GANDLF 0.1.3.dev20250217__py3-none-any.whl → 0.1.3.dev20250219__py3-none-any.whl

GANDLF/cli/main_run.py

@@ -19,6 +19,7 @@ def main_run(
     device: str,
     resume: bool,
     reset: bool,
+    _profile: Optional[bool] = False,
     output_dir: Optional[str] = None,
 ) -> None:
     """
@@ -98,6 +99,7 @@ def main_run(
                 device=device,
                 resume=resume,
                 reset=reset,
+                _profile=_profile,
             )
     else:
         data_full, headers = parseTrainingCSV(file_data_full, train=train_mode)

GANDLF/entrypoints/run.py

@@ -24,6 +24,7 @@ def _run(
     reset_flag: bool,
     resume_flag: bool,
     output_path: Optional[str],
+    _profile: Optional[bool] = False,
 ):
     if model_dir is None and output_path:
         model_dir = output_path
@@ -60,6 +61,7 @@ def _run(
     logging.debug(f"{reset_flag=}")
     logging.debug(f"{resume_flag=}")
     logging.debug(f"{output_path=}")
+    logging.debug(f"{_profile=}")
 
     main_run(
         data_csv=input_data,
@@ -70,6 +72,7 @@ def _run(
         resume=resume_flag,
         reset=reset_flag,
         output_dir=output_path,
+        _profile=_profile,
     )
     print("Finished.")
 
@@ -145,6 +148,12 @@ def _run(
     default=None,
     help="Output file which will contain the logs.",
 )
+@click.option(
+    "--profile",
+    "-pf",
+    is_flag=True,
+    help="Track the run time and memory consumption for each layer",
+)
 @append_copyright_to_help
 def new_way(
     config: str,
@@ -156,6 +165,7 @@ def new_way(
     resume: bool,
     output_path: str,
     raw_input: str,
+    profile: bool,
     log_file: str,
 ):
     """Semantic segmentation, regression, and classification for medical images using Deep Learning."""
@@ -170,6 +180,7 @@ def new_way(
         reset_flag=reset,
         resume_flag=resume,
         output_path=output_path,
+        _profile=profile,
     )
 
 

GANDLF/training_manager.py

@@ -1,6 +1,7 @@
 import pandas as pd
 import os, pickle, shutil
 from pathlib import Path
+from torch.profiler import profile, ProfilerActivity
 
 from GANDLF.compute import training_loop
 from GANDLF.utils import get_dataframe, split_data
@@ -145,6 +146,7 @@ def TrainingManager_split(
     device: str,
     resume: bool,
     reset: bool,
+    _profile: bool,
 ):
     """
     This is the training manager that ties all the training functionality together
@@ -158,6 +160,8 @@ def TrainingManager_split(
         device (str): The device to perform computations on.
         resume (bool): Whether the previous run will be resumed or not.
         reset (bool): Whether the previous run will be reset or not.
+        _profile(bool):Whether the we want the profile activity or not.
+
     """
     currentModelConfigPickle = os.path.join(outputDir, "parameters.pkl")
     currentModelConfigYaml = os.path.join(outputDir, "config.yaml")
@@ -178,11 +182,27 @@ def TrainingManager_split(
         with open(currentModelConfigYaml, "w") as handle:
             yaml.dump(parameters, handle, default_flow_style=False)
 
-    training_loop(
-        training_data=dataframe_train,
-        validation_data=dataframe_validation,
-        output_dir=outputDir,
-        device=device,
-        params=parameters,
-        testing_data=dataframe_testing,
-    )
+    if _profile:
+        with profile(
+            activities=[ProfilerActivity.CPU, ProfilerActivity.CUDA],
+            profile_memory=True,
+            record_shapes=True,
+        ) as prof:
+            training_loop(
+                training_data=dataframe_train,
+                validation_data=dataframe_validation,
+                output_dir=outputDir,
+                device=device,
+                params=parameters,
+                testing_data=dataframe_testing,
+            )
+        print(prof.key_averages().table(sort_by="cpu_time_total", row_limit=10))
+    else:
+        training_loop(
+            training_data=dataframe_train,
+            validation_data=dataframe_validation,
+            output_dir=outputDir,
+            device=device,
+            params=parameters,
+            testing_data=dataframe_testing,
+        )

GANDLF/version.py

@@ -1 +1 @@
-__version__ = "0.1.3-dev20250217"
+__version__ = "0.1.3-dev20250219"

{GANDLF-0.1.3.dev20250217.dist-info → GANDLF-0.1.3.dev20250219.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.2
 Name: GANDLF
-Version: 0.1.3.dev20250217
+Version: 0.1.3.dev20250219
 Summary: PyTorch-based framework that handles segmentation/regression/classification using various DL architectures for medical imaging.
 Author: MLCommons
 Author-email: gandlf@mlcommons.org

{GANDLF-0.1.3.dev20250217.dist-info → GANDLF-0.1.3.dev20250219.dist-info}/RECORD

@@ -4,8 +4,8 @@ GANDLF/inference_manager.py,sha256=ncT8HFo46IIpD_mw8i2mmOnMkhvPrWJITfiNQ1uBIco,4
 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=FXvQ4p3DELzR2MtfG1ANsOL1X9Oo99X8rm4npJ7xLlo,7302
-GANDLF/version.py,sha256=wYhOU5yEFXHDcFkcrP79NOpeCMjXY19aK4CZPDAaeXs,34
+GANDLF/training_manager.py,sha256=t7zcOVdgu5AhOhY544joxfTNR00ixnXQfQ4GWLk2o6Y,8058
+GANDLF/version.py,sha256=hWsD3CO6U-PDppam4lwKhmncOJ1h6Thk_sCTg11NTfQ,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
@@ -14,7 +14,7 @@ GANDLF/cli/data_split_saver.py,sha256=72ygy9s3INt2NFAfSW4j9dxxmuuvfzfBTF0Hwh0nYB
 GANDLF/cli/deploy.py,sha256=55mnId66_-KOWROwPj9OEePENWm58BYFBvn_kWOdil8,15153
 GANDLF/cli/generate_metrics.py,sha256=t9Ecr8Vva03JBX_Og70QRnvJtmSXQg1q8YxlyoC_9DY,18981
 GANDLF/cli/huggingface_hub_handler.py,sha256=vGQYwDiT3Y8yk_xLNkB8DgW1rYpEcwYp0TCdCO5oWTs,4631
-GANDLF/cli/main_run.py,sha256=e4QMKti7AEaKI4NU4dlO64weS7UgwVXCanbDHdV2oXk,4415
+GANDLF/cli/main_run.py,sha256=Du14psJsqS2wUe8XkfmdlQQutlNO7RYqoK-VNOslA0I,4488
 GANDLF/cli/patch_extraction.py,sha256=30RpBfjpwE9GLRSSD7JRqwoHngESQL0eOt09n_5r18Q,3555
 GANDLF/cli/post_training_model_optimization.py,sha256=cuPqUGrFcTIfhT67lAxpnywt8t9yrlqyHUl6wjr18qo,2111
 GANDLF/cli/preprocess_and_save.py,sha256=pvOI5oaM-GLDF2TdK9F9j_KMyvypNh155Hut_AvZphg,8814
@@ -71,7 +71,7 @@ GANDLF/entrypoints/optimize_model.py,sha256=w3A1n2jvH5s2bp9m3E3rUX1wd1J4Tt_zfOD3
 GANDLF/entrypoints/patch_miner.py,sha256=StrdmbAiECPpsN1AoZo75Mc1y-UAmKFyNfFmJrnHOg4,3095
 GANDLF/entrypoints/preprocess.py,sha256=-2XbLmRkQossOpZCU0HvvWWuKbefq6OE_Bf2HeHoYNk,5571
 GANDLF/entrypoints/recover_config.py,sha256=3eyYbQJMPcgZz6NDZFpJadbgUdnMF6chudRKqmBaJ4E,3712
-GANDLF/entrypoints/run.py,sha256=ChOpM5Cx1R2WbFo5zW3q0BuFpNXhTa7EXMdHAzcFtSk,9294
+GANDLF/entrypoints/run.py,sha256=6A3OQw7DEeuJ_tPYnz4QovnI2sem09taAsq82gPZ6b8,9570
 GANDLF/entrypoints/split_csv.py,sha256=TZMpYjzPXD8koOdB7kokJYStQcfMzQD0z_Nysxvuxwo,3662
 GANDLF/entrypoints/subcommands.py,sha256=LyYgN5bOAF5K6laGWChe_CBi02RmPhIS7nYpiojOC0w,1768
 GANDLF/entrypoints/verify_install.py,sha256=E204smRPuH7Fv4rBPkjVXmxMPB_Tzd2lTAdVxp2hNhY,1370
@@ -159,9 +159,9 @@ GANDLF/utils/modelio.py,sha256=tWeTwVTvQy5I5hydxNZz4N8xEU3lHMayMa9gx5-Vr7Q,8016
 GANDLF/utils/parameter_processing.py,sha256=DA7ZEsizWWLJZnCxBnDNh1NyA-bw5oirOvodiZZWbIk,5675
 GANDLF/utils/tensor.py,sha256=AOwNTQfw9mnsomGwOF2Q_rdDS1WANlIatB0hhZN0gSg,21504
 GANDLF/utils/write_parse.py,sha256=bTBNxIaIGgjusq1mlHA8hioKZ6XmEJWFhfZWAQz2a9I,9197
-GANDLF-0.1.3.dev20250217.dist-info/LICENSE,sha256=GlZPAfA4eckod8IVayhBXkqCpESXf6cc9BGli_Jwims,11357
-GANDLF-0.1.3.dev20250217.dist-info/METADATA,sha256=fw4EmhX23h0XptxJLiYl2l4Vi5jld3KvHTdDAVEi9KA,9726
-GANDLF-0.1.3.dev20250217.dist-info/WHEEL,sha256=In9FTNxeP60KnTkGw7wk6mJPYd_dQSjEZmXdBdMCI-8,91
-GANDLF-0.1.3.dev20250217.dist-info/entry_points.txt,sha256=agwocNI7Upi-sFDe1rMl71dGN8YhCBB7WJmtBHRF4jg,902
-GANDLF-0.1.3.dev20250217.dist-info/top_level.txt,sha256=i5D9wEbQhl085_9Lx2m7x-9Zu6nlx1tjYYbuSihG09E,7
-GANDLF-0.1.3.dev20250217.dist-info/RECORD,,
+GANDLF-0.1.3.dev20250219.dist-info/LICENSE,sha256=GlZPAfA4eckod8IVayhBXkqCpESXf6cc9BGli_Jwims,11357
+GANDLF-0.1.3.dev20250219.dist-info/METADATA,sha256=Sqleri1tKJa6abRvtCEQvMZYR07nD3qPP0EGbvObO14,9726
+GANDLF-0.1.3.dev20250219.dist-info/WHEEL,sha256=In9FTNxeP60KnTkGw7wk6mJPYd_dQSjEZmXdBdMCI-8,91
+GANDLF-0.1.3.dev20250219.dist-info/entry_points.txt,sha256=agwocNI7Upi-sFDe1rMl71dGN8YhCBB7WJmtBHRF4jg,902
+GANDLF-0.1.3.dev20250219.dist-info/top_level.txt,sha256=i5D9wEbQhl085_9Lx2m7x-9Zu6nlx1tjYYbuSihG09E,7
+GANDLF-0.1.3.dev20250219.dist-info/RECORD,,