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Merge branch 'master' into hf_cli4
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sarthakpati authored Aug 20, 2024
2 parents f8c3e6a + 41a0705 commit 4651320
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Showing 18 changed files with 141 additions and 13 deletions.
1 change: 1 addition & 0 deletions .github/PULL_REQUEST_TEMPLATE.md
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Expand Up @@ -23,3 +23,4 @@ Note that if a box is left unchecked, PR merges will take longer than usual.
- [ ] [Usage documentation](https://github.com/mlcommons/GaNDLF/blob/master/docs) has been updated, if appropriate.
- [ ] Tests added or modified to [cover the changes](https://app.codecov.io/gh/mlcommons/GaNDLF); if coverage is reduced, please give explanation.
- [ ] If customized dependency installation is required (i.e., a separate `pip install` step is needed for PR to be functional), please ensure it is reflected in all the files that control the CI, namely: [python-test.yml](https://github.com/mlcommons/GaNDLF/blob/master/.github/workflows/python-test.yml), and all docker files [[1](https://github.com/mlcommons/GaNDLF/blob/master/Dockerfile-CPU),[2](https://github.com/mlcommons/GaNDLF/blob/devcontainer_build_fix/Dockerfile-CUDA11.6),[3](https://github.com/mlcommons/GaNDLF/blob/master/Dockerfile-ROCm)].
- [ ] The `logging` library is being used and no `print` statements are left.
9 changes: 8 additions & 1 deletion GANDLF/entrypoints/anonymizer.py
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Expand Up @@ -62,9 +62,16 @@ 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."""
logger_setup(log_file)
_anonymize_images(input_dir, output_file, config, modality)


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2 changes: 1 addition & 1 deletion GANDLF/entrypoints/cli_tool.py
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Expand Up @@ -12,7 +12,7 @@
def gandlf(ctx):
"""GANDLF command-line tool."""
ctx.ensure_object(dict)
logger_setup()
# logger_setup()


# registers subcommands: `gandlf anonymizer`, `gandlf run`, etc.
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9 changes: 8 additions & 1 deletion GANDLF/entrypoints/collect_stats.py
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Expand Up @@ -191,9 +191,16 @@ def _collect_stats(model_dir: str, output_dir: str):
required=True,
help="Output directory to save stats and plot",
)
@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: str, output_dir: str):
def new_way(model_dir: str, output_dir: str, log_file: str):
"""Collect statistics from different testing/validation combinations from output directory."""
logger_setup(log_file)
_collect_stats(model_dir=model_dir, output_dir=output_dir)


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10 changes: 9 additions & 1 deletion GANDLF/entrypoints/config_generator.py
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Expand Up @@ -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."""

logger_setup(log_file)
_generate_config(config, strategy, output)


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9 changes: 9 additions & 0 deletions GANDLF/entrypoints/construct_csv.py
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Expand Up @@ -90,15 +90,24 @@ 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."""

logger_setup(log_file)
_construct_csv(
input_dir=input_dir,
channels_id=channels_id,
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10 changes: 9 additions & 1 deletion GANDLF/entrypoints/debug_info.py
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Expand Up @@ -39,9 +39,17 @@ def _debug_info(verbose: bool):
is_flag=True,
help="If passed, prints all packages installed as well",
)
@click.option(
"--log-file",
type=click.Path(),
default=None,
help="Output file which will contain the logs.",
)
@append_copyright_to_help
def new_way(verbose: bool):
def new_way(verbose: bool, log_file):
"""Displays detailed info about system environment: library versions, settings, etc."""

logger_setup(log_file)
_debug_info(verbose=verbose)


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8 changes: 8 additions & 0 deletions GANDLF/entrypoints/deploy.py
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Expand Up @@ -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],
Expand All @@ -136,8 +142,10 @@ def new_way(
output_dir: str,
requires_gpu: bool,
entrypoint: Optional[str],
log_file: str,
):
"""Generate frozen/deployable versions of trained GaNDLF models."""
logger_setup(log_file)
_deploy(
model=model,
config=config,
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9 changes: 9 additions & 0 deletions GANDLF/entrypoints/generate_metrics.py
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Expand Up @@ -53,6 +53,12 @@ def _generate_metrics(
default=-1,
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(
"--log-file",
type=click.Path(),
default=None,
help="Output file which will contain the logs.",
)
@click.option("--raw-input", hidden=True)
@append_copyright_to_help
def new_way(
Expand All @@ -61,8 +67,11 @@ def new_way(
output_file: Optional[str],
missing_prediction: int,
raw_input: str,
log_file: str,
):
"""Metrics calculator."""

logger_setup(log_file)
_generate_metrics(
input_data=input_data,
config=config,
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13 changes: 12 additions & 1 deletion GANDLF/entrypoints/optimize_model.py
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Expand Up @@ -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."""

logger_setup(log_file)
_optimize_model(model=model, config=config, output_path=output_path)


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10 changes: 9 additions & 1 deletion GANDLF/entrypoints/patch_miner.py
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Expand Up @@ -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, log_file: str, config: Optional[str]):
"""Construct patches from whole slide image(s)."""

logger_setup(log_file)
_mine_patches(input_path=input_csv, output_dir=output_dir, config=config)


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9 changes: 9 additions & 0 deletions GANDLF/entrypoints/preprocess.py
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Expand Up @@ -82,6 +82,12 @@ 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,
Expand All @@ -90,8 +96,11 @@ 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."""

logger_setup(log_file)
_preprocess(
config=config,
input_data=input_data,
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10 changes: 9 additions & 1 deletion GANDLF/entrypoints/recover_config.py
Original file line number Diff line number Diff line change
Expand Up @@ -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."""

logger_setup(log_file)
_recover_config(model_dir=model_dir, mlcube=mlcube, output_file=output_file)


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9 changes: 9 additions & 0 deletions GANDLF/entrypoints/run.py
Original file line number Diff line number Diff line change
Expand Up @@ -141,6 +141,12 @@ 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,
Expand All @@ -152,8 +158,11 @@ 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."""

logger_setup(log_file)
_run(
config=config,
input_data=input_data,
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10 changes: 9 additions & 1 deletion GANDLF/entrypoints/split_csv.py
Original file line number Diff line number Diff line change
Expand Up @@ -49,9 +49,17 @@ 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, log_file: str, config: Optional[str]):
"""Split the data into training, validation, and testing sets and save them as csvs in the output directory."""

logger_setup(log_file)
_split_csv(input_csv, output_dir, config)


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9 changes: 8 additions & 1 deletion GANDLF/entrypoints/verify_install.py
Original file line number Diff line number Diff line change
Expand Up @@ -23,9 +23,16 @@ 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."""
logger_setup(log_file)
_verify_install()


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2 changes: 1 addition & 1 deletion GANDLF/utils/gandlf_logging.py
Original file line number Diff line number Diff line change
Expand Up @@ -40,9 +40,9 @@ def logger_setup(log_file=None, config_path="logging_config.yaml") -> None:
log_tmp_file = log_file
if log_file is None: # create tmp file
log_tmp_file = _create_tmp_log_file()
logging.info(f"The logs are saved in {log_tmp_file}")
_create_log_file(log_tmp_file)
_configure_logging_with_logfile(log_tmp_file, config_path)
logging.info(f"The logs are saved in {log_tmp_file}")


class InfoOnlyFilter(logging.Filter):
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15 changes: 13 additions & 2 deletions docs/extending.md
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Expand Up @@ -137,6 +137,16 @@ bash
### Use loggers instead of print
We use the native `logging` [library](https://docs.python.org/3/library/logging.html) for logs management. This gets automatically configured when GaNDLF gets launched. So, if you are extending the code, please use loggers instead of prints.

Here is an example how `root logger` can be used
```
def my_new_cool_function(df: pd.DataFrame):
logging.debug("Message for debug file only")
logging.info("Hi GaNDLF user, I greet you in the CLI output")
logging.error(f"A detailed message about any error if needed. Exception: {str(e)}, params: {params}, df shape: {df.shape}")
# do NOT use normal print statements
# print("Hi GaNDLF user!")
```

Here is an example how logger can be used:

```
Expand All @@ -148,16 +158,17 @@ def my_new_cool_function(df: pd.DataFrame):
# print("Hi GaNDLF user!") # don't use prints please.
```


### What and where is logged

GaNDLF logs are splitted into multiple parts:
- CLI output: only `info` messages are shown here
- debug file: all messages are shown
- stderr: display `warning`, `error`, or `critical` messages

By default, the logs are flushed to console.
By default, the logs are saved in the `/tmp/.gandlf` dir.
The logs are **saved** in the path that is defined by the '--log-file' parameter in the CLI commands.
If the path is not provided or an error is raised, the logs will be flushed to console.




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