/usr/lib/python2.7/dist-packages/stfio/stfio.py is in python-stfio 0.13.19-1.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
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# Version 2.0.12
#
# Do not make changes to this file unless you know what you are doing--modify
# the SWIG interface file instead.
"""
The stfio module provides functions to read/write data from/to
common electrophysiology file formats
"""
from sys import version_info
if version_info >= (2,6,0):
def swig_import_helper():
from os.path import dirname
import imp
fp = None
try:
fp, pathname, description = imp.find_module('_stfio', [dirname(__file__)])
except ImportError:
import _stfio
return _stfio
if fp is not None:
try:
_mod = imp.load_module('_stfio', fp, pathname, description)
finally:
fp.close()
return _mod
_stfio = swig_import_helper()
del swig_import_helper
else:
import _stfio
del version_info
try:
_swig_property = property
except NameError:
pass # Python < 2.2 doesn't have 'property'.
def _swig_setattr_nondynamic(self,class_type,name,value,static=1):
if (name == "thisown"): return self.this.own(value)
if (name == "this"):
if type(value).__name__ == 'SwigPyObject':
self.__dict__[name] = value
return
method = class_type.__swig_setmethods__.get(name,None)
if method: return method(self,value)
if (not static):
self.__dict__[name] = value
else:
raise AttributeError("You cannot add attributes to %s" % self)
def _swig_setattr(self,class_type,name,value):
return _swig_setattr_nondynamic(self,class_type,name,value,0)
def _swig_getattr(self,class_type,name):
if (name == "thisown"): return self.this.own()
method = class_type.__swig_getmethods__.get(name,None)
if method: return method(self)
raise AttributeError(name)
def _swig_repr(self):
try: strthis = "proxy of " + self.this.__repr__()
except: strthis = ""
return "<%s.%s; %s >" % (self.__class__.__module__, self.__class__.__name__, strthis,)
try:
_object = object
_newclass = 1
except AttributeError:
class _object : pass
_newclass = 0
class Recording(_object):
__swig_setmethods__ = {}
__setattr__ = lambda self, name, value: _swig_setattr(self, Recording, name, value)
__swig_getmethods__ = {}
__getattr__ = lambda self, name: _swig_getattr(self, Recording, name)
__repr__ = _swig_repr
def __init__(self, *args):
this = _stfio.new_Recording(*args)
try: self.this.append(this)
except: self.this = this
__swig_destroy__ = _stfio.delete_Recording
__del__ = lambda self : None;
__swig_setmethods__["dt"] = _stfio.Recording_dt_set
__swig_getmethods__["dt"] = _stfio.Recording_dt_get
if _newclass:dt = _swig_property(_stfio.Recording_dt_get, _stfio.Recording_dt_set)
__swig_setmethods__["file_description"] = _stfio.Recording_file_description_set
__swig_getmethods__["file_description"] = _stfio.Recording_file_description_get
if _newclass:file_description = _swig_property(_stfio.Recording_file_description_get, _stfio.Recording_file_description_set)
__swig_setmethods__["time"] = _stfio.Recording_time_set
__swig_getmethods__["time"] = _stfio.Recording_time_get
if _newclass:time = _swig_property(_stfio.Recording_time_get, _stfio.Recording_time_set)
__swig_setmethods__["date"] = _stfio.Recording_date_set
__swig_getmethods__["date"] = _stfio.Recording_date_get
if _newclass:date = _swig_property(_stfio.Recording_date_get, _stfio.Recording_date_set)
__swig_setmethods__["comment"] = _stfio.Recording_comment_set
__swig_getmethods__["comment"] = _stfio.Recording_comment_get
if _newclass:comment = _swig_property(_stfio.Recording_comment_get, _stfio.Recording_comment_set)
__swig_setmethods__["xunits"] = _stfio.Recording_xunits_set
__swig_getmethods__["xunits"] = _stfio.Recording_xunits_get
if _newclass:xunits = _swig_property(_stfio.Recording_xunits_get, _stfio.Recording_xunits_set)
__swig_setmethods__["datetime"] = _stfio.Recording_datetime_set
__swig_getmethods__["datetime"] = _stfio.Recording_datetime_get
if _newclass:datetime = _swig_property(_stfio.Recording_datetime_get, _stfio.Recording_datetime_set)
def __getitem__(self, *args): return _stfio.Recording___getitem__(self, *args)
def __len__(self): return _stfio.Recording___len__(self)
def write(self, *args):
"""
Writes a Recording to a file.
Arguments:
fname -- file name
#ifndef TEST_MINIMAL
ftype -- file type (string). At present, only "hdf5" is supported.
#else
ftype -- file type (string). At present, "hdf5", "gdf", "cfs" and "ibw" are supported.
#endif // TEST_MINIMAL
verbose-- Show info while writing
Returns:
True upon successful completion.
Writes a Recording to a file.
Arguments:
fname -- file name
#ifndef TEST_MINIMAL
ftype -- file type (string). At present, only "hdf5" is supported.
#else
ftype -- file type (string). At present, "hdf5", "gdf", "cfs" and "ibw" are supported.
#endif // TEST_MINIMAL
verbose-- Show info while writing
Returns:
True upon successful completion.
Writes a Recording to a file.
Arguments:
fname -- file name
#ifndef TEST_MINIMAL
ftype -- file type (string). At present, only "hdf5" is supported.
#else
ftype -- file type (string). At present, "hdf5", "gdf", "cfs" and "ibw" are supported.
#endif // TEST_MINIMAL
verbose-- Show info while writing
Returns:
True upon successful completion.
"""
return _stfio.Recording_write(self, *args)
def aspandas(self):
import sys
import numpy as np
has_pandas = True
try:
import pandas as pd
except ImportError:
has_pandas = False
if has_pandas:
chnames = [ch.name for ch in self]
channels = np.array([np.concatenate([sec for sec in ch]) for ch in self])
date_range = pd.date_range(start=self.datetime, periods=channels.shape[1],
freq='%dU' % np.round(self.dt*1e3))
return pd.DataFrame(channels.transpose(), index=date_range, columns=chnames)
else:
sys.stderr.write("Pandas is not available on this system\n")
return None
Recording_swigregister = _stfio.Recording_swigregister
Recording_swigregister(Recording)
class Channel(_object):
__swig_setmethods__ = {}
__setattr__ = lambda self, name, value: _swig_setattr(self, Channel, name, value)
__swig_getmethods__ = {}
__getattr__ = lambda self, name: _swig_getattr(self, Channel, name)
__repr__ = _swig_repr
def __init__(self, *args):
this = _stfio.new_Channel(*args)
try: self.this.append(this)
except: self.this = this
__swig_destroy__ = _stfio.delete_Channel
__del__ = lambda self : None;
__swig_setmethods__["name"] = _stfio.Channel_name_set
__swig_getmethods__["name"] = _stfio.Channel_name_get
if _newclass:name = _swig_property(_stfio.Channel_name_get, _stfio.Channel_name_set)
__swig_setmethods__["yunits"] = _stfio.Channel_yunits_set
__swig_getmethods__["yunits"] = _stfio.Channel_yunits_get
if _newclass:yunits = _swig_property(_stfio.Channel_yunits_get, _stfio.Channel_yunits_set)
def __getitem__(self, *args): return _stfio.Channel___getitem__(self, *args)
def __len__(self): return _stfio.Channel___len__(self)
Channel_swigregister = _stfio.Channel_swigregister
Channel_swigregister(Channel)
class Section(_object):
__swig_setmethods__ = {}
__setattr__ = lambda self, name, value: _swig_setattr(self, Section, name, value)
__swig_getmethods__ = {}
__getattr__ = lambda self, name: _swig_getattr(self, Section, name)
__repr__ = _swig_repr
def __init__(self, *args):
this = _stfio.new_Section(*args)
try: self.this.append(this)
except: self.this = this
__swig_destroy__ = _stfio.delete_Section
__del__ = lambda self : None;
def __getitem__(self, *args): return _stfio.Section___getitem__(self, *args)
def __len__(self): return _stfio.Section___len__(self)
def asarray(self):
"""Returns the section as a numpy array."""
return _stfio.Section_asarray(self)
Section_swigregister = _stfio.Section_swigregister
Section_swigregister(Section)
def _read(*args):
"""
_read(filename, ftype, verbose, Data) -> bool
Reads a file and returns a recording object.
Arguments:
filename -- file name
#ifndef TEST_MINIMAL
ftype -- File type
#else
ftype -- File type (obsolete)
#endif // TEST_MINIMAL
verbose -- Show info while reading
Returns:
A recording object.
"""
return _stfio._read(*args)
import os
class StfIOException(Exception):
""" raises Exceptions for the Stfio module """
def __init__(self, error_msg):
self.msg = error_msg
def __str__(self):
return repr(self.msg)
filetype = {
'.dat':'cfs',
'.h5':'hdf5',
'.abf':'abf',
'.atf':'atf',
'.axgd':'axg',
'.axgx':'axg'}
def read(fname, ftype=None, verbose=False):
"""Reads a file and returns a Recording object.
Arguments:
fname -- file name
#ifndef TEST_MINIMAL
ftype -- file type (string); can be one of:
"cfs" - CED filing system
"hdf5" - HDF5
"abf" - Axon binary file
"atf" - Axon text file
"axg" - Axograph X binary file
"heka" - HEKA binary file
if ftype is None (default), it will be guessed from the
extension.
#else
ftype -- file type (string) is obsolete.
in the past it has been used to determine the file type.
Now an automated file type identification is used, and this
parameter become obsolete; eventually it will be removed.
#endif // TEST_MINIMAL
verbose-- Show info while reading file
Returns:
A Recording object.
"""
if not os.path.exists(fname):
raise StfIOException('File %s does not exist' % fname)
if ftype is None:
ext = os.path.splitext(fname)[1]
try:
ftype = filetype[ext]
except KeyError:
raise StfIOException('Couldn\'t guess file type from extension (%s)' % ext)
rec = Recording()
if not _read(fname, ftype, verbose, rec):
raise StfIOException('Error reading file')
if verbose:
print("")
return rec
# This file is compatible with both classic and new-style classes.
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