set split_level as the default configuration and removed fast configu…

…ration
MHubAI · Dec 3, 2024 · 290c7fd · 290c7fd
1 parent 8ef8980
commit 290c7fd
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Showing 3 changed files with 1 addition and 47 deletions.
diff --git a/models/mrsegmentator/config/default.yml b/models/mrsegmentator/config/default.yml
@@ -19,7 +19,6 @@ modules:
       mod: '%Modality'
 
   MRSegmentatorMLRunner:
-    use_fast_mode: false
 
   DsegConverter:
     model_name: MRSegmentator

diff --git a/models/mrsegmentator/config/fast.yml b/models/mrsegmentator/config/fast.yml
diff --git a/models/mrsegmentator/utils/MRSegmentatorMLRunner.py b/models/mrsegmentator/utils/MRSegmentatorMLRunner.py
@@ -19,11 +19,8 @@
 # register custom segmentation before class definition
 Segment.register("SPINE", name="Spine")
 
-@IO.Config('use_fast_mode', bool, False, the="flag to set to run MRSegmentator in a faster mode")
 class MRSegmentatorMLRunner(Module):
 
-    use_fast_mode: bool
-
     @IO.Instance()
     @IO.Input('in_data', 'nifti:mod=ct|mr', the="input whole body mr/ct scan")
     @IO.Output('out_data', 'segmentations.nii.gz', 'nifti:mod=seg:model=MRSegmentator:roi=SPLEEN,RIGHT_KIDNEY,LEFT_KIDNEY,GALLBLADDER,LIVER,STOMACH,PANCREAS,RIGHT_ADRENAL_GLAND,LEFT_ADRENAL_GLAND,LEFT_LUNG,RIGHT_LUNG,HEART,AORTA,INFERIOR_VENA_CAVA,PORTAL_AND_SPLENIC_VEIN,LEFT_ILIAC_ARTERY,RIGHT_ILIAC_ARTERY,ESOPHAGUS,SMALL_INTESTINE,DUODENUM,COLON,URINARY_BLADDER,SPINE,SACRUM,LEFT_HIP,RIGHT_HIP,LEFT_FEMUR,RIGHT_FEMUR,LEFT_AUTOCHTHONOUS_BACK_MUSCLE,RIGHT_AUTOCHTHONOUS_BACK_MUSCLE,LEFT_ILIOPSOAS,RIGHT_ILIOPSOAS,LEFT_GLUTEUS_MAXIMUS,RIGHT_GLUTEUS_MAXIMUS,LEFT_GLUTEUS_MEDIUS,RIGHT_GLUTEUS_MEDIUS,LEFT_GLUTEUS_MINIMUS,RIGHT_GLUTEUS_MINIMUS', data='in_data', the="output segmentation mask containing all labels")
@@ -34,16 +31,7 @@ def task(self, instance: Instance, in_data: InstanceData, out_data: InstanceData
         bash_command  = ["mrsegmentator"]
         bash_command += ["-i", in_data.abspath]
         bash_command += ["--outdir", tmp_dir]
-        bash_command += ["--nproc_export", "1"]
-        bash_command += ["--nproc", "1"]
-        bash_command += ["--batchsize", "1"]
-
-        if self.use_fast_mode:
-            self.v("Running MRSegmentator in lower memory footprint mode ('--split_level', 1)")
-            self.v("Note: This increases runtime and possibly reduces segmentation performance.")
-            bash_command += ["--split_level", "1"]
-        else:
-            self.v("Running MRSegmentator in default mode.")
+        bash_command += ["--split_level", "1"]
 
         self.v(">> run: ", " ".join(bash_command))