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 main():
logging.basicConfig(level=logging.INFO)
args = parse_command_line_arguments()
_LG.info('Loading {}'.format(args.input))
fcs = load_fcs(args.input)
_LG.info('Applying logicle transform.')
# 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)
_LG.info('Saving the result to {}'.format(args.output))
fcs.save(args.output)