Script to merge volume tracing into on-disk segmentation (#3431)

* [WIP] script to merge volume tracing into on-disk segmentation

* group by segmentation files, overwrite the necessary files

* implement pr feedback

Author: fm3

tools/merge-volume-into-data-layer/.gitignore

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+*.zip
+tmp-*

tools/merge-volume-into-data-layer/main.py

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+#!/usr/bin/env python3
+
+from argparse import ArgumentParser
+import zipfile
+import shutil
+import os
+import sys
+import random
+import string
+import wkw
+import numpy as np
+import re
+from operator import add
+
+def main():
+    args = create_parser().parse_args()
+    confirmation_prompt(args)
+    tracing_tmpdir_path = extract_tracing_zip(args)
+
+    tracing_dataset = wkw.Dataset.open(os.path.join(tracing_tmpdir_path, '1'))
+    segmentation_dataset = wkw.Dataset.open(os.path.join(args.segmentation_path, '1'))
+
+    assert(tracing_dataset.header.num_channels == segmentation_dataset.header.num_channels)
+    assert(tracing_dataset.header.voxel_type == segmentation_dataset.header.voxel_type)
+
+    tracing_bboxes = file_bboxes(tracing_dataset)
+    segmentation_bboxes = file_bboxes(segmentation_dataset)
+
+    bboxes_grouped = group_tracing_bboxes(tracing_bboxes, segmentation_bboxes)
+
+    print("Found {} tracing files, which will affect {} segmentation files".format(len(tracing_bboxes), len(bboxes_grouped)))
+
+    segmentation_file_len_voxels = segmentation_dataset.header.block_len * segmentation_dataset.header.file_len
+
+    for counter, bbox_group_key in enumerate(bboxes_grouped):
+        segmentation_bbox = bboxes_grouped[bbox_group_key][0]
+        tracing_bboxes = bboxes_grouped[bbox_group_key][1]
+
+        print("Reading segmentation file {} of {}, bounding box: {}...".format(counter+1, len(bboxes_grouped), segmentation_bbox))
+        data = segmentation_dataset.read(segmentation_bbox[0], segmentation_bbox[1])
+
+        print("  Overwriting tracing buckets in memory...")
+        for tracing_bbox in tracing_bboxes:
+            print("    Overwriting", tracing_bbox)
+            tracing_data = tracing_dataset.read(tracing_bbox[0], tracing_bbox[1])
+            topleft = list(map(lambda x: x % segmentation_file_len_voxels, tracing_bbox[0]))
+            shape = tracing_bbox[1]
+            bottomright = list( map(add, topleft, shape) )
+            data[0:1, topleft[0]:bottomright[0], topleft[1]:bottomright[1], topleft[2]:bottomright[2]] = tracing_data
+
+        print("  Writing segmentation file back to disk...")
+        segmentation_dataset.write([0, 0, 0], data)
+    print("Cleaning up temporary files...")
+    shutil.rmtree(tracing_tmpdir_path)
+    print("Done.")
+
+def confirmation_prompt(args):
+    if not args.yes:
+        answer = input("Are you sure you want to modify the data in {}? This cannot be undone. To continue, type “yes”: ".format(args.segmentation_path))
+        if answer != "yes":
+            print("Aborting")
+            sys.exit(0)
+
+def extract_tracing_zip(args):
+    tracing_tmpdir_path = tmp_filename()
+    os.makedirs(tracing_tmpdir_path)
+    with zipfile.ZipFile(args.tracing_path) as outer_zip:
+        if 'data.zip' in outer_zip.namelist():
+            outfile_path = os.path.join(tracing_tmpdir_path, 'data.zip')
+            with outer_zip.open('data.zip') as data_zip, open(outfile_path, 'wb') as outfile:
+                shutil.copyfileobj(data_zip, outfile)
+                extract_data_zip(outfile_path, tracing_tmpdir_path)
+            os.remove(outfile_path)
+        else:
+            extract_data_zip(args.tracing_path)
+    return tracing_tmpdir_path
+
+def extract_data_zip(path, tracing_tmpdir_path):
+    with zipfile.ZipFile(path) as file:
+        zipfile.ZipFile.extractall(file, path=tracing_tmpdir_path)
+
+def group_tracing_bboxes(tracing_bboxes, segmentation_bboxes):
+    grouped = {}
+    for tracing_bbox in tracing_bboxes:
+        segmentation_bbox = matching_segmentation_bbox(segmentation_bboxes, tracing_bbox)
+        if not str(segmentation_bbox) in grouped:
+            grouped[str(segmentation_bbox)] = (segmentation_bbox, [])
+        grouped[str(segmentation_bbox)][1].append(tracing_bbox)
+    return grouped
+
+def matching_segmentation_bbox(segmentation_bboxes, tracing_bbox):
+    for segmentation_bbox in segmentation_bboxes:
+        if     (segmentation_bbox[0][0] <= tracing_bbox[0][0]
+            and segmentation_bbox[0][1] <= tracing_bbox[0][1]
+            and segmentation_bbox[0][2] <= tracing_bbox[0][2]
+            and segmentation_bbox[1][0] >= tracing_bbox[1][0]
+            and segmentation_bbox[1][1] >= tracing_bbox[1][1]
+            and segmentation_bbox[1][2] >= tracing_bbox[1][2]):
+                return segmentation_bbox
+    print("Error: tracing extends outside of segmentation data. Stopping, no data was modified.")
+    sys.exit(1)
+
+def file_bboxes(dataset):
+    file_len_voxels = dataset.header.block_len * dataset.header.file_len
+    p = re.compile('(.*)/z([0-9]+)/y([0-9]+)/x([0-9]+).wkw')
+    bboxes = []
+    for file in dataset.list_files():
+        m = p.match(file)
+        file_coords = [m.group(4), m.group(3), m.group(2)]
+        offset = [int(x) * file_len_voxels for x in file_coords]
+        shape = [file_len_voxels, file_len_voxels, file_len_voxels]
+        bboxes.append((offset, shape))
+    return bboxes
+
+def create_parser():
+    parser = ArgumentParser()
+    parser.add_argument('tracing_path', help='Volume tracing zip file')
+    parser.add_argument('segmentation_path', help='Directory containing the segmentation to overwrite. (Path should not include zoom level)')
+    parser.add_argument('-y', '--yes', action="store_true", help='Skip the confirmation prompt')
+    return parser
+
+def tmp_filename():
+    return 'tmp-' + ''.join(random.choice(string.ascii_uppercase + string.digits) for _ in range(10))
+
+if __name__ == '__main__':
+    main()

tools/merge-volume-into-data-layer/requirements.txt

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+wkw
+argparse
+numpy