Merge pull request #112 from BrainLesion/feature/2025-algorithms

Feature/2025 algorithms

Author: neuronflow

README.md

@@ -3,12 +3,13 @@
 from brats.core.inpainting_algorithms import Inpainter
 from brats.core.missing_mri_algorithms import MissingMRI
 from brats.core.segmentation_algorithms import (
-    AdultGliomaPostTreatmentSegmenter,
     AdultGliomaPreTreatmentSegmenter,
+    AdultGliomaPreAndPostTreatmentSegmenter,
     AfricaSegmenter,
     GoATSegmenter,
     MeningiomaSegmenter,
     MetastasesSegmenter,
+    MeningiomaRTSegmenter,
     PediatricSegmenter,
 )
 

brats/__init__.py

@@ -26,8 +26,17 @@ class Algorithms(str, Enum):
     pass
 
 
-class AdultGliomaPostTreatmentAlgorithms(Algorithms):
-    """Constants for the available adult glioma post treatment segmentation algorithms."""
+class AdultGliomaPreAndPostTreatmentAlgorithms(Algorithms):
+    """Constants for the available adult glioma pre and post treatment segmentation algorithms."""
+
+    BraTS25_1 = "BraTS25_1"
+    """ BraTS25 Adult Glioma Segmentation 1st place """
+    BraTS25_2 = "BraTS25_2"
+    """ BraTS25 Adult Glioma Segmentation 2nd place """
+    BraTS25_3A = "BraTS25_3A"
+    """ BraTS25 Adult Glioma Segmentation 3rd place (tie) """
+    BraTS25_3B = "BraTS25_3B"
+    """ BraTS25 Adult Glioma Segmentation 3rd place (tie) """
 
     BraTS24_1 = "BraTS24_1"
     """ BraTS24 Adult Glioma Segmentation 1st place """
@@ -48,8 +57,15 @@ class AdultGliomaPreTreatmentAlgorithms(Algorithms):
     """BraTS23 Adult Glioma Segmentation 3rd place (GPU only)"""
 
 
-class MeningiomaAlgorithms(Algorithms):
-    """Constants for the available meningioma segmentation algorithms."""
+class MeningiomaRTAlgorithms(Algorithms):
+    """Constants for the available meningioma segmentation - Radio Therapy algorithms."""
+
+    BraTS25_1 = "BraTS25_1"
+    """ BraTS25 Meningioma Segmentation 1st place """
+    BraTS25_2 = "BraTS25_2"
+    """ BraTS25 Meningioma Segmentation 2nd place """
+    BraTS25_3 = "BraTS25_3"
+    """ BraTS25 Meningioma Segmentation 3rd place """
 
     BraTS24_1 = "BraTS24_1"
     """ BraTS24 Meningioma Segmentation 1st place """
@@ -58,6 +74,15 @@ class MeningiomaAlgorithms(Algorithms):
     BraTS24_3 = "BraTS24_3"
     """ BraTS24 Meningioma Segmentation 3rd place """
 
+
+class MeningiomaAlgorithms(Algorithms):
+    """Constants for the available meningioma segmentation algorithms."""
+
+    BraTS25_1 = "BraTS25_1"
+    """BraTS25 Meningioma Segmentation 1st place """
+    BraTS25_2 = "BraTS25_2"
+    """BraTS25 Meningioma Segmentation 2nd place """
+
     BraTS23_1 = "BraTS23_1"
     """BraTS23 Meningioma Segmentation 1st place (GPU only)"""
     BraTS23_2 = "BraTS23_2"
@@ -69,6 +94,15 @@ class MeningiomaAlgorithms(Algorithms):
 class PediatricAlgorithms(Algorithms):
     """Constants for the available pediatric segmentation algorithms."""
 
+    BraTS25_1A = "BraTS25_1A"
+    """ BraTS25 Pediatric Segmentation 1st place (tie)"""
+    BraTS25_1B = "BraTS25_1B"
+    """ BraTS25 Pediatric Segmentation 1st place (tie)"""
+    BraTS25_1C = "BraTS25_1C"
+    """ BraTS25 Pediatric Segmentation 1st place (tie)"""
+    BraTS25_1D = "BraTS25_1D"
+    """ BraTS25 Pediatric Segmentation 1st place (tie)"""
+
     BraTS24_1 = "BraTS24_1"
     """ BraTS24 Pediatric Segmentation 1st place """
     BraTS24_2 = "BraTS24_2"
@@ -87,6 +121,15 @@ class PediatricAlgorithms(Algorithms):
 class AfricaAlgorithms(Algorithms):
     """Constants for the available africa segmentation algorithms."""
 
+    BraTS25_1 = "BraTS25_1"
+    """ BraTS25 BraTS-SSA Segmentation 1st place """
+    BraTS25_2A = "BraTS25_2A"
+    """ BraTS25 BraTS-SSA Segmentation 2nd place (Tie)"""
+    BraTS25_2B = "BraTS25_2B"
+    """ BraTS25 BraTS-SSA Segmentation 2nd place (Tie) """
+    BraTS25_3 = "BraTS25_3"
+    """ BraTS25 BraTS-SSA Segmentation 3rd place """
+
     BraTS24_1 = "BraTS24_1"
     """ BraTS24 BraTS-Africa Segmentation 1st place """
     BraTS24_2 = "BraTS24_2"
@@ -105,6 +148,11 @@ class AfricaAlgorithms(Algorithms):
 class MetastasesAlgorithms(Algorithms):
     """Constants for the available Inpainting algorithms."""
 
+    BraTS25_1 = "BraTS25_1"
+    """BraTS25  Brain Metastases Segmentation 1st place"""
+    BraTS25_2 = "BraTS25_2"
+    """BraTS25  Brain Metastases Segmentation 2nd place"""
+
     BraTS23_1 = "BraTS23_1"
     """BraTS23  Brain Metastases Segmentation 1st place (GPU only)"""
     BraTS23_2 = "BraTS23_2"
@@ -116,6 +164,13 @@ class MetastasesAlgorithms(Algorithms):
 class InpaintingAlgorithms(Algorithms):
     """Constants for the available BraTS Inpainting algorithms."""
 
+    BraTS25_1A = "BraTS25_1A"
+    """ BraTS25  Inpainting shared 1st place (tie) """
+    BraTS25_1B = "BraTS25_1B"
+    """ BraTS25  Inpainting shared 1st place (tie)"""
+    BraTS25_2 = "BraTS25_2"
+    """ BraTS25  Inpainting 2nd place """
+
     BraTS24_1 = "BraTS24_1"
     """ BraTS24  Inpainting 1st place """
     BraTS24_2 = "BraTS24_2"
@@ -132,21 +187,38 @@ class InpaintingAlgorithms(Algorithms):
 
 
 class MissingMRIAlgorithms(Algorithms):
-    """Constants for the available missing mri  algorithms."""
+    """Constants for the available missing mri algorithms."""
+
+    BraTS25_1 = "BraTS25_1"
+    """ BraTS25  MissingMRI 1st place """
+    BraTS25_2 = "BraTS25_2"
+    """ BraTS25  MissingMRI 2nd place """
+    BraTS25_3 = "BraTS25_3"
+    """ BraTS25  MissingMRI 3rd place """
 
     BraTS24_1 = "BraTS24_1"
     """ BraTS24  MissingMRI 1st place """
     BraTS24_2 = "BraTS24_2"
     """ BraTS24  MissingMRI 2nd place """
     BraTS24_3 = "BraTS24_3"
     """ BraTS24  MissingMRI 3rd place """
+
     BraTS23_1 = "BraTS23_1"
     """ BraTS23  MissingMRI 1st place """
 
 
 class GoATAlgorithms(Algorithms):
     """Constants for the available missing mri  algorithms."""
 
+    BraTS25_1A = "BraTS25_1A"
+    """ BraTS25 Generalizability Across Tumors (BraTS-GoAT) 1st place (tie) """
+    BraTS25_1B = "BraTS25_1B"
+    """ BraTS25 Generalizability Across Tumors (BraTS-GoAT) 1st place (tie) """
+    BraTS25_1C = "BraTS25_1C"
+    """ BraTS25 Generalizability Across Tumors (BraTS-GoAT) 1st place (tie) """
+    BraTS25_1D = "BraTS25_1D"
+    """ BraTS25 Generalizability Across Tumors (BraTS-GoAT) 1st place (tie) """
+
     BraTS24_1 = "BraTS24_1"
     """ BraTS24 Generalizability Across Tumors (BraTS-GoAT) 1st place (The only submission)"""
 
@@ -161,10 +233,11 @@ class GoATAlgorithms(Algorithms):
 ADULT_GLIOMA_PRE_TREATMENT_SEGMENTATION_ALGORITHMS = (
     META_DIR / "adult_glioma_pre_treatment.yml"
 )
-ADULT_GLIOMA_POST_TREATMENT_SEGMENTATION_ALGORITHMS = (
-    META_DIR / "adult_glioma_post_treatment.yml"
+ADULT_GLIOMA_PRE_AND_POST_TREATMENT_SEGMENTATION_ALGORITHMS = (
+    META_DIR / "adult_glioma_pre_and_post_treatment.yml"
 )
 MENINGIOMA_SEGMENTATION_ALGORITHMS = META_DIR / "meningioma.yml"
+MENINGIOMA_RT_SEGMENTATION_ALGORITHMS = META_DIR / "meningioma_rt.yml"
 PEDIATRIC_SEGMENTATION_ALGORITHMS = META_DIR / "pediatric.yml"
 AFRICA_SEGMENTATION_ALGORITHMS = META_DIR / "africa.yml"
 METASTASES_SEGMENTATION_ALGORITHMS = META_DIR / "metastases.yml"

brats/constants.py

@@ -11,6 +11,7 @@
 from brats.utils.algorithm_config import load_algorithms
 from brats.constants import OUTPUT_NAME_SCHEMA, Algorithms, Task
 from brats.utils.data_handling import InferenceSetup
+from brats.utils.exceptions import AlgorithmConfigException
 
 
 class BraTSAlgorithm(ABC):
@@ -23,7 +24,7 @@ def __init__(
         algorithm: Algorithms,
         algorithms_file_path: Path,
         task: Task,
-        cuda_devices: Optional[str] = "0",
+        cuda_devices: str = "0",
         force_cpu: bool = False,
     ):
         # inference device setup
@@ -34,6 +35,10 @@ def __init__(
         self.algorithm_list = load_algorithms(file_path=algorithms_file_path)
         # save algorithm identifier for logging etc.
         self.algorithm_key = algorithm.value
+        if self.algorithm_key not in self.algorithm_list:
+            raise AlgorithmConfigException(
+                f"Algorithm {self.algorithm_key} not found in {algorithms_file_path}"
+            )
         # data for selected algorithm
         self.algorithm = self.algorithm_list[algorithm.value]
 
@@ -63,8 +68,21 @@ def _standardize_batch_inputs(
         """
         pass
 
+    def extract_identifier_from_subject_id(self, subject_id: str) -> str:
+        """
+        Extract the index from the subject ID
+        Args:
+            subject_id (str): Subject ID of the input
+        Returns:
+            str: Extracted identifier
+        """
+        return "-".join(subject_id.split("-")[-2:])
+
     def _process_single_output(
-        self, tmp_output_folder: Path | str, subject_id: str, output_file: Path
+        self,
+        tmp_output_folder: Path | str,
+        subject_id: str,
+        output_file: Path,
     ) -> None:
         """
         Process the output of a single inference run and save it in the specified file.
@@ -79,9 +97,14 @@ def _process_single_output(
             # Missing MRI has no fixed names since the missing modality differs and is included in the name
             algorithm_output = Path(tmp_output_folder).iterdir().__next__()
         else:
-            algorithm_output = Path(tmp_output_folder) / OUTPUT_NAME_SCHEMA[
-                self.task
-            ].format(subject_id=subject_id)
+            # extract id from subject id, i.e. BraTS-MEN-00000-000 => 00000-000
+            identifier = self.extract_identifier_from_subject_id(subject_id)
+            possible_output = list(Path(tmp_output_folder).glob(f"*{identifier}*"))
+            if len(possible_output) == 0:
+                raise FileNotFoundError(
+                    f"No output found for subject {subject_id} in {tmp_output_folder}"
+                )
+            algorithm_output = possible_output[0]
 
         # ensure path exists and rename output to the desired path
         output_file = Path(output_file).absolute()
@@ -123,9 +146,15 @@ def _process_batch_output(
                     / f"{external_name}{'-' + modality if modality else ''}.nii.gz"
                 )
             else:
-                algorithm_output = Path(tmp_output_folder) / OUTPUT_NAME_SCHEMA[
-                    self.task
-                ].format(subject_id=internal_name)
+                identifier = self.extract_identifier_from_subject_id(internal_name)
+                possible_outputs = list(Path(tmp_output_folder).glob(f"*{identifier}*"))
+                if len(possible_outputs) == 0:
+                    logger.error(
+                        f"No output found for subject {internal_name} in {tmp_output_folder}"
+                    )
+                    continue
+                algorithm_output = possible_outputs[0]
+
                 output_file = output_folder / f"{external_name}.nii.gz"
             shutil.move(algorithm_output, output_file)
 
@@ -166,7 +195,7 @@ def _infer_single(
             self._process_single_output(
                 tmp_output_folder=tmp_output_folder,
                 subject_id=subject_id,
-                output_file=output_file,
+                output_file=Path(output_file),
             )
             logger.info(f"Saved output to: {Path(output_file).absolute()}")