comparison spyboat_cli.py @ 4:a4c6fcf2c456 draft

"planemo upload commit 0584e8878deaf91614c6bb3c0122975300132c25"

3:4d7f30a7e2f6

import spyboat
import output_report

logging.basicConfig(level=logging.INFO, stream=sys.stdout, force=True)
logger = logging.getLogger('wrapper')

# ----------command line parameters ---------------

parser = argparse.ArgumentParser(description='Process some arguments.')

# ------------Read the input----------------------------------------
try:
    movie = spyboat.open_tif(arguments.input_path)
except FileNotFoundError:
    logger.critical(f"Couldn't open {arguments.input_path}, check movie storage directory!")

    sys.exit(1)

# -------- Do (optional) spatial downsampling ---------------------------

scale_factor = arguments.rescale

# defaults to None

    if arguments.report_img_path != '.':
        logger.info(f'Creating report directory {arguments.report_img_path}')
        os.mkdir(arguments.report_img_path)    

    # make 6 times 4 snapshots each
    Nsnap = 6
    NFrames = movie.shape[0]
    # show only frames at least one Tmin
    # away from the edge (-effects)
    start_frame = int(Wkwargs['Tmin']/Wkwargs['dt'])        
    

4:a4c6fcf2c456

import spyboat
import output_report

logging.basicConfig(level=logging.INFO, stream=sys.stdout, force=True)
logger = logging.getLogger('spyboat-cli')

# ----------command line parameters ---------------

parser = argparse.ArgumentParser(description='Process some arguments.')

# ------------Read the input----------------------------------------
try:
    movie = spyboat.open_tif(arguments.input_path)
except FileNotFoundError:
    logger.critical(f"Couldn't open {arguments.input_path}, check movie storage directory!")
    sys.exit(1)
# problems get logged in 'open_tif'
if movie is None:
    sys.exit(1)
# -------- Do (optional) spatial downsampling ---------------------------

scale_factor = arguments.rescale

# defaults to None

    if arguments.report_img_path != '.':
        logger.info(f'Creating report directory {arguments.report_img_path}')
        os.mkdir(arguments.report_img_path)    

    # 4 snapshots each
    Nsnap = 7
    NFrames = movie.shape[0]
    # show only frames at least one Tmin
    # away from the edge (-effects)
    start_frame = int(Wkwargs['Tmin']/Wkwargs['dt'])