ch2_result_center = np.mean(centers, axis=0) ch2_result_radius = np.max( np.sqrt((centers - ch2_result_center)**2)) sid = ch2['slice_id'] slice2roi[pid][sid] = { 'roi_center': tuple(ch2_result_center), 'roi_radii': (ch2_result_radius, ch2_result_radius) } filename = data_path.split('/')[-1] + '_slice2roi_joni.pkl' with open(filename, 'w') as f: pickle.dump(slice2roi, f) print 'saved to ', filename return slice2roi if __name__ == '__main__': parser = argparse.ArgumentParser(description=__doc__) required = parser.add_argument_group('required arguments') #required.add_argument('-c', '--config', # help='configuration to run', # required=True) args = parser.parse_args() data_paths = [PKL_TRAIN_DATA_PATH, PKL_TEST_DATA_PATH] log_path = LOGS_PATH + "generate_roi.log" with print_to_file(log_path): for d in data_paths: get_slice2roi(d, plot=True) print "log saved to '%s'" % log_path
centers = np.array(ch2_centers) ch2_result_center = np.mean(centers, axis=0) ch2_result_radius = np.max(np.sqrt((centers - ch2_result_center) ** 2)) sid = ch2["slice_id"] slice2roi[pid][sid] = { "roi_center": tuple(ch2_result_center), "roi_radii": (ch2_result_radius, ch2_result_radius), } filename = data_path.split("/")[-1] + "_slice2roi_joni.pkl" with open(filename, "w") as f: pickle.dump(slice2roi, f) print "saved to ", filename return slice2roi if __name__ == "__main__": parser = argparse.ArgumentParser(description=__doc__) required = parser.add_argument_group("required arguments") # required.add_argument('-c', '--config', # help='configuration to run', # required=True) args = parser.parse_args() data_paths = [PKL_TRAIN_DATA_PATH, PKL_TEST_DATA_PATH] log_path = LOGS_PATH + "generate_roi.log" with print_to_file(log_path): for d in data_paths: get_slice2roi(d, plot=True) print "log saved to '%s'" % log_path
) train_data["intermediates"] = iter_train(0) pickle.dump(train_data, open(metadata_path + "-dump", "wb")) return if __name__ == "__main__": parser = argparse.ArgumentParser(description=__doc__) required = parser.add_argument_group('required arguments') required.add_argument('-c', '--config', help='configuration to run', required=True) args = parser.parse_args() set_configuration(args.config) expid = utils.generate_expid(args.config) log_file = LOGS_PATH + "%s.log" % expid with print_to_file(log_file): print "Running configuration:", config().__name__ print "Current git version:", utils.get_git_revision_hash() train_model(expid) print "log saved to '%s'" % log_file predict_model(expid) print "log saved to '%s'" % log_file