multielectrode_grasp/code/python-neo/neo/io/asciispiketrainio.py

# -*- coding: utf-8 -*-

"""
Classe for reading/writing SpikeTrains in a text file.
It is the simple case where different spiketrains are written line by line.

Supported : Read/Write

Author: sgarcia

"""

import os

import numpy as np
import quantities as pq

from neo.io.baseio import BaseIO
from neo.core import Segment, SpikeTrain


class AsciiSpikeTrainIO(BaseIO):
    """

    Classe for reading/writing SpikeTrains in a text file.
    Each Spiketrain is a line.

    Usage:
        >>> from neo import io
        >>> r = io.AsciiSpikeTrainIO( filename = 'File_ascii_spiketrain_1.txt')
        >>> seg = r.read_segment(lazy = False, cascade = True,)
        >>> print seg.spiketrains     # doctest: +ELLIPSIS, +NORMALIZE_WHITESPACE
        [<SpikeTrain(array([ 3.89981604,  4.73258781,  0.608428  ,  4.60246277,  1.23805797,
        ...

    """

    is_readable        = True
    is_writable        = True

    supported_objects  = [Segment , SpikeTrain]
    readable_objects   = [Segment]
    writeable_objects  = [Segment]

    has_header         = False
    is_streameable     = False

    read_params        = {
                            Segment : [
                                        ('delimiter' , {'value' :  '\t', 'possible' : ['\t' , ' ' , ',' , ';'] }) ,
                                        ('t_start' , { 'value' : 0., } ),
                                        ]
                            }
    write_params       = {
                            Segment : [
                                        ('delimiter' , {'value' :  '\t', 'possible' : ['\t' , ' ' , ',' , ';'] }) ,
                                        ]
                            }

    name               = None
    extensions          = [ 'txt' ]

    mode = 'file'


    def __init__(self , filename = None) :
        """
        This class read/write SpikeTrains in a text file.
        Each row is a spiketrain.

        **Arguments**

        filename : the filename to read/write

        """
        BaseIO.__init__(self)
        self.filename = filename

    def read_segment(self,
                            lazy = False,
                            cascade = True,
                            delimiter = '\t',
                            t_start = 0.*pq.s,
                            unit = pq.s,
                            ):
        """
        Arguments:
            delimiter  :  columns delimiter in file  '\t' or one space or two space or ',' or ';'
            t_start : time start of all spiketrain 0 by default
            unit : unit of spike times, can be a str or directly a Quantities
        """
        unit = pq.Quantity(1, unit)

        seg = Segment(file_origin = os.path.basename(self.filename))
        if not cascade:
            return seg

        f = open(self.filename, 'Ur')
        for i,line in enumerate(f) :
            alldata = line[:-1].split(delimiter)
            if alldata[-1] == '': alldata = alldata[:-1]
            if alldata[0] == '': alldata = alldata[1:]
            if lazy:
                spike_times = [ ]
                t_stop = t_start
            else:
                spike_times = np.array(alldata).astype('f')
                t_stop = spike_times.max()*unit

            sptr = SpikeTrain(spike_times*unit, t_start=t_start, t_stop=t_stop)
            if lazy:
                sptr.lazy_shape = len(alldata)

            sptr.annotate(channel_index = i)
            seg.spiketrains.append(sptr)
        f.close()

        seg.create_many_to_one_relationship()
        return seg

    def write_segment(self, segment,
                                delimiter = '\t',
                                ):
        """
        Write SpikeTrain of a Segment in a txt file.
        Each row is a spiketrain.

         Arguments:
            segment : the segment to write. Only analog signals will be written.
            delimiter  :  columns delimiter in file  '\t' or one space or two space or ',' or ';'

            information of t_start is lost

        """

        f = open(self.filename, 'w')
        for s,sptr in enumerate(segment.spiketrains) :
            for ts in sptr :
                f.write('%f%s'% (ts , delimiter) )
            f.write('\n')
        f.close()