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Diffstat (limited to 'silx/io/octaveh5.py')
| -rw-r--r-- | silx/io/octaveh5.py | 171 |
1 files changed, 0 insertions, 171 deletions
diff --git a/silx/io/octaveh5.py b/silx/io/octaveh5.py deleted file mode 100644 index 84fa726..0000000 --- a/silx/io/octaveh5.py +++ /dev/null @@ -1,171 +0,0 @@ -# coding: utf-8 -# /*########################################################################## -# Copyright (C) 2016-2020 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. -# -# ############################################################################*/ -""" -Python h5 module and octave h5 module have different ways to deal with -h5 files. -This module is used to make the link between octave and python using such files. -(python is using a dictionary and octave a struct ) - -This module provides tool to set HDF5 file for fasttomo input. - -Here is an example of a simple read and write : - -.. code-block:: python - :emphasize-lines: 3,5 - - # writing a structure - myStruct = {'MKEEP_MASK': 0.0, 'UNSHARP_SIGMA': 0.80000000000000004 } - writer = Octaveh5().open("my_h5file", 'a') - writer.write('mt_struct_name', myStruct) - - # reading a h5 file - reader = Octaveh5().open("my_h5file") - strucDict = reader.get('mt_struct_name') - -.. note:: These functions depend on the `h5py <http://www.h5py.org/>`_ - library, which is a mandatory dependency for `silx`. - -""" - -import logging -logger = logging.getLogger(__name__) -import numpy as np -import h5py - -__authors__ = ["C. Nemoz", "H. Payno"] -__license__ = "MIT" -__date__ = "05/10/2016" - - -class Octaveh5(object): - """This class allows communication between octave and python using hdf5 format. - """ - - def __init__(self, octave_targetted_version=3.8): - """Constructor - - :param octave_targetted_version: the version of Octave for which we want to write this hdf5 file. - - This is needed because for old Octave version we need to had a hack(adding one extra character) - """ - self.file = None - self.octave_targetted_version = octave_targetted_version - - def open(self, h5file, mode='r'): - """Open the h5 file which has been write by octave - - :param h5file: The path of the file to read - :param mode: the opening mode of the file :'r', 'w'... - """ - try: - self.file = h5py.File(h5file, mode) - return self - except IOError as e: - if mode == 'a': - reason = "\n %s: Can t find or create " % h5file - else: - reason = "\n %s: File not found" % h5file - self.file = None - - logger.info(reason) - raise e - - def get(self, struct_name): - """Read octave equivalent structures in hdf5 file - - :param struct_name: the identification of the top level identity we want to get from an hdf5 structure - :return: the dictionnary of the requested struct. None if can t find it - """ - if self.file is None: - info = "No file currently open" - logger.info(info) - return None - - data_dict = {} - grr = (list(self.file[struct_name].items())[1])[1] - try: - gr_level2 = grr.items() - except AttributeError: - reason = "no gr_level2" - logger.info(reason) - return None - - for key, val in iter(dict(gr_level2).items()): - data_dict[str(key)] = list(val.items())[1][1][()] - - if list(val.items())[0][1][()] != np.string_('sq_string'): - data_dict[str(key)] = float(data_dict[str(key)]) - else: - if list(val.items())[0][1][()] == np.string_('sq_string'): - # in the case the string has been stored as an nd-array of char - if type(data_dict[str(key)]) is np.ndarray: - data_dict[str(key)] = "".join(chr(item) for item in data_dict[str(key)]) - else: - data_dict[str(key)] = data_dict[str(key)].decode('UTF-8') - - # In the case Octave have added an extra character at the end - if self.octave_targetted_version < 3.8: - data_dict[str(key)] = data_dict[str(key)][:-1] - - return data_dict - - def write(self, struct_name, data_dict): - """write data_dict under the group struct_name in the open hdf5 file - - :param struct_name: the identificatioon of the structure to write in the hdf5 - :param data_dict: The python dictionnary containing the informations to write - """ - if self.file is None: - info = "No file currently open" - logger.info(info) - return - - group_l1 = self.file.create_group(struct_name) - group_l1.attrs['OCTAVE_GLOBAL'] = np.uint8(1) - group_l1.attrs['OCTAVE_NEW_FORMAT'] = np.uint8(1) - group_l1.create_dataset("type", data=np.string_('scalar struct'), dtype="|S14") - group_l2 = group_l1.create_group('value') - for ftparams in data_dict: - group_l3 = group_l2.create_group(ftparams) - group_l3.attrs['OCTAVE_NEW_FORMAT'] = np.uint8(1) - if type(data_dict[ftparams]) == str: - group_l3.create_dataset("type", (), data=np.string_('sq_string'), dtype="|S10") - if self.octave_targetted_version < 3.8: - group_l3.create_dataset("value", data=np.string_(data_dict[ftparams] + '0')) - else: - group_l3.create_dataset("value", data=np.string_(data_dict[ftparams])) - else: - group_l3.create_dataset("type", (), data=np.string_('scalar'), dtype="|S7") - group_l3.create_dataset("value", data=data_dict[ftparams]) - - def close(self): - """Close the file after calling read function - """ - if self.file: - self.file.close() - - def __del__(self): - """Destructor - """ - self.close() |