hub/venv/lib/python3.7/site-packages/scipy/io/idl.py

# IDLSave - a python module to read IDL 'save' files
# Copyright (c) 2010 Thomas P. Robitaille

# Many thanks to Craig Markwardt for publishing the Unofficial Format
# Specification for IDL .sav files, without which this Python module would not
# exist (http://cow.physics.wisc.edu/~craigm/idl/savefmt).

# This code was developed by with permission from ITT Visual Information
# Systems. IDL(r) is a registered trademark of ITT Visual Information Systems,
# Inc. for their Interactive Data Language software.

# Permission is hereby granted, free of charge, to any person obtaining a
# copy of this software and associated documentation files (the "Software"),
# to deal in the Software without restriction, including without limitation
# the rights to use, copy, modify, merge, publish, distribute, sublicense,
# and/or sell copies of the Software, and to permit persons to whom the
# Software is furnished to do so, subject to the following conditions:

# The above copyright notice and this permission notice shall be included in
# all copies or substantial portions of the Software.

# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
# FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
# DEALINGS IN THE SOFTWARE.

from __future__ import division, print_function, absolute_import

__all__ = ['readsav']

import struct
import numpy as np
from numpy.compat import asstr
import tempfile
import zlib
import warnings

# Define the different data types that can be found in an IDL save file
DTYPE_DICT = {1: '>u1',
              2: '>i2',
              3: '>i4',
              4: '>f4',
              5: '>f8',
              6: '>c8',
              7: '|O',
              8: '|O',
              9: '>c16',
              10: '|O',
              11: '|O',
              12: '>u2',
              13: '>u4',
              14: '>i8',
              15: '>u8'}

# Define the different record types that can be found in an IDL save file
RECTYPE_DICT = {0: "START_MARKER",
                1: "COMMON_VARIABLE",
                2: "VARIABLE",
                3: "SYSTEM_VARIABLE",
                6: "END_MARKER",
                10: "TIMESTAMP",
                12: "COMPILED",
                13: "IDENTIFICATION",
                14: "VERSION",
                15: "HEAP_HEADER",
                16: "HEAP_DATA",
                17: "PROMOTE64",
                19: "NOTICE",
                20: "DESCRIPTION"}

# Define a dictionary to contain structure definitions
STRUCT_DICT = {}


def _align_32(f):
    '''Align to the next 32-bit position in a file'''

    pos = f.tell()
    if pos % 4 != 0:
        f.seek(pos + 4 - pos % 4)
    return


def _skip_bytes(f, n):
    '''Skip `n` bytes'''
    f.read(n)
    return


def _read_bytes(f, n):
    '''Read the next `n` bytes'''
    return f.read(n)


def _read_byte(f):
    '''Read a single byte'''
    return np.uint8(struct.unpack('>B', f.read(4)[:1])[0])


def _read_long(f):
    '''Read a signed 32-bit integer'''
    return np.int32(struct.unpack('>l', f.read(4))[0])


def _read_int16(f):
    '''Read a signed 16-bit integer'''
    return np.int16(struct.unpack('>h', f.read(4)[2:4])[0])


def _read_int32(f):
    '''Read a signed 32-bit integer'''
    return np.int32(struct.unpack('>i', f.read(4))[0])


def _read_int64(f):
    '''Read a signed 64-bit integer'''
    return np.int64(struct.unpack('>q', f.read(8))[0])


def _read_uint16(f):
    '''Read an unsigned 16-bit integer'''
    return np.uint16(struct.unpack('>H', f.read(4)[2:4])[0])


def _read_uint32(f):
    '''Read an unsigned 32-bit integer'''
    return np.uint32(struct.unpack('>I', f.read(4))[0])


def _read_uint64(f):
    '''Read an unsigned 64-bit integer'''
    return np.uint64(struct.unpack('>Q', f.read(8))[0])


def _read_float32(f):
    '''Read a 32-bit float'''
    return np.float32(struct.unpack('>f', f.read(4))[0])


def _read_float64(f):
    '''Read a 64-bit float'''
    return np.float64(struct.unpack('>d', f.read(8))[0])


class Pointer(object):
    '''Class used to define pointers'''

    def __init__(self, index):
        self.index = index
        return


class ObjectPointer(Pointer):
    '''Class used to define object pointers'''
    pass


def _read_string(f):
    '''Read a string'''
    length = _read_long(f)
    if length > 0:
        chars = _read_bytes(f, length)
        _align_32(f)
        chars = asstr(chars)
    else:
        chars = ''
    return chars


def _read_string_data(f):
    '''Read a data string (length is specified twice)'''
    length = _read_long(f)
    if length > 0:
        length = _read_long(f)
        string_data = _read_bytes(f, length)
        _align_32(f)
    else:
        string_data = ''
    return string_data


def _read_data(f, dtype):
    '''Read a variable with a specified data type'''
    if dtype == 1:
        if _read_int32(f) != 1:
            raise Exception("Error occurred while reading byte variable")
        return _read_byte(f)
    elif dtype == 2:
        return _read_int16(f)
    elif dtype == 3:
        return _read_int32(f)
    elif dtype == 4:
        return _read_float32(f)
    elif dtype == 5:
        return _read_float64(f)
    elif dtype == 6:
        real = _read_float32(f)
        imag = _read_float32(f)
        return np.complex64(real + imag * 1j)
    elif dtype == 7:
        return _read_string_data(f)
    elif dtype == 8:
        raise Exception("Should not be here - please report this")
    elif dtype == 9:
        real = _read_float64(f)
        imag = _read_float64(f)
        return np.complex128(real + imag * 1j)
    elif dtype == 10:
        return Pointer(_read_int32(f))
    elif dtype == 11:
        return ObjectPointer(_read_int32(f))
    elif dtype == 12:
        return _read_uint16(f)
    elif dtype == 13:
        return _read_uint32(f)
    elif dtype == 14:
        return _read_int64(f)
    elif dtype == 15:
        return _read_uint64(f)
    else:
        raise Exception("Unknown IDL type: %i - please report this" % dtype)


def _read_structure(f, array_desc, struct_desc):
    '''
    Read a structure, with the array and structure descriptors given as
    `array_desc` and `structure_desc` respectively.
    '''

    nrows = array_desc['nelements']
    columns = struct_desc['tagtable']

    dtype = []
    for col in columns:
        if col['structure'] or col['array']:
            dtype.append(((col['name'].lower(), col['name']), np.object_))
        else:
            if col['typecode'] in DTYPE_DICT:
                dtype.append(((col['name'].lower(), col['name']),
                                    DTYPE_DICT[col['typecode']]))
            else:
                raise Exception("Variable type %i not implemented" %
                                                            col['typecode'])

    structure = np.recarray((nrows, ), dtype=dtype)

    for i in range(nrows):
        for col in columns:
            dtype = col['typecode']
            if col['structure']:
                structure[col['name']][i] = _read_structure(f,
                                      struct_desc['arrtable'][col['name']],
                                      struct_desc['structtable'][col['name']])
            elif col['array']:
                structure[col['name']][i] = _read_array(f, dtype,
                                      struct_desc['arrtable'][col['name']])
            else:
                structure[col['name']][i] = _read_data(f, dtype)

    # Reshape structure if needed
    if array_desc['ndims'] > 1:
        dims = array_desc['dims'][:int(array_desc['ndims'])]
        dims.reverse()
        structure = structure.reshape(dims)

    return structure


def _read_array(f, typecode, array_desc):
    '''
    Read an array of type `typecode`, with the array descriptor given as
    `array_desc`.
    '''

    if typecode in [1, 3, 4, 5, 6, 9, 13, 14, 15]:

        if typecode == 1:
            nbytes = _read_int32(f)
            if nbytes != array_desc['nbytes']:
                warnings.warn("Not able to verify number of bytes from header")

        # Read bytes as numpy array
        array = np.frombuffer(f.read(array_desc['nbytes']),
                              dtype=DTYPE_DICT[typecode])

    elif typecode in [2, 12]:

        # These are 2 byte types, need to skip every two as they are not packed

        array = np.frombuffer(f.read(array_desc['nbytes']*2),
                              dtype=DTYPE_DICT[typecode])[1::2]

    else:

        # Read bytes into list
        array = []
        for i in range(array_desc['nelements']):
            dtype = typecode
            data = _read_data(f, dtype)
            array.append(data)

        array = np.array(array, dtype=np.object_)

    # Reshape array if needed
    if array_desc['ndims'] > 1:
        dims = array_desc['dims'][:int(array_desc['ndims'])]
        dims.reverse()
        array = array.reshape(dims)

    # Go to next alignment position
    _align_32(f)

    return array


def _read_record(f):
    '''Function to read in a full record'''

    record = {'rectype': _read_long(f)}

    nextrec = _read_uint32(f)
    nextrec += _read_uint32(f) * 2**32

    _skip_bytes(f, 4)

    if not record['rectype'] in RECTYPE_DICT:
        raise Exception("Unknown RECTYPE: %i" % record['rectype'])

    record['rectype'] = RECTYPE_DICT[record['rectype']]

    if record['rectype'] in ["VARIABLE", "HEAP_DATA"]:

        if record['rectype'] == "VARIABLE":
            record['varname'] = _read_string(f)
        else:
            record['heap_index'] = _read_long(f)
            _skip_bytes(f, 4)

        rectypedesc = _read_typedesc(f)

        if rectypedesc['typecode'] == 0:

            if nextrec == f.tell():
                record['data'] = None  # Indicates NULL value
            else:
                raise ValueError("Unexpected type code: 0")

        else:

            varstart = _read_long(f)
            if varstart != 7:
                raise Exception("VARSTART is not 7")

            if rectypedesc['structure']:
                record['data'] = _read_structure(f, rectypedesc['array_desc'],
                                                    rectypedesc['struct_desc'])
            elif rectypedesc['array']:
                record['data'] = _read_array(f, rectypedesc['typecode'],
                                                rectypedesc['array_desc'])
            else:
                dtype = rectypedesc['typecode']
                record['data'] = _read_data(f, dtype)

    elif record['rectype'] == "TIMESTAMP":

        _skip_bytes(f, 4*256)
        record['date'] = _read_string(f)
        record['user'] = _read_string(f)
        record['host'] = _read_string(f)

    elif record['rectype'] == "VERSION":

        record['format'] = _read_long(f)
        record['arch'] = _read_string(f)
        record['os'] = _read_string(f)
        record['release'] = _read_string(f)

    elif record['rectype'] == "IDENTIFICATON":

        record['author'] = _read_string(f)
        record['title'] = _read_string(f)
        record['idcode'] = _read_string(f)

    elif record['rectype'] == "NOTICE":

        record['notice'] = _read_string(f)

    elif record['rectype'] == "DESCRIPTION":

        record['description'] = _read_string_data(f)

    elif record['rectype'] == "HEAP_HEADER":

        record['nvalues'] = _read_long(f)
        record['indices'] = [_read_long(f) for _ in range(record['nvalues'])]

    elif record['rectype'] == "COMMONBLOCK":

        record['nvars'] = _read_long(f)
        record['name'] = _read_string(f)
        record['varnames'] = [_read_string(f) for _ in range(record['nvars'])]

    elif record['rectype'] == "END_MARKER":

        record['end'] = True

    elif record['rectype'] == "UNKNOWN":

        warnings.warn("Skipping UNKNOWN record")

    elif record['rectype'] == "SYSTEM_VARIABLE":

        warnings.warn("Skipping SYSTEM_VARIABLE record")

    else:

        raise Exception("record['rectype']=%s not implemented" %
                                                            record['rectype'])

    f.seek(nextrec)

    return record


def _read_typedesc(f):
    '''Function to read in a type descriptor'''

    typedesc = {'typecode': _read_long(f), 'varflags': _read_long(f)}

    if typedesc['varflags'] & 2 == 2:
        raise Exception("System variables not implemented")

    typedesc['array'] = typedesc['varflags'] & 4 == 4
    typedesc['structure'] = typedesc['varflags'] & 32 == 32

    if typedesc['structure']:
        typedesc['array_desc'] = _read_arraydesc(f)
        typedesc['struct_desc'] = _read_structdesc(f)
    elif typedesc['array']:
        typedesc['array_desc'] = _read_arraydesc(f)

    return typedesc


def _read_arraydesc(f):
    '''Function to read in an array descriptor'''

    arraydesc = {'arrstart': _read_long(f)}

    if arraydesc['arrstart'] == 8:

        _skip_bytes(f, 4)

        arraydesc['nbytes'] = _read_long(f)
        arraydesc['nelements'] = _read_long(f)
        arraydesc['ndims'] = _read_long(f)

        _skip_bytes(f, 8)

        arraydesc['nmax'] = _read_long(f)

        arraydesc['dims'] = [_read_long(f) for _ in range(arraydesc['nmax'])]

    elif arraydesc['arrstart'] == 18:

        warnings.warn("Using experimental 64-bit array read")

        _skip_bytes(f, 8)

        arraydesc['nbytes'] = _read_uint64(f)
        arraydesc['nelements'] = _read_uint64(f)
        arraydesc['ndims'] = _read_long(f)

        _skip_bytes(f, 8)

        arraydesc['nmax'] = 8

        arraydesc['dims'] = []
        for d in range(arraydesc['nmax']):
            v = _read_long(f)
            if v != 0:
                raise Exception("Expected a zero in ARRAY_DESC")
            arraydesc['dims'].append(_read_long(f))

    else:

        raise Exception("Unknown ARRSTART: %i" % arraydesc['arrstart'])

    return arraydesc


def _read_structdesc(f):
    '''Function to read in a structure descriptor'''

    structdesc = {}

    structstart = _read_long(f)
    if structstart != 9:
        raise Exception("STRUCTSTART should be 9")

    structdesc['name'] = _read_string(f)
    predef = _read_long(f)
    structdesc['ntags'] = _read_long(f)
    structdesc['nbytes'] = _read_long(f)

    structdesc['predef'] = predef & 1
    structdesc['inherits'] = predef & 2
    structdesc['is_super'] = predef & 4

    if not structdesc['predef']:

        structdesc['tagtable'] = [_read_tagdesc(f)
                                  for _ in range(structdesc['ntags'])]

        for tag in structdesc['tagtable']:
            tag['name'] = _read_string(f)

        structdesc['arrtable'] = {tag['name']: _read_arraydesc(f)
                                  for tag in structdesc['tagtable']
                                  if tag['array']}

        structdesc['structtable'] = {tag['name']: _read_structdesc(f)
                                     for tag in structdesc['tagtable']
                                     if tag['structure']}

        if structdesc['inherits'] or structdesc['is_super']:
            structdesc['classname'] = _read_string(f)
            structdesc['nsupclasses'] = _read_long(f)
            structdesc['supclassnames'] = [
                _read_string(f) for _ in range(structdesc['nsupclasses'])]
            structdesc['supclasstable'] = [
                _read_structdesc(f) for _ in range(structdesc['nsupclasses'])]

        STRUCT_DICT[structdesc['name']] = structdesc

    else:

        if not structdesc['name'] in STRUCT_DICT:
            raise Exception("PREDEF=1 but can't find definition")

        structdesc = STRUCT_DICT[structdesc['name']]

    return structdesc


def _read_tagdesc(f):
    '''Function to read in a tag descriptor'''

    tagdesc = {'offset': _read_long(f)}

    if tagdesc['offset'] == -1:
        tagdesc['offset'] = _read_uint64(f)

    tagdesc['typecode'] = _read_long(f)
    tagflags = _read_long(f)

    tagdesc['array'] = tagflags & 4 == 4
    tagdesc['structure'] = tagflags & 32 == 32
    tagdesc['scalar'] = tagdesc['typecode'] in DTYPE_DICT
    # Assume '10'x is scalar

    return tagdesc


def _replace_heap(variable, heap):

    if isinstance(variable, Pointer):

        while isinstance(variable, Pointer):

            if variable.index == 0:
                variable = None
            else:
                if variable.index in heap:
                    variable = heap[variable.index]
                else:
                    warnings.warn("Variable referenced by pointer not found "
                                  "in heap: variable will be set to None")
                    variable = None

        replace, new = _replace_heap(variable, heap)

        if replace:
            variable = new

        return True, variable

    elif isinstance(variable, np.core.records.recarray):

        # Loop over records
        for ir, record in enumerate(variable):

            replace, new = _replace_heap(record, heap)

            if replace:
                variable[ir] = new

        return False, variable

    elif isinstance(variable, np.core.records.record):

        # Loop over values
        for iv, value in enumerate(variable):

            replace, new = _replace_heap(value, heap)

            if replace:
                variable[iv] = new

        return False, variable

    elif isinstance(variable, np.ndarray):

        # Loop over values if type is np.object_
        if variable.dtype.type is np.object_:

            for iv in range(variable.size):

                replace, new = _replace_heap(variable.item(iv), heap)

                if replace:
                    variable.itemset(iv, new)

        return False, variable

    else:

        return False, variable


class AttrDict(dict):
    '''
    A case-insensitive dictionary with access via item, attribute, and call
    notations:

        >>> d = AttrDict()
        >>> d['Variable'] = 123
        >>> d['Variable']
        123
        >>> d.Variable
        123
        >>> d.variable
        123
        >>> d('VARIABLE')
        123
    '''

    def __init__(self, init={}):
        dict.__init__(self, init)

    def __getitem__(self, name):
        return super(AttrDict, self).__getitem__(name.lower())

    def __setitem__(self, key, value):
        return super(AttrDict, self).__setitem__(key.lower(), value)

    __getattr__ = __getitem__
    __setattr__ = __setitem__
    __call__ = __getitem__


def readsav(file_name, idict=None, python_dict=False,
            uncompressed_file_name=None, verbose=False):
    """
    Read an IDL .sav file.

    Parameters
    ----------
    file_name : str
        Name of the IDL save file.
    idict : dict, optional
        Dictionary in which to insert .sav file variables.
    python_dict : bool, optional
        By default, the object return is not a Python dictionary, but a
        case-insensitive dictionary with item, attribute, and call access
        to variables. To get a standard Python dictionary, set this option
        to True.
    uncompressed_file_name : str, optional
        This option only has an effect for .sav files written with the
        /compress option. If a file name is specified, compressed .sav
        files are uncompressed to this file. Otherwise, readsav will use
        the `tempfile` module to determine a temporary filename
        automatically, and will remove the temporary file upon successfully
        reading it in.
    verbose : bool, optional
        Whether to print out information about the save file, including
        the records read, and available variables.

    Returns
    -------
    idl_dict : AttrDict or dict
        If `python_dict` is set to False (default), this function returns a
        case-insensitive dictionary with item, attribute, and call access
        to variables. If `python_dict` is set to True, this function
        returns a Python dictionary with all variable names in lowercase.
        If `idict` was specified, then variables are written to the
        dictionary specified, and the updated dictionary is returned.

    """

    # Initialize record and variable holders
    records = []
    if python_dict or idict:
        variables = {}
    else:
        variables = AttrDict()

    # Open the IDL file
    f = open(file_name, 'rb')

    # Read the signature, which should be 'SR'
    signature = _read_bytes(f, 2)
    if signature != b'SR':
        raise Exception("Invalid SIGNATURE: %s" % signature)

    # Next, the record format, which is '\x00\x04' for normal .sav
    # files, and '\x00\x06' for compressed .sav files.
    recfmt = _read_bytes(f, 2)

    if recfmt == b'\x00\x04':
        pass

    elif recfmt == b'\x00\x06':

        if verbose:
            print("IDL Save file is compressed")

        if uncompressed_file_name:
            fout = open(uncompressed_file_name, 'w+b')
        else:
            fout = tempfile.NamedTemporaryFile(suffix='.sav')

        if verbose:
            print(" -> expanding to %s" % fout.name)

        # Write header
        fout.write(b'SR\x00\x04')

        # Cycle through records
        while True:

            # Read record type
            rectype = _read_long(f)
            fout.write(struct.pack('>l', int(rectype)))

            # Read position of next record and return as int
            nextrec = _read_uint32(f)
            nextrec += _read_uint32(f) * 2**32

            # Read the unknown 4 bytes
            unknown = f.read(4)

            # Check if the end of the file has been reached
            if RECTYPE_DICT[rectype] == 'END_MARKER':
                fout.write(struct.pack('>I', int(nextrec) % 2**32))
                fout.write(struct.pack('>I', int((nextrec - (nextrec % 2**32)) / 2**32)))
                fout.write(unknown)
                break

            # Find current position
            pos = f.tell()

            # Decompress record
            rec_string = zlib.decompress(f.read(nextrec-pos))

            # Find new position of next record
            nextrec = fout.tell() + len(rec_string) + 12

            # Write out record
            fout.write(struct.pack('>I', int(nextrec % 2**32)))
            fout.write(struct.pack('>I', int((nextrec - (nextrec % 2**32)) / 2**32)))
            fout.write(unknown)
            fout.write(rec_string)

        # Close the original compressed file
        f.close()

        # Set f to be the decompressed file, and skip the first four bytes
        f = fout
        f.seek(4)

    else:
        raise Exception("Invalid RECFMT: %s" % recfmt)

    # Loop through records, and add them to the list
    while True:
        r = _read_record(f)
        records.append(r)
        if 'end' in r:
            if r['end']:
                break

    # Close the file
    f.close()

    # Find heap data variables
    heap = {}
    for r in records:
        if r['rectype'] == "HEAP_DATA":
            heap[r['heap_index']] = r['data']

    # Find all variables
    for r in records:
        if r['rectype'] == "VARIABLE":
            replace, new = _replace_heap(r['data'], heap)
            if replace:
                r['data'] = new
            variables[r['varname'].lower()] = r['data']

    if verbose:

        # Print out timestamp info about the file
        for record in records:
            if record['rectype'] == "TIMESTAMP":
                print("-"*50)
                print("Date: %s" % record['date'])
                print("User: %s" % record['user'])
                print("Host: %s" % record['host'])
                break

        # Print out version info about the file
        for record in records:
            if record['rectype'] == "VERSION":
                print("-"*50)
                print("Format: %s" % record['format'])
                print("Architecture: %s" % record['arch'])
                print("Operating System: %s" % record['os'])
                print("IDL Version: %s" % record['release'])
                break

        # Print out identification info about the file
        for record in records:
            if record['rectype'] == "IDENTIFICATON":
                print("-"*50)
                print("Author: %s" % record['author'])
                print("Title: %s" % record['title'])
                print("ID Code: %s" % record['idcode'])
                break

        # Print out descriptions saved with the file
        for record in records:
            if record['rectype'] == "DESCRIPTION":
                print("-"*50)
                print("Description: %s" % record['description'])
                break

        print("-"*50)
        print("Successfully read %i records of which:" %
                                            (len(records)))

        # Create convenience list of record types
        rectypes = [r['rectype'] for r in records]

        for rt in set(rectypes):
            if rt != 'END_MARKER':
                print(" - %i are of type %s" % (rectypes.count(rt), rt))
        print("-"*50)

        if 'VARIABLE' in rectypes:
            print("Available variables:")
            for var in variables:
                print(" - %s [%s]" % (var, type(variables[var])))
            print("-"*50)

    if idict:
        for var in variables:
            idict[var] = variables[var]
        return idict
    else:
        return variables