/usr/lib/python2.7/dist-packages/neo/io/neuroscopeio.py is in python-neo 0.3.3-2.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 | # -*- coding: utf-8 -*-
"""
Reading from neuroscope format files.
Ref: http://neuroscope.sourceforge.net/
It is an old format from Buzsaki's lab.
Supported: Read
#TODO:
SpikeTrain file '.clu' '.res'
EventArray '.ext.evt' or '.evt.ext'
Author: sgarcia
"""
# needed for python 3 compatibility
from __future__ import absolute_import
import os
from xml.etree import ElementTree
import numpy as np
import quantities as pq
from neo.io.baseio import BaseIO
from neo.io.rawbinarysignalio import RawBinarySignalIO
from neo.core import (Block, Segment, RecordingChannel, RecordingChannelGroup,
AnalogSignal)
from neo.io.tools import create_many_to_one_relationship
class NeuroScopeIO(BaseIO):
"""
"""
is_readable = True
is_writable = False
supported_objects = [ Block, Segment , AnalogSignal, RecordingChannel, RecordingChannelGroup]
readable_objects = [ Block ]
writeable_objects = [ ]
has_header = False
is_streameable = False
read_params = {
Segment : [ ]
}
# do not supported write so no GUI stuff
write_params = None
name = 'NeuroScope'
extensions = [ 'xml' ]
mode = 'file'
def __init__(self , filename = None) :
"""
Arguments:
filename : the filename
"""
BaseIO.__init__(self)
self.filename = filename
def read_block(self,
lazy = False,
cascade = True,
):
"""
"""
tree = ElementTree.parse(self.filename)
root = tree.getroot()
acq = root.find('acquisitionSystem')
nbits = int(acq.find('nBits').text)
nbchannel = int(acq.find('nChannels').text)
sampling_rate = float(acq.find('samplingRate').text)*pq.Hz
voltage_range = float(acq.find('voltageRange').text)
#offset = int(acq.find('offset').text)
amplification = float(acq.find('amplification').text)
bl = Block(file_origin = os.path.basename(self.filename).replace('.xml', ''))
if cascade:
seg = Segment()
bl.segments.append(seg)
# RC and RCG
rc_list = [ ]
for i, xml_rcg in enumerate(root.find('anatomicalDescription').find('channelGroups').findall('group')):
rcg = RecordingChannelGroup(name = 'Group {}'.format(i))
bl.recordingchannelgroups.append(rcg)
for xml_rc in xml_rcg:
rc = RecordingChannel(index = int(xml_rc.text))
rc_list.append(rc)
rcg.recordingchannels.append(rc)
rc.recordingchannelgroups.append(rcg)
rcg.channel_indexes = np.array([rc.index for rc in rcg.recordingchannels], dtype = int)
rcg.channel_names = np.array(['Channel{}'.format(rc.index) for rc in rcg.recordingchannels], dtype = 'S')
# AnalogSignals
reader = RawBinarySignalIO(filename = self.filename.replace('.xml', '.dat'))
seg2 = reader.read_segment(cascade = True, lazy = lazy,
sampling_rate = sampling_rate,
t_start = 0.*pq.s,
unit = pq.V, nbchannel = nbchannel,
bytesoffset = 0,
dtype = np.int16 if nbits<=16 else np.int32,
rangemin = -voltage_range/2.,
rangemax = voltage_range/2.,)
for s, sig in enumerate(seg2.analogsignals):
if not lazy:
sig /= amplification
sig.segment = seg
seg.analogsignals.append(sig)
rc_list[s].analogsignals.append(sig)
create_many_to_one_relationship(bl)
return bl
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