add AbdomenAtlas conversion script

nnunetv2/dataset_conversion/Dataset224_AbdomenAtlas1.0.py

@@ -0,0 +1,45 @@
+from batchgenerators.utilities.file_and_folder_operations import *
+import shutil
+from nnunetv2.dataset_conversion.generate_dataset_json import generate_dataset_json
+
+
+if __name__ == '__main__':
+    base = '/home/isensee/Downloads/AbdomenAtlas1.0Mini'
+    cases = subdirs(base, join=False, prefix='BDMAP')
+
+    target_dataset_id = 224
+    target_dataset_name = f'Dataset{target_dataset_id:3.0f}_AbdomenAtlas1.0'
+
+    raw_dir = '/home/isensee/drives/E132-Projekte/Projects/Helmholtz_Imaging_ACVL/2024_JHU_benchmark'
+    maybe_mkdir_p(join(raw_dir, target_dataset_name))
+    imagesTr = join(raw_dir, target_dataset_name, 'imagesTr')
+    labelsTr = join(raw_dir, target_dataset_name, 'labelsTr')
+    maybe_mkdir_p(imagesTr)
+    maybe_mkdir_p(labelsTr)
+
+    for case in cases:
+        shutil.copy(join(base, case, 'ct.nii.gz'), join(imagesTr, case + '_0000.nii.gz'))
+        shutil.copy(join(base, case, 'combined_labels.nii.gz'), join(labelsTr, case + '.nii.gz'))
+
+    labels = {
+        "background": 0,
+        "aorta": 1,
+        "gall_bladder": 2,
+        "kidney_left": 3,
+        "kidney_right": 4,
+        "liver": 5,
+        "pancreas": 6,
+        "postcava": 7,
+        "spleen": 8,
+        "stomach": 9
+    }
+
+    generate_dataset_json(
+        join(raw_dir, target_dataset_name),
+        {0: 'nonCT'},  # this was a mistake we did at the beginning and we keep it like that here for consistency
+        labels,
+        len(cases),
+        '.nii.gz',
+        None,
+        target_dataset_name
+    )