fix: Updating alignment dimensions and offsets to Angstrom (#323)

* Updating alignment dimensions and offsets to Angstrom * Updating dimensions to image size
chanzuckerberg · Oct 16, 2024 · e4a74a2 · e4a74a2
1 parent 5fac83e
commit e4a74a2
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Showing 3 changed files with 39 additions and 37 deletions.
diff --git a/ingestion_tools/scripts/importers/alignment.py b/ingestion_tools/scripts/importers/alignment.py
@@ -120,7 +120,9 @@ 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()
-        return tomogram.get_source_volume_info().get_dimensions()
+        voxel_size = round(tomogram.get_source_volume_info().voxel_size, 3)
+        dim = tomogram.get_source_volume_info().get_dimensions()
+        return {d: voxel_size * dim[d] for d in "xyz"}
 
     def is_default_alignment(self) -> bool:
         return "default" in self.file_paths

diff --git a/ingestion_tools/scripts/tests/s3_import/test_alignments.py b/ingestion_tools/scripts/tests/s3_import/test_alignments.py
@@ -166,7 +166,7 @@ def test_alignment_import_item(
         "tilt_offset": -0.3,
         "tilt_path": f"{prefix}/{id_prefix}/TS_run1.tlt",
         "tiltx_path": f"{prefix}/{id_prefix}/TS_run1.xtilt",
-        "volume_dimension": {"x": 6, "y": 8, "z": 10},
+        "volume_dimension": {"x": 13.48 * 6, "y": 13.48 * 8, "z": 13.48 * 10},
         "volume_offset": {"x": -1, "y": 2, "z": -3},
         "x_rotation_offset": -2.3,
     }
@@ -243,7 +243,7 @@ def test_alignment_import_item_aretomo(
         "tilt_offset": -0.3,
         "tilt_path": None,
         "tiltx_path": None,
-        "volume_dimension": {"x": 6, "y": 8, "z": 10},
+        "volume_dimension": {"x": 13.48 * 6, "y": 13.48 * 8, "z": 13.48 * 10},
         "volume_offset": {"x": -1, "y": 2, "z": -3},
         "x_rotation_offset": -2.3,
     }
@@ -281,7 +281,7 @@ def test_default_alignment_import_with_tomograms(
         "tilt_offset": 0,
         "tilt_path": None,
         "tiltx_path": None,
-        "volume_dimension": {"x": 6, "y": 8, "z": 10},
+        "volume_dimension": {"x": 13.48 * 6, "y": 13.48 * 8, "z": 13.48 * 10},
         "volume_offset": {"x": 0, "y": 0, "z": 0},
         "x_rotation_offset": 0,
     }

diff --git a/schema/core/v2.0.0/metadata.yaml b/schema/core/v2.0.0/metadata.yaml
@@ -752,65 +752,65 @@ classes:
     attributes:
       x:
         any_of:
-          - range: integer
-          - range: IntegerFormattedString
+          - range: float
+          - range: FloatFormattedString
         required: true
-        description: Number of pixels in the 3D data fast axis
+        description: X dimension of the reconstruction volume in angstrom
         unit:
-          descriptive_name: pixels
-          symbol: px
+          descriptive_name: Angstrom
+          symbol: Å
       y:
         any_of:
-          - range: integer
-          - range: IntegerFormattedString
+        - range: float
+        - range: FloatFormattedString
         required: true
-        description: Number of pixels in the 3D data medium axis
+        description: Y dimension of the reconstruction volume in angstrom
         unit:
-          descriptive_name: pixels
-          symbol: px
+          descriptive_name: Angstrom
+          symbol: Å
       z:
         any_of:
-          - range: integer
-          - range: IntegerFormattedString
+        - range: float
+        - range: FloatFormattedString
         required: true
-        description: Number of pixels in the 3D data slow axis.  This is the image projection direction at zero stage tilt
+        description: Z dimension of the reconstruction volume in angstrom
         unit:
-          descriptive_name: pixels
-          symbol: px
+          descriptive_name: Angstrom
+          symbol: Å
 
   AlignmentOffset:
     description: &desc_alignment_offset The offset of a alignment in voxels in each dimension relative to the canonical tomogram.
     attributes:
       x:
         any_of:
-          - range: integer
-          - range: cdp-common:IntegerFormattedString
+          - range: float
+          - range: cdp-common:FloatFormattedString
         required: true
-        description: x offset relative to the canonical tomogram in pixels
-        ifabsent: "int(0)"
+        description: X shift of the reconstruction volume in angstrom
+        ifabsent: "float(0)"
         unit:
-          descriptive_name: pixels
-          symbol: px
+          descriptive_name: Angstrom
+          symbol: Å
       y:
         any_of:
-          - range: integer
-          - range: cdp-common:IntegerFormattedString
+        - range: float
+        - range: cdp-common:FloatFormattedString
         required: true
-        description: y offset relative to the canonical tomogram in pixels
-        ifabsent: "int(0)"
+        description: Y shift of the reconstruction volume in angstrom
+        ifabsent: "float(0)"
         unit:
-          descriptive_name: pixels
-          symbol: px
+          descriptive_name: Angstrom
+          symbol: Å
       z:
         any_of:
-          - range: integer
-          - range: cdp-common:IntegerFormattedString
+        - range: float
+        - range: cdp-common:FloatFormattedString
         required: true
-        ifabsent: "int(0)"
-        description: z offset relative to the canonical tomogram in pixels
+        description: Z shift of the reconstruction volume in angstrom
+        ifabsent: "float(0)"
         unit:
-          descriptive_name: pixels
-          symbol: px
+          descriptive_name: Angstrom
+          symbol: Å
 
 
   Alignment: