commands

These functions are used in the bioimageio command line interface defined in bioimageio.core.cli.

Functions:

Name	Description
package	Save a resource's metadata with its associated files.
test	Test a bioimageio resource.
validate_format	DEPRECATED; Access the existing validation_summary attribute instead.

Attributes:

Name	Type	Description
WeightFormatArgAll
WeightFormatArgAny

WeightFormatArgAll module-attribute

WeightFormatArgAll = Literal['keras_hdf5', 'onnx', 'pytorch_state_dict', 'tensorflow_saved_model_bundle', 'torchscript', 'all']

Used by:

• API Reference  commands
  •  package
  •  test

WeightFormatArgAny module-attribute

WeightFormatArgAny = Literal['keras_hdf5', 'onnx', 'pytorch_state_dict', 'tensorflow_saved_model_bundle', 'torchscript', 'any']

package

package(descr: ResourceDescr, path: Path, *, weight_format: WeightFormatArgAll = 'all')

Save a resource's metadata with its associated files.

If path does not have a .zip suffix this command will save the

package as an unzipped folder instead.

Parameters:

Name	Type	Description	Default
descr	ResourceDescr	a bioimageio resource description	required
path	Path	output path	required
weight_format	WeightFormatArgAll	include only this single weight-format (if not 'all').	'all'

Source code in src/bioimageio/core/commands.py

def package(
    descr: ResourceDescr,
    path: Path,
    *,
    weight_format: WeightFormatArgAll = "all",
):
    """Save a resource's metadata with its associated files.

    Note: If `path` does not have a `.zip` suffix this command will save the
          package as an unzipped folder instead.

    Args:
        descr: a bioimageio resource description
        path: output path
        weight_format: include only this single weight-format (if not 'all').
    """
    if isinstance(descr, InvalidDescr):
        logged = descr.validation_summary.save()
        msg = f"Invalid {descr.type} description."
        if logged:
            msg += f" Details saved to {logged}."

        raise ValueError(msg)

    if weight_format == "all":
        weights_priority_order = None
    else:
        weights_priority_order = (weight_format,)

    if path.suffix == ".zip":
        _ = save_bioimageio_package(
            descr,
            output_path=path,
            weights_priority_order=weights_priority_order,
        )
    else:
        _ = save_bioimageio_package_as_folder(
            descr,
            output_path=path,
            weights_priority_order=weights_priority_order,
        )
    return 0

test

test(descr: Union[ResourceDescr, InvalidDescr], *, weight_format: WeightFormatArgAll = 'all', devices: Optional[Union[str, Sequence[str]]] = None, summary: Union[Literal['display'], Path, Sequence[Union[Literal['display'], Path]]] = 'display', runtime_env: Union[Literal['currently-active', 'as-described'], Path] = 'currently-active', determinism: Literal['seed_only', 'full'] = 'seed_only', format_version: Union[FormatVersionPlaceholder, str] = 'discover', working_dir: Optional[Path] = None) -> int

Test a bioimageio resource.

Arguments as described in bioimageio.core.cli.TestCmd

Source code in src/bioimageio/core/commands.py

def test(
    descr: Union[ResourceDescr, InvalidDescr],
    *,
    weight_format: WeightFormatArgAll = "all",
    devices: Optional[Union[str, Sequence[str]]] = None,
    summary: Union[
        Literal["display"], Path, Sequence[Union[Literal["display"], Path]]
    ] = "display",
    runtime_env: Union[
        Literal["currently-active", "as-described"], Path
    ] = "currently-active",
    determinism: Literal["seed_only", "full"] = "seed_only",
    format_version: Union[FormatVersionPlaceholder, str] = "discover",
    working_dir: Optional[Path] = None,
) -> int:
    """Test a bioimageio resource.

    Arguments as described in [bioimageio.core.cli.TestCmd][]
    """
    if isinstance(descr, InvalidDescr):
        test_summary = descr.validation_summary
    else:
        test_summary = test_description(
            descr,
            format_version=format_version,
            weight_format=None if weight_format == "all" else weight_format,
            devices=[devices] if isinstance(devices, str) else devices,
            runtime_env=runtime_env,
            determinism=determinism,
            working_dir=working_dir,
        )

    _ = test_summary.log(summary)
    return 0 if test_summary.status == "passed" else 1

validate_format

validate_format(descr: Union[ResourceDescr, InvalidDescr], summary: Union[Path, Sequence[Path]] = ())

DEPRECATED; Access the existing validation_summary attribute instead. validate the meta data format of a bioimageio resource

Parameters:

Name	Type	Description	Default
descr	Union[ResourceDescr, InvalidDescr]	a bioimageio resource description	required

Source code in src/bioimageio/core/commands.py

def validate_format(
    descr: Union[ResourceDescr, InvalidDescr],
    summary: Union[Path, Sequence[Path]] = (),
):
    """DEPRECATED; Access the existing `validation_summary` attribute instead.
    validate the meta data format of a bioimageio resource

    Args:
        descr: a bioimageio resource description
    """
    _ = descr.validation_summary.save(summary)
    return 0 if descr.validation_summary.status in ("valid-format", "passed") else 1