""" Module for reading and writing matlab (TM) .mat files """ # Authors: Travis Oliphant, Matthew Brett from __future__ import division, print_function, absolute_import import numpy as np from scipy.lib.six import string_types from .miobase import get_matfile_version, docfiller from .mio4 import MatFile4Reader, MatFile4Writer from .mio5 import MatFile5Reader, MatFile5Writer __all__ = ['mat_reader_factory', 'loadmat', 'savemat', 'whosmat'] def _open_file(file_like, appendmat): ''' Open `file_like` and return as file-like object ''' if isinstance(file_like, string_types): try: return open(file_like, 'rb') except IOError as e: if appendmat and not file_like.endswith('.mat'): file_like += '.mat' return open(file_like, 'rb') raise IOError(e) # not a string - maybe file-like object try: file_like.read(0) except AttributeError: raise IOError('Reader needs file name or open file-like object') return file_like @docfiller def mat_reader_factory(file_name, appendmat=True, **kwargs): """Create reader for matlab .mat format files Parameters ---------- %(file_arg)s %(append_arg)s %(load_args)s %(struct_arg)s Returns ------- matreader : MatFileReader object Initialized instance of MatFileReader class matching the mat file type detected in `filename`. """ byte_stream = _open_file(file_name, appendmat) mjv, mnv = get_matfile_version(byte_stream) if mjv == 0: return MatFile4Reader(byte_stream, **kwargs) elif mjv == 1: return MatFile5Reader(byte_stream, **kwargs) elif mjv == 2: raise NotImplementedError('Please use HDF reader for matlab v7.3 files') else: raise TypeError('Did not recognize version %s' % mjv) @docfiller def loadmat(file_name, mdict=None, appendmat=True, **kwargs): """ Load MATLAB file Parameters ---------- file_name : str Name of the mat file (do not need .mat extension if appendmat==True) Can also pass open file-like object. m_dict : dict, optional Dictionary in which to insert matfile variables. appendmat : bool, optional True to append the .mat extension to the end of the given filename, if not already present. byte_order : str or None, optional None by default, implying byte order guessed from mat file. Otherwise can be one of ('native', '=', 'little', '<', 'BIG', '>'). mat_dtype : bool, optional If True, return arrays in same dtype as would be loaded into MATLAB (instead of the dtype with which they are saved). squeeze_me : bool, optional Whether to squeeze unit matrix dimensions or not. chars_as_strings : bool, optional Whether to convert char arrays to string arrays. matlab_compatible : bool, optional Returns matrices as would be loaded by MATLAB (implies squeeze_me=False, chars_as_strings=False, mat_dtype=True, struct_as_record=True). struct_as_record : bool, optional Whether to load MATLAB structs as numpy record arrays, or as old-style numpy arrays with dtype=object. Setting this flag to False replicates the behavior of scipy version 0.7.x (returning numpy object arrays). The default setting is True, because it allows easier round-trip load and save of MATLAB files. verify_compressed_data_integrity : bool, optional Whether the length of compressed sequences in the MATLAB file should be checked, to ensure that they are not longer than we expect. It is advisable to enable this (the default) because overlong compressed sequences in MATLAB files generally indicate that the files have experienced some sort of corruption. variable_names : None or sequence If None (the default) - read all variables in file. Otherwise `variable_names` should be a sequence of strings, giving names of the matlab variables to read from the file. The reader will skip any variable with a name not in this sequence, possibly saving some read processing. Returns ------- mat_dict : dict dictionary with variable names as keys, and loaded matrices as values Notes ----- v4 (Level 1.0), v6 and v7 to 7.2 matfiles are supported. You will need an HDF5 python library to read matlab 7.3 format mat files. Because scipy does not supply one, we do not implement the HDF5 / 7.3 interface here. """ variable_names = kwargs.pop('variable_names', None) MR = mat_reader_factory(file_name, appendmat, **kwargs) matfile_dict = MR.get_variables(variable_names) if mdict is not None: mdict.update(matfile_dict) else: mdict = matfile_dict if isinstance(file_name, string_types): MR.mat_stream.close() return mdict @docfiller def savemat(file_name, mdict, appendmat=True, format='5', long_field_names=False, do_compression=False, oned_as='row'): """ Save a dictionary of names and arrays into a MATLAB-style .mat file. This saves the array objects in the given dictionary to a MATLAB- style .mat file. Parameters ---------- file_name : str or file-like object Name of the .mat file (.mat extension not needed if ``appendmat == True``). Can also pass open file_like object. mdict : dict Dictionary from which to save matfile variables. appendmat : bool, optional True (the default) to append the .mat extension to the end of the given filename, if not already present. format : {'5', '4'}, string, optional '5' (the default) for MATLAB 5 and up (to 7.2), '4' for MATLAB 4 .mat files long_field_names : bool, optional False (the default) - maximum field name length in a structure is 31 characters which is the documented maximum length. True - maximum field name length in a structure is 63 characters which works for MATLAB 7.6+ do_compression : bool, optional Whether or not to compress matrices on write. Default is False. oned_as : {'row', 'column'}, optional If 'column', write 1-D numpy arrays as column vectors. If 'row', write 1-D numpy arrays as row vectors. See also -------- mio4.MatFile4Writer mio5.MatFile5Writer """ file_is_string = isinstance(file_name, string_types) if file_is_string: if appendmat and file_name[-4:] != ".mat": file_name = file_name + ".mat" file_stream = open(file_name, 'wb') else: if not hasattr(file_name, 'write'): raise IOError('Writer needs file name or writeable ' 'file-like object') file_stream = file_name if format == '4': if long_field_names: raise ValueError("Long field names are not available for version 4 files") MW = MatFile4Writer(file_stream, oned_as) elif format == '5': MW = MatFile5Writer(file_stream, do_compression=do_compression, unicode_strings=True, long_field_names=long_field_names, oned_as=oned_as) else: raise ValueError("Format should be '4' or '5'") MW.put_variables(mdict) if file_is_string: file_stream.close() @docfiller def whosmat(file_name, appendmat=True, **kwargs): """ List variables inside a MATLAB file .. versionadded:: 0.12.0 Parameters ---------- %(file_arg)s %(append_arg)s %(load_args)s %(struct_arg)s Returns ------- variables : list of tuples A list of tuples, where each tuple holds the matrix name (a string), its shape (tuple of ints), and its data class (a string). Possible data classes are: int8, uint8, int16, uint16, int32, uint32, int64, uint64, single, double, cell, struct, object, char, sparse, function, opaque, logical, unknown. Notes ----- v4 (Level 1.0), v6 and v7 to 7.2 matfiles are supported. You will need an HDF5 python library to read matlab 7.3 format mat files. Because scipy does not supply one, we do not implement the HDF5 / 7.3 interface here. """ ML = mat_reader_factory(file_name, **kwargs) variables = ML.list_variables() if isinstance(file_name, string_types): ML.mat_stream.close() return variables