scipy 1.16.1__cp314-cp314t-macosx_14_0_x86_64.whl

scipy/io/matlab/_miobase.py

@@ -0,0 +1,435 @@
+# Authors: Travis Oliphant, Matthew Brett
+
+"""
+Base classes for MATLAB file stream reading.
+
+MATLAB is a registered trademark of the Mathworks inc.
+"""
+
+from typing import Final
+
+import numpy as np
+from scipy._lib import doccer
+
+from . import _byteordercodes as boc
+
+__all__ = [
+    'MatReadError', 'MatReadWarning', 'MatWriteError', 'MatWriteWarning',
+]
+
+class MatReadError(Exception):
+    """Exception indicating a read issue."""
+
+
+class MatWriteError(Exception):
+    """Exception indicating a write issue."""
+
+
+class MatReadWarning(UserWarning):
+    """Warning class for read issues."""
+
+class MatWriteWarning(UserWarning):
+    """Warning class for write 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: Final = 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
+
+
+_HDR_N_BYTES = 20
+
+
+def _get_matfile_version(fileobj):
+    # Mat4 files have a zero somewhere in first 4 bytes
+    fileobj.seek(0)
+    hdr_bytes = fileobj.read(_HDR_N_BYTES)
+    if len(hdr_bytes) < _HDR_N_BYTES:
+        raise MatReadError("Mat file appears to be truncated")
+    if hdr_bytes.count(0) == _HDR_N_BYTES:
+        raise MatReadError("Mat file appears to be corrupt "
+                           f"(first {_HDR_N_BYTES} bytes == 0)")
+    mopt_ints = np.ndarray(shape=(4,), dtype=np.uint8, buffer=hdr_bytes[:4])
+    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(f'1-D option "{oned_as}" is strange')
+    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

scipy/io/matlab/byteordercodes.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__: list[str] = []
+
+
+def __dir__():
+    return __all__
+
+
+def __getattr__(name):
+    return _sub_module_deprecation(sub_package="io.matlab", module="byteordercodes",
+                                   private_modules=["_byteordercodes"], all=__all__,
+                                   attribute=name)

scipy/io/matlab/mio.py

@@ -0,0 +1,16 @@
+# 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__ = ["loadmat", "savemat", "whosmat"]  # noqa: F822
+
+def __dir__():
+    return __all__
+
+
+def __getattr__(name):
+    return _sub_module_deprecation(sub_package="io.matlab", module="mio",
+                                   private_modules=["_mio"], all=__all__,
+                                   attribute=name)

scipy/io/matlab/mio4.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__: list[str] = []
+
+
+def __dir__():
+    return __all__
+
+
+def __getattr__(name):
+    return _sub_module_deprecation(sub_package="io.matlab", module="mio4",
+                                   private_modules=["_mio4"], all=__all__,
+                                   attribute=name)

scipy/io/matlab/mio5.py

@@ -0,0 +1,19 @@
+# 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__ = [  # noqa: F822
+    'MatWriteError', 'MatReadError', 'MatReadWarning', 'MatlabObject',
+    'MatlabFunction', 'mat_struct', 'varmats_from_mat',
+]
+
+def __dir__():
+    return __all__
+
+
+def __getattr__(name):
+    return _sub_module_deprecation(sub_package="io.matlab", module="mio5",
+                                   private_modules=["_mio5"], all=__all__,
+                                   attribute=name)

scipy/io/matlab/mio5_params.py

@@ -0,0 +1,18 @@
+# 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__ = [  # noqa: F822
+    'MatlabFunction', 'MatlabObject', 'MatlabOpaque', 'mat_struct',
+]
+
+def __dir__():
+    return __all__
+
+
+def __getattr__(name):
+    return _sub_module_deprecation(sub_package="io.matlab", module="mio5_params",
+                                   private_modules=["_mio5_params"], all=__all__,
+                                   attribute=name)

scipy/io/matlab/mio5_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__: list[str] = []
+
+
+def __dir__():
+    return __all__
+
+
+def __getattr__(name):
+    return _sub_module_deprecation(sub_package="io.matlab", module="mio5_utils",
+                                   private_modules=["_mio5_utils"], all=__all__,
+                                   attribute=name)

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__: list[str] = []
+
+
+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)

scipy/io/matlab/miobase.py

@@ -0,0 +1,16 @@
+# 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__ = ["MatReadError", "MatReadWarning", "MatWriteError"]  # noqa: F822
+
+def __dir__():
+    return __all__
+
+
+def __getattr__(name):
+    return _sub_module_deprecation(sub_package="io.matlab", module="miobase",
+                                   private_modules=["_miobase"], all=__all__,
+                                   attribute=name)

scipy/io/matlab/streams.py

@@ -0,0 +1,16 @@
+# 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__: list[str] = []
+
+def __dir__():
+    return __all__
+
+
+def __getattr__(name):
+    return _sub_module_deprecation(sub_package="io.matlab", module="streams",
+                                   private_modules=["_streams"], all=__all__,
+                                   attribute=name)

scipy/io/matlab/tests/data/japanese_utf8.txt

@@ -0,0 +1,5 @@
+Japanese: 
+すべての人間は、生まれながらにして自由であり、
+かつ、尊厳と権利と について平等である。
+人間は、理性と良心とを授けられており、
+互いに同胞の精神をもって行動しなければならない。