def test_SpatialTemporalReceptiveField():
locations = [[3.0, 4.0], [3.0, 5.0], [2.0, 4.0], [2.0, 5.0], [3.0, 4.0],
[3.0, 5.0], [2.0, 4.0], [2.0, 5.0]]
signs = [1, 1, 1, 1, -1, -1, -1, -1]
traces = [[np.arange(4)], [np.arange(1, 5)], [np.arange(2, 6)],
[np.arange(3, 7)], [np.arange(5, 9)], [np.arange(6, 10)],
[np.arange(7, 11)], [np.arange(8, 12)]]
traces = [np.array(t) for t in traces]
time = np.arange(4, 8)
STRF = sca.SpatialTemporalReceptiveField(locations, signs, traces, time)
assert (STRF.data['traces'][0][0][1] == 8)
assert (STRF.data['sign'][4] == 1)
assert (np.array_equal(STRF.get_locations()[2], np.array([3., 4., -1.])))
newLocations = [[location[0] + 1, location[1] + 1]
for location in locations[0:4]]
newSigns = [1, 1, 1, 1]
STRF.add_traces(newLocations, newSigns, traces[0:4])
assert (STRF.data['traces'][7][1][2] == 4)
def test_SpatialTemporalReceptiveField_IO():
locations = [[3.0, 4.0], [3.0, 5.0], [2.0, 4.0], [2.0, 5.0], [3.0, 4.0],
[3.0, 5.0], [2.0, 4.0], [2.0, 5.0]]
signs = [1, 1, 1, 1, -1, -1, -1, -1]
traces = [[np.arange(4)], [np.arange(1, 5)], [np.arange(2, 6)],
[np.arange(3, 7)], [np.arange(5, 9)], [np.arange(6, 10)],
[np.arange(7, 11)], [np.arange(8, 12)]]
time = np.arange(4, 8)
STRF = sca.SpatialTemporalReceptiveField(locations, signs, traces, time)
if os.path.isfile(testH5Path): os.remove(testH5Path)
testFile = h5py.File(testH5Path)
STRFGroup = testFile.create_group('spatial_temporal_receptive_field')
STRF.to_h5_group(STRFGroup)
testFile.close()
h5File = h5py.File(testH5Path)
STRF = sca.SpatialTemporalReceptiveField.from_h5_group(
h5File['spatial_temporal_receptive_field'])
h5File.close()
assert (STRF.data['traces'][3][0][1] == 7)
probe_traces.append(
plane_traces[:, curr_frame_start:curr_frame_end])
plane_roi_traces.append(np.array(probe_traces))
print('probe: {} / {}; shape: {}'.format(probe_ind + 1, len(probe_ns),
np.array(probe_traces).shape))
# plane_roi_traces = np.array(plane_roi_traces)
print('saving ...')
for roi_ind in range(roi_num):
print "roi: {} / {}".format(roi_ind + 1, roi_num)
curr_unit_traces = [pt[:, roi_ind, :] for pt in plane_roi_traces]
curr_unit_traces = [list(t) for t in curr_unit_traces]
curr_strf = sca.SpatialTemporalReceptiveField(
locations=probe_locations,
signs=probe_signs,
traces=curr_unit_traces,
time=plane_t,
# trigger_ts=trigger_ts_lst,
trigger_ts=None,
name='roi_{:04d}'.format(roi_ind),
trace_data_type=trace_source)
curr_strf_grp = plane_strf_grp.create_group(
'strf_roi_{:04d}'.format(roi_ind))
curr_strf.to_h5_group(curr_strf_grp)
nwb_f.close()
curr_frame_end = curr_frame_start + plane_chunk_frame_dur
if curr_frame_start >= 0 and curr_frame_end <= len(plane_trace_ts):
probe_traces.append(
plane_traces[:, curr_frame_start:curr_frame_end])
plane_roi_traces.append(np.array(probe_traces))
print('probe: {} / {}; shape: {}'.format(probe_ind + 1, len(probe_ns),
np.array(probe_traces).shape))
# plane_roi_traces = np.array(plane_roi_traces)
print('saving ...')
for roi_ind in range(roi_num):
print "roi: {} / {}".format(roi_ind + 1, roi_num)
curr_unit_traces = [pt[:, roi_ind, :] for pt in plane_roi_traces]
curr_unit_traces = [list(t) for t in curr_unit_traces]
curr_strf = sca.SpatialTemporalReceptiveField(
probe_locations,
probe_signs,
curr_unit_traces,
plane_t,
name='roi_{:04d}'.format(roi_ind),
trace_data_type=trace_source)
curr_strf_grp = plane_strf_grp.create_group(
'strf_roi_{:04d}'.format(roi_ind))
curr_strf.to_h5_group(curr_strf_grp)
nwb_f.close()