def main(): parser = argparse.ArgumentParser(__doc__) parser.add_argument('data_file', help="Path to data file") args = parser.parse_args() dm = DataManager(args.data_file) print dm.spath('some_stack')
def dthresh_and_dt(isq_filename): dm = DataManager(isq_filename, working_base='/Users/hartleym/working/ct_analysis') input_path = dm.spath('raw_stack') output_path = dm.spath('threshdt') def dthresh(image): thresh = threshold_otsu(image) thresholded = image > thresh dt = distance_transform_cdt(thresholded) return dt > 18 apply_stack_transform(input_path, output_path, dthresh)
def dconvert_isq_file(isq_filename): dm = DataManager(isq_filename) stack_path = dm.spath('raw_stack') convert_large_isq_file(isq_filename, stack_path)
def main(): parser = argparse.ArgumentParser() parser.add_argument('filename', help='Path to ISQ file') args = parser.parse_args() dm = DataManager(args.filename) stack = Image3D.from_path(dm.spath('stripped')) seed_labels = find_seed_centroids(stack) stage = {} stage['name'] = dm.name stage['seeds'] = seed_labels with open(dm.spath('seeds.yml'), 'w') as f: yaml.dump(stage, f)
def populate_queue(queue, fn): dm = DataManager(fn) seeds_dir = dm.spath('seeds') isolated_dir = dm.spath('isolated_seeds') docker_seeds_dir = '/working/C0000230/seeds' docker_isolated_dir = '/working/C0000230/isolated_seeds' for seed_file in os.listdir(seeds_dir)[2:3]: input_file = os.path.join(docker_seeds_dir, seed_file) output_file = os.path.join(docker_isolated_dir, seed_file) print input_file, output_file command = make_command(input_file, output_file) subprocess.call(command)
def dcc_centroids(isq_filename): dm = DataManager(isq_filename, working_base='/Users/hartleym/working/ct_analysis') input_path = dm.spath('threshdt') with open('centroids.txt', 'w') as f: for n, image in enumerate(yield_stack_from_path(input_path)): centroids = find_component_centroids(image) for c in centroids: f.write("{}\n".format(c + [n]))
def spikey_redis(fn): r = redis.StrictRedis(host='192.168.99.100') dm = DataManager(fn) seeds_dir = dm.spath('seeds') isolated_dir = dm.spath('isolated_seeds') docker_seeds_dir = '/working/C0000230/seeds' docker_isolated_dir = '/working/C0000230/isolated_seeds' prefix = 'python /code/ct_pod_analysis/scripts/isolate_single_seed.py' for seed_file in os.listdir(seeds_dir)[2:10]: input_file = os.path.join(docker_seeds_dir, seed_file) output_file = os.path.join(docker_isolated_dir, seed_file) command = "{} {} {}".format(prefix, input_file, output_file) r.lpush("tasks", command)