Merge pull request #545 from AllenCell/hotfix/prediction-updates-cyto…

…-dl==0.4.1 Update prediction to use cyto-dl==0.4.1
AllenCell · Nov 1, 2024 · ea92306 · ea92306
2 parents d29161b + cc96c6f
commit ea92306
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Showing 9 changed files with 4 additions and 6 deletions.
diff --git a/src/allencell_ml_segmenter/_tests/services/test_prediction_service.py b/src/allencell_ml_segmenter/_tests/services/test_prediction_service.py
@@ -150,7 +150,7 @@ def test_build_overrides() -> None:
         / "0_exp"
         / "prediction_output_test"
     )
-    assert overrides["data.transforms.predict.transforms[1].reader[0].C"] == 3
+    assert overrides["input_channel"] == 3
     assert overrides["data.columns"] == ["raw", "split"]
     assert overrides["data.split_column"] == "split"
 

diff --git a/...s/output_test_folder/target/output_1.tiff → ...iles/output_test_folder/seg/output_1.tiff b/...s/output_test_folder/target/output_1.tiff → ...iles/output_test_folder/seg/output_1.tiff
diff --git a/...s/output_test_folder/target/output_2.tiff → ...iles/output_test_folder/seg/output_2.tiff b/...s/output_test_folder/target/output_2.tiff → ...iles/output_test_folder/seg/output_2.tiff
diff --git a/...ut_test_folder_extra/target/output_1.tiff → ...utput_test_folder_extra/seg/output_1.tiff b/...ut_test_folder_extra/target/output_1.tiff → ...utput_test_folder_extra/seg/output_1.tiff
diff --git a/...ut_test_folder_extra/target/output_2.tiff → ...utput_test_folder_extra/seg/output_2.tiff b/...ut_test_folder_extra/target/output_2.tiff → ...utput_test_folder_extra/seg/output_2.tiff
diff --git a/...ut_test_folder_extra/target/output_3.tiff → ...utput_test_folder_extra/seg/output_3.tiff b/...ut_test_folder_extra/target/output_3.tiff → ...utput_test_folder_extra/seg/output_3.tiff
diff --git a/...ut_test_folder_extra/target/output_4.tiff → ...utput_test_folder_extra/seg/output_4.tiff b/...ut_test_folder_extra/target/output_4.tiff → ...utput_test_folder_extra/seg/output_4.tiff
diff --git a/src/allencell_ml_segmenter/prediction/model.py b/src/allencell_ml_segmenter/prediction/model.py
@@ -81,7 +81,7 @@ def get_output_seg_directory(self) -> Optional[Path]:
         Gets path to where segmentation predictions are stored.
         """
         return (
-            self._output_directory / "target"
+            self._output_directory / "seg"
             if self._output_directory is not None
             else None
         )

diff --git a/src/allencell_ml_segmenter/services/prediction_service.py b/src/allencell_ml_segmenter/services/prediction_service.py
@@ -157,10 +157,8 @@ def build_overrides(self, checkpoint: Path) -> dict[str, Any]:
         channel: Optional[int] = (
             self._prediction_model.get_image_input_channel_index()
         )
-        if channel:
-            overrides["data.transforms.predict.transforms[1].reader[0].C"] = (
-                channel
-            )
+        if channel is not None:
+            overrides["input_channel"] = channel
 
         # selecting hardware- GPU if available (and correct drivers installed),
         # CPU otherwise.