/
formatsubmission.py
39 lines (34 loc) · 1.32 KB
/
formatsubmission.py
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from rungala import get_paths
import argparse
import numpy as np
import h5py
import tifffile
import os
H5_SUFFIX = "-0.50.lzf.h5"
TIF_SUFFIX = "-0.50.tif"
H5_KEY = "stack"
ID_DELIMITER = "AND"
def format(cues_id, features_id, exec_id, outfile_name):
paths = get_paths("gala-segment", "test", "whole", "only", cues_id, features_id, exec_id, "only")
seg_path = os.path.join(paths["output_dir"], paths["experiment_name"]+H5_SUFFIX)
if len(outfile_name) < 1:
out_path = os.path.join(paths["output_dir"], paths["experiment_name"]+TIF_SUFFIX)
else:
out_path = os.path.join(paths["output_dir"], outfile_name)
seg_h5 = h5py.File(seg_path, "r")
seg_np = np.array(seg_h5[H5_KEY]).astype(np.int16)
print "saving to",out_path
tifffile.imsave(out_path, seg_np)
def main():
# traintest, size, volume_id, cues_id
parser = argparse.ArgumentParser()
parser.add_argument("cues_id", type=str)
parser.add_argument("features_id", type=str)
parser.add_argument("--outfile-name", type=str, default="",
help="special id to target")
parser.add_argument("--exec-id", type=str, default="",
help="special id to target")
args = parser.parse_args()
format(args.cues_id, args.features_id, args.exec_id, args.outfile_name)
if __name__ == "__main__":
main()