Reading nd datasets

webknossos/examples/download_segments.py

@@ -14,7 +14,7 @@ def main() -> None:
     )
     mag_view = dataset.get_segmentation_layers()[0].get_mag(MAG)
 
-    z = mag_view.bounding_box.topleft.z
+    z = mag_view.bounding_box.get_bounds("z")[0]
     with mag_view.get_buffered_slice_reader() as reader:
         for slice_data in reader:
             slice_data = slice_data[0]  # First channel only

webknossos/examples/download_tiff_stack.py

@@ -15,7 +15,7 @@ def main() -> None:
     )
     mag_view = dataset.get_layer(LAYER_NAME).get_mag(MAG)
 
-    z = mag_view.bounding_box.topleft.z
+    z = mag_view.bounding_box.get_bounds("z")[0]
     with mag_view.get_buffered_slice_reader() as reader:
         for slice_data in reader:
             slice_data = slice_data[0]  # First channel only

webknossos/script_collection/reading_nd_data.py

@@ -0,0 +1,65 @@
+from pathlib import Path
+
+from tifffile import imwrite
+
+import webknossos as wk
+from webknossos.geometry.nd_bounding_box import NDBoundingBox
+
+TIF_PATH = Path(".") / "webknossos" / "testdata" / "4D" / "4D_series"
+OUTPUT = Path(".") / "testoutput" / "4D_series"
+
+
+def from_images_import():
+    dataset = wk.Dataset.from_images(
+        TIF_PATH,
+        OUTPUT,
+        voxel_size=(10, 10, 10),
+        data_format="zarr3",
+        compress=True,
+        use_bioformats=True,
+    )
+    layer = dataset.get_color_layers()[0]
+    mag_view = layer.get_finest_mag()
+    # data = mag_view.read()[0, 0, 0, :, :]
+
+    for bbox in layer.bounding_box.chunk((439, 167, 5)):
+        with mag_view.get_buffered_slice_reader(absolute_bounding_box=bbox) as reader:
+            for i, slice_data in enumerate(reader):
+                imwrite(
+                    f"l4_sample_tiff/tiff_{i}_from_bbox{bbox}.tiff",
+                    slice_data,
+                )
+
+
+def open_existing_dataset():
+    ds = wk.Dataset.open(OUTPUT)
+    layer = ds.get_color_layers()[0]
+    mag_view = layer.get_finest_mag()
+    read_bbox = NDBoundingBox(
+        topleft=(0, 0, 0, 0),
+        size=(1, 1, 439, 167),
+        axes=("t", "z", "y", "x"),
+        index=(1, 2, 3, 4),
+    )
+    data = mag_view.read(absolute_bounding_box=read_bbox)
+    assert data.shape == (1,) + read_bbox.size
+    data = mag_view.read(
+        absolute_bounding_box=NDBoundingBox(
+            topleft=(0, 0, 0, 0),
+            size=(1, 1, 439, 167),
+            axes=("t", "z", "y", "x"),
+            index=(1, 2, 3, 4),
+        )
+    )
+
+    imwrite("l4_sample_tiff/test.tiff", data)
+
+
+def main() -> None:
+    """Imports a dataset with more than 3 dimensions."""
+    from_images_import()
+    # open_existing_dataset()
+
+
+if __name__ == "__main__":
+    main()

webknossos/tests/dataset/test_add_layer_from_images.py

@@ -43,6 +43,26 @@ def test_compare_tifffile(tmp_path: Path) -> None:
         assert np.array_equal(data[:, :, z_index], comparison_slice)
 
 
+def test_compare_nd_tifffile(tmp_path: Path) -> None:
+    ds = wk.Dataset(tmp_path, (1, 1, 1))
+    l = ds.add_layer_from_images(
+        "testdata/4D/4D_series/4D-series.ome.tif",
+        layer_name="color",
+        category="color",
+        topleft=(100, 100, 55),
+        use_bioformats=True,
+        data_format="zarr3",
+        chunk_shape=(8, 8, 8),
+        chunks_per_shard=(8, 8, 8),
+    )
+    assert l.bounding_box.topleft == wk.VecInt(0, 55, 100, 100)
+    assert l.bounding_box.size == wk.VecInt(7, 5, 167, 439)
+    assert np.array_equal(
+        l.get_finest_mag().read()[0],
+        TiffFile("testdata/4D/4D_series/4D-series.ome.tif").asarray(),
+    )
+
+
 REPO_IMAGES_ARGS: List[
     Tuple[Union[str, List[Path]], Dict[str, Any], str, int, Tuple[int, int, int]]
 ] = [

webknossos/tests/test_examples.py

@@ -312,7 +312,7 @@ def test_download_segments() -> None:
 
         assert (
             len(list(output_path.iterdir()))
-            == 2 * mag_view.layer.bounding_box.size.z / mag_view.mag.z
+            == 2 * mag_view.layer.bounding_box.get_3d("size").z / mag_view.mag.z
         )
 
 
@@ -329,7 +329,7 @@ def test_download_tiff_stack() -> None:
 
         assert (
             len(list(output_path.iterdir()))
-            == mag_view.bounding_box.size.z / mag_view.mag.z
+            == mag_view.bounding_box.get_3d("size").z / mag_view.mag.z
         )
 
 

webknossos/webknossos/annotation/annotation.py

@@ -476,7 +476,7 @@ def _load_from_zip(cls, content: Union[str, PathLike, BinaryIO]) -> "Annotation"
         assert len(nml_paths) > 0, "Couldn't find an nml file in the supplied zip-file."
         assert (
             len(nml_paths) == 1
-        ), f"There must be exactly one nml file in the zip-file, buf found {len(nml_paths)}."
+        ), f"There must be exactly one nml file in the zip-file, but found {len(nml_paths)}."
         with nml_paths[0].open(mode="rb") as f:
             return cls._load_from_nml(nml_paths[0].stem, f, possible_volume_paths=paths)