GANDLF 0.1.4__py3-none-any.whl → 0.1.6.dev20251109__py3-none-any.whl

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/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/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/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/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/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/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/version.py

@@ -1,5 +1 @@
-#!/usr/bin/env python3
-# -*- coding: UTF-8 -*-
-
-# check GaNDLF wiki for versioning and release guidelines: https://github.com/mlcommons/GaNDLF/wiki
-__version__ = "0.1.4"
+__version__ = "0.1.6-dev20251109"

{gandlf-0.1.4.dist-info → gandlf-0.1.6.dev20251109.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: GANDLF
-Version: 0.1.4
+Version: 0.1.6.dev20251109
 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.dist-info → gandlf-0.1.6.dev20251109.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=M1zbN1EmLVtrLi5zYCd_nLaggSzKXNthBUWrc42uHo0,170
+GANDLF/version.py,sha256=T_UNbVsixOTPH9NDpzIMB22zTro3LXJA38K5KwO3KJI,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
@@ -27,7 +27,7 @@ GANDLF/compute/loss_and_metric.py,sha256=vKta--M_2cvsqDfeGLFcE5UZNyfHYkOyjqxlc3x
 GANDLF/compute/step.py,sha256=di8zk8EgRKu5y0-Aq0aBTgrKo30SWM8wdLsnVeDaZqU,4765
 GANDLF/compute/training_loop.py,sha256=TI0aDov1K2OjbmB1LxDVtuZzbB99_wIiTu22tsH4GS0,24871
 GANDLF/configuration/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-GANDLF/configuration/default_config.py,sha256=utmsmxTzyNSOz_E7SNQCxXMjbQ3H9RII-e9iBFALrb8,3069
+GANDLF/configuration/default_config.py,sha256=S2h1SI2gHJbKdYtfc8fQBsB1dMIfLmYLRIcbus7p3GE,3069
 GANDLF/configuration/differential_privacy_config.py,sha256=nvLoBt11VTD_pGsQD8cmmgv-XMVZR5s0I-dkKrLhRXE,584
 GANDLF/configuration/exclude_parameters.py,sha256=rg754BoaWBMmdKVgrmFSmtsw9uw7V9Yi-VXcXPp1edY,46
 GANDLF/configuration/model_config.py,sha256=CFlTU7ypX5FzPDj-UMDDQXThHkgLeqvPEtPy79dZwdU,3313
@@ -37,7 +37,7 @@ GANDLF/configuration/parameters_config.py,sha256=p31KVVwWVjOSifWoXPuUKynzyeeUoTS
 GANDLF/configuration/patch_sampler_config.py,sha256=1CFjhB7Idfdw0ckXlyVwK-dDBKYlcuXrDi-uRdJjPA4,357
 GANDLF/configuration/post_processing_config.py,sha256=Wx1YYuKnuxP0bgN5j9rQWUk3cD4-XJ_hE3cB-7xvTpg,349
 GANDLF/configuration/pre_processing_config.py,sha256=qjaSzdsDn3M5W5j4eUN21GknTTPSFlR8b9_69dbl-m8,3322
-GANDLF/configuration/scheduler_config.py,sha256=OKhXBrDKAM1YFROnrDy7H_V5Zs2GRkUWzaVkWTVfEu0,3308
+GANDLF/configuration/scheduler_config.py,sha256=QLuXbgpdeJrDmW5sgku2f1Qn4Q0AQtCSTeK6JQBjBno,3414
 GANDLF/configuration/user_defined_config.py,sha256=_-OejzxteociR4NM7xrtOKfWBfUmjRvNr_SMmdcZCYc,5179
 GANDLF/configuration/utils.py,sha256=p0bzaOKRvGi-beB99dBfkfl4rTDJ1F9xar78YJbii4U,3247
 GANDLF/configuration/validators.py,sha256=Mz0SmVQhF2cTyUs5Otxn_7T6L0MoaPRHPoOYimks96o,19875
@@ -125,7 +125,7 @@ GANDLF/models/imagenet_unet.py,sha256=vTAuckJ0Bs9nfe2G0nKISqgxWArIYdM4poGpTk56QY
 GANDLF/models/imagenet_vgg.py,sha256=FrMNLIxCtaMHWZ9JO7pWtoXTT1f8eVDuREx9108Aw2g,10367
 GANDLF/models/light_unet.py,sha256=jzcTHH7kv_ikriYxIe7fbQJkmwOQZzePW4KLCW2FGWM,6645
 GANDLF/models/light_unet_multilayer.py,sha256=xrKy--lljbCX7U2eYjpFZA69C6qlHmA5W-fEckPBll4,4534
-GANDLF/models/lightning_module.py,sha256=kZhlCSD_JLJFFqVRGUEz1CgvENWHqVgc418_fvbQdkk,83347
+GANDLF/models/lightning_module.py,sha256=QLBL-QKp5DADHn8PpGjAJO4l3J7M4WI95kymPFvfGOk,83332
 GANDLF/models/modelBase.py,sha256=NFmKcEylNchm0LVqwRoD_iIMFj36IsaKwVCPJPLux3g,5752
 GANDLF/models/resnet.py,sha256=0PB7sGSLHUq2F6tyHYqxepmU1eBccSwCzBrD7Qmc280,16987
 GANDLF/models/sdnet.py,sha256=uhHvOHRTAx4ANxv2lKXfBn6Bg4Broqzb77qekVjXeFI,14528
@@ -166,9 +166,9 @@ GANDLF/privacy/opacus/config_parsing.py,sha256=1x9XTrRA-zVJI8dieVDECL-RWd4SlOsk6
 GANDLF/privacy/opacus/model_handling.py,sha256=LSFo_TtCHwFhThJ9i7agWFjxVx1aABHC3bIUVLReFPs,6437
 GANDLF/privacy/opacus/opacus_anonymization_manager.py,sha256=8VzMtezagKlkaI6x-UL7NPiXIIFQ014Iw9atsCy_46w,9549
 GANDLF/privacy/opacus/training_utils.py,sha256=ejXUIhLNjRzTebF-7uCYUluK7jyINDOpLe2yhOKacJg,3683
-GANDLF/schedulers/__init__.py,sha256=jMTea7kX7zawFrtjVDKHDLIfBgt7GD-G2z9_eKjI1_A,1320
+GANDLF/schedulers/__init__.py,sha256=2Uni-hJKqzoRoo7B_4hhbGW1nvudhGBZc6EPBVYJnn8,1475
 GANDLF/schedulers/wrap_monai.py,sha256=_kP3ArUIFK3x3u0nQV8Gi2oPruMIGGTSZxa4bSygGPs,400
-GANDLF/schedulers/wrap_torch.py,sha256=NuCAmYMKgYeFzO1PEiHfnFaHpzuQU0DsK5NOi-gVxOo,6746
+GANDLF/schedulers/wrap_torch.py,sha256=S0Aoo3vHEYlumgngANKGlM86fE3W15ReaWxmb4KthD8,7165
 GANDLF/utils/__init__.py,sha256=F74QIQ6dZL8cOIsZkU-VfDdcHewUW959GXRvDfphGCk,1725
 GANDLF/utils/data_splitter.py,sha256=IBVsLYo4y28G6LedbLPYWyiAUiaLxD4wWZD4EZC2D6I,10174
 GANDLF/utils/exceptions.py,sha256=SmEGzCbc5mXxjylmA9XE4PXZdmkkfOjrEh473cWTAvA,100
@@ -177,14 +177,14 @@ GANDLF/utils/generic.py,sha256=NyJgaeCdryBlHMziPPLmWtIk450u042NWQgs_qh7knw,11744
 GANDLF/utils/handle_collisions.py,sha256=UFgfrddQqeipOdpKk0Mo-wwJ-TYTESNZyXzEyQeaLdI,3082
 GANDLF/utils/imaging.py,sha256=_qCgvIXHZW_k_IUYLU95G5L5yoozxCRCYxo65TI-95U,15983
 GANDLF/utils/modelbase.py,sha256=MJ1ufJGQ-ZgfYWTg7o4f-Iz78d7SYiyxN7MT8bnNDaw,950
-GANDLF/utils/modelio.py,sha256=9koLUn3wCODtNOYA2abtxkqxfLgEG07Bhh-NYIrtWOc,8084
+GANDLF/utils/modelio.py,sha256=xmzAn7P0kqJd_Gcf17nMcV784poW2qpi3AY483Tk2ko,8247
 GANDLF/utils/parameter_processing.py,sha256=DA7ZEsizWWLJZnCxBnDNh1NyA-bw5oirOvodiZZWbIk,5675
 GANDLF/utils/pred_target_processors.py,sha256=aatXJ6jdJaNAHa_tPzHfC1gOQrPYJLtg-cYeUFvkM_s,2701
-GANDLF/utils/tensor.py,sha256=AOwNTQfw9mnsomGwOF2Q_rdDS1WANlIatB0hhZN0gSg,21504
+GANDLF/utils/tensor.py,sha256=SbcTyWs_qaFTnxpFlJHiq9xNKesDu7t0YZsm9eUnDSk,21565
 GANDLF/utils/write_parse.py,sha256=HROxskhet-uIdUJmz16z_7p9r0mf8hWsqQFygwZ8ap0,9202
-gandlf-0.1.4.dist-info/licenses/LICENSE,sha256=GlZPAfA4eckod8IVayhBXkqCpESXf6cc9BGli_Jwims,11357
-gandlf-0.1.4.dist-info/METADATA,sha256=qvx9jEiSPd2XFxeU3aLHp7vVrxDqtmtxG2MDkNaPZ3E,9892
-gandlf-0.1.4.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
-gandlf-0.1.4.dist-info/entry_points.txt,sha256=agwocNI7Upi-sFDe1rMl71dGN8YhCBB7WJmtBHRF4jg,902
-gandlf-0.1.4.dist-info/top_level.txt,sha256=i5D9wEbQhl085_9Lx2m7x-9Zu6nlx1tjYYbuSihG09E,7
-gandlf-0.1.4.dist-info/RECORD,,
+gandlf-0.1.6.dev20251109.dist-info/licenses/LICENSE,sha256=GlZPAfA4eckod8IVayhBXkqCpESXf6cc9BGli_Jwims,11357
+gandlf-0.1.6.dev20251109.dist-info/METADATA,sha256=OwoTI2uOcWtOPKnPAMJcAcJkq7QxpplOvVT0-nEPnpI,9904
+gandlf-0.1.6.dev20251109.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
+gandlf-0.1.6.dev20251109.dist-info/entry_points.txt,sha256=agwocNI7Upi-sFDe1rMl71dGN8YhCBB7WJmtBHRF4jg,902
+gandlf-0.1.6.dev20251109.dist-info/top_level.txt,sha256=i5D9wEbQhl085_9Lx2m7x-9Zu6nlx1tjYYbuSihG09E,7
+gandlf-0.1.6.dev20251109.dist-info/RECORD,,