diff options
Diffstat (limited to 'silx/io/utils.py')
| -rw-r--r-- | silx/io/utils.py | 138 |
1 files changed, 107 insertions, 31 deletions
diff --git a/silx/io/utils.py b/silx/io/utils.py index 654bfe3..930c84e 100644 --- a/silx/io/utils.py +++ b/silx/io/utils.py @@ -1,6 +1,6 @@ # coding: utf-8 # /*########################################################################## -# Copyright (C) 2016-2018 European Synchrotron Radiation Facility +# Copyright (C) 2016-2019 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 @@ -27,29 +27,26 @@ __authors__ = ["P. Knobel", "V. Valls"] __license__ = "MIT" __date__ = "18/04/2018" -import numpy + +import enum import os.path import sys import time import logging import collections +import numpy +import six + 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 = None - h5py_import_error = e +import h5py try: import h5pyd except ImportError as e: h5pyd = None - h5py_import_error = e logger = logging.getLogger(__name__) @@ -88,10 +85,9 @@ def supported_extensions(flat_formats=True): 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", "*.hdf5"]) - formats["NeXus files"] = set(["*.nx", "*.nxs", "*.h5", "*.hdf", "*.hdf5"]) + formats = collections.OrderedDict() + formats["HDF5 files"] = set(["*.h5", "*.hdf", "*.hdf5"]) + formats["NeXus files"] = set(["*.nx", "*.nxs", "*.h5", "*.hdf", "*.hdf5"]) formats["NeXus layout from spec files"] = set(["*.dat", "*.spec", "*.mca"]) if flat_formats: try: @@ -106,6 +102,7 @@ def supported_extensions(flat_formats=True): extensions.append("*.npy") formats["Numpy binary files"] = set(extensions) + formats["Coherent X-Ray Imaging files"] = set(["*.cxi"]) return formats @@ -405,10 +402,6 @@ def h5ls(h5group, lvl=0): .. note:: This function requires `h5py <http://www.h5py.org/>`_ to be installed. """ - if h5py is None: - logger.error("h5ls requires h5py") - raise h5py_import_error - h5repr = '' if is_group(h5group): h5f = h5group @@ -466,9 +459,8 @@ def _open_local_file(filename): debugging_info.append((sys.exc_info(), "File '%s' can't be read as a numpy file." % filename)) - if h5py is not None: - if h5py.is_hdf5(filename): - return h5py.File(filename, "r") + if h5py.is_hdf5(filename): + return h5py.File(filename, "r") try: from . import fabioh5 @@ -616,13 +608,12 @@ def _get_classes_type(): _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 + _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 if h5pyd is not None: _CLASSES_TYPE[h5pyd.Dataset] = H5Type.DATASET @@ -695,9 +686,6 @@ 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 type_ = get_h5_class(obj) @@ -836,3 +824,91 @@ def get_data(url): raise ValueError("Scheme '%s' not supported" % url.scheme()) return data + + +def rawfile_to_h5_external_dataset(bin_file, output_url, shape, dtype, + overwrite=False): + """ + Create a HDF5 dataset at `output_url` pointing to the given vol_file. + + Either `shape` or `info_file` must be provided. + + :param str bin_file: Path to the .vol file + :param DataUrl output_url: HDF5 URL where to save the external dataset + :param tuple shape: Shape of the volume + :param numpy.dtype dtype: Data type of the volume elements (default: float32) + :param bool overwrite: True to allow overwriting (default: False). + """ + assert isinstance(output_url, silx.io.url.DataUrl) + assert isinstance(shape, (tuple, list)) + v_majeur, v_mineur, v_micro = h5py.version.version.split('.') + if v_majeur <= '2' and v_mineur < '9': + raise Exception('h5py >= 2.9 should be installed to access the ' + 'external feature.') + + with h5py.File(output_url.file_path()) as _h5_file: + if output_url.data_path() in _h5_file: + if overwrite is False: + raise ValueError('data_path already exists') + else: + logger.warning('will overwrite path %s' % output_url.data_path()) + del _h5_file[output_url.data_path()] + external = [(bin_file, 0, h5py.h5f.UNLIMITED)] + _h5_file.create_dataset(output_url.data_path(), + shape, + dtype=dtype, + external=external) + + +def vol_to_h5_external_dataset(vol_file, output_url, info_file=None, + vol_dtype=numpy.float32, overwrite=False): + """ + Create a HDF5 dataset at `output_url` pointing to the given vol_file. + + If the vol_file.info containing the shape is not on the same folder as the + vol-file then you should specify her location. + + :param str vol_file: Path to the .vol file + :param DataUrl output_url: HDF5 URL where to save the external dataset + :param Union[str,None] info_file: + .vol.info file name written by pyhst and containing the shape information + :param numpy.dtype vol_dtype: Data type of the volume elements (default: float32) + :param bool overwrite: True to allow overwriting (default: False). + :raises ValueError: If fails to read shape from the .vol.info file + """ + _info_file = info_file + if _info_file is None: + _info_file = vol_file + '.info' + if not os.path.exists(_info_file): + logger.error('info_file not given and %s does not exists, please' + 'specify .vol.info file' % _info_file) + return + + def info_file_to_dict(): + ddict = {} + with builtin_open(info_file, "r") as _file: + lines = _file.readlines() + for line in lines: + if not '=' in line: + continue + l = line.rstrip().replace(' ', '') + l = l.split('#')[0] + key, value = l.split('=') + ddict[key.lower()] = value + return ddict + + ddict = info_file_to_dict() + if 'num_x' not in ddict or 'num_y' not in ddict or 'num_z' not in ddict: + raise ValueError( + 'Unable to retrieve volume shape from %s' % info_file) + + dimX = int(ddict['num_x']) + dimY = int(ddict['num_y']) + dimZ = int(ddict['num_z']) + shape = (dimZ, dimY, dimX) + + return rawfile_to_h5_external_dataset(bin_file=vol_file, + output_url=output_url, + shape=shape, + dtype=vol_dtype, + overwrite=overwrite) |