GANDLF 0.1.4.dev20250707__py3-none-any.whl → 0.1.5.dev20250709__py3-none-any.whl

GANDLF/metrics/segmentation_panoptica.py

@@ -1,6 +1,7 @@
 from pathlib import Path
-import tempfile
+import os
 
+from typing import Optional
 import numpy as np
 
 from panoptica import Panoptica_Evaluator
@@ -9,8 +10,8 @@ from panoptica import Panoptica_Evaluator
 def generate_instance_segmentation(
     prediction: np.ndarray,
     target: np.ndarray,
-    parameters: dict = None,
-    panoptica_config_path: str = None,
+    parameters: dict,
+    panoptica_config_path: Optional[str] = None,
 ) -> dict:
     """
     Evaluate a single exam using Panoptica.
@@ -19,29 +20,27 @@ def generate_instance_segmentation(
         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.
+        parameters (dict): The GaNDLF parameters from which panoptica config is to be extracted.
         panoptica_config_path (str): The path to the Panoptica configuration file.
 
     Returns:
         dict: The evaluation results.
     """
 
-    cwd = Path(__file__).parent.absolute()
+    os.environ["PANOPTICA_CITATION_REMINDER"] = "False"
+
     # the parameters dict takes precedence over the panoptica_config_path
-    panoptica_config = parameters.get("panoptica_config", None)
-    if panoptica_config is None:
+    evaluator = parameters.get("panoptica_config", None)
+    if evaluator is None:
+        cwd = Path(__file__).parent.absolute()
         panoptica_config_path = (
-            cwd / "panoptica_config_brats.yaml"
+            str(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)
+        evaluator = Panoptica_Evaluator.load_from_config(panoptica_config_path)
+
+    assert evaluator is not None, "Panoptica evaluator could not be initialized."
 
     # call evaluate
     group2result = evaluator.evaluate(prediction_arr=prediction, reference_arr=target)

GANDLF/version.py

@@ -1 +1 @@
-__version__ = "0.1.4-dev20250707"
+__version__ = "0.1.5-dev20250709"

{gandlf-0.1.4.dev20250707.dist-info → gandlf-0.1.5.dev20250709.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: GANDLF
-Version: 0.1.4.dev20250707
+Version: 0.1.5.dev20250709
 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.dev20250707.dist-info → gandlf-0.1.5.dev20250709.dist-info}/RECORD

@@ -5,7 +5,7 @@ GANDLF/logger.py,sha256=oamQ1SOTTpAnC8vQ67o211Q6_bExGg_hAuqlHGlJfAI,2951
 GANDLF/logging_config.yaml,sha256=9XxRxAKtLn5ehT1khpR8wEiJGW64sx1lylAspM5KaWk,1337
 GANDLF/parseConfig.py,sha256=jO-ybIPxLw23OWDvFdTukbft0ZM8UOofGnoL2C5CEps,754
 GANDLF/training_manager.py,sha256=AZlf-fl7KAwZgyre8-0M5lAyma6NvtiGX6XT51AJdxU,11436
-GANDLF/version.py,sha256=aUD6n0l6GU99YL_r_OUbcz48uaESPsxSIr0HcUgtMm8,34
+GANDLF/version.py,sha256=mnOEOwW-y5mRKKq51jXVfaB7yp_oCF4ajPpScc4Y6eM,34
 GANDLF/anonymize/__init__.py,sha256=Nxig-jM-a-aKlK09PNi1zhNulEpLTyjnsY_oGQKdjhQ,1953
 GANDLF/anonymize/convert_to_nifti.py,sha256=MOfSDncFGJGb-EQP9sFGn0yuKpX010Ioi2KNwttaex8,1339
 GANDLF/cli/__init__.py,sha256=F05eyL2HKyWkHczRZuPE_Z2Yg685P9ARYxTwz6njGeQ,784
@@ -111,7 +111,7 @@ GANDLF/metrics/metric_calculators.py,sha256=c-NAl84yniTWjMKePBlf0TsCIJnYHODplt8H
 GANDLF/metrics/panoptica_config_brats.yaml,sha256=mTGSQuJoENuy84gZd2tHV0Dfl7GX5nIeE_46q5Vczx4,2685
 GANDLF/metrics/regression.py,sha256=Ca58jo9OL1GdjB2ZvQCcrKWz9F67iY5rcbnQxT-LpcU,4584
 GANDLF/metrics/segmentation.py,sha256=zqWEI6LuphFM0Nsm0sG2XeqAxpNJnoK1Z9q4FJt58c8,25645
-GANDLF/metrics/segmentation_panoptica.py,sha256=aFGF3q_Fnf5vIWaJDMHcs2Az_fb23l2cvvifnCkgPO0,1611
+GANDLF/metrics/segmentation_panoptica.py,sha256=TNphTIU4C3e-hu62sDpRDW_h6_za9g_7TgEjEgaRclE,1598
 GANDLF/metrics/synthesis.py,sha256=IfYit-R0O5ZUfmsWfLD6BqcLjjoEiotx0lUdsXWlbao,6730
 GANDLF/models/MSDNet.py,sha256=mzBkw_kQigSDTxaR7tojhdI4ECIQ65i_qiCrNaZmBHI,3442
 GANDLF/models/__init__.py,sha256=3SwskWonRW1AduPe6CYQWucU8ZBkkfJUpEF34I0NWP0,4286
@@ -182,9 +182,9 @@ GANDLF/utils/parameter_processing.py,sha256=DA7ZEsizWWLJZnCxBnDNh1NyA-bw5oirOvod
 GANDLF/utils/pred_target_processors.py,sha256=aatXJ6jdJaNAHa_tPzHfC1gOQrPYJLtg-cYeUFvkM_s,2701
 GANDLF/utils/tensor.py,sha256=AOwNTQfw9mnsomGwOF2Q_rdDS1WANlIatB0hhZN0gSg,21504
 GANDLF/utils/write_parse.py,sha256=HROxskhet-uIdUJmz16z_7p9r0mf8hWsqQFygwZ8ap0,9202
-gandlf-0.1.4.dev20250707.dist-info/licenses/LICENSE,sha256=GlZPAfA4eckod8IVayhBXkqCpESXf6cc9BGli_Jwims,11357
-gandlf-0.1.4.dev20250707.dist-info/METADATA,sha256=5ChBddmfEN7ncF2b6dv1ZGCiJf9d2GMd9NHXHmAzjfo,9904
-gandlf-0.1.4.dev20250707.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
-gandlf-0.1.4.dev20250707.dist-info/entry_points.txt,sha256=agwocNI7Upi-sFDe1rMl71dGN8YhCBB7WJmtBHRF4jg,902
-gandlf-0.1.4.dev20250707.dist-info/top_level.txt,sha256=i5D9wEbQhl085_9Lx2m7x-9Zu6nlx1tjYYbuSihG09E,7
-gandlf-0.1.4.dev20250707.dist-info/RECORD,,
+gandlf-0.1.5.dev20250709.dist-info/licenses/LICENSE,sha256=GlZPAfA4eckod8IVayhBXkqCpESXf6cc9BGli_Jwims,11357
+gandlf-0.1.5.dev20250709.dist-info/METADATA,sha256=2E8SDmCeaQXUSBljeHCx3ciqkoDvBlQ-Rw_CPcD_eN4,9904
+gandlf-0.1.5.dev20250709.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
+gandlf-0.1.5.dev20250709.dist-info/entry_points.txt,sha256=agwocNI7Upi-sFDe1rMl71dGN8YhCBB7WJmtBHRF4jg,902
+gandlf-0.1.5.dev20250709.dist-info/top_level.txt,sha256=i5D9wEbQhl085_9Lx2m7x-9Zu6nlx1tjYYbuSihG09E,7
+gandlf-0.1.5.dev20250709.dist-info/RECORD,,