spine updates

StanfordMIMI · Dec 3, 2023 · 79a8b25 · 79a8b25
1 parent bc21bd8
commit 79a8b25
Showing 1 changed file with 44 additions and 59 deletions.
diff --git a/comp2comp/spine/spine.py b/comp2comp/spine/spine.py
@@ -57,66 +57,51 @@ def __call__(self, inference_pipeline):
         # )
         os.environ["TOTALSEG_WEIGHTS_PATH"] = self.model_dir
 
-        cache_dir = "/dataNAS/people/lblankem/install_testing_v1/Comp2Comp/outputs/2023-11-30_14-21-29/medstar/abdct/studies"
-
-        split_output_dir = str(self.output_dir).split("/")
-        study_name = split_output_dir[-2]
-        series_name = split_output_dir[-1]
-
-        cache_image_path = os.path.join(cache_dir, study_name, series_name, "segmentations/converted_dcm.nii.gz")
-        cache_seg_path = os.path.join(cache_dir, study_name, series_name, "segmentations/spine_seg.nii.gz")
-
-        if os.path.exists(cache_image_path) and os.path.exists(cache_seg_path):
-            print("Using cached spine segmentation.")
-            seg = nib.load(cache_seg_path)
-            mv = nib.load(cache_image_path)
-
-        else:
-            seg = totalsegmentator(
-                input=os.path.join(self.output_dir_segmentations, "converted_dcm.nii.gz"),
-                output=os.path.join(self.output_dir_segmentations, "segmentation.nii"),
-                task_ids=[292],
-                ml=True,
-                nr_thr_resamp=1,
-                nr_thr_saving=6,
-                fast=False,
-                nora_tag="None",
-                preview=False,
-                task="total",
-                # roi_subset=[
-                #     "vertebrae_T12",
-                #     "vertebrae_L1",
-                #     "vertebrae_L2",
-                #     "vertebrae_L3",
-                #     "vertebrae_L4",
-                #     "vertebrae_L5",
-                # ],
-                roi_subset=None,
-                statistics=False,
-                radiomics=False,
-                crop_path=None,
-                body_seg=False,
-                force_split=False,
-                output_type="nifti",
-                quiet=False,
-                verbose=False,
-                test=0,
-                skip_saving=True,
-                device="gpu",
-                license_number=None,
-                statistics_exclude_masks_at_border=True,
-                no_derived_masks=False,
-                v1_order=False,
-            )
-            mv = nib.load(
-                os.path.join(self.output_dir_segmentations, "converted_dcm.nii.gz")
-            )
+        seg = totalsegmentator(
+            input=os.path.join(self.output_dir_segmentations, "converted_dcm.nii.gz"),
+            output=os.path.join(self.output_dir_segmentations, "segmentation.nii"),
+            task_ids=[292],
+            ml=True,
+            nr_thr_resamp=1,
+            nr_thr_saving=6,
+            fast=False,
+            nora_tag="None",
+            preview=False,
+            task="total",
+            # roi_subset=[
+            #     "vertebrae_T12",
+            #     "vertebrae_L1",
+            #     "vertebrae_L2",
+            #     "vertebrae_L3",
+            #     "vertebrae_L4",
+            #     "vertebrae_L5",
+            # ],
+            roi_subset=None,
+            statistics=False,
+            radiomics=False,
+            crop_path=None,
+            body_seg=False,
+            force_split=False,
+            output_type="nifti",
+            quiet=False,
+            verbose=False,
+            test=0,
+            skip_saving=True,
+            device="gpu",
+            license_number=None,
+            statistics_exclude_masks_at_border=True,
+            no_derived_masks=False,
+            v1_order=False,
+        )
+        mv = nib.load(
+            os.path.join(self.output_dir_segmentations, "converted_dcm.nii.gz")
+        )
 
-            # save the seg
-            nib.save(
-                seg,
-                os.path.join(self.output_dir_segmentations, "spine_seg.nii.gz"),
-            )
+        # save the seg
+        nib.save(
+            seg,
+            os.path.join(self.output_dir_segmentations, "spine_seg.nii.gz"),
+        )
 
         # inference_pipeline.segmentation = nib.load(
         #     os.path.join(self.output_dir_segmentations, "segmentation.nii")