python-stfio 0.15.4-1 / usr / lib / python2.7 / dist-packages / stfio / stfio.py

# This file was automatically generated by SWIG (http://www.swig.org).
# Version 3.0.10
#
# 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 as _swig_python_version_info
if _swig_python_version_info >= (2, 7, 0):
    def swig_import_helper():
        import importlib
        pkg = __name__.rpartition('.')[0]
        mname = '.'.join((pkg, '_stfio')).lstrip('.')
        try:
            return importlib.import_module(mname)
        except ImportError:
            return importlib.import_module('_stfio')
    _stfio = swig_import_helper()
    del swig_import_helper
elif _swig_python_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 _swig_python_version_info
try:
    _swig_property = property
except NameError:
    pass  # Python < 2.2 doesn't have 'property'.

try:
    import builtins as __builtin__
except ImportError:
    import __builtin__

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):
        if _newclass:
            object.__setattr__(self, name, value)
        else:
            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("'%s' object has no attribute '%s'" % (class_type.__name__, name))


def _swig_repr(self):
    try:
        strthis = "proxy of " + self.this.__repr__()
    except __builtin__.Exception:
        strthis = ""
    return "<%s.%s; %s >" % (self.__class__.__module__, self.__class__.__name__, strthis,)

try:
    _object = object
    _newclass = 1
except __builtin__.Exception:
    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 __builtin__.Exception:
            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, at):
        return _stfio.Recording___getitem__(self, at)

    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 __builtin__.Exception:
            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, at):
        return _stfio.Channel___getitem__(self, at)

    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, nparray):
        this = _stfio.new_Section(nparray)
        try:
            self.this.append(this)
        except __builtin__.Exception:
            self.this = this
    __swig_destroy__ = _stfio.delete_Section
    __del__ = lambda self: None

    def __getitem__(self, at):
        return _stfio.Section___getitem__(self, at)

    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(filename, ftype, verbose, Data):
    """
    _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(filename, ftype, verbose, Data)

def detect_events(*args, **kwargs):
    """
    detect_events(data, templ, dt, mode, norm=True, lowpass=0.5, highpass=0.0001) -> PyObject *



    Arguments:

    """
    return _stfio.detect_events(*args, **kwargs)

def peak_detection(invec, threshold, min_distance):
    """
    peak_detection(invec, threshold, min_distance) -> PyObject *



    Arguments:

    """
    return _stfio.peak_detection(invec, threshold, min_distance)

def risetime(invec, base, amp, frac=0.2):
    """
    risetime(invec, base, amp, frac=0.2) -> double



    Arguments:

    """
    return _stfio.risetime(invec, base, amp, frac)

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


def read_tdms(fn):
    import numpy as np
    import sys
    try:
        from nptdms import TdmsFile
    except ImportError:
        sys.stderr.write("nptdms module unavailable")
        return None

    tdms_file = TdmsFile(fn)

    try:
        times = np.array(
            [[channel.data
              for channel in tdms_file.group_channels(group)
              if channel.data is not None]
             for group in tdms_file.groups()
             if group.lower() == "time"][0][0])
        dt = np.mean(np.diff(times))
    except IndexError:
        if not "Sampling Rate" in tdms_file.object().properties.keys():
            dt = 1.0
        else:
            sr = tdms_file.object().properties['Sampling Rate']
            if sr > 0:
                dt = 1e3/sr
            else:
                dt = 1.0
    chlist = [Channel(
        [Section(channel.data)
         for channel in tdms_file.group_channels(group)
         if channel.data is not None])
        for group in tdms_file.groups()
        if group.lower() != "time"]
    chlist[0].xunits = "mV"
    chlist[1].yunits = "pA"
    rec = Recording(chlist)
    rec.dt = dt
    rec.xunits = "ms"
    sys.stderr.write(fn + "\n")
    return rec

# This file is compatible with both classic and new-style classes.