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