Coverage for src/bioimageio/core/__init__.py: 100%

1"""bioimageio.core --- core functionality for BioImage.IO resources 

2 

3The main focus on this library is to provide functionality to run prediction with 

4BioImage.IO models, including standardized pre- and postprocessing operations. 

5The BioImage.IO models (and other resources) are described by---and can be loaded with---the bioimageio.spec package. 

6 

7See `predict` and `predict_many` for straight-forward model inference 

8and `create_prediction_pipeline` for finer control of the inference process. 

9 

10Other notable bioimageio.core functionalities include: 

11- Testing BioImage.IO resources beyond format validation, e.g. by generating model outputs from test inputs. 

12 See `test_model` or for arbitrary resource types `test_description`. 

13- Extending available model weight formats by converting existing ones, see `add_weights`. 

14- Creating and manipulating `Sample`s consisting of tensors with associated statistics. 

15- Computing statistics on datasets (represented as sequences of samples), see `compute_dataset_measures`. 

16""" 

17# ruff: noqa: E402 

18 

19__version__ = "0.11.0" 

20from loguru import logger 

21 

22logger.disable("bioimageio.core") 

23 

24 

25from bioimageio.spec import ValidationSummary as ValidationSummary 

26from bioimageio.spec import build_description as build_description 

27from bioimageio.spec import dump_description as dump_description 

28from bioimageio.spec import load_dataset_description as load_dataset_description 

29from bioimageio.spec import load_description as load_description 

30from bioimageio.spec import ( 

31 load_description_and_validate_format_only as load_description_and_validate_format_only, 

32) 

33from bioimageio.spec import load_model_description as load_model_description 

34from bioimageio.spec import save_bioimageio_package as save_bioimageio_package 

35from bioimageio.spec import ( 

36 save_bioimageio_package_as_folder as save_bioimageio_package_as_folder, 

37) 

38from bioimageio.spec import save_bioimageio_yaml_only as save_bioimageio_yaml_only 

39from bioimageio.spec import validate_format as validate_format 

40 

41from . import axis as axis 

42from . import backends as backends 

43from . import block_meta as block_meta 

44from . import cli as cli 

45from . import commands as commands 

46from . import common as common 

47from . import digest_spec as digest_spec 

48from . import io as io 

49from . import prediction as prediction 

50from . import proc_ops as proc_ops 

51from . import proc_setup as proc_setup 

52from . import sample as sample 

53from . import stat_calculators as stat_calculators 

54from . import stat_measures as stat_measures 

55from . import tensor as tensor 

56from . import weight_converters as weight_converters 

57from ._prediction_pipeline import IntermediatePrediction as IntermediatePrediction 

58from ._prediction_pipeline import PredictionPipeline as PredictionPipeline 

59from ._prediction_pipeline import RemotePredictionPipeline as RemotePredictionPipeline 

60from ._prediction_pipeline import ( 

61 create_prediction_pipeline as create_prediction_pipeline, 

62) 

63from ._prediction_pipeline import ( 

64 create_remote_prediction_pipeline as create_remote_prediction_pipeline, 

65) 

66from ._resource_tests import enable_determinism as enable_determinism 

67from ._resource_tests import load_description_and_test as load_description_and_test 

68from ._resource_tests import test_description as test_description 

69from ._resource_tests import test_model as test_model 

70from ._sample_serializer import SampleSerializer as SampleSerializer 

71from ._settings import Settings as Settings 

72from ._settings import settings as settings 

73 

74# reexports from bioimageio.core submodules 

75from .axis import Axis as Axis 

76from .axis import AxisId as AxisId 

77from .backends import create_model_adapter as create_model_adapter 

78from .block_meta import BlockMeta as BlockMeta 

79from .common import MemberId as MemberId 

80from .prediction import predict as predict 

81from .prediction import predict_many as predict_many 

82from .sample import Sample as Sample 

83from .sample import SampleBlock as SampleBlock 

84from .sample import SampleBlockMeta as SampleBlockMeta 

85from .stat_calculators import compute_dataset_measures as compute_dataset_measures 

86from .stat_calculators import compute_measures as compute_measures 

87from .stat_calculators import compute_sample_measures as compute_sample_measures 

88from .stat_measures import Stat as Stat 

89from .tensor import Tensor as Tensor 

90from .weight_converters import add_weights as add_weights 

91 

92# aliases 

93test_resource = test_description 

94"""alias of `test_description`""" 

95load_resource = load_description 

96"""alias of `load_description`""" 

97load_model = load_model_description 

98"""alias of `load_model_description`"""