def setup():
global DIRPATH
DIRPATH = tempfile.mkdtemp()
# Create DAT file.
raw_data = create_trace(nsamples, nchannels)
for start, end in excerpts(nsamples, nexcerpts=10, excerpt_size=10):
raw_data[start:end] += np.random.randint(low=-10000, high=10000,
size=(10, nchannels))
raw_data.tofile(op.join(DIRPATH, dat_filename))
# Create PRM file.
prm = get_params(**{
'raw_data_files': dat_filename,
'experiment_name': name,
'nchannels': nchannels,
'sample_rate': sample_rate,
'detect_spikes': 'positive',
'prb_file': prb_filename,
})
prm_contents = pydict_to_python(prm)
with open(op.join(DIRPATH, prm_filename), 'w') as f:
f.write(prm_contents)
# Create PRB file.
prb_contents = """
nchannels = %NCHANNELS%
channel_groups = {0:
{
'channels': list(range(nchannels)),
'graph': [(i, i + 1) for i in range(nchannels - 1)],
}
}""".replace('%NCHANNELS%', str(nchannels)).replace(' ', '')
with open(op.join(DIRPATH, prb_filename), 'w') as f:
f.write(prb_contents)
def _load_files_info(prm_filename, dir=None):
dir_, filename = op.split(prm_filename)
dir = dir or dir_
basename, ext = op.splitext(filename)
if ext == '':
ext = '.prm'
prm_filename = op.join(dir, basename + ext)
assert op.exists(prm_filename)
# Load PRM file.
prm = get_params(prm_filename)
nchannels = prm.get('nchannels')
assert nchannels > 0
# Find PRB path in PRM file, and load it.
prb_filename = prm.get('prb_file')
if not op.exists(prb_filename):
prb_filename = op.join(dir, prb_filename)
prb = load_probe(prb_filename)
# Find raw data source.
data = prm.get('raw_data_files')
if isinstance(data, basestring):
if data.endswith('.dat'):
data = [data]
if isinstance(data, list):
for i in range(len(data)):
if not op.exists(data[i]):
data[i] = op.join(dir, data[i])
experiment_name = prm.get('experiment_name')
return dict(prm=prm, prb=prb, experiment_name=experiment_name, nchannels=nchannels,
data=data, dir=dir)
def _load_files_info(prm_filename, dir=None):
dir_, filename = op.split(prm_filename)
dir = dir or dir_
basename, ext = op.splitext(filename)
if ext == '':
ext = '.prm'
prm_filename = op.join(dir, basename + ext)
assert op.exists(prm_filename)
# Load PRM file.
prm = get_params(prm_filename)
nchannels = prm.get('nchannels')
assert nchannels > 0
# Find PRB path in PRM file, and load it.
prb_filename = prm.get('prb_file')
if not op.exists(prb_filename):
prb_filename = op.join(dir, prb_filename)
prb = load_probe(prb_filename)
# Find raw data source.
data = prm.get('raw_data_files')
if isinstance(data, basestring):
if data.endswith('.dat'):
data = [data]
if isinstance(data, list):
for i in range(len(data)):
if not op.exists(data[i]):
data[i] = op.join(dir, data[i])
experiment_name = prm.get('experiment_name')
return dict(prm=prm,
prb=prb,
experiment_name=experiment_name,
nchannels=nchannels,
data=data,
dir=dir)
def setup():
global DIRPATH
DIRPATH = tempfile.mkdtemp()
# Create DAT file.
raw_data = create_trace(nsamples, nchannels)
for start, end in excerpts(nsamples, nexcerpts=10, excerpt_size=10):
raw_data[start:end] += np.random.randint(low=-10000,
high=10000,
size=(10, nchannels))
raw_data.tofile(op.join(DIRPATH, dat_filename))
# Create PRM file.
prm = get_params(
**{
'raw_data_files': dat_filename,
'experiment_name': name,
'nchannels': nchannels,
'sample_rate': sample_rate,
'detect_spikes': 'positive',
'prb_file': prb_filename,
})
prm_contents = pydict_to_python(prm)
with open(op.join(DIRPATH, prm_filename), 'w') as f:
f.write(prm_contents)
# Create PRB file.
prb_contents = """
nchannels = %NCHANNELS%
channel_groups = {0:
{
'channels': list(range(nchannels)),
'graph': [(i, i + 1) for i in range(nchannels - 1)],
}
}""".replace('%NCHANNELS%', str(nchannels)).replace(' ', '')
with open(op.join(DIRPATH, prb_filename), 'w') as f:
f.write(prb_contents)
def test_get_params():
assert get_params(sample_rate=1).get('filter_butter_order', None) == 3
assert get_params(sample_rate=1,
filter_butter_order=1)['filter_butter_order'] == 1
def test_get_params():
assert get_params(sample_rate=1).get('filter_butter_order', None) == 3
assert get_params(sample_rate=1, filter_butter_order=1)['filter_butter_order'] == 1