cta aorta

nnunetv2/dataset_conversion/Dataset021_CTAAorta.py

@@ -0,0 +1,71 @@
+from batchgenerators.utilities.file_and_folder_operations import *
+import shutil
+from nnunetv2.dataset_conversion.generate_dataset_json import generate_dataset_json
+from nnunetv2.paths import nnUNet_raw
+import SimpleITK as sitk
+
+
+if __name__ == '__main__':
+    """
+    
+    """
+    # extracted traiing.zip file is here
+    base = '/home/isensee/Downloads/'
+    target_dataset_id = 21
+    target_dataset_name = f'Dataset{target_dataset_id:03.0f}_CTAAorta'
+
+    maybe_mkdir_p(join(nnUNet_raw, target_dataset_name))
+    imagesTr = join(nnUNet_raw, target_dataset_name, 'imagesTr')
+    labelsTr = join(nnUNet_raw, target_dataset_name, 'labelsTr')
+    maybe_mkdir_p(imagesTr)
+    maybe_mkdir_p(labelsTr)
+
+    cases = subfiles(join(base, 'images'), join=False, prefix='subject')
+    for case in cases:
+        outname = case.replace('_CTA.mha', '')
+        im = sitk.ReadImage(join(base, 'images', case))
+        sitk.WriteImage(im, join(imagesTr, outname + '_0000.nii.gz'))
+
+        seg = sitk.ReadImage(join(base, 'masks', case.replace('_CTA.mha', '_label.mha')))
+        sitk.WriteImage(seg, join(labelsTr, outname + '.nii.gz'))
+
+    labels = {
+            "background": 0,
+            "Zone_0": 1,
+            "Innominate": 2,
+            "Zone_1": 3,
+            "Left_Common_Carotid": 4,
+            "Zone_2": 5,
+            "Left_Subclavian_Artery": 6,
+            "Zone_3": 7,
+            "Zone_4": 8,
+            "Zone_5": 9,
+            "Zone_6": 10,
+            "Celiac_Artery": 11,
+            "Zone_7": 12,
+            "SMA": 13,
+            "Zone_8": 14,
+            "Right_Renal_Artery": 15,
+            "Left_Renal_Artery": 16,
+            "Zone_9": 17,
+            "Zone_10_R_(Right_Common_Iliac_Artery)": 18,
+            "Zone_10_L_(Left_Common_Iliac_Artery)": 19,
+            "Right_Internal_Iliac_Artery_Dice_Score": 20,
+            "Left_Internal_Iliac_Artery_Dice_Score": 21,
+            "Zone_11_R_(Right_External_Iliac_Artery)": 22,
+            "Zone_11_L_(Left_External_Iliac_Artery)": 23
+        }
+
+
+    generate_dataset_json(
+        join(nnUNet_raw, target_dataset_name),
+        {0: 'CT'},
+        labels,
+        len(cases),
+        '.nii.gz',
+        None,
+        target_dataset_name,
+        overwrite_image_reader_writer='NibabelIOWithReorient',
+        reference='https://aortaseg24.grand-challenge.org/',
+        license='see ref'
+    )