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- """
- Tests of neo.io.brainwaref32io
- """
- import os.path
- import unittest
- import numpy as np
- import quantities as pq
- from neo.core import Block, Segment, SpikeTrain, Group
- from neo.io import BrainwareF32IO
- 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
- 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)
- gr = Group(file_origin=filenameorig)
- block.groups.append(gr)
- try:
- with np.load(filename, allow_pickle=True) as f32obj:
- f32file = list(f32obj.items())[0][1].flatten()
- except OSError as exc:
- if 'as a pickle' in exc.message:
- block.create_many_to_one_relationship()
- 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]
- gr.spiketrains.append(train)
- block.segments.append(segment)
- block.create_many_to_one_relationship()
- 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
- suffix = '_f32_py3.npz'
- 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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