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__ = "0.9.6" 

20from loguru import logger 

21 

22logger.disable("bioimageio.core") 

23 

24import bioimageio.spec 

25 

26from . import axis as axis 

27from . import backends as backends 

28from . import block_meta as block_meta 

29from . import cli as cli 

30from . import commands as commands 

31from . import common as common 

32from . import digest_spec as digest_spec 

33from . import io as io 

34from . import model_adapters as model_adapters 

35from . import prediction as prediction 

36from . import proc_ops as proc_ops 

37from . import proc_setup as proc_setup 

38from . import sample as sample 

39from . import stat_calculators as stat_calculators 

40from . import stat_measures as stat_measures 

41from . import tensor as tensor 

42from . import weight_converters as weight_converters 

43from ._prediction_pipeline import PredictionPipeline as PredictionPipeline 

44from ._prediction_pipeline import ( 

45 create_prediction_pipeline as create_prediction_pipeline, 

46) 

47from ._resource_tests import enable_determinism as enable_determinism 

48from ._resource_tests import load_description_and_test as load_description_and_test 

49from ._resource_tests import test_description as test_description 

50from ._resource_tests import test_model as test_model 

51from ._settings import Settings as Settings 

52from ._settings import settings as settings 

53 

54# reexports from bioimageio.spec 

55build_description = bioimageio.spec.build_description 

56dump_description = bioimageio.spec.dump_description 

57load_dataset_description = bioimageio.spec.load_dataset_description 

58load_description = bioimageio.spec.load_description 

59load_description_and_validate_format_only = ( 

60 bioimageio.spec.load_description_and_validate_format_only 

61) 

62load_model_description = bioimageio.spec.load_model_description 

63save_bioimageio_package = bioimageio.spec.save_bioimageio_package 

64save_bioimageio_package_as_folder = bioimageio.spec.save_bioimageio_package_as_folder 

65save_bioimageio_yaml_only = bioimageio.spec.save_bioimageio_yaml_only 

66validate_format = bioimageio.spec.validate_format 

67ValidationSummary = bioimageio.spec.ValidationSummary 

68 

69 

70# reexports from bioimageio.core submodules 

71add_weights = weight_converters.add_weights 

72Axis = axis.Axis 

73AxisId = axis.AxisId 

74BlockMeta = block_meta.BlockMeta 

75compute_dataset_measures = stat_calculators.compute_dataset_measures 

76create_model_adapter = backends.create_model_adapter 

77MemberId = common.MemberId 

78predict = prediction.predict 

79predict_many = prediction.predict_many 

80Sample = sample.Sample 

81Stat = stat_measures.Stat 

82Tensor = tensor.Tensor 

83 

84# aliases 

85test_resource = test_description 

86"""alias of `test_description`""" 

87load_resource = load_description 

88"""alias of `load_description`""" 

89load_model = load_model_description 

90"""alias of `load_model_description`"""