997 lines
32 KiB
Python
997 lines
32 KiB
Python
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"""
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Matrix Market I/O in Python.
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See http://math.nist.gov/MatrixMarket/formats.html
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for information about the Matrix Market format.
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"""
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#
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# Author: Pearu Peterson <pearu@cens.ioc.ee>
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# Created: October, 2004
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#
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# References:
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# http://math.nist.gov/MatrixMarket/
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#
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import os
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import numpy as np
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from numpy import (asarray, real, imag, conj, zeros, ndarray, concatenate,
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ones, can_cast)
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from scipy.sparse import coo_matrix, isspmatrix
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__all__ = ['mminfo', 'mmread', 'mmwrite', 'MMFile']
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# -----------------------------------------------------------------------------
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def asstr(s):
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if isinstance(s, bytes):
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return s.decode('latin1')
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return str(s)
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def mminfo(source):
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"""
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Return size and storage parameters from Matrix Market file-like 'source'.
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Parameters
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----------
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source : str or file-like
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Matrix Market filename (extension .mtx) or open file-like object
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Returns
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-------
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rows : int
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Number of matrix rows.
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cols : int
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Number of matrix columns.
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entries : int
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Number of non-zero entries of a sparse matrix
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or rows*cols for a dense matrix.
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format : str
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Either 'coordinate' or 'array'.
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field : str
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Either 'real', 'complex', 'pattern', or 'integer'.
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symmetry : str
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Either 'general', 'symmetric', 'skew-symmetric', or 'hermitian'.
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Examples
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--------
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>>> from io import StringIO
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>>> from scipy.io import mminfo
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>>> text = '''%%MatrixMarket matrix coordinate real general
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... 5 5 7
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... 2 3 1.0
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... 3 4 2.0
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... 3 5 3.0
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... 4 1 4.0
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... 4 2 5.0
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... 4 3 6.0
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... 4 4 7.0
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... '''
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``mminfo(source)`` returns the number of rows, number of columns,
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format, field type and symmetry attribute of the source file.
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>>> mminfo(StringIO(text))
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(5, 5, 7, 'coordinate', 'real', 'general')
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"""
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return MMFile.info(source)
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# -----------------------------------------------------------------------------
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def mmread(source):
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"""
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Reads the contents of a Matrix Market file-like 'source' into a matrix.
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Parameters
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----------
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source : str or file-like
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Matrix Market filename (extensions .mtx, .mtz.gz)
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or open file-like object.
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Returns
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-------
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a : ndarray or coo_matrix
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Dense or sparse matrix depending on the matrix format in the
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Matrix Market file.
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Examples
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--------
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>>> from io import StringIO
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>>> from scipy.io import mmread
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>>> text = '''%%MatrixMarket matrix coordinate real general
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... 5 5 7
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... 2 3 1.0
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... 3 4 2.0
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... 3 5 3.0
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... 4 1 4.0
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... 4 2 5.0
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... 4 3 6.0
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... 4 4 7.0
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... '''
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``mmread(source)`` returns the data as sparse matrix in COO format.
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>>> m = mmread(StringIO(text))
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>>> m
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<5x5 sparse matrix of type '<class 'numpy.float64'>'
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with 7 stored elements in COOrdinate format>
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>>> m.A
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array([[0., 0., 0., 0., 0.],
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[0., 0., 1., 0., 0.],
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[0., 0., 0., 2., 3.],
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[4., 5., 6., 7., 0.],
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[0., 0., 0., 0., 0.]])
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"""
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return MMFile().read(source)
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# -----------------------------------------------------------------------------
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def mmwrite(target, a, comment='', field=None, precision=None, symmetry=None):
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r"""
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Writes the sparse or dense array `a` to Matrix Market file-like `target`.
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Parameters
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----------
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target : str or file-like
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Matrix Market filename (extension .mtx) or open file-like object.
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a : array like
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Sparse or dense 2-D array.
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comment : str, optional
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Comments to be prepended to the Matrix Market file.
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field : None or str, optional
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Either 'real', 'complex', 'pattern', or 'integer'.
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precision : None or int, optional
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Number of digits to display for real or complex values.
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symmetry : None or str, optional
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Either 'general', 'symmetric', 'skew-symmetric', or 'hermitian'.
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If symmetry is None the symmetry type of 'a' is determined by its
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values.
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Returns
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-------
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None
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Examples
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--------
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>>> from io import BytesIO
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>>> import numpy as np
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>>> from scipy.sparse import coo_matrix
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>>> from scipy.io import mmwrite
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Write a small NumPy array to a matrix market file. The file will be
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written in the ``'array'`` format.
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>>> a = np.array([[1.0, 0, 0, 0], [0, 2.5, 0, 6.25]])
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>>> target = BytesIO()
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>>> mmwrite(target, a)
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>>> print(target.getvalue().decode('latin1'))
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%%MatrixMarket matrix array real general
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%
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2 4
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1.0000000000000000e+00
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0.0000000000000000e+00
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0.0000000000000000e+00
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2.5000000000000000e+00
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0.0000000000000000e+00
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0.0000000000000000e+00
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0.0000000000000000e+00
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6.2500000000000000e+00
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Add a comment to the output file, and set the precision to 3.
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>>> target = BytesIO()
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>>> mmwrite(target, a, comment='\n Some test data.\n', precision=3)
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>>> print(target.getvalue().decode('latin1'))
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%%MatrixMarket matrix array real general
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%
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% Some test data.
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%
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2 4
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1.000e+00
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0.000e+00
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0.000e+00
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2.500e+00
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0.000e+00
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0.000e+00
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0.000e+00
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6.250e+00
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Convert to a sparse matrix before calling ``mmwrite``. This will
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result in the output format being ``'coordinate'`` rather than
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``'array'``.
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>>> target = BytesIO()
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>>> mmwrite(target, coo_matrix(a), precision=3)
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>>> print(target.getvalue().decode('latin1'))
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%%MatrixMarket matrix coordinate real general
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%
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2 4 3
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1 1 1.00e+00
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2 2 2.50e+00
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2 4 6.25e+00
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Write a complex Hermitian array to a matrix market file. Note that
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only six values are actually written to the file; the other values
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are implied by the symmetry.
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>>> z = np.array([[3, 1+2j, 4-3j], [1-2j, 1, -5j], [4+3j, 5j, 2.5]])
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>>> z
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array([[ 3. +0.j, 1. +2.j, 4. -3.j],
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[ 1. -2.j, 1. +0.j, -0. -5.j],
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[ 4. +3.j, 0. +5.j, 2.5+0.j]])
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>>> target = BytesIO()
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>>> mmwrite(target, z, precision=2)
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>>> print(target.getvalue().decode('latin1'))
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%%MatrixMarket matrix array complex hermitian
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%
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3 3
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3.00e+00 0.00e+00
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1.00e+00 -2.00e+00
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4.00e+00 3.00e+00
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1.00e+00 0.00e+00
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0.00e+00 5.00e+00
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2.50e+00 0.00e+00
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"""
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MMFile().write(target, a, comment, field, precision, symmetry)
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###############################################################################
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class MMFile:
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__slots__ = ('_rows',
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'_cols',
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'_entries',
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'_format',
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'_field',
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'_symmetry')
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@property
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def rows(self):
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return self._rows
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@property
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def cols(self):
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return self._cols
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@property
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def entries(self):
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return self._entries
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@property
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def format(self):
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return self._format
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@property
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def field(self):
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return self._field
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@property
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def symmetry(self):
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return self._symmetry
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@property
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def has_symmetry(self):
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return self._symmetry in (self.SYMMETRY_SYMMETRIC,
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self.SYMMETRY_SKEW_SYMMETRIC,
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self.SYMMETRY_HERMITIAN)
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# format values
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FORMAT_COORDINATE = 'coordinate'
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FORMAT_ARRAY = 'array'
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FORMAT_VALUES = (FORMAT_COORDINATE, FORMAT_ARRAY)
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@classmethod
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def _validate_format(self, format):
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if format not in self.FORMAT_VALUES:
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raise ValueError('unknown format type %s, must be one of %s' %
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(format, self.FORMAT_VALUES))
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# field values
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FIELD_INTEGER = 'integer'
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FIELD_UNSIGNED = 'unsigned-integer'
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FIELD_REAL = 'real'
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FIELD_COMPLEX = 'complex'
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FIELD_PATTERN = 'pattern'
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FIELD_VALUES = (FIELD_INTEGER, FIELD_UNSIGNED, FIELD_REAL, FIELD_COMPLEX,
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FIELD_PATTERN)
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@classmethod
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def _validate_field(self, field):
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if field not in self.FIELD_VALUES:
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raise ValueError('unknown field type %s, must be one of %s' %
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(field, self.FIELD_VALUES))
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# symmetry values
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SYMMETRY_GENERAL = 'general'
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SYMMETRY_SYMMETRIC = 'symmetric'
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SYMMETRY_SKEW_SYMMETRIC = 'skew-symmetric'
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SYMMETRY_HERMITIAN = 'hermitian'
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SYMMETRY_VALUES = (SYMMETRY_GENERAL, SYMMETRY_SYMMETRIC,
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SYMMETRY_SKEW_SYMMETRIC, SYMMETRY_HERMITIAN)
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@classmethod
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def _validate_symmetry(self, symmetry):
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if symmetry not in self.SYMMETRY_VALUES:
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raise ValueError('unknown symmetry type %s, must be one of %s' %
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(symmetry, self.SYMMETRY_VALUES))
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DTYPES_BY_FIELD = {FIELD_INTEGER: 'intp',
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FIELD_UNSIGNED: 'uint64',
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FIELD_REAL: 'd',
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FIELD_COMPLEX: 'D',
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FIELD_PATTERN: 'd'}
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# -------------------------------------------------------------------------
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@staticmethod
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def reader():
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pass
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# -------------------------------------------------------------------------
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@staticmethod
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def writer():
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pass
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# -------------------------------------------------------------------------
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@classmethod
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def info(self, source):
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"""
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Return size, storage parameters from Matrix Market file-like 'source'.
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Parameters
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|
|
----------
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|
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source : str or file-like
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|
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Matrix Market filename (extension .mtx) or open file-like object
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Returns
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-------
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rows : int
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Number of matrix rows.
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cols : int
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Number of matrix columns.
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entries : int
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Number of non-zero entries of a sparse matrix
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or rows*cols for a dense matrix.
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format : str
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Either 'coordinate' or 'array'.
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field : str
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Either 'real', 'complex', 'pattern', or 'integer'.
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symmetry : str
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Either 'general', 'symmetric', 'skew-symmetric', or 'hermitian'.
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"""
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stream, close_it = self._open(source)
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try:
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# read and validate header line
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line = stream.readline()
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mmid, matrix, format, field, symmetry = \
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[asstr(part.strip()) for part in line.split()]
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if not mmid.startswith('%%MatrixMarket'):
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raise ValueError('source is not in Matrix Market format')
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if not matrix.lower() == 'matrix':
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raise ValueError("Problem reading file header: " + line)
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# http://math.nist.gov/MatrixMarket/formats.html
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if format.lower() == 'array':
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format = self.FORMAT_ARRAY
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elif format.lower() == 'coordinate':
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format = self.FORMAT_COORDINATE
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# skip comments
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# line.startswith('%')
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while line and line[0] in ['%', 37]:
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line = stream.readline()
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# skip empty lines
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while not line.strip():
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line = stream.readline()
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split_line = line.split()
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if format == self.FORMAT_ARRAY:
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if not len(split_line) == 2:
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raise ValueError("Header line not of length 2: " +
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line.decode('ascii'))
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rows, cols = map(int, split_line)
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||
|
|
entries = rows * cols
|
||
|
|
else:
|
||
|
|
if not len(split_line) == 3:
|
||
|
|
raise ValueError("Header line not of length 3: " +
|
||
|
|
line.decode('ascii'))
|
||
|
|
rows, cols, entries = map(int, split_line)
|
||
|
|
|
||
|
|
return (rows, cols, entries, format, field.lower(),
|
||
|
|
symmetry.lower())
|
||
|
|
|
||
|
|
finally:
|
||
|
|
if close_it:
|
||
|
|
stream.close()
|
||
|
|
|
||
|
|
# -------------------------------------------------------------------------
|
||
|
|
@staticmethod
|
||
|
|
def _open(filespec, mode='rb'):
|
||
|
|
""" Return an open file stream for reading based on source.
|
||
|
|
|
||
|
|
If source is a file name, open it (after trying to find it with mtx and
|
||
|
|
gzipped mtx extensions). Otherwise, just return source.
|
||
|
|
|
||
|
|
Parameters
|
||
|
|
----------
|
||
|
|
filespec : str or file-like
|
||
|
|
String giving file name or file-like object
|
||
|
|
mode : str, optional
|
||
|
|
Mode with which to open file, if `filespec` is a file name.
|
||
|
|
|
||
|
|
Returns
|
||
|
|
-------
|
||
|
|
fobj : file-like
|
||
|
|
Open file-like object.
|
||
|
|
close_it : bool
|
||
|
|
True if the calling function should close this file when done,
|
||
|
|
false otherwise.
|
||
|
|
"""
|
||
|
|
# If 'filespec' is path-like (str, pathlib.Path, os.DirEntry, other class
|
||
|
|
# implementing a '__fspath__' method), try to convert it to str. If this
|
||
|
|
# fails by throwing a 'TypeError', assume it's an open file handle and
|
||
|
|
# return it as-is.
|
||
|
|
try:
|
||
|
|
filespec = os.fspath(filespec)
|
||
|
|
except TypeError:
|
||
|
|
return filespec, False
|
||
|
|
|
||
|
|
# 'filespec' is definitely a str now
|
||
|
|
|
||
|
|
# open for reading
|
||
|
|
if mode[0] == 'r':
|
||
|
|
|
||
|
|
# determine filename plus extension
|
||
|
|
if not os.path.isfile(filespec):
|
||
|
|
if os.path.isfile(filespec+'.mtx'):
|
||
|
|
filespec = filespec + '.mtx'
|
||
|
|
elif os.path.isfile(filespec+'.mtx.gz'):
|
||
|
|
filespec = filespec + '.mtx.gz'
|
||
|
|
elif os.path.isfile(filespec+'.mtx.bz2'):
|
||
|
|
filespec = filespec + '.mtx.bz2'
|
||
|
|
# open filename
|
||
|
|
if filespec.endswith('.gz'):
|
||
|
|
import gzip
|
||
|
|
stream = gzip.open(filespec, mode)
|
||
|
|
elif filespec.endswith('.bz2'):
|
||
|
|
import bz2
|
||
|
|
stream = bz2.BZ2File(filespec, 'rb')
|
||
|
|
else:
|
||
|
|
stream = open(filespec, mode)
|
||
|
|
|
||
|
|
# open for writing
|
||
|
|
else:
|
||
|
|
if filespec[-4:] != '.mtx':
|
||
|
|
filespec = filespec + '.mtx'
|
||
|
|
stream = open(filespec, mode)
|
||
|
|
|
||
|
|
return stream, True
|
||
|
|
|
||
|
|
# -------------------------------------------------------------------------
|
||
|
|
@staticmethod
|
||
|
|
def _get_symmetry(a):
|
||
|
|
m, n = a.shape
|
||
|
|
if m != n:
|
||
|
|
return MMFile.SYMMETRY_GENERAL
|
||
|
|
issymm = True
|
||
|
|
isskew = True
|
||
|
|
isherm = a.dtype.char in 'FD'
|
||
|
|
|
||
|
|
# sparse input
|
||
|
|
if isspmatrix(a):
|
||
|
|
# check if number of nonzero entries of lower and upper triangle
|
||
|
|
# matrix are equal
|
||
|
|
a = a.tocoo()
|
||
|
|
(row, col) = a.nonzero()
|
||
|
|
if (row < col).sum() != (row > col).sum():
|
||
|
|
return MMFile.SYMMETRY_GENERAL
|
||
|
|
|
||
|
|
# define iterator over symmetric pair entries
|
||
|
|
a = a.todok()
|
||
|
|
|
||
|
|
def symm_iterator():
|
||
|
|
for ((i, j), aij) in a.items():
|
||
|
|
if i > j:
|
||
|
|
aji = a[j, i]
|
||
|
|
yield (aij, aji, False)
|
||
|
|
elif i == j:
|
||
|
|
yield (aij, aij, True)
|
||
|
|
|
||
|
|
# non-sparse input
|
||
|
|
else:
|
||
|
|
# define iterator over symmetric pair entries
|
||
|
|
def symm_iterator():
|
||
|
|
for j in range(n):
|
||
|
|
for i in range(j, n):
|
||
|
|
aij, aji = a[i][j], a[j][i]
|
||
|
|
yield (aij, aji, i == j)
|
||
|
|
|
||
|
|
# check for symmetry
|
||
|
|
# yields aij, aji, is_diagonal
|
||
|
|
for (aij, aji, is_diagonal) in symm_iterator():
|
||
|
|
if isskew and is_diagonal and aij != 0:
|
||
|
|
isskew = False
|
||
|
|
else:
|
||
|
|
if issymm and aij != aji:
|
||
|
|
issymm = False
|
||
|
|
with np.errstate(over="ignore"):
|
||
|
|
# This can give a warning for uint dtypes, so silence that
|
||
|
|
if isskew and aij != -aji:
|
||
|
|
isskew = False
|
||
|
|
if isherm and aij != conj(aji):
|
||
|
|
isherm = False
|
||
|
|
if not (issymm or isskew or isherm):
|
||
|
|
break
|
||
|
|
|
||
|
|
# return symmetry value
|
||
|
|
if issymm:
|
||
|
|
return MMFile.SYMMETRY_SYMMETRIC
|
||
|
|
if isskew:
|
||
|
|
return MMFile.SYMMETRY_SKEW_SYMMETRIC
|
||
|
|
if isherm:
|
||
|
|
return MMFile.SYMMETRY_HERMITIAN
|
||
|
|
return MMFile.SYMMETRY_GENERAL
|
||
|
|
|
||
|
|
# -------------------------------------------------------------------------
|
||
|
|
@staticmethod
|
||
|
|
def _field_template(field, precision):
|
||
|
|
return {MMFile.FIELD_REAL: '%%.%ie\n' % precision,
|
||
|
|
MMFile.FIELD_INTEGER: '%i\n',
|
||
|
|
MMFile.FIELD_UNSIGNED: '%u\n',
|
||
|
|
MMFile.FIELD_COMPLEX: '%%.%ie %%.%ie\n' %
|
||
|
|
(precision, precision)
|
||
|
|
}.get(field, None)
|
||
|
|
|
||
|
|
# -------------------------------------------------------------------------
|
||
|
|
def __init__(self, **kwargs):
|
||
|
|
self._init_attrs(**kwargs)
|
||
|
|
|
||
|
|
# -------------------------------------------------------------------------
|
||
|
|
def read(self, source):
|
||
|
|
"""
|
||
|
|
Reads the contents of a Matrix Market file-like 'source' into a matrix.
|
||
|
|
|
||
|
|
Parameters
|
||
|
|
----------
|
||
|
|
source : str or file-like
|
||
|
|
Matrix Market filename (extensions .mtx, .mtz.gz)
|
||
|
|
or open file object.
|
||
|
|
|
||
|
|
Returns
|
||
|
|
-------
|
||
|
|
a : ndarray or coo_matrix
|
||
|
|
Dense or sparse matrix depending on the matrix format in the
|
||
|
|
Matrix Market file.
|
||
|
|
"""
|
||
|
|
stream, close_it = self._open(source)
|
||
|
|
|
||
|
|
try:
|
||
|
|
self._parse_header(stream)
|
||
|
|
return self._parse_body(stream)
|
||
|
|
|
||
|
|
finally:
|
||
|
|
if close_it:
|
||
|
|
stream.close()
|
||
|
|
|
||
|
|
# -------------------------------------------------------------------------
|
||
|
|
def write(self, target, a, comment='', field=None, precision=None,
|
||
|
|
symmetry=None):
|
||
|
|
"""
|
||
|
|
Writes sparse or dense array `a` to Matrix Market file-like `target`.
|
||
|
|
|
||
|
|
Parameters
|
||
|
|
----------
|
||
|
|
target : str or file-like
|
||
|
|
Matrix Market filename (extension .mtx) or open file-like object.
|
||
|
|
a : array like
|
||
|
|
Sparse or dense 2-D array.
|
||
|
|
comment : str, optional
|
||
|
|
Comments to be prepended to the Matrix Market file.
|
||
|
|
field : None or str, optional
|
||
|
|
Either 'real', 'complex', 'pattern', or 'integer'.
|
||
|
|
precision : None or int, optional
|
||
|
|
Number of digits to display for real or complex values.
|
||
|
|
symmetry : None or str, optional
|
||
|
|
Either 'general', 'symmetric', 'skew-symmetric', or 'hermitian'.
|
||
|
|
If symmetry is None the symmetry type of 'a' is determined by its
|
||
|
|
values.
|
||
|
|
"""
|
||
|
|
|
||
|
|
stream, close_it = self._open(target, 'wb')
|
||
|
|
|
||
|
|
try:
|
||
|
|
self._write(stream, a, comment, field, precision, symmetry)
|
||
|
|
|
||
|
|
finally:
|
||
|
|
if close_it:
|
||
|
|
stream.close()
|
||
|
|
else:
|
||
|
|
stream.flush()
|
||
|
|
|
||
|
|
# -------------------------------------------------------------------------
|
||
|
|
def _init_attrs(self, **kwargs):
|
||
|
|
"""
|
||
|
|
Initialize each attributes with the corresponding keyword arg value
|
||
|
|
or a default of None
|
||
|
|
"""
|
||
|
|
|
||
|
|
attrs = self.__class__.__slots__
|
||
|
|
public_attrs = [attr[1:] for attr in attrs]
|
||
|
|
invalid_keys = set(kwargs.keys()) - set(public_attrs)
|
||
|
|
|
||
|
|
if invalid_keys:
|
||
|
|
raise ValueError('''found %s invalid keyword arguments, please only
|
||
|
|
use %s''' % (tuple(invalid_keys),
|
||
|
|
public_attrs))
|
||
|
|
|
||
|
|
for attr in attrs:
|
||
|
|
setattr(self, attr, kwargs.get(attr[1:], None))
|
||
|
|
|
||
|
|
# -------------------------------------------------------------------------
|
||
|
|
def _parse_header(self, stream):
|
||
|
|
rows, cols, entries, format, field, symmetry = \
|
||
|
|
self.__class__.info(stream)
|
||
|
|
self._init_attrs(rows=rows, cols=cols, entries=entries, format=format,
|
||
|
|
field=field, symmetry=symmetry)
|
||
|
|
|
||
|
|
# -------------------------------------------------------------------------
|
||
|
|
def _parse_body(self, stream):
|
||
|
|
rows, cols, entries, format, field, symm = (self.rows, self.cols,
|
||
|
|
self.entries, self.format,
|
||
|
|
self.field, self.symmetry)
|
||
|
|
|
||
|
|
try:
|
||
|
|
from scipy.sparse import coo_matrix
|
||
|
|
except ImportError:
|
||
|
|
coo_matrix = None
|
||
|
|
|
||
|
|
dtype = self.DTYPES_BY_FIELD.get(field, None)
|
||
|
|
|
||
|
|
has_symmetry = self.has_symmetry
|
||
|
|
is_integer = field == self.FIELD_INTEGER
|
||
|
|
is_unsigned_integer = field == self.FIELD_UNSIGNED
|
||
|
|
is_complex = field == self.FIELD_COMPLEX
|
||
|
|
is_skew = symm == self.SYMMETRY_SKEW_SYMMETRIC
|
||
|
|
is_herm = symm == self.SYMMETRY_HERMITIAN
|
||
|
|
is_pattern = field == self.FIELD_PATTERN
|
||
|
|
|
||
|
|
if format == self.FORMAT_ARRAY:
|
||
|
|
a = zeros((rows, cols), dtype=dtype)
|
||
|
|
line = 1
|
||
|
|
i, j = 0, 0
|
||
|
|
if is_skew:
|
||
|
|
a[i, j] = 0
|
||
|
|
if i < rows - 1:
|
||
|
|
i += 1
|
||
|
|
while line:
|
||
|
|
line = stream.readline()
|
||
|
|
# line.startswith('%')
|
||
|
|
if not line or line[0] in ['%', 37] or not line.strip():
|
||
|
|
continue
|
||
|
|
if is_integer:
|
||
|
|
aij = int(line)
|
||
|
|
elif is_unsigned_integer:
|
||
|
|
aij = int(line)
|
||
|
|
elif is_complex:
|
||
|
|
aij = complex(*map(float, line.split()))
|
||
|
|
else:
|
||
|
|
aij = float(line)
|
||
|
|
a[i, j] = aij
|
||
|
|
if has_symmetry and i != j:
|
||
|
|
if is_skew:
|
||
|
|
a[j, i] = -aij
|
||
|
|
elif is_herm:
|
||
|
|
a[j, i] = conj(aij)
|
||
|
|
else:
|
||
|
|
a[j, i] = aij
|
||
|
|
if i < rows-1:
|
||
|
|
i = i + 1
|
||
|
|
else:
|
||
|
|
j = j + 1
|
||
|
|
if not has_symmetry:
|
||
|
|
i = 0
|
||
|
|
else:
|
||
|
|
i = j
|
||
|
|
if is_skew:
|
||
|
|
a[i, j] = 0
|
||
|
|
if i < rows-1:
|
||
|
|
i += 1
|
||
|
|
|
||
|
|
if is_skew:
|
||
|
|
if not (i in [0, j] and j == cols - 1):
|
||
|
|
raise ValueError("Parse error, did not read all lines.")
|
||
|
|
else:
|
||
|
|
if not (i in [0, j] and j == cols):
|
||
|
|
raise ValueError("Parse error, did not read all lines.")
|
||
|
|
|
||
|
|
elif format == self.FORMAT_COORDINATE and coo_matrix is None:
|
||
|
|
# Read sparse matrix to dense when coo_matrix is not available.
|
||
|
|
a = zeros((rows, cols), dtype=dtype)
|
||
|
|
line = 1
|
||
|
|
k = 0
|
||
|
|
while line:
|
||
|
|
line = stream.readline()
|
||
|
|
# line.startswith('%')
|
||
|
|
if not line or line[0] in ['%', 37] or not line.strip():
|
||
|
|
continue
|
||
|
|
l = line.split()
|
||
|
|
i, j = map(int, l[:2])
|
||
|
|
i, j = i-1, j-1
|
||
|
|
if is_integer:
|
||
|
|
aij = int(l[2])
|
||
|
|
elif is_unsigned_integer:
|
||
|
|
aij = int(l[2])
|
||
|
|
elif is_complex:
|
||
|
|
aij = complex(*map(float, l[2:]))
|
||
|
|
else:
|
||
|
|
aij = float(l[2])
|
||
|
|
a[i, j] = aij
|
||
|
|
if has_symmetry and i != j:
|
||
|
|
if is_skew:
|
||
|
|
a[j, i] = -aij
|
||
|
|
elif is_herm:
|
||
|
|
a[j, i] = conj(aij)
|
||
|
|
else:
|
||
|
|
a[j, i] = aij
|
||
|
|
k = k + 1
|
||
|
|
if not k == entries:
|
||
|
|
ValueError("Did not read all entries")
|
||
|
|
|
||
|
|
elif format == self.FORMAT_COORDINATE:
|
||
|
|
# Read sparse COOrdinate format
|
||
|
|
|
||
|
|
if entries == 0:
|
||
|
|
# empty matrix
|
||
|
|
return coo_matrix((rows, cols), dtype=dtype)
|
||
|
|
|
||
|
|
I = zeros(entries, dtype='intc')
|
||
|
|
J = zeros(entries, dtype='intc')
|
||
|
|
if is_pattern:
|
||
|
|
V = ones(entries, dtype='int8')
|
||
|
|
elif is_integer:
|
||
|
|
V = zeros(entries, dtype='intp')
|
||
|
|
elif is_unsigned_integer:
|
||
|
|
V = zeros(entries, dtype='uint64')
|
||
|
|
elif is_complex:
|
||
|
|
V = zeros(entries, dtype='complex')
|
||
|
|
else:
|
||
|
|
V = zeros(entries, dtype='float')
|
||
|
|
|
||
|
|
entry_number = 0
|
||
|
|
for line in stream:
|
||
|
|
# line.startswith('%')
|
||
|
|
if not line or line[0] in ['%', 37] or not line.strip():
|
||
|
|
continue
|
||
|
|
|
||
|
|
if entry_number+1 > entries:
|
||
|
|
raise ValueError("'entries' in header is smaller than "
|
||
|
|
"number of entries")
|
||
|
|
l = line.split()
|
||
|
|
I[entry_number], J[entry_number] = map(int, l[:2])
|
||
|
|
|
||
|
|
if not is_pattern:
|
||
|
|
if is_integer:
|
||
|
|
V[entry_number] = int(l[2])
|
||
|
|
elif is_unsigned_integer:
|
||
|
|
V[entry_number] = int(l[2])
|
||
|
|
elif is_complex:
|
||
|
|
V[entry_number] = complex(*map(float, l[2:]))
|
||
|
|
else:
|
||
|
|
V[entry_number] = float(l[2])
|
||
|
|
entry_number += 1
|
||
|
|
if entry_number < entries:
|
||
|
|
raise ValueError("'entries' in header is larger than "
|
||
|
|
"number of entries")
|
||
|
|
|
||
|
|
I -= 1 # adjust indices (base 1 -> base 0)
|
||
|
|
J -= 1
|
||
|
|
|
||
|
|
if has_symmetry:
|
||
|
|
mask = (I != J) # off diagonal mask
|
||
|
|
od_I = I[mask]
|
||
|
|
od_J = J[mask]
|
||
|
|
od_V = V[mask]
|
||
|
|
|
||
|
|
I = concatenate((I, od_J))
|
||
|
|
J = concatenate((J, od_I))
|
||
|
|
|
||
|
|
if is_skew:
|
||
|
|
od_V *= -1
|
||
|
|
elif is_herm:
|
||
|
|
od_V = od_V.conjugate()
|
||
|
|
|
||
|
|
V = concatenate((V, od_V))
|
||
|
|
|
||
|
|
a = coo_matrix((V, (I, J)), shape=(rows, cols), dtype=dtype)
|
||
|
|
else:
|
||
|
|
raise NotImplementedError(format)
|
||
|
|
|
||
|
|
return a
|
||
|
|
|
||
|
|
# ------------------------------------------------------------------------
|
||
|
|
def _write(self, stream, a, comment='', field=None, precision=None,
|
||
|
|
symmetry=None):
|
||
|
|
if isinstance(a, list) or isinstance(a, ndarray) or \
|
||
|
|
isinstance(a, tuple) or hasattr(a, '__array__'):
|
||
|
|
rep = self.FORMAT_ARRAY
|
||
|
|
a = asarray(a)
|
||
|
|
if len(a.shape) != 2:
|
||
|
|
raise ValueError('Expected 2 dimensional array')
|
||
|
|
rows, cols = a.shape
|
||
|
|
|
||
|
|
if field is not None:
|
||
|
|
|
||
|
|
if field == self.FIELD_INTEGER:
|
||
|
|
if not can_cast(a.dtype, 'intp'):
|
||
|
|
raise OverflowError("mmwrite does not support integer "
|
||
|
|
"dtypes larger than native 'intp'.")
|
||
|
|
a = a.astype('intp')
|
||
|
|
elif field == self.FIELD_REAL:
|
||
|
|
if a.dtype.char not in 'fd':
|
||
|
|
a = a.astype('d')
|
||
|
|
elif field == self.FIELD_COMPLEX:
|
||
|
|
if a.dtype.char not in 'FD':
|
||
|
|
a = a.astype('D')
|
||
|
|
|
||
|
|
else:
|
||
|
|
if not isspmatrix(a):
|
||
|
|
raise ValueError('unknown matrix type: %s' % type(a))
|
||
|
|
|
||
|
|
rep = 'coordinate'
|
||
|
|
rows, cols = a.shape
|
||
|
|
|
||
|
|
typecode = a.dtype.char
|
||
|
|
|
||
|
|
if precision is None:
|
||
|
|
if typecode in 'fF':
|
||
|
|
precision = 8
|
||
|
|
else:
|
||
|
|
precision = 16
|
||
|
|
if field is None:
|
||
|
|
kind = a.dtype.kind
|
||
|
|
if kind == 'i':
|
||
|
|
if not can_cast(a.dtype, 'intp'):
|
||
|
|
raise OverflowError("mmwrite does not support integer "
|
||
|
|
"dtypes larger than native 'intp'.")
|
||
|
|
field = 'integer'
|
||
|
|
elif kind == 'f':
|
||
|
|
field = 'real'
|
||
|
|
elif kind == 'c':
|
||
|
|
field = 'complex'
|
||
|
|
elif kind == 'u':
|
||
|
|
field = 'unsigned-integer'
|
||
|
|
else:
|
||
|
|
raise TypeError('unexpected dtype kind ' + kind)
|
||
|
|
|
||
|
|
if symmetry is None:
|
||
|
|
symmetry = self._get_symmetry(a)
|
||
|
|
|
||
|
|
# validate rep, field, and symmetry
|
||
|
|
self.__class__._validate_format(rep)
|
||
|
|
self.__class__._validate_field(field)
|
||
|
|
self.__class__._validate_symmetry(symmetry)
|
||
|
|
|
||
|
|
# write initial header line
|
||
|
|
data = f'%%MatrixMarket matrix {rep} {field} {symmetry}\n'
|
||
|
|
stream.write(data.encode('latin1'))
|
||
|
|
|
||
|
|
# write comments
|
||
|
|
for line in comment.split('\n'):
|
||
|
|
data = '%%%s\n' % (line)
|
||
|
|
stream.write(data.encode('latin1'))
|
||
|
|
|
||
|
|
template = self._field_template(field, precision)
|
||
|
|
# write dense format
|
||
|
|
if rep == self.FORMAT_ARRAY:
|
||
|
|
# write shape spec
|
||
|
|
data = '%i %i\n' % (rows, cols)
|
||
|
|
stream.write(data.encode('latin1'))
|
||
|
|
|
||
|
|
if field in (self.FIELD_INTEGER, self.FIELD_REAL,
|
||
|
|
self.FIELD_UNSIGNED):
|
||
|
|
if symmetry == self.SYMMETRY_GENERAL:
|
||
|
|
for j in range(cols):
|
||
|
|
for i in range(rows):
|
||
|
|
data = template % a[i, j]
|
||
|
|
stream.write(data.encode('latin1'))
|
||
|
|
|
||
|
|
elif symmetry == self.SYMMETRY_SKEW_SYMMETRIC:
|
||
|
|
for j in range(cols):
|
||
|
|
for i in range(j + 1, rows):
|
||
|
|
data = template % a[i, j]
|
||
|
|
stream.write(data.encode('latin1'))
|
||
|
|
|
||
|
|
else:
|
||
|
|
for j in range(cols):
|
||
|
|
for i in range(j, rows):
|
||
|
|
data = template % a[i, j]
|
||
|
|
stream.write(data.encode('latin1'))
|
||
|
|
|
||
|
|
elif field == self.FIELD_COMPLEX:
|
||
|
|
|
||
|
|
if symmetry == self.SYMMETRY_GENERAL:
|
||
|
|
for j in range(cols):
|
||
|
|
for i in range(rows):
|
||
|
|
aij = a[i, j]
|
||
|
|
data = template % (real(aij), imag(aij))
|
||
|
|
stream.write(data.encode('latin1'))
|
||
|
|
else:
|
||
|
|
for j in range(cols):
|
||
|
|
for i in range(j, rows):
|
||
|
|
aij = a[i, j]
|
||
|
|
data = template % (real(aij), imag(aij))
|
||
|
|
stream.write(data.encode('latin1'))
|
||
|
|
|
||
|
|
elif field == self.FIELD_PATTERN:
|
||
|
|
raise ValueError('pattern type inconsisted with dense format')
|
||
|
|
|
||
|
|
else:
|
||
|
|
raise TypeError('Unknown field type %s' % field)
|
||
|
|
|
||
|
|
# write sparse format
|
||
|
|
else:
|
||
|
|
coo = a.tocoo() # convert to COOrdinate format
|
||
|
|
|
||
|
|
# if symmetry format used, remove values above main diagonal
|
||
|
|
if symmetry != self.SYMMETRY_GENERAL:
|
||
|
|
lower_triangle_mask = coo.row >= coo.col
|
||
|
|
coo = coo_matrix((coo.data[lower_triangle_mask],
|
||
|
|
(coo.row[lower_triangle_mask],
|
||
|
|
coo.col[lower_triangle_mask])),
|
||
|
|
shape=coo.shape)
|
||
|
|
|
||
|
|
# write shape spec
|
||
|
|
data = '%i %i %i\n' % (rows, cols, coo.nnz)
|
||
|
|
stream.write(data.encode('latin1'))
|
||
|
|
|
||
|
|
template = self._field_template(field, precision-1)
|
||
|
|
|
||
|
|
if field == self.FIELD_PATTERN:
|
||
|
|
for r, c in zip(coo.row+1, coo.col+1):
|
||
|
|
data = "%i %i\n" % (r, c)
|
||
|
|
stream.write(data.encode('latin1'))
|
||
|
|
elif field in (self.FIELD_INTEGER, self.FIELD_REAL,
|
||
|
|
self.FIELD_UNSIGNED):
|
||
|
|
for r, c, d in zip(coo.row+1, coo.col+1, coo.data):
|
||
|
|
data = ("%i %i " % (r, c)) + (template % d)
|
||
|
|
stream.write(data.encode('latin1'))
|
||
|
|
elif field == self.FIELD_COMPLEX:
|
||
|
|
for r, c, d in zip(coo.row+1, coo.col+1, coo.data):
|
||
|
|
data = ("%i %i " % (r, c)) + (template % (d.real, d.imag))
|
||
|
|
stream.write(data.encode('latin1'))
|
||
|
|
else:
|
||
|
|
raise TypeError('Unknown field type %s' % field)
|
||
|
|
|
||
|
|
|
||
|
|
def _is_fromfile_compatible(stream):
|
||
|
|
"""
|
||
|
|
Check whether `stream` is compatible with numpy.fromfile.
|
||
|
|
|
||
|
|
Passing a gzipped file object to ``fromfile/fromstring`` doesn't work with
|
||
|
|
Python 3.
|
||
|
|
"""
|
||
|
|
|
||
|
|
bad_cls = []
|
||
|
|
try:
|
||
|
|
import gzip
|
||
|
|
bad_cls.append(gzip.GzipFile)
|
||
|
|
except ImportError:
|
||
|
|
pass
|
||
|
|
try:
|
||
|
|
import bz2
|
||
|
|
bad_cls.append(bz2.BZ2File)
|
||
|
|
except ImportError:
|
||
|
|
pass
|
||
|
|
|
||
|
|
bad_cls = tuple(bad_cls)
|
||
|
|
return not isinstance(stream, bad_cls)
|