diff options
Diffstat (limited to 'src/silx/io/fabioh5.py')
| -rwxr-xr-x | src/silx/io/fabioh5.py | 132 |
1 files changed, 68 insertions, 64 deletions
diff --git a/src/silx/io/fabioh5.py b/src/silx/io/fabioh5.py index c5ef964..89e838b 100755 --- a/src/silx/io/fabioh5.py +++ b/src/silx/io/fabioh5.py @@ -1,5 +1,5 @@ # /*########################################################################## -# Copyright (C) 2016-2021 European Synchrotron Radiation Facility +# Copyright (C) 2016-2023 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 @@ -31,7 +31,6 @@ """ -import collections import datetime import logging import numbers @@ -77,19 +76,6 @@ def supported_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.""" @@ -108,8 +94,7 @@ class FrameData(commonh5.LazyLoadableDataset): return self.__fabio_reader.get_data() def _update_cache(self): - if isinstance(self.__fabio_reader.fabio_file(), - fabio.file_series.file_series): + if isinstance(self.__fabio_reader.fabio_file(), fabio.file_series.file_series): # Reading all the files is taking too much time # Reach the information from the only first frame first_image = self.__fabio_reader.fabio_file().first_image() @@ -140,9 +125,9 @@ class FrameData(commonh5.LazyLoadableDataset): def __getitem__(self, item): # optimization for fetching a single frame if data not already loaded if not self._is_initialized: - if isinstance(item, int) and \ - isinstance(self.__fabio_reader.fabio_file(), - fabio.file_series.file_series): + if isinstance(item, int) and isinstance( + self.__fabio_reader.fabio_file(), fabio.file_series.file_series + ): if item < 0: # negative indexing item += len(self) @@ -158,8 +143,7 @@ class RawHeaderData(commonh5.LazyLoadableDataset): self.__fabio_reader = fabio_reader def _create_data(self): - """Initialize hold data by merging all headers of each frames. - """ + """Initialize hold data by merging all headers of each frames.""" headers = [] types = set([]) for fabio_frame in self.__fabio_reader.iter_frames(): @@ -199,8 +183,7 @@ class RawHeaderData(commonh5.LazyLoadableDataset): class MetadataGroup(commonh5.LazyLoadableGroup): - """Abstract class for groups containing a reference to a fabio image. - """ + """Abstract class for groups containing a reference to a fabio image.""" def __init__(self, name, metadata_reader, kind, parent=None, attrs=None): commonh5.LazyLoadableGroup.__init__(self, name, parent, attrs) @@ -220,8 +203,7 @@ class MetadataGroup(commonh5.LazyLoadableGroup): class DetectorGroup(commonh5.LazyLoadableGroup): - """Define the detector group (sub group of instrument) using Fabio data. - """ + """Define the detector group (sub group of instrument) using Fabio data.""" def __init__(self, name, fabio_reader, parent=None, attrs=None): if attrs is None: @@ -241,8 +223,7 @@ class DetectorGroup(commonh5.LazyLoadableGroup): class ImageGroup(commonh5.LazyLoadableGroup): - """Define the image group (sub group of measurement) using Fabio data. - """ + """Define the image group (sub group of measurement) using Fabio data.""" def __init__(self, name, fabio_reader, parent=None, attrs=None): commonh5.LazyLoadableGroup.__init__(self, name, parent, attrs) @@ -281,8 +262,7 @@ class NxDataPreviewGroup(commonh5.LazyLoadableGroup): class SampleGroup(commonh5.LazyLoadableGroup): - """Define the image group (sub group of measurement) using Fabio data. - """ + """Define the image group (sub group of measurement) using Fabio data.""" def __init__(self, name, fabio_reader, parent=None): attrs = {"NXclass": "NXsample"} @@ -309,8 +289,7 @@ class SampleGroup(commonh5.LazyLoadableGroup): class MeasurementGroup(commonh5.LazyLoadableGroup): - """Define the measurement group for fabio file. - """ + """Define the measurement group for fabio file.""" def __init__(self, name, fabio_reader, parent=None, attrs=None): commonh5.LazyLoadableGroup.__init__(self, name, parent, attrs) @@ -369,9 +348,13 @@ class FabioReader(object): 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.") + 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.") + raise TypeError( + "Parameters fabio_image and file_series are mutually exclusive." + ) self.__must_be_closed = False @@ -382,14 +365,18 @@ class FabioReader(object): if isinstance(fabio_image, fabio.fabioimage.FabioImage): self.__fabio_file = fabio_image else: - raise TypeError("FabioImage expected but %s found.", fabio_image.__class__) + 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) + self.__fabio_file = fabio.file_series.file_series(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__) + raise TypeError( + "file_series or list expected but %s found.", file_series.__class__ + ) def close(self): """Close the object, and free up associated resources. @@ -401,10 +388,7 @@ class FabioReader(object): may fail. """ if self.__must_be_closed: - # Make sure the API of fabio provide it a 'close' method - # TODO the test can be removed if fabio version >= 0.8 - if hasattr(self.__fabio_file, "close"): - self.__fabio_file.close() + self.__fabio_file.close() self.__fabio_file = None def fabio_file(self): @@ -428,7 +412,7 @@ class FabioReader(object): 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) + 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): @@ -514,7 +498,9 @@ class FabioReader(object): 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) + old = self._set_vector_normalization( + at_least_32bits=True, signed_type=True + ) else: old = None value = self._convert_metadata_vector(value) @@ -590,7 +576,7 @@ class FabioReader(object): return previous def _normalize_vector_type(self, dtype): - """Normalize the """ + """Normalize the""" if self.__at_least_32bits: if numpy.issubdtype(dtype, numpy.signedinteger): dtype = numpy.result_type(dtype, numpy.uint32) @@ -602,7 +588,7 @@ class FabioReader(object): 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)) + signed = numpy.dtype("%s%i" % ("i", dtype.itemsize)) dtype = numpy.result_type(dtype, signed) return dtype @@ -652,7 +638,7 @@ class FabioReader(object): if result_type.kind == "S": none_value = b"" elif result_type.kind == "U": - none_value = u"" + none_value = "" elif result_type.kind == "f": none_value = numpy.float64("NaN") elif result_type.kind == "i": @@ -692,7 +678,7 @@ class FabioReader(object): # convert to a numpy associative array key_dtype = numpy.min_scalar_type(list(value.keys())) value_dtype = numpy.min_scalar_type(list(value.values())) - associative_type = [('key', key_dtype), ('value', value_dtype)] + associative_type = [("key", key_dtype), ("value", value_dtype)] assert key_dtype.kind != "O" and value_dtype.kind != "O" return numpy.array(list(value.items()), dtype=associative_type) if isinstance(value, numbers.Number): @@ -702,7 +688,7 @@ class FabioReader(object): if isinstance(value, bytes): try: - value = value.decode('utf-8') + value = value.decode("utf-8") except UnicodeDecodeError: return numpy.void(value) @@ -818,7 +804,7 @@ class EdfFabioReader(FabioReader): pos_values = header.get(pos_values_key, "") pos_values = pos_values.split() - result = collections.OrderedDict() + result = {} nbitems = max(len(mnemonic_values), len(pos_values)) for i in range(nbitems): if i < len(mnemonic_values): @@ -874,7 +860,9 @@ class EdfFabioReader(FabioReader): if len(ub_data) > 9: _logger.warning("UB_mne and UB_pos contains more than expected keys.") if len(s_data) > 6: - _logger.warning("sample_mne and sample_pos contains more than expected keys.") + _logger.warning( + "sample_mne and sample_pos contains more than expected keys." + ) data = numpy.array([s_data["U0"], s_data["U1"], s_data["U2"]], dtype=float) unit_cell_abc = data @@ -882,10 +870,16 @@ class EdfFabioReader(FabioReader): data = numpy.array([s_data["U3"], s_data["U4"], s_data["U5"]], dtype=float) unit_cell_alphabetagamma = data - ub_matrix = numpy.array([[ - [ub_data["UB0"], ub_data["UB1"], ub_data["UB2"]], - [ub_data["UB3"], ub_data["UB4"], ub_data["UB5"]], - [ub_data["UB6"], ub_data["UB7"], ub_data["UB8"]]]], dtype=float) + ub_matrix = numpy.array( + [ + [ + [ub_data["UB0"], ub_data["UB1"], ub_data["UB2"]], + [ub_data["UB3"], ub_data["UB4"], ub_data["UB5"]], + [ub_data["UB6"], ub_data["UB7"], ub_data["UB8"]], + ] + ], + dtype=float, + ) self.__unit_cell_abc = unit_cell_abc self.__unit_cell_alphabetagamma = unit_cell_alphabetagamma @@ -939,8 +933,7 @@ class EdfFabioReader(FabioReader): class File(commonh5.File): - """Class which handle a fabio image as a mimick of a h5py.File. - """ + """Class which handle a fabio image as a mimick of a h5py.File.""" def __init__(self, file_name=None, fabio_image=None, file_series=None): """ @@ -953,15 +946,19 @@ class File(commonh5.File): 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) + self.__fabio_reader = self.create_fabio_reader( + file_name, fabio_image, file_series + ) if fabio_image is not None: file_name = fabio_image.filename scan = self.create_scan_group(self.__fabio_reader) - attrs = {"NX_class": "NXroot", - "file_time": datetime.datetime.now().isoformat(), - "creator": "silx %s" % silx_version, - "default": scan.basename} + attrs = { + "NX_class": "NXroot", + "file_time": datetime.datetime.now().isoformat(), + "creator": "silx %s" % silx_version, + "default": scan.basename, + } if file_name is not None: attrs["file_name"] = file_name commonh5.File.__init__(self, name=file_name, attrs=attrs) @@ -981,9 +978,16 @@ class File(commonh5.File): } scan = commonh5.Group("scan_0", attrs=scan_attrs) instrument = commonh5.Group("instrument", attrs={"NX_class": "NXinstrument"}) - measurement = MeasurementGroup("measurement", fabio_reader, attrs={"NX_class": "NXcollection"}) + 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"}) + positioners = MetadataGroup( + "positioners", + fabio_reader, + FabioReader.POSITIONER, + attrs={"NX_class": "NXpositioner"}, + ) raw_header = RawHeaderData("scan_header", fabio_reader, self) detector = DetectorGroup("detector_0", fabio_reader) @@ -1031,7 +1035,7 @@ class File(commonh5.File): elif first_image is not None: use_edf_reader = isinstance(first_image, fabio.edfimage.EdfImage) else: - assert(False) + assert False if use_edf_reader: reader = EdfFabioReader(file_name, fabio_image, file_series) |