def test_compute_volume_corrected_nm(self): image_set = ImageSet(self.repo, path_list=['mrna/arhgdia/2h/']) vcnm = image_set.compute_volume_corrected_nm() self.assertAlmostEqual(0.029713582957013474, vcnm, places=5)
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( constants.analysis_config['FIGURE_OUTPUT_PATH'].format( root_dir=global_root_dir), tgt_image_name) plot.bar_profile(nms, tgt_fp, plot_colors) logger.info("Generated image at {}", str(tgt_fp).split("analysis/")[1])