fix: consider both scan rotation and stage rotation for tfs metadata

delmic · Mar 1, 2024 · b1d918b · b1d918b
1 parent 018cab4
commit b1d918b
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Showing 2 changed files with 5 additions and 2 deletions.
diff --git a/src/odemis/dataio/test/tiff_test.py b/src/odemis/dataio/test/tiff_test.py
@@ -2369,14 +2369,15 @@ def test_convert_thermo_fisher_to_odemis_metadata(self):
             model.MD_PIXEL_SIZE: (2.69792e-07, 2.69792e-07),
             model.MD_DWELL_TIME: 1e-6,
             model.MD_POS: (0.000133417, -0.000717625),
-            model.MD_ROTATION: 0.0,
+            model.MD_ROTATION: 0.0,     
             model.MD_EBEAM_VOLTAGE: 2000.0,
             model.MD_EBEAM_CURRENT: 1.41708e-11,
             model.MD_EBEAM_SPOT_DIAM: 5.181,
             model.MD_ACQ_TYPE: model.MD_AT_EM,
             model.MD_DET_TYPE: model.MD_DT_NORMAL,
             model.MD_DESCRIPTION: os.path.basename(TFS_FILENAME).replace(".tif", ""),
         }
+        # TODO: add a test with scan rotation + stage rotation
 
         for key in md.keys():
             self.assertIn(key, data.content[0].metadata)

diff --git a/src/odemis/dataio/tiff.py b/src/odemis/dataio/tiff.py
@@ -2743,7 +2743,9 @@ def _convert_thermo_fisher_to_odemis_metadata(metadata: str) -> dict:
     try:
         # beam metadata
         beam_type = tfs_md["Beam"]["beam"]
-        md[model.MD_ROTATION] = float(tfs_md[beam_type]["scanrotation"])
+        # add stage rotation to scan rotation, as odemis does not have stage rotation metadata
+        stage_rotation = float(tfs_md["Stage"].get("rotation", 0))
+        md[model.MD_ROTATION] = float(tfs_md[beam_type]["scanrotation"]) + stage_rotation
         md[model.MD_EBEAM_VOLTAGE] = float(tfs_md[beam_type]["hv"])
         md[model.MD_EBEAM_CURRENT] = float(tfs_md[beam_type]["beamcurrent"])