GANDLF 0.1.4.dev20250707__tar.gz → 0.1.5__tar.gz

{gandlf-0.1.4.dev20250707 → gandlf-0.1.5}/Dockerfile-CPU

@@ -19,7 +19,7 @@ RUN apt-get install -y libjpeg8-dev zlib1g-dev libffi-dev libgl1
 # fix pip version because of weird PyYAML issue
 RUN python3.11 -m pip install --upgrade pip
 # EXPLICITLY install cpu versions of torch/torchvision (not all versions have +cpu modes on PyPI...)
-RUN python3.11 -m pip install torch==2.5.0 torchvision==0.20.0 torchaudio==2.5.0 --index-url https://download.pytorch.org/whl/cpu
+RUN python3.11 -m pip install torch==2.7.1 torchvision==0.22.1 torchaudio==2.7.1 --index-url https://download.pytorch.org/whl/cpu
 RUN python3.11 -m pip install openvino-dev opencv-python-headless
 
 # Do some dependency installation separately here to make layer caching more efficient

{gandlf-0.1.4.dev20250707 → gandlf-0.1.5}/Dockerfile-CUDA11.8

@@ -21,7 +21,7 @@ RUN apt install -y python3-pip
 RUN apt-get install -y libjpeg8-dev zlib1g-dev libffi-dev libgl1
 # fix pip version because of weird PyYAML issue
 RUN python3.11 -m pip install --upgrade pip
-RUN python3.11 -m pip install torch==2.5.0 torchvision==0.20.0 torchaudio==2.5.0 --index-url https://download.pytorch.org/whl/cu118
+RUN python3.11 -m pip install torch==2.7.1 torchvision==0.22.1 torchaudio==2.7.1 --index-url https://download.pytorch.org/whl/cu118
 RUN python3.11 -m pip install openvino-dev opencv-python-headless
 
 # Do some dependency installation separately here to make layer caching more efficient

gandlf-0.1.4.dev20250707/Dockerfile-CUDA12.1 → gandlf-0.1.5/Dockerfile-CUDA12.6

@@ -1,4 +1,4 @@
-FROM nvidia/cuda:12.1.0-devel-ubuntu22.04
+FROM nvidia/cuda:12.6.3-cudnn-devel-ubuntu22.04
 LABEL github="https://github.com/mlcommons/GaNDLF"
 LABEL docs="https://mlcommons.github.io/GaNDLF/"
 LABEL version=1.0
@@ -21,7 +21,7 @@ RUN apt install -y python3-pip
 RUN apt-get install -y libjpeg8-dev zlib1g-dev libffi-dev libgl1
 # fix pip version because of weird PyYAML issue
 RUN python3.11 -m pip install --upgrade pip
-RUN python3.11 -m pip install torch==2.5.0 torchvision==0.20.0 torchaudio==2.5.0 --index-url https://download.pytorch.org/whl/cu121
+RUN python3.11 -m pip install torch==2.7.1 torchvision==0.22.1 torchaudio==2.7.1 --index-url https://download.pytorch.org/whl/cu126
 RUN python3.11 -m pip install openvino-dev opencv-python-headless
 
 # Do some dependency installation separately here to make layer caching more efficient

{gandlf-0.1.4.dev20250707 → gandlf-0.1.5}/Dockerfile-ROCm

@@ -1,4 +1,4 @@
-FROM rocm/pytorch:rocm6.1_ubuntu22.04_py3.10_pytorch_2.4
+FROM rocm/pytorch:rocm6.3.4_ubuntu22.04_py3.10_pytorch_release_2.4.0
 LABEL github="https://github.com/mlcommons/GaNDLF"
 LABEL docs="https://mlcommons.github.io/GaNDLF/"
 LABEL version=1.0
@@ -19,7 +19,7 @@ RUN apt install -y python3-pip
 RUN apt-get install -y python3.11 python3-pip libjpeg8-dev zlib1g-dev python3-dev libpython3.11-dev libffi-dev libgl1
 # fix pip version because of weird PyYAML issue
 RUN python3.11 -m pip install --upgrade pip
-RUN python3.11 -m pip install torch==2.5.0 torchvision==0.20.0 torchaudio==2.5.0 --index-url https://download.pytorch.org/whl/rocm6.1
+RUN python3.11 -m pip install torch==2.7.1 torchvision==0.22.1 torchaudio==2.7.1 --index-url https://download.pytorch.org/whl/rocm6.3
 RUN python3.11 -m pip install openvino-dev opencv-python-headless
 
 # Do some dependency installation separately here to make layer caching more efficient

{gandlf-0.1.4.dev20250707 → gandlf-0.1.5}/GANDLF/configuration/default_config.py

@@ -34,7 +34,7 @@ class DefaultParameters(BaseModel):
         default=10, description="Number of samples per volume."
     )
     q_num_workers: int = Field(
-        default=4, description="Number of worker threads to use."
+        default=0, description="Number of worker threads to use."
     )
     num_epochs: int = Field(default=100, description="Total number of epochs to train.")
     patience: int = Field(

{gandlf-0.1.4.dev20250707 → gandlf-0.1.5}/GANDLF/configuration/scheduler_config.py

@@ -84,7 +84,9 @@ schedulers_dict_config = {
     "reduce-on-plateau": ReduceOnPlateauConfig,
     "plateau": ReduceOnPlateauConfig,
     "reduceonplateau": ReduceOnPlateauConfig,
+    "cosineannealingwarmrestarts": CosineannealingConfig,
     "cosineannealing": CosineannealingConfig,
+    "cosineannealinglr": CosineannealingConfig,
     "warmupcosineschedule": WarmupcosinescheduleConfig,
     "wcs": WarmupcosinescheduleConfig,
 }

{gandlf-0.1.4.dev20250707 → gandlf-0.1.5}/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-0.1.4.dev20250707 → gandlf-0.1.5}/GANDLF/models/lightning_module.py

@@ -1713,7 +1713,7 @@ class GandlfLightningModule(pl.LightningModule):
             print(f"Previous latest model loaded from {self.model_paths['latest']}.")
         else:
             raise RuntimeError(
-                "No model found to load. Please train the model before running inference."
+                f"Best/latest models not found to load: {self.model_paths}"
             )
 
     @rank_zero_only

{gandlf-0.1.4.dev20250707 → gandlf-0.1.5}/GANDLF/schedulers/__init__.py

@@ -6,7 +6,8 @@ from .wrap_torch import (
     exp,
     step,
     reduce_on_plateau,
-    cosineannealing,
+    cosineannealingwarmrestarts,
+    cosineannealingLR,
 )
 
 from .wrap_monai import warmupcosineschedule
@@ -24,7 +25,9 @@ global_schedulers_dict = {
     "reduce-on-plateau": reduce_on_plateau,
     "plateau": reduce_on_plateau,
     "reduceonplateau": reduce_on_plateau,
-    "cosineannealing": cosineannealing,
+    "cosineannealing": cosineannealingwarmrestarts,
+    "cosineannealingwarmrestarts": cosineannealingwarmrestarts,
+    "cosineannealinglr": cosineannealingLR,
     "warmupcosineschedule": warmupcosineschedule,
     "wcs": warmupcosineschedule,
 }

{gandlf-0.1.4.dev20250707 → gandlf-0.1.5}/GANDLF/schedulers/wrap_torch.py

@@ -5,6 +5,7 @@ from torch.optim.lr_scheduler import (
     StepLR,
     ReduceLROnPlateau,
     CosineAnnealingWarmRestarts,
+    CosineAnnealingLR,
 )
 import math
 
@@ -169,14 +170,25 @@ def reduce_on_plateau(parameters):
     )
 
 
-def cosineannealing(parameters):
+def cosineannealingwarmrestarts(parameters):
     parameters["scheduler"]["T_0"] = parameters["scheduler"].get("T_0", 5)
     parameters["scheduler"]["T_mult"] = parameters["scheduler"].get("T_mult", 1)
-    parameters["scheduler"]["min_lr"] = parameters["scheduler"].get("min_lr", 0.001)
+    parameters["scheduler"]["eta_min"] = parameters["scheduler"].get("eta_min", 0.001)
 
     return CosineAnnealingWarmRestarts(
         parameters["optimizer_object"],
         T_0=parameters["scheduler"]["T_0"],
         T_mult=parameters["scheduler"]["T_mult"],
-        eta_min=parameters["scheduler"]["min_lr"],
+        eta_min=parameters["scheduler"]["eta_min"],
+    )
+
+
+def cosineannealingLR(parameters):
+    parameters["scheduler"]["T_max"] = parameters["scheduler"].get("T_max", 50)
+    parameters["scheduler"]["eta_min"] = parameters["scheduler"].get("eta_min", 0.001)
+
+    return CosineAnnealingLR(
+        parameters["optimizer_object"],
+        T_max=parameters["scheduler"]["T_max"],
+        eta_min=parameters["scheduler"]["eta_min"],
     )

{gandlf-0.1.4.dev20250707 → gandlf-0.1.5}/GANDLF/utils/modelio.py

@@ -175,7 +175,9 @@ def load_model(
     Returns:
         dict: Model dictionary containing model parameters and metadata.
     """
-    model_dict = torch.load(path, map_location=device)
+    # For PyTorch 2.7+, use weights_only=False to maintain backward compatibility
+    # This prevents the new security warning in PyTorch 2.7+
+    model_dict = torch.load(path, map_location=device, weights_only=False)
 
     # check if the model dictionary is complete
     if full_sanity_check:

{gandlf-0.1.4.dev20250707 → gandlf-0.1.5}/GANDLF/utils/tensor.py

@@ -290,7 +290,8 @@ def get_class_imbalance_weights_classification(
         np.fromiter(penalty_dict.values(), dtype=np.float64).sum()
         + sys.float_info.epsilon
     )
-    for i in range(params["model"]["num_classes"]):
+    # Only normalize penalties for classes that actually exist in penalty_dict
+    for i in penalty_dict.keys():
         penalty_dict[i] /= penalty_sum
 
     # passing None for sampling_weights because there is no clear way to calculate this for classification tasks which do not have a label

gandlf-0.1.5/GANDLF/version.py

@@ -0,0 +1,5 @@
+#!/usr/bin/env python3
+# -*- coding: UTF-8 -*-
+
+# check GaNDLF wiki for versioning and release guidelines: https://github.com/mlcommons/GaNDLF/wiki
+__version__ = "0.1.5"

{gandlf-0.1.4.dev20250707 → gandlf-0.1.5}/GANDLF.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: GANDLF
-Version: 0.1.4.dev20250707
+Version: 0.1.5
 Summary: PyTorch-based framework that handles segmentation/regression/classification using various DL architectures for medical imaging.
 Author: MLCommons
 Author-email: gandlf@mlcommons.org
@@ -18,9 +18,9 @@ Classifier: Topic :: Scientific/Engineering :: Medical Science Apps.
 Requires-Python: >3.9, <3.13
 Description-Content-Type: text/markdown
 License-File: LICENSE
-Requires-Dist: torch==2.5.0
+Requires-Dist: torch==2.7.1
 Requires-Dist: black==23.11.0
-Requires-Dist: lightning==2.4.0
+Requires-Dist: lightning==2.5.2
 Requires-Dist: numpy==1.26.4
 Requires-Dist: scipy
 Requires-Dist: SimpleITK!=2.0.*

{gandlf-0.1.4.dev20250707 → gandlf-0.1.5}/GANDLF.egg-info/SOURCES.txt

@@ -3,7 +3,7 @@ CODE_OF_CONDUCT.md
 CONTRIBUTING.md
 Dockerfile-CPU
 Dockerfile-CUDA11.8
-Dockerfile-CUDA12.1
+Dockerfile-CUDA12.6
 Dockerfile-ROCm
 LICENSE
 MANIFEST.in

{gandlf-0.1.4.dev20250707 → gandlf-0.1.5}/GANDLF.egg-info/requires.txt

@@ -1,6 +1,6 @@
-torch==2.5.0
+torch==2.7.1
 black==23.11.0
-lightning==2.4.0
+lightning==2.5.2
 numpy==1.26.4
 scipy
 SimpleITK!=2.0.*

{gandlf-0.1.4.dev20250707 → gandlf-0.1.5}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: GANDLF
-Version: 0.1.4.dev20250707
+Version: 0.1.5
 Summary: PyTorch-based framework that handles segmentation/regression/classification using various DL architectures for medical imaging.
 Author: MLCommons
 Author-email: gandlf@mlcommons.org
@@ -18,9 +18,9 @@ Classifier: Topic :: Scientific/Engineering :: Medical Science Apps.
 Requires-Python: >3.9, <3.13
 Description-Content-Type: text/markdown
 License-File: LICENSE
-Requires-Dist: torch==2.5.0
+Requires-Dist: torch==2.7.1
 Requires-Dist: black==23.11.0
-Requires-Dist: lightning==2.4.0
+Requires-Dist: lightning==2.5.2
 Requires-Dist: numpy==1.26.4
 Requires-Dist: scipy
 Requires-Dist: SimpleITK!=2.0.*

{gandlf-0.1.4.dev20250707 → gandlf-0.1.5}/setup.py

@@ -38,9 +38,9 @@ toplevel_package_excludes = ["testing*"]
 # specifying version for `black` separately because it is also used to [check for lint](https://github.com/mlcommons/GaNDLF/blob/master/.github/workflows/black.yml)
 black_version = "23.11.0"
 requirements = [
-    "torch==2.5.0",
+    "torch==2.7.1",
     f"black=={black_version}",
-    "lightning==2.4.0",
+    "lightning==2.5.2",
     "numpy==1.26.4",
     "scipy",
     "SimpleITK!=2.0.*",

gandlf-0.1.4.dev20250707/GANDLF/version.py

@@ -1 +0,0 @@
-__version__ = "0.1.4-dev20250707"