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.gitattributes

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+*.arrow filter=lfs diff=lfs merge=lfs -text
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+*.bz2 filter=lfs diff=lfs merge=lfs -text
+*.ckpt filter=lfs diff=lfs merge=lfs -text
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inference.sh

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+export nnUNet_N_proc_DA=36
+export nnUNet_results="./nnUNet_results"
+export nnUNet_predictions="./nnUNet_predictions"
+export nnUNet_eval="./nnUNet_eval"
+export PYTHONWARNINGS="ignore"
+
+GPU_ID=0 
+DATASET=1356
+
+TRAINER=nnUNetTrainer 
+
+CUDA_VISIBLE_DEVICES=$GPU_ID nnUNetv2_predict -d $DATASET -i $nnUNet_eval/Dataset1356/imagesTs/ -o $nnUNet_predictions/ -tr $TRAINER -d $DATASET -c 3d_fullres -f all -p nnUNetResEncUNetLPlans --continue_prediction 

masks_BDMAP.py

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+import os
+import numpy as np
+import nibabel as nib
+import argparse
+from tqdm import tqdm
+from concurrent.futures import ProcessPoolExecutor, as_completed
+from multiprocessing import cpu_count
+
+# label mapping
+label_mapping =[
+    ('aorta.nii.gz', 1),
+    ('gall_bladder.nii.gz', 2),
+    ('kidney_left.nii.gz', 3),
+    ('kidney_right.nii.gz', 4),
+    ('liver.nii.gz', 5),
+    ('pancreas_body.nii.gz', 6),
+    ('pancreas_head.nii.gz', 7),
+    ('pancreas_tail.nii.gz', 8),
+    ('postcava.nii.gz', 9),
+    ('spleen.nii.gz', 10),
+    ('stomach.nii.gz', 11),
+    ('adrenal_gland_left.nii.gz', 12),
+    ('adrenal_gland_right.nii.gz', 13),
+    ('bladder.nii.gz', 14),
+    ('celiac_trunk.nii.gz', 15),
+    ('colon.nii.gz', 16),
+    ('duodenum.nii.gz', 17),
+    ('esophagus.nii.gz', 18),
+    ('prostate.nii.gz', 19),
+    ('rectum.nii.gz', 20),
+    ('lung_left.nii.gz', 21),
+    ('lung_right.nii.gz', 22),
+    ('vertebrae_L5.nii.gz', 23),
+    ('vertebrae_L4.nii.gz', 24),
+    ('vertebrae_L3.nii.gz', 25),
+    ('vertebrae_L2.nii.gz', 26),
+    ('vertebrae_L1.nii.gz', 27),
+    ('vertebrae_T12.nii.gz', 28),
+    ('vertebrae_T11.nii.gz', 29),
+    ('vertebrae_T10.nii.gz', 30),
+    ('vertebrae_T9.nii.gz', 31),
+    ('vertebrae_T8.nii.gz', 32),
+    ('trachea.nii.gz', 33),
+    ('heart.nii.gz', 34),
+    ('hip_left.nii.gz', 35),
+    ('hip_right.nii.gz', 36),
+    ('sacrum.nii.gz', 37),
+    ('uterus.nii.gz', 38),
+    ('liver_lesion.nii.gz', 39),
+    ('pancreatic_lesion.nii.gz', 40),
+    ('kidney_lesion.nii.gz', 41),
+    ('colon_lesion.nii.gz', 42)
+]
+
+
+
+
+def process_case(file_name, source_dir, output_dir):
+    if not file_name.endswith(".nii.gz"):
+        return None
+
+    case_name = file_name.replace(".nii.gz", "")
+    input_path = os.path.join(source_dir, file_name)
+
+    try:
+        img = nib.load(input_path)
+        data = img.get_fdata()
+
+        case_output_dir = os.path.join(output_dir, case_name, "segmentations")
+        os.makedirs(case_output_dir, exist_ok=True)
+
+        saved = False  
+
+        for label_name, label_value in label_mapping:
+            mask = np.zeros_like(data, dtype=np.uint8)
+
+            if isinstance(label_value, list):
+                for val in label_value:
+                    mask[data == val] = 1
+            else:
+                mask[data == label_value] = 1
+            
+            mask_nifti = nib.Nifti1Image(mask, img.affine, img.header)
+            output_path = os.path.join(case_output_dir, label_name)
+            nib.save(mask_nifti, output_path)
+            saved = True
+
+        return f"finished: {case_name}" if saved else f" {case_name}"
+
+    except Exception as e:
+        return f"process {case_name} error: {e}"
+
+def process_all_cases(source_dir, output_dir):
+    cases = [f for f in os.listdir(source_dir) if f.endswith(".nii.gz")]
+
+    print(f">> finding {len(cases)} cases, starting...")
+    print('>> {} CPU cores are secured.'.format(int(cpu_count()*0.9)))
+    results = []
+    with ProcessPoolExecutor(max_workers=int(cpu_count()*0.9)) as executor:
+        futures = {executor.submit(process_case, case, source_dir, output_dir): case for case in cases}
+
+        for future in tqdm(as_completed(futures), total=len(futures), desc="Processing"):
+            case = futures[future]
+            try:
+                result = future.result()
+                if result:
+                    results.append(result)
+            except Exception as e:
+                results.append(f"case {case} error: {e}")
+
+    for res in results:
+        print(res)
+
+    print(f"All finished! (Split){source_dir}")
+
+def main():
+    parser = argparse.ArgumentParser(description="split combined label")
+    parser.add_argument("--source_dir", required=True, help="input path")
+    parser.add_argument("--output_dir", drequired=True, help="output path")
+    args = parser.parse_args()
+
+    process_all_cases(args.source_dir, args.output_dir)
+
+if __name__ == "__main__":
+    main()
+
+
+

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