def test_load_file_fail():
this_file_path = os.path.realpath(__file__)
this_dir_name = os.path.dirname(this_file_path)
file_name = os.path.join(this_dir_name, 'no_file.h5')
with pytest.raises(IOError) as ex:
_ = ws.loadDataFile(file_name)
assert 'The file' in str(ex.value)
file_name = os.path.join(this_dir_name, 'no_h5.h6')
with pytest.raises(RuntimeError) as ex:
_ = ws.loadDataFile(file_name)
assert 'File must be a WaveSurfer-generated HDF5 (.h5) file.' in str(ex.value)
def test_version_higher_then_latest():
this_file_path = os.path.realpath(__file__)
this_dir_name = os.path.dirname(this_file_path)
file_name = os.path.join(this_dir_name, 'ws_v100_data.h5')
with pytest.raises(RuntimeWarning) as ex:
_ = ws.loadDataFile(file_name)
assert 'You are reading a WaveSurfer file version this module was not' in str(ex.value)
def test_type_single():
this_file_path = os.path.realpath(__file__)
this_dir_name = os.path.dirname(this_file_path)
file_name = os.path.join(this_dir_name, 'test2.h5')
dataAsDict = ws.loadDataFile(file_name, format_string='single')
scan = dataAsDict['sweep_0001']['analogScans']
assert scan.dtype == 'float32'
assert np.allclose(scan.mean(axis=1), np.array([1.78443789, 1.78402293]))
def test_type_raw():
this_file_path = os.path.realpath(__file__)
this_dir_name = os.path.dirname(this_file_path)
file_name = os.path.join(this_dir_name, 'test2.h5')
dataAsDict = ws.loadDataFile(file_name, format_string='raw') # conversion to scaled data would fail for this file
scan = dataAsDict['sweep_0001']['analogScans']
assert scan.dtype == 'int16'
assert np.allclose(scan.mean(axis=1), np.array([5565.12903571, 5563.84042857]))
def test_version_higher():
this_file_path = os.path.realpath(__file__)
this_dir_name = os.path.dirname(this_file_path)
file_name = os.path.join(this_dir_name, 'ws_v1p0p2_data.h5')
with pytest.warns(RuntimeWarning) as record:
_ = ws.loadDataFile(file_name)
# check that only one warning was raised
assert len(record) == 1
# check that the message matches
assert 'You are reading a WaveSurfer file version this module was not' in record[
0].message.args[0]
def test_loading_newer_file_with_funnier_sampling_rate():
this_file_path = os.path.realpath(__file__)
this_dir_name = os.path.dirname(this_file_path)
file_name = os.path.join(this_dir_name, '29997_Hz_sampling_rate_0p913_0001.h5')
data_file_as_struct = ws.loadDataFile(file_name, 'raw')
# The nominal sampling rate was 29997, but the returned
# sampling rate should be 100e6/3333 for both acq and stim.
returned_acq_sampling_rate = data_file_as_struct['header']['Acquisition']['SampleRate']
n_timebase_ticks_per_acq_sample = 100e6 / returned_acq_sampling_rate # should be exactly 3333
assert n_timebase_ticks_per_acq_sample == 3333
returned_stim_sampling_rate = data_file_as_struct['header']['Stimulation']['SampleRate']
n_timebase_ticks_per_stim_sample = 100e6 / returned_stim_sampling_rate # should be exactly 3333
assert n_timebase_ticks_per_stim_sample == 3333
def test_loading_newer_file_with_funny_sampling_rate():
this_file_path = os.path.realpath(__file__)
this_dir_name = os.path.dirname(this_file_path)
file_name = os.path.join(this_dir_name, '30_kHz_sampling_rate_0p913_0001.h5')
data_file_as_struct = ws.loadDataFile(file_name, 'raw')
# The requested sampling rate was 30000, but this version of WS
# coerces that in the UI to an acheivable rate, which should be
# ~30003 Hz, to make (100 Mhz)/fs an integer.
returned_acq_sampling_rate = data_file_as_struct['header']['Acquisition']['SampleRate']
n_timebase_ticks_per_acq_sample = 100e6 / returned_acq_sampling_rate # should be exactly 3333
assert n_timebase_ticks_per_acq_sample == 3333
returned_stim_sampling_rate = data_file_as_struct['header']['Stimulation']['SampleRate']
n_timebase_ticks_per_stim_sample = 100e6 / returned_stim_sampling_rate # should be exactly 3333
assert n_timebase_ticks_per_stim_sample == 3333
def test_loading_older_file_with_funny_sampling_rate():
this_file_path = os.path.realpath(__file__)
this_dir_name = os.path.dirname(this_file_path)
file_name = os.path.join(this_dir_name, '30_kHz_sampling_rate_0p912_0001.h5')
data_file_as_struct = ws.loadDataFile(file_name, 'raw') # conversion to scaled data would fail for this file
# The nominal sampling rate was 30000, but the returned
# sampling rate should be ~30003 Hz, to make (100 Mhz)/fs an
# integer.
returned_acq_sampling_rate = data_file_as_struct['header']['Acquisition']['SampleRate']
n_timebase_ticks_per_acq_sample = 100e6 / returned_acq_sampling_rate # should be exactly 3333
assert n_timebase_ticks_per_acq_sample == 3333
returned_stim_sampling_rate = data_file_as_struct['header']['Stimulation']['SampleRate']
n_timebase_ticks_per_stim_sample = 100e6 / returned_stim_sampling_rate # should be exactly 3333
assert n_timebase_ticks_per_stim_sample == 3333
def load_wavesurfer_file(WS_path):
#%%
ws_data = ws.loadDataFile(filename=WS_path, format_string='double' )
units = np.array(ws_data['header']['AIChannelUnits']).astype(str)
channelnames = np.array(ws_data['header']['AIChannelNames']).astype(str)
commandchannel = np.asarray(ws_data['header']['AOChannelNames'],str) =='Command'
commandunit = np.asarray(ws_data['header']['AOChannelUnits'],str)[np.where(commandchannel)[0][0]]
ephysidx = (channelnames == 'Voltage').argmax()
if 'A' in commandunit:
recording_mode = 'CC'
else:
recording_mode = 'VC'
framatimesidx = (channelnames == 'FrameTrigger').argmax()
keys = list(ws_data.keys())
del keys[keys=='header']
if len(keys)>1:
print('MULTIPLE SWEEPS! HANDLE ME!!')
time.sleep(1000)
sweep = ws_data[keys[0]]
sRate = ws_data['header']['AcquisitionSampleRate'][0][0]
voltage = sweep['analogScans'][ephysidx,:]
#%
if units[ephysidx] == 'mV':
voltage =voltage/1000
units[ephysidx] = 'V'
if units[ephysidx] == 'pA':
voltage =voltage/10**12
units[ephysidx] = 'A'
if units[ephysidx] == 'nA':
voltage =voltage/10**9
units[ephysidx] = 'A'
frame_trigger = sweep['analogScans'][framatimesidx,:]
timestamp = ws_data['header']['ClockAtRunStart']
#%
# =============================================================================
# plt.plot(voltage)
# plt.plot(peaks,voltage[peaks],'ro')
# =============================================================================
#%%
return voltage, frame_trigger, sRate, recording_mode, timestamp , units[ephysidx]
def test_loading_0p933_file():
this_file_path = os.path.realpath(__file__)
this_dir_name = os.path.dirname(this_file_path)
file_name = os.path.join(this_dir_name, 'ws_0p933_data_0001.h5')
dataAsDict = ws.loadDataFile(file_name)
acq_sampling_rate = float(dataAsDict['header']['Acquisition']['SampleRate'])
assert acq_sampling_rate == 20e3
n_a_i_channels = dataAsDict['header']['Acquisition']['AnalogChannelScales'].size
assert n_a_i_channels == 1
n_active_a_i_channels = int(dataAsDict['header']['Acquisition']['IsChannelActive'].sum())
assert n_active_a_i_channels == 1
stim_sampling_rate = dataAsDict['header']['Stimulation']['SampleRate']
assert stim_sampling_rate == 20e3
x = dataAsDict['sweep_0001']['analogScans']
assert x.dtype == 'float64'
assert np.absolute(np.max(x[0]) - 5) < 0.01
assert np.absolute(np.min(x[0]) - 0) < 0.01
assert np.allclose(x.mean(axis=1), np.array([2.49962616]))
def test_loading_file():
this_file_path = os.path.realpath(__file__)
this_dir_name = os.path.dirname(this_file_path)
file_name = os.path.join(this_dir_name, 'test2.h5')
dataAsDict = ws.loadDataFile(file_name)
scan = dataAsDict['sweep_0001']['analogScans']
assert scan.dtype == 'float64'
assert np.allclose(scan.mean(axis=1), np.array([1.78443789, 1.78402293]))
acq_sampling_rate = float(dataAsDict['header']['AcquisitionSampleRate'])
assert acq_sampling_rate == 20e3
n_a_i_channels = int(dataAsDict['header']['NAIChannels'])
assert n_a_i_channels == 3
n_active_a_i_channels = int(dataAsDict['header']['IsAIChannelActive'].sum())
assert n_active_a_i_channels == 2
stim_sampling_rate = dataAsDict['header']['StimulationSampleRate']
assert stim_sampling_rate == 20e3
x = dataAsDict['sweep_0001']['analogScans']
assert np.absolute(np.max(x[0]) - 5) < 0.01
assert np.absolute(np.min(x[0]) - 0) < 0.01
def test_loading_0p74_file():
this_file_path = os.path.realpath(__file__)
this_dir_name = os.path.dirname(this_file_path)
file_name = os.path.join(this_dir_name, 'ws_0p74_data_0001.h5')
dataAsDict = ws.loadDataFile(file_name, 'raw') # conversion to scaled data would fail for this file
acq_sampling_rate = float(dataAsDict['header']['Acquisition']['SampleRate'])
assert acq_sampling_rate == 20e3
n_a_i_channels = dataAsDict['header']['Acquisition']['ChannelScales'].size
assert n_a_i_channels == 4
n_active_a_i_channels = int(dataAsDict['header']['Acquisition']['IsChannelActive'].sum())
assert n_active_a_i_channels == 4
stim_sampling_rate = dataAsDict['header']['Stimulation']['SampleRate']
assert stim_sampling_rate == 20e3
x_as_int16 = dataAsDict['trial_0001']
assert x_as_int16.dtype == 'int16'
assert np.max(x_as_int16[0]) == 15204
assert np.min(x_as_int16[0]) == 2
x = x_as_int16.astype('float64')
assert np.allclose(x.mean(axis=1), np.array([7603.29115, 7594.2194, 7598.7204, 7594.06135]))