# -*- 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 import unittest import numpy as np import quantities as pq from neo.core import Block, ChannelIndex, Segment, SpikeTrain, Unit 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 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) chx = ChannelIndex(file_origin=filenameorig, index=np.array([], dtype=np.int), channel_names=np.array([], dtype='S')) unit = Unit(file_origin=filenameorig) # load objects into their containers block.channel_indexes.append(chx) chx.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: 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] unit.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 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()