tiffstack_to_wkw

#!/usr/bin/env python

import argparse
import code # for code.interact(local=dict(globals(), **locals()) ) debugging
import glob
import numpy as np
import os
import webknossos
import webknossos.dataset

######################
# Make a wkw out of a tiff stack

def main():
    cfg = handle_args()
    files=sorted(glob.glob(os.path.join(cfg.src, "*.tiff")))

    dataset = webknossos.Dataset(dataset_path=cfg.dest, voxel_size=(8,8,8), name=cfg.dset_name, exist_ok=False)
    dataset.add_layer_from_images(images=files, layer_name="seg", batch_size=cfg.batch_size, category=webknossos.dataset.SEGMENTATION_CATEGORY)


def handle_args():
    parser = argparse.ArgumentParser(description="This does a thing")
    parser.add_argument("src",  help="Directory containing tiff stack")
    parser.add_argument("dest", help="Target directory")
    parser.add_argument("--dset_name", default="export_1720537802", help="Webknossos name for dataset")
    parser.add_argument("--batch_size", default=32, type=int, help="Batch size for ingest")
    parser.add_argument("--verbose",    help="Be noisier")
    ret = parser.parse_args()
    return ret

#####
if __name__ == '__main__':
    main()