GANDLF 0.1.4.dev20250609__tar.gz → 0.1.4.dev20250610__tar.gz

{gandlf-0.1.4.dev20250609 → gandlf-0.1.4.dev20250610}/GANDLF/cli/generate_metrics.py

@@ -10,7 +10,11 @@ import SimpleITK as sitk
 import numpy as np
 
 from GANDLF.config_manager import ConfigManager
-from GANDLF.utils import find_problem_type_from_parameters, one_hot
+from GANDLF.utils import (
+    find_problem_type_from_parameters,
+    one_hot,
+    sanity_check_on_file_readers,
+)
 from GANDLF.metrics import (
     overall_stats,
     structural_similarity_index,
@@ -176,6 +180,9 @@ def generate_metrics_dict(
         for _, row in tqdm(input_df.iterrows(), total=input_df.shape[0]):
             current_subject_id = row["SubjectID"]
             overall_stats_dict[current_subject_id] = {}
+            sanity_check_on_file_readers(
+                row["Target"], row["Prediction"], current_subject_id
+            )
             label_image = torchio.LabelMap(row["Target"])
             pred_image = torchio.LabelMap(row["Prediction"])
             label_tensor = label_image.data
@@ -264,17 +271,20 @@ def generate_metrics_dict(
         for _, row in tqdm(input_df.iterrows(), total=input_df.shape[0]):
             current_subject_id = row["SubjectID"]
             overall_stats_dict[current_subject_id] = {}
+            sanity_check_on_file_readers(
+                row["Target"], row["Prediction"], current_subject_id
+            )
             label_image = torchio.LabelMap(row["Target"])
             pred_image = torchio.LabelMap(row["Prediction"])
             label_tensor = label_image.data
             pred_tensor = pred_image.data
             spacing = label_image.spacing
-            if label_tensor.data.shape[-1] == 1:
-                spacing = spacing[0:2]
-            # add dimension for batch
-            parameters["subject_spacing"] = torch.Tensor(spacing).unsqueeze(0)
-            label_array = label_tensor.unsqueeze(0).numpy()
-            pred_array = pred_tensor.unsqueeze(0).numpy()
+            # if label_tensor.data.shape[-1] == 1:
+            #     spacing = spacing[0:2]
+            # remove dimension to ensure 3D tensors
+            if label_tensor.data.ndim == 4:
+                label_array = label_tensor.squeeze(0).numpy().astype(int)
+                pred_array = pred_tensor.squeeze(0).numpy().astype(int)
 
             overall_stats_dict[current_subject_id] = generate_instance_segmentation(
                 prediction=pred_array, target=label_array
@@ -340,6 +350,9 @@ def generate_metrics_dict(
         for _, row in tqdm(input_df.iterrows(), total=input_df.shape[0]):
             current_subject_id = row["SubjectID"]
             overall_stats_dict[current_subject_id] = {}
+            sanity_check_on_file_readers(
+                row["Target"], row["Prediction"], current_subject_id
+            )
             target_image = __fix_2d_tensor(torchio.ScalarImage(row["Target"]).data)
             pred_image = __fix_2d_tensor(torchio.ScalarImage(row["Prediction"]).data)
             # if "Mask" is not in the row, we assume that the whole image is the mask

{gandlf-0.1.4.dev20250609 → gandlf-0.1.4.dev20250610}/GANDLF/metrics/panoptica_config_brats.yaml

@@ -13,7 +13,10 @@ edge_case_handler: !EdgeCaseHandler
     !Metric IOU: !MetricZeroTPEdgeCaseHandling {empty_prediction_result: !EdgeCaseResult ZERO,
       empty_reference_result: !EdgeCaseResult ZERO, no_instances_result: !EdgeCaseResult NAN,
       normal: !EdgeCaseResult ZERO}
-    !Metric ASSD: !MetricZeroTPEdgeCaseHandling {empty_prediction_result: !EdgeCaseResult INF,
+    !Metric NSD: !MetricZeroTPEdgeCaseHandling {empty_prediction_result: !EdgeCaseResult INF,
+      empty_reference_result: !EdgeCaseResult INF, no_instances_result: !EdgeCaseResult NAN,
+      normal: !EdgeCaseResult INF}
+    !Metric HD95: !MetricZeroTPEdgeCaseHandling {empty_prediction_result: !EdgeCaseResult INF,
       empty_reference_result: !EdgeCaseResult INF, no_instances_result: !EdgeCaseResult NAN,
       normal: !EdgeCaseResult INF}
     !Metric RVD: !MetricZeroTPEdgeCaseHandling {empty_prediction_result: !EdgeCaseResult NAN,
@@ -27,24 +30,27 @@ global_metrics: [!Metric DSC]
 instance_approximator: !ConnectedComponentsInstanceApproximator {cca_backend: null}
 instance_matcher: !NaiveThresholdMatching {allow_many_to_one: false, matching_metric: !Metric IOU,
   matching_threshold: 0.5}
-instance_metrics: [!Metric DSC, !Metric IOU, !Metric ASSD, !Metric RVD]
+instance_metrics: [!Metric DSC, !Metric IOU, !Metric RVD, !Metric NSD, !Metric HD95]
 log_times: false
 save_group_times: false
 segmentation_class_groups: !SegmentationClassGroups
   groups:
-    ed: !LabelGroup
+    snfh: !LabelGroup
       single_instance: false
       value_labels: [2]
     et: !LabelGroup
       single_instance: false
       value_labels: [3]
-    net: !LabelGroup
+    netc: !LabelGroup
       single_instance: false
       value_labels: [1]
+    rc: !LabelGroup
+      single_instance: false
+      value_labels: [4]
     tc: !LabelMergeGroup
       single_instance: false
-      value_labels: [1, 3]
+      value_labels: [1, 3, 4]
     wt: !LabelMergeGroup
       single_instance: false
-      value_labels: [1, 2, 3]
+      value_labels: [1, 2, 3, 4]
 verbose: false

{gandlf-0.1.4.dev20250609 → gandlf-0.1.4.dev20250610}/GANDLF/utils/__init__.py

@@ -7,6 +7,7 @@ from .imaging import (
     resize_image,
     resample_image,
     perform_sanity_check_on_subject,
+    sanity_check_on_file_readers,
     write_training_patches,
     get_correct_padding_size,
     applyCustomColorMap,

{gandlf-0.1.4.dev20250609 → gandlf-0.1.4.dev20250610}/GANDLF/utils/imaging.py

@@ -123,6 +123,56 @@ def softer_sanity_check(
     return result
 
 
+def sanity_check_on_file_readers(
+    file_reader_0: Union[str, sitk.ImageFileReader],
+    file_reader_1: Union[str, sitk.ImageFileReader],
+    subject_id: Optional[str] = "",
+    threshold: Optional[float] = 0.00001,
+) -> bool:
+    """
+    This function performs a sanity check on the file readers to ensure that the properties of the images are consistent.
+
+    Args:
+        file_reader_0 (Union[str, sitk.ImageFileReader]): The first file reader.
+        file_reader_1 (Union[str, sitk.ImageFileReader]): The second file reader.
+        threshold (Optional[float], optional): The threshold for comparison. Defaults to 0.00001.
+
+    Returns:
+        bool: True if the sanity check passes.
+    """
+
+    if isinstance(file_reader_0, str):
+        temp_file = file_reader_0
+        file_reader_0 = sitk.ImageFileReader()
+        file_reader_0.SetFileName(temp_file)
+        file_reader_0.ReadImageInformation()
+
+    if isinstance(file_reader_1, str):
+        temp_file = file_reader_1
+        file_reader_1 = sitk.ImageFileReader()
+        file_reader_1.SetFileName(temp_file)
+        file_reader_1.ReadImageInformation()
+    # this check needs to be absolute
+    assert file_reader_0.GetDimension() == file_reader_1.GetDimension(), (
+        "Dimensions for Subject '" + subject_id + "' are not consistent."
+    )
+
+    # other checks can be softer
+    assert softer_sanity_check(
+        file_reader_0.GetOrigin(), file_reader_1.GetOrigin(), threshold=threshold
+    ), ("Origin for Subject '" + subject_id + "' are not consistent.")
+
+    assert softer_sanity_check(
+        file_reader_0.GetDirection(), file_reader_1.GetDirection(), threshold=threshold
+    ), ("Orientation for Subject '" + subject_id + "' are not consistent.")
+
+    assert softer_sanity_check(
+        file_reader_0.GetSpacing(), file_reader_1.GetSpacing(), threshold=threshold
+    ), ("Spacing for Subject '" + subject_id + "' are not consistent.")
+
+    return True
+
+
 def perform_sanity_check_on_subject(subject: torchio.Subject, parameters: dict) -> bool:
     """
     This function performs a sanity check on the image modalities in input subject to ensure that they are consistent.
@@ -169,39 +219,11 @@ def perform_sanity_check_on_subject(subject: torchio.Subject, parameters: dict)
             else:
                 file_reader_current = _get_itkimage_or_filereader(subject[str(key)])
 
-                # this check needs to be absolute
-                assert (
-                    file_reader_base.GetDimension()
-                    == file_reader_current.GetDimension()
-                ), (
-                    "Dimensions for Subject '"
-                    + subject["subject_id"]
-                    + "' are not consistent."
-                )
-
-                # other checks can be softer
-                assert softer_sanity_check(
-                    file_reader_base.GetOrigin(), file_reader_current.GetOrigin()
-                ), (
-                    "Origin for Subject '"
-                    + subject["subject_id"]
-                    + "' are not consistent."
-                )
-
-                assert softer_sanity_check(
-                    file_reader_base.GetDirection(), file_reader_current.GetDirection()
-                ), (
-                    "Orientation for Subject '"
-                    + subject["subject_id"]
-                    + "' are not consistent."
-                )
-
-                assert softer_sanity_check(
-                    file_reader_base.GetSpacing(), file_reader_current.GetSpacing()
-                ), (
-                    "Spacing for Subject '"
-                    + subject["subject_id"]
-                    + "' are not consistent."
+                sanity_check_on_file_readers(
+                    file_reader_base,
+                    file_reader_current,
+                    subject_id=subject["subject_id"],
+                    threshold=parameters.get("sanity_check_threshold", 0.00001),
                 )
 
     return True

gandlf-0.1.4.dev20250610/GANDLF/version.py

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

{gandlf-0.1.4.dev20250609 → gandlf-0.1.4.dev20250610}/GANDLF.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: GANDLF
-Version: 0.1.4.dev20250609
+Version: 0.1.4.dev20250610
 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.dev20250609 → gandlf-0.1.4.dev20250610}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: GANDLF
-Version: 0.1.4.dev20250609
+Version: 0.1.4.dev20250610
 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.dev20250609/GANDLF/version.py

@@ -1 +0,0 @@
-__version__ = "0.1.4-dev20250609"