GANDLF 0.1.4.dev20250610__tar.gz → 0.1.4.dev20250612__tar.gz

{gandlf-0.1.4.dev20250610 → gandlf-0.1.4.dev20250612}/GANDLF/cli/generate_metrics.py

@@ -287,7 +287,7 @@ def generate_metrics_dict(
                 pred_array = pred_tensor.squeeze(0).numpy().astype(int)
 
             overall_stats_dict[current_subject_id] = generate_instance_segmentation(
-                prediction=pred_array, target=label_array
+                prediction=pred_array, target=label_array, parameters=parameters
             )
 
     elif problem_type == "synthesis":

gandlf-0.1.4.dev20250612/GANDLF/metrics/segmentation_panoptica.py

@@ -0,0 +1,50 @@
+from pathlib import Path
+import tempfile
+
+import numpy as np
+
+from panoptica import Panoptica_Evaluator
+
+
+def generate_instance_segmentation(
+    prediction: np.ndarray,
+    target: np.ndarray,
+    parameters: dict = None,
+    panoptica_config_path: str = None,
+) -> dict:
+    """
+    Evaluate a single exam using Panoptica.
+
+    Args:
+        prediction (np.ndarray): The input prediction containing objects.
+        label_path (str): The path to the reference label.
+        target (np.ndarray): The input target containing objects.
+        panoptica_config_path (str): The path to the Panoptica configuration file.
+
+    Returns:
+        dict: The evaluation results.
+    """
+
+    cwd = Path(__file__).parent.absolute()
+    # the parameters dict takes precedence over the panoptica_config_path
+    panoptica_config = parameters.get("panoptica_config", None)
+    if panoptica_config is None:
+        panoptica_config_path = (
+            cwd / "panoptica_config_brats.yaml"
+            if panoptica_config_path is None
+            else panoptica_config_path
+        )
+    else:
+        # write the panoptica config to a file
+        panoptica_config_path = tempfile.NamedTemporaryFile(
+            mode="w", delete=False, suffix=".yaml"
+        ).name
+        with open(panoptica_config_path, "w") as f:
+            f.write(panoptica_config)
+    evaluator = Panoptica_Evaluator.load_from_config(panoptica_config_path)
+
+    # call evaluate
+    group2result = evaluator.evaluate(prediction_arr=prediction, reference_arr=target)
+
+    results = {k: r.to_dict() for k, r in group2result.items()}
+    return results

gandlf-0.1.4.dev20250612/GANDLF/version.py

@@ -0,0 +1 @@
+__version__ = "0.1.4-dev20250612"

{gandlf-0.1.4.dev20250610 → gandlf-0.1.4.dev20250612}/GANDLF.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: GANDLF
-Version: 0.1.4.dev20250610
+Version: 0.1.4.dev20250612
 Summary: PyTorch-based framework that handles segmentation/regression/classification using various DL architectures for medical imaging.
 Author: MLCommons
 Author-email: gandlf@mlcommons.org

{gandlf-0.1.4.dev20250610 → gandlf-0.1.4.dev20250612}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: GANDLF
-Version: 0.1.4.dev20250610
+Version: 0.1.4.dev20250612
 Summary: PyTorch-based framework that handles segmentation/regression/classification using various DL architectures for medical imaging.
 Author: MLCommons
 Author-email: gandlf@mlcommons.org

gandlf-0.1.4.dev20250610/GANDLF/metrics/segmentation_panoptica.py

@@ -1,35 +0,0 @@
-from pathlib import Path
-
-import numpy as np
-
-from panoptica import Panoptica_Evaluator
-
-
-def generate_instance_segmentation(
-    prediction: np.ndarray, target: np.ndarray, panoptica_config_path: str = None
-) -> dict:
-    """
-    Evaluate a single exam using Panoptica.
-
-    Args:
-        prediction (np.ndarray): The input prediction containing objects.
-        label_path (str): The path to the reference label.
-        panoptica_config_path (str): The path to the Panoptica configuration file.
-
-    Returns:
-        dict: The evaluation results.
-    """
-
-    cwd = Path(__file__).parent.absolute()
-    panoptica_config_path = (
-        cwd / "panoptica_config_brats.yaml"
-        if panoptica_config_path is None
-        else panoptica_config_path
-    )
-    evaluator = Panoptica_Evaluator.load_from_config(panoptica_config_path)
-
-    # call evaluate
-    group2result = evaluator.evaluate(prediction_arr=prediction, reference_arr=target)
-
-    results = {k: r.to_dict() for k, r in group2result.items()}
-    return results

gandlf-0.1.4.dev20250610/GANDLF/version.py

@@ -1 +0,0 @@
-__version__ = "0.1.4-dev20250610"