diff --git a/ckpts/universal/global_step40/zero/24.mlp.dense_h_to_4h_swiglu.weight/fp32.pt b/ckpts/universal/global_step40/zero/24.mlp.dense_h_to_4h_swiglu.weight/fp32.pt new file mode 100644 index 0000000000000000000000000000000000000000..f245cd3badb2003a0bfa3427cf05dad21fe46fa6 --- /dev/null +++ b/ckpts/universal/global_step40/zero/24.mlp.dense_h_to_4h_swiglu.weight/fp32.pt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:372171cd4c686202bff2cba46f1afeed84a35ae94991a2f2b575171d34f76e7f +size 33555533 diff --git a/venv/lib/python3.10/site-packages/scipy/io/matlab/__init__.py b/venv/lib/python3.10/site-packages/scipy/io/matlab/__init__.py new file mode 100644 index 0000000000000000000000000000000000000000..3f3257cca30b6b2d7fff4e3f27ac0c9bce135a0f --- /dev/null +++ b/venv/lib/python3.10/site-packages/scipy/io/matlab/__init__.py @@ -0,0 +1,63 @@ +""" +MATLAB® file utilities (:mod:`scipy.io.matlab`) +=============================================== + +.. currentmodule:: scipy.io.matlab + +This submodule is meant to provide lower-level file utilities related to reading +and writing MATLAB files. + +.. autosummary:: + :toctree: generated/ + + matfile_version - Get the MATLAB file version + MatReadError - Exception indicating a read issue + MatReadWarning - Warning class for read issues + MatWriteError - Exception indicating a write issue + mat_struct - Class used when ``struct_as_record=False`` + +.. autosummary:: + :toctree: generated/ + :template: autosummary/ndarray_subclass.rst + :nosignatures: + + MatlabObject - Class for a MATLAB object + MatlabOpaque - Class for a MATLAB opaque matrix + MatlabFunction - Class for a MATLAB function object + +The following utilities that live in the :mod:`scipy.io` +namespace also exist in this namespace: + +.. autosummary:: + :toctree: generated/ + + loadmat - Read a MATLAB style mat file (version 4 through 7.1) + savemat - Write a MATLAB style mat file (version 4 through 7.1) + whosmat - List contents of a MATLAB style mat file (version 4 through 7.1) + +Notes +----- +MATLAB(R) is a registered trademark of The MathWorks, Inc., 3 Apple Hill +Drive, Natick, MA 01760-2098, USA. + +""" +# Matlab file read and write utilities +from ._mio import loadmat, savemat, whosmat +from ._mio5 import MatlabFunction +from ._mio5_params import MatlabObject, MatlabOpaque, mat_struct +from ._miobase import (matfile_version, MatReadError, MatReadWarning, + MatWriteError) + +# Deprecated namespaces, to be removed in v2.0.0 +from .import (mio, mio5, mio5_params, mio4, byteordercodes, + miobase, mio_utils, streams, mio5_utils) + +__all__ = [ + 'loadmat', 'savemat', 'whosmat', 'MatlabObject', + 'matfile_version', 'MatReadError', 'MatReadWarning', + 'MatWriteError', 'mat_struct', 'MatlabOpaque', 'MatlabFunction' +] + +from scipy._lib._testutils import PytestTester +test = PytestTester(__name__) +del PytestTester diff --git 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issue.""" + + +class MatWriteError(Exception): + """Exception indicating a write issue.""" + + +class MatReadWarning(UserWarning): + """Warning class for read issues.""" + + +doc_dict = \ + {'file_arg': + '''file_name : str + Name of the mat file (do not need .mat extension if + appendmat==True) Can also pass open file-like object.''', + 'append_arg': + '''appendmat : bool, optional + True to append the .mat extension to the end of the given + filename, if not already present. Default is True.''', + 'load_args': + '''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_arg': + '''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.''', + 'matstream_arg': + '''mat_stream : file-like + Object with file API, open for reading.''', + 'long_fields': + '''long_field_names : bool, optional + * False - maximum field name length in a structure is 31 characters + which is the documented maximum length. This is the default. + * True - maximum field name length in a structure is 63 characters + which works for MATLAB 7.6''', + 'do_compression': + '''do_compression : bool, optional + Whether to compress matrices on write. Default is False.''', + 'oned_as': + '''oned_as : {'row', 'column'}, optional + If 'column', write 1-D NumPy arrays as column vectors. + If 'row', write 1D NumPy arrays as row vectors.''', + 'unicode_strings': + '''unicode_strings : bool, optional + If True, write strings as Unicode, else MATLAB usual encoding.'''} + +docfiller = doccer.filldoc(doc_dict) + +''' + + Note on architecture +====================== + +There are three sets of parameters relevant for reading files. The +first are *file read parameters* - containing options that are common +for reading the whole file, and therefore every variable within that +file. At the moment these are: + +* mat_stream +* dtypes (derived from byte code) +* byte_order +* chars_as_strings +* squeeze_me +* struct_as_record (MATLAB 5 files) +* class_dtypes (derived from order code, MATLAB 5 files) +* codecs (MATLAB 5 files) +* uint16_codec (MATLAB 5 files) + +Another set of parameters are those that apply only to the current +variable being read - the *header*: + +* header related variables (different for v4 and v5 mat files) +* is_complex +* mclass +* var_stream + +With the header, we need ``next_position`` to tell us where the next +variable in the stream is. + +Then, for each element in a matrix, there can be *element read +parameters*. An element is, for example, one element in a MATLAB cell +array. At the moment, these are: + +* mat_dtype + +The file-reading object contains the *file read parameters*. The +*header* is passed around as a data object, or may be read and discarded +in a single function. The *element read parameters* - the mat_dtype in +this instance, is passed into a general post-processing function - see +``mio_utils`` for details. +''' + + +def convert_dtypes(dtype_template, order_code): + ''' Convert dtypes in mapping to given order + + Parameters + ---------- + dtype_template : mapping + mapping with values returning numpy dtype from ``np.dtype(val)`` + order_code : str + an order code suitable for using in ``dtype.newbyteorder()`` + + Returns + ------- + dtypes : mapping + mapping where values have been replaced by + ``np.dtype(val).newbyteorder(order_code)`` + + ''' + dtypes = dtype_template.copy() + for k in dtypes: + dtypes[k] = np.dtype(dtypes[k]).newbyteorder(order_code) + return dtypes + + +def read_dtype(mat_stream, a_dtype): + """ + Generic get of byte stream data of known type + + Parameters + ---------- + mat_stream : file_like object + MATLAB (tm) mat file stream + a_dtype : dtype + dtype of array to read. `a_dtype` is assumed to be correct + endianness. + + Returns + ------- + arr : ndarray + Array of dtype `a_dtype` read from stream. + + """ + num_bytes = a_dtype.itemsize + arr = np.ndarray(shape=(), + dtype=a_dtype, + buffer=mat_stream.read(num_bytes), + order='F') + return arr + + +def matfile_version(file_name, *, appendmat=True): + """ + Return major, minor tuple depending on apparent mat file type + + Where: + + #. 0,x -> version 4 format mat files + #. 1,x -> version 5 format mat files + #. 2,x -> version 7.3 format mat files (HDF format) + + Parameters + ---------- + file_name : str + Name of the mat file (do not need .mat extension if + appendmat==True). Can also pass open file-like object. + appendmat : bool, optional + True to append the .mat extension to the end of the given + filename, if not already present. Default is True. + + Returns + ------- + major_version : {0, 1, 2} + major MATLAB File format version + minor_version : int + minor MATLAB file format version + + Raises + ------ + MatReadError + If the file is empty. + ValueError + The matfile version is unknown. + + Notes + ----- + Has the side effect of setting the file read pointer to 0 + """ + from ._mio import _open_file_context + with _open_file_context(file_name, appendmat=appendmat) as fileobj: + return _get_matfile_version(fileobj) + + +get_matfile_version = matfile_version + + +def _get_matfile_version(fileobj): + # Mat4 files have a zero somewhere in first 4 bytes + fileobj.seek(0) + mopt_bytes = fileobj.read(4) + if len(mopt_bytes) == 0: + raise MatReadError("Mat file appears to be empty") + mopt_ints = np.ndarray(shape=(4,), dtype=np.uint8, buffer=mopt_bytes) + if 0 in mopt_ints: + fileobj.seek(0) + return (0,0) + # For 5 format or 7.3 format we need to read an integer in the + # header. Bytes 124 through 128 contain a version integer and an + # endian test string + fileobj.seek(124) + tst_str = fileobj.read(4) + fileobj.seek(0) + maj_ind = int(tst_str[2] == b'I'[0]) + maj_val = int(tst_str[maj_ind]) + min_val = int(tst_str[1 - maj_ind]) + ret = (maj_val, min_val) + if maj_val in (1, 2): + return ret + raise ValueError('Unknown mat file type, version {}, {}'.format(*ret)) + + +def matdims(arr, oned_as='column'): + """ + Determine equivalent MATLAB dimensions for given array + + Parameters + ---------- + arr : ndarray + Input array + oned_as : {'column', 'row'}, optional + Whether 1-D arrays are returned as MATLAB row or column matrices. + Default is 'column'. + + Returns + ------- + dims : tuple + Shape tuple, in the form MATLAB expects it. + + Notes + ----- + We had to decide what shape a 1 dimensional array would be by + default. ``np.atleast_2d`` thinks it is a row vector. The + default for a vector in MATLAB (e.g., ``>> 1:12``) is a row vector. + + Versions of scipy up to and including 0.11 resulted (accidentally) + in 1-D arrays being read as column vectors. For the moment, we + maintain the same tradition here. + + Examples + -------- + >>> import numpy as np + >>> from scipy.io.matlab._miobase import matdims + >>> matdims(np.array(1)) # NumPy scalar + (1, 1) + >>> matdims(np.array([1])) # 1-D array, 1 element + (1, 1) + >>> matdims(np.array([1,2])) # 1-D array, 2 elements + (2, 1) + >>> matdims(np.array([[2],[3]])) # 2-D array, column vector + (2, 1) + >>> matdims(np.array([[2,3]])) # 2-D array, row vector + (1, 2) + >>> matdims(np.array([[[2,3]]])) # 3-D array, rowish vector + (1, 1, 2) + >>> matdims(np.array([])) # empty 1-D array + (0, 0) + >>> matdims(np.array([[]])) # empty 2-D array + (0, 0) + >>> matdims(np.array([[[]]])) # empty 3-D array + (0, 0, 0) + + Optional argument flips 1-D shape behavior. + + >>> matdims(np.array([1,2]), 'row') # 1-D array, 2 elements + (1, 2) + + The argument has to make sense though + + >>> matdims(np.array([1,2]), 'bizarre') + Traceback (most recent call last): + ... + ValueError: 1-D option "bizarre" is strange + + """ + shape = arr.shape + if shape == (): # scalar + return (1, 1) + if len(shape) == 1: # 1D + if shape[0] == 0: + return (0, 0) + elif oned_as == 'column': + return shape + (1,) + elif oned_as == 'row': + return (1,) + shape + else: + raise ValueError('1-D option "%s" is strange' + % oned_as) + return shape + + +class MatVarReader: + ''' Abstract class defining required interface for var readers''' + def __init__(self, file_reader): + pass + + def read_header(self): + ''' Returns header ''' + pass + + def array_from_header(self, header): + ''' Reads array given header ''' + pass + + +class MatFileReader: + """ Base object for reading mat files + + To make this class functional, you will need to override the + following methods: + + matrix_getter_factory - gives object to fetch next matrix from stream + guess_byte_order - guesses file byte order from file + """ + + @docfiller + def __init__(self, mat_stream, + byte_order=None, + mat_dtype=False, + squeeze_me=False, + chars_as_strings=True, + matlab_compatible=False, + struct_as_record=True, + verify_compressed_data_integrity=True, + simplify_cells=False): + ''' + Initializer for mat file reader + + mat_stream : file-like + object with file API, open for reading + %(load_args)s + ''' + # Initialize stream + self.mat_stream = mat_stream + self.dtypes = {} + if not byte_order: + byte_order = self.guess_byte_order() + else: + byte_order = boc.to_numpy_code(byte_order) + self.byte_order = byte_order + self.struct_as_record = struct_as_record + if matlab_compatible: + self.set_matlab_compatible() + else: + self.squeeze_me = squeeze_me + self.chars_as_strings = chars_as_strings + self.mat_dtype = mat_dtype + self.verify_compressed_data_integrity = verify_compressed_data_integrity + self.simplify_cells = simplify_cells + if simplify_cells: + self.squeeze_me = True + self.struct_as_record = False + + def set_matlab_compatible(self): + ''' Sets options to return arrays as MATLAB loads them ''' + self.mat_dtype = True + self.squeeze_me = False + self.chars_as_strings = False + + def guess_byte_order(self): + ''' As we do not know what file type we have, assume native ''' + return boc.native_code + + def end_of_stream(self): + b = self.mat_stream.read(1) + curpos = self.mat_stream.tell() + self.mat_stream.seek(curpos-1) + return len(b) == 0 + + +def arr_dtype_number(arr, num): + ''' Return dtype for given number of items per element''' + return np.dtype(arr.dtype.str[:2] + str(num)) + + +def arr_to_chars(arr): + ''' Convert string array to char array ''' + dims = list(arr.shape) + if not dims: + dims = [1] + dims.append(int(arr.dtype.str[2:])) + arr = np.ndarray(shape=dims, + dtype=arr_dtype_number(arr, 1), + buffer=arr) + empties = [arr == np.array('', dtype=arr.dtype)] + if not np.any(empties): + return arr + arr = arr.copy() + arr[tuple(empties)] = ' ' + return arr diff --git a/venv/lib/python3.10/site-packages/scipy/io/matlab/mio_utils.py b/venv/lib/python3.10/site-packages/scipy/io/matlab/mio_utils.py new file mode 100644 index 0000000000000000000000000000000000000000..62d32965e0197f60d7c34efbc6f39c6c904b6f49 --- /dev/null +++ b/venv/lib/python3.10/site-packages/scipy/io/matlab/mio_utils.py @@ -0,0 +1,17 @@ +# This file is not meant for public use and will be removed in SciPy v2.0.0. +# Use the `scipy.io.matlab` namespace for importing the functions +# included below. + +from scipy._lib.deprecation import _sub_module_deprecation + +__all__ = ['squeeze_element', 'chars_to_strings'] # noqa: F822 + + +def __dir__(): + return __all__ + + +def __getattr__(name): + return _sub_module_deprecation(sub_package="io.matlab", module="mio_utils", + private_modules=["_mio_utils"], all=__all__, + attribute=name) diff --git a/venv/lib/python3.10/site-packages/scipy/io/matlab/tests/__init__.py b/venv/lib/python3.10/site-packages/scipy/io/matlab/tests/__init__.py new file mode 100644 index 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0000000000000000000000000000000000000000..76c51d01388a1770b348bc603ebfdd51bc011f0c Binary files /dev/null and b/venv/lib/python3.10/site-packages/scipy/io/matlab/tests/data/testvec_4_GLNX86.mat differ diff --git a/venv/lib/python3.10/site-packages/scipy/io/matlab/tests/test_byteordercodes.py b/venv/lib/python3.10/site-packages/scipy/io/matlab/tests/test_byteordercodes.py new file mode 100644 index 0000000000000000000000000000000000000000..535434d188ff575029cc7a0de807b0daa7348f73 --- /dev/null +++ b/venv/lib/python3.10/site-packages/scipy/io/matlab/tests/test_byteordercodes.py @@ -0,0 +1,29 @@ +''' Tests for byteorder module ''' + +import sys + +from numpy.testing import assert_ +from pytest import raises as assert_raises + +import scipy.io.matlab._byteordercodes as sibc + + +def test_native(): + native_is_le = sys.byteorder == 'little' + assert_(sibc.sys_is_le == native_is_le) + + +def test_to_numpy(): + if sys.byteorder == 'little': + assert_(sibc.to_numpy_code('native') == '<') + assert_(sibc.to_numpy_code('swapped') == '>') + else: + assert_(sibc.to_numpy_code('native') == '>') + assert_(sibc.to_numpy_code('swapped') == '<') + assert_(sibc.to_numpy_code('native') == sibc.to_numpy_code('=')) + assert_(sibc.to_numpy_code('big') == '>') + for code in ('little', '<', 'l', 'L', 'le'): + assert_(sibc.to_numpy_code(code) == '<') + for code in ('big', '>', 'b', 'B', 'be'): + assert_(sibc.to_numpy_code(code) == '>') + assert_raises(ValueError, sibc.to_numpy_code, 'silly string') diff --git a/venv/lib/python3.10/site-packages/scipy/io/matlab/tests/test_mio.py b/venv/lib/python3.10/site-packages/scipy/io/matlab/tests/test_mio.py new file mode 100644 index 0000000000000000000000000000000000000000..cd3ee2fb35c381c0a12c7aee15e4e160ef74ac1b --- /dev/null +++ b/venv/lib/python3.10/site-packages/scipy/io/matlab/tests/test_mio.py @@ -0,0 +1,1339 @@ +''' Nose test generators + +Need function load / save / roundtrip tests + +''' +import os +from collections import OrderedDict +from os.path import join as pjoin, dirname +from glob import glob +from io import BytesIO +import re +from tempfile import mkdtemp + +import warnings +import shutil +import gzip + +from numpy.testing import (assert_array_equal, assert_array_almost_equal, + assert_equal, assert_, assert_warns, assert_allclose) +import pytest +from pytest import raises as assert_raises + +import numpy as np +from numpy import array +import scipy.sparse as SP + +import scipy.io +from scipy.io.matlab import MatlabOpaque, MatlabFunction, MatlabObject +import scipy.io.matlab._byteordercodes as boc +from scipy.io.matlab._miobase import ( + matdims, MatWriteError, MatReadError, matfile_version) +from scipy.io.matlab._mio import mat_reader_factory, loadmat, savemat, whosmat +from scipy.io.matlab._mio5 import ( + MatFile5Writer, MatFile5Reader, varmats_from_mat, to_writeable, + EmptyStructMarker) +import scipy.io.matlab._mio5_params as mio5p +from scipy._lib._util import VisibleDeprecationWarning + + +test_data_path = pjoin(dirname(__file__), 'data') + + +def mlarr(*args, **kwargs): + """Convenience function to return matlab-compatible 2-D array.""" + arr = np.array(*args, **kwargs) + arr.shape = matdims(arr) + return arr + + +# Define cases to test +theta = np.pi/4*np.arange(9,dtype=float).reshape(1,9) +case_table4 = [ + {'name': 'double', + 'classes': {'testdouble': 'double'}, + 'expected': {'testdouble': theta} + }] +case_table4.append( + {'name': 'string', + 'classes': {'teststring': 'char'}, + 'expected': {'teststring': + array(['"Do nine men interpret?" "Nine men," I nod.'])} + }) +case_table4.append( + {'name': 'complex', + 'classes': {'testcomplex': 'double'}, + 'expected': {'testcomplex': np.cos(theta) + 1j*np.sin(theta)} + }) +A = np.zeros((3,5)) +A[0] = list(range(1,6)) +A[:,0] = list(range(1,4)) +case_table4.append( + {'name': 'matrix', + 'classes': {'testmatrix': 'double'}, + 'expected': {'testmatrix': A}, + }) +case_table4.append( + {'name': 'sparse', + 'classes': {'testsparse': 'sparse'}, + 'expected': {'testsparse': SP.coo_matrix(A)}, + }) +B = A.astype(complex) +B[0,0] += 1j +case_table4.append( + {'name': 'sparsecomplex', + 'classes': {'testsparsecomplex': 'sparse'}, + 'expected': {'testsparsecomplex': SP.coo_matrix(B)}, + }) +case_table4.append( + {'name': 'multi', + 'classes': {'theta': 'double', 'a': 'double'}, + 'expected': {'theta': theta, 'a': A}, + }) +case_table4.append( + {'name': 'minus', + 'classes': {'testminus': 'double'}, + 'expected': {'testminus': mlarr(-1)}, + }) +case_table4.append( + {'name': 'onechar', + 'classes': {'testonechar': 'char'}, + 'expected': {'testonechar': array(['r'])}, + }) +# Cell arrays stored as object arrays +CA = mlarr(( # tuple for object array creation + [], + mlarr([1]), + mlarr([[1,2]]), + mlarr([[1,2,3]])), dtype=object).reshape(1,-1) +CA[0,0] = array( + ['This cell contains this string and 3 arrays of increasing length']) +case_table5 = [ + {'name': 'cell', + 'classes': {'testcell': 'cell'}, + 'expected': {'testcell': CA}}] +CAE = mlarr(( # tuple for object array creation + mlarr(1), + mlarr(2), + mlarr([]), + mlarr([]), + mlarr(3)), dtype=object).reshape(1,-1) +objarr = np.empty((1,1),dtype=object) +objarr[0,0] = mlarr(1) +case_table5.append( + {'name': 'scalarcell', + 'classes': {'testscalarcell': 'cell'}, + 'expected': {'testscalarcell': objarr} + }) +case_table5.append( + {'name': 'emptycell', + 'classes': {'testemptycell': 'cell'}, + 'expected': {'testemptycell': CAE}}) +case_table5.append( + {'name': 'stringarray', + 'classes': {'teststringarray': 'char'}, + 'expected': {'teststringarray': array( + ['one ', 'two ', 'three'])}, + }) +case_table5.append( + {'name': '3dmatrix', + 'classes': {'test3dmatrix': 'double'}, + 'expected': { + 'test3dmatrix': np.transpose(np.reshape(list(range(1,25)), (4,3,2)))} + }) +st_sub_arr = array([np.sqrt(2),np.exp(1),np.pi]).reshape(1,3) +dtype = [(n, object) for n in ['stringfield', 'doublefield', 'complexfield']] +st1 = np.zeros((1,1), dtype) +st1['stringfield'][0,0] = array(['Rats live on no evil star.']) +st1['doublefield'][0,0] = st_sub_arr +st1['complexfield'][0,0] = st_sub_arr * (1 + 1j) +case_table5.append( + {'name': 'struct', + 'classes': {'teststruct': 'struct'}, + 'expected': {'teststruct': st1} + }) +CN = np.zeros((1,2), dtype=object) +CN[0,0] = mlarr(1) +CN[0,1] = np.zeros((1,3), dtype=object) +CN[0,1][0,0] = mlarr(2, dtype=np.uint8) +CN[0,1][0,1] = mlarr([[3]], dtype=np.uint8) +CN[0,1][0,2] = np.zeros((1,2), dtype=object) +CN[0,1][0,2][0,0] = mlarr(4, dtype=np.uint8) +CN[0,1][0,2][0,1] = mlarr(5, dtype=np.uint8) +case_table5.append( + {'name': 'cellnest', + 'classes': {'testcellnest': 'cell'}, + 'expected': {'testcellnest': CN}, + }) +st2 = np.empty((1,1), dtype=[(n, object) for n in ['one', 'two']]) +st2[0,0]['one'] = mlarr(1) +st2[0,0]['two'] = np.empty((1,1), dtype=[('three', object)]) +st2[0,0]['two'][0,0]['three'] = array(['number 3']) +case_table5.append( + {'name': 'structnest', + 'classes': {'teststructnest': 'struct'}, + 'expected': {'teststructnest': st2} + }) +a = np.empty((1,2), dtype=[(n, object) for n in ['one', 'two']]) +a[0,0]['one'] = mlarr(1) +a[0,0]['two'] = mlarr(2) +a[0,1]['one'] = array(['number 1']) +a[0,1]['two'] = array(['number 2']) +case_table5.append( + {'name': 'structarr', + 'classes': {'teststructarr': 'struct'}, + 'expected': {'teststructarr': a} + }) +ODT = np.dtype([(n, object) for n in + ['expr', 'inputExpr', 'args', + 'isEmpty', 'numArgs', 'version']]) +MO = MatlabObject(np.zeros((1,1), dtype=ODT), 'inline') +m0 = MO[0,0] +m0['expr'] = array(['x']) +m0['inputExpr'] = array([' x = INLINE_INPUTS_{1};']) +m0['args'] = array(['x']) +m0['isEmpty'] = mlarr(0) +m0['numArgs'] = mlarr(1) +m0['version'] = mlarr(1) +case_table5.append( + {'name': 'object', + 'classes': {'testobject': 'object'}, + 'expected': {'testobject': MO} + }) +fp_u_str = open(pjoin(test_data_path, 'japanese_utf8.txt'), 'rb') +u_str = fp_u_str.read().decode('utf-8') +fp_u_str.close() +case_table5.append( + {'name': 'unicode', + 'classes': {'testunicode': 'char'}, + 'expected': {'testunicode': array([u_str])} + }) +case_table5.append( + {'name': 'sparse', + 'classes': {'testsparse': 'sparse'}, + 'expected': {'testsparse': SP.coo_matrix(A)}, + }) +case_table5.append( + {'name': 'sparsecomplex', + 'classes': {'testsparsecomplex': 'sparse'}, + 'expected': {'testsparsecomplex': SP.coo_matrix(B)}, + }) +case_table5.append( + {'name': 'bool', + 'classes': {'testbools': 'logical'}, + 'expected': {'testbools': + array([[True], [False]])}, + }) + +case_table5_rt = case_table5[:] +# Inline functions can't be concatenated in matlab, so RT only +case_table5_rt.append( + {'name': 'objectarray', + 'classes': {'testobjectarray': 'object'}, + 'expected': {'testobjectarray': np.repeat(MO, 2).reshape(1,2)}}) + + +def types_compatible(var1, var2): + """Check if types are same or compatible. + + 0-D numpy scalars are compatible with bare python scalars. + """ + type1 = type(var1) + type2 = type(var2) + if type1 is type2: + return True + if type1 is np.ndarray and var1.shape == (): + return type(var1.item()) is type2 + if type2 is np.ndarray and var2.shape == (): + return type(var2.item()) is type1 + return False + + +def _check_level(label, expected, actual): + """ Check one level of a potentially nested array """ + if SP.issparse(expected): # allow different types of sparse matrices + assert_(SP.issparse(actual)) + assert_array_almost_equal(actual.toarray(), + expected.toarray(), + err_msg=label, + decimal=5) + return + # Check types are as expected + assert_(types_compatible(expected, actual), + f"Expected type {type(expected)}, got {type(actual)} at {label}") + # A field in a record array may not be an ndarray + # A scalar from a record array will be type np.void + if not isinstance(expected, + (np.void, np.ndarray, MatlabObject)): + assert_equal(expected, actual) + return + # This is an ndarray-like thing + assert_(expected.shape == actual.shape, + msg=f'Expected shape {expected.shape}, got {actual.shape} at {label}') + ex_dtype = expected.dtype + if ex_dtype.hasobject: # array of objects + if isinstance(expected, MatlabObject): + assert_equal(expected.classname, actual.classname) + for i, ev in enumerate(expected): + level_label = "%s, [%d], " % (label, i) + _check_level(level_label, ev, actual[i]) + return + if ex_dtype.fields: # probably recarray + for fn in ex_dtype.fields: + level_label = f"{label}, field {fn}, " + _check_level(level_label, + expected[fn], actual[fn]) + return + if ex_dtype.type in (str, # string or bool + np.str_, + np.bool_): + assert_equal(actual, expected, err_msg=label) + return + # Something numeric + assert_array_almost_equal(actual, expected, err_msg=label, decimal=5) + + +def _load_check_case(name, files, case): + for file_name in files: + matdict = loadmat(file_name, struct_as_record=True) + label = f"test {name}; file {file_name}" + for k, expected in case.items(): + k_label = f"{label}, variable {k}" + assert_(k in matdict, "Missing key at %s" % k_label) + _check_level(k_label, expected, matdict[k]) + + +def _whos_check_case(name, files, case, classes): + for file_name in files: + label = f"test {name}; file {file_name}" + + whos = whosmat(file_name) + + expected_whos = [ + (k, expected.shape, classes[k]) for k, expected in case.items()] + + whos.sort() + expected_whos.sort() + assert_equal(whos, expected_whos, + f"{label}: {whos!r} != {expected_whos!r}" + ) + + +# Round trip tests +def _rt_check_case(name, expected, format): + mat_stream = BytesIO() + savemat(mat_stream, expected, format=format) + mat_stream.seek(0) + _load_check_case(name, [mat_stream], expected) + + +# generator for tests +def _cases(version, filt='test%(name)s_*.mat'): + if version == '4': + cases = case_table4 + elif version == '5': + cases = case_table5 + else: + assert version == '5_rt' + cases = case_table5_rt + for case in cases: + name = case['name'] + expected = case['expected'] + if filt is None: + files = None + else: + use_filt = pjoin(test_data_path, filt % dict(name=name)) + files = glob(use_filt) + assert len(files) > 0, \ + f"No files for test {name} using filter {filt}" + classes = case['classes'] + yield name, files, expected, classes + + +@pytest.mark.parametrize('version', ('4', '5')) +def test_load(version): + for case in _cases(version): + _load_check_case(*case[:3]) + + +@pytest.mark.parametrize('version', ('4', '5')) +def test_whos(version): + for case in _cases(version): + _whos_check_case(*case) + + +# generator for round trip tests +@pytest.mark.parametrize('version, fmts', [ + ('4', ['4', '5']), + ('5_rt', ['5']), +]) +def test_round_trip(version, fmts): + for case in _cases(version, filt=None): + for fmt in fmts: + _rt_check_case(case[0], case[2], fmt) + + +def test_gzip_simple(): + xdense = np.zeros((20,20)) + xdense[2,3] = 2.3 + xdense[4,5] = 4.5 + x = SP.csc_matrix(xdense) + + name = 'gzip_test' + expected = {'x':x} + format = '4' + + tmpdir = mkdtemp() + try: + fname = pjoin(tmpdir,name) + mat_stream = gzip.open(fname, mode='wb') + savemat(mat_stream, expected, format=format) + mat_stream.close() + + mat_stream = gzip.open(fname, mode='rb') + actual = loadmat(mat_stream, struct_as_record=True) + mat_stream.close() + finally: + shutil.rmtree(tmpdir) + + assert_array_almost_equal(actual['x'].toarray(), + expected['x'].toarray(), + err_msg=repr(actual)) + + +def test_multiple_open(): + # Ticket #1039, on Windows: check that files are not left open + tmpdir = mkdtemp() + try: + x = dict(x=np.zeros((2, 2))) + + fname = pjoin(tmpdir, "a.mat") + + # Check that file is not left open + savemat(fname, x) + os.unlink(fname) + savemat(fname, x) + loadmat(fname) + os.unlink(fname) + + # Check that stream is left open + f = open(fname, 'wb') + savemat(f, x) + f.seek(0) + f.close() + + f = open(fname, 'rb') + loadmat(f) + f.seek(0) + f.close() + finally: + shutil.rmtree(tmpdir) + + +def test_mat73(): + # Check any hdf5 files raise an error + filenames = glob( + pjoin(test_data_path, 'testhdf5*.mat')) + assert_(len(filenames) > 0) + for filename in filenames: + fp = open(filename, 'rb') + assert_raises(NotImplementedError, + loadmat, + fp, + struct_as_record=True) + fp.close() + + +def test_warnings(): + # This test is an echo of the previous behavior, which was to raise a + # warning if the user triggered a search for mat files on the Python system + # path. We can remove the test in the next version after upcoming (0.13). + fname = pjoin(test_data_path, 'testdouble_7.1_GLNX86.mat') + with warnings.catch_warnings(): + warnings.simplefilter('error') + # This should not generate a warning + loadmat(fname, struct_as_record=True) + # This neither + loadmat(fname, struct_as_record=False) + + +def test_regression_653(): + # Saving a dictionary with only invalid keys used to raise an error. Now we + # save this as an empty struct in matlab space. + sio = BytesIO() + savemat(sio, {'d':{1:2}}, format='5') + back = loadmat(sio)['d'] + # Check we got an empty struct equivalent + assert_equal(back.shape, (1,1)) + assert_equal(back.dtype, np.dtype(object)) + assert_(back[0,0] is None) + + +def test_structname_len(): + # Test limit for length of field names in structs + lim = 31 + fldname = 'a' * lim + st1 = np.zeros((1,1), dtype=[(fldname, object)]) + savemat(BytesIO(), {'longstruct': st1}, format='5') + fldname = 'a' * (lim+1) + st1 = np.zeros((1,1), dtype=[(fldname, object)]) + assert_raises(ValueError, savemat, BytesIO(), + {'longstruct': st1}, format='5') + + +def test_4_and_long_field_names_incompatible(): + # Long field names option not supported in 4 + my_struct = np.zeros((1,1),dtype=[('my_fieldname',object)]) + assert_raises(ValueError, savemat, BytesIO(), + {'my_struct':my_struct}, format='4', long_field_names=True) + + +def test_long_field_names(): + # Test limit for length of field names in structs + lim = 63 + fldname = 'a' * lim + st1 = np.zeros((1,1), dtype=[(fldname, object)]) + savemat(BytesIO(), {'longstruct': st1}, format='5',long_field_names=True) + fldname = 'a' * (lim+1) + st1 = np.zeros((1,1), dtype=[(fldname, object)]) + assert_raises(ValueError, savemat, BytesIO(), + {'longstruct': st1}, format='5',long_field_names=True) + + +def test_long_field_names_in_struct(): + # Regression test - long_field_names was erased if you passed a struct + # within a struct + lim = 63 + fldname = 'a' * lim + cell = np.ndarray((1,2),dtype=object) + st1 = np.zeros((1,1), dtype=[(fldname, object)]) + cell[0,0] = st1 + cell[0,1] = st1 + savemat(BytesIO(), {'longstruct': cell}, format='5',long_field_names=True) + # + # Check to make sure it fails with long field names off + # + assert_raises(ValueError, savemat, BytesIO(), + {'longstruct': cell}, format='5', long_field_names=False) + + +def test_cell_with_one_thing_in_it(): + # Regression test - make a cell array that's 1 x 2 and put two + # strings in it. It works. Make a cell array that's 1 x 1 and put + # a string in it. It should work but, in the old days, it didn't. + cells = np.ndarray((1,2),dtype=object) + cells[0,0] = 'Hello' + cells[0,1] = 'World' + savemat(BytesIO(), {'x': cells}, format='5') + + cells = np.ndarray((1,1),dtype=object) + cells[0,0] = 'Hello, world' + savemat(BytesIO(), {'x': cells}, format='5') + + +def test_writer_properties(): + # Tests getting, setting of properties of matrix writer + mfw = MatFile5Writer(BytesIO()) + assert_equal(mfw.global_vars, []) + mfw.global_vars = ['avar'] + assert_equal(mfw.global_vars, ['avar']) + assert_equal(mfw.unicode_strings, False) + mfw.unicode_strings = True + assert_equal(mfw.unicode_strings, True) + assert_equal(mfw.long_field_names, False) + mfw.long_field_names = True + assert_equal(mfw.long_field_names, True) + + +def test_use_small_element(): + # Test whether we're using small data element or not + sio = BytesIO() + wtr = MatFile5Writer(sio) + # First check size for no sde for name + arr = np.zeros(10) + wtr.put_variables({'aaaaa': arr}) + w_sz = len(sio.getvalue()) + # Check small name results in largish difference in size + sio.truncate(0) + sio.seek(0) + wtr.put_variables({'aaaa': arr}) + assert_(w_sz - len(sio.getvalue()) > 4) + # Whereas increasing name size makes less difference + sio.truncate(0) + sio.seek(0) + wtr.put_variables({'aaaaaa': arr}) + assert_(len(sio.getvalue()) - w_sz < 4) + + +def test_save_dict(): + # Test that both dict and OrderedDict can be saved (as recarray), + # loaded as matstruct, and preserve order + ab_exp = np.array([[(1, 2)]], dtype=[('a', object), ('b', object)]) + for dict_type in (dict, OrderedDict): + # Initialize with tuples to keep order + d = dict_type([('a', 1), ('b', 2)]) + stream = BytesIO() + savemat(stream, {'dict': d}) + stream.seek(0) + vals = loadmat(stream)['dict'] + assert_equal(vals.dtype.names, ('a', 'b')) + assert_array_equal(vals, ab_exp) + + +def test_1d_shape(): + # New 5 behavior is 1D -> row vector + arr = np.arange(5) + for format in ('4', '5'): + # Column is the default + stream = BytesIO() + savemat(stream, {'oned': arr}, format=format) + vals = loadmat(stream) + assert_equal(vals['oned'].shape, (1, 5)) + # can be explicitly 'column' for oned_as + stream = BytesIO() + savemat(stream, {'oned':arr}, + format=format, + oned_as='column') + vals = loadmat(stream) + assert_equal(vals['oned'].shape, (5,1)) + # but different from 'row' + stream = BytesIO() + savemat(stream, {'oned':arr}, + format=format, + oned_as='row') + vals = loadmat(stream) + assert_equal(vals['oned'].shape, (1,5)) + + +def test_compression(): + arr = np.zeros(100).reshape((5,20)) + arr[2,10] = 1 + stream = BytesIO() + savemat(stream, {'arr':arr}) + raw_len = len(stream.getvalue()) + vals = loadmat(stream) + assert_array_equal(vals['arr'], arr) + stream = BytesIO() + savemat(stream, {'arr':arr}, do_compression=True) + compressed_len = len(stream.getvalue()) + vals = loadmat(stream) + assert_array_equal(vals['arr'], arr) + assert_(raw_len > compressed_len) + # Concatenate, test later + arr2 = arr.copy() + arr2[0,0] = 1 + stream = BytesIO() + savemat(stream, {'arr':arr, 'arr2':arr2}, do_compression=False) + vals = loadmat(stream) + assert_array_equal(vals['arr2'], arr2) + stream = BytesIO() + savemat(stream, {'arr':arr, 'arr2':arr2}, do_compression=True) + vals = loadmat(stream) + assert_array_equal(vals['arr2'], arr2) + + +def test_single_object(): + stream = BytesIO() + savemat(stream, {'A':np.array(1, dtype=object)}) + + +def test_skip_variable(): + # Test skipping over the first of two variables in a MAT file + # using mat_reader_factory and put_variables to read them in. + # + # This is a regression test of a problem that's caused by + # using the compressed file reader seek instead of the raw file + # I/O seek when skipping over a compressed chunk. + # + # The problem arises when the chunk is large: this file has + # a 256x256 array of random (uncompressible) doubles. + # + filename = pjoin(test_data_path,'test_skip_variable.mat') + # + # Prove that it loads with loadmat + # + d = loadmat(filename, struct_as_record=True) + assert_('first' in d) + assert_('second' in d) + # + # Make the factory + # + factory, file_opened = mat_reader_factory(filename, struct_as_record=True) + # + # This is where the factory breaks with an error in MatMatrixGetter.to_next + # + d = factory.get_variables('second') + assert_('second' in d) + factory.mat_stream.close() + + +def test_empty_struct(): + # ticket 885 + filename = pjoin(test_data_path,'test_empty_struct.mat') + # before ticket fix, this would crash with ValueError, empty data + # type + d = loadmat(filename, struct_as_record=True) + a = d['a'] + assert_equal(a.shape, (1,1)) + assert_equal(a.dtype, np.dtype(object)) + assert_(a[0,0] is None) + stream = BytesIO() + arr = np.array((), dtype='U') + # before ticket fix, this used to give data type not understood + savemat(stream, {'arr':arr}) + d = loadmat(stream) + a2 = d['arr'] + assert_array_equal(a2, arr) + + +def test_save_empty_dict(): + # saving empty dict also gives empty struct + stream = BytesIO() + savemat(stream, {'arr': {}}) + d = loadmat(stream) + a = d['arr'] + assert_equal(a.shape, (1,1)) + assert_equal(a.dtype, np.dtype(object)) + assert_(a[0,0] is None) + + +def assert_any_equal(output, alternatives): + """ Assert `output` is equal to at least one element in `alternatives` + """ + one_equal = False + for expected in alternatives: + if np.all(output == expected): + one_equal = True + break + assert_(one_equal) + + +def test_to_writeable(): + # Test to_writeable function + res = to_writeable(np.array([1])) # pass through ndarrays + assert_equal(res.shape, (1,)) + assert_array_equal(res, 1) + # Dict fields can be written in any order + expected1 = np.array([(1, 2)], dtype=[('a', '|O8'), ('b', '|O8')]) + expected2 = np.array([(2, 1)], dtype=[('b', '|O8'), ('a', '|O8')]) + alternatives = (expected1, expected2) + assert_any_equal(to_writeable({'a':1,'b':2}), alternatives) + # Fields with underscores discarded + assert_any_equal(to_writeable({'a':1,'b':2, '_c':3}), alternatives) + # Not-string fields discarded + assert_any_equal(to_writeable({'a':1,'b':2, 100:3}), alternatives) + # String fields that are valid Python identifiers discarded + assert_any_equal(to_writeable({'a':1,'b':2, '99':3}), alternatives) + # Object with field names is equivalent + + class klass: + pass + + c = klass + c.a = 1 + c.b = 2 + assert_any_equal(to_writeable(c), alternatives) + # empty list and tuple go to empty array + res = to_writeable([]) + assert_equal(res.shape, (0,)) + assert_equal(res.dtype.type, np.float64) + res = to_writeable(()) + assert_equal(res.shape, (0,)) + assert_equal(res.dtype.type, np.float64) + # None -> None + assert_(to_writeable(None) is None) + # String to strings + assert_equal(to_writeable('a string').dtype.type, np.str_) + # Scalars to numpy to NumPy scalars + res = to_writeable(1) + assert_equal(res.shape, ()) + assert_equal(res.dtype.type, np.array(1).dtype.type) + assert_array_equal(res, 1) + # Empty dict returns EmptyStructMarker + assert_(to_writeable({}) is EmptyStructMarker) + # Object does not have (even empty) __dict__ + assert_(to_writeable(object()) is None) + # Custom object does have empty __dict__, returns EmptyStructMarker + + class C: + pass + + assert_(to_writeable(c()) is EmptyStructMarker) + # dict keys with legal characters are convertible + res = to_writeable({'a': 1})['a'] + assert_equal(res.shape, (1,)) + assert_equal(res.dtype.type, np.object_) + # Only fields with illegal characters, falls back to EmptyStruct + assert_(to_writeable({'1':1}) is EmptyStructMarker) + assert_(to_writeable({'_a':1}) is EmptyStructMarker) + # Unless there are valid fields, in which case structured array + assert_equal(to_writeable({'1':1, 'f': 2}), + np.array([(2,)], dtype=[('f', '|O8')])) + + +def test_recarray(): + # check roundtrip of structured array + dt = [('f1', 'f8'), + ('f2', 'S10')] + arr = np.zeros((2,), dtype=dt) + arr[0]['f1'] = 0.5 + arr[0]['f2'] = 'python' + arr[1]['f1'] = 99 + arr[1]['f2'] = 'not perl' + stream = BytesIO() + savemat(stream, {'arr': arr}) + d = loadmat(stream, struct_as_record=False) + a20 = d['arr'][0,0] + assert_equal(a20.f1, 0.5) + assert_equal(a20.f2, 'python') + d = loadmat(stream, struct_as_record=True) + a20 = d['arr'][0,0] + assert_equal(a20['f1'], 0.5) + assert_equal(a20['f2'], 'python') + # structs always come back as object types + assert_equal(a20.dtype, np.dtype([('f1', 'O'), + ('f2', 'O')])) + a21 = d['arr'].flat[1] + assert_equal(a21['f1'], 99) + assert_equal(a21['f2'], 'not perl') + + +def test_save_object(): + class C: + pass + c = C() + c.field1 = 1 + c.field2 = 'a string' + stream = BytesIO() + savemat(stream, {'c': c}) + d = loadmat(stream, struct_as_record=False) + c2 = d['c'][0,0] + assert_equal(c2.field1, 1) + assert_equal(c2.field2, 'a string') + d = loadmat(stream, struct_as_record=True) + c2 = d['c'][0,0] + assert_equal(c2['field1'], 1) + assert_equal(c2['field2'], 'a string') + + +def test_read_opts(): + # tests if read is seeing option sets, at initialization and after + # initialization + arr = np.arange(6).reshape(1,6) + stream = BytesIO() + savemat(stream, {'a': arr}) + rdr = MatFile5Reader(stream) + back_dict = rdr.get_variables() + rarr = back_dict['a'] + assert_array_equal(rarr, arr) + rdr = MatFile5Reader(stream, squeeze_me=True) + assert_array_equal(rdr.get_variables()['a'], arr.reshape((6,))) + rdr.squeeze_me = False + assert_array_equal(rarr, arr) + rdr = MatFile5Reader(stream, byte_order=boc.native_code) + assert_array_equal(rdr.get_variables()['a'], arr) + # inverted byte code leads to error on read because of swapped + # header etc. + rdr = MatFile5Reader(stream, byte_order=boc.swapped_code) + assert_raises(Exception, rdr.get_variables) + rdr.byte_order = boc.native_code + assert_array_equal(rdr.get_variables()['a'], arr) + arr = np.array(['a string']) + stream.truncate(0) + stream.seek(0) + savemat(stream, {'a': arr}) + rdr = MatFile5Reader(stream) + assert_array_equal(rdr.get_variables()['a'], arr) + rdr = MatFile5Reader(stream, chars_as_strings=False) + carr = np.atleast_2d(np.array(list(arr.item()), dtype='U1')) + assert_array_equal(rdr.get_variables()['a'], carr) + rdr.chars_as_strings = True + assert_array_equal(rdr.get_variables()['a'], arr) + + +def test_empty_string(): + # make sure reading empty string does not raise error + estring_fname = pjoin(test_data_path, 'single_empty_string.mat') + fp = open(estring_fname, 'rb') + rdr = MatFile5Reader(fp) + d = rdr.get_variables() + fp.close() + assert_array_equal(d['a'], np.array([], dtype='U1')) + # Empty string round trip. Matlab cannot distinguish + # between a string array that is empty, and a string array + # containing a single empty string, because it stores strings as + # arrays of char. There is no way of having an array of char that + # is not empty, but contains an empty string. + stream = BytesIO() + savemat(stream, {'a': np.array([''])}) + rdr = MatFile5Reader(stream) + d = rdr.get_variables() + assert_array_equal(d['a'], np.array([], dtype='U1')) + stream.truncate(0) + stream.seek(0) + savemat(stream, {'a': np.array([], dtype='U1')}) + rdr = MatFile5Reader(stream) + d = rdr.get_variables() + assert_array_equal(d['a'], np.array([], dtype='U1')) + stream.close() + + +def test_corrupted_data(): + import zlib + for exc, fname in [(ValueError, 'corrupted_zlib_data.mat'), + (zlib.error, 'corrupted_zlib_checksum.mat')]: + with open(pjoin(test_data_path, fname), 'rb') as fp: + rdr = MatFile5Reader(fp) + assert_raises(exc, rdr.get_variables) + + +def test_corrupted_data_check_can_be_disabled(): + with open(pjoin(test_data_path, 'corrupted_zlib_data.mat'), 'rb') as fp: + rdr = MatFile5Reader(fp, verify_compressed_data_integrity=False) + rdr.get_variables() + + +def test_read_both_endian(): + # make sure big- and little- endian data is read correctly + for fname in ('big_endian.mat', 'little_endian.mat'): + fp = open(pjoin(test_data_path, fname), 'rb') + rdr = MatFile5Reader(fp) + d = rdr.get_variables() + fp.close() + assert_array_equal(d['strings'], + np.array([['hello'], + ['world']], dtype=object)) + assert_array_equal(d['floats'], + np.array([[2., 3.], + [3., 4.]], dtype=np.float32)) + + +def test_write_opposite_endian(): + # We don't support writing opposite endian .mat files, but we need to behave + # correctly if the user supplies an other-endian NumPy array to write out. + float_arr = np.array([[2., 3.], + [3., 4.]]) + int_arr = np.arange(6).reshape((2, 3)) + uni_arr = np.array(['hello', 'world'], dtype='U') + stream = BytesIO() + savemat(stream, { + 'floats': float_arr.byteswap().view(float_arr.dtype.newbyteorder()), + 'ints': int_arr.byteswap().view(int_arr.dtype.newbyteorder()), + 'uni_arr': uni_arr.byteswap().view(uni_arr.dtype.newbyteorder()), + }) + rdr = MatFile5Reader(stream) + d = rdr.get_variables() + assert_array_equal(d['floats'], float_arr) + assert_array_equal(d['ints'], int_arr) + assert_array_equal(d['uni_arr'], uni_arr) + stream.close() + + +def test_logical_array(): + # The roundtrip test doesn't verify that we load the data up with the + # correct (bool) dtype + with open(pjoin(test_data_path, 'testbool_8_WIN64.mat'), 'rb') as fobj: + rdr = MatFile5Reader(fobj, mat_dtype=True) + d = rdr.get_variables() + x = np.array([[True], [False]], dtype=np.bool_) + assert_array_equal(d['testbools'], x) + assert_equal(d['testbools'].dtype, x.dtype) + + +def test_logical_out_type(): + # Confirm that bool type written as uint8, uint8 class + # See gh-4022 + stream = BytesIO() + barr = np.array([False, True, False]) + savemat(stream, {'barray': barr}) + stream.seek(0) + reader = MatFile5Reader(stream) + reader.initialize_read() + reader.read_file_header() + hdr, _ = reader.read_var_header() + assert_equal(hdr.mclass, mio5p.mxUINT8_CLASS) + assert_equal(hdr.is_logical, True) + var = reader.read_var_array(hdr, False) + assert_equal(var.dtype.type, np.uint8) + + +def test_roundtrip_zero_dimensions(): + stream = BytesIO() + savemat(stream, {'d':np.empty((10, 0))}) + d = loadmat(stream) + assert d['d'].shape == (10, 0) + + +def test_mat4_3d(): + # test behavior when writing 3-D arrays to matlab 4 files + stream = BytesIO() + arr = np.arange(24).reshape((2,3,4)) + assert_raises(ValueError, savemat, stream, {'a': arr}, True, '4') + + +def test_func_read(): + func_eg = pjoin(test_data_path, 'testfunc_7.4_GLNX86.mat') + fp = open(func_eg, 'rb') + rdr = MatFile5Reader(fp) + d = rdr.get_variables() + fp.close() + assert isinstance(d['testfunc'], MatlabFunction) + stream = BytesIO() + wtr = MatFile5Writer(stream) + assert_raises(MatWriteError, wtr.put_variables, d) + + +def test_mat_dtype(): + double_eg = pjoin(test_data_path, 'testmatrix_6.1_SOL2.mat') + fp = open(double_eg, 'rb') + rdr = MatFile5Reader(fp, mat_dtype=False) + d = rdr.get_variables() + fp.close() + assert_equal(d['testmatrix'].dtype.kind, 'u') + + fp = open(double_eg, 'rb') + rdr = MatFile5Reader(fp, mat_dtype=True) + d = rdr.get_variables() + fp.close() + assert_equal(d['testmatrix'].dtype.kind, 'f') + + +def test_sparse_in_struct(): + # reproduces bug found by DC where Cython code was insisting on + # ndarray return type, but getting sparse matrix + st = {'sparsefield': SP.coo_matrix(np.eye(4))} + stream = BytesIO() + savemat(stream, {'a':st}) + d = loadmat(stream, struct_as_record=True) + assert_array_equal(d['a'][0, 0]['sparsefield'].toarray(), np.eye(4)) + + +def test_mat_struct_squeeze(): + stream = BytesIO() + in_d = {'st':{'one':1, 'two':2}} + savemat(stream, in_d) + # no error without squeeze + loadmat(stream, struct_as_record=False) + # previous error was with squeeze, with mat_struct + loadmat(stream, struct_as_record=False, squeeze_me=True) + + +def test_scalar_squeeze(): + stream = BytesIO() + in_d = {'scalar': [[0.1]], 'string': 'my name', 'st':{'one':1, 'two':2}} + savemat(stream, in_d) + out_d = loadmat(stream, squeeze_me=True) + assert_(isinstance(out_d['scalar'], float)) + assert_(isinstance(out_d['string'], str)) + assert_(isinstance(out_d['st'], np.ndarray)) + + +def test_str_round(): + # from report by Angus McMorland on mailing list 3 May 2010 + stream = BytesIO() + in_arr = np.array(['Hello', 'Foob']) + out_arr = np.array(['Hello', 'Foob ']) + savemat(stream, dict(a=in_arr)) + res = loadmat(stream) + # resulted in ['HloolFoa', 'elWrdobr'] + assert_array_equal(res['a'], out_arr) + stream.truncate(0) + stream.seek(0) + # Make Fortran ordered version of string + in_str = in_arr.tobytes(order='F') + in_from_str = np.ndarray(shape=a.shape, + dtype=in_arr.dtype, + order='F', + buffer=in_str) + savemat(stream, dict(a=in_from_str)) + assert_array_equal(res['a'], out_arr) + # unicode save did lead to buffer too small error + stream.truncate(0) + stream.seek(0) + in_arr_u = in_arr.astype('U') + out_arr_u = out_arr.astype('U') + savemat(stream, {'a': in_arr_u}) + res = loadmat(stream) + assert_array_equal(res['a'], out_arr_u) + + +def test_fieldnames(): + # Check that field names are as expected + stream = BytesIO() + savemat(stream, {'a': {'a':1, 'b':2}}) + res = loadmat(stream) + field_names = res['a'].dtype.names + assert_equal(set(field_names), {'a', 'b'}) + + +def test_loadmat_varnames(): + # Test that we can get just one variable from a mat file using loadmat + mat5_sys_names = ['__globals__', + '__header__', + '__version__'] + for eg_file, sys_v_names in ( + (pjoin(test_data_path, 'testmulti_4.2c_SOL2.mat'), []), (pjoin( + test_data_path, 'testmulti_7.4_GLNX86.mat'), mat5_sys_names)): + vars = loadmat(eg_file) + assert_equal(set(vars.keys()), set(['a', 'theta'] + sys_v_names)) + vars = loadmat(eg_file, variable_names='a') + assert_equal(set(vars.keys()), set(['a'] + sys_v_names)) + vars = loadmat(eg_file, variable_names=['a']) + assert_equal(set(vars.keys()), set(['a'] + sys_v_names)) + vars = loadmat(eg_file, variable_names=['theta']) + assert_equal(set(vars.keys()), set(['theta'] + sys_v_names)) + vars = loadmat(eg_file, variable_names=('theta',)) + assert_equal(set(vars.keys()), set(['theta'] + sys_v_names)) + vars = loadmat(eg_file, variable_names=[]) + assert_equal(set(vars.keys()), set(sys_v_names)) + vnames = ['theta'] + vars = loadmat(eg_file, variable_names=vnames) + assert_equal(vnames, ['theta']) + + +def test_round_types(): + # Check that saving, loading preserves dtype in most cases + arr = np.arange(10) + stream = BytesIO() + for dts in ('f8','f4','i8','i4','i2','i1', + 'u8','u4','u2','u1','c16','c8'): + stream.truncate(0) + stream.seek(0) # needed for BytesIO in Python 3 + savemat(stream, {'arr': arr.astype(dts)}) + vars = loadmat(stream) + assert_equal(np.dtype(dts), vars['arr'].dtype) + + +def test_varmats_from_mat(): + # Make a mat file with several variables, write it, read it back + names_vars = (('arr', mlarr(np.arange(10))), + ('mystr', mlarr('a string')), + ('mynum', mlarr(10))) + + # Dict like thing to give variables in defined order + class C: + def items(self): + return names_vars + stream = BytesIO() + savemat(stream, C()) + varmats = varmats_from_mat(stream) + assert_equal(len(varmats), 3) + for i in range(3): + name, var_stream = varmats[i] + exp_name, exp_res = names_vars[i] + assert_equal(name, exp_name) + res = loadmat(var_stream) + assert_array_equal(res[name], exp_res) + + +def test_one_by_zero(): + # Test 1x0 chars get read correctly + func_eg = pjoin(test_data_path, 'one_by_zero_char.mat') + fp = open(func_eg, 'rb') + rdr = MatFile5Reader(fp) + d = rdr.get_variables() + fp.close() + assert_equal(d['var'].shape, (0,)) + + +def test_load_mat4_le(): + # We were getting byte order wrong when reading little-endian floa64 dense + # matrices on big-endian platforms + mat4_fname = pjoin(test_data_path, 'test_mat4_le_floats.mat') + vars = loadmat(mat4_fname) + assert_array_equal(vars['a'], [[0.1, 1.2]]) + + +def test_unicode_mat4(): + # Mat4 should save unicode as latin1 + bio = BytesIO() + var = {'second_cat': 'Schrödinger'} + savemat(bio, var, format='4') + var_back = loadmat(bio) + assert_equal(var_back['second_cat'], var['second_cat']) + + +def test_logical_sparse(): + # Test we can read logical sparse stored in mat file as bytes. + # See https://github.com/scipy/scipy/issues/3539. + # In some files saved by MATLAB, the sparse data elements (Real Part + # Subelement in MATLAB speak) are stored with apparent type double + # (miDOUBLE) but are in fact single bytes. + filename = pjoin(test_data_path,'logical_sparse.mat') + # Before fix, this would crash with: + # ValueError: indices and data should have the same size + d = loadmat(filename, struct_as_record=True) + log_sp = d['sp_log_5_4'] + assert_(isinstance(log_sp, SP.csc_matrix)) + assert_equal(log_sp.dtype.type, np.bool_) + assert_array_equal(log_sp.toarray(), + [[True, True, True, False], + [False, False, True, False], + [False, False, True, False], + [False, False, False, False], + [False, False, False, False]]) + + +def test_empty_sparse(): + # Can we read empty sparse matrices? + sio = BytesIO() + import scipy.sparse + empty_sparse = scipy.sparse.csr_matrix([[0,0],[0,0]]) + savemat(sio, dict(x=empty_sparse)) + sio.seek(0) + res = loadmat(sio) + assert_array_equal(res['x'].shape, empty_sparse.shape) + assert_array_equal(res['x'].toarray(), 0) + # Do empty sparse matrices get written with max nnz 1? + # See https://github.com/scipy/scipy/issues/4208 + sio.seek(0) + reader = MatFile5Reader(sio) + reader.initialize_read() + reader.read_file_header() + hdr, _ = reader.read_var_header() + assert_equal(hdr.nzmax, 1) + + +def test_empty_mat_error(): + # Test we get a specific warning for an empty mat file + sio = BytesIO() + assert_raises(MatReadError, loadmat, sio) + + +def test_miuint32_compromise(): + # Reader should accept miUINT32 for miINT32, but check signs + # mat file with miUINT32 for miINT32, but OK values + filename = pjoin(test_data_path, 'miuint32_for_miint32.mat') + res = loadmat(filename) + assert_equal(res['an_array'], np.arange(10)[None, :]) + # mat file with miUINT32 for miINT32, with negative value + filename = pjoin(test_data_path, 'bad_miuint32.mat') + with assert_raises(ValueError): + loadmat(filename) + + +def test_miutf8_for_miint8_compromise(): + # Check reader accepts ascii as miUTF8 for array names + filename = pjoin(test_data_path, 'miutf8_array_name.mat') + res = loadmat(filename) + assert_equal(res['array_name'], [[1]]) + # mat file with non-ascii utf8 name raises error + filename = pjoin(test_data_path, 'bad_miutf8_array_name.mat') + with assert_raises(ValueError): + loadmat(filename) + + +def test_bad_utf8(): + # Check that reader reads bad UTF with 'replace' option + filename = pjoin(test_data_path,'broken_utf8.mat') + res = loadmat(filename) + assert_equal(res['bad_string'], + b'\x80 am broken'.decode('utf8', 'replace')) + + +def test_save_unicode_field(tmpdir): + filename = os.path.join(str(tmpdir), 'test.mat') + test_dict = {'a':{'b':1,'c':'test_str'}} + savemat(filename, test_dict) + + +def test_save_custom_array_type(tmpdir): + class CustomArray: + def __array__(self, dtype=None, copy=None): + return np.arange(6.0).reshape(2, 3) + a = CustomArray() + filename = os.path.join(str(tmpdir), 'test.mat') + savemat(filename, {'a': a}) + out = loadmat(filename) + assert_array_equal(out['a'], np.array(a)) + + +def test_filenotfound(): + # Check the correct error is thrown + assert_raises(OSError, loadmat, "NotExistentFile00.mat") + assert_raises(OSError, loadmat, "NotExistentFile00") + + +def test_simplify_cells(): + # Test output when simplify_cells=True + filename = pjoin(test_data_path, 'testsimplecell.mat') + res1 = loadmat(filename, simplify_cells=True) + res2 = loadmat(filename, simplify_cells=False) + assert_(isinstance(res1["s"], dict)) + assert_(isinstance(res2["s"], np.ndarray)) + assert_array_equal(res1["s"]["mycell"], np.array(["a", "b", "c"])) + + +@pytest.mark.parametrize('version, filt, regex', [ + (0, '_4*_*', None), + (1, '_5*_*', None), + (1, '_6*_*', None), + (1, '_7*_*', '^((?!hdf5).)*$'), # not containing hdf5 + (2, '_7*_*', '.*hdf5.*'), + (1, '8*_*', None), +]) +def test_matfile_version(version, filt, regex): + use_filt = pjoin(test_data_path, 'test*%s.mat' % filt) + files = glob(use_filt) + if regex is not None: + files = [file for file in files if re.match(regex, file) is not None] + assert len(files) > 0, \ + f"No files for version {version} using filter {filt}" + for file in files: + got_version = matfile_version(file) + assert got_version[0] == version + + +def test_opaque(): + """Test that we can read a MatlabOpaque object.""" + data = loadmat(pjoin(test_data_path, 'parabola.mat')) + assert isinstance(data['parabola'], MatlabFunction) + assert isinstance(data['parabola'].item()[3].item()[3], MatlabOpaque) + + +def test_opaque_simplify(): + """Test that we can read a MatlabOpaque object when simplify_cells=True.""" + data = loadmat(pjoin(test_data_path, 'parabola.mat'), simplify_cells=True) + assert isinstance(data['parabola'], MatlabFunction) + + +def test_deprecation(): + """Test that access to previous attributes still works.""" + # This should be accessible immediately from scipy.io import + with assert_warns(DeprecationWarning): + scipy.io.matlab.mio5_params.MatlabOpaque + + # These should be importable but warn as well + with assert_warns(DeprecationWarning): + from scipy.io.matlab.miobase import MatReadError # noqa: F401 + + +def test_gh_17992(tmp_path): + rng = np.random.default_rng(12345) + outfile = tmp_path / "lists.mat" + array_one = rng.random((5,3)) + array_two = rng.random((6,3)) + list_of_arrays = [array_one, array_two] + # warning suppression only needed for NumPy < 1.24.0 + with np.testing.suppress_warnings() as sup: + sup.filter(VisibleDeprecationWarning) + savemat(outfile, + {'data': list_of_arrays}, + long_field_names=True, + do_compression=True) + # round trip check + new_dict = {} + loadmat(outfile, + new_dict) + assert_allclose(new_dict["data"][0][0], array_one) + assert_allclose(new_dict["data"][0][1], array_two) + + +def test_gh_19659(tmp_path): + d = { + "char_array": np.array([list("char"), list("char")], dtype="U1"), + "string_array": np.array(["string", "string"]), + } + outfile = tmp_path / "tmp.mat" + # should not error: + savemat(outfile, d, format="4") diff --git a/venv/lib/python3.10/site-packages/scipy/io/matlab/tests/test_mio5_utils.py b/venv/lib/python3.10/site-packages/scipy/io/matlab/tests/test_mio5_utils.py new file mode 100644 index 0000000000000000000000000000000000000000..b3f27114c4a4ed10c1a2526058f4d0dbbd0e5638 --- /dev/null +++ b/venv/lib/python3.10/site-packages/scipy/io/matlab/tests/test_mio5_utils.py @@ -0,0 +1,179 @@ +""" Testing mio5_utils Cython module + +""" +import sys + +from io import BytesIO + +import numpy as np + +from numpy.testing import assert_array_equal, assert_equal, assert_ +from pytest import raises as assert_raises + +import scipy.io.matlab._byteordercodes as boc +import scipy.io.matlab._streams as streams +import scipy.io.matlab._mio5_params as mio5p +import scipy.io.matlab._mio5_utils as m5u + + +def test_byteswap(): + for val in ( + 1, + 0x100, + 0x10000): + a = np.array(val, dtype=np.uint32) + b = a.byteswap() + c = m5u.byteswap_u4(a) + assert_equal(b.item(), c) + d = m5u.byteswap_u4(c) + assert_equal(a.item(), d) + + +def _make_tag(base_dt, val, mdtype, sde=False): + ''' Makes a simple matlab tag, full or sde ''' + base_dt = np.dtype(base_dt) + bo = boc.to_numpy_code(base_dt.byteorder) + byte_count = base_dt.itemsize + if not sde: + udt = bo + 'u4' + padding = 8 - (byte_count % 8) + all_dt = [('mdtype', udt), + ('byte_count', udt), + ('val', base_dt)] + if padding: + all_dt.append(('padding', 'u1', padding)) + else: # is sde + udt = bo + 'u2' + padding = 4-byte_count + if bo == '<': # little endian + all_dt = [('mdtype', udt), + ('byte_count', udt), + ('val', base_dt)] + else: # big endian + all_dt = [('byte_count', udt), + ('mdtype', udt), + ('val', base_dt)] + if padding: + all_dt.append(('padding', 'u1', padding)) + tag = np.zeros((1,), dtype=all_dt) + tag['mdtype'] = mdtype + tag['byte_count'] = byte_count + tag['val'] = val + return tag + + +def _write_stream(stream, *strings): + stream.truncate(0) + stream.seek(0) + for s in strings: + stream.write(s) + stream.seek(0) + + +def _make_readerlike(stream, byte_order=boc.native_code): + class R: + pass + r = R() + r.mat_stream = stream + r.byte_order = byte_order + r.struct_as_record = True + r.uint16_codec = sys.getdefaultencoding() + r.chars_as_strings = False + r.mat_dtype = False + r.squeeze_me = False + return r + + +def test_read_tag(): + # mainly to test errors + # make reader-like thing + str_io = BytesIO() + r = _make_readerlike(str_io) + c_reader = m5u.VarReader5(r) + # This works for StringIO but _not_ BytesIO + assert_raises(OSError, c_reader.read_tag) + # bad SDE + tag = _make_tag('i4', 1, mio5p.miINT32, sde=True) + tag['byte_count'] = 5 + _write_stream(str_io, tag.tobytes()) + assert_raises(ValueError, c_reader.read_tag) + + +def test_read_stream(): + tag = _make_tag('i4', 1, mio5p.miINT32, sde=True) + tag_str = tag.tobytes() + str_io = BytesIO(tag_str) + st = streams.make_stream(str_io) + s = streams._read_into(st, tag.itemsize) + assert_equal(s, tag.tobytes()) + + +def test_read_numeric(): + # make reader-like thing + str_io = BytesIO() + r = _make_readerlike(str_io) + # check simplest of tags + for base_dt, val, mdtype in (('u2', 30, mio5p.miUINT16), + ('i4', 1, mio5p.miINT32), + ('i2', -1, mio5p.miINT16)): + for byte_code in ('<', '>'): + r.byte_order = byte_code + c_reader = m5u.VarReader5(r) + assert_equal(c_reader.little_endian, byte_code == '<') + assert_equal(c_reader.is_swapped, byte_code != boc.native_code) + for sde_f in (False, True): + dt = np.dtype(base_dt).newbyteorder(byte_code) + a = _make_tag(dt, val, mdtype, sde_f) + a_str = a.tobytes() + _write_stream(str_io, a_str) + el = c_reader.read_numeric() + assert_equal(el, val) + # two sequential reads + _write_stream(str_io, a_str, a_str) + el = c_reader.read_numeric() + assert_equal(el, val) + el = c_reader.read_numeric() + assert_equal(el, val) + + +def test_read_numeric_writeable(): + # make reader-like thing + str_io = BytesIO() + r = _make_readerlike(str_io, '<') + c_reader = m5u.VarReader5(r) + dt = np.dtype('' + rdr.mat_stream.read(4) # presumably byte padding + mdict = read_minimat_vars(rdr) + fp.close() + return mdict + + +def test_jottings(): + # example + fname = os.path.join(test_data_path, 'parabola.mat') + read_workspace_vars(fname) diff --git a/venv/lib/python3.10/site-packages/scipy/io/matlab/tests/test_mio_utils.py b/venv/lib/python3.10/site-packages/scipy/io/matlab/tests/test_mio_utils.py new file mode 100644 index 0000000000000000000000000000000000000000..1d19a9797faa2221307a7330b69fffa26410f624 --- /dev/null +++ b/venv/lib/python3.10/site-packages/scipy/io/matlab/tests/test_mio_utils.py @@ -0,0 +1,45 @@ +""" Testing + +""" + +import numpy as np + +from numpy.testing import assert_array_equal, assert_ + +from scipy.io.matlab._mio_utils import squeeze_element, chars_to_strings + + +def test_squeeze_element(): + a = np.zeros((1,3)) + assert_array_equal(np.squeeze(a), squeeze_element(a)) + # 0-D output from squeeze gives scalar + sq_int = squeeze_element(np.zeros((1,1), dtype=float)) + assert_(isinstance(sq_int, float)) + # Unless it's a structured array + sq_sa = squeeze_element(np.zeros((1,1),dtype=[('f1', 'f')])) + assert_(isinstance(sq_sa, np.ndarray)) + # Squeezing empty arrays maintain their dtypes. + sq_empty = squeeze_element(np.empty(0, np.uint8)) + assert sq_empty.dtype == np.uint8 + + +def test_chars_strings(): + # chars as strings + strings = ['learn ', 'python', 'fast ', 'here '] + str_arr = np.array(strings, dtype='U6') # shape (4,) + chars = [list(s) for s in strings] + char_arr = np.array(chars, dtype='U1') # shape (4,6) + assert_array_equal(chars_to_strings(char_arr), str_arr) + ca2d = char_arr.reshape((2,2,6)) + sa2d = str_arr.reshape((2,2)) + assert_array_equal(chars_to_strings(ca2d), sa2d) + ca3d = char_arr.reshape((1,2,2,6)) + sa3d = str_arr.reshape((1,2,2)) + assert_array_equal(chars_to_strings(ca3d), sa3d) + # Fortran ordered arrays + char_arrf = np.array(chars, dtype='U1', order='F') # shape (4,6) + assert_array_equal(chars_to_strings(char_arrf), str_arr) + # empty array + arr = np.array([['']], dtype='U1') + out_arr = np.array([''], dtype='U1') + assert_array_equal(chars_to_strings(arr), out_arr) diff --git a/venv/lib/python3.10/site-packages/scipy/io/matlab/tests/test_miobase.py b/venv/lib/python3.10/site-packages/scipy/io/matlab/tests/test_miobase.py new file mode 100644 index 0000000000000000000000000000000000000000..e07024f980823ce54ef7aa9ad08586f426d94b25 --- /dev/null +++ b/venv/lib/python3.10/site-packages/scipy/io/matlab/tests/test_miobase.py @@ -0,0 +1,32 @@ +""" Testing miobase module +""" + +import numpy as np + +from numpy.testing import assert_equal +from pytest import raises as assert_raises + +from scipy.io.matlab._miobase import matdims + + +def test_matdims(): + # Test matdims dimension finder + assert_equal(matdims(np.array(1)), (1, 1)) # NumPy scalar + assert_equal(matdims(np.array([1])), (1, 1)) # 1-D array, 1 element + assert_equal(matdims(np.array([1,2])), (2, 1)) # 1-D array, 2 elements + assert_equal(matdims(np.array([[2],[3]])), (2, 1)) # 2-D array, column vector + assert_equal(matdims(np.array([[2,3]])), (1, 2)) # 2-D array, row vector + # 3d array, rowish vector + assert_equal(matdims(np.array([[[2,3]]])), (1, 1, 2)) + assert_equal(matdims(np.array([])), (0, 0)) # empty 1-D array + assert_equal(matdims(np.array([[]])), (1, 0)) # empty 2-D array + assert_equal(matdims(np.array([[[]]])), (1, 1, 0)) # empty 3-D array + assert_equal(matdims(np.empty((1, 0, 1))), (1, 0, 1)) # empty 3-D array + # Optional argument flips 1-D shape behavior. + assert_equal(matdims(np.array([1,2]), 'row'), (1, 2)) # 1-D array, 2 elements + # The argument has to make sense though + assert_raises(ValueError, matdims, np.array([1,2]), 'bizarre') + # Check empty sparse matrices get their own shape + from scipy.sparse import csr_matrix, csc_matrix + assert_equal(matdims(csr_matrix(np.zeros((3, 3)))), (3, 3)) + assert_equal(matdims(csc_matrix(np.zeros((2, 2)))), (2, 2)) diff --git a/venv/lib/python3.10/site-packages/scipy/io/matlab/tests/test_pathological.py b/venv/lib/python3.10/site-packages/scipy/io/matlab/tests/test_pathological.py new file mode 100644 index 0000000000000000000000000000000000000000..c5c86decb7e90f69f293e90eba74fb47dd4f1277 --- /dev/null +++ b/venv/lib/python3.10/site-packages/scipy/io/matlab/tests/test_pathological.py @@ -0,0 +1,33 @@ +""" Test reading of files not conforming to matlab specification + +We try and read any file that matlab reads, these files included +""" +from os.path import dirname, join as pjoin + +from numpy.testing import assert_ +from pytest import raises as assert_raises + +from scipy.io.matlab._mio import loadmat + +TEST_DATA_PATH = pjoin(dirname(__file__), 'data') + + +def test_multiple_fieldnames(): + # Example provided by Dharhas Pothina + # Extracted using mio5.varmats_from_mat + multi_fname = pjoin(TEST_DATA_PATH, 'nasty_duplicate_fieldnames.mat') + vars = loadmat(multi_fname) + funny_names = vars['Summary'].dtype.names + assert_({'_1_Station_Q', '_2_Station_Q', + '_3_Station_Q'}.issubset(funny_names)) + + +def test_malformed1(): + # Example from gh-6072 + # Contains malformed header data, which previously resulted into a + # buffer overflow. + # + # Should raise an exception, not segfault + fname = pjoin(TEST_DATA_PATH, 'malformed1.mat') + with open(fname, 'rb') as f: + assert_raises(ValueError, loadmat, f) diff --git a/venv/lib/python3.10/site-packages/scipy/io/matlab/tests/test_streams.py b/venv/lib/python3.10/site-packages/scipy/io/matlab/tests/test_streams.py new file mode 100644 index 0000000000000000000000000000000000000000..d8768d8e9251c6e47debeb65dff3ec056d38ee56 --- /dev/null +++ b/venv/lib/python3.10/site-packages/scipy/io/matlab/tests/test_streams.py @@ -0,0 +1,232 @@ +""" Testing + +""" + +import os +import zlib + +from io import BytesIO + + +from tempfile import mkstemp +from contextlib import contextmanager + +import numpy as np + +from numpy.testing import assert_, assert_equal +from pytest import raises as assert_raises + +from scipy.io.matlab._streams import (make_stream, + GenericStream, ZlibInputStream, + _read_into, _read_string, BLOCK_SIZE) + + +@contextmanager +def setup_test_file(): + val = b'a\x00string' + fd, fname = mkstemp() + + with os.fdopen(fd, 'wb') as fs: + fs.write(val) + with open(fname, 'rb') as fs: + gs = BytesIO(val) + cs = BytesIO(val) + yield fs, gs, cs + os.unlink(fname) + + +def test_make_stream(): + with setup_test_file() as (fs, gs, cs): + # test stream initialization + assert_(isinstance(make_stream(gs), GenericStream)) + + +def test_tell_seek(): + with setup_test_file() as (fs, gs, cs): + for s in (fs, gs, cs): + st = make_stream(s) + res = st.seek(0) + assert_equal(res, 0) + assert_equal(st.tell(), 0) + res = st.seek(5) + assert_equal(res, 0) + assert_equal(st.tell(), 5) + res = st.seek(2, 1) + assert_equal(res, 0) + assert_equal(st.tell(), 7) + res = st.seek(-2, 2) + assert_equal(res, 0) + assert_equal(st.tell(), 6) + + +def test_read(): + with setup_test_file() as (fs, gs, cs): + for s in (fs, gs, cs): + st = make_stream(s) + st.seek(0) + res = st.read(-1) + assert_equal(res, b'a\x00string') + st.seek(0) + res = st.read(4) + assert_equal(res, b'a\x00st') + # read into + st.seek(0) + res = _read_into(st, 4) + assert_equal(res, b'a\x00st') + res = _read_into(st, 4) + assert_equal(res, b'ring') + assert_raises(OSError, _read_into, st, 2) + # read alloc + st.seek(0) + res = _read_string(st, 4) + assert_equal(res, b'a\x00st') + res = _read_string(st, 4) + assert_equal(res, b'ring') + assert_raises(OSError, _read_string, st, 2) + + +class TestZlibInputStream: + def _get_data(self, size): + data = np.random.randint(0, 256, size).astype(np.uint8).tobytes() + compressed_data = zlib.compress(data) + stream = BytesIO(compressed_data) + return stream, len(compressed_data), data + + def test_read(self): + SIZES = [0, 1, 10, BLOCK_SIZE//2, BLOCK_SIZE-1, + BLOCK_SIZE, BLOCK_SIZE+1, 2*BLOCK_SIZE-1] + + READ_SIZES = [BLOCK_SIZE//2, BLOCK_SIZE-1, + BLOCK_SIZE, BLOCK_SIZE+1] + + def check(size, read_size): + compressed_stream, compressed_data_len, data = self._get_data(size) + stream = ZlibInputStream(compressed_stream, compressed_data_len) + data2 = b'' + so_far = 0 + while True: + block = stream.read(min(read_size, + size - so_far)) + if not block: + break + so_far += len(block) + data2 += block + assert_equal(data, data2) + + for size in SIZES: + for read_size in READ_SIZES: + check(size, read_size) + + def test_read_max_length(self): + size = 1234 + data = np.random.randint(0, 256, size).astype(np.uint8).tobytes() + compressed_data = zlib.compress(data) + compressed_stream = BytesIO(compressed_data + b"abbacaca") + stream = ZlibInputStream(compressed_stream, len(compressed_data)) + + stream.read(len(data)) + assert_equal(compressed_stream.tell(), len(compressed_data)) + + assert_raises(OSError, stream.read, 1) + + def test_read_bad_checksum(self): + data = np.random.randint(0, 256, 10).astype(np.uint8).tobytes() + compressed_data = zlib.compress(data) + + # break checksum + compressed_data = (compressed_data[:-1] + + bytes([(compressed_data[-1] + 1) & 255])) + + compressed_stream = BytesIO(compressed_data) + stream = ZlibInputStream(compressed_stream, len(compressed_data)) + + assert_raises(zlib.error, stream.read, len(data)) + + def test_seek(self): + compressed_stream, compressed_data_len, data = self._get_data(1024) + + stream = ZlibInputStream(compressed_stream, compressed_data_len) + + stream.seek(123) + p = 123 + assert_equal(stream.tell(), p) + d1 = stream.read(11) + assert_equal(d1, data[p:p+11]) + + stream.seek(321, 1) + p = 123+11+321 + assert_equal(stream.tell(), p) + d2 = stream.read(21) + assert_equal(d2, data[p:p+21]) + + stream.seek(641, 0) + p = 641 + assert_equal(stream.tell(), p) + d3 = stream.read(11) + assert_equal(d3, data[p:p+11]) + + assert_raises(OSError, stream.seek, 10, 2) + assert_raises(OSError, stream.seek, -1, 1) + assert_raises(ValueError, stream.seek, 1, 123) + + stream.seek(10000, 1) + assert_raises(OSError, stream.read, 12) + + def test_seek_bad_checksum(self): + data = np.random.randint(0, 256, 10).astype(np.uint8).tobytes() + compressed_data = zlib.compress(data) + + # break checksum + compressed_data = (compressed_data[:-1] + + bytes([(compressed_data[-1] + 1) & 255])) + + compressed_stream = BytesIO(compressed_data) + stream = ZlibInputStream(compressed_stream, len(compressed_data)) + + assert_raises(zlib.error, stream.seek, len(data)) + + def test_all_data_read(self): + compressed_stream, compressed_data_len, data = self._get_data(1024) + stream = ZlibInputStream(compressed_stream, compressed_data_len) + assert_(not stream.all_data_read()) + stream.seek(512) + assert_(not stream.all_data_read()) + stream.seek(1024) + assert_(stream.all_data_read()) + + def test_all_data_read_overlap(self): + COMPRESSION_LEVEL = 6 + + data = np.arange(33707000).astype(np.uint8).tobytes() + compressed_data = zlib.compress(data, COMPRESSION_LEVEL) + compressed_data_len = len(compressed_data) + + # check that part of the checksum overlaps + assert_(compressed_data_len == BLOCK_SIZE + 2) + + compressed_stream = BytesIO(compressed_data) + stream = ZlibInputStream(compressed_stream, compressed_data_len) + assert_(not stream.all_data_read()) + stream.seek(len(data)) + assert_(stream.all_data_read()) + + def test_all_data_read_bad_checksum(self): + COMPRESSION_LEVEL = 6 + + data = np.arange(33707000).astype(np.uint8).tobytes() + compressed_data = zlib.compress(data, COMPRESSION_LEVEL) + compressed_data_len = len(compressed_data) + + # check that part of the checksum overlaps + assert_(compressed_data_len == BLOCK_SIZE + 2) + + # break checksum + compressed_data = (compressed_data[:-1] + + bytes([(compressed_data[-1] + 1) & 255])) + + compressed_stream = BytesIO(compressed_data) + stream = ZlibInputStream(compressed_stream, compressed_data_len) + assert_(not stream.all_data_read()) + stream.seek(len(data)) + + assert_raises(zlib.error, stream.all_data_read)