def base_logicle_test(self, original_file, transed_file):
diff_threshold = 1.0
fcs, fcs_trans = load_test_data(original_file, transed_file)
compensate(fcs)
# Currently applying logicle transform takes a lot of time, and
# we want to run this script inside CircleCI without timeout.
# So we put the processing into subprocess and periodically print
# status.
run_and_check(lambda: apply_logicle_transform(fcs, ), 300)
channel_info = fcs.meta['_channels_']
result = {}
fail = False
for channel in channel_info['$PnN']:
if channel == 'Time':
continue
val0 = fcs[channel].values
val1 = fcs_trans[channel].values
denom = (val0 + val1) / 2 + 1
numer = np.abs(val0 - val1)
diff = 100 * np.mean(numer / denom)
result[channel] = diff
if diff > diff_threshold:
fail = True
_LG.info(result)
self.assertTrue(not fail)
def base_logicle_test(self, original_file, transed_file):
diff_threshold = 1.0
fcs, fcs_trans = load_test_data(original_file, transed_file)
compensate(fcs)
# Currently applying logicle transform takes a lot of time, and
# we want to run this script inside CircleCI without timeout.
# So we put the processing into subprocess and periodically print
# status.
run_and_check(lambda: apply_logicle_transform(fcs,), 300)
channel_info = fcs.meta['_channels_']
result = {}
fail = False
for channel in channel_info['$PnN']:
if channel == 'Time':
continue
val0 = fcs[channel].values
val1 = fcs_trans[channel].values
denom = (val0 + val1) / 2 + 1
numer = np.abs(val0 - val1)
diff = 100 * np.mean(numer/denom)
result[channel] = diff
if diff > diff_threshold:
fail = True
_LG.info(result)
self.assertTrue(not fail)
def _process_fcs_file(filename):
# TODO: Remove this script
fcs = FCMeasurement(ID='Test Sample', datafile=filename)
fcs_format = fcs.meta['__header__']['FCS format']
if int(float(fcs_format[3:])) not in [2, 3]:
raise RuntimeError('{} is not supported.'.format(fcs_format))
if fcs.meta['$DATATYPE'] == 'I':
_LG.info('Not processing integer type')
return fcs
compensate(fcs)
apply_logicle_transform(fcs)
