bioimageio.core.commands

  1"""These functions are used in the bioimageio command line interface
  2defined in `bioimageio.core.cli`."""
  3
  4from pathlib import Path
  5from typing import Optional, Sequence, Union
  6
  7from typing_extensions import Literal
  8
  9from bioimageio.core.common import SupportedWeightsFormat
 10from bioimageio.spec import (
 11    InvalidDescr,
 12    ResourceDescr,
 13    save_bioimageio_package,
 14    save_bioimageio_package_as_folder,
 15)
 16from bioimageio.spec._internal.types import FormatVersionPlaceholder
 17
 18from ._resource_tests import test_description
 19
 20WeightFormatArgAll = Literal[SupportedWeightsFormat, "all"]
 21WeightFormatArgAny = Literal[SupportedWeightsFormat, "any"]
 22
 23
 24def test(
 25    descr: Union[ResourceDescr, InvalidDescr],
 26    *,
 27    weight_format: WeightFormatArgAll = "all",
 28    devices: Optional[Union[str, Sequence[str]]] = None,
 29    summary: Union[
 30        Literal["display"], Path, Sequence[Union[Literal["display"], Path]]
 31    ] = "display",
 32    runtime_env: Union[
 33        Literal["currently-active", "as-described"], Path
 34    ] = "currently-active",
 35    determinism: Literal["seed_only", "full"] = "seed_only",
 36    format_version: Union[FormatVersionPlaceholder, str] = "discover",
 37) -> int:
 38    """Test a bioimageio resource.
 39
 40    Arguments as described in `bioimageio.core.cli.TestCmd`
 41    """
 42    if isinstance(descr, InvalidDescr):
 43        test_summary = descr.validation_summary
 44    else:
 45        test_summary = test_description(
 46            descr,
 47            format_version=format_version,
 48            weight_format=None if weight_format == "all" else weight_format,
 49            devices=[devices] if isinstance(devices, str) else devices,
 50            runtime_env=runtime_env,
 51            determinism=determinism,
 52        )
 53
 54    _ = test_summary.log(summary)
 55    return 0 if test_summary.status == "passed" else 1
 56
 57
 58def validate_format(
 59    descr: Union[ResourceDescr, InvalidDescr],
 60    summary: Union[Path, Sequence[Path]] = (),
 61):
 62    """DEPRECATED; Access the existing `validation_summary` attribute instead.
 63    validate the meta data format of a bioimageio resource
 64
 65    Args:
 66        descr: a bioimageio resource description
 67    """
 68    _ = descr.validation_summary.save(summary)
 69    return 0 if descr.validation_summary.status in ("valid-format", "passed") else 1
 70
 71
 72# TODO: absorb into `save_bioimageio_package`
 73def package(
 74    descr: ResourceDescr,
 75    path: Path,
 76    *,
 77    weight_format: WeightFormatArgAll = "all",
 78):
 79    """Save a resource's metadata with its associated files.
 80
 81    Note: If `path` does not have a `.zip` suffix this command will save the
 82          package as an unzipped folder instead.
 83
 84    Args:
 85        descr: a bioimageio resource description
 86        path: output path
 87        weight-format: include only this single weight-format (if not 'all').
 88    """
 89    if isinstance(descr, InvalidDescr):
 90        logged = descr.validation_summary.save()
 91        msg = f"Invalid {descr.type} description."
 92        if logged:
 93            msg += f" Details saved to {logged}."
 94
 95        raise ValueError(msg)
 96
 97    if weight_format == "all":
 98        weights_priority_order = None
 99    else:
100        weights_priority_order = (weight_format,)
101
102    if path.suffix == ".zip":
103        _ = save_bioimageio_package(
104            descr,
105            output_path=path,
106            weights_priority_order=weights_priority_order,
107        )
108    else:
109        _ = save_bioimageio_package_as_folder(
110            descr,
111            output_path=path,
112            weights_priority_order=weights_priority_order,
113        )
114    return 0