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# 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.
# Define the different data types that can be found in an IDL save file 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 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
'''Align to the next 32-bit position in a file'''
pos = f.tell() if pos % 4 != 0: f.seek(pos + 4 - pos % 4) return
'''Skip `n` bytes''' f.read(n) return
'''Read the next `n` bytes''' return f.read(n)
'''Read a single byte''' return np.uint8(struct.unpack('>B', f.read(4)[:1])[0])
'''Read a signed 32-bit integer''' return np.int32(struct.unpack('>l', f.read(4))[0])
'''Read a signed 16-bit integer''' return np.int16(struct.unpack('>h', f.read(4)[2:4])[0])
'''Read a signed 32-bit integer''' return np.int32(struct.unpack('>i', f.read(4))[0])
'''Read a signed 64-bit integer''' return np.int64(struct.unpack('>q', f.read(8))[0])
'''Read an unsigned 16-bit integer''' return np.uint16(struct.unpack('>H', f.read(4)[2:4])[0])
'''Read an unsigned 32-bit integer''' return np.uint32(struct.unpack('>I', f.read(4))[0])
'''Read an unsigned 64-bit integer''' return np.uint64(struct.unpack('>Q', f.read(8))[0])
'''Read a 32-bit float''' return np.float32(struct.unpack('>f', f.read(4))[0])
'''Read a 64-bit float''' return np.float64(struct.unpack('>d', f.read(8))[0])
'''Class used to define pointers'''
self.index = index return
'''Class used to define object pointers'''
'''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
'''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
'''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)
''' 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
''' 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
'''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'] = [] for i in range(record['nvalues']): record['indices'].append(_read_long(f))
elif record['rectype'] == "COMMONBLOCK":
record['nvars'] = _read_long(f) record['name'] = _read_string(f) record['varnames'] = [] for i in range(record['nvars']): record['varnames'].append(_read_string(f))
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
'''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
'''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'] = [] for d in range(arraydesc['nmax']): arraydesc['dims'].append(_read_long(f))
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
'''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'] = [] for t in range(structdesc['ntags']): structdesc['tagtable'].append(_read_tagdesc(f))
for tag in structdesc['tagtable']: tag['name'] = _read_string(f)
structdesc['arrtable'] = {} for tag in structdesc['tagtable']: if tag['array']: structdesc['arrtable'][tag['name']] = _read_arraydesc(f)
structdesc['structtable'] = {} for tag in structdesc['tagtable']: if tag['structure']: structdesc['structtable'][tag['name']] = _read_structdesc(f)
if structdesc['inherits'] or structdesc['is_super']: structdesc['classname'] = _read_string(f) structdesc['nsupclasses'] = _read_long(f) structdesc['supclassnames'] = [] for s in range(structdesc['nsupclasses']): structdesc['supclassnames'].append(_read_string(f)) structdesc['supclasstable'] = [] for s in range(structdesc['nsupclasses']): structdesc['supclasstable'].append(_read_structdesc(f))
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
'''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
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
''' 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 '''
dict.__init__(self, init)
return super(AttrDict, self).__getitem__(name.lower())
return super(AttrDict, self).__setitem__(key.lower(), value)
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 |