/usr/lib/python2.7/dist-packages/neo/test/iotest/test_brainwaref32io.py is in python-neo 0.3.3-2.
This file is owned by root:root, with mode 0o644.
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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 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 | # -*- coding: utf-8 -*-
"""
Tests of neo.io.brainwaref32io
"""
# needed for python 3 compatibility
from __future__ import absolute_import, division, print_function
import os.path
import sys
try:
import unittest2 as unittest
except ImportError:
import unittest
import numpy as np
import quantities as pq
from neo.core import Block, RecordingChannelGroup, Segment, SpikeTrain, Unit
from neo.io import BrainwareF32IO
from neo.io.tools import create_many_to_one_relationship
from neo.test.iotest.common_io_test import BaseTestIO
from neo.test.tools import (assert_same_sub_schema,
assert_neo_object_is_compliant)
from neo.test.iotest.tools import create_generic_reader
PY_VER = sys.version_info[0]
def proc_f32(filename):
'''Load an f32 file that has already been processed by the official matlab
file converter. That matlab data is saved to an m-file, which is then
converted to a numpy '.npz' file. This numpy file is the file actually
loaded. This function converts it to a neo block and returns the block.
This block can be compared to the block produced by BrainwareF32IO to
make sure BrainwareF32IO is working properly
block = proc_f32(filename)
filename: The file name of the numpy file to load. It should end with
'*_f32_py?.npz'. This will be converted to a neo 'file_origin' property
with the value '*.f32', so the filename to compare should fit that pattern.
'py?' should be 'py2' for the python 2 version of the numpy file or 'py3'
for the python 3 version of the numpy file.
example: filename = 'file1_f32_py2.npz'
f32 file name = 'file1.f32'
'''
filenameorig = os.path.basename(filename[:-12]+'.f32')
# create the objects to store other objects
block = Block(file_origin=filenameorig)
rcg = RecordingChannelGroup(file_origin=filenameorig)
rcg.channel_indexes = np.array([], dtype=np.int)
rcg.channel_names = np.array([], dtype='S')
unit = Unit(file_origin=filenameorig)
# load objects into their containers
block.recordingchannelgroups.append(rcg)
rcg.units.append(unit)
try:
with np.load(filename) as f32obj:
f32file = f32obj.items()[0][1].flatten()
except IOError as exc:
if 'as a pickle' in exc.message:
create_many_to_one_relationship(block)
return block
else:
raise
sweeplengths = [res[0, 0].tolist() for res in f32file['sweeplength']]
stims = [res.flatten().tolist() for res in f32file['stim']]
sweeps = [res['spikes'].flatten() for res in f32file['sweep'] if res.size]
fullf32 = zip(sweeplengths, stims, sweeps)
for sweeplength, stim, sweep in fullf32:
for trainpts in sweep:
if trainpts.size:
trainpts = trainpts.flatten().astype('float32')
else:
trainpts = []
paramnames = ['Param%s' % i for i in range(len(stim))]
params = dict(zip(paramnames, stim))
train = SpikeTrain(trainpts, units=pq.ms,
t_start=0, t_stop=sweeplength,
file_origin=filenameorig)
segment = Segment(file_origin=filenameorig, **params)
segment.spiketrains = [train]
unit.spiketrains.append(train)
block.segments.append(segment)
create_many_to_one_relationship(block)
return block
class BrainwareF32IOTestCase(BaseTestIO, unittest.TestCase):
'''
Unit test testcase for neo.io.BrainwareF32IO
'''
ioclass = BrainwareF32IO
read_and_write_is_bijective = False
# These are the files it tries to read and test for compliance
files_to_test = ['block_300ms_4rep_1clust_part_ch1.f32',
'block_500ms_5rep_empty_fullclust_ch1.f32',
'block_500ms_5rep_empty_partclust_ch1.f32',
'interleaved_500ms_5rep_ch2.f32',
'interleaved_500ms_5rep_nospikes_ch1.f32',
'multi_500ms_mulitrep_ch1.f32',
'random_500ms_12rep_noclust_part_ch2.f32',
'sequence_500ms_5rep_ch2.f32']
# add the appropriate suffix depending on the python version
suffix = '_f32_py%s.npz' % PY_VER
files_to_download = files_to_test[:]
# add the reference files to the list of files to download
files_to_compare = []
for fname in files_to_test:
if fname:
files_to_compare.append(os.path.splitext(fname)[0] + suffix)
# Will fetch from g-node if they don't already exist locally
# How does it know to do this before any of the other tests?
files_to_download = files_to_test + files_to_compare
def test_reading_same(self):
for ioobj, path in self.iter_io_objects(return_path=True):
obj_reader_base = create_generic_reader(ioobj, target=False)
obj_reader_single = create_generic_reader(ioobj)
obj_base = obj_reader_base()
obj_single = obj_reader_single()
try:
assert_same_sub_schema(obj_base, obj_single)
except BaseException as exc:
exc.args += ('from ' + os.path.basename(path),)
raise
def test_against_reference(self):
for obj, path in self.iter_objects(return_path=True):
filename = os.path.basename(path)
refpath = os.path.splitext(path)[0] + self.suffix
refobj = proc_f32(refpath)
try:
assert_neo_object_is_compliant(obj)
assert_neo_object_is_compliant(refobj)
assert_same_sub_schema(obj, refobj)
except BaseException as exc:
exc.args += ('from ' + filename,)
raise
if __name__ == '__main__':
unittest.main()
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