[FIX] remove redundant classes parameter to writing segmentations

Author: sophiamaedler

src/scportrait/pipeline/_utils/sdata_io.py

@@ -242,7 +242,6 @@ def _write_segmentation_object_sdata(
         self,
         segmentation_object: Labels2DModel,
         segmentation_label: str,
-        classes: set[str] | None = None,
         overwrite: bool = False,
     ) -> None:
         """Write segmentation object to SpatialData.
@@ -268,7 +267,6 @@ def _write_segmentation_sdata(
         self,
         segmentation: xarray.DataArray | np.ndarray,
         segmentation_label: str,
-        classes: set[str] | None = None,
         chunks: ChunkSize2D = (1000, 1000),
         overwrite: bool = False,
     ) -> None:
@@ -292,7 +290,7 @@ def _write_segmentation_sdata(
         if not get_chunk_size(mask) == chunks:
             mask.data = mask.data.rechunk(chunks)
 
-        self._write_segmentation_object_sdata(mask, segmentation_label, classes=classes, overwrite=overwrite)
+        self._write_segmentation_object_sdata(mask, segmentation_label, overwrite=overwrite)
 
     def _write_points_object_sdata(self, points: PointsModel, points_name: str, overwrite: bool = False) -> None:
         """Write points object to SpatialData.

src/scportrait/pipeline/segmentation/segmentation.py

@@ -307,16 +307,12 @@ def _save_segmentation_sdata(self, labels, classes, masks=None):
             if "nuclei" in masks:
                 ix = masks.index("nuclei")
 
-                self.filehandler._write_segmentation_sdata(
-                    labels[ix], self.nuc_seg_name, classes=classes, overwrite=self.overwrite
-                )
+                self.filehandler._write_segmentation_sdata(labels[ix], self.nuc_seg_name, overwrite=self.overwrite)
                 self.filehandler._add_centers(self.nuc_seg_name, overwrite=self.overwrite)
 
             if "cytosol" in masks:
                 ix = masks.index("cytosol")
-                self.filehandler._write_segmentation_sdata(
-                    labels[ix], self.cyto_seg_name, classes=classes, overwrite=self.overwrite
-                )
+                self.filehandler._write_segmentation_sdata(labels[ix], self.cyto_seg_name, overwrite=self.overwrite)
                 self.filehandler._add_centers(self.cyto_seg_name, overwrite=self.overwrite)
 
     def save_map(self, map_name):

src/scportrait/pipeline/segmentation/workflows.py

@@ -587,13 +587,11 @@ def _perform_size_filtering(
                         self.filehandler._write_segmentation_sdata(
                             mask,
                             segmentation_label=f"debugging_seg_size_filter_results_{mask_name}",
-                            classes=filter.ids,
                         )
                     else:
                         self.filehandler._write_segmentation_sdata(
                             mask[0],
                             segmentation_label=f"debugging_seg_size_filter_results_{mask_name}",
-                            classes=filter.ids,
                         )
                     # then this does not need to be plotted as it can be visualized from there
                     plot_results = False
@@ -700,10 +698,10 @@ def _perform_mask_matching_filtering(
                 if self.save_filter_results:
                     # add filtering results to sdata object
                     self.filehandler._write_segmentation_sdata(
-                        mask_nuc[0], segmentation_label="debugging_seg_match_mask_results_nucleus", classes=None
+                        mask_nuc[0], segmentation_label="debugging_seg_match_mask_results_nucleus"
                     )
                     self.filehandler._write_segmentation_sdata(
-                        mask_cyto[0], segmentation_label="debugging_seg_match_mask_result_cytosol", classes=None
+                        mask_cyto[0], segmentation_label="debugging_seg_match_mask_result_cytosol"
                     )
 
                     # then no plotting needs to be performed as the results can be viewed in the sdata object