619 lines
20 KiB
Python
619 lines
20 KiB
Python
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''' Classes for read / write of matlab (TM) 4 files
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'''
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from __future__ import division, print_function, absolute_import
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import sys
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import warnings
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import numpy as np
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from numpy.compat import asbytes, asstr
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import scipy.sparse
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from scipy._lib.six import string_types
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from .miobase import (MatFileReader, docfiller, matdims, read_dtype,
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convert_dtypes, arr_to_chars, arr_dtype_number)
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from .mio_utils import squeeze_element, chars_to_strings
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from functools import reduce
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SYS_LITTLE_ENDIAN = sys.byteorder == 'little'
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miDOUBLE = 0
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miSINGLE = 1
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miINT32 = 2
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miINT16 = 3
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miUINT16 = 4
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miUINT8 = 5
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mdtypes_template = {
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miDOUBLE: 'f8',
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miSINGLE: 'f4',
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miINT32: 'i4',
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miINT16: 'i2',
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miUINT16: 'u2',
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miUINT8: 'u1',
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'header': [('mopt', 'i4'),
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('mrows', 'i4'),
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('ncols', 'i4'),
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('imagf', 'i4'),
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('namlen', 'i4')],
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'U1': 'U1',
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}
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np_to_mtypes = {
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'f8': miDOUBLE,
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'c32': miDOUBLE,
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'c24': miDOUBLE,
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'c16': miDOUBLE,
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'f4': miSINGLE,
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'c8': miSINGLE,
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'i4': miINT32,
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'i2': miINT16,
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'u2': miUINT16,
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'u1': miUINT8,
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'S1': miUINT8,
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}
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# matrix classes
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mxFULL_CLASS = 0
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mxCHAR_CLASS = 1
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mxSPARSE_CLASS = 2
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order_codes = {
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0: '<',
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1: '>',
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2: 'VAX D-float', # !
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3: 'VAX G-float',
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4: 'Cray', # !!
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}
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mclass_info = {
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mxFULL_CLASS: 'double',
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mxCHAR_CLASS: 'char',
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mxSPARSE_CLASS: 'sparse',
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}
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class VarHeader4(object):
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# Mat4 variables never logical or global
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is_logical = False
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is_global = False
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def __init__(self,
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name,
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dtype,
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mclass,
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dims,
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is_complex):
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self.name = name
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self.dtype = dtype
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self.mclass = mclass
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self.dims = dims
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self.is_complex = is_complex
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class VarReader4(object):
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''' Class to read matlab 4 variables '''
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def __init__(self, file_reader):
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self.file_reader = file_reader
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self.mat_stream = file_reader.mat_stream
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self.dtypes = file_reader.dtypes
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self.chars_as_strings = file_reader.chars_as_strings
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self.squeeze_me = file_reader.squeeze_me
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def read_header(self):
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''' Read and return header for variable '''
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data = read_dtype(self.mat_stream, self.dtypes['header'])
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name = self.mat_stream.read(int(data['namlen'])).strip(b'\x00')
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if data['mopt'] < 0 or data['mopt'] > 5000:
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raise ValueError('Mat 4 mopt wrong format, byteswapping problem?')
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M, rest = divmod(data['mopt'], 1000) # order code
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if M not in (0, 1):
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warnings.warn("We do not support byte ordering '%s'; returned "
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"data may be corrupt" % order_codes[M],
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UserWarning)
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O, rest = divmod(rest, 100) # unused, should be 0
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if O != 0:
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raise ValueError('O in MOPT integer should be 0, wrong format?')
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P, rest = divmod(rest, 10) # data type code e.g miDOUBLE (see above)
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T = rest # matrix type code e.g. mxFULL_CLASS (see above)
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dims = (data['mrows'], data['ncols'])
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is_complex = data['imagf'] == 1
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dtype = self.dtypes[P]
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return VarHeader4(
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name,
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dtype,
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T,
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dims,
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is_complex)
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def array_from_header(self, hdr, process=True):
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mclass = hdr.mclass
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if mclass == mxFULL_CLASS:
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arr = self.read_full_array(hdr)
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elif mclass == mxCHAR_CLASS:
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arr = self.read_char_array(hdr)
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if process and self.chars_as_strings:
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arr = chars_to_strings(arr)
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elif mclass == mxSPARSE_CLASS:
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# no current processing (below) makes sense for sparse
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return self.read_sparse_array(hdr)
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else:
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raise TypeError('No reader for class code %s' % mclass)
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if process and self.squeeze_me:
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return squeeze_element(arr)
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return arr
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def read_sub_array(self, hdr, copy=True):
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''' Mat4 read using header `hdr` dtype and dims
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Parameters
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----------
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hdr : object
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object with attributes ``dtype``, ``dims``. dtype is assumed to be
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the correct endianness
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copy : bool, optional
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copies array before return if True (default True)
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(buffer is usually read only)
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Returns
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-------
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arr : ndarray
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of dtype givem by `hdr` ``dtype`` and shape givem by `hdr` ``dims``
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'''
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dt = hdr.dtype
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dims = hdr.dims
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num_bytes = dt.itemsize
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for d in dims:
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num_bytes *= d
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buffer = self.mat_stream.read(int(num_bytes))
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if len(buffer) != num_bytes:
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raise ValueError("Not enough bytes to read matrix '%s'; is this "
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"a badly-formed file? Consider listing matrices "
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"with `whosmat` and loading named matrices with "
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"`variable_names` kwarg to `loadmat`" % hdr.name)
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arr = np.ndarray(shape=dims,
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dtype=dt,
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buffer=buffer,
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order='F')
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if copy:
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arr = arr.copy()
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return arr
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def read_full_array(self, hdr):
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''' Full (rather than sparse) matrix getter
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Read matrix (array) can be real or complex
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Parameters
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----------
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hdr : ``VarHeader4`` instance
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Returns
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-------
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arr : ndarray
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complex array if ``hdr.is_complex`` is True, otherwise a real
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numeric array
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'''
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if hdr.is_complex:
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# avoid array copy to save memory
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res = self.read_sub_array(hdr, copy=False)
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res_j = self.read_sub_array(hdr, copy=False)
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return res + (res_j * 1j)
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return self.read_sub_array(hdr)
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def read_char_array(self, hdr):
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''' latin-1 text matrix (char matrix) reader
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Parameters
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----------
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hdr : ``VarHeader4`` instance
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Returns
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-------
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arr : ndarray
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with dtype 'U1', shape given by `hdr` ``dims``
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'''
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arr = self.read_sub_array(hdr).astype(np.uint8)
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S = arr.tostring().decode('latin-1')
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return np.ndarray(shape=hdr.dims,
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dtype=np.dtype('U1'),
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buffer=np.array(S)).copy()
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def read_sparse_array(self, hdr):
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''' Read and return sparse matrix type
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Parameters
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----------
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hdr : ``VarHeader4`` instance
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Returns
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-------
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arr : ``scipy.sparse.coo_matrix``
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with dtype ``float`` and shape read from the sparse matrix data
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Notes
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-----
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MATLAB 4 real sparse arrays are saved in a N+1 by 3 array format, where
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N is the number of non-zero values. Column 1 values [0:N] are the
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(1-based) row indices of the each non-zero value, column 2 [0:N] are the
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column indices, column 3 [0:N] are the (real) values. The last values
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[-1,0:2] of the rows, column indices are shape[0] and shape[1]
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respectively of the output matrix. The last value for the values column
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is a padding 0. mrows and ncols values from the header give the shape of
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the stored matrix, here [N+1, 3]. Complex data is saved as a 4 column
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matrix, where the fourth column contains the imaginary component; the
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last value is again 0. Complex sparse data do *not* have the header
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``imagf`` field set to True; the fact that the data are complex is only
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detectable because there are 4 storage columns
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'''
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res = self.read_sub_array(hdr)
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tmp = res[:-1,:]
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# All numbers are float64 in Matlab, but Scipy sparse expects int shape
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dims = (int(res[-1,0]), int(res[-1,1]))
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I = np.ascontiguousarray(tmp[:,0],dtype='intc') # fixes byte order also
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J = np.ascontiguousarray(tmp[:,1],dtype='intc')
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I -= 1 # for 1-based indexing
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J -= 1
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if res.shape[1] == 3:
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V = np.ascontiguousarray(tmp[:,2],dtype='float')
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else:
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V = np.ascontiguousarray(tmp[:,2],dtype='complex')
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V.imag = tmp[:,3]
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return scipy.sparse.coo_matrix((V,(I,J)), dims)
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def shape_from_header(self, hdr):
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'''Read the shape of the array described by the header.
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The file position after this call is unspecified.
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'''
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mclass = hdr.mclass
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if mclass == mxFULL_CLASS:
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shape = tuple(map(int, hdr.dims))
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elif mclass == mxCHAR_CLASS:
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shape = tuple(map(int, hdr.dims))
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if self.chars_as_strings:
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shape = shape[:-1]
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elif mclass == mxSPARSE_CLASS:
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dt = hdr.dtype
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dims = hdr.dims
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if not (len(dims) == 2 and dims[0] >= 1 and dims[1] >= 1):
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return ()
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# Read only the row and column counts
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self.mat_stream.seek(dt.itemsize * (dims[0] - 1), 1)
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rows = np.ndarray(shape=(1,), dtype=dt,
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buffer=self.mat_stream.read(dt.itemsize))
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self.mat_stream.seek(dt.itemsize * (dims[0] - 1), 1)
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cols = np.ndarray(shape=(1,), dtype=dt,
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buffer=self.mat_stream.read(dt.itemsize))
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shape = (int(rows), int(cols))
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else:
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raise TypeError('No reader for class code %s' % mclass)
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if self.squeeze_me:
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shape = tuple([x for x in shape if x != 1])
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return shape
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class MatFile4Reader(MatFileReader):
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''' Reader for Mat4 files '''
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@docfiller
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def __init__(self, mat_stream, *args, **kwargs):
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''' Initialize matlab 4 file reader
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%(matstream_arg)s
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%(load_args)s
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'''
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super(MatFile4Reader, self).__init__(mat_stream, *args, **kwargs)
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self._matrix_reader = None
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def guess_byte_order(self):
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self.mat_stream.seek(0)
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mopt = read_dtype(self.mat_stream, np.dtype('i4'))
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self.mat_stream.seek(0)
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if mopt == 0:
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return '<'
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if mopt < 0 or mopt > 5000:
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# Number must have been byteswapped
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return SYS_LITTLE_ENDIAN and '>' or '<'
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# Not byteswapped
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return SYS_LITTLE_ENDIAN and '<' or '>'
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def initialize_read(self):
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''' Run when beginning read of variables
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Sets up readers from parameters in `self`
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'''
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self.dtypes = convert_dtypes(mdtypes_template, self.byte_order)
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self._matrix_reader = VarReader4(self)
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def read_var_header(self):
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''' Read and return header, next position
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Parameters
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----------
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None
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Returns
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-------
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header : object
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object that can be passed to self.read_var_array, and that
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has attributes ``name`` and ``is_global``
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next_position : int
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position in stream of next variable
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'''
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hdr = self._matrix_reader.read_header()
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n = reduce(lambda x, y: x*y, hdr.dims, 1) # fast product
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remaining_bytes = hdr.dtype.itemsize * n
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if hdr.is_complex and not hdr.mclass == mxSPARSE_CLASS:
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remaining_bytes *= 2
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next_position = self.mat_stream.tell() + remaining_bytes
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return hdr, next_position
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def read_var_array(self, header, process=True):
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''' Read array, given `header`
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Parameters
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----------
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header : header object
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object with fields defining variable header
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process : {True, False}, optional
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If True, apply recursive post-processing during loading of array.
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Returns
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-------
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arr : array
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||
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array with post-processing applied or not according to
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`process`.
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'''
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return self._matrix_reader.array_from_header(header, process)
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def get_variables(self, variable_names=None):
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''' get variables from stream as dictionary
|
||
|
|
|
||
|
|
Parameters
|
||
|
|
----------
|
||
|
|
variable_names : None or str or sequence of str, optional
|
||
|
|
variable name, or sequence of variable names to get from Mat file /
|
||
|
|
file stream. If None, then get all variables in file
|
||
|
|
'''
|
||
|
|
if isinstance(variable_names, string_types):
|
||
|
|
variable_names = [variable_names]
|
||
|
|
elif variable_names is not None:
|
||
|
|
variable_names = list(variable_names)
|
||
|
|
self.mat_stream.seek(0)
|
||
|
|
# set up variable reader
|
||
|
|
self.initialize_read()
|
||
|
|
mdict = {}
|
||
|
|
while not self.end_of_stream():
|
||
|
|
hdr, next_position = self.read_var_header()
|
||
|
|
name = asstr(hdr.name)
|
||
|
|
if variable_names is not None and name not in variable_names:
|
||
|
|
self.mat_stream.seek(next_position)
|
||
|
|
continue
|
||
|
|
mdict[name] = self.read_var_array(hdr)
|
||
|
|
self.mat_stream.seek(next_position)
|
||
|
|
if variable_names is not None:
|
||
|
|
variable_names.remove(name)
|
||
|
|
if len(variable_names) == 0:
|
||
|
|
break
|
||
|
|
return mdict
|
||
|
|
|
||
|
|
def list_variables(self):
|
||
|
|
''' list variables from stream '''
|
||
|
|
self.mat_stream.seek(0)
|
||
|
|
# set up variable reader
|
||
|
|
self.initialize_read()
|
||
|
|
vars = []
|
||
|
|
while not self.end_of_stream():
|
||
|
|
hdr, next_position = self.read_var_header()
|
||
|
|
name = asstr(hdr.name)
|
||
|
|
shape = self._matrix_reader.shape_from_header(hdr)
|
||
|
|
info = mclass_info.get(hdr.mclass, 'unknown')
|
||
|
|
vars.append((name, shape, info))
|
||
|
|
|
||
|
|
self.mat_stream.seek(next_position)
|
||
|
|
return vars
|
||
|
|
|
||
|
|
|
||
|
|
def arr_to_2d(arr, oned_as='row'):
|
||
|
|
''' Make ``arr`` exactly two dimensional
|
||
|
|
|
||
|
|
If `arr` has more than 2 dimensions, raise a ValueError
|
||
|
|
|
||
|
|
Parameters
|
||
|
|
----------
|
||
|
|
arr : array
|
||
|
|
oned_as : {'row', 'column'}, optional
|
||
|
|
Whether to reshape 1D vectors as row vectors or column vectors.
|
||
|
|
See documentation for ``matdims`` for more detail
|
||
|
|
|
||
|
|
Returns
|
||
|
|
-------
|
||
|
|
arr2d : array
|
||
|
|
2D version of the array
|
||
|
|
'''
|
||
|
|
dims = matdims(arr, oned_as)
|
||
|
|
if len(dims) > 2:
|
||
|
|
raise ValueError('Matlab 4 files cannot save arrays with more than '
|
||
|
|
'2 dimensions')
|
||
|
|
return arr.reshape(dims)
|
||
|
|
|
||
|
|
|
||
|
|
class VarWriter4(object):
|
||
|
|
def __init__(self, file_writer):
|
||
|
|
self.file_stream = file_writer.file_stream
|
||
|
|
self.oned_as = file_writer.oned_as
|
||
|
|
|
||
|
|
def write_bytes(self, arr):
|
||
|
|
self.file_stream.write(arr.tostring(order='F'))
|
||
|
|
|
||
|
|
def write_string(self, s):
|
||
|
|
self.file_stream.write(s)
|
||
|
|
|
||
|
|
def write_header(self, name, shape, P=miDOUBLE, T=mxFULL_CLASS, imagf=0):
|
||
|
|
''' Write header for given data options
|
||
|
|
|
||
|
|
Parameters
|
||
|
|
----------
|
||
|
|
name : str
|
||
|
|
name of variable
|
||
|
|
shape : sequence
|
||
|
|
Shape of array as it will be read in matlab
|
||
|
|
P : int, optional
|
||
|
|
code for mat4 data type, one of ``miDOUBLE, miSINGLE, miINT32,
|
||
|
|
miINT16, miUINT16, miUINT8``
|
||
|
|
T : int, optional
|
||
|
|
code for mat4 matrix class, one of ``mxFULL_CLASS, mxCHAR_CLASS,
|
||
|
|
mxSPARSE_CLASS``
|
||
|
|
imagf : int, optional
|
||
|
|
flag indicating complex
|
||
|
|
'''
|
||
|
|
header = np.empty((), mdtypes_template['header'])
|
||
|
|
M = not SYS_LITTLE_ENDIAN
|
||
|
|
O = 0
|
||
|
|
header['mopt'] = (M * 1000 +
|
||
|
|
O * 100 +
|
||
|
|
P * 10 +
|
||
|
|
T)
|
||
|
|
header['mrows'] = shape[0]
|
||
|
|
header['ncols'] = shape[1]
|
||
|
|
header['imagf'] = imagf
|
||
|
|
header['namlen'] = len(name) + 1
|
||
|
|
self.write_bytes(header)
|
||
|
|
self.write_string(asbytes(name + '\0'))
|
||
|
|
|
||
|
|
def write(self, arr, name):
|
||
|
|
''' Write matrix `arr`, with name `name`
|
||
|
|
|
||
|
|
Parameters
|
||
|
|
----------
|
||
|
|
arr : array_like
|
||
|
|
array to write
|
||
|
|
name : str
|
||
|
|
name in matlab workspace
|
||
|
|
'''
|
||
|
|
# we need to catch sparse first, because np.asarray returns an
|
||
|
|
# an object array for scipy.sparse
|
||
|
|
if scipy.sparse.issparse(arr):
|
||
|
|
self.write_sparse(arr, name)
|
||
|
|
return
|
||
|
|
arr = np.asarray(arr)
|
||
|
|
dt = arr.dtype
|
||
|
|
if not dt.isnative:
|
||
|
|
arr = arr.astype(dt.newbyteorder('='))
|
||
|
|
dtt = dt.type
|
||
|
|
if dtt is np.object_:
|
||
|
|
raise TypeError('Cannot save object arrays in Mat4')
|
||
|
|
elif dtt is np.void:
|
||
|
|
raise TypeError('Cannot save void type arrays')
|
||
|
|
elif dtt in (np.unicode_, np.string_):
|
||
|
|
self.write_char(arr, name)
|
||
|
|
return
|
||
|
|
self.write_numeric(arr, name)
|
||
|
|
|
||
|
|
def write_numeric(self, arr, name):
|
||
|
|
arr = arr_to_2d(arr, self.oned_as)
|
||
|
|
imagf = arr.dtype.kind == 'c'
|
||
|
|
try:
|
||
|
|
P = np_to_mtypes[arr.dtype.str[1:]]
|
||
|
|
except KeyError:
|
||
|
|
if imagf:
|
||
|
|
arr = arr.astype('c128')
|
||
|
|
else:
|
||
|
|
arr = arr.astype('f8')
|
||
|
|
P = miDOUBLE
|
||
|
|
self.write_header(name,
|
||
|
|
arr.shape,
|
||
|
|
P=P,
|
||
|
|
T=mxFULL_CLASS,
|
||
|
|
imagf=imagf)
|
||
|
|
if imagf:
|
||
|
|
self.write_bytes(arr.real)
|
||
|
|
self.write_bytes(arr.imag)
|
||
|
|
else:
|
||
|
|
self.write_bytes(arr)
|
||
|
|
|
||
|
|
def write_char(self, arr, name):
|
||
|
|
arr = arr_to_chars(arr)
|
||
|
|
arr = arr_to_2d(arr, self.oned_as)
|
||
|
|
dims = arr.shape
|
||
|
|
self.write_header(
|
||
|
|
name,
|
||
|
|
dims,
|
||
|
|
P=miUINT8,
|
||
|
|
T=mxCHAR_CLASS)
|
||
|
|
if arr.dtype.kind == 'U':
|
||
|
|
# Recode unicode to latin1
|
||
|
|
n_chars = np.product(dims)
|
||
|
|
st_arr = np.ndarray(shape=(),
|
||
|
|
dtype=arr_dtype_number(arr, n_chars),
|
||
|
|
buffer=arr)
|
||
|
|
st = st_arr.item().encode('latin-1')
|
||
|
|
arr = np.ndarray(shape=dims, dtype='S1', buffer=st)
|
||
|
|
self.write_bytes(arr)
|
||
|
|
|
||
|
|
def write_sparse(self, arr, name):
|
||
|
|
''' Sparse matrices are 2D
|
||
|
|
|
||
|
|
See docstring for VarReader4.read_sparse_array
|
||
|
|
'''
|
||
|
|
A = arr.tocoo() # convert to sparse COO format (ijv)
|
||
|
|
imagf = A.dtype.kind == 'c'
|
||
|
|
ijv = np.zeros((A.nnz + 1, 3+imagf), dtype='f8')
|
||
|
|
ijv[:-1,0] = A.row
|
||
|
|
ijv[:-1,1] = A.col
|
||
|
|
ijv[:-1,0:2] += 1 # 1 based indexing
|
||
|
|
if imagf:
|
||
|
|
ijv[:-1,2] = A.data.real
|
||
|
|
ijv[:-1,3] = A.data.imag
|
||
|
|
else:
|
||
|
|
ijv[:-1,2] = A.data
|
||
|
|
ijv[-1,0:2] = A.shape
|
||
|
|
self.write_header(
|
||
|
|
name,
|
||
|
|
ijv.shape,
|
||
|
|
P=miDOUBLE,
|
||
|
|
T=mxSPARSE_CLASS)
|
||
|
|
self.write_bytes(ijv)
|
||
|
|
|
||
|
|
|
||
|
|
class MatFile4Writer(object):
|
||
|
|
''' Class for writing matlab 4 format files '''
|
||
|
|
def __init__(self, file_stream, oned_as=None):
|
||
|
|
self.file_stream = file_stream
|
||
|
|
if oned_as is None:
|
||
|
|
oned_as = 'row'
|
||
|
|
self.oned_as = oned_as
|
||
|
|
self._matrix_writer = None
|
||
|
|
|
||
|
|
def put_variables(self, mdict, write_header=None):
|
||
|
|
''' Write variables in `mdict` to stream
|
||
|
|
|
||
|
|
Parameters
|
||
|
|
----------
|
||
|
|
mdict : mapping
|
||
|
|
mapping with method ``items`` return name, contents pairs
|
||
|
|
where ``name`` which will appeak in the matlab workspace in
|
||
|
|
file load, and ``contents`` is something writeable to a
|
||
|
|
matlab file, such as a numpy array.
|
||
|
|
write_header : {None, True, False}
|
||
|
|
If True, then write the matlab file header before writing the
|
||
|
|
variables. If None (the default) then write the file header
|
||
|
|
if we are at position 0 in the stream. By setting False
|
||
|
|
here, and setting the stream position to the end of the file,
|
||
|
|
you can append variables to a matlab file
|
||
|
|
'''
|
||
|
|
# there is no header for a matlab 4 mat file, so we ignore the
|
||
|
|
# ``write_header`` input argument. It's there for compatibility
|
||
|
|
# with the matlab 5 version of this method
|
||
|
|
self._matrix_writer = VarWriter4(self)
|
||
|
|
for name, var in mdict.items():
|
||
|
|
self._matrix_writer.write(var, name)
|