetString(PyExc_RuntimeError, + "_PyLong_AsByteArray() not available in PyPy, cannot convert large numbers"); +#else + long val; + PyObject *v = __Pyx_PyNumber_Int(x); + #if PY_MAJOR_VERSION < 3 + if (likely(v) && !PyLong_Check(v)) { + PyObject *tmp = v; + v = PyNumber_Long(tmp); + Py_DECREF(tmp); + } + #endif + if (likely(v)) { + int one = 1; int is_little = (int)*(unsigned char *)&one; + unsigned char *bytes = (unsigned char *)&val; + int ret = _PyLong_AsByteArray((PyLongObject *)v, + bytes, sizeof(val), + is_little, !is_unsigned); + Py_DECREF(v); + if (likely(!ret)) + return val; + } +#endif + return (long) -1; + } + } else { + long val; + PyObject *tmp = __Pyx_PyNumber_Int(x); + if (!tmp) return (long) -1; + val = __Pyx_PyInt_As_long(tmp); + Py_DECREF(tmp); + return val; + } +raise_overflow: + PyErr_SetString(PyExc_OverflowError, + "value too large to convert to long"); + return (long) -1; +raise_neg_overflow: + PyErr_SetString(PyExc_OverflowError, + "can't convert negative value to long"); + return (long) -1; +} + +#if CYTHON_CCOMPLEX #ifdef __cplusplus static CYTHON_INLINE __pyx_t_float_complex __pyx_t_float_complex_from_parts(float x, float y) { return ::std::complex< float >(x, y); @@ -23352,86 +21006,60 @@ bad: } #endif -/* Arithmetic */ - #if CYTHON_CCOMPLEX +#if CYTHON_CCOMPLEX #else - static CYTHON_INLINE int __Pyx_c_eq_float(__pyx_t_float_complex a, __pyx_t_float_complex b) { + static CYTHON_INLINE int __Pyx_c_eqf(__pyx_t_float_complex a, __pyx_t_float_complex b) { return (a.real == b.real) && (a.imag == b.imag); } - static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_sum_float(__pyx_t_float_complex a, __pyx_t_float_complex b) { + static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_sumf(__pyx_t_float_complex a, __pyx_t_float_complex b) { __pyx_t_float_complex z; z.real = a.real + b.real; z.imag = a.imag + b.imag; return z; } - static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_diff_float(__pyx_t_float_complex a, __pyx_t_float_complex b) { + static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_difff(__pyx_t_float_complex a, __pyx_t_float_complex b) { __pyx_t_float_complex z; z.real = a.real - b.real; z.imag = a.imag - b.imag; return z; } - static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_prod_float(__pyx_t_float_complex a, __pyx_t_float_complex b) { + static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_prodf(__pyx_t_float_complex a, __pyx_t_float_complex b) { __pyx_t_float_complex z; z.real = a.real * b.real - a.imag * b.imag; z.imag = a.real * b.imag + a.imag * b.real; return z; } - #if 1 - static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_quot_float(__pyx_t_float_complex a, __pyx_t_float_complex b) { - if (b.imag == 0) { - return __pyx_t_float_complex_from_parts(a.real / b.real, a.imag / b.real); - } else if (fabsf(b.real) >= fabsf(b.imag)) { - if (b.real == 0 && b.imag == 0) { - return __pyx_t_float_complex_from_parts(a.real / b.real, a.imag / b.imag); - } else { - float r = b.imag / b.real; - float s = 1.0 / (b.real + b.imag * r); - return __pyx_t_float_complex_from_parts( - (a.real + a.imag * r) * s, (a.imag - a.real * r) * s); - } - } else { - float r = b.real / b.imag; - float s = 1.0 / (b.imag + b.real * r); - return __pyx_t_float_complex_from_parts( - (a.real * r + a.imag) * s, (a.imag * r - a.real) * s); - } - } - #else - static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_quot_float(__pyx_t_float_complex a, __pyx_t_float_complex b) { - if (b.imag == 0) { - return __pyx_t_float_complex_from_parts(a.real / b.real, a.imag / b.real); - } else { - float denom = b.real * b.real + b.imag * b.imag; - return __pyx_t_float_complex_from_parts( - (a.real * b.real + a.imag * b.imag) / denom, - (a.imag * b.real - a.real * b.imag) / denom); - } + static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_quotf(__pyx_t_float_complex a, __pyx_t_float_complex b) { + __pyx_t_float_complex z; + float denom = b.real * b.real + b.imag * b.imag; + z.real = (a.real * b.real + a.imag * b.imag) / denom; + z.imag = (a.imag * b.real - a.real * b.imag) / denom; + return z; } - #endif - static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_neg_float(__pyx_t_float_complex a) { + static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_negf(__pyx_t_float_complex a) { __pyx_t_float_complex z; z.real = -a.real; z.imag = -a.imag; return z; } - static CYTHON_INLINE int __Pyx_c_is_zero_float(__pyx_t_float_complex a) { + static CYTHON_INLINE int __Pyx_c_is_zerof(__pyx_t_float_complex a) { return (a.real == 0) && (a.imag == 0); } - static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_conj_float(__pyx_t_float_complex a) { + static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_conjf(__pyx_t_float_complex a) { __pyx_t_float_complex z; z.real = a.real; z.imag = -a.imag; return z; } #if 1 - static CYTHON_INLINE float __Pyx_c_abs_float(__pyx_t_float_complex z) { + static CYTHON_INLINE float __Pyx_c_absf(__pyx_t_float_complex z) { #if !defined(HAVE_HYPOT) || defined(_MSC_VER) return sqrtf(z.real*z.real + z.imag*z.imag); #else return hypotf(z.real, z.imag); #endif } - static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_pow_float(__pyx_t_float_complex a, __pyx_t_float_complex b) { + static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_powf(__pyx_t_float_complex a, __pyx_t_float_complex b) { __pyx_t_float_complex z; float r, lnr, theta, z_r, z_theta; if (b.imag == 0 && b.real == (int)b.real) { @@ -23449,32 +21077,24 @@ bad: case 1: return a; case 2: - z = __Pyx_c_prod_float(a, a); - return __Pyx_c_prod_float(a, a); + z = __Pyx_c_prodf(a, a); + return __Pyx_c_prodf(a, a); case 3: - z = __Pyx_c_prod_float(a, a); - return __Pyx_c_prod_float(z, a); + z = __Pyx_c_prodf(a, a); + return __Pyx_c_prodf(z, a); case 4: - z = __Pyx_c_prod_float(a, a); - return __Pyx_c_prod_float(z, z); + z = __Pyx_c_prodf(a, a); + return __Pyx_c_prodf(z, z); } } if (a.imag == 0) { if (a.real == 0) { return a; - } else if (b.imag == 0) { - z.real = powf(a.real, b.real); - z.imag = 0; - return z; - } else if (a.real > 0) { - r = a.real; - theta = 0; - } else { - r = -a.real; - theta = atan2f(0, -1); } + r = a.real; + theta = 0; } else { - r = __Pyx_c_abs_float(a); + r = __Pyx_c_absf(a); theta = atan2f(a.imag, a.real); } lnr = logf(r); @@ -23487,8 +21107,7 @@ bad: #endif #endif -/* Declarations */ - #if CYTHON_CCOMPLEX +#if CYTHON_CCOMPLEX #ifdef __cplusplus static CYTHON_INLINE __pyx_t_double_complex __pyx_t_double_complex_from_parts(double x, double y) { return ::std::complex< double >(x, y); @@ -23507,86 +21126,60 @@ bad: } #endif -/* Arithmetic */ - #if CYTHON_CCOMPLEX +#if CYTHON_CCOMPLEX #else - static CYTHON_INLINE int __Pyx_c_eq_double(__pyx_t_double_complex a, __pyx_t_double_complex b) { + static CYTHON_INLINE int __Pyx_c_eq(__pyx_t_double_complex a, __pyx_t_double_complex b) { return (a.real == b.real) && (a.imag == b.imag); } - static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_sum_double(__pyx_t_double_complex a, __pyx_t_double_complex b) { + static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_sum(__pyx_t_double_complex a, __pyx_t_double_complex b) { __pyx_t_double_complex z; z.real = a.real + b.real; z.imag = a.imag + b.imag; return z; } - static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_diff_double(__pyx_t_double_complex a, __pyx_t_double_complex b) { + static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_diff(__pyx_t_double_complex a, __pyx_t_double_complex b) { __pyx_t_double_complex z; z.real = a.real - b.real; z.imag = a.imag - b.imag; return z; } - static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_prod_double(__pyx_t_double_complex a, __pyx_t_double_complex b) { + static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_prod(__pyx_t_double_complex a, __pyx_t_double_complex b) { __pyx_t_double_complex z; z.real = a.real * b.real - a.imag * b.imag; z.imag = a.real * b.imag + a.imag * b.real; return z; } - #if 1 - static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_quot_double(__pyx_t_double_complex a, __pyx_t_double_complex b) { - if (b.imag == 0) { - return __pyx_t_double_complex_from_parts(a.real / b.real, a.imag / b.real); - } else if (fabs(b.real) >= fabs(b.imag)) { - if (b.real == 0 && b.imag == 0) { - return __pyx_t_double_complex_from_parts(a.real / b.real, a.imag / b.imag); - } else { - double r = b.imag / b.real; - double s = 1.0 / (b.real + b.imag * r); - return __pyx_t_double_complex_from_parts( - (a.real + a.imag * r) * s, (a.imag - a.real * r) * s); - } - } else { - double r = b.real / b.imag; - double s = 1.0 / (b.imag + b.real * r); - return __pyx_t_double_complex_from_parts( - (a.real * r + a.imag) * s, (a.imag * r - a.real) * s); - } - } - #else - static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_quot_double(__pyx_t_double_complex a, __pyx_t_double_complex b) { - if (b.imag == 0) { - return __pyx_t_double_complex_from_parts(a.real / b.real, a.imag / b.real); - } else { - double denom = b.real * b.real + b.imag * b.imag; - return __pyx_t_double_complex_from_parts( - (a.real * b.real + a.imag * b.imag) / denom, - (a.imag * b.real - a.real * b.imag) / denom); - } + static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_quot(__pyx_t_double_complex a, __pyx_t_double_complex b) { + __pyx_t_double_complex z; + double denom = b.real * b.real + b.imag * b.imag; + z.real = (a.real * b.real + a.imag * b.imag) / denom; + z.imag = (a.imag * b.real - a.real * b.imag) / denom; + return z; } - #endif - static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_neg_double(__pyx_t_double_complex a) { + static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_neg(__pyx_t_double_complex a) { __pyx_t_double_complex z; z.real = -a.real; z.imag = -a.imag; return z; } - static CYTHON_INLINE int __Pyx_c_is_zero_double(__pyx_t_double_complex a) { + static CYTHON_INLINE int __Pyx_c_is_zero(__pyx_t_double_complex a) { return (a.real == 0) && (a.imag == 0); } - static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_conj_double(__pyx_t_double_complex a) { + static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_conj(__pyx_t_double_complex a) { __pyx_t_double_complex z; z.real = a.real; z.imag = -a.imag; return z; } #if 1 - static CYTHON_INLINE double __Pyx_c_abs_double(__pyx_t_double_complex z) { + static CYTHON_INLINE double __Pyx_c_abs(__pyx_t_double_complex z) { #if !defined(HAVE_HYPOT) || defined(_MSC_VER) return sqrt(z.real*z.real + z.imag*z.imag); #else return hypot(z.real, z.imag); #endif } - static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_pow_double(__pyx_t_double_complex a, __pyx_t_double_complex b) { + static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_pow(__pyx_t_double_complex a, __pyx_t_double_complex b) { __pyx_t_double_complex z; double r, lnr, theta, z_r, z_theta; if (b.imag == 0 && b.real == (int)b.real) { @@ -23604,32 +21197,24 @@ bad: case 1: return a; case 2: - z = __Pyx_c_prod_double(a, a); - return __Pyx_c_prod_double(a, a); + z = __Pyx_c_prod(a, a); + return __Pyx_c_prod(a, a); case 3: - z = __Pyx_c_prod_double(a, a); - return __Pyx_c_prod_double(z, a); + z = __Pyx_c_prod(a, a); + return __Pyx_c_prod(z, a); case 4: - z = __Pyx_c_prod_double(a, a); - return __Pyx_c_prod_double(z, z); + z = __Pyx_c_prod(a, a); + return __Pyx_c_prod(z, z); } } if (a.imag == 0) { if (a.real == 0) { return a; - } else if (b.imag == 0) { - z.real = pow(a.real, b.real); - z.imag = 0; - return z; - } else if (a.real > 0) { - r = a.real; - theta = 0; - } else { - r = -a.real; - theta = atan2(0, -1); } + r = a.real; + theta = 0; } else { - r = __Pyx_c_abs_double(a); + r = __Pyx_c_abs(a); theta = atan2(a.imag, a.real); } lnr = log(r); @@ -23642,453 +21227,36 @@ bad: #endif #endif -/* CIntToPy */ - static CYTHON_INLINE PyObject* __Pyx_PyInt_From_enum__NPY_TYPES(enum NPY_TYPES value) { - const enum NPY_TYPES neg_one = (enum NPY_TYPES) -1, const_zero = (enum NPY_TYPES) 0; - const int is_unsigned = neg_one > const_zero; - if (is_unsigned) { - if (sizeof(enum NPY_TYPES) < sizeof(long)) { - return PyInt_FromLong((long) value); - } else if (sizeof(enum NPY_TYPES) <= sizeof(unsigned long)) { - return PyLong_FromUnsignedLong((unsigned long) value); -#ifdef HAVE_LONG_LONG - } else if (sizeof(enum NPY_TYPES) <= sizeof(unsigned PY_LONG_LONG)) { - return PyLong_FromUnsignedLongLong((unsigned PY_LONG_LONG) value); -#endif - } - } else { - if (sizeof(enum NPY_TYPES) <= sizeof(long)) { - return PyInt_FromLong((long) value); -#ifdef HAVE_LONG_LONG - } else if (sizeof(enum NPY_TYPES) <= sizeof(PY_LONG_LONG)) { - return PyLong_FromLongLong((PY_LONG_LONG) value); -#endif - } - } - { - int one = 1; int little = (int)*(unsigned char *)&one; - unsigned char *bytes = (unsigned char *)&value; - return _PyLong_FromByteArray(bytes, sizeof(enum NPY_TYPES), - little, !is_unsigned); - } -} - -/* CIntFromPy */ - static CYTHON_INLINE int __Pyx_PyInt_As_int(PyObject *x) { - const int neg_one = (int) -1, const_zero = (int) 0; - const int is_unsigned = neg_one > const_zero; -#if PY_MAJOR_VERSION < 3 - if (likely(PyInt_Check(x))) { - if (sizeof(int) < sizeof(long)) { - __PYX_VERIFY_RETURN_INT(int, long, PyInt_AS_LONG(x)) - } else { - long val = PyInt_AS_LONG(x); - if (is_unsigned && unlikely(val < 0)) { - goto raise_neg_overflow; - } - return (int) val; - } - } else -#endif - if (likely(PyLong_Check(x))) { - if (is_unsigned) { -#if CYTHON_USE_PYLONG_INTERNALS - const digit* digits = ((PyLongObject*)x)->ob_digit; - switch (Py_SIZE(x)) { - case 0: return (int) 0; - case 1: __PYX_VERIFY_RETURN_INT(int, digit, digits[0]) - case 2: - if (8 * sizeof(int) > 1 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(int, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(int) >= 2 * PyLong_SHIFT) { - return (int) (((((int)digits[1]) << PyLong_SHIFT) | (int)digits[0])); - } - } - break; - case 3: - if (8 * sizeof(int) > 2 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(int, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(int) >= 3 * PyLong_SHIFT) { - return (int) (((((((int)digits[2]) << PyLong_SHIFT) | (int)digits[1]) << PyLong_SHIFT) | (int)digits[0])); - } - } - break; - case 4: - if (8 * sizeof(int) > 3 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(int, unsigned long, (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(int) >= 4 * PyLong_SHIFT) { - return (int) (((((((((int)digits[3]) << PyLong_SHIFT) | (int)digits[2]) << PyLong_SHIFT) | (int)digits[1]) << PyLong_SHIFT) | (int)digits[0])); - } - } - break; - } -#endif -#if CYTHON_COMPILING_IN_CPYTHON - if (unlikely(Py_SIZE(x) < 0)) { - goto raise_neg_overflow; - } -#else - { - int result = PyObject_RichCompareBool(x, Py_False, Py_LT); - if (unlikely(result < 0)) - return (int) -1; - if (unlikely(result == 1)) - goto raise_neg_overflow; - } -#endif - if (sizeof(int) <= sizeof(unsigned long)) { - __PYX_VERIFY_RETURN_INT_EXC(int, unsigned long, PyLong_AsUnsignedLong(x)) -#ifdef HAVE_LONG_LONG - } else if (sizeof(int) <= sizeof(unsigned PY_LONG_LONG)) { - __PYX_VERIFY_RETURN_INT_EXC(int, unsigned PY_LONG_LONG, PyLong_AsUnsignedLongLong(x)) -#endif - } - } else { -#if CYTHON_USE_PYLONG_INTERNALS - const digit* digits = ((PyLongObject*)x)->ob_digit; - switch (Py_SIZE(x)) { - case 0: return (int) 0; - case -1: __PYX_VERIFY_RETURN_INT(int, sdigit, (sdigit) (-(sdigit)digits[0])) - case 1: __PYX_VERIFY_RETURN_INT(int, digit, +digits[0]) - case -2: - if (8 * sizeof(int) - 1 > 1 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(int, long, -(long) (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(int) - 1 > 2 * PyLong_SHIFT) { - return (int) (((int)-1)*(((((int)digits[1]) << PyLong_SHIFT) | (int)digits[0]))); - } - } - break; - case 2: - if (8 * sizeof(int) > 1 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(int, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(int) - 1 > 2 * PyLong_SHIFT) { - return (int) ((((((int)digits[1]) << PyLong_SHIFT) | (int)digits[0]))); - } - } - break; - case -3: - if (8 * sizeof(int) - 1 > 2 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(int, long, -(long) (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(int) - 1 > 3 * PyLong_SHIFT) { - return (int) (((int)-1)*(((((((int)digits[2]) << PyLong_SHIFT) | (int)digits[1]) << PyLong_SHIFT) | (int)digits[0]))); - } - } - break; - case 3: - if (8 * sizeof(int) > 2 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(int, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(int) - 1 > 3 * PyLong_SHIFT) { - return (int) ((((((((int)digits[2]) << PyLong_SHIFT) | (int)digits[1]) << PyLong_SHIFT) | (int)digits[0]))); - } - } - break; - case -4: - if (8 * sizeof(int) - 1 > 3 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(int, long, -(long) (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(int) - 1 > 4 * PyLong_SHIFT) { - return (int) (((int)-1)*(((((((((int)digits[3]) << PyLong_SHIFT) | (int)digits[2]) << PyLong_SHIFT) | (int)digits[1]) << PyLong_SHIFT) | (int)digits[0]))); - } - } - break; - case 4: - if (8 * sizeof(int) > 3 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(int, unsigned long, (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(int) - 1 > 4 * PyLong_SHIFT) { - return (int) ((((((((((int)digits[3]) << PyLong_SHIFT) | (int)digits[2]) << PyLong_SHIFT) | (int)digits[1]) << PyLong_SHIFT) | (int)digits[0]))); - } - } - break; - } -#endif - if (sizeof(int) <= sizeof(long)) { - __PYX_VERIFY_RETURN_INT_EXC(int, long, PyLong_AsLong(x)) -#ifdef HAVE_LONG_LONG - } else if (sizeof(int) <= sizeof(PY_LONG_LONG)) { - __PYX_VERIFY_RETURN_INT_EXC(int, PY_LONG_LONG, PyLong_AsLongLong(x)) -#endif - } - } - { -#if CYTHON_COMPILING_IN_PYPY && !defined(_PyLong_AsByteArray) - PyErr_SetString(PyExc_RuntimeError, - "_PyLong_AsByteArray() not available in PyPy, cannot convert large numbers"); -#else - int val; - PyObject *v = __Pyx_PyNumber_IntOrLong(x); - #if PY_MAJOR_VERSION < 3 - if (likely(v) && !PyLong_Check(v)) { - PyObject *tmp = v; - v = PyNumber_Long(tmp); - Py_DECREF(tmp); - } - #endif - if (likely(v)) { - int one = 1; int is_little = (int)*(unsigned char *)&one; - unsigned char *bytes = (unsigned char *)&val; - int ret = _PyLong_AsByteArray((PyLongObject *)v, - bytes, sizeof(val), - is_little, !is_unsigned); - Py_DECREF(v); - if (likely(!ret)) - return val; - } -#endif - return (int) -1; - } - } else { - int val; - PyObject *tmp = __Pyx_PyNumber_IntOrLong(x); - if (!tmp) return (int) -1; - val = __Pyx_PyInt_As_int(tmp); - Py_DECREF(tmp); - return val; - } -raise_overflow: - PyErr_SetString(PyExc_OverflowError, - "value too large to convert to int"); - return (int) -1; -raise_neg_overflow: - PyErr_SetString(PyExc_OverflowError, - "can't convert negative value to int"); - return (int) -1; -} - -/* CIntFromPy */ - static CYTHON_INLINE long __Pyx_PyInt_As_long(PyObject *x) { - const long neg_one = (long) -1, const_zero = (long) 0; - const int is_unsigned = neg_one > const_zero; -#if PY_MAJOR_VERSION < 3 - if (likely(PyInt_Check(x))) { - if (sizeof(long) < sizeof(long)) { - __PYX_VERIFY_RETURN_INT(long, long, PyInt_AS_LONG(x)) - } else { - long val = PyInt_AS_LONG(x); - if (is_unsigned && unlikely(val < 0)) { - goto raise_neg_overflow; - } - return (long) val; - } - } else -#endif - if (likely(PyLong_Check(x))) { - if (is_unsigned) { -#if CYTHON_USE_PYLONG_INTERNALS - const digit* digits = ((PyLongObject*)x)->ob_digit; - switch (Py_SIZE(x)) { - case 0: return (long) 0; - case 1: __PYX_VERIFY_RETURN_INT(long, digit, digits[0]) - case 2: - if (8 * sizeof(long) > 1 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(long, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(long) >= 2 * PyLong_SHIFT) { - return (long) (((((long)digits[1]) << PyLong_SHIFT) | (long)digits[0])); - } - } - break; - case 3: - if (8 * sizeof(long) > 2 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(long, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(long) >= 3 * PyLong_SHIFT) { - return (long) (((((((long)digits[2]) << PyLong_SHIFT) | (long)digits[1]) << PyLong_SHIFT) | (long)digits[0])); - } - } - break; - case 4: - if (8 * sizeof(long) > 3 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(long, unsigned long, (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(long) >= 4 * PyLong_SHIFT) { - return (long) (((((((((long)digits[3]) << PyLong_SHIFT) | (long)digits[2]) << PyLong_SHIFT) | (long)digits[1]) << PyLong_SHIFT) | (long)digits[0])); - } - } - break; - } -#endif -#if CYTHON_COMPILING_IN_CPYTHON - if (unlikely(Py_SIZE(x) < 0)) { - goto raise_neg_overflow; - } -#else - { - int result = PyObject_RichCompareBool(x, Py_False, Py_LT); - if (unlikely(result < 0)) - return (long) -1; - if (unlikely(result == 1)) - goto raise_neg_overflow; - } -#endif - if (sizeof(long) <= sizeof(unsigned long)) { - __PYX_VERIFY_RETURN_INT_EXC(long, unsigned long, PyLong_AsUnsignedLong(x)) -#ifdef HAVE_LONG_LONG - } else if (sizeof(long) <= sizeof(unsigned PY_LONG_LONG)) { - __PYX_VERIFY_RETURN_INT_EXC(long, unsigned PY_LONG_LONG, PyLong_AsUnsignedLongLong(x)) -#endif - } - } else { -#if CYTHON_USE_PYLONG_INTERNALS - const digit* digits = ((PyLongObject*)x)->ob_digit; - switch (Py_SIZE(x)) { - case 0: return (long) 0; - case -1: __PYX_VERIFY_RETURN_INT(long, sdigit, (sdigit) (-(sdigit)digits[0])) - case 1: __PYX_VERIFY_RETURN_INT(long, digit, +digits[0]) - case -2: - if (8 * sizeof(long) - 1 > 1 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(long, long, -(long) (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(long) - 1 > 2 * PyLong_SHIFT) { - return (long) (((long)-1)*(((((long)digits[1]) << PyLong_SHIFT) | (long)digits[0]))); - } - } - break; - case 2: - if (8 * sizeof(long) > 1 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 2 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(long, unsigned long, (((((unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(long) - 1 > 2 * PyLong_SHIFT) { - return (long) ((((((long)digits[1]) << PyLong_SHIFT) | (long)digits[0]))); - } - } - break; - case -3: - if (8 * sizeof(long) - 1 > 2 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(long, long, -(long) (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(long) - 1 > 3 * PyLong_SHIFT) { - return (long) (((long)-1)*(((((((long)digits[2]) << PyLong_SHIFT) | (long)digits[1]) << PyLong_SHIFT) | (long)digits[0]))); - } - } - break; - case 3: - if (8 * sizeof(long) > 2 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 3 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(long, unsigned long, (((((((unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(long) - 1 > 3 * PyLong_SHIFT) { - return (long) ((((((((long)digits[2]) << PyLong_SHIFT) | (long)digits[1]) << PyLong_SHIFT) | (long)digits[0]))); - } - } - break; - case -4: - if (8 * sizeof(long) - 1 > 3 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(long, long, -(long) (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(long) - 1 > 4 * PyLong_SHIFT) { - return (long) (((long)-1)*(((((((((long)digits[3]) << PyLong_SHIFT) | (long)digits[2]) << PyLong_SHIFT) | (long)digits[1]) << PyLong_SHIFT) | (long)digits[0]))); - } - } - break; - case 4: - if (8 * sizeof(long) > 3 * PyLong_SHIFT) { - if (8 * sizeof(unsigned long) > 4 * PyLong_SHIFT) { - __PYX_VERIFY_RETURN_INT(long, unsigned long, (((((((((unsigned long)digits[3]) << PyLong_SHIFT) | (unsigned long)digits[2]) << PyLong_SHIFT) | (unsigned long)digits[1]) << PyLong_SHIFT) | (unsigned long)digits[0]))) - } else if (8 * sizeof(long) - 1 > 4 * PyLong_SHIFT) { - return (long) ((((((((((long)digits[3]) << PyLong_SHIFT) | (long)digits[2]) << PyLong_SHIFT) | (long)digits[1]) << PyLong_SHIFT) | (long)digits[0]))); - } - } - break; - } -#endif - if (sizeof(long) <= sizeof(long)) { - __PYX_VERIFY_RETURN_INT_EXC(long, long, PyLong_AsLong(x)) -#ifdef HAVE_LONG_LONG - } else if (sizeof(long) <= sizeof(PY_LONG_LONG)) { - __PYX_VERIFY_RETURN_INT_EXC(long, PY_LONG_LONG, PyLong_AsLongLong(x)) -#endif - } - } - { -#if CYTHON_COMPILING_IN_PYPY && !defined(_PyLong_AsByteArray) - PyErr_SetString(PyExc_RuntimeError, - "_PyLong_AsByteArray() not available in PyPy, cannot convert large numbers"); -#else - long val; - PyObject *v = __Pyx_PyNumber_IntOrLong(x); - #if PY_MAJOR_VERSION < 3 - if (likely(v) && !PyLong_Check(v)) { - PyObject *tmp = v; - v = PyNumber_Long(tmp); - Py_DECREF(tmp); - } - #endif - if (likely(v)) { - int one = 1; int is_little = (int)*(unsigned char *)&one; - unsigned char *bytes = (unsigned char *)&val; - int ret = _PyLong_AsByteArray((PyLongObject *)v, - bytes, sizeof(val), - is_little, !is_unsigned); - Py_DECREF(v); - if (likely(!ret)) - return val; - } -#endif - return (long) -1; - } - } else { - long val; - PyObject *tmp = __Pyx_PyNumber_IntOrLong(x); - if (!tmp) return (long) -1; - val = __Pyx_PyInt_As_long(tmp); - Py_DECREF(tmp); - return val; - } -raise_overflow: - PyErr_SetString(PyExc_OverflowError, - "value too large to convert to long"); - return (long) -1; -raise_neg_overflow: - PyErr_SetString(PyExc_OverflowError, - "can't convert negative value to long"); - return (long) -1; -} - -/* SwapException */ - #if CYTHON_FAST_THREAD_STATE -static CYTHON_INLINE void __Pyx__ExceptionSwap(PyThreadState *tstate, PyObject **type, PyObject **value, PyObject **tb) { +static CYTHON_INLINE void __Pyx_ExceptionSwap(PyObject **type, PyObject **value, PyObject **tb) { PyObject *tmp_type, *tmp_value, *tmp_tb; +#if CYTHON_COMPILING_IN_CPYTHON + PyThreadState *tstate = PyThreadState_GET(); tmp_type = tstate->exc_type; tmp_value = tstate->exc_value; tmp_tb = tstate->exc_traceback; tstate->exc_type = *type; tstate->exc_value = *value; tstate->exc_traceback = *tb; - *type = tmp_type; - *value = tmp_value; - *tb = tmp_tb; -} #else -static CYTHON_INLINE void __Pyx_ExceptionSwap(PyObject **type, PyObject **value, PyObject **tb) { - PyObject *tmp_type, *tmp_value, *tmp_tb; PyErr_GetExcInfo(&tmp_type, &tmp_value, &tmp_tb); PyErr_SetExcInfo(*type, *value, *tb); +#endif *type = tmp_type; *value = tmp_value; *tb = tmp_tb; } -#endif -/* CoroutineBase */ - #include <structmember.h> -#include <frameobject.h> -static PyObject *__Pyx_Coroutine_Send(PyObject *self, PyObject *value); -static PyObject *__Pyx_Coroutine_Close(PyObject *self); -static PyObject *__Pyx_Coroutine_Throw(PyObject *gen, PyObject *args); -#define __Pyx_Coroutine_Undelegate(gen) Py_CLEAR((gen)->yieldfrom) +static PyObject *__Pyx_Generator_Next(PyObject *self); +static PyObject *__Pyx_Generator_Send(PyObject *self, PyObject *value); +static PyObject *__Pyx_Generator_Close(PyObject *self); +static PyObject *__Pyx_Generator_Throw(PyObject *gen, PyObject *args); +static PyTypeObject *__pyx_GeneratorType = 0; +#define __Pyx_Generator_CheckExact(obj) (Py_TYPE(obj) == __pyx_GeneratorType) +#define __Pyx_Generator_Undelegate(gen) Py_CLEAR((gen)->yieldfrom) #if 1 || PY_VERSION_HEX < 0x030300B0 static int __Pyx_PyGen_FetchStopIterationValue(PyObject **pvalue) { PyObject *et, *ev, *tb; PyObject *value = NULL; - __Pyx_PyThreadState_declare - __Pyx_PyThreadState_assign __Pyx_ErrFetch(&et, &ev, &tb); if (!et) { Py_XDECREF(tb); @@ -24097,47 +21265,25 @@ static int __Pyx_PyGen_FetchStopIterationValue(PyObject **pvalue) { *pvalue = Py_None; return 0; } + if (unlikely(et != PyExc_StopIteration) && + unlikely(!PyErr_GivenExceptionMatches(et, PyExc_StopIteration))) { + __Pyx_ErrRestore(et, ev, tb); + return -1; + } if (likely(et == PyExc_StopIteration)) { - if (!ev) { - Py_INCREF(Py_None); - value = Py_None; - } -#if PY_VERSION_HEX >= 0x030300A0 - else if (Py_TYPE(ev) == (PyTypeObject*)PyExc_StopIteration) { - value = ((PyStopIterationObject *)ev)->value; - Py_INCREF(value); - Py_DECREF(ev); - } -#endif - else if (unlikely(PyTuple_Check(ev))) { - if (PyTuple_GET_SIZE(ev) >= 1) { -#if CYTHON_ASSUME_SAFE_MACROS && !CYTHON_AVOID_BORROWED_REFS - value = PyTuple_GET_ITEM(ev, 0); - Py_INCREF(value); -#else - value = PySequence_ITEM(ev, 0); -#endif - } else { + if (likely(!ev) || !PyObject_IsInstance(ev, PyExc_StopIteration)) { + if (!ev) { Py_INCREF(Py_None); - value = Py_None; + ev = Py_None; } - Py_DECREF(ev); - } - else if (!PyObject_TypeCheck(ev, (PyTypeObject*)PyExc_StopIteration)) { - value = ev; - } - if (likely(value)) { Py_XDECREF(tb); Py_DECREF(et); - *pvalue = value; + *pvalue = ev; return 0; } - } else if (!PyErr_GivenExceptionMatches(et, PyExc_StopIteration)) { - __Pyx_ErrRestore(et, ev, tb); - return -1; } PyErr_NormalizeException(&et, &ev, &tb); - if (unlikely(!PyObject_TypeCheck(ev, (PyTypeObject*)PyExc_StopIteration))) { + if (unlikely(!PyObject_IsInstance(ev, PyExc_StopIteration))) { __Pyx_ErrRestore(et, ev, tb); return -1; } @@ -24149,10 +21295,10 @@ static int __Pyx_PyGen_FetchStopIterationValue(PyObject **pvalue) { Py_DECREF(ev); #else { - PyObject* args = __Pyx_PyObject_GetAttrStr(ev, __pyx_n_s_args); + PyObject* args = PyObject_GetAttr(ev, __pyx_n_s_args); Py_DECREF(ev); if (likely(args)) { - value = PySequence_GetItem(args, 0); + value = PyObject_GetItem(args, 0); Py_DECREF(args); } if (unlikely(!value)) { @@ -24167,7 +21313,7 @@ static int __Pyx_PyGen_FetchStopIterationValue(PyObject **pvalue) { } #endif static CYTHON_INLINE -void __Pyx_Coroutine_ExceptionClear(__pyx_CoroutineObject *self) { +void __Pyx_Generator_ExceptionClear(__pyx_GeneratorObject *self) { PyObject *exc_type = self->exc_type; PyObject *exc_value = self->exc_value; PyObject *exc_traceback = self->exc_traceback; @@ -24179,7 +21325,7 @@ void __Pyx_Coroutine_ExceptionClear(__pyx_CoroutineObject *self) { Py_XDECREF(exc_traceback); } static CYTHON_INLINE -int __Pyx_Coroutine_CheckRunning(__pyx_CoroutineObject *gen) { +int __Pyx_Generator_CheckRunning(__pyx_GeneratorObject *gen) { if (unlikely(gen->is_running)) { PyErr_SetString(PyExc_ValueError, "generator already executing"); @@ -24188,9 +21334,8 @@ int __Pyx_Coroutine_CheckRunning(__pyx_CoroutineObject *gen) { return 0; } static CYTHON_INLINE -PyObject *__Pyx_Coroutine_SendEx(__pyx_CoroutineObject *self, PyObject *value) { +PyObject *__Pyx_Generator_SendEx(__pyx_GeneratorObject *self, PyObject *value) { PyObject *retval; - __Pyx_PyThreadState_declare assert(!self->is_running); if (unlikely(self->resume_label == 0)) { if (unlikely(value && value != Py_None)) { @@ -24204,22 +21349,22 @@ PyObject *__Pyx_Coroutine_SendEx(__pyx_CoroutineObject *self, PyObject *value) { PyErr_SetNone(PyExc_StopIteration); return NULL; } - __Pyx_PyThreadState_assign if (value) { -#if CYTHON_COMPILING_IN_PYPY || CYTHON_COMPILING_IN_PYSTON +#if CYTHON_COMPILING_IN_PYPY #else if (self->exc_traceback) { + PyThreadState *tstate = PyThreadState_GET(); PyTracebackObject *tb = (PyTracebackObject *) self->exc_traceback; PyFrameObject *f = tb->tb_frame; - Py_XINCREF(__pyx_tstate->frame); + Py_XINCREF(tstate->frame); assert(f->f_back == NULL); - f->f_back = __pyx_tstate->frame; + f->f_back = tstate->frame; } #endif __Pyx_ExceptionSwap(&self->exc_type, &self->exc_value, &self->exc_traceback); } else { - __Pyx_Coroutine_ExceptionClear(self); + __Pyx_Generator_ExceptionClear(self); } self->is_running = 1; retval = self->body((PyObject *) self, value); @@ -24227,7 +21372,7 @@ PyObject *__Pyx_Coroutine_SendEx(__pyx_CoroutineObject *self, PyObject *value) { if (retval) { __Pyx_ExceptionSwap(&self->exc_type, &self->exc_value, &self->exc_traceback); -#if CYTHON_COMPILING_IN_PYPY || CYTHON_COMPILING_IN_PYSTON +#if CYTHON_COMPILING_IN_PYPY #else if (self->exc_traceback) { PyTracebackObject *tb = (PyTracebackObject *) self->exc_traceback; @@ -24236,49 +21381,50 @@ PyObject *__Pyx_Coroutine_SendEx(__pyx_CoroutineObject *self, PyObject *value) { } #endif } else { - __Pyx_Coroutine_ExceptionClear(self); - } - return retval; -} -static CYTHON_INLINE -PyObject *__Pyx_Coroutine_MethodReturn(PyObject *retval) { - if (unlikely(!retval && !PyErr_Occurred())) { - PyErr_SetNone(PyExc_StopIteration); + __Pyx_Generator_ExceptionClear(self); } return retval; } static CYTHON_INLINE -PyObject *__Pyx_Coroutine_FinishDelegation(__pyx_CoroutineObject *gen) { +PyObject *__Pyx_Generator_FinishDelegation(__pyx_GeneratorObject *gen) { PyObject *ret; PyObject *val = NULL; - __Pyx_Coroutine_Undelegate(gen); + __Pyx_Generator_Undelegate(gen); __Pyx_PyGen_FetchStopIterationValue(&val); - ret = __Pyx_Coroutine_SendEx(gen, val); + ret = __Pyx_Generator_SendEx(gen, val); Py_XDECREF(val); return ret; } -static PyObject *__Pyx_Coroutine_Send(PyObject *self, PyObject *value) { - PyObject *retval; - __pyx_CoroutineObject *gen = (__pyx_CoroutineObject*) self; +static PyObject *__Pyx_Generator_Next(PyObject *self) { + __pyx_GeneratorObject *gen = (__pyx_GeneratorObject*) self; PyObject *yf = gen->yieldfrom; - if (unlikely(__Pyx_Coroutine_CheckRunning(gen))) + if (unlikely(__Pyx_Generator_CheckRunning(gen))) + return NULL; + if (yf) { + PyObject *ret; + gen->is_running = 1; + ret = Py_TYPE(yf)->tp_iternext(yf); + gen->is_running = 0; + if (likely(ret)) { + return ret; + } + return __Pyx_Generator_FinishDelegation(gen); + } + return __Pyx_Generator_SendEx(gen, Py_None); +} +static PyObject *__Pyx_Generator_Send(PyObject *self, PyObject *value) { + __pyx_GeneratorObject *gen = (__pyx_GeneratorObject*) self; + PyObject *yf = gen->yieldfrom; + if (unlikely(__Pyx_Generator_CheckRunning(gen))) return NULL; if (yf) { PyObject *ret; gen->is_running = 1; - #ifdef __Pyx_Generator_USED if (__Pyx_Generator_CheckExact(yf)) { - ret = __Pyx_Coroutine_Send(yf, value); - } else - #endif - #ifdef __Pyx_Coroutine_USED - if (__Pyx_Coroutine_CheckExact(yf)) { - ret = __Pyx_Coroutine_Send(yf, value); - } else - #endif - { + ret = __Pyx_Generator_Send(yf, value); + } else { if (value == Py_None) - ret = Py_TYPE(yf)->tp_iternext(yf); + ret = PyIter_Next(yf); else ret = __Pyx_PyObject_CallMethod1(yf, __pyx_n_s_send, value); } @@ -24286,33 +21432,21 @@ static PyObject *__Pyx_Coroutine_Send(PyObject *self, PyObject *value) { if (likely(ret)) { return ret; } - retval = __Pyx_Coroutine_FinishDelegation(gen); - } else { - retval = __Pyx_Coroutine_SendEx(gen, value); + return __Pyx_Generator_FinishDelegation(gen); } - return __Pyx_Coroutine_MethodReturn(retval); + return __Pyx_Generator_SendEx(gen, value); } -static int __Pyx_Coroutine_CloseIter(__pyx_CoroutineObject *gen, PyObject *yf) { +static int __Pyx_Generator_CloseIter(__pyx_GeneratorObject *gen, PyObject *yf) { PyObject *retval = NULL; int err = 0; - #ifdef __Pyx_Generator_USED if (__Pyx_Generator_CheckExact(yf)) { - retval = __Pyx_Coroutine_Close(yf); + retval = __Pyx_Generator_Close(yf); if (!retval) return -1; - } else - #endif - #ifdef __Pyx_Coroutine_USED - if (__Pyx_Coroutine_CheckExact(yf)) { - retval = __Pyx_Coroutine_Close(yf); - if (!retval) - return -1; - } else - #endif - { + } else { PyObject *meth; gen->is_running = 1; - meth = __Pyx_PyObject_GetAttrStr(yf, __pyx_n_s_close); + meth = PyObject_GetAttr(yf, __pyx_n_s_close); if (unlikely(!meth)) { if (!PyErr_ExceptionMatches(PyExc_AttributeError)) { PyErr_WriteUnraisable(yf); @@ -24329,44 +21463,22 @@ static int __Pyx_Coroutine_CloseIter(__pyx_CoroutineObject *gen, PyObject *yf) { Py_XDECREF(retval); return err; } -static PyObject *__Pyx_Generator_Next(PyObject *self) { - __pyx_CoroutineObject *gen = (__pyx_CoroutineObject*) self; - PyObject *yf = gen->yieldfrom; - if (unlikely(__Pyx_Coroutine_CheckRunning(gen))) - return NULL; - if (yf) { - PyObject *ret; - gen->is_running = 1; - #ifdef __Pyx_Generator_USED - if (__Pyx_Generator_CheckExact(yf)) { - ret = __Pyx_Generator_Next(yf); - } else - #endif - ret = Py_TYPE(yf)->tp_iternext(yf); - gen->is_running = 0; - if (likely(ret)) { - return ret; - } - return __Pyx_Coroutine_FinishDelegation(gen); - } - return __Pyx_Coroutine_SendEx(gen, Py_None); -} -static PyObject *__Pyx_Coroutine_Close(PyObject *self) { - __pyx_CoroutineObject *gen = (__pyx_CoroutineObject *) self; +static PyObject *__Pyx_Generator_Close(PyObject *self) { + __pyx_GeneratorObject *gen = (__pyx_GeneratorObject *) self; PyObject *retval, *raised_exception; PyObject *yf = gen->yieldfrom; int err = 0; - if (unlikely(__Pyx_Coroutine_CheckRunning(gen))) + if (unlikely(__Pyx_Generator_CheckRunning(gen))) return NULL; if (yf) { Py_INCREF(yf); - err = __Pyx_Coroutine_CloseIter(gen, yf); - __Pyx_Coroutine_Undelegate(gen); + err = __Pyx_Generator_CloseIter(gen, yf); + __Pyx_Generator_Undelegate(gen); Py_DECREF(yf); } if (err == 0) PyErr_SetNone(PyExc_GeneratorExit); - retval = __Pyx_Coroutine_SendEx(gen, NULL); + retval = __Pyx_Generator_SendEx(gen, NULL); if (retval) { Py_DECREF(retval); PyErr_SetString(PyExc_RuntimeError, @@ -24386,40 +21498,32 @@ static PyObject *__Pyx_Coroutine_Close(PyObject *self) { } return NULL; } -static PyObject *__Pyx_Coroutine_Throw(PyObject *self, PyObject *args) { - __pyx_CoroutineObject *gen = (__pyx_CoroutineObject *) self; +static PyObject *__Pyx_Generator_Throw(PyObject *self, PyObject *args) { + __pyx_GeneratorObject *gen = (__pyx_GeneratorObject *) self; PyObject *typ; PyObject *tb = NULL; PyObject *val = NULL; PyObject *yf = gen->yieldfrom; if (!PyArg_UnpackTuple(args, (char *)"throw", 1, 3, &typ, &val, &tb)) return NULL; - if (unlikely(__Pyx_Coroutine_CheckRunning(gen))) + if (unlikely(__Pyx_Generator_CheckRunning(gen))) return NULL; if (yf) { PyObject *ret; Py_INCREF(yf); if (PyErr_GivenExceptionMatches(typ, PyExc_GeneratorExit)) { - int err = __Pyx_Coroutine_CloseIter(gen, yf); + int err = __Pyx_Generator_CloseIter(gen, yf); Py_DECREF(yf); - __Pyx_Coroutine_Undelegate(gen); + __Pyx_Generator_Undelegate(gen); if (err < 0) - return __Pyx_Coroutine_MethodReturn(__Pyx_Coroutine_SendEx(gen, NULL)); + return __Pyx_Generator_SendEx(gen, NULL); goto throw_here; } gen->is_running = 1; - #ifdef __Pyx_Generator_USED if (__Pyx_Generator_CheckExact(yf)) { - ret = __Pyx_Coroutine_Throw(yf, args); - } else - #endif - #ifdef __Pyx_Coroutine_USED - if (__Pyx_Coroutine_CheckExact(yf)) { - ret = __Pyx_Coroutine_Throw(yf, args); - } else - #endif - { - PyObject *meth = __Pyx_PyObject_GetAttrStr(yf, __pyx_n_s_throw); + ret = __Pyx_Generator_Throw(yf, args); + } else { + PyObject *meth = PyObject_GetAttr(yf, __pyx_n_s_throw); if (unlikely(!meth)) { Py_DECREF(yf); if (!PyErr_ExceptionMatches(PyExc_AttributeError)) { @@ -24427,7 +21531,7 @@ static PyObject *__Pyx_Coroutine_Throw(PyObject *self, PyObject *args) { return NULL; } PyErr_Clear(); - __Pyx_Coroutine_Undelegate(gen); + __Pyx_Generator_Undelegate(gen); gen->is_running = 0; goto throw_here; } @@ -24437,16 +21541,16 @@ static PyObject *__Pyx_Coroutine_Throw(PyObject *self, PyObject *args) { gen->is_running = 0; Py_DECREF(yf); if (!ret) { - ret = __Pyx_Coroutine_FinishDelegation(gen); + ret = __Pyx_Generator_FinishDelegation(gen); } - return __Pyx_Coroutine_MethodReturn(ret); + return ret; } throw_here: __Pyx_Raise(typ, val, tb, NULL); - return __Pyx_Coroutine_MethodReturn(__Pyx_Coroutine_SendEx(gen, NULL)); + return __Pyx_Generator_SendEx(gen, NULL); } -static int __Pyx_Coroutine_traverse(PyObject *self, visitproc visit, void *arg) { - __pyx_CoroutineObject *gen = (__pyx_CoroutineObject *) self; +static int __Pyx_Generator_traverse(PyObject *self, visitproc visit, void *arg) { + __pyx_GeneratorObject *gen = (__pyx_GeneratorObject *) self; Py_VISIT(gen->closure); Py_VISIT(gen->classobj); Py_VISIT(gen->yieldfrom); @@ -24455,8 +21559,8 @@ static int __Pyx_Coroutine_traverse(PyObject *self, visitproc visit, void *arg) Py_VISIT(gen->exc_traceback); return 0; } -static int __Pyx_Coroutine_clear(PyObject *self) { - __pyx_CoroutineObject *gen = (__pyx_CoroutineObject *) self; +static int __Pyx_Generator_clear(PyObject *self) { + __pyx_GeneratorObject *gen = (__pyx_GeneratorObject *) self; Py_CLEAR(gen->closure); Py_CLEAR(gen->classobj); Py_CLEAR(gen->yieldfrom); @@ -24467,8 +21571,8 @@ static int __Pyx_Coroutine_clear(PyObject *self) { Py_CLEAR(gen->gi_qualname); return 0; } -static void __Pyx_Coroutine_dealloc(PyObject *self) { - __pyx_CoroutineObject *gen = (__pyx_CoroutineObject *) self; +static void __Pyx_Generator_dealloc(PyObject *self) { + __pyx_GeneratorObject *gen = (__pyx_GeneratorObject *) self; PyObject_GC_UnTrack(gen); if (gen->gi_weakreflist != NULL) PyObject_ClearWeakRefs(self); @@ -24485,23 +21589,21 @@ static void __Pyx_Coroutine_dealloc(PyObject *self) { } PyObject_GC_UnTrack(self); } - __Pyx_Coroutine_clear(self); + __Pyx_Generator_clear(self); PyObject_GC_Del(gen); } -static void __Pyx_Coroutine_del(PyObject *self) { +static void __Pyx_Generator_del(PyObject *self) { PyObject *res; PyObject *error_type, *error_value, *error_traceback; - __pyx_CoroutineObject *gen = (__pyx_CoroutineObject *) self; - __Pyx_PyThreadState_declare + __pyx_GeneratorObject *gen = (__pyx_GeneratorObject *) self; if (gen->resume_label <= 0) return ; #if PY_VERSION_HEX < 0x030400a1 assert(self->ob_refcnt == 0); self->ob_refcnt = 1; #endif - __Pyx_PyThreadState_assign __Pyx_ErrFetch(&error_type, &error_value, &error_traceback); - res = __Pyx_Coroutine_Close(self); + res = __Pyx_Generator_Close(self); if (res == NULL) PyErr_WriteUnraisable(self); else @@ -24529,15 +21631,13 @@ static void __Pyx_Coroutine_del(PyObject *self) { #endif } static PyObject * -__Pyx_Coroutine_get_name(__pyx_CoroutineObject *self) +__Pyx_Generator_get_name(__pyx_GeneratorObject *self) { - PyObject *name = self->gi_name; - if (unlikely(!name)) name = Py_None; - Py_INCREF(name); - return name; + Py_INCREF(self->gi_name); + return self->gi_name; } static int -__Pyx_Coroutine_set_name(__pyx_CoroutineObject *self, PyObject *value) +__Pyx_Generator_set_name(__pyx_GeneratorObject *self, PyObject *value) { PyObject *tmp; #if PY_MAJOR_VERSION >= 3 @@ -24556,15 +21656,13 @@ __Pyx_Coroutine_set_name(__pyx_CoroutineObject *self, PyObject *value) return 0; } static PyObject * -__Pyx_Coroutine_get_qualname(__pyx_CoroutineObject *self) +__Pyx_Generator_get_qualname(__pyx_GeneratorObject *self) { - PyObject *name = self->gi_qualname; - if (unlikely(!name)) name = Py_None; - Py_INCREF(name); - return name; + Py_INCREF(self->gi_qualname); + return self->gi_qualname; } static int -__Pyx_Coroutine_set_qualname(__pyx_CoroutineObject *self, PyObject *value) +__Pyx_Generator_set_qualname(__pyx_GeneratorObject *self, PyObject *value) { PyObject *tmp; #if PY_MAJOR_VERSION >= 3 @@ -24582,160 +21680,37 @@ __Pyx_Coroutine_set_qualname(__pyx_CoroutineObject *self, PyObject *value) Py_XDECREF(tmp); return 0; } -static __pyx_CoroutineObject *__Pyx__Coroutine_New( - PyTypeObject* type, __pyx_coroutine_body_t body, PyObject *closure, - PyObject *name, PyObject *qualname, PyObject *module_name) { - __pyx_CoroutineObject *gen = PyObject_GC_New(__pyx_CoroutineObject, type); - if (gen == NULL) - return NULL; - gen->body = body; - gen->closure = closure; - Py_XINCREF(closure); - gen->is_running = 0; - gen->resume_label = 0; - gen->classobj = NULL; - gen->yieldfrom = NULL; - gen->exc_type = NULL; - gen->exc_value = NULL; - gen->exc_traceback = NULL; - gen->gi_weakreflist = NULL; - Py_XINCREF(qualname); - gen->gi_qualname = qualname; - Py_XINCREF(name); - gen->gi_name = name; - Py_XINCREF(module_name); - gen->gi_modulename = module_name; - PyObject_GC_Track(gen); - return gen; -} - -/* PatchModuleWithCoroutine */ - static PyObject* __Pyx_Coroutine_patch_module(PyObject* module, const char* py_code) { -#if defined(__Pyx_Generator_USED) || defined(__Pyx_Coroutine_USED) - int result; - PyObject *globals, *result_obj; - globals = PyDict_New(); if (unlikely(!globals)) goto ignore; - result = PyDict_SetItemString(globals, "_cython_coroutine_type", - #ifdef __Pyx_Coroutine_USED - (PyObject*)__pyx_CoroutineType); - #else - Py_None); - #endif - if (unlikely(result < 0)) goto ignore; - result = PyDict_SetItemString(globals, "_cython_generator_type", - #ifdef __Pyx_Generator_USED - (PyObject*)__pyx_GeneratorType); - #else - Py_None); - #endif - if (unlikely(result < 0)) goto ignore; - if (unlikely(PyDict_SetItemString(globals, "_module", module) < 0)) goto ignore; - if (unlikely(PyDict_SetItemString(globals, "__builtins__", __pyx_b) < 0)) goto ignore; - result_obj = PyRun_String(py_code, Py_file_input, globals, globals); - if (unlikely(!result_obj)) goto ignore; - Py_DECREF(result_obj); - Py_DECREF(globals); - return module; -ignore: - Py_XDECREF(globals); - PyErr_WriteUnraisable(module); - if (unlikely(PyErr_WarnEx(PyExc_RuntimeWarning, "Cython module failed to patch module with custom type", 1) < 0)) { - Py_DECREF(module); - module = NULL; - } -#else - py_code++; -#endif - return module; -} - -/* PatchGeneratorABC */ - #if defined(__Pyx_Generator_USED) || defined(__Pyx_Coroutine_USED) -static PyObject* __Pyx_patch_abc_module(PyObject *module); -static PyObject* __Pyx_patch_abc_module(PyObject *module) { - module = __Pyx_Coroutine_patch_module( - module, "" -"if _cython_generator_type is not None:\n" -" try: Generator = _module.Generator\n" -" except AttributeError: pass\n" -" else: Generator.register(_cython_generator_type)\n" -"if _cython_coroutine_type is not None:\n" -" try: Coroutine = _module.Coroutine\n" -" except AttributeError: pass\n" -" else: Coroutine.register(_cython_coroutine_type)\n" - ); - return module; -} -#endif -static int __Pyx_patch_abc(void) { -#if defined(__Pyx_Generator_USED) || defined(__Pyx_Coroutine_USED) - static int abc_patched = 0; - if (!abc_patched) { - PyObject *module; - module = PyImport_ImportModule((PY_VERSION_HEX >= 0x03030000) ? "collections.abc" : "collections"); - if (!module) { - PyErr_WriteUnraisable(NULL); - if (unlikely(PyErr_WarnEx(PyExc_RuntimeWarning, - ((PY_VERSION_HEX >= 0x03030000) ? - "Cython module failed to register with collections.abc module" : - "Cython module failed to register with collections module"), 1) < 0)) { - return -1; - } - } else { - module = __Pyx_patch_abc_module(module); - abc_patched = 1; - if (unlikely(!module)) - return -1; - Py_DECREF(module); - } - module = PyImport_ImportModule("backports_abc"); - if (module) { - module = __Pyx_patch_abc_module(module); - Py_XDECREF(module); - } - if (!module) { - PyErr_Clear(); - } - } -#else - if (0) __Pyx_Coroutine_patch_module(NULL, NULL); -#endif - return 0; -} - -/* Generator */ - static PyMethodDef __pyx_Generator_methods[] = { - {"send", (PyCFunction) __Pyx_Coroutine_Send, METH_O, - (char*) PyDoc_STR("send(arg) -> send 'arg' into generator,\nreturn next yielded value or raise StopIteration.")}, - {"throw", (PyCFunction) __Pyx_Coroutine_Throw, METH_VARARGS, - (char*) PyDoc_STR("throw(typ[,val[,tb]]) -> raise exception in generator,\nreturn next yielded value or raise StopIteration.")}, - {"close", (PyCFunction) __Pyx_Coroutine_Close, METH_NOARGS, - (char*) PyDoc_STR("close() -> raise GeneratorExit inside generator.")}, - {0, 0, 0, 0} -}; -static PyMemberDef __pyx_Generator_memberlist[] = { - {(char *) "gi_running", T_BOOL, offsetof(__pyx_CoroutineObject, is_running), READONLY, NULL}, - {(char*) "gi_yieldfrom", T_OBJECT, offsetof(__pyx_CoroutineObject, yieldfrom), READONLY, - (char*) PyDoc_STR("object being iterated by 'yield from', or None")}, - {0, 0, 0, 0, 0} -}; static PyGetSetDef __pyx_Generator_getsets[] = { - {(char *) "__name__", (getter)__Pyx_Coroutine_get_name, (setter)__Pyx_Coroutine_set_name, + {(char *) "__name__", (getter)__Pyx_Generator_get_name, (setter)__Pyx_Generator_set_name, (char*) PyDoc_STR("name of the generator"), 0}, - {(char *) "__qualname__", (getter)__Pyx_Coroutine_get_qualname, (setter)__Pyx_Coroutine_set_qualname, + {(char *) "__qualname__", (getter)__Pyx_Generator_get_qualname, (setter)__Pyx_Generator_set_qualname, (char*) PyDoc_STR("qualified name of the generator"), 0}, {0, 0, 0, 0, 0} }; +static PyMemberDef __pyx_Generator_memberlist[] = { + {(char *) "gi_running", T_BOOL, offsetof(__pyx_GeneratorObject, is_running), READONLY, NULL}, + {0, 0, 0, 0, 0} +}; +static PyMethodDef __pyx_Generator_methods[] = { + {"send", (PyCFunction) __Pyx_Generator_Send, METH_O, 0}, + {"throw", (PyCFunction) __Pyx_Generator_Throw, METH_VARARGS, 0}, + {"close", (PyCFunction) __Pyx_Generator_Close, METH_NOARGS, 0}, + {0, 0, 0, 0} +}; static PyTypeObject __pyx_GeneratorType_type = { PyVarObject_HEAD_INIT(0, 0) "generator", - sizeof(__pyx_CoroutineObject), + sizeof(__pyx_GeneratorObject), 0, - (destructor) __Pyx_Coroutine_dealloc, + (destructor) __Pyx_Generator_dealloc, 0, 0, 0, +#if PY_MAJOR_VERSION < 3 0, +#else + 0, +#endif 0, 0, 0, @@ -24748,10 +21723,10 @@ static PyTypeObject __pyx_GeneratorType_type = { 0, Py_TPFLAGS_DEFAULT | Py_TPFLAGS_HAVE_GC | Py_TPFLAGS_HAVE_FINALIZE, 0, - (traverseproc) __Pyx_Coroutine_traverse, + (traverseproc) __Pyx_Generator_traverse, 0, 0, - offsetof(__pyx_CoroutineObject, gi_weakreflist), + offsetof(__pyx_GeneratorObject, gi_weakreflist), 0, (iternextfunc) __Pyx_Generator_Next, __pyx_Generator_methods, @@ -24775,25 +21750,48 @@ static PyTypeObject __pyx_GeneratorType_type = { #if PY_VERSION_HEX >= 0x030400a1 0, #else - __Pyx_Coroutine_del, + __Pyx_Generator_del, #endif 0, #if PY_VERSION_HEX >= 0x030400a1 - __Pyx_Coroutine_del, + __Pyx_Generator_del, #endif }; +static __pyx_GeneratorObject *__Pyx_Generator_New(__pyx_generator_body_t body, + PyObject *closure, PyObject *name, PyObject *qualname) { + __pyx_GeneratorObject *gen = + PyObject_GC_New(__pyx_GeneratorObject, &__pyx_GeneratorType_type); + if (gen == NULL) + return NULL; + gen->body = body; + gen->closure = closure; + Py_XINCREF(closure); + gen->is_running = 0; + gen->resume_label = 0; + gen->classobj = NULL; + gen->yieldfrom = NULL; + gen->exc_type = NULL; + gen->exc_value = NULL; + gen->exc_traceback = NULL; + gen->gi_weakreflist = NULL; + Py_XINCREF(qualname); + gen->gi_qualname = qualname; + Py_XINCREF(name); + gen->gi_name = name; + PyObject_GC_Track(gen); + return gen; +} static int __pyx_Generator_init(void) { __pyx_GeneratorType_type.tp_getattro = PyObject_GenericGetAttr; __pyx_GeneratorType_type.tp_iter = PyObject_SelfIter; __pyx_GeneratorType = __Pyx_FetchCommonType(&__pyx_GeneratorType_type); - if (unlikely(!__pyx_GeneratorType)) { + if (__pyx_GeneratorType == NULL) { return -1; } return 0; } -/* CheckBinaryVersion */ - static int __Pyx_check_binary_version(void) { +static int __Pyx_check_binary_version(void) { char ctversion[4], rtversion[4]; PyOS_snprintf(ctversion, 4, "%d.%d", PY_MAJOR_VERSION, PY_MINOR_VERSION); PyOS_snprintf(rtversion, 4, "%s", Py_GetVersion()); @@ -24808,8 +21806,7 @@ static int __pyx_Generator_init(void) { return 0; } -/* ModuleImport */ - #ifndef __PYX_HAVE_RT_ImportModule +#ifndef __PYX_HAVE_RT_ImportModule #define __PYX_HAVE_RT_ImportModule static PyObject *__Pyx_ImportModule(const char *name) { PyObject *py_name = 0; @@ -24826,8 +21823,7 @@ bad: } #endif -/* TypeImport */ - #ifndef __PYX_HAVE_RT_ImportType +#ifndef __PYX_HAVE_RT_ImportType #define __PYX_HAVE_RT_ImportType static PyTypeObject *__Pyx_ImportType(const char *module_name, const char *class_name, size_t size, int strict) @@ -24873,14 +21869,14 @@ static PyTypeObject *__Pyx_ImportType(const char *module_name, const char *class #endif if (!strict && (size_t)basicsize > size) { PyOS_snprintf(warning, sizeof(warning), - "%s.%s size changed, may indicate binary incompatibility. Expected %zd, got %zd", - module_name, class_name, basicsize, size); + "%s.%s size changed, may indicate binary incompatibility", + module_name, class_name); if (PyErr_WarnEx(NULL, warning, 0) < 0) goto bad; } else if ((size_t)basicsize != size) { PyErr_Format(PyExc_ValueError, - "%.200s.%.200s has the wrong size, try recompiling. Expected %zd, got %zd", - module_name, class_name, basicsize, size); + "%.200s.%.200s has the wrong size, try recompiling", + module_name, class_name); goto bad; } return (PyTypeObject *)result; @@ -24891,8 +21887,7 @@ bad: } #endif -/* InitStrings */ - static int __Pyx_InitStrings(__Pyx_StringTabEntry *t) { +static int __Pyx_InitStrings(__Pyx_StringTabEntry *t) { while (t->p) { #if PY_MAJOR_VERSION < 3 if (t->is_unicode) { @@ -24930,7 +21925,7 @@ static CYTHON_INLINE char* __Pyx_PyObject_AsString(PyObject* o) { return __Pyx_PyObject_AsStringAndSize(o, &ignore); } static CYTHON_INLINE char* __Pyx_PyObject_AsStringAndSize(PyObject* o, Py_ssize_t *length) { -#if CYTHON_COMPILING_IN_CPYTHON && (__PYX_DEFAULT_STRING_ENCODING_IS_ASCII || __PYX_DEFAULT_STRING_ENCODING_IS_DEFAULT) +#if __PYX_DEFAULT_STRING_ENCODING_IS_ASCII || __PYX_DEFAULT_STRING_ENCODING_IS_DEFAULT if ( #if PY_MAJOR_VERSION < 3 && __PYX_DEFAULT_STRING_ENCODING_IS_ASCII __Pyx_sys_getdefaultencoding_not_ascii && @@ -24971,7 +21966,7 @@ static CYTHON_INLINE char* __Pyx_PyObject_AsStringAndSize(PyObject* o, Py_ssize_ #endif } else #endif -#if (!CYTHON_COMPILING_IN_PYPY) || (defined(PyByteArray_AS_STRING) && defined(PyByteArray_GET_SIZE)) +#if !CYTHON_COMPILING_IN_PYPY if (PyByteArray_Check(o)) { *length = PyByteArray_GET_SIZE(o); return PyByteArray_AS_STRING(o); @@ -24992,10 +21987,8 @@ static CYTHON_INLINE int __Pyx_PyObject_IsTrue(PyObject* x) { if (is_true | (x == Py_False) | (x == Py_None)) return is_true; else return PyObject_IsTrue(x); } -static CYTHON_INLINE PyObject* __Pyx_PyNumber_IntOrLong(PyObject* x) { -#if CYTHON_USE_TYPE_SLOTS +static CYTHON_INLINE PyObject* __Pyx_PyNumber_Int(PyObject* x) { PyNumberMethods *m; -#endif const char *name = NULL; PyObject *res = NULL; #if PY_MAJOR_VERSION < 3 @@ -25003,10 +21996,9 @@ static CYTHON_INLINE PyObject* __Pyx_PyNumber_IntOrLong(PyObject* x) { #else if (PyLong_Check(x)) #endif - return __Pyx_NewRef(x); -#if CYTHON_USE_TYPE_SLOTS + return Py_INCREF(x), x; m = Py_TYPE(x)->tp_as_number; - #if PY_MAJOR_VERSION < 3 +#if PY_MAJOR_VERSION < 3 if (m && m->nb_int) { name = "int"; res = PyNumber_Int(x); @@ -25015,14 +22007,11 @@ static CYTHON_INLINE PyObject* __Pyx_PyNumber_IntOrLong(PyObject* x) { name = "long"; res = PyNumber_Long(x); } - #else +#else if (m && m->nb_int) { name = "int"; res = PyNumber_Long(x); } - #endif -#else - res = PyNumber_Int(x); #endif if (res) { #if PY_MAJOR_VERSION < 3 @@ -25047,55 +22036,18 @@ static CYTHON_INLINE Py_ssize_t __Pyx_PyIndex_AsSsize_t(PyObject* b) { Py_ssize_t ival; PyObject *x; #if PY_MAJOR_VERSION < 3 - if (likely(PyInt_CheckExact(b))) { - if (sizeof(Py_ssize_t) >= sizeof(long)) - return PyInt_AS_LONG(b); - else - return PyInt_AsSsize_t(x); - } + if (likely(PyInt_CheckExact(b))) + return PyInt_AS_LONG(b); #endif if (likely(PyLong_CheckExact(b))) { - #if CYTHON_USE_PYLONG_INTERNALS - const digit* digits = ((PyLongObject*)b)->ob_digit; - const Py_ssize_t size = Py_SIZE(b); - if (likely(__Pyx_sst_abs(size) <= 1)) { - ival = likely(size) ? digits[0] : 0; - if (size == -1) ival = -ival; - return ival; - } else { - switch (size) { - case 2: - if (8 * sizeof(Py_ssize_t) > 2 * PyLong_SHIFT) { - return (Py_ssize_t) (((((size_t)digits[1]) << PyLong_SHIFT) | (size_t)digits[0])); - } - break; - case -2: - if (8 * sizeof(Py_ssize_t) > 2 * PyLong_SHIFT) { - return -(Py_ssize_t) (((((size_t)digits[1]) << PyLong_SHIFT) | (size_t)digits[0])); - } - break; - case 3: - if (8 * sizeof(Py_ssize_t) > 3 * PyLong_SHIFT) { - return (Py_ssize_t) (((((((size_t)digits[2]) << PyLong_SHIFT) | (size_t)digits[1]) << PyLong_SHIFT) | (size_t)digits[0])); - } - break; - case -3: - if (8 * sizeof(Py_ssize_t) > 3 * PyLong_SHIFT) { - return -(Py_ssize_t) (((((((size_t)digits[2]) << PyLong_SHIFT) | (size_t)digits[1]) << PyLong_SHIFT) | (size_t)digits[0])); - } - break; - case 4: - if (8 * sizeof(Py_ssize_t) > 4 * PyLong_SHIFT) { - return (Py_ssize_t) (((((((((size_t)digits[3]) << PyLong_SHIFT) | (size_t)digits[2]) << PyLong_SHIFT) | (size_t)digits[1]) << PyLong_SHIFT) | (size_t)digits[0])); - } - break; - case -4: - if (8 * sizeof(Py_ssize_t) > 4 * PyLong_SHIFT) { - return -(Py_ssize_t) (((((((((size_t)digits[3]) << PyLong_SHIFT) | (size_t)digits[2]) << PyLong_SHIFT) | (size_t)digits[1]) << PyLong_SHIFT) | (size_t)digits[0])); - } - break; - } - } + #if CYTHON_COMPILING_IN_CPYTHON && PY_MAJOR_VERSION >= 3 + #if CYTHON_USE_PYLONG_INTERNALS + switch (Py_SIZE(b)) { + case -1: return -(sdigit)((PyLongObject*)b)->ob_digit[0]; + case 0: return 0; + case 1: return ((PyLongObject*)b)->ob_digit[0]; + } + #endif #endif return PyLong_AsSsize_t(b); } diff --git a/silx/io/specfile.pyx b/silx/io/specfile.pyx index 35f425b..39e8816 100644 --- a/silx/io/specfile.pyx +++ b/silx/io/specfile.pyx @@ -614,7 +614,7 @@ class Scan(object): def _string_to_char_star(string_): """Convert a string to ASCII encoded bytes when using python3""" - if sys.version.startswith("3") and not isinstance(string_, bytes): + if sys.version_info[0] >= 3 and not isinstance(string_, bytes): return bytes(string_, "ascii") return string_ @@ -629,15 +629,14 @@ def is_specfile(filename): """ if not os.path.isfile(filename): return False - # test for presence of #S or #F in first two lines - f = open(filename) - for i, line in enumerate(f): - if line.startswith("#S ") or line.startswith("#F "): - f.close() + # test for presence of #S or #F in first 10 lines + with open(filename, "rb") as f: + chunk = f.read(2500) + for i, line in enumerate(chunk.split(b"\n")): + if line.startswith(b"#S ") or line.startswith(b"#F "): return True if i >= 10: break - f.close() return False @@ -681,10 +680,15 @@ cdef class SpecFile(object): def __dealloc__(self): """Destructor: Calls SfClose(self.handle)""" + self.close() + + def close(self): + """Close the file descriptor""" # handle is NULL if SfOpen failed if self.handle: if specfile_wrapper.SfClose(self.handle): _logger.warning("Error while closing SpecFile") + self.handle = NULL def __len__(self): """Return the number of scans in the SpecFile diff --git a/silx/io/specfile/src/locale_management.c b/silx/io/specfile/src/locale_management.c index 163ed75..62111cc 100644 --- a/silx/io/specfile/src/locale_management.c +++ b/silx/io/specfile/src/locale_management.c @@ -24,15 +24,23 @@ #include <stdlib.h> #ifdef _GNU_SOURCE -#include <xlocale.h> -#include <locale.h> +# include <locale.h> +# ifdef __GLIBC__ +# include <features.h> +# if !((__GLIBC__ > 2) || ((__GLIBC__ == 2) && (__GLIBC_MINOR__ > 25))) +# /* strtod_l has been moved to stdlib.h since glibc 2.26 */ +# include <xlocale.h> +# endif +# else +# include <xlocale.h> +# endif #else -#ifdef PYMCA_POSIX -#else -#ifdef SPECFILE_POSIX -#include <locale.h> -#endif -#endif +# ifdef PYMCA_POSIX +# else +# ifdef SPECFILE_POSIX +# include <locale.h> +# endif +# endif #endif #include <string.h> diff --git a/silx/io/specfilewrapper.py b/silx/io/specfilewrapper.py index 005e54e..01e185c 100644 --- a/silx/io/specfilewrapper.py +++ b/silx/io/specfilewrapper.py @@ -1,6 +1,6 @@ # coding: utf-8 # /*######################################################################### -# Copyright (C) 2016 European Synchrotron Radiation Facility +# Copyright (C) 2016-2018 European Synchrotron Radiation Facility # # Permission is hereby granted, free of charge, to any person obtaining a copy # of this software and associated documentation files (the "Software"), to deal @@ -332,7 +332,7 @@ class scandata(Scan): # noqa lines. If ``key`` does not match any header line, return empty list. :return: List of scan header lines - :rtype: list[str] + :rtype: List[str] """ if key.strip() == "": return self.scan_header diff --git a/silx/io/spech5.py b/silx/io/spech5.py index 81a7a7e..a112fe0 100644 --- a/silx/io/spech5.py +++ b/silx/io/spech5.py @@ -1,6 +1,6 @@ # coding: utf-8 # /*########################################################################## -# Copyright (C) 2016-2017 European Synchrotron Radiation Facility +# Copyright (C) 2016-2018 European Synchrotron Radiation Facility # # Permission is hereby granted, free of charge, to any person obtaining a copy # of this software and associated documentation files (the "Software"), to deal @@ -157,20 +157,30 @@ You can test for existence of data or groups:: >>> "spam" in sfh5["1.1"] False -Strings are stored encoded as ``numpy.string_``, as recommended by -`the h5py documentation <http://docs.h5py.org/en/latest/strings.html>`_. -This ensures maximum compatibility with third party software libraries, -when saving a :class:`SpecH5` to a HDF5 file using :mod:`silx.io.spectoh5`. +.. note:: -The type ``numpy.string_`` is a byte-string format. The consequence of this -is that you should decode strings before using them in **Python 3**:: + Text used to be stored with a dtype ``numpy.string_`` in silx versions + prior to *0.7.0*. The type ``numpy.string_`` is a byte-string format. + The consequence of this is that you had to decode strings before using + them in **Python 3**:: - >>> from silx.io.spech5 import SpecH5 - >>> sfh5 = SpecH5("31oct98.dat") - >>> sfh5["/68.1/title"] - b'68 ascan tx3 -28.5 -24.5 20 0.5' - >>> sfh5["/68.1/title"].decode() - '68 ascan tx3 -28.5 -24.5 20 0.5' + >>> from silx.io.spech5 import SpecH5 + >>> sfh5 = SpecH5("31oct98.dat") + >>> sfh5["/68.1/title"] + b'68 ascan tx3 -28.5 -24.5 20 0.5' + >>> sfh5["/68.1/title"].decode() + '68 ascan tx3 -28.5 -24.5 20 0.5' + + From silx version *0.7.0* onwards, text is now stored as unicode. This + corresponds to the default text type in python 3, and to the *unicode* + type in Python 2. + + To be on the safe side, you can test for the presence of a *decode* + attribute, to ensure that you always work with unicode text:: + + >>> title = sfh5["/68.1/title"] + >>> if hasattr(title, "decode"): + ... title = title.decode() """ @@ -178,28 +188,32 @@ import datetime import logging import numpy import re -import sys import io +import h5py from silx import version as silx_version from .specfile import SpecFile from . import commonh5 +from silx.third_party import six __authors__ = ["P. Knobel", "D. Naudet"] __license__ = "MIT" -__date__ = "23/08/2017" +__date__ = "01/03/2018" logger1 = logging.getLogger(__name__) -try: - import h5py -except ImportError: - h5py = None - logger1.debug("Module h5py optional.", exc_info=True) + +text_dtype = h5py.special_dtype(vlen=six.text_type) -string_types = (basestring,) if sys.version_info[0] == 2 else (str,) # noqa -integer_types = (int, long,) if sys.version_info[0] == 2 else (int,) # noqa +def to_h5py_utf8(str_list): + """Convert a string or a list of strings to a numpy array of + unicode strings that can be written to HDF5 as utf-8. + + This ensures that the type will be consistent between python 2 and + python 3, if attributes or datasets are saved to an HDF5 file. + """ + return numpy.array(str_list, dtype=text_dtype) def _get_number_of_mca_analysers(scan): @@ -457,10 +471,9 @@ class SpecH5NodeDataset(commonh5.Dataset, SpecH5Dataset): def __init__(self, name, data, parent=None, attrs=None): # get proper value types, to inherit from numpy # attributes (dtype, shape, size) - if isinstance(data, string_types): - # use bytes for maximum compatibility - # (see http://docs.h5py.org/en/latest/strings.html) - value = numpy.string_(data) + if isinstance(data, six.string_types): + # use unicode (utf-8 when saved to HDF5 output) + value = to_h5py_utf8(data) elif isinstance(data, float): # use 32 bits for float scalars value = numpy.float32(data) @@ -472,7 +485,8 @@ class SpecH5NodeDataset(commonh5.Dataset, SpecH5Dataset): data_kind = array.dtype.kind if data_kind in ["S", "U"]: - value = numpy.asarray(array, dtype=numpy.string_) + value = numpy.asarray(array, + dtype=text_dtype) elif data_kind in ["f"]: value = numpy.asarray(array, dtype=numpy.float32) else: @@ -547,12 +561,12 @@ class SpecH5(commonh5.File, SpecH5Group): self._sf = SpecFile(filename) - attrs = {"NX_class": "NXroot", - "file_time": datetime.datetime.now().isoformat(), - "file_name": filename, - "creator": "silx %s" % silx_version} + attrs = {"NX_class": to_h5py_utf8("NXroot"), + "file_time": to_h5py_utf8( + datetime.datetime.now().isoformat()), + "file_name": to_h5py_utf8(filename), + "creator": to_h5py_utf8("silx spech5 %s" % silx_version)} commonh5.File.__init__(self, filename, attrs=attrs) - assert self.attrs["NX_class"] == "NXroot" for scan_key in self._sf.keys(): scan = self._sf[scan_key] @@ -560,7 +574,7 @@ class SpecH5(commonh5.File, SpecH5Group): self.add_node(scan_group) def close(self): - # or del self._sf? + self._sf.close() self._sf = None @@ -573,10 +587,13 @@ class ScanGroup(commonh5.Group, SpecH5Group): :param scan: specfile.Scan object """ commonh5.Group.__init__(self, scan_key, parent=parent, - attrs={"NX_class": "NXentry"}) + attrs={"NX_class": to_h5py_utf8("NXentry")}) + # take title in #S after stripping away scan number and spaces + s_hdr_line = scan.scan_header_dict["S"] + title = s_hdr_line.lstrip("0123456789").lstrip() self.add_node(SpecH5NodeDataset(name="title", - data=scan.scan_header_dict["S"], + data=to_h5py_utf8(title), parent=self)) if "D" in scan.scan_header_dict: @@ -603,7 +620,7 @@ class ScanGroup(commonh5.Group, SpecH5Group): scan_key) start_time_str = "" self.add_node(SpecH5NodeDataset(name="start_time", - data=start_time_str, + data=to_h5py_utf8(start_time_str), parent=self)) self.add_node(InstrumentGroup(parent=self, scan=scan)) @@ -620,7 +637,7 @@ class InstrumentGroup(commonh5.Group, SpecH5Group): :param scan: specfile.Scan object """ commonh5.Group.__init__(self, name="instrument", parent=parent, - attrs={"NX_class": "NXinstrument"}) + attrs={"NX_class": to_h5py_utf8("NXinstrument")}) self.add_node(InstrumentSpecfileGroup(parent=self, scan=scan)) self.add_node(PositionersGroup(parent=self, scan=scan)) @@ -635,21 +652,23 @@ class InstrumentGroup(commonh5.Group, SpecH5Group): class InstrumentSpecfileGroup(commonh5.Group, SpecH5Group): def __init__(self, parent, scan): commonh5.Group.__init__(self, name="specfile", parent=parent, - attrs={"NX_class": "NXcollection"}) - self.add_node(SpecH5NodeDataset(name="file_header", - data="\n".join(scan.file_header), - parent=self, - attrs={})) - self.add_node(SpecH5NodeDataset(name="scan_header", - data="\n".join(scan.scan_header), - parent=self, - attrs={})) + attrs={"NX_class": to_h5py_utf8("NXcollection")}) + self.add_node(SpecH5NodeDataset( + name="file_header", + data=to_h5py_utf8(scan.file_header), + parent=self, + attrs={})) + self.add_node(SpecH5NodeDataset( + name="scan_header", + data=to_h5py_utf8(scan.scan_header), + parent=self, + attrs={})) class PositionersGroup(commonh5.Group, SpecH5Group): def __init__(self, parent, scan): commonh5.Group.__init__(self, name="positioners", parent=parent, - attrs={"NX_class": "NXcollection"}) + attrs={"NX_class": to_h5py_utf8("NXcollection")}) for motor_name in scan.motor_names: safe_motor_name = motor_name.replace("/", "%") if motor_name in scan.labels and scan.data.shape[0] > 0: @@ -668,11 +687,14 @@ class InstrumentMcaGroup(commonh5.Group, SpecH5Group): def __init__(self, parent, analyser_index, scan): name = "mca_%d" % analyser_index commonh5.Group.__init__(self, name=name, parent=parent, - attrs={"NX_class": "NXdetector"}) + attrs={"NX_class": to_h5py_utf8("NXdetector")}) - self.add_node(McaDataDataset(parent=self, + mcaDataDataset = McaDataDataset(parent=self, analyser_index=analyser_index, - scan=scan)) + scan=scan) + self.add_node(mcaDataDataset) + spectrum_length = mcaDataDataset.shape[-1] + mcaDataDataset = None if len(scan.mca.channels) == 1: # single @CALIB line applying to multiple devices @@ -681,6 +703,21 @@ class InstrumentMcaGroup(commonh5.Group, SpecH5Group): else: calibration_dataset = scan.mca.calibration[analyser_index] channels_dataset = scan.mca.channels[analyser_index] + + channels_length = len(channels_dataset) + if (channels_length > 1) and (spectrum_length > 0): + logger1.info("Spectrum and channels length mismatch") + # this should always be the case + if channels_length > spectrum_length: + channels_dataset = channels_dataset[:spectrum_length] + elif channels_length < spectrum_length: + # only trust first channel and increment + channel0 = channels_dataset[0] + increment = channels_dataset[1] - channels_dataset[0] + channels_dataset = numpy.linspace(channel0, + channel0 + increment * spectrum_length, + spectrum_length, endpoint=False) + self.add_node(SpecH5NodeDataset(name="calibration", data=calibration_dataset, parent=self)) @@ -707,7 +744,7 @@ class McaDataDataset(SpecH5LazyNodeDataset): def __init__(self, parent, analyser_index, scan): commonh5.LazyLoadableDataset.__init__( self, name="data", parent=parent, - attrs={"interpretation": "spectrum", }) + attrs={"interpretation": to_h5py_utf8("spectrum"),}) self._scan = scan self._analyser_index = analyser_index self._shape = None @@ -741,7 +778,7 @@ class McaDataDataset(SpecH5LazyNodeDataset): def __getitem__(self, item): # optimization for fetching a single spectrum if data not already loaded if not self._is_initialized: - if isinstance(item, integer_types): + if isinstance(item, six.integer_types): if item < 0: # negative indexing item += len(self) @@ -750,7 +787,7 @@ class McaDataDataset(SpecH5LazyNodeDataset): # accessing a slice or element of a single spectrum [i, j:k] try: spectrum_idx, channel_idx_or_slice = item - assert isinstance(spectrum_idx, integer_types) + assert isinstance(spectrum_idx, six.integer_types) except (ValueError, TypeError, AssertionError): pass else: @@ -770,7 +807,7 @@ class MeasurementGroup(commonh5.Group, SpecH5Group): :param scan: specfile.Scan object """ commonh5.Group.__init__(self, name="measurement", parent=parent, - attrs={"NX_class": "NXcollection", }) + attrs={"NX_class": to_h5py_utf8("NXcollection"),}) for label in scan.labels: safe_label = label.replace("/", "%") self.add_node(SpecH5NodeDataset(name=safe_label, @@ -805,23 +842,23 @@ class SampleGroup(commonh5.Group, SpecH5Group): :param scan: specfile.Scan object """ commonh5.Group.__init__(self, name="sample", parent=parent, - attrs={"NX_class": "NXsample", }) + attrs={"NX_class": to_h5py_utf8("NXsample"),}) if _unit_cell_in_scan(scan): self.add_node(SpecH5NodeDataset(name="unit_cell", data=_parse_unit_cell(scan.scan_header_dict["G1"]), parent=self, - attrs={"interpretation": "scalar"})) + attrs={"interpretation": to_h5py_utf8("scalar")})) self.add_node(SpecH5NodeDataset(name="unit_cell_abc", data=_parse_unit_cell(scan.scan_header_dict["G1"])[0, 0:3], parent=self, - attrs={"interpretation": "scalar"})) + attrs={"interpretation": to_h5py_utf8("scalar")})) self.add_node(SpecH5NodeDataset(name="unit_cell_alphabetagamma", data=_parse_unit_cell(scan.scan_header_dict["G1"])[0, 3:6], parent=self, - attrs={"interpretation": "scalar"})) + attrs={"interpretation": to_h5py_utf8("scalar")})) if _ub_matrix_in_scan(scan): self.add_node(SpecH5NodeDataset(name="ub_matrix", data=_parse_UB_matrix(scan.scan_header_dict["G3"]), parent=self, - attrs={"interpretation": "scalar"})) + attrs={"interpretation": to_h5py_utf8("scalar")})) diff --git a/silx/io/test/__init__.py b/silx/io/test/__init__.py index 2510ae2..a309ee9 100644 --- a/silx/io/test/__init__.py +++ b/silx/io/test/__init__.py @@ -24,7 +24,7 @@ __authors__ = ["T. Vincent", "P. Knobel"] __license__ = "MIT" -__date__ = "20/09/2017" +__date__ = "08/12/2017" import unittest @@ -39,6 +39,7 @@ from .test_utils import suite as test_utils_suite from .test_nxdata import suite as test_nxdata_suite from .test_commonh5 import suite as test_commonh5_suite from .test_rawh5 import suite as test_rawh5_suite +from .test_url import suite as test_url_suite def suite(): @@ -54,4 +55,5 @@ def suite(): test_suite.addTest(test_nxdata_suite()) test_suite.addTest(test_commonh5_suite()) test_suite.addTest(test_rawh5_suite()) + test_suite.addTest(test_url_suite()) return test_suite diff --git a/silx/io/test/test_dictdump.py b/silx/io/test/test_dictdump.py index 15d5fdc..9cd054c 100644 --- a/silx/io/test/test_dictdump.py +++ b/silx/io/test/test_dictdump.py @@ -25,7 +25,7 @@ __authors__ = ["P. Knobel"] __license__ = "MIT" -__date__ = "10/02/2017" +__date__ = "17/01/2018" from collections import OrderedDict import numpy @@ -41,9 +41,12 @@ except ImportError: from collections import defaultdict +from silx.utils.testutils import TestLogging + from ..configdict import ConfigDict -from ..dictdump import dicttoh5, dicttojson, dicttoini, dump +from ..dictdump import dicttoh5, dicttojson, dump from ..dictdump import h5todict, load +from ..dictdump import logger as dictdump_logger def tree(): @@ -93,6 +96,24 @@ class TestDictToH5(unittest.TestCase): min(ddict["city attributes"]["Europe"]["France"]["Grenoble"]["coordinates"]), 5.7196) + def testH5Overwrite(self): + dd = ConfigDict({'t': True}) + + dicttoh5(h5file=self.h5_fname, treedict=dd, mode='a') + dd = ConfigDict({'t': False}) + with TestLogging(dictdump_logger, warning=1): + dicttoh5(h5file=self.h5_fname, treedict=dd, mode='a', + overwrite_data=False) + + res = h5todict(self.h5_fname) + assert(res['t'] == True) + + dicttoh5(h5file=self.h5_fname, treedict=dd, mode='a', + overwrite_data=True) + + res = h5todict(self.h5_fname) + assert(res['t'] == False) + @unittest.skipIf(h5py_missing, "Could not import h5py") class TestH5ToDict(unittest.TestCase): diff --git a/silx/io/test/test_fabioh5.py b/silx/io/test/test_fabioh5.py index d9459ae..5fbf0d0 100644 --- a/silx/io/test/test_fabioh5.py +++ b/silx/io/test/test_fabioh5.py @@ -1,6 +1,6 @@ # coding: utf-8 # /*########################################################################## -# Copyright (C) 2016-2017 European Synchrotron Radiation Facility +# Copyright (C) 2016-2018 European Synchrotron Radiation Facility # # Permission is hereby granted, free of charge, to any person obtaining a copy # of this software and associated documentation files (the "Software"), to deal @@ -25,10 +25,9 @@ __authors__ = ["V. Valls"] __license__ = "MIT" -__date__ = "04/10/2017" +__date__ = "24/02/2018" import os -import sys import logging import numpy import unittest @@ -289,6 +288,28 @@ class TestFabioH5(unittest.TestCase): self.assertIn(d.dtype.char, ['d', 'f']) numpy.testing.assert_array_almost_equal(d[...], expected) + def test_interpretation_mca_edf(self): + """EDF files with two or more headers starting with "MCA" + must have @interpretation = "spectrum" an the data.""" + header = { + "Title": "zapimage samy -4.975 -5.095 80 500 samz -4.091 -4.171 70 0", + "MCA a": -23.812, + "MCA b": 2.7107, + "MCA c": 8.1164e-06} + + data = numpy.array([[0, 0], [0, 0]], dtype=numpy.int8) + fabio_image = fabio.edfimage.EdfImage(data=data, header=header) + h5_image = fabioh5.File(fabio_image=fabio_image) + + data_dataset = h5_image["/scan_0/measurement/image_0/data"] + self.assertEquals(data_dataset.attrs["interpretation"], "spectrum") + + data_dataset = h5_image["/scan_0/instrument/detector_0/data"] + self.assertEquals(data_dataset.attrs["interpretation"], "spectrum") + + data_dataset = h5_image["/scan_0/measurement/image_0/info/data"] + self.assertEquals(data_dataset.attrs["interpretation"], "spectrum") + def test_get_api(self): result = self.h5_image.get("scan_0", getclass=True, getlink=True) self.assertIs(result, h5py.HardLink) @@ -356,6 +377,95 @@ class TestFabioH5(unittest.TestCase): self.assertIsInstance(data[...], numpy.ndarray) +class TestFabioH5MultiFrames(unittest.TestCase): + + @classmethod + def setUpClass(cls): + if fabio is None: + raise unittest.SkipTest("fabio is needed") + if h5py is None: + raise unittest.SkipTest("h5py is needed") + + names = ["A", "B", "C", "D"] + values = [["32000", "-10", "5.0", "1"], + ["-32000", "-10", "5.0", "1"]] + + fabio_file = None + + for i in range(10): + header = { + "image_id": "%d" % i, + "integer": "-100", + "float": "1.0", + "string": "hi!", + "list_integer": "100 50 0", + "list_float": "1.0 2.0 3.5", + "string_looks_like_list": "2000 hi!", + "motor_mne": " ".join(names), + "motor_pos": " ".join(values[i % len(values)]), + "counter_mne": " ".join(names), + "counter_pos": " ".join(values[i % len(values)]) + } + for iname, name in enumerate(names): + header[name] = values[i % len(values)][iname] + + data = numpy.array([[i, 11], [12, 13], [14, 15]], dtype=numpy.int64) + if fabio_file is None: + fabio_file = fabio.edfimage.EdfImage(data=data, header=header) + else: + fabio_file.appendFrame(data=data, header=header) + + cls.fabio_file = fabio_file + cls.fabioh5 = fabioh5.File(fabio_image=fabio_file) + + def test_others(self): + others = self.fabioh5["/scan_0/instrument/detector_0/others"] + dataset = others["A"] + self.assertGreaterEqual(dataset.dtype.itemsize, 1) + self.assertEqual(dataset.dtype.kind, "i") + dataset = others["B"] + self.assertGreaterEqual(dataset.dtype.itemsize, 1) + self.assertEqual(dataset.dtype.kind, "i") + dataset = others["C"] + self.assertGreaterEqual(dataset.dtype.itemsize, 1) + self.assertEqual(dataset.dtype.kind, "f") + dataset = others["D"] + self.assertGreaterEqual(dataset.dtype.itemsize, 1) + self.assertEqual(dataset.dtype.kind, "u") + + def test_positioners(self): + counters = self.fabioh5["/scan_0/instrument/positioners"] + # At least 32 bits, no unsigned values + dataset = counters["A"] + self.assertGreaterEqual(dataset.dtype.itemsize, 4) + self.assertEqual(dataset.dtype.kind, "i") + dataset = counters["B"] + self.assertGreaterEqual(dataset.dtype.itemsize, 4) + self.assertEqual(dataset.dtype.kind, "i") + dataset = counters["C"] + self.assertGreaterEqual(dataset.dtype.itemsize, 4) + self.assertEqual(dataset.dtype.kind, "f") + dataset = counters["D"] + self.assertGreaterEqual(dataset.dtype.itemsize, 4) + self.assertEqual(dataset.dtype.kind, "i") + + def test_counters(self): + counters = self.fabioh5["/scan_0/measurement"] + # At least 32 bits, no unsigned values + dataset = counters["A"] + self.assertGreaterEqual(dataset.dtype.itemsize, 4) + self.assertEqual(dataset.dtype.kind, "i") + dataset = counters["B"] + self.assertGreaterEqual(dataset.dtype.itemsize, 4) + self.assertEqual(dataset.dtype.kind, "i") + dataset = counters["C"] + self.assertGreaterEqual(dataset.dtype.itemsize, 4) + self.assertEqual(dataset.dtype.kind, "f") + dataset = counters["D"] + self.assertGreaterEqual(dataset.dtype.itemsize, 4) + self.assertEqual(dataset.dtype.kind, "i") + + class TestFabioH5WithEdf(unittest.TestCase): @classmethod @@ -388,12 +498,6 @@ class TestFabioH5WithEdf(unittest.TestCase): def tearDownClass(cls): cls.fabio_image = None cls.h5_image = None - if sys.platform == "win32" and fabio is not None: - # gc collect is needed to close a file descriptor - # opened by fabio and not released. - # https://github.com/silx-kit/fabio/issues/167 - import gc - gc.collect() shutil.rmtree(cls.tmp_directory) def test_reserved_format_metadata(self): @@ -406,11 +510,70 @@ class TestFabioH5WithEdf(unittest.TestCase): self.assertNotIn("/scan_0/instrument/detector_0/others/HeaderID", self.h5_image) +class TestFabioH5WithFileSeries(unittest.TestCase): + + @classmethod + def setUpClass(cls): + if fabio is None: + raise unittest.SkipTest("fabio is needed") + if h5py is None: + raise unittest.SkipTest("h5py is needed") + + cls.tmp_directory = tempfile.mkdtemp() + + cls.edf_filenames = [] + + for i in range(10): + filename = os.path.join(cls.tmp_directory, "test_%04d.edf" % i) + cls.edf_filenames.append(filename) + + header = { + "image_id": "%d" % i, + "integer": "-100", + "float": "1.0", + "string": "hi!", + "list_integer": "100 50 0", + "list_float": "1.0 2.0 3.5", + "string_looks_like_list": "2000 hi!", + } + data = numpy.array([[i, 11], [12, 13], [14, 15]], dtype=numpy.int64) + fabio_image = fabio.edfimage.edfimage(data, header) + fabio_image.write(filename) + + @classmethod + def tearDownClass(cls): + shutil.rmtree(cls.tmp_directory) + + def _testH5Image(self, h5_image): + # test data + dataset = h5_image["/scan_0/instrument/detector_0/data"] + self.assertEquals(dataset.h5py_class, h5py.Dataset) + self.assertTrue(isinstance(dataset[()], numpy.ndarray)) + self.assertEquals(dataset.dtype.kind, "i") + self.assertEquals(dataset.shape, (10, 3, 2)) + self.assertEquals(list(dataset[:, 0, 0]), list(range(10))) + self.assertEquals(dataset.attrs["interpretation"], "image") + # test metatdata + dataset = h5_image["/scan_0/instrument/detector_0/others/image_id"] + self.assertEquals(list(dataset[...]), list(range(10))) + + def testFileList(self): + h5_image = fabioh5.File(file_series=self.edf_filenames) + self._testH5Image(h5_image) + + def testFileSeries(self): + file_series = fabioh5._FileSeries(self.edf_filenames) + h5_image = fabioh5.File(file_series=file_series) + self._testH5Image(h5_image) + + def suite(): loadTests = unittest.defaultTestLoader.loadTestsFromTestCase test_suite = unittest.TestSuite() test_suite.addTest(loadTests(TestFabioH5)) + test_suite.addTest(loadTests(TestFabioH5MultiFrames)) test_suite.addTest(loadTests(TestFabioH5WithEdf)) + test_suite.addTest(loadTests(TestFabioH5WithFileSeries)) return test_suite diff --git a/silx/io/test/test_nxdata.py b/silx/io/test/test_nxdata.py index f891db9..f7ea8a4 100644 --- a/silx/io/test/test_nxdata.py +++ b/silx/io/test/test_nxdata.py @@ -1,6 +1,6 @@ # coding: utf-8 # /*########################################################################## -# Copyright (C) 2016-2017 European Synchrotron Radiation Facility +# Copyright (C) 2016-2018 European Synchrotron Radiation Facility # # Permission is hereby granted, free of charge, to any person obtaining a copy # of this software and associated documentation files (the "Software"), to deal @@ -25,7 +25,7 @@ __authors__ = ["P. Knobel"] __license__ = "MIT" -__date__ = "27/09/2016" +__date__ = "27/01/2018" try: import h5py @@ -36,6 +36,10 @@ import tempfile import unittest from .. import nxdata +from silx.third_party import six + +text_dtype = h5py.special_dtype(vlen=six.text_type) + @unittest.skipIf(h5py is None, "silx.io.nxdata tests depend on h5py") class TestNXdata(unittest.TestCase): @@ -71,9 +75,16 @@ class TestNXdata(unittest.TestCase): g1d0 = g1d.create_group("1D_spectrum") g1d0.attrs["NX_class"] = "NXdata" g1d0.attrs["signal"] = "count" + g1d0.attrs["auxiliary_signals"] = numpy.array(["count2", "count3"], + dtype=text_dtype) g1d0.attrs["axes"] = "energy_calib" - g1d0.attrs["uncertainties"] = b"energy_errors", + g1d0.attrs["uncertainties"] = numpy.array(["energy_errors", ], + dtype=text_dtype) g1d0.create_dataset("count", data=numpy.arange(10)) + g1d0.create_dataset("count2", data=0.5 * numpy.arange(10)) + d = g1d0.create_dataset("count3", data=0.4 * numpy.arange(10)) + d.attrs["long_name"] = "3rd counter" + g1d0.create_dataset("title", data="Title as dataset (like nexpy)") g1d0.create_dataset("energy_calib", data=(10, 5)) # 10 * idx + 5 g1d0.create_dataset("energy_errors", data=3.14 * numpy.random.rand(10)) @@ -86,7 +97,7 @@ class TestNXdata(unittest.TestCase): g1d2 = g1d.create_group("4D_spectra") g1d2.attrs["NX_class"] = "NXdata" g1d2.attrs["signal"] = "counts" - g1d2.attrs["axes"] = b"energy", + g1d2.attrs["axes"] = numpy.array(["energy", ], dtype=text_dtype) ds = g1d2.create_dataset("counts", data=numpy.arange(2 * 2 * 3 * 10).reshape((2, 2, 3, 10))) ds.attrs["interpretation"] = "spectrum" ds = g1d2.create_dataset("errors", data=4.5 * numpy.random.rand(2, 2, 3, 10)) @@ -103,8 +114,11 @@ class TestNXdata(unittest.TestCase): g2d0 = g2d.create_group("2D_regular_image") g2d0.attrs["NX_class"] = "NXdata" g2d0.attrs["signal"] = "image" - g2d0.attrs["axes"] = b"rows_calib", b"columns_coordinates" + g2d0.attrs["auxiliary_signals"] = "image2" + g2d0.attrs["axes"] = numpy.array(["rows_calib", "columns_coordinates"], + dtype=text_dtype) g2d0.create_dataset("image", data=numpy.arange(4 * 6).reshape((4, 6))) + g2d0.create_dataset("image2", data=numpy.arange(4 * 6).reshape((4, 6))) ds = g2d0.create_dataset("rows_calib", data=(10, 5)) ds.attrs["long_name"] = "Calibrated Y" g2d0.create_dataset("columns_coordinates", data=0.5 + 0.02 * numpy.arange(6)) @@ -112,7 +126,9 @@ class TestNXdata(unittest.TestCase): g2d1 = g2d.create_group("2D_irregular_data") g2d1.attrs["NX_class"] = "NXdata" g2d1.attrs["signal"] = "data" - g2d1.attrs["axes"] = b"rows_coordinates", b"columns_coordinates" + g2d1.attrs["title"] = "Title as group attr" + g2d1.attrs["axes"] = numpy.array(["rows_coordinates", "columns_coordinates"], + dtype=text_dtype) g2d1.create_dataset("data", data=numpy.arange(64 * 128).reshape((64, 128))) g2d1.create_dataset("rows_coordinates", data=numpy.arange(64) + numpy.random.rand(64)) g2d1.create_dataset("columns_coordinates", data=numpy.arange(128) + 2.5 * numpy.random.rand(128)) @@ -126,19 +142,33 @@ class TestNXdata(unittest.TestCase): g2d3 = g2d.create_group("5D_images") g2d3.attrs["NX_class"] = "NXdata" g2d3.attrs["signal"] = "images" - g2d3.attrs["axes"] = b"rows_coordinates", b"columns_coordinates" + g2d3.attrs["axes"] = numpy.array(["rows_coordinates", "columns_coordinates"], + dtype=text_dtype) ds = g2d3.create_dataset("images", data=numpy.arange(2 * 2 * 2 * 4 * 6).reshape((2, 2, 2, 4, 6))) ds.attrs["interpretation"] = "image" g2d3.create_dataset("rows_coordinates", data=5 + 10 * numpy.arange(4)) g2d3.create_dataset("columns_coordinates", data=0.5 + 0.02 * numpy.arange(6)) + g2d4 = g2d.create_group("RGBA_image") + g2d4.attrs["NX_class"] = "NXdata" + g2d4.attrs["signal"] = "image" + g2d4.attrs["axes"] = numpy.array(["rows_calib", "columns_coordinates"], + dtype=text_dtype) + rgba_image = numpy.linspace(0, 1, num=7*8*3).reshape((7, 8, 3)) + rgba_image[:, :, 1] = 1 - rgba_image[:, :, 1] # invert G channel to add some color + ds = g2d4.create_dataset("image", data=rgba_image) + ds.attrs["interpretation"] = "rgba-image" + ds = g2d4.create_dataset("rows_calib", data=(10, 5)) + ds.attrs["long_name"] = "Calibrated Y" + g2d4.create_dataset("columns_coordinates", data=0.5+0.02*numpy.arange(8)) + # SCATTER g = self.h5f.create_group("scatters") gd0 = g.create_group("x_y_scatter") gd0.attrs["NX_class"] = "NXdata" gd0.attrs["signal"] = "y" - gd0.attrs["axes"] = b"x", + gd0.attrs["axes"] = numpy.array(["x", ], dtype=text_dtype) gd0.create_dataset("y", data=numpy.random.rand(128) - 0.5) gd0.create_dataset("x", data=2 * numpy.random.rand(128)) gd0.create_dataset("x_errors", data=0.05 * numpy.random.rand(128)) @@ -147,7 +177,7 @@ class TestNXdata(unittest.TestCase): gd1 = g.create_group("x_y_value_scatter") gd1.attrs["NX_class"] = "NXdata" gd1.attrs["signal"] = "values" - gd1.attrs["axes"] = b"x", b"y" + gd1.attrs["axes"] = numpy.array(["x", "y"], dtype=text_dtype) gd1.create_dataset("values", data=3.14 * numpy.random.rand(128)) gd1.create_dataset("y", data=numpy.random.rand(128)) gd1.create_dataset("y_errors", data=0.02 * numpy.random.rand(128)) @@ -199,6 +229,7 @@ class TestNXdata(unittest.TestCase): def testSpectra(self): nxd = nxdata.NXdata(self.h5f["spectra/1D_spectrum"]) self.assertTrue(nxd.signal_is_1d) + self.assertTrue(nxd.is_curve) self.assertTrue(numpy.array_equal(numpy.array(nxd.signal), numpy.arange(10))) self.assertEqual(nxd.axes_names, ["energy_calib"]) @@ -208,9 +239,18 @@ class TestNXdata(unittest.TestCase): self.assertIsNone(nxd.errors) self.assertFalse(nxd.is_scatter or nxd.is_x_y_value_scatter) self.assertIsNone(nxd.interpretation) + self.assertEqual(nxd.title, "Title as dataset (like nexpy)") + + self.assertEqual(nxd.auxiliary_signals_dataset_names, + ["count2", "count3"]) + self.assertEqual(nxd.auxiliary_signals_names, + ["count2", "3rd counter"]) + self.assertAlmostEqual(nxd.auxiliary_signals[1][2], + 0.8) # numpy.arange(10) * 0.4 nxd = nxdata.NXdata(self.h5f["spectra/2D_spectra"]) self.assertTrue(nxd.signal_is_2d) + self.assertTrue(nxd.is_curve) self.assertEqual(nxd.axes_names, [None, None]) self.assertEqual(nxd.axes_dataset_names, [None, None]) self.assertEqual(nxd.axes, [None, None]) @@ -221,6 +261,7 @@ class TestNXdata(unittest.TestCase): nxd = nxdata.NXdata(self.h5f["spectra/4D_spectra"]) self.assertFalse(nxd.signal_is_0d or nxd.signal_is_1d or nxd.signal_is_2d or nxd.signal_is_3d) + self.assertTrue(nxd.is_curve) self.assertEqual(nxd.axes_names, [None, None, None, "Calibrated energy"]) self.assertEqual(nxd.axes_dataset_names, @@ -242,15 +283,19 @@ class TestNXdata(unittest.TestCase): def testImages(self): nxd = nxdata.NXdata(self.h5f["images/2D_regular_image"]) self.assertTrue(nxd.signal_is_2d) + self.assertTrue(nxd.is_image) self.assertEqual(nxd.axes_names, ["Calibrated Y", "columns_coordinates"]) self.assertEqual(list(nxd.axes_dataset_names), ["rows_calib", "columns_coordinates"]) self.assertIsNone(nxd.errors) self.assertFalse(nxd.is_scatter or nxd.is_x_y_value_scatter) self.assertIsNone(nxd.interpretation) + self.assertEqual(len(nxd.auxiliary_signals), 1) + self.assertEqual(nxd.auxiliary_signals_names, ["image2"]) nxd = nxdata.NXdata(self.h5f["images/2D_irregular_data"]) self.assertTrue(nxd.signal_is_2d) + self.assertTrue(nxd.is_image) self.assertEqual(nxd.axes_dataset_names, nxd.axes_names) self.assertEqual(list(nxd.axes_dataset_names), @@ -259,8 +304,10 @@ class TestNXdata(unittest.TestCase): self.assertIsNone(nxd.errors) self.assertFalse(nxd.is_scatter or nxd.is_x_y_value_scatter) self.assertIsNone(nxd.interpretation) + self.assertEqual(nxd.title, "Title as group attr") nxd = nxdata.NXdata(self.h5f["images/5D_images"]) + self.assertTrue(nxd.is_image) self.assertFalse(nxd.signal_is_0d or nxd.signal_is_1d or nxd.signal_is_2d or nxd.signal_is_3d) self.assertEqual(nxd.axes_names, @@ -271,6 +318,16 @@ class TestNXdata(unittest.TestCase): self.assertFalse(nxd.is_scatter or nxd.is_x_y_value_scatter) self.assertEqual(nxd.interpretation, "image") + nxd = nxdata.NXdata(self.h5f["images/RGBA_image"]) + self.assertTrue(nxd.is_image) + self.assertEqual(nxd.interpretation, "rgba-image") + self.assertTrue(nxd.signal_is_3d) + self.assertEqual(nxd.axes_names, ["Calibrated Y", + "columns_coordinates", + None]) + self.assertEqual(list(nxd.axes_dataset_names), + ["rows_calib", "columns_coordinates", None]) + def testScatters(self): nxd = nxdata.NXdata(self.h5f["scatters/x_y_scatter"]) self.assertTrue(nxd.signal_is_1d) @@ -301,10 +358,206 @@ class TestNXdata(unittest.TestCase): self.assertIsNone(nxd.interpretation) +@unittest.skipIf(h5py is None, "silx.io.nxdata tests depend on h5py") +class TestLegacyNXdata(unittest.TestCase): + def setUp(self): + tmp = tempfile.NamedTemporaryFile(prefix="nxdata_legacy_examples_", + suffix=".h5", delete=True) + tmp.file.close() + self.h5fname = tmp.name + self.h5f = h5py.File(tmp.name, "w") + + def tearDown(self): + self.h5f.close() + + def testSignalAttrOnDataset(self): + g = self.h5f.create_group("2D") + g.attrs["NX_class"] = "NXdata" + + ds0 = g.create_dataset("image0", + data=numpy.arange(4 * 6).reshape((4, 6))) + ds0.attrs["signal"] = 1 + ds0.attrs["long_name"] = "My first image" + + ds1 = g.create_dataset("image1", + data=numpy.arange(4 * 6).reshape((4, 6))) + ds1.attrs["signal"] = "2" + ds1.attrs["long_name"] = "My 2nd image" + + ds2 = g.create_dataset("image2", + data=numpy.arange(4 * 6).reshape((4, 6))) + ds2.attrs["signal"] = 3 + + nxd = nxdata.NXdata(self.h5f["2D"]) + + self.assertEqual(nxd.signal_dataset_name, "image0") + self.assertEqual(nxd.signal_name, "My first image") + self.assertEqual(nxd.signal.shape, + (4, 6)) + + self.assertEqual(len(nxd.auxiliary_signals), 2) + self.assertEqual(nxd.auxiliary_signals[1].shape, + (4, 6)) + + self.assertEqual(nxd.auxiliary_signals_dataset_names, + ["image1", "image2"]) + self.assertEqual(nxd.auxiliary_signals_names, + ["My 2nd image", "image2"]) + + def testAxesOnSignalDataset(self): + g = self.h5f.create_group("2D") + g.attrs["NX_class"] = "NXdata" + + ds0 = g.create_dataset("image0", + data=numpy.arange(4 * 6).reshape((4, 6))) + ds0.attrs["signal"] = 1 + ds0.attrs["axes"] = "yaxis:xaxis" + + ds1 = g.create_dataset("yaxis", + data=numpy.arange(4)) + ds2 = g.create_dataset("xaxis", + data=numpy.arange(6)) + + nxd = nxdata.NXdata(self.h5f["2D"]) + + self.assertEqual(nxd.axes_dataset_names, + ["yaxis", "xaxis"]) + self.assertTrue(numpy.array_equal(nxd.axes[0], + numpy.arange(4))) + self.assertTrue(numpy.array_equal(nxd.axes[1], + numpy.arange(6))) + + def testAxesOnAxesDatasets(self): + g = self.h5f.create_group("2D") + g.attrs["NX_class"] = "NXdata" + + ds0 = g.create_dataset("image0", + data=numpy.arange(4 * 6).reshape((4, 6))) + ds0.attrs["signal"] = 1 + ds1 = g.create_dataset("yaxis", + data=numpy.arange(4)) + ds1.attrs["axis"] = 0 + ds2 = g.create_dataset("xaxis", + data=numpy.arange(6)) + ds2.attrs["axis"] = "1" + + nxd = nxdata.NXdata(self.h5f["2D"]) + self.assertEqual(nxd.axes_dataset_names, + ["yaxis", "xaxis"]) + self.assertTrue(numpy.array_equal(nxd.axes[0], + numpy.arange(4))) + self.assertTrue(numpy.array_equal(nxd.axes[1], + numpy.arange(6))) + + +class TestSaveNXdata(unittest.TestCase): + def setUp(self): + tmp = tempfile.NamedTemporaryFile(prefix="nxdata", + suffix=".h5", delete=True) + tmp.file.close() + self.h5fname = tmp.name + + def testSimpleSave(self): + sig = numpy.array([0, 1, 2]) + a0 = numpy.array([2, 3, 4]) + a1 = numpy.array([3, 4, 5]) + nxdata.save_NXdata(filename=self.h5fname, + signal=sig, + axes=[a0, a1], + signal_name="sig", + axes_names=["a0", "a1"], + nxentry_name="a", + nxdata_name="mydata") + + h5f = h5py.File(self.h5fname, "r") + self.assertTrue(nxdata.is_valid_nxdata(h5f["a/mydata"])) + + nxd = nxdata.NXdata(h5f["/a/mydata"]) + self.assertTrue(numpy.array_equal(nxd.signal, + sig)) + self.assertTrue(numpy.array_equal(nxd.axes[0], + a0)) + + h5f.close() + + def testSimplestSave(self): + sig = numpy.array([0, 1, 2]) + nxdata.save_NXdata(filename=self.h5fname, + signal=sig) + + h5f = h5py.File(self.h5fname, "r") + + self.assertTrue(nxdata.is_valid_nxdata(h5f["/entry/data0"])) + + nxd = nxdata.NXdata(h5f["/entry/data0"]) + self.assertTrue(numpy.array_equal(nxd.signal, + sig)) + h5f.close() + + def testSaveDefaultAxesNames(self): + sig = numpy.array([0, 1, 2]) + a0 = numpy.array([2, 3, 4]) + a1 = numpy.array([3, 4, 5]) + nxdata.save_NXdata(filename=self.h5fname, + signal=sig, + axes=[a0, a1], + signal_name="sig", + axes_names=None, + axes_long_names=["a", "b"], + nxentry_name="a", + nxdata_name="mydata") + + h5f = h5py.File(self.h5fname, "r") + self.assertTrue(nxdata.is_valid_nxdata(h5f["a/mydata"])) + + nxd = nxdata.NXdata(h5f["/a/mydata"]) + self.assertTrue(numpy.array_equal(nxd.signal, + sig)) + self.assertTrue(numpy.array_equal(nxd.axes[0], + a0)) + self.assertEqual(nxd.axes_dataset_names, + [u"dim0", u"dim1"]) + self.assertEqual(nxd.axes_names, + [u"a", u"b"]) + + h5f.close() + + def testSaveToExistingEntry(self): + h5f = h5py.File(self.h5fname, "w") + g = h5f.create_group("myentry") + g.attrs["NX_class"] = "NXentry" + h5f.close() + + sig = numpy.array([0, 1, 2]) + a0 = numpy.array([2, 3, 4]) + a1 = numpy.array([3, 4, 5]) + nxdata.save_NXdata(filename=self.h5fname, + signal=sig, + axes=[a0, a1], + signal_name="sig", + axes_names=["a0", "a1"], + nxentry_name="myentry", + nxdata_name="toto") + + h5f = h5py.File(self.h5fname, "r") + self.assertTrue(nxdata.is_valid_nxdata(h5f["myentry/toto"])) + + nxd = nxdata.NXdata(h5f["myentry/toto"]) + self.assertTrue(numpy.array_equal(nxd.signal, + sig)) + self.assertTrue(numpy.array_equal(nxd.axes[0], + a0)) + h5f.close() + + def suite(): test_suite = unittest.TestSuite() test_suite.addTest( unittest.defaultTestLoader.loadTestsFromTestCase(TestNXdata)) + test_suite.addTest( + unittest.defaultTestLoader.loadTestsFromTestCase(TestLegacyNXdata)) + test_suite.addTest( + unittest.defaultTestLoader.loadTestsFromTestCase(TestSaveNXdata)) return test_suite diff --git a/silx/io/test/test_specfile.py b/silx/io/test/test_specfile.py index 0aef2e2..9236fee 100644 --- a/silx/io/test/test_specfile.py +++ b/silx/io/test/test_specfile.py @@ -25,9 +25,9 @@ __authors__ = ["P. Knobel", "V.A. Sole"] __license__ = "MIT" -__date__ = "03/08/2017" +__date__ = "17/01/2018" + -import gc import locale import logging import numpy @@ -36,7 +36,7 @@ import sys import tempfile import unittest -from silx.test import utils +from silx.utils import testutils from ..specfile import SpecFile, Scan from .. import specfile @@ -136,14 +136,14 @@ class TestSpecFile(unittest.TestCase): @classmethod def setUpClass(cls): fd, cls.fname1 = tempfile.mkstemp(text=False) - if sys.version < '3.0': + if sys.version_info < (3, ): os.write(fd, sftext) else: os.write(fd, bytes(sftext, 'ascii')) os.close(fd) fd2, cls.fname2 = tempfile.mkstemp(text=False) - if sys.version < '3.0': + if sys.version_info < (3, ): os.write(fd2, sftext[370:923]) else: os.write(fd2, bytes(sftext[370:923], 'ascii')) @@ -151,7 +151,7 @@ class TestSpecFile(unittest.TestCase): fd3, cls.fname3 = tempfile.mkstemp(text=False) txt = sftext[371:923] - if sys.version < '3.0': + if sys.version_info < (3, ): os.write(fd3, txt) else: os.write(fd3, bytes(txt, 'ascii')) @@ -177,16 +177,9 @@ class TestSpecFile(unittest.TestCase): self.scan1_no_fhdr_crash = self.sf_no_fhdr_crash[0] def tearDown(self): - del self.sf - del self.sf_no_fhdr - del self.scan1 - del self.scan1_2 - del self.scan25 - del self.scan1_no_fhdr - del self.sf_no_fhdr_crash - del self.scan1_no_fhdr_crash - del self.empty_scan - gc.collect() + self.sf.close() + self.sf_no_fhdr.close() + self.sf_no_fhdr_crash.close() def test_open(self): self.assertIsInstance(self.sf, SpecFile) @@ -376,7 +369,7 @@ class TestSpecFile(unittest.TestCase): self.assertEqual(self.scan25.mca.channels, []) - @utils.test_logging(specfile._logger.name, warning=1) + @testutils.test_logging(specfile._logger.name, warning=1) def test_empty_scan(self): """Test reading a scan with no data points""" self.assertEqual(len(self.empty_scan.labels), @@ -389,7 +382,7 @@ class TestSFLocale(unittest.TestCase): @classmethod def setUpClass(cls): fd, cls.fname = tempfile.mkstemp(text=False) - if sys.version < '3.0': + if sys.version_info < (3, ): os.write(fd, sftext) else: os.write(fd, bytes(sftext, 'ascii')) @@ -399,13 +392,12 @@ class TestSFLocale(unittest.TestCase): def tearDownClass(cls): os.unlink(cls.fname) locale.setlocale(locale.LC_NUMERIC, loc) # restore saved locale - gc.collect() def crunch_data(self): self.sf3 = SpecFile(self.fname) self.assertAlmostEqual(self.sf3[0].data_line(1)[2], 1.56) - del self.sf3 + self.sf3.close() @unittest.skipIf(not try_DE, "de_DE.utf8 locale not installed") def test_locale_de_DE(self): diff --git a/silx/io/test/test_specfilewrapper.py b/silx/io/test/test_specfilewrapper.py index c5b0f39..2f463fa 100644 --- a/silx/io/test/test_specfilewrapper.py +++ b/silx/io/test/test_specfilewrapper.py @@ -27,7 +27,6 @@ __authors__ = ["P. Knobel"] __license__ = "MIT" __date__ = "15/05/2017" -import gc import locale import logging import numpy @@ -114,23 +113,15 @@ class TestSpecfilewrapper(unittest.TestCase): @classmethod def setUpClass(cls): fd, cls.fname1 = tempfile.mkstemp(text=False) - if sys.version < '3.0': + if sys.version_info < (3, ): os.write(fd, sftext) else: os.write(fd, bytes(sftext, 'ascii')) os.close(fd) - fd2, cls.fname2 = tempfile.mkstemp(text=False) - if sys.version < '3.0': - os.write(fd2, sftext[370:-97]) - else: - os.write(fd2, bytes(sftext[370:-97], 'ascii')) - os.close(fd2) - @classmethod def tearDownClass(cls): os.unlink(cls.fname1) - os.unlink(cls.fname2) def setUp(self): self.sf = Specfile(self.fname1) @@ -139,11 +130,7 @@ class TestSpecfilewrapper(unittest.TestCase): self.scan25 = self.sf.select("25.1") def tearDown(self): - del self.sf - del self.scan1 - del self.scan1_2 - del self.scan25 - gc.collect() + self.sf.close() def test_number_of_scans(self): self.assertEqual(3, len(self.sf)) diff --git a/silx/io/test/test_spech5.py b/silx/io/test/test_spech5.py index 1d04c6f..b842243 100644 --- a/silx/io/test/test_spech5.py +++ b/silx/io/test/test_spech5.py @@ -1,6 +1,6 @@ # coding: utf-8 # /*########################################################################## -# Copyright (C) 2016-2017 European Synchrotron Radiation Facility +# Copyright (C) 2016-2018 European Synchrotron Radiation Facility # # Permission is hereby granted, free of charge, to any person obtaining a copy # of this software and associated documentation files (the "Software"), to deal @@ -22,7 +22,6 @@ # # ############################################################################*/ """Tests for spech5""" -import gc from numpy import array_equal import os import io @@ -32,11 +31,10 @@ import unittest import datetime from functools import partial -from silx.test import utils +from silx.utils import testutils from .. import spech5 -from ..spech5 import (SpecH5, SpecH5Group, - SpecH5Dataset, spec_date_to_iso8601) +from ..spech5 import (SpecH5, SpecH5Dataset, spec_date_to_iso8601) from .. import specfile try: @@ -46,7 +44,7 @@ except ImportError: __authors__ = ["P. Knobel"] __license__ = "MIT" -__date__ = "26/07/2017" +__date__ = "12/02/2018" sftext = """#F /tmp/sf.dat #E 1455180875 @@ -216,7 +214,7 @@ class TestSpecH5(unittest.TestCase): @classmethod def setUpClass(cls): fd, cls.fname = tempfile.mkstemp() - if sys.version < '3.0': + if sys.version_info < (3, ): os.write(fd, sftext) else: os.write(fd, bytes(sftext, 'ascii')) @@ -230,9 +228,7 @@ class TestSpecH5(unittest.TestCase): self.sfh5 = SpecH5(self.fname) def tearDown(self): - # fix Win32 permission error when deleting temp file - del self.sfh5 - gc.collect() + self.sfh5.close() def testContainsFile(self): self.assertIn("/1.2/measurement", self.sfh5) @@ -275,9 +271,9 @@ class TestSpecH5(unittest.TestCase): def testDate(self): # start time is in Iso8601 format self.assertEqual(self.sfh5["/1.1/start_time"], - b"2016-02-11T09:55:20") + u"2016-02-11T09:55:20") self.assertEqual(self.sfh5["25.1/start_time"], - b"2015-03-14T03:53:50") + u"2015-03-14T03:53:50") def testDatasetInstanceAttr(self): """The SpecH5Dataset objects must implement some dummy attributes @@ -299,7 +295,7 @@ class TestSpecH5(unittest.TestCase): -3) self.assertEqual(self.sfh5.get("/1.1/start_time", default=-3), - b"2016-02-11T09:55:20") + u"2016-02-11T09:55:20") def testGetClass(self): """Test :meth:`SpecH5Group.get`""" @@ -355,33 +351,22 @@ class TestSpecH5(unittest.TestCase): def testHeader(self): file_header = self.sfh5["/1.2/instrument/specfile/file_header"] scan_header = self.sfh5["/1.2/instrument/specfile/scan_header"] - # convert ndarray(dtype=numpy.string_) to str - if sys.version < '3.0': - file_header = str(file_header[()]) - scan_header = str(scan_header[()]) - else: - file_header = str(file_header.astype(str)) - scan_header = str(scan_header.astype(str)) # File header has 10 lines - self.assertEqual(len(file_header.split("\n")), 10) + self.assertEqual(len(file_header), 10) # 1.2 has 9 scan & mca header lines - self.assertEqual(len(scan_header.split("\n")), 9) + self.assertEqual(len(scan_header), 9) # line 4 of file header self.assertEqual( - file_header.split("\n")[3], - "#C imaging User = opid17") + file_header[3], + u"#C imaging User = opid17") # line 4 of scan header scan_header = self.sfh5["25.1/instrument/specfile/scan_header"] - if sys.version < '3.0': - scan_header = str(scan_header[()]) - else: - scan_header = str(scan_header[()].astype(str)) self.assertEqual( - scan_header.split("\n")[3], - "#P1 4.74255 6.197579 2.238283") + scan_header[3], + u"#P1 4.74255 6.197579 2.238283") def testLinks(self): self.assertTrue( @@ -493,7 +478,7 @@ class TestSpecH5(unittest.TestCase): def testTitle(self): self.assertEqual(self.sfh5["/25.1/title"], - b"25 ascan c3th 1.33245 1.52245 40 0.15") + u"ascan c3th 1.33245 1.52245 40 0.15") def testValues(self): group = self.sfh5["/25.1"] @@ -582,9 +567,9 @@ class TestSpecH5(unittest.TestCase): # All 0 values self.assertNotIn("sample", self.sfh5["/1001.1"]) with self.assertRaises(KeyError): - uc = self.sfh5["/1001.1/sample/unit_cell"] + self.sfh5["/1001.1/sample/unit_cell"] - @utils.test_logging(spech5.logger1.name, warning=2) + @testutils.test_logging(spech5.logger1.name, warning=2) def testOpenFileDescriptor(self): """Open a SpecH5 file from a file descriptor""" with io.open(self.sfh5.filename) as f: @@ -593,6 +578,7 @@ class TestSpecH5(unittest.TestCase): name_list = [] # check if the object is working self.sfh5.visit(name_list.append) + sfh5.close() sftext_multi_mca_headers = """ @@ -624,7 +610,7 @@ class TestSpecH5MultiMca(unittest.TestCase): @classmethod def setUpClass(cls): fd, cls.fname = tempfile.mkstemp(text=False) - if sys.version < '3.0': + if sys.version_info < (3, ): os.write(fd, sftext_multi_mca_headers) else: os.write(fd, bytes(sftext_multi_mca_headers, 'ascii')) @@ -638,9 +624,7 @@ class TestSpecH5MultiMca(unittest.TestCase): self.sfh5 = SpecH5(self.fname) def tearDown(self): - # fix Win32 permission error when deleting temp file - del self.sfh5 - gc.collect() + self.sfh5.close() def testMcaCalib(self): mca0_calib = self.sfh5["/1.1/measurement/mca_0/info/calibration"] @@ -691,7 +675,7 @@ sftext_no_cols = r"""#F C:/DATA\test.mca #D Thu Jul 7 08:40:19 2016 #C no data cols, one mca analyser, single spectrum #@MCA %16C -#@CHANN 151 29 29 1 +#@CHANN 151 0 150 1 #@CALIB 0 2 0 @A 789 784 788 814 847 862 880 904 925 955 987 1015 1031 1070 1111 1139 \ 1203 1236 1290 1392 1492 1558 1688 1813 1977 2119 2346 2699 3121 3542 4102 4970 \ @@ -756,7 +740,7 @@ class TestSpecH5NoDataCols(unittest.TestCase): @classmethod def setUpClass(cls): fd, cls.fname = tempfile.mkstemp() - if sys.version < '3.0': + if sys.version_info < (3, ): os.write(fd, sftext_no_cols) else: os.write(fd, bytes(sftext_no_cols, 'ascii')) @@ -770,9 +754,7 @@ class TestSpecH5NoDataCols(unittest.TestCase): self.sfh5 = SpecH5(self.fname) def tearDown(self): - # fix Win32 permission error when deleting temp file - del self.sfh5 - gc.collect() + self.sfh5.close() def testScan1(self): # 1.1: single analyser, single spectrum, 151 channels @@ -829,7 +811,7 @@ class TestSpecH5SlashInLabels(unittest.TestCase): @classmethod def setUpClass(cls): fd, cls.fname = tempfile.mkstemp() - if sys.version < '3.0': + if sys.version_info < (3, ): os.write(fd, sf_text_slash) else: os.write(fd, bytes(sf_text_slash, 'ascii')) @@ -843,9 +825,7 @@ class TestSpecH5SlashInLabels(unittest.TestCase): self.sfh5 = SpecH5(self.fname) def tearDown(self): - # fix Win32 permission error when deleting temp file - del self.sfh5 - gc.collect() + self.sfh5.close() def testLabels(self): """Ensure `/` is substituted with `%` and diff --git a/silx/io/test/test_spectoh5.py b/silx/io/test/test_spectoh5.py index 421c48b..8020731 100644 --- a/silx/io/test/test_spectoh5.py +++ b/silx/io/test/test_spectoh5.py @@ -1,6 +1,6 @@ # coding: utf-8 # /*########################################################################## -# Copyright (C) 2016-2017 European Synchrotron Radiation Facility +# Copyright (C) 2016-2018 European Synchrotron Radiation Facility # # Permission is hereby granted, free of charge, to any person obtaining a copy # of this software and associated documentation files (the "Software"), to deal @@ -23,8 +23,7 @@ # ############################################################################*/ """Tests for SpecFile to HDF5 converter""" -import gc -from numpy import array_equal, string_ +from numpy import array_equal import os import sys import tempfile @@ -41,7 +40,7 @@ else: __authors__ = ["P. Knobel"] __license__ = "MIT" -__date__ = "02/06/2017" +__date__ = "12/02/2018" sftext = """#F /tmp/sf.dat @@ -93,7 +92,7 @@ class TestConvertSpecHDF5(unittest.TestCase): @classmethod def setUpClass(cls): fd, cls.spec_fname = tempfile.mkstemp(text=False) - if sys.version < '3.0': + if sys.version_info < (3, ): os.write(fd, sftext) else: os.write(fd, bytes(sftext, 'ascii')) @@ -115,11 +114,9 @@ class TestConvertSpecHDF5(unittest.TestCase): self.h5f = h5py.File(self.h5_fname, "a") def tearDown(self): - del self.sfh5 self.h5f.close() - del self.h5f + self.sfh5.close() os.unlink(self.h5_fname) - gc.collect() def testAppendToHDF5(self): write_to_h5(self.sfh5, self.h5f, h5path="/foo/bar/spam") @@ -141,24 +138,22 @@ class TestConvertSpecHDF5(unittest.TestCase): def testTitle(self): """Test the value of a dataset""" title12 = self.h5f["/1.2/title"].value - if sys.version > '3.0': - title12 = title12.decode() self.assertEqual(title12, - "1 aaaaaa") + u"aaaaaa") def testAttrs(self): # Test root group (file) attributes self.assertEqual(self.h5f.attrs["NX_class"], - string_("NXroot")) + u"NXroot") # Test dataset attributes ds = self.h5f["/1.2/instrument/mca_1/data"] self.assertTrue("interpretation" in ds.attrs) self.assertEqual(list(ds.attrs.values()), - [string_("spectrum")]) + [u"spectrum"]) # Test group attributes grp = self.h5f["1.1"] self.assertEqual(grp.attrs["NX_class"], - string_("NXentry")) + u"NXentry") self.assertEqual(len(list(grp.attrs.keys())), 1) diff --git a/silx/io/test/test_url.py b/silx/io/test/test_url.py new file mode 100644 index 0000000..5093fc2 --- /dev/null +++ b/silx/io/test/test_url.py @@ -0,0 +1,209 @@ +# coding: utf-8 +# /*########################################################################## +# Copyright (C) 2016-2017 European Synchrotron Radiation Facility +# +# Permission is hereby granted, free of charge, to any person obtaining a copy +# of this software and associated documentation files (the "Software"), to deal +# in the Software without restriction, including without limitation the rights +# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell +# copies of the Software, and to permit persons to whom the Software is +# furnished to do so, subject to the following conditions: +# +# The above copyright notice and this permission notice shall be included in +# all copies or substantial portions of the Software. +# +# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR +# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, +# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE +# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER +# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, +# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN +# THE SOFTWARE. +# +# ############################################################################*/ +"""Tests for url module""" + +__authors__ = ["V. Valls"] +__license__ = "MIT" +__date__ = "29/01/2018" + + +import unittest +from ..url import DataUrl + + +class TestDataUrl(unittest.TestCase): + + def assertUrl(self, url, expected): + self.assertEqual(url.is_valid(), expected[0]) + self.assertEqual(url.is_absolute(), expected[1]) + self.assertEqual(url.scheme(), expected[2]) + self.assertEqual(url.file_path(), expected[3]) + self.assertEqual(url.data_path(), expected[4]) + self.assertEqual(url.data_slice(), expected[5]) + + def test_fabio_absolute(self): + url = DataUrl("fabio:///data/image.edf?slice=2") + expected = [True, True, "fabio", "/data/image.edf", None, (2, )] + self.assertUrl(url, expected) + + def test_fabio_absolute_windows(self): + url = DataUrl("fabio:///C:/data/image.edf?slice=2") + expected = [True, True, "fabio", "C:/data/image.edf", None, (2, )] + self.assertUrl(url, expected) + + def test_silx_absolute(self): + url = DataUrl("silx:///data/image.h5?path=/data/dataset&slice=1,5") + expected = [True, True, "silx", "/data/image.h5", "/data/dataset", (1, 5)] + self.assertUrl(url, expected) + + def test_commandline_shell_separator(self): + url = DataUrl("silx:///data/image.h5::path=/data/dataset&slice=1,5") + expected = [True, True, "silx", "/data/image.h5", "/data/dataset", (1, 5)] + self.assertUrl(url, expected) + + def test_silx_absolute2(self): + url = DataUrl("silx:///data/image.edf?/scan_0/detector/data") + expected = [True, True, "silx", "/data/image.edf", "/scan_0/detector/data", None] + self.assertUrl(url, expected) + + def test_silx_absolute_windows(self): + url = DataUrl("silx:///C:/data/image.h5?/scan_0/detector/data") + expected = [True, True, "silx", "C:/data/image.h5", "/scan_0/detector/data", None] + self.assertUrl(url, expected) + + def test_silx_relative(self): + url = DataUrl("silx:./image.h5") + expected = [True, False, "silx", "./image.h5", None, None] + self.assertUrl(url, expected) + + def test_fabio_relative(self): + url = DataUrl("fabio:./image.edf") + expected = [True, False, "fabio", "./image.edf", None, None] + self.assertUrl(url, expected) + + def test_silx_relative2(self): + url = DataUrl("silx:image.h5") + expected = [True, False, "silx", "image.h5", None, None] + self.assertUrl(url, expected) + + def test_fabio_relative2(self): + url = DataUrl("fabio:image.edf") + expected = [True, False, "fabio", "image.edf", None, None] + self.assertUrl(url, expected) + + def test_file_relative(self): + url = DataUrl("image.edf") + expected = [True, False, None, "image.edf", None, None] + self.assertUrl(url, expected) + + def test_file_relative2(self): + url = DataUrl("./foo/bar/image.edf") + expected = [True, False, None, "./foo/bar/image.edf", None, None] + self.assertUrl(url, expected) + + def test_file_relative3(self): + url = DataUrl("foo/bar/image.edf") + expected = [True, False, None, "foo/bar/image.edf", None, None] + self.assertUrl(url, expected) + + def test_file_absolute(self): + url = DataUrl("/data/image.edf") + expected = [True, True, None, "/data/image.edf", None, None] + self.assertUrl(url, expected) + + def test_file_absolute_windows(self): + url = DataUrl("C:/data/image.edf") + expected = [True, True, None, "C:/data/image.edf", None, None] + self.assertUrl(url, expected) + + def test_absolute_with_path(self): + url = DataUrl("/foo/foobar.h5?/foo/bar") + expected = [True, True, None, "/foo/foobar.h5", "/foo/bar", None] + self.assertUrl(url, expected) + + def test_windows_file_data_slice(self): + url = DataUrl("C:/foo/foobar.h5?path=/foo/bar&slice=5,1") + expected = [True, True, None, "C:/foo/foobar.h5", "/foo/bar", (5, 1)] + self.assertUrl(url, expected) + + def test_scheme_file_data_slice(self): + url = DataUrl("silx:/foo/foobar.h5?path=/foo/bar&slice=5,1") + expected = [True, True, "silx", "/foo/foobar.h5", "/foo/bar", (5, 1)] + self.assertUrl(url, expected) + + def test_scheme_windows_file_data_slice(self): + url = DataUrl("silx:C:/foo/foobar.h5?path=/foo/bar&slice=5,1") + expected = [True, True, "silx", "C:/foo/foobar.h5", "/foo/bar", (5, 1)] + self.assertUrl(url, expected) + + def test_empty(self): + url = DataUrl("") + expected = [False, False, None, "", None, None] + self.assertUrl(url, expected) + + def test_unknown_scheme(self): + url = DataUrl("foo:/foo/foobar.h5?path=/foo/bar&slice=5,1") + expected = [False, True, "foo", "/foo/foobar.h5", "/foo/bar", (5, 1)] + self.assertUrl(url, expected) + + def test_slice(self): + url = DataUrl("/a.h5?path=/b&slice=5,1") + expected = [True, True, None, "/a.h5", "/b", (5, 1)] + self.assertUrl(url, expected) + + def test_slice_ellipsis(self): + url = DataUrl("/a.h5?path=/b&slice=...") + expected = [True, True, None, "/a.h5", "/b", (Ellipsis, )] + self.assertUrl(url, expected) + + def test_slice_slicing(self): + url = DataUrl("/a.h5?path=/b&slice=:") + expected = [True, True, None, "/a.h5", "/b", (slice(None), )] + self.assertUrl(url, expected) + + def test_slice_missing_element(self): + url = DataUrl("/a.h5?path=/b&slice=5,,1") + expected = [False, True, None, "/a.h5", "/b", None] + self.assertUrl(url, expected) + + def test_slice_no_elements(self): + url = DataUrl("/a.h5?path=/b&slice=") + expected = [False, True, None, "/a.h5", "/b", None] + self.assertUrl(url, expected) + + def test_create_relative_url(self): + url = DataUrl(scheme="silx", file_path="./foo.h5", data_path="/", data_slice=(5, 1)) + self.assertFalse(url.is_absolute()) + url2 = DataUrl(url.path()) + self.assertEqual(url, url2) + + def test_create_absolute_url(self): + url = DataUrl(scheme="silx", file_path="/foo.h5", data_path="/", data_slice=(5, 1)) + url2 = DataUrl(url.path()) + self.assertEqual(url, url2) + + def test_create_absolute_windows_url(self): + url = DataUrl(scheme="silx", file_path="C:/foo.h5", data_path="/", data_slice=(5, 1)) + url2 = DataUrl(url.path()) + self.assertEqual(url, url2) + + def test_create_slice_url(self): + url = DataUrl(scheme="silx", file_path="/foo.h5", data_path="/", data_slice=(5, 1, Ellipsis, slice(None))) + url2 = DataUrl(url.path()) + self.assertEqual(url, url2) + + def test_wrong_url(self): + url = DataUrl(scheme="silx", file_path="/foo.h5", data_slice=(5, 1)) + self.assertFalse(url.is_valid()) + + +def suite(): + test_suite = unittest.TestSuite() + loadTests = unittest.defaultTestLoader.loadTestsFromTestCase + test_suite.addTest(loadTests(TestDataUrl)) + return test_suite + + +if __name__ == '__main__': + unittest.main(defaultTest='suite') diff --git a/silx/io/test/test_utils.py b/silx/io/test/test_utils.py index 09074bb..53e001c 100644 --- a/silx/io/test/test_utils.py +++ b/silx/io/test/test_utils.py @@ -30,9 +30,9 @@ import re import shutil import tempfile import unittest -import sys from .. import utils +import silx.io.url try: import h5py @@ -48,7 +48,7 @@ except ImportError: __authors__ = ["P. Knobel"] __license__ = "MIT" -__date__ = "28/09/2017" +__date__ = "12/02/2018" expected_spec1 = r"""#F .* @@ -110,9 +110,9 @@ class TestSave(unittest.TestCase): def test_save_csv(self): utils.save1D(self.csv_fname, self.x, self.y, - xlabel=self.xlab, ylabels=self.ylabs, - filetype="csv", fmt=["%d", "%.2f", "%.2e"], - csvdelim=";", autoheader=True) + xlabel=self.xlab, ylabels=self.ylabs, + filetype="csv", fmt=["%d", "%.2f", "%.2e"], + csvdelim=";", autoheader=True) csvf = open(self.csv_fname) actual_csv = csvf.read() @@ -125,22 +125,20 @@ class TestSave(unittest.TestCase): and converting it to a named record array""" npyf = open(self.npy_fname, "wb") utils.save1D(npyf, self.x, self.y, - xlabel=self.xlab, ylabels=self.ylabs) + xlabel=self.xlab, ylabels=self.ylabs) npyf.close() npy_recarray = numpy.load(self.npy_fname) self.assertEqual(npy_recarray.shape, (3,)) - self.assertTrue( - numpy.array_equal( - npy_recarray['Ordinate1'], - numpy.array((4, 5, 6)))) + self.assertTrue(numpy.array_equal(npy_recarray['Ordinate1'], + numpy.array((4, 5, 6)))) def test_savespec_filename(self): """Save SpecFile using savespec()""" utils.savespec(self.spec_fname, self.x, self.y[0], xlabel=self.xlab, - ylabel=self.ylabs[0], fmt=["%d", "%.2f"], close_file=True, - scan_number=1) + ylabel=self.ylabs[0], fmt=["%d", "%.2f"], + close_file=True, scan_number=1) specf = open(self.spec_fname) actual_spec = specf.read() @@ -152,15 +150,15 @@ class TestSave(unittest.TestCase): """Save SpecFile using savespec(), passing a file handle""" # first savespec:Â open, write file header, save y[0] as scan 1, # return file handle - specf = utils.savespec(self.spec_fname, self.x, self.y[0], xlabel=self.xlab, - ylabel=self.ylabs[0], fmt=["%d", "%.2f"], - close_file=False) + specf = utils.savespec(self.spec_fname, self.x, self.y[0], + xlabel=self.xlab, ylabel=self.ylabs[0], + fmt=["%d", "%.2f"], close_file=False) # second savespec:Â save y[1] as scan 2, close file utils.savespec(specf, self.x, self.y[1], xlabel=self.xlab, - ylabel=self.ylabs[1], fmt=["%d", "%.2f"], - write_file_header=False, close_file=True, - scan_number=2) + ylabel=self.ylabs[1], fmt=["%d", "%.2f"], + write_file_header=False, close_file=True, + scan_number=2) specf = open(self.spec_fname) actual_spec = specf.read() @@ -171,7 +169,7 @@ class TestSave(unittest.TestCase): def test_save_spec(self): """Save SpecFile using save()""" utils.save1D(self.spec_fname, self.x, self.y, xlabel=self.xlab, - ylabels=self.ylabs, filetype="spec", fmt=["%d", "%.2f"]) + ylabels=self.ylabs, filetype="spec", fmt=["%d", "%.2f"]) specf = open(self.spec_fname) actual_spec = specf.read() @@ -192,7 +190,7 @@ class TestSave(unittest.TestCase): self.y = [[4, 5, 6], [7, 8, 9]] self.ylabs = ["Ordinate1", "Ordinate2"] utils.save1D(self.csv_fname, self.x, self.y, - autoheader=True, fmt=["%d", "%.2f", "%.2e"]) + autoheader=True, fmt=["%d", "%.2f", "%.2e"]) csvf = open(self.csv_fname) actual_csv = csvf.read() @@ -242,15 +240,12 @@ class TestH5Ls(unittest.TestCase): self.assertIn("+foo", lines) self.assertIn("\t+bar", lines) - self.assertMatchAnyStringInList( - r'\t\t<HDF5 dataset "tmp": shape \(3,\), type "<i[48]">', - lines) - self.assertMatchAnyStringInList( - r'\t\t<HDF5 dataset "spam": shape \(2, 2\), type "<i[48]">', - lines) - self.assertMatchAnyStringInList( - r'\t<HDF5 dataset "data": shape \(1,\), type "<f[48]">', - lines) + match = r'\t\t<HDF5 dataset "tmp": shape \(3,\), type "<i[48]">' + self.assertMatchAnyStringInList(match, lines) + match = r'\t\t<HDF5 dataset "spam": shape \(2, 2\), type "<i[48]">' + self.assertMatchAnyStringInList(match, lines) + match = r'\t<HDF5 dataset "data": shape \(1,\), type "<f[48]">' + self.assertMatchAnyStringInList(match, lines) os.unlink(self.h5_fname) @@ -325,12 +320,6 @@ class TestOpen(unittest.TestCase): @classmethod def tearDownClass(cls): - if sys.platform == "win32" and fabio is not None: - # gc collect is needed to close a file descriptor - # opened by fabio and not released. - # https://github.com/silx-kit/fabio/issues/167 - import gc - gc.collect() shutil.rmtree(cls.tmp_directory) def testH5(self): @@ -410,6 +399,30 @@ class TestOpen(unittest.TestCase): # load it self.assertRaises(IOError, utils.open, self.missing_filename) + def test_silx_scheme(self): + if h5py is None: + self.skipTest("H5py is missing") + url = silx.io.url.DataUrl(scheme="silx", file_path=self.h5_filename, data_path="/") + with utils.open(url.path()) as f: + self.assertIsNotNone(f) + self.assertTrue(silx.io.utils.is_file(f)) + + def test_fabio_scheme(self): + if h5py is None: + self.skipTest("H5py is missing") + if fabio is None: + self.skipTest("Fabio is missing") + url = silx.io.url.DataUrl(scheme="fabio", file_path=self.edf_filename) + self.assertRaises(IOError, utils.open, url.path()) + + def test_bad_url(self): + url = silx.io.url.DataUrl(scheme="sil", file_path=self.h5_filename) + self.assertRaises(IOError, utils.open, url.path()) + + def test_sliced_url(self): + url = silx.io.url.DataUrl(file_path=self.h5_filename, data_slice=(5,)) + self.assertRaises(IOError, utils.open, url.path()) + class TestNodes(unittest.TestCase): """Test `silx.io.utils.is_` functions.""" @@ -443,7 +456,7 @@ class TestNodes(unittest.TestCase): class Foo(object): def __init__(self): - self.h5py_class = h5py.File + self.h5_class = utils.H5Type.FILE obj = Foo() self.assertTrue(utils.is_file(obj)) self.assertTrue(utils.is_group(obj)) @@ -455,7 +468,7 @@ class TestNodes(unittest.TestCase): class Foo(object): def __init__(self): - self.h5py_class = h5py.Group + self.h5_class = utils.H5Type.GROUP obj = Foo() self.assertFalse(utils.is_file(obj)) self.assertTrue(utils.is_group(obj)) @@ -467,7 +480,7 @@ class TestNodes(unittest.TestCase): class Foo(object): def __init__(self): - self.h5py_class = h5py.Dataset + self.h5_class = utils.H5Type.DATASET obj = Foo() self.assertFalse(utils.is_file(obj)) self.assertFalse(utils.is_group(obj)) @@ -491,13 +504,142 @@ class TestNodes(unittest.TestCase): class Foo(object): def __init__(self): - self.h5py_class = int + self.h5_class = int obj = Foo() self.assertFalse(utils.is_file(obj)) self.assertFalse(utils.is_group(obj)) self.assertFalse(utils.is_dataset(obj)) +class TestGetData(unittest.TestCase): + """Test `silx.io.utils.get_data` function.""" + + @classmethod + def setUpClass(cls): + cls.tmp_directory = tempfile.mkdtemp() + cls.createResources(cls.tmp_directory) + + @classmethod + def createResources(cls, directory): + + if h5py is not None: + cls.h5_filename = os.path.join(directory, "test.h5") + h5 = h5py.File(cls.h5_filename, mode="w") + h5["group/group/scalar"] = 50 + h5["group/group/array"] = [1, 2, 3, 4, 5] + h5["group/group/array2d"] = [[1, 2, 3, 4, 5], [6, 7, 8, 9, 10]] + h5.close() + + cls.spec_filename = os.path.join(directory, "test.dat") + utils.savespec(cls.spec_filename, [1], [1.1], xlabel="x", ylabel="y", + fmt=["%d", "%.2f"], close_file=True, scan_number=1) + + if fabio is not None: + cls.edf_filename = os.path.join(directory, "test.edf") + cls.edf_multiframe_filename = os.path.join(directory, "test_multi.edf") + header = fabio.fabioimage.OrderedDict() + header["integer"] = "10" + data = numpy.array([[10, 50], [50, 10]]) + fabiofile = fabio.edfimage.EdfImage(data, header) + fabiofile.write(cls.edf_filename) + fabiofile.appendFrame(data=data, header=header) + fabiofile.write(cls.edf_multiframe_filename) + + cls.txt_filename = os.path.join(directory, "test.txt") + f = io.open(cls.txt_filename, "w+t") + f.write(u"Kikoo") + f.close() + + cls.missing_filename = os.path.join(directory, "test.missing") + + @classmethod + def tearDownClass(cls): + shutil.rmtree(cls.tmp_directory) + + def test_hdf5_scalar(self): + if h5py is None: + self.skipTest("H5py is missing") + url = "silx:%s?/group/group/scalar" % self.h5_filename + data = utils.get_data(url=url) + self.assertEqual(data, 50) + + def test_hdf5_array(self): + if h5py is None: + self.skipTest("H5py is missing") + url = "silx:%s?/group/group/array" % self.h5_filename + data = utils.get_data(url=url) + self.assertEqual(data.shape, (5, )) + self.assertEqual(data[0], 1) + + def test_hdf5_array_slice(self): + if h5py is None: + self.skipTest("H5py is missing") + url = "silx:%s?path=/group/group/array2d&slice=1" % self.h5_filename + data = utils.get_data(url=url) + self.assertEqual(data.shape, (5, )) + self.assertEqual(data[0], 6) + + def test_hdf5_array_slice_out_of_range(self): + if h5py is None: + self.skipTest("H5py is missing") + url = "silx:%s?path=/group/group/array2d&slice=5" % self.h5_filename + self.assertRaises(ValueError, utils.get_data, url) + + def test_edf_using_silx(self): + if h5py is None: + self.skipTest("H5py is missing") + if fabio is None: + self.skipTest("fabio is missing") + url = "silx:%s?/scan_0/instrument/detector_0/data" % self.edf_filename + data = utils.get_data(url=url) + self.assertEqual(data.shape, (2, 2)) + self.assertEqual(data[0, 0], 10) + + def test_fabio_frame(self): + if fabio is None: + self.skipTest("fabio is missing") + url = "fabio:%s?slice=1" % self.edf_multiframe_filename + data = utils.get_data(url=url) + self.assertEqual(data.shape, (2, 2)) + self.assertEqual(data[0, 0], 10) + + def test_fabio_singleframe(self): + if fabio is None: + self.skipTest("fabio is missing") + url = "fabio:%s?slice=0" % self.edf_filename + data = utils.get_data(url=url) + self.assertEqual(data.shape, (2, 2)) + self.assertEqual(data[0, 0], 10) + + def test_fabio_too_much_frames(self): + if fabio is None: + self.skipTest("fabio is missing") + url = "fabio:%s?slice=..." % self.edf_multiframe_filename + self.assertRaises(ValueError, utils.get_data, url) + + def test_fabio_no_frame(self): + if fabio is None: + self.skipTest("fabio is missing") + url = "fabio:%s" % self.edf_filename + data = utils.get_data(url=url) + self.assertEqual(data.shape, (2, 2)) + self.assertEqual(data[0, 0], 10) + + def test_unsupported_scheme(self): + url = "foo:/foo/bar" + self.assertRaises(ValueError, utils.get_data, url) + + def test_no_scheme(self): + if fabio is None: + self.skipTest("fabio is missing") + url = "%s?path=/group/group/array2d&slice=5" % self.h5_filename + self.assertRaises((ValueError, IOError), utils.get_data, url) + + def test_file_not_exists(self): + url = "silx:/foo/bar" + self.assertRaises(IOError, utils.get_data, url) + + def suite(): loadTests = unittest.defaultTestLoader.loadTestsFromTestCase test_suite = unittest.TestSuite() @@ -505,6 +647,7 @@ def suite(): test_suite.addTest(loadTests(TestH5Ls)) test_suite.addTest(loadTests(TestOpen)) test_suite.addTest(loadTests(TestNodes)) + test_suite.addTest(loadTests(TestGetData)) return test_suite diff --git a/silx/io/url.py b/silx/io/url.py new file mode 100644 index 0000000..ba62a81 --- /dev/null +++ b/silx/io/url.py @@ -0,0 +1,366 @@ +# coding: utf-8 +# /*########################################################################## +# +# Copyright (c) 2016-2017 European Synchrotron Radiation Facility +# +# Permission is hereby granted, free of charge, to any person obtaining a copy +# of this software and associated documentation files (the "Software"), to deal +# in the Software without restriction, including without limitation the rights +# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell +# copies of the Software, and to permit persons to whom the Software is +# furnished to do so, subject to the following conditions: +# +# The above copyright notice and this permission notice shall be included in +# all copies or substantial portions of the Software. +# +# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR +# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, +# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE +# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER +# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, +# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN +# THE SOFTWARE. +# +# ###########################################################################*/ +"""URL module""" + +__authors__ = ["V. Valls"] +__license__ = "MIT" +__date__ = "29/01/2018" + +import logging +from silx.third_party import six +parse = six.moves.urllib.parse + + +_logger = logging.getLogger(__name__) + + +class DataUrl(object): + """Non-mutable object to parse a string representing a resource data + locator. + + It supports: + + - path to file and path inside file to the data + - data slicing + - fabio or silx access to the data + - absolute and relative file access + + >>> # fabio access using absolute path + >>> DataUrl("fabio:///data/image.edf?slice=2") + >>> DataUrl("fabio:///C:/data/image.edf?slice=2") + + >>> # silx access using absolute path + >>> DataUrl("silx:///data/image.h5?path=/data/dataset&slice=1,5") + >>> DataUrl("silx:///data/image.edf?path=/scan_0/detector/data") + >>> DataUrl("silx:///C:/data/image.edf?path=/scan_0/detector/data") + + >>> # `path=` can be omited if there is no other query keys + >>> DataUrl("silx:///data/image.h5?/data/dataset") + >>> # is the same as + >>> DataUrl("silx:///data/image.h5?path=/data/dataset") + + >>> # `::` can be used instead of `?` which can be useful with shell in + >>> # command lines + >>> DataUrl("silx:///data/image.h5::/data/dataset") + >>> # is the same as + >>> DataUrl("silx:///data/image.h5?/data/dataset") + + >>> # Relative path access + >>> DataUrl("silx:./image.h5") + >>> DataUrl("fabio:./image.edf") + >>> DataUrl("silx:image.h5") + >>> DataUrl("fabio:image.edf") + + >>> # Is also support parsing of file access for convenience + >>> DataUrl("./foo/bar/image.edf") + >>> DataUrl("C:/data/") + + :param str path: Path representing a link to a data. If specified, other + arguments are not used. + :param str file_path: Link to the file containing the the data. + None if there is no data selection. + :param str data_path: Data selection applyed to the data file selected. + None if there is no data selection. + :param Tuple[int,slice,Ellipse] data_slice: Slicing applyed of the selected + data. None if no slicing applyed. + :param Union[str,None] scheme: Scheme of the URL. "silx", "fabio" + is supported. Other strings can be provided, but :meth:`is_valid` will + be false. + """ + def __init__(self, path=None, file_path=None, data_path=None, data_slice=None, scheme=None): + self.__is_valid = False + if path is not None: + assert(file_path is None) + assert(data_path is None) + assert(data_slice is None) + assert(scheme is None) + self.__parse_from_path(path) + else: + self.__file_path = file_path + self.__data_path = data_path + self.__data_slice = data_slice + self.__scheme = scheme + self.__path = None + self.__check_validity() + + def __eq__(self, other): + if self.is_valid() != other.is_valid(): + return False + if self.is_valid(): + if self.__scheme != other.scheme(): + return False + if self.__file_path != other.file_path(): + return False + if self.__data_path != other.data_path(): + return False + if self.__data_slice != other.data_slice(): + return False + return True + else: + return self.__path == other.path() + + def __ne__(self, other): + return not (self == other) + + def __repr__(self): + return str(self) + + def __str__(self): + if self.is_valid() or self.__path is None: + def quote_string(string): + if isinstance(string, six.string_types): + return "'%s'" % string + else: + return string + + template = "DataUrl(valid=%s, scheme=%s, file_path=%s, data_path=%s, data_slice=%s)" + return template % (self.__is_valid, + quote_string(self.__scheme), + quote_string(self.__file_path), + quote_string(self.__data_path), + self.__data_slice) + else: + template = "DataUrl(valid=%s, string=%s)" + return template % (self.__is_valid, self.__path) + + def __check_validity(self): + """Check the validity of the attributes.""" + if self.__file_path in [None, ""]: + self.__is_valid = False + return + + if self.__scheme is None: + self.__is_valid = True + elif self.__scheme == "fabio": + self.__is_valid = self.__data_path is None + elif self.__scheme == "silx": + # If there is a slice you must have a data path + # But you can have a data path without slice + slice_implies_data = (self.__data_path is None and self.__data_slice is None) or self.__data_path is not None + self.__is_valid = slice_implies_data + else: + self.__is_valid = False + + @staticmethod + def _parse_slice(slice_string): + """Parse a slicing sequence and return an associated tuple. + + It supports a sequence of `...`, `:`, and integers separated by a coma. + + :rtype: tuple + """ + def str_to_slice(string): + if string == "...": + return Ellipsis + elif string == ":": + return slice(None) + else: + return int(string) + + if slice_string == "": + raise ValueError("An empty slice is not valid") + + tokens = slice_string.split(",") + data_slice = [] + for t in tokens: + try: + data_slice.append(str_to_slice(t)) + except ValueError: + raise ValueError("'%s' is not a valid slicing" % t) + return tuple(data_slice) + + def __parse_from_path(self, path): + """Parse the path and initialize attributes. + + :param str path: Path representing the URL. + """ + self.__path = path + path = path.replace("::", "?", 1) + url = parse.urlparse(path) + + is_valid = True + + if len(url.scheme) <= 2: + # Windows driver + scheme = None + pos = self.__path.index(url.path) + file_path = self.__path[0:pos] + url.path + else: + scheme = url.scheme if url.scheme is not "" else None + file_path = url.path + + # Check absolute windows path + if len(file_path) > 2 and file_path[0] == '/': + if file_path[1] == ":" or file_path[2] == ":": + file_path = file_path[1:] + + self.__scheme = scheme + self.__file_path = file_path + + query = parse.parse_qsl(url.query, keep_blank_values=True) + if len(query) == 1 and query[0][1] == "": + # there is no query keys + data_path = query[0][0] + data_slice = None + else: + merged_query = {} + for name, value in query: + if name in query: + merged_query[name].append(value) + else: + merged_query[name] = [value] + + def pop_single_value(merged_query, name): + if name in merged_query: + values = merged_query.pop(name) + if len(values) > 1: + _logger.warning("More than one query key named '%s'. The last one is used.", name) + value = values[-1] + else: + value = None + return value + + data_path = pop_single_value(merged_query, "path") + data_slice = pop_single_value(merged_query, "slice") + if data_slice is not None: + try: + data_slice = self._parse_slice(data_slice) + except ValueError: + is_valid = False + data_slice = None + + for key in merged_query.keys(): + _logger.warning("Query key %s unsupported. Key skipped.", key) + + self.__data_path = data_path + self.__data_slice = data_slice + + if is_valid: + self.__check_validity() + else: + self.__is_valid = False + + def is_valid(self): + """Returns true if the URL is valid. Else attributes can be None. + + :rtype: bool + """ + return self.__is_valid + + def path(self): + """Returns the string representing the URL. + + :rtype: str + """ + if self.__path is not None: + return self.__path + + def slice_to_string(data_slice): + if data_slice == Ellipsis: + return "..." + elif data_slice == slice(None): + return ":" + elif isinstance(data_slice, int): + return str(data_slice) + else: + raise TypeError("Unexpected slicing type. Found %s" % type(data_slice)) + + if self.__data_path is not None and self.__data_slice is None: + query = self.__data_path + else: + queries = [] + if self.__data_path is not None: + queries.append("path=" + self.__data_path) + if self.__data_slice is not None: + data_slice = ",".join([slice_to_string(s) for s in self.__data_slice]) + queries.append("slice=" + data_slice) + query = "&".join(queries) + + path = "" + if self.__file_path is not None: + path += self.__file_path + + if query != "": + path = path + "?" + query + + if self.__scheme is not None: + if self.is_absolute(): + if path.startswith("/"): + path = self.__scheme + "://" + path + else: + path = self.__scheme + ":///" + path + else: + path = self.__scheme + ":" + path + + return path + + def is_absolute(self): + """Returns true if the file path is an absolute path. + + :rtype: bool + """ + file_path = self.file_path() + if len(file_path) > 0: + if file_path[0] == "/": + return True + if len(file_path) > 2: + # Windows + if file_path[1] == ":" or file_path[2] == ":": + return True + elif len(file_path) > 1: + # Windows + if file_path[1] == ":": + return True + return False + + def file_path(self): + """Returns the path to the file containing the data. + + :rtype: str + """ + return self.__file_path + + def data_path(self): + """Returns the path inside the file to the data. + + :rtype: str + """ + return self.__data_path + + def data_slice(self): + """Returns the slicing applyed to the data. + + It is a tuple containing numbers, slice or ellipses. + + :rtype: Tuple[int, slice, Ellipse] + """ + return self.__data_slice + + def scheme(self): + """Returns the scheme. It can be None if no scheme is specified. + + :rtype: Union[str, None] + """ + return self.__scheme diff --git a/silx/io/utils.py b/silx/io/utils.py index 361a28b..be19fdb 100644 --- a/silx/io/utils.py +++ b/silx/io/utils.py @@ -1,6 +1,6 @@ # coding: utf-8 # /*########################################################################## -# Copyright (C) 2016-2017 European Synchrotron Radiation Facility +# Copyright (C) 2016-2018 European Synchrotron Radiation Facility # # Permission is hereby granted, free of charge, to any person obtaining a copy # of this software and associated documentation files (the "Software"), to deal @@ -23,36 +23,88 @@ # ############################################################################*/ """ I/O utility functions""" +__authors__ = ["P. Knobel", "V. Valls"] +__license__ = "MIT" +__date__ = "14/02/2018" + import numpy import os.path import sys import time import logging +import collections -from silx.utils.deprecation import deprecated from silx.utils.proxy import Proxy +from silx.third_party import six +from silx.third_party import enum +import silx.io.url try: import h5py except ImportError as e: - h5py_missing = True + h5py = None h5py_import_error = e -else: - h5py_missing = False - -__authors__ = ["P. Knobel", "V. Valls"] -__license__ = "MIT" -__date__ = "28/09/2017" +try: + import h5pyd +except ImportError as e: + h5pyd = None + h5py_import_error = e logger = logging.getLogger(__name__) + +class H5Type(enum.Enum): + """Identify a set of HDF5 concepts""" + DATASET = 1 + GROUP = 2 + FILE = 3 + SOFT_LINK = 4 + EXTERNAL_LINK = 5 + HARD_LINK = 6 + + +_CLASSES_TYPE = None +"""Store mapping between classes and types""" + string_types = (basestring,) if sys.version_info[0] == 2 else (str,) # noqa builtin_open = open +def supported_extensions(flat_formats=True): + """Returns the list file extensions supported by `silx.open`. + + The result filter out formats when the expected module is not available. + + :param bool flat_formats: If true, also include flat formats like npy or + edf (while the expected module is available) + :returns: A dictionary indexed by file description and containing a set of + extensions (an extension is a string like "\*.ext"). + :rtype: Dict[str, Set[str]] + """ + formats = {} + if h5py is not None: + formats["HDF5 files"] = set(["*.h5", "*.hdf"]) + formats["NeXus files"] = set(["*.nx", "*.nxs", "*.h5", "*.hdf"]) + formats["NeXus layout from spec files"] = set(["*.dat", "*.spec", "*.mca"]) + if flat_formats: + try: + from silx.io import fabioh5 + except ImportError: + fabioh5 = None + if fabioh5 is not None: + formats["NeXus layout from fabio files"] = set(fabioh5.supported_extensions()) + + extensions = ["*.npz"] + if flat_formats: + extensions.append("*.npy") + + formats["Numpy binary files"] = set(extensions) + return formats + + def save1D(fname, x, y, xlabel=None, ylabels=None, filetype=None, fmt="%.7g", csvdelim=";", newline="\n", header="", footer="", comments="#", autoheader=False): @@ -349,7 +401,7 @@ def h5ls(h5group, lvl=0): .. note:: This function requires `h5py <http://www.h5py.org/>`_ to be installed. """ - if h5py_missing: + if h5py is None: logger.error("h5ls requires h5py") raise h5py_import_error @@ -379,7 +431,7 @@ def h5ls(h5group, lvl=0): return h5repr -def _open(filename): +def _open_local_file(filename): """ Load a file as an `h5py.File`-like object. @@ -399,42 +451,43 @@ def _open(filename): raise IOError("Filename '%s' must be a file path" % filename) debugging_info = [] + try: + _, extension = os.path.splitext(filename) - _, extension = os.path.splitext(filename) + if extension in [".npz", ".npy"]: + try: + from . import rawh5 + return rawh5.NumpyFile(filename) + except (IOError, ValueError) as e: + debugging_info.append((sys.exc_info(), + "File '%s' can't be read as a numpy file." % filename)) - if not h5py_missing: - if h5py.is_hdf5(filename): - return h5py.File(filename, "r") + if h5py is not None: + if h5py.is_hdf5(filename): + return h5py.File(filename, "r") - if extension in [".npz", ".npy"]: try: - from . import rawh5 - return rawh5.NumpyFile(filename) - except (IOError, ValueError) as e: + from . import fabioh5 + return fabioh5.File(filename) + except ImportError: + debugging_info.append((sys.exc_info(), "fabioh5 can't be loaded.")) + except Exception: debugging_info.append((sys.exc_info(), - "File '%s' can't be read as a numpy file." % filename)) + "File '%s' can't be read as fabio file." % filename)) - try: - from . import fabioh5 - return fabioh5.File(filename) - except ImportError: - debugging_info.append((sys.exc_info(), "fabioh5 can't be loaded.")) - except Exception: - debugging_info.append((sys.exc_info(), - "File '%s' can't be read as fabio file." % filename)) + try: + from . import spech5 + return spech5.SpecH5(filename) + except ImportError: + debugging_info.append((sys.exc_info(), + "spech5 can't be loaded.")) + except IOError: + debugging_info.append((sys.exc_info(), + "File '%s' can't be read as spec file." % filename)) + finally: + for exc_info, message in debugging_info: + logger.debug(message, exc_info=exc_info) - try: - from . import spech5 - return spech5.SpecH5(filename) - except ImportError: - debugging_info.append((sys.exc_info(), - "spech5 can't be loaded.")) - except IOError: - debugging_info.append((sys.exc_info(), - "File '%s' can't be read as spec file." % filename)) - - for exc_info, message in debugging_info: - logger.debug(message, exc_info=exc_info) raise IOError("File '%s' can't be read as HDF5" % filename) @@ -452,16 +505,24 @@ class _MainNode(Proxy): def __init__(self, h5_node, h5_file): super(_MainNode, self).__init__(h5_node) self.__file = h5_file - self.__class = get_h5py_class(h5_node) + self.__class = get_h5_class(h5_node) + + @property + def h5_class(self): + """Returns the HDF5 class which is mimicked by this class. + + :rtype: H5Type + """ + return self.__class @property def h5py_class(self): """Returns the h5py classes which is mimicked by this class. It can be one of `h5py.File, h5py.Group` or `h5py.Dataset`. - :rtype: Class + :rtype: h5py class """ - return self.__class + return h5type_to_h5py_class(self.__class) def __enter__(self): return self @@ -496,44 +557,129 @@ def open(filename): # pylint:disable=redefined-builtin :raises: IOError if the file can't be loaded or path can't be found :rtype: h5py-like node """ - if "::" in filename: - filename, h5_path = filename.split("::") + url = silx.io.url.DataUrl(filename) + + if url.scheme() in [None, "file", "silx"]: + # That's a local file + if not url.is_valid(): + raise IOError("URL '%s' is not valid" % filename) + h5_file = _open_local_file(url.file_path()) + elif url.scheme() in ["fabio"]: + raise IOError("URL '%s' containing fabio scheme is not supported" % filename) else: - filename, h5_path = filename, "/" + # That's maybe an URL supported by h5pyd + uri = six.moves.urllib.parse.urlparse(filename) + if h5pyd is None: + raise IOError("URL '%s' unsupported. Try to install h5pyd." % filename) + path = uri.path + endpoint = "%s://%s" % (uri.scheme, uri.netloc) + if path.startswith("/"): + path = path[1:] + return h5pyd.File(path, 'r', endpoint=endpoint) + + if url.data_slice(): + raise IOError("URL '%s' containing slicing is not supported" % filename) + + if url.data_path() in [None, "/", ""]: + # The full file is requested + return h5_file + else: + # Only a children is requested + if url.data_path() not in h5_file: + msg = "File '%s' does not contain path '%s'." % (filename, url.data_path()) + raise IOError(msg) + node = h5_file[url.data_path()] + proxy = _MainNode(node, h5_file) + return proxy - h5_file = _open(filename) - if h5_path in ["/", ""]: - # Short cut - return h5_file +def _get_classes_type(): + """Returns a mapping between Python classes and HDF5 concepts. + + This function allow an lazy initialization to avoid recurssive import + of modules. + """ + global _CLASSES_TYPE + from . import commonh5 + + if _CLASSES_TYPE is not None: + return _CLASSES_TYPE - if h5_path not in h5_file: - msg = "File '%s' do not contains path '%s'." % (filename, h5_path) - raise IOError(msg) + _CLASSES_TYPE = collections.OrderedDict() - node = h5_file[h5_path] - proxy = _MainNode(node, h5_file) - return proxy + _CLASSES_TYPE[commonh5.Dataset] = H5Type.DATASET + _CLASSES_TYPE[commonh5.File] = H5Type.FILE + _CLASSES_TYPE[commonh5.Group] = H5Type.GROUP + _CLASSES_TYPE[commonh5.SoftLink] = H5Type.SOFT_LINK + if h5py is not None: + _CLASSES_TYPE[h5py.Dataset] = H5Type.DATASET + _CLASSES_TYPE[h5py.File] = H5Type.FILE + _CLASSES_TYPE[h5py.Group] = H5Type.GROUP + _CLASSES_TYPE[h5py.SoftLink] = H5Type.SOFT_LINK + _CLASSES_TYPE[h5py.HardLink] = H5Type.HARD_LINK + _CLASSES_TYPE[h5py.ExternalLink] = H5Type.EXTERNAL_LINK -@deprecated -def load(filename): + if h5pyd is not None: + _CLASSES_TYPE[h5pyd.Dataset] = H5Type.DATASET + _CLASSES_TYPE[h5pyd.File] = H5Type.FILE + _CLASSES_TYPE[h5pyd.Group] = H5Type.GROUP + _CLASSES_TYPE[h5pyd.SoftLink] = H5Type.SOFT_LINK + _CLASSES_TYPE[h5pyd.HardLink] = H5Type.HARD_LINK + _CLASSES_TYPE[h5pyd.ExternalLink] = H5Type.EXTERNAL_LINK + + return _CLASSES_TYPE + + +def get_h5_class(obj=None, class_=None): """ - Load a file as an `h5py.File`-like object. + Returns the HDF5 type relative to the object or to the class. - Format supported: - - h5 files, if `h5py` module is installed - - Spec files if `SpecFile` module is installed + :param obj: Instance of an object + :param class_: A class + :rtype: H5Type + """ + if class_ is None: + class_ = obj.__class__ - .. deprecated:: 0.4 - Use :meth:`open`, or :meth:`silx.io.open`. Will be removed in - Silx 0.5. + classes = _get_classes_type() + t = classes.get(class_, None) + if t is not None: + return t - :param str filename: A filename - :raises: IOError if the file can't be loaded as an h5py.File like object - :rtype: h5py.File + if obj is not None: + if hasattr(obj, "h5_class"): + return obj.h5_class + + for referencedClass_, type_ in classes.items(): + if issubclass(class_, referencedClass_): + classes[class_] = type_ + return type_ + + classes[class_] = None + return None + + +def h5type_to_h5py_class(type_): + """ + Returns an h5py class from an H5Type. None if nothing found. + + :param H5Type type_: + :rtype: H5py class """ - return open(filename) + if type_ == H5Type.FILE: + return h5py.File + if type_ == H5Type.GROUP: + return h5py.Group + if type_ == H5Type.DATASET: + return h5py.Dataset + if type_ == H5Type.SOFT_LINK: + return h5py.SoftLink + if type_ == H5Type.HARD_LINK: + return h5py.HardLink + if type_ == H5Type.EXTERNAL_LINK: + return h5py.ExternalLink + return None def get_h5py_class(obj): @@ -545,12 +691,13 @@ def get_h5py_class(obj): :param obj: An object :return: An h5py object """ + if h5py is None: + logger.error("get_h5py_class/is_file/is_group/is_dataset requires h5py") + raise h5py_import_error if hasattr(obj, "h5py_class"): return obj.h5py_class - elif isinstance(obj, (h5py.File, h5py.Group, h5py.Dataset, h5py.SoftLink)): - return obj.__class__ - else: - return None + type_ = get_h5_class(obj) + return h5type_to_h5py_class(type_) def is_file(obj): @@ -559,22 +706,18 @@ def is_file(obj): :param obj: An object """ - class_ = get_h5py_class(obj) - if class_ is None: - return False - return issubclass(class_, h5py.File) + t = get_h5_class(obj) + return t == H5Type.FILE def is_group(obj): """ - True if the object is a h5py.Group-like object. + True if the object is a h5py.Group-like object. A file is a group. :param obj: An object """ - class_ = get_h5py_class(obj) - if class_ is None: - return False - return issubclass(class_, h5py.Group) + t = get_h5_class(obj) + return t in [H5Type.GROUP, H5Type.FILE] def is_dataset(obj): @@ -583,10 +726,8 @@ def is_dataset(obj): :param obj: An object """ - class_ = get_h5py_class(obj) - if class_ is None: - return False - return issubclass(class_, h5py.Dataset) + t = get_h5_class(obj) + return t == H5Type.DATASET def is_softlink(obj): @@ -595,19 +736,99 @@ def is_softlink(obj): :param obj: An object """ - class_ = get_h5py_class(obj) - if class_ is None: - return False - return issubclass(class_, h5py.SoftLink) + t = get_h5_class(obj) + return t == H5Type.SOFT_LINK -if h5py_missing: - def raise_h5py_missing(obj): - logger.error("get_h5py_class/is_file/is_group/is_dataset requires h5py") - raise h5py_import_error +def get_data(url): + """Returns a numpy data from an URL. + + Examples: + + >>> # 1st frame from an EDF using silx.io.open + >>> data = silx.io.get_data("silx:/users/foo/image.edf::/scan_0/instrument/detector_0/data[0]") + + >>> # 1st frame from an EDF using fabio + >>> data = silx.io.get_data("fabio:/users/foo/image.edf::[0]") + + Yet 2 schemes are supported by the function. + + - If `silx` scheme is used, the file is opened using + :meth:`silx.io.open` + and the data is reach using usually NeXus paths. + - If `fabio` scheme is used, the file is opened using :meth:`fabio.open` + from the FabIO library. + No data path have to be specified, but each frames can be accessed + using the data slicing. + This shortcut of :meth:`silx.io.open` allow to have a faster access to + the data. + + .. seealso:: :class:`silx.io.url.DataUrl` + + :param Union[str,silx.io.url.DataUrl]: A data URL + :rtype: Union[numpy.ndarray, numpy.generic] + :raises ImportError: If the mandatory library to read the file is not + available. + :raises ValueError: If the URL is not valid or do not match the data + :raises IOError: If the file is not found or in case of internal error of + :meth:`fabio.open` or :meth:`silx.io.open`. In this last case more + informations are displayed in debug mode. + """ + if not isinstance(url, silx.io.url.DataUrl): + url = silx.io.url.DataUrl(url) + + if not url.is_valid(): + raise ValueError("URL '%s' is not valid" % url.path()) + + if not os.path.exists(url.file_path()): + raise IOError("File '%s' not found" % url.file_path()) + + if url.scheme() == "silx": + data_path = url.data_path() + data_slice = url.data_slice() + + with open(url.file_path()) as h5: + if data_path not in h5: + raise ValueError("Data path from URL '%s' not found" % url.path()) + data = h5[data_path] + + if not silx.io.is_dataset(data): + raise ValueError("Data path from URL '%s' is not a dataset" % url.path()) + + if data_slice is not None: + data = data[data_slice] + else: + # works for scalar and array + data = data[()] + + elif url.scheme() == "fabio": + import fabio + data_slice = url.data_slice() + if data_slice is None: + data_slice = (0, ) + if data_slice is None or len(data_slice) != 1: + raise ValueError("Fabio slice expect a single frame, but %s found" % data_slice) + index = data_slice[0] + if not isinstance(index, int): + raise ValueError("Fabio slice expect a single integer, but %s found" % data_slice) + + try: + fabio_file = fabio.open(url.file_path()) + except Exception: + logger.debug("Error while opening %s with fabio", url.file_path(), exc_info=True) + raise IOError("Error while opening %s with fabio (use debug for more information)" % url.path()) + + if fabio_file.nframes == 1: + if index != 0: + raise ValueError("Only a single frame availalbe. Slice %s out of range" % index) + data = fabio_file.data + else: + data = fabio_file.getframe(index).data + + # There is no explicit close + fabio_file = None + + else: + raise ValueError("Scheme '%s' not supported" % url.scheme()) - get_h5py_class = raise_h5py_missing - is_file = raise_h5py_missing - is_group = raise_h5py_missing - is_dataset = raise_h5py_missing - is_softlink = raise_h5py_missing + return data |