Merge remote-tracking branch 'origin' into kaloster/docs-update

ingestion_tools/scripts/importers/alignment.py

@@ -120,7 +120,7 @@ def get_tomogram_volume_dimension(self) -> dict:
         if not tomogram:
             # If no source tomogram is found don't create a default alignment metadata file.
             raise TomogramNotFoundError()
-        voxel_size = round(tomogram.get_source_volume_info().voxel_size, 3)
+        voxel_size = round(tomogram.get_voxel_spacing().as_float(), 3)
         dim = tomogram.get_source_volume_info().get_dimensions()
         return {d: voxel_size * dim[d] for d in "xyz"}
 

ingestion_tools/scripts/importers/visualization_precompute.py

@@ -2,8 +2,6 @@
 from pathlib import Path
 from typing import Any
 
-from cryoet_data_portal_neuroglancer.precompute import points, segmentation_mask
-
 from common import colors
 from common.config import DepositionImportConfig
 from common.finders import DefaultImporterFactory
@@ -90,6 +88,10 @@ def neuroglancer_precompute(self, output_prefix: str, voxel_spacing: float) -> N
         precompute_path = self._get_neuroglancer_precompute_path(annotation_path, output_prefix)
         metadata = self.annotation.metadata
         tmp_path = fs.localwritable(precompute_path)
+        # Importing this at runtime instead of compile time since zfpy (a dependency of this
+        # module) cannot be imported successfully on darwin/ARM machines.
+        from cryoet_data_portal_neuroglancer.precompute import points
+
         points.encode_annotation(
             self.annotation.get_output_data(annotation_path),
             metadata,
@@ -136,6 +138,10 @@ def neuroglancer_precompute(self, output_prefix: str, voxel_spacing: float) -> N
         precompute_path = self._get_neuroglancer_precompute_path(annotation_path, output_prefix)
         tmp_path = fs.localwritable(precompute_path)
         zarr_file_path = fs.destformat(self.annotation.get_output_filename(annotation_path, "zarr"))
+        # Importing this at runtime instead of compile time since zfpy (a dependency of this
+        # module) cannot be imported successfully on darwin/ARM machines.
+        from cryoet_data_portal_neuroglancer.precompute import segmentation_mask
+
         segmentation_mask.encode_segmentation(
             zarr_file_path,
             Path(tmp_path),

ingestion_tools/scripts/tests/s3_import/test_alignments.py

@@ -281,7 +281,7 @@ def test_default_alignment_import_with_tomograms(
         "tilt_offset": 0,
         "tilt_path": None,
         "tiltx_path": None,
-        "volume_dimension": {"x": 13.48 * 6, "y": 13.48 * 8, "z": 13.48 * 10},
+        "volume_dimension": {"x": 4.123 * 6, "y": 4.123 * 8, "z": 4.123 * 10},
         "volume_offset": {"x": 0, "y": 0, "z": 0},
         "x_rotation_offset": 0,
     }