fixed doing the labeling step first before adding the ivd and eps

spineps/phase_labeling.py

@@ -33,6 +33,7 @@ def perform_labeling_step(model: VertLabelingClassifier, img_nii: NII, vert_nii:
         model.load()
     # run model
     labelmap = run_model_for_vert_labeling(model, img_nii, vert_nii)[0]
+
     # relabel according to labelmap
     return vert_nii.map_labels_(labelmap)
 
@@ -64,6 +65,7 @@ def run_model_for_vert_labeling(
     )
     assert len(orig_label) == len(fpath_post), f"{len(orig_label)} != {len(fpath_post)}"
     labelmap = {orig_label[idx]: fpath_post[idx] for idx in range(len(orig_label))}
+
     return labelmap, fcost, fpath, fpath_post, costlist, min_costs_path, predictions
 
 

spineps/phase_post.py

@@ -17,13 +17,16 @@
     np_volume,
 )
 
+from spineps.phase_labeling import VertLabelingClassifier, perform_labeling_step
 from spineps.seg_pipeline import logger, vertebra_subreg_labels
 from spineps.utils.proc_functions import fix_wrong_posterior_instance_label
 
 
 def phase_postprocess_combined(
+    img_nii: NII,
     seg_nii: NII,
     vert_nii: NII,
+    model_labeling: VertLabelingClassifier | None,
     debug_data: dict | None,
     labeling_offset: int = 0,
     proc_assign_missing_cc: bool = True,
@@ -36,6 +39,7 @@ def phase_postprocess_combined(
 ) -> tuple[NII, NII]:
     logger.print("Post process", Log_Type.STAGE)
     with logger:
+        img_nii.assert_affine(other=seg_nii)
         seg_nii.assert_affine(other=vert_nii)
         # Post process semantic mask
         ###################
@@ -54,6 +58,7 @@ def phase_postprocess_combined(
         seg_uncropped = seg_nii.copy()
 
         # Crop down
+        img_nii.apply_crop_(crop_slices)
         vert_nii.apply_crop_(crop_slices)
         seg_nii.apply_crop_(crop_slices)
 
@@ -79,8 +84,8 @@ def phase_postprocess_combined(
 
         # Label vertebra top -> down
         whole_vert_nii_cleaned, vert_labels = label_instance_top_to_bottom(whole_vert_nii_cleaned, labeling_offset=labeling_offset)
-        # if labeling_offset != 0:
-        #    whole_vert_nii_cleaned.map_labels_({i: i + 1 for i in vert_labels if i != 0}, verbose=verbose)
+        if model_labeling is not None:
+            whole_vert_nii_cleaned = perform_labeling_step(model=model_labeling, img_nii=img_nii, vert_nii=whole_vert_nii_cleaned)
         logger.print(f"Labeled {len(vert_labels)} vertebra instances from top to bottom")
         vert_arr_cleaned = add_ivd_ep_vert_label(whole_vert_nii_cleaned, seg_nii_cleaned)
         vert_arr_cleaned[seg_nii_cleaned.get_seg_array() == v_name2idx["S1"]] = v_name2idx["S1"]

spineps/seg_run.py

@@ -470,8 +470,10 @@ def process_img_nii(  # noqa: C901
             seg_nii_back.assert_affine(other=input_nii)
             # use both seg_raw and vert_raw to clean each other, add ivd_ep ...
             seg_nii_clean, vert_nii_clean = phase_postprocess_combined(
+                img_nii=input_nii_,
                 seg_nii=seg_nii_back,
                 vert_nii=whole_vert_nii,
+                model_labeling=model_labeling,
                 debug_data=debug_data_run,
                 labeling_offset=vertebra_instance_labeling_offset - 1,
                 proc_clean_inst_by_sem=proc_clean_inst_by_sem,
@@ -484,10 +486,6 @@ def process_img_nii(  # noqa: C901
             vert_nii_clean.assert_affine(other=input_nii)
             # input_package.make_nii_from_this(seg_nii_clean)
             # input_package.make_nii_from_this(vert_nii_clean)
-
-            if model_labeling is not None:
-                vert_nii_clean = perform_labeling_step(model=model_labeling, img_nii=input_nii, vert_nii=vert_nii_clean)
-
             seg_nii_clean.save(out_spine, verbose=logger)
             vert_nii_clean.save(out_vert, verbose=logger)
             done_something = True