Extract sub-volume of n5 file

Author: schilling40

scripts/extract_block.py

@@ -0,0 +1,68 @@
+import os
+import argparse
+import numpy as np
+import h5py
+import z5py
+
+"""
+This script extracts data around an input center coordinate in a given ROI halo.
+"""
+
+
+def main(input_file, output_dir, input_key, resolution, coords, roi_halo):
+    """
+
+    :param str input_file: File path to input folder in n5 format
+    :param str output_dir: output directory for saving cropped n5 file as <basename>_crop.n5
+    :param str input_key: Key for accessing volume in n5 format, e.g. 'setup0/s0'
+    :param float resolution: Resolution of input data in micrometer
+    :param str coords: Center coordinates of extracted 3D volume in format 'z,y,x'
+    :param str roi_halo: ROI halo of extracted 3D volume in format 'z,y,x'
+    """
+
+    coords =  [int(r) for r in coords.split(",")]
+    roi_halo = [int(r) for r in roi_halo.split(",")]
+
+    input_content = list(filter(None, input_file.split("/")))
+    basename = "".join(input_content[-1].split(".")[:-1])
+    input_dir = input_file.split(basename)[0]
+    input_dir = os.path.abspath(input_dir)
+
+    if "" == output_dir:
+        output_dir = input_dir
+
+    input_key = "setup0/timepoint0/s0"
+
+    output_file = os.path.join(output_dir, basename + "_crop" + ".n5")
+
+    #M_LR_000167_R, coords = '806,1042,1334', coords = (z, y, x) compared to MoBIE view
+
+    coords = np.array(coords)
+    coords = coords / resolution
+    coords = np.round(coords).astype(np.int32)
+
+    roi = tuple(slice(co - rh, co + rh) for co, rh in zip(coords, roi_halo))
+
+    with z5py.File(input_file, "r") as f:
+        raw = f[input_key][roi]
+
+    with z5py.File(output_file, "w") as f_out:
+        f_out.create_dataset("raw", data=raw, compression="gzip")
+
+if __name__ == "__main__":
+
+    parser = argparse.ArgumentParser(
+        description="Script to extract region of interest (ROI) block around center coordinate.")
+
+    parser.add_argument('input', type=str, help="Input file in n5 format.")
+    parser.add_argument('-o', "--output", type=str, default="", help="Output directory")
+    parser.add_argument('-c', "--coord", type=str, required=True, help="3D coordinate in format 'z,y,x' as center of extracted block. Dimensions are inversed to view in MoBIE (x y z) -> (z y x)")
+
+    parser.add_argument('-k', "--input_key", type=str, default="setup0/timepoint0/s0", help="Input key for data in input file")
+    parser.add_argument('-r', "--resolution", type=float, default=0.38, help="Resolution of input in micrometer")
+
+    parser.add_argument("--roi_halo", type=str, default="128,128,64", help="ROI halo around center coordinate")
+
+    args = parser.parse_args()
+
+    main(args.input, args.output, args.input_key, args.resolution, args.coord, args.roi_halo)