def test_1plane_1chan_with_batches_metrics_and_exported_to_nwb_format(
test_ops):
"""
Tests for case with 1 plane and 1 channel with multiple batches. Results are saved to nwb format
then checked to see if it contains the necessary parts for use with GUI.
"""
test_ops['tiff_list'] = ['input_1500.tif']
test_ops['do_regmetrics'] = True
test_ops['save_NWB'] = True
outputs_to_check = ['F', 'Fneu', 'spks', 'iscell']
suite2p.run_s2p(ops=test_ops)
utils.check_output(test_ops['save_path0'],
outputs_to_check,
test_ops['data_path'][0],
test_ops['nplanes'],
test_ops['nchannels'],
added_tag='1500')
# Read Nwb data and make sure it's identical to output data
stat, ops, F, Fneu, spks, iscell, probcell, redcell, probredcell = \
io.read_nwb(str(Path(test_ops['save_path0']).joinpath('suite2p').joinpath('ophys.nwb')))
utils.compare_list_of_outputs(
0, outputs_to_check,
utils.get_list_of_output_data(outputs_to_check, test_ops['save_path0'],
0),
[
F, Fneu, spks,
np.concatenate([
iscell.astype(np.float32)[:, np.newaxis],
probcell.astype(np.float32)[:, np.newaxis]
],
axis=1)
])
def test_1plane_1chan_with_batches_metrics_and_exported_to_nwb_format(test_ops):
"""
Tests for case with 1 plane and 1 channel with multiple batches. Results are saved to nwb format
then checked to see if it contains the necessary parts for use with GUI.
"""
test_ops.update({
'tiff_list': ['input_1500.tif'],
'do_regmetrics': True,
'save_NWB': True,
})
suite2p.run_s2p(ops=test_ops)
nplanes = test_ops['nplanes']
assert all(utils.check_output(
output_root=test_ops['save_path0'],
outputs_to_check=get_outputs_to_check(test_ops['nchannels']),
test_data_dir=test_ops['data_path'][0].joinpath(f"{nplanes}plane{test_ops['nchannels']}chan1500/suite2p/"),
nplanes=nplanes,
))
# Read Nwb data and make sure it's identical to output data
stat, ops, F, Fneu, spks, iscell, probcell, redcell, probredcell = \
io.read_nwb(str(Path(test_ops['save_path0']).joinpath('suite2p/ophys.nwb')))
assert all(utils.compare_list_of_outputs(
0,
get_outputs_to_check(test_ops['nchannels']),
utils.get_list_of_output_data(get_outputs_to_check(test_ops['nchannels']), test_ops['save_path0'], 0),
[F, Fneu, np.stack([iscell.astype(np.float32), probcell.astype(np.float32)]).T, spks, stat],
))
def test_2plane_2chan_with_batches(test_ops):
"""
Tests for case with 2 planes and 2 channels with multiple batches. Runs twice to check for consistency.
"""
for _ in range(2):
ops = test_ops.copy()
ops.update({
'tiff_list': ['input_1500.tif'],
'batch_size': 200,
'nplanes': 2,
'nchannels': 2,
'reg_tif': True,
'reg_tif_chan2': True,
})
nplanes = ops['nplanes']
suite2p.run_s2p(ops=ops)
outputs_to_check = ['F', 'iscell', 'stat']
#if ops['nchannels'] == 2:
# outputs_to_check.extend(['F_chan2', 'Fneu_chan2'])
for i in range(nplanes):
assert all(utils.compare_list_of_outputs(
outputs_to_check,
utils.get_list_of_data(outputs_to_check, ops['data_path'][0].joinpath(f"{nplanes}plane{ops['nchannels']}chan1500/suite2p/plane{i}")),
utils.get_list_of_data(outputs_to_check, Path(ops['save_path0']).joinpath(f"suite2p/plane{i}")),
))
def temp_test_1plane_2chan_sourcery(test_ops):
"""
Tests for case with 1 plane and 2 channel.
"""
test_ops.update({
'nchannels': 2,
'sparse_mode': 0,
'tiff_list': ['input.tif'],
'keep_movie_raw': True
})
suite2p.run_s2p(ops=test_ops)
nplanes = test_ops['nplanes']
outputs_to_check = ['F', 'iscell', 'stat']
for i in range(nplanes):
assert all(utils.compare_list_of_outputs(
outputs_to_check,
utils.get_list_of_data(outputs_to_check, test_ops['data_path'][0].joinpath(f"{nplanes}plane{test_ops['nchannels']}chan/suite2p/plane{i}")),
utils.get_list_of_data(outputs_to_check, Path(test_ops['save_path0']).joinpath(f"suite2p/plane{i}")),
))
def test_mesoscan_2plane_2z(test_ops):
"""
Tests for case with 2 planes and 2 ROIs for a mesoscan.
"""
with open('data/test_data/mesoscan/ops.json') as f:
meso_ops = json.load(f)
test_ops['data_path'] = [Path(test_ops['data_path'][0]).joinpath('mesoscan')]
for key in meso_ops.keys():
if key not in ['data_path', 'save_path0', 'do_registration', 'roidetect']:
test_ops[key] = meso_ops[key]
test_ops['delete_bin'] = False
suite2p.run_s2p(ops=test_ops)
nplanes = test_ops['nplanes'] * test_ops['nrois']
outputs_to_check = ['F', 'iscell', 'stat']
for i in range(nplanes):
assert all(utils.compare_list_of_outputs(
outputs_to_check,
utils.get_list_of_data(outputs_to_check, test_ops['data_path'][0].joinpath(f'suite2p/plane{i}')),
utils.get_list_of_data(outputs_to_check, Path(test_ops['save_path0']).joinpath(f"suite2p/plane{i}")),
))
def test_extraction_output_2plane2chan(test_ops):
test_ops.update({
'nchannels': 2,
'nplanes': 2,
})
detection_dir = test_ops['data_path'][0].joinpath('detection')
ops = prepare_for_extraction(
test_ops,
[[
detection_dir.joinpath('pre_registered01.npy'),
detection_dir.joinpath('pre_registered02.npy')
],
[
detection_dir.joinpath('pre_registered11.npy'),
detection_dir.joinpath('pre_registered12.npy')
]],
(404, 360),
)
ops[0]['meanImg_chan2'] = np.load(
detection_dir.joinpath('meanImg_chan2p0.npy'))
ops[1]['meanImg_chan2'] = np.load(
detection_dir.joinpath('meanImg_chan2p1.npy'))
extract_wrapper(ops)
nplanes = test_ops['nplanes']
outputs_to_check = ['F', 'Fneu', 'F_chan2', 'Fneu_chan2', 'stat', 'spks']
for i in range(nplanes):
assert all(
utils.compare_list_of_outputs(
outputs_to_check,
utils.get_list_of_data(
outputs_to_check,
Path(test_ops['data_path'][0].joinpath(
f"{nplanes}plane{test_ops['nchannels']}chan/suite2p/plane{i}"
))),
utils.get_list_of_data(
outputs_to_check,
Path(
test_ops['save_path0']).joinpath(f"suite2p/plane{i}")),
))
def test_extraction_output_1plane1chan(test_ops):
ops = prepare_for_extraction(
test_ops,
[[test_ops['data_path'][0].joinpath('detection/pre_registered.npy')]],
(404, 360))
extract_wrapper(ops)
nplanes = test_ops['nplanes']
outputs_to_check = ['F', 'Fneu', 'stat', 'spks']
for i in range(nplanes):
assert all(
utils.compare_list_of_outputs(
outputs_to_check,
utils.get_list_of_data(
outputs_to_check,
Path(test_ops['data_path'][0]).joinpath(
f"{nplanes}plane{test_ops['nchannels']}chan/suite2p/plane{i}"
)),
utils.get_list_of_data(
outputs_to_check,
Path(
test_ops['save_path0']).joinpath(f"suite2p/plane{i}")),
))
def test_1plane_1chan_with_batches_metrics_and_exported_to_nwb_format(test_ops):
"""
Tests for case with 1 plane and 1 channel with multiple batches. Results are saved to nwb format
then checked to see if it contains the necessary parts for use with GUI.
"""
test_ops.update({
'tiff_list': ['input_1500.tif'],
'do_regmetrics': True,
'save_NWB': True
})
suite2p.run_s2p(ops=test_ops)
nplanes = test_ops['nplanes']
outputs_to_check = ['F', 'stat']
for i in range(nplanes):
assert all(utils.compare_list_of_outputs(
outputs_to_check,
utils.get_list_of_data(outputs_to_check, test_ops['data_path'][0].joinpath(f"{nplanes}plane{test_ops['nchannels']}chan1500/suite2p/plane{i}")),
utils.get_list_of_data(outputs_to_check, Path(test_ops['save_path0']).joinpath(f"suite2p/plane{i}")),
))
# Read Nwb data and make sure it's identical to output data
stat, ops, F, Fneu, spks, iscell, probcell, redcell, probredcell = \
io.read_nwb(str(Path(test_ops['save_path0']).joinpath('suite2p/ophys.nwb')))
output_dir = Path(test_ops['save_path0']).joinpath(f"suite2p/plane0")
output_name_list = ['F', 'stat']
data_list_one = utils.get_list_of_data(output_name_list, output_dir)
data_list_two = [F, stat]
for output, data1, data2 in zip(output_name_list, data_list_one, data_list_two):
if output == 'stat': # where the elements of npy arrays are dictionaries (e.g: stat.npy)
for gt_dict, output_dict in zip(data1, data2):
for k in gt_dict.keys():
if k=='ypix' or k=='xpix': # todo: these both are different from the original; footprint and overlap are different, std key doesn't exist in output_dict.
assert np.allclose(gt_dict[k], output_dict[k], rtol=1e-4, atol=5e-2)
elif output == 'iscell': # just check the first column; are cells/noncells classified the same way?
assert np.array_equal(data1[:, 0], data2[:, 0])
else:
assert np.allclose(data1, data2, rtol=1e-4, atol=5e-2)