Add configuration to allow using itk or pydicom_seg for DICOM SEG (#1854)

* Add configuration to allow using ITK or pydicom_seg for generating DICOM SEG

Signed-off-by: José Frias <josefrias@bmd-software.com>

* Fix mypy issue when dealing with str and converting to bool in MONAI_LABEL_USE_ITK_FOR_DICOM_SEG config

Signed-off-by: José Frias <josefrias@bmd-software.com>

---------

Signed-off-by: José Frias <josefrias@bmd-software.com>

Author: joselfrias

monailabel/config.py

@@ -9,6 +9,7 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 import os
+from distutils.util import strtobool
 from importlib.metadata import distributions
 from typing import Any, Dict, List, Optional
 
@@ -115,6 +116,10 @@ class Settings(BaseSettings):
         else "https://huggingface.co/facebook/sam2-hiera-large/resolve/main/sam2_hiera_l.yaml"
     )
 
+    MONAI_LABEL_USE_ITK_FOR_DICOM_SEG: bool = bool(
+        strtobool(os.environ.get("MONAI_LABEL_USE_ITK_FOR_DICOM_SEG", "True"))
+    )
+
     model_config = SettingsConfigDict(
         env_file=".env",
         case_sensitive=True,

monailabel/datastore/utils/convert.py

@@ -23,6 +23,7 @@
 from monai.transforms import LoadImage
 from pydicom.filereader import dcmread
 
+from monailabel.config import settings
 from monailabel.datastore.utils.colors import GENERIC_ANATOMY_COLORS
 from monailabel.transform.writer import write_itk
 from monailabel.utils.others.generic import run_command
@@ -80,7 +81,12 @@ def binary_to_image(reference_image, label, dtype=np.uint8, file_ext=".nii.gz"):
     return output_file
 
 
-def nifti_to_dicom_seg(series_dir, label, label_info, file_ext="*", use_itk=True) -> str:
+def nifti_to_dicom_seg(series_dir, label, label_info, file_ext="*", use_itk=None) -> str:
+
+    # Only use config if no explicit override
+    if use_itk is None:
+        use_itk = settings.MONAI_LABEL_USE_ITK_FOR_DICOM_SEG
+
     start = time.time()
 
     label_np, meta_dict = LoadImage(image_only=False)(label)

monailabel/endpoints/infer.py

@@ -183,7 +183,7 @@ def run_inference(
         suffixes = [".nii", ".nii.gz", ".nrrd"]
         image_path = [image_uri.replace(suffix, "") for suffix in suffixes if image_uri.endswith(suffix)][0]
         res_img = result.get("file") if result.get("file") else result.get("label")
-        dicom_seg_file = nifti_to_dicom_seg(image_path, res_img, p.get("label_info"), use_itk=True)
+        dicom_seg_file = nifti_to_dicom_seg(image_path, res_img, p.get("label_info"))
         result["dicom_seg"] = dicom_seg_file
 
     return send_response(instance.datastore(), result, output, background_tasks)