Create move_dataset_slices_by_one.py (#453)

* Create move_dataset_slices_by_one.py

* Update webknossos/examples/move_dataset_slices_by_one.py

Co-authored-by: R Schwanhold <[email protected]>

* incorporate PR feedback

* move script to script-collection

* add script-collection to linting and typechecking

* format

Co-authored-by: R Schwanhold <[email protected]>

Author: philippotto

webknossos/lint.sh

@@ -4,3 +4,4 @@ set -eEuo pipefail
 pylint -j4 webknossos
 # pylint -j4 tests/**/*.py  # TODO add linting for tests
 pylint -j4 examples/*.py
+pylint -j4 script-collection/*.py

webknossos/script-collection/move_dataset_slices_by_one.py

@@ -0,0 +1,86 @@
+from argparse import ArgumentParser
+from pathlib import Path
+from typing import Tuple
+
+from wkcuber.utils import (  # pylint: disable=import-error
+    add_distribution_flags,
+    add_scale_flag,
+    get_executor_for_args,
+    named_partial,
+)
+
+from webknossos.dataset import Dataset, MagView, View
+
+
+def create_parser() -> ArgumentParser:
+    parser = ArgumentParser(
+        description="Copies a given dataset layer in mag1 while moving all slices from z+1 to z. Can be used to fix off-by-one errors."
+    )
+
+    parser.add_argument("source_path", help="Path to input WKW dataset", type=Path)
+
+    parser.add_argument(
+        "target_path",
+        help="WKW dataset with which to compare the input dataset.",
+        type=Path,
+    )
+
+    parser.add_argument(
+        "--layer_name",
+        "-l",
+        help="Name of the layer to compare (if not provided, all layers are compared)",
+        default=None,
+    )
+
+    add_distribution_flags(parser)
+    add_scale_flag(parser)
+
+    return parser
+
+
+def move_by_one(
+    src_mag: MagView,
+    args: Tuple[View, int],
+) -> None:
+    chunk_view, i = args
+    del i
+    size = chunk_view.size
+    dst_offset = chunk_view.global_offset
+
+    src_offset = (
+        dst_offset[0],
+        dst_offset[1],
+        dst_offset[2] + 1,
+    )
+
+    data = src_mag.read(src_offset, size)
+    chunk_view.write(data)
+
+
+def main() -> None:
+
+    args = create_parser().parse_args()
+
+    src_dataset = Dataset(args.source_path)
+    src_layer = src_dataset.get_layer(args.layer_name)
+    src_mag = src_layer.get_mag("1")
+
+    dst_dataset = Dataset.get_or_create(args.target_path, args.scale)
+    dst_layer = dst_dataset.add_layer(args.layer_name, "color")
+    dst_layer.bounding_box = src_layer.bounding_box
+
+    dst_mag = dst_layer.get_or_add_mag("1")
+
+    dst_view = dst_mag.get_view()
+
+    with get_executor_for_args(args) as executor:
+        func = named_partial(move_by_one, src_mag)
+        dst_view.for_each_chunk(
+            func,
+            chunk_size=dst_mag._get_file_dimensions(),
+            executor=executor,
+        )
+
+
+if __name__ == "__main__":
+    main()

webknossos/typecheck.sh

@@ -9,3 +9,6 @@ python -m mypy -p tests --disallow-untyped-defs --show-error-codes --strict-equa
 
 echo "Typecheck examples..."
 python -m mypy -p examples --disallow-untyped-defs --show-error-codes --strict-equality --namespace-packages --no-implicit-optional
+
+echo "Typecheck script-collection..."
+python -m mypy -p script-collection --disallow-untyped-defs --show-error-codes --strict-equality --namespace-packages --no-implicit-optional