add --log-file par to cli commands

GANDLF/entrypoints/anonymizer.py

@@ -12,7 +12,7 @@
 from GANDLF.anonymize import run_anonymizer
 from GANDLF.cli import copyrightMessage
 from GANDLF.entrypoints import append_copyright_to_help
-from GANDLF.utils.gandlf_logging import logger_setup
+from GANDLF.utils import logger_setup
 
 
 def _anonymize_images(
@@ -63,9 +63,17 @@ def _anonymize_images(
     type=click.Path(),
     help="Output directory or file which will contain the image(s) after anonymization.",
 )
+@click.option(
+    "--log-file",
+    type=click.Path(),
+    default=None,
+    help="Output file which will contain the logs.",
+)
 @append_copyright_to_help
-def new_way(input_dir, config, modality, output_file):
+def new_way(input_dir, config, modality, output_file, log_file):
     """Anonymize images/scans in the data directory."""
+    if log_file is not None:
+        logger_setup(log_file)
     _anonymize_images(input_dir, output_file, config, modality)
 
 

GANDLF/entrypoints/config_generator.py

@@ -34,9 +34,17 @@ def _generate_config(config: str, strategy: str, output: str):
     type=click.Path(file_okay=False, dir_okay=True),
     help="Path to output directory.",
 )
+@click.option(
+    "--log-file",
+    type=click.Path(),
+    default=None,
+    help="Output file which will contain the logs.",
+)
 @append_copyright_to_help
-def new_way(config, strategy, output):
+def new_way(config, strategy, output, log_file):
     """Generate multiple GaNDLF configurations based on a single baseline GaNDLF for experimentation."""
+    if log_file is not None:
+        logger_setup(log_file)
     _generate_config(config, strategy, output)
 
 

GANDLF/entrypoints/construct_csv.py

@@ -91,15 +91,24 @@ def _construct_csv(
     help="If True, paths in the output data CSV will always be relative to the location"
     " of the output data CSV itself.",
 )
+@click.option(
+    "--log-file",
+    type=click.Path(),
+    default=None,
+    help="Output file which will contain the logs.",
+)
 @append_copyright_to_help
 def new_way(
     input_dir: str,
     channels_id: str,
     label_id: Optional[str],
     output_file: str,
     relativize_paths: bool,
+    log_file: str,
 ):
     """Generate training/inference CSV from data directory."""
+    if log_file is not None:
+        logger_setup(log_file)
     _construct_csv(
         input_dir=input_dir,
         channels_id=channels_id,

GANDLF/entrypoints/debug_info.py

@@ -25,9 +25,17 @@ def _debug_info():
 
 
 @click.command()
+@click.option(
+    "--log-file",
+    type=click.Path(),
+    default=None,
+    help="Output file which will contain the logs.",
+)
 @append_copyright_to_help
-def new_way():
+def new_way(log_file):
     """Displays detailed info about system environment: library versions, settings, etc."""
+    if log_file is not None:
+        logger_setup(log_file)
     _debug_info()
 
 

GANDLF/entrypoints/deploy.py

@@ -126,6 +126,12 @@ def _deploy(
     help="An optional custom python entrypoint script to use instead of the default specified in mlcube.yaml."
     " (Only for inference and metrics)",
 )
+@click.option(
+    "--log-file",
+    type=click.Path(),
+    default=None,
+    help="Output file which will contain the logs.",
+)
 @append_copyright_to_help
 def new_way(
     model: Optional[str],
@@ -136,8 +142,11 @@ def new_way(
     output_dir: str,
     requires_gpu: bool,
     entrypoint: Optional[str],
+    log_file: str,
 ):
     """Generate frozen/deployable versions of trained GaNDLF models."""
+    if log_file is not None:
+        logger_setup(log_file)
     _deploy(
         model=model,
         config=config,

GANDLF/entrypoints/generate_metrics.py

@@ -54,15 +54,24 @@ def _generate_metrics(
     help="The value to use for missing predictions as penalty; if `-1`, this does not get added. This is only used in the case where the targets and predictions are passed independently.",
 )
 @click.option("--raw-input", hidden=True)
+@click.option(
+    "--log-file",
+    type=click.Path(),
+    default=None,
+    help="Output file which will contain the logs.",
+)
 @append_copyright_to_help
 def new_way(
     config: str,
     input_data: str,
     output_file: Optional[str],
     missing_prediction: int,
     raw_input: str,
+    log_file: str,
 ):
     """Metrics calculator."""
+    if log_file is not None:
+        logger_setup(log_file)
     _generate_metrics(
         input_data=input_data,
         config=config,

GANDLF/entrypoints/optimize_model.py

@@ -46,11 +46,22 @@ def _optimize_model(
     required=False,
     type=click.Path(exists=True, file_okay=True, dir_okay=False),
 )
+@click.option(
+    "--log-file",
+    type=click.Path(),
+    default=None,
+    help="Output file which will contain the logs.",
+)
 @append_copyright_to_help
 def new_way(
-    model: str, config: Optional[str] = None, output_path: Optional[str] = None
+    model: str,
+    log_file: str,
+    config: Optional[str] = None,
+    output_path: Optional[str] = None,
 ):
     """Generate optimized versions of trained GaNDLF models."""
+    if log_file is not None:
+        logger_setup(log_file)
     _optimize_model(model=model, config=config, output_path=output_path)
 
 

GANDLF/entrypoints/patch_miner.py

@@ -42,9 +42,17 @@ def _mine_patches(input_path: str, output_dir: str, config: Optional[str]):
     help="config (in YAML) for running the patch miner. Needs 'scale' and 'patch_size' to be defined, "
     "otherwise defaults to 16 and (256, 256), respectively.",
 )
+@click.option(
+    "--log-file",
+    type=click.Path(),
+    default=None,
+    help="Output file which will contain the logs.",
+)
 @append_copyright_to_help
-def new_way(input_csv: str, output_dir: str, config: Optional[str]):
+def new_way(input_csv: str, output_dir: str, config: Optional[str], log_file):
     """Construct patches from whole slide image(s)."""
+    if log_file is not None:
+        logger_setup(log_file)
     _mine_patches(input_path=input_csv, output_dir=output_dir, config=config)
 
 

GANDLF/entrypoints/preprocess.py

@@ -81,6 +81,12 @@ def _preprocess(
     is_flag=True,
     help="If passed, applies zero cropping during output creation.",
 )
+@click.option(
+    "--log-file",
+    type=click.Path(),
+    default=None,
+    help="Output file which will contain the logs.",
+)
 @append_copyright_to_help
 def new_way(
     config: str,
@@ -89,8 +95,11 @@ def new_way(
     label_pad: str,
     apply_augs: bool,
     crop_zero: bool,
+    log_file: str,
 ):
     """Generate training/inference data which are preprocessed to reduce resource footprint during computation."""
+    if log_file is not None:
+        logger_setup(log_file)
     _preprocess(
         config=config,
         input_data=input_data,

GANDLF/entrypoints/recover_config.py

@@ -47,10 +47,18 @@ def _recover_config(model_dir: Optional[str], mlcube: bool, output_file: str):
     type=click.Path(file_okay=True, dir_okay=False),
     help="Path to an output file where the config will be written.",
 )
+@click.option(
+    "--log-file",
+    type=click.Path(),
+    default=None,
+    help="Output file which will contain the logs.",
+)
 @append_copyright_to_help
-def new_way(model_dir, mlcube, output_file):
+def new_way(model_dir, mlcube, output_file, log_file):
     """Recovers a config file from a GaNDLF model. If used from within a deployed GaNDLF MLCube,
     attempts to extract the config from the embedded model."""
+    if log_file is not None:
+        logger_setup(log_file)
     _recover_config(model_dir=model_dir, mlcube=mlcube, output_file=output_file)
 
 

GANDLF/entrypoints/run.py

@@ -146,6 +146,12 @@ def _run(
     help="Location to save the output of the inference session. Not used for training.",
 )
 @click.option("--raw-input", hidden=True)
+@click.option(
+    "--log-file",
+    type=click.Path(),
+    default=None,
+    help="Output file which will contain the logs.",
+)
 @append_copyright_to_help
 def new_way(
     config: str,
@@ -157,8 +163,11 @@ def new_way(
     resume: bool,
     output_path: str,
     raw_input: str,
+    log_file: str,
 ):
     """Semantic segmentation, regression, and classification for medical images using Deep Learning."""
+    if log_file is not None:
+        logger_setup(log_file)
     _run(
         config=config,
         input_data=input_data,

GANDLF/entrypoints/split_csv.py

@@ -50,9 +50,17 @@ def _split_csv(input_csv: str, output_dir: str, config_path: Optional[str]):
     help="The GaNDLF config (in YAML) with the `nested_training` key specified to the folds needed.",
     type=click.Path(exists=True, file_okay=True, dir_okay=False),
 )
+@click.option(
+    "--log-file",
+    type=click.Path(),
+    default=None,
+    help="Output file which will contain the logs.",
+)
 @append_copyright_to_help
-def new_way(input_csv: str, output_dir: str, config: Optional[str]):
+def new_way(input_csv: str, output_dir: str, config: Optional[str], log_file: str):
     """Split the data into training, validation, and testing sets and save them as csvs in the output directory."""
+    if log_file is not None:
+        logger_setup(log_file)
     _split_csv(input_csv, output_dir, config)
 
 

GANDLF/entrypoints/verify_install.py

@@ -30,9 +30,17 @@ def _verify_install():
 
 
 @click.command()
+@click.option(
+    "--log-file",
+    type=click.Path(),
+    default=None,
+    help="Output file which will contain the logs.",
+)
 @append_copyright_to_help
-def new_way():
+def new_way(log_file):
     """Verify GaNDLF installation."""
+    if log_file is not None:
+        logger_setup(log_file)
     _verify_install()