Coverage for src/bioimageio/spec/utils.py: 92%

1"""Utility functions for bioimage.io specifications (mostly IO).""" 

2 

3from __future__ import annotations 

4 

5import json 

6import shutil 

7from typing import Any, TypedDict 

8 

9import pydantic 

10from imageio.v3 import imread # pyright: ignore[reportUnknownVariableType] 

11from loguru import logger 

12from numpy.typing import NDArray 

13 

14from ._description import ensure_description_is_dataset as ensure_description_is_dataset 

15from ._description import ensure_description_is_model as ensure_description_is_model 

16from ._internal._settings import settings 

17from ._internal.io import FileDescr 

18from ._internal.io import download as download 

19from ._internal.io import extract_file_name as extract_file_name 

20from ._internal.io import get_reader as get_reader 

21from ._internal.io import get_sha256 as get_sha256 

22from ._internal.io import ( 

23 identify_bioimageio_yaml_file_name as identify_bioimageio_yaml_file_name, 

24) 

25from ._internal.io import interprete_file_source as interprete_file_source 

26from ._internal.io import is_valid_bioimageio_yaml_name as is_valid_bioimageio_yaml_name 

27from ._internal.io_basics import ZipPath 

28from ._internal.io_utils import load_array as load_array 

29from ._internal.io_utils import open_bioimageio_yaml as open_bioimageio_yaml 

30from ._internal.io_utils import read_yaml as read_yaml 

31from ._internal.io_utils import save_array as save_array 

32from ._internal.io_utils import write_yaml as write_yaml 

33from ._internal.types import PermissiveFileSource, RelativeFilePath 

34from ._internal.utils import files 

35 

36get_file_name = extract_file_name 

37 

38 

39class SpdxLicenseEntry(TypedDict): 

40 isDeprecatedLicenseId: bool 

41 isKnownByZenodo: bool 

42 isOsiApproved: bool 

43 licenseId: str 

44 name: str 

45 reference: str 

46 

47 

48class SpdxLicenses(TypedDict): 

49 licenseListVersion: str 

50 licenses: list[SpdxLicenseEntry] 

51 releaseDate: str 

52 

53 

54def get_spdx_licenses() -> SpdxLicenses: 

55 """get details of the SPDX licenses known to bioimageio.spec""" 

56 with ( 

57 files("bioimageio.spec") 

58 .joinpath("static/spdx_licenses.json") 

59 .open("r", encoding="utf-8") 

60 ) as f: 

61 return json.load(f) 

62 

63 

64def get_bioimageio_json_schema() -> dict[str, Any]: 

65 """get the bioimageio specification as a JSON schema""" 

66 with ( 

67 files("bioimageio.spec") 

68 .joinpath("static/bioimageio_schema.json") 

69 .open("r", encoding="utf-8") 

70 ) as f: 

71 return json.load(f) 

72 

73 

74def load_image( 

75 source: FileDescr | ZipPath | PermissiveFileSource, 

76) -> NDArray[Any]: 

77 """load a single image as numpy array 

78 

79 Args: 

80 source: image source 

81 """ 

82 

83 source = _interprete_file_source(source) 

84 

85 if source.suffix == ".npy": 

86 return load_array(source) 

87 else: 

88 reader = get_reader(source) 

89 return imread(reader.read(), extension=source.suffix) # pyright: ignore[reportUnknownVariableType] 

90 

91 

92def _interprete_file_source(source: FileDescr | ZipPath | PermissiveFileSource): 

93 if isinstance(source, (FileDescr, ZipPath)): 

94 parsed_source = source 

95 elif isinstance(source, (str, pydantic.AnyUrl)): 

96 parsed_source = interprete_file_source(source) 

97 else: 

98 parsed_source = source 

99 

100 if isinstance(parsed_source, RelativeFilePath): 

101 parsed_source = parsed_source.absolute() 

102 

103 return parsed_source 

104 

105 

106def empty_cache(): 

107 """Empty the bioimageio disk cache.""" 

108 

109 shutil.rmtree(settings.cache_path) 

110 settings.cache_path.mkdir(parents=True, exist_ok=True) 

111 logger.info("Emptied cache at {}", settings.cache_path)