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.spec import (
 10    InvalidDescr,
 11    ResourceDescr,
 12    save_bioimageio_package,
 13    save_bioimageio_package_as_folder,
 14)
 15from bioimageio.spec._internal.types import FormatVersionPlaceholder
 16
 17from ._resource_tests import test_description
 18
 19# unfortunately this does not work with py3.9 and pydantic 2.11
 20# from bioimageio.core.common import SupportedWeightsFormat
 21# WeightFormatArgAll = Literal[SupportedWeightsFormat, "all"]
 22# WeightFormatArgAny = Literal[SupportedWeightsFormat, "any"]
 23# so we write out the literal explicitly
 24WeightFormatArgAll = Literal[
 25    "keras_hdf5",
 26    "onnx",
 27    "pytorch_state_dict",
 28    "tensorflow_saved_model_bundle",
 29    "torchscript",
 30    "all",
 31]
 32WeightFormatArgAny = Literal[
 33    "keras_hdf5",
 34    "onnx",
 35    "pytorch_state_dict",
 36    "tensorflow_saved_model_bundle",
 37    "torchscript",
 38    "any",
 39]
 40
 41
 42def test(
 43    descr: Union[ResourceDescr, InvalidDescr],
 44    *,
 45    weight_format: WeightFormatArgAll = "all",
 46    devices: Optional[Union[str, Sequence[str]]] = None,
 47    summary: Union[
 48        Literal["display"], Path, Sequence[Union[Literal["display"], Path]]
 49    ] = "display",
 50    runtime_env: Union[
 51        Literal["currently-active", "as-described"], Path
 52    ] = "currently-active",
 53    determinism: Literal["seed_only", "full"] = "seed_only",
 54    format_version: Union[FormatVersionPlaceholder, str] = "discover",
 55) -> int:
 56    """Test a bioimageio resource.
 57
 58    Arguments as described in `bioimageio.core.cli.TestCmd`
 59    """
 60    if isinstance(descr, InvalidDescr):
 61        test_summary = descr.validation_summary
 62    else:
 63        test_summary = test_description(
 64            descr,
 65            format_version=format_version,
 66            weight_format=None if weight_format == "all" else weight_format,
 67            devices=[devices] if isinstance(devices, str) else devices,
 68            runtime_env=runtime_env,
 69            determinism=determinism,
 70        )
 71
 72    _ = test_summary.log(summary)
 73    return 0 if test_summary.status == "passed" else 1
 74
 75
 76def validate_format(
 77    descr: Union[ResourceDescr, InvalidDescr],
 78    summary: Union[Path, Sequence[Path]] = (),
 79):
 80    """DEPRECATED; Access the existing `validation_summary` attribute instead.
 81    validate the meta data format of a bioimageio resource
 82
 83    Args:
 84        descr: a bioimageio resource description
 85    """
 86    _ = descr.validation_summary.save(summary)
 87    return 0 if descr.validation_summary.status in ("valid-format", "passed") else 1
 88
 89
 90# TODO: absorb into `save_bioimageio_package`
 91def package(
 92    descr: ResourceDescr,
 93    path: Path,
 94    *,
 95    weight_format: WeightFormatArgAll = "all",
 96):
 97    """Save a resource's metadata with its associated files.
 98
 99    Note: If `path` does not have a `.zip` suffix this command will save the
100          package as an unzipped folder instead.
101
102    Args:
103        descr: a bioimageio resource description
104        path: output path
105        weight-format: include only this single weight-format (if not 'all').
106    """
107    if isinstance(descr, InvalidDescr):
108        logged = descr.validation_summary.save()
109        msg = f"Invalid {descr.type} description."
110        if logged:
111            msg += f" Details saved to {logged}."
112
113        raise ValueError(msg)
114
115    if weight_format == "all":
116        weights_priority_order = None
117    else:
118        weights_priority_order = (weight_format,)
119
120    if path.suffix == ".zip":
121        _ = save_bioimageio_package(
122            descr,
123            output_path=path,
124            weights_priority_order=weights_priority_order,
125        )
126    else:
127        _ = save_bioimageio_package_as_folder(
128            descr,
129            output_path=path,
130            weights_priority_order=weights_priority_order,
131        )
132    return 0