bioimageio.core.commands

 1"""These functions implement the logic of 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.model.v0_5 import WeightsFormat
16
17from ._resource_tests import test_description
18
19WeightFormatArgAll = Literal[WeightsFormat, "all"]
20WeightFormatArgAny = Literal[WeightsFormat, "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    decimal: int = 4,
29) -> int:
30    """test a bioimageio resource
31
32    Args:
33        source: Path or URL to the bioimageio resource description file
34                (bioimageio.yaml or rdf.yaml) or to a zipped resource
35        weight_format: (model only) The weight format to use
36        devices: Device(s) to use for testing
37        decimal: Precision for numerical comparisons
38    """
39    if isinstance(descr, InvalidDescr):
40        descr.validation_summary.display()
41        return 1
42
43    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        decimal=decimal,
48    )
49    summary.display()
50    return 0 if summary.status == "passed" else 1
51
52
53def validate_format(
54    descr: Union[ResourceDescr, InvalidDescr],
55):
56    """validate the meta data format of a bioimageio resource
57
58    Args:
59        descr: a bioimageio resource description
60    """
61    descr.validation_summary.display()
62    return 0 if descr.validation_summary.status == "passed" else 1
63
64
65def package(
66    descr: ResourceDescr, path: Path, *, weight_format: WeightFormatArgAll = "all"
67):
68    """Save a resource's metadata with its associated files.
69
70    Note: If `path` does not have a `.zip` suffix this command will save the
71          package as an unzipped folder instead.
72
73    Args:
74        descr: a bioimageio resource description
75        path: output path
76        weight-format: include only this single weight-format (if not 'all').
77    """
78    if isinstance(descr, InvalidDescr):
79        descr.validation_summary.display()
80        raise ValueError("resource description is invalid")
81
82    if weight_format == "all":
83        weights_priority_order = None
84    else:
85        weights_priority_order = (weight_format,)
86
87    if path.suffix == ".zip":
88        _ = save_bioimageio_package(
89            descr,
90            output_path=path,
91            weights_priority_order=weights_priority_order,
92        )
93    else:
94        _ = save_bioimageio_package_as_folder(
95            descr,
96            output_path=path,
97            weights_priority_order=weights_priority_order,
98        )
99    return 0