def test_compute_surface_corrected_nm(self):
image_set = ImageSet(self.repo, path_list=['mrna/arhgdia/2h/'])
result = image_set.compute_surface_corrected_nm()
self.assertAlmostEqual(result, 0.1010903526279469, places=5)
for i, gene in enumerate(
tqdm.tqdm(constants.dataset_config['MRNA_GENES'],
desc="Genes")):
nms = []
tgt_image_name = constants.analysis_config[
'FIGURE_NAME_FORMAT_BARPLOT'].format(gene=gene)
tgt_fp = pathlib.Path(
constants.analysis_config['FIGURE_OUTPUT_PATH'].format(
root_dir=global_root_dir), tgt_image_name)
for timepoint in tqdm.tqdm(
constants.dataset_config['TIMEPOINTS_MRNA'],
desc="Timepoint"):
imageset = ImageSet(repo, [
"{0}/{1}/{2}/".format(molecule_type, gene, timepoint)
])
nm = imageset.compute_surface_corrected_nm()
nms.append(nm)
plot.bar_profile(nms, tgt_fp, plot_colors[i])
logger.info("Generated image at {}",
str(tgt_fp).split("analysis/")[1])
else:
timepoint = '3h'
nms = []
for i, gene in enumerate(constants.analysis_config['MRNA_GENES']):
imageset = ImageSet(
repo,
['{0}/{1}/{2}/'.format(molecule_type, gene, timepoint)])
nms.append(imageset.compute_volume_corrected_nm())
tgt_image_name = constants.analysis_config[
'FIGURE_NAME_FORMAT_VOLUME']
tgt_fp = pathlib.Path(
