common

Used by:

• API Reference  core  MemberId

Classes:

Name	Description
CropWidth
Halo
OverlapWidth
PadWidth
SliceInfo

Attributes:

Name	Type	Description
BlockIndex
BlocksizeParameter		Parameter to determine a concrete size for paramtrized axis sizes defined by
CropWhere
CropWidthLike
DTypeStr
Frozen
HaloLike
K
MemberId		ID of a Sample member, see bioimageio.core.sample.Sample
PadMode
PadWhere
PadWidthLike
PerMember
QuantileMethod		Methods to use when the desired quantile lies between two data points.
SampleId		ID of a sample, see bioimageio.core.sample.Sample
SupportedWeightsFormat
T
TotalNumberOfBlocks
V

BlockIndex module-attribute

BlockIndex = int

Used by:

• API Reference
  •  block  Block
  •  block_meta  BlockMeta
  •  sample
    •  SampleBlock
    •  SampleBlockBase
    •  SampleBlockMeta
    •  SampleBlockWithOrigin

BlocksizeParameter module-attribute

BlocksizeParameter = Union[v0_5.ParameterizedSize_N, Mapping[Tuple[MemberId, AxisId], v0_5.ParameterizedSize_N]]

Parameter to determine a concrete size for paramtrized axis sizes defined by bioimageio.spec.model.v0_5.ParameterizedSize.

Used by:

• API Reference
  •  core
    •  PredictionPipeline
    •  create_prediction_pipeline
  •  prediction  predict

CropWhere module-attribute

CropWhere = _Where

CropWidthLike module-attribute

CropWidthLike = _LeftRightLike[CropWidth]

DTypeStr module-attribute

DTypeStr = Literal['bool', 'float32', 'float64', 'int8', 'int16', 'int32', 'int64', 'uint8', 'uint16', 'uint32', 'uint64']

Used by:

• API Reference  proc_ops  EnsureDtype

Frozen module-attribute

Frozen = MappingProxyType

HaloLike module-attribute

HaloLike = _LeftRightLike[Halo]

Used by:

• API Reference
  •  block  split_tensor_into_blocks
  •  block_meta
    •  split_multiple_shapes_into_blocks
    •  split_shape_into_blocks

K module-attribute

K = TypeVar('K', bound=Hashable)

MemberId module-attribute

MemberId = v0_5.TensorId

ID of a Sample member, see bioimageio.core.sample.Sample

Returned by:

• API Reference  digest_spec
  •  get_member_id
  •  get_member_ids

Used by:

• API Reference
  •  common
    •  BlocksizeParameter
    •  PerMember
  •  core  MemberId
  •  digest_spec  get_io_sample_block_metas
  •  prediction
    •  predict
    •  predict_many
  •  proc_ops
    •  Binarize
    •  Clip
    •  EnsureDtype
    •  FixedZeroMeanUnitVariance
    •  ScaleLinear
    •  ScaleMeanVariance
    •  ScaleRange
    •  Sigmoid
    •  Softmax
    •  ZeroMeanUnitVariance
  •  sample
    •  LinearSampleAxisTransform
    •  Sample
    •  SampleBlock
    •  SampleBlockBase
    •  SampleBlockMeta
    •  SampleBlockWithOrigin
  •  stat_calculators
    •  CrickQuantilesCalculator
    •  MeanCalculator
    •  MeanQuantilesCalculator
    •  MeanVarStdCalculator
    •  NaiveSampleMeasureCalculator
    •  SampleQuantilesCalculator

PadMode module-attribute

PadMode = Literal['edge', 'reflect', 'symmetric']

Used by:

• API Reference
  •  block  split_tensor_into_blocks
  •  sample  sample_block_generator

PadWhere module-attribute

PadWhere = _Where

PadWidthLike module-attribute

PadWidthLike = _LeftRightLike[PadWidth]

PerMember module-attribute

PerMember = Mapping[MemberId, T]

Returned by:

• API Reference
  •  block_meta  split_multiple_shapes_into_blocks
  •  digest_spec  get_block_transform

Used by:

• API Reference
  •  block_meta  split_multiple_shapes_into_blocks
  •  digest_spec
    •  create_sample_for_model
    •  get_input_halo
    •  get_io_sample_block_metas
    •  load_sample_for_model
  •  io  save_sample
  •  prediction
    •  predict
    •  predict_many
  •  sample
    •  SampleBlock
    •  SampleBlockBase
    •  SampleBlockMeta
    •  SampleBlockWithOrigin
    •  sample_block_generator
    •  sample_block_meta_generator

QuantileMethod module-attribute

QuantileMethod = Literal['inverted_cdf', 'linear']

Methods to use when the desired quantile lies between two data points. See https://numpy.org/devdocs/reference/generated/numpy.quantile.html#numpy-quantile for details.

Note

Only relevant for SampleQuantile measures, as DatasetQuantile measures computed by [bioimageio.core.stat_calculators.][] are approximations (and use the "linear" method for each sample quantiles)

Warning

Limited choices to map more easily to bioimageio.spec descriptions. Current implementations: - bioimageio.spec.model.v0_5.ClipKwargs implies "inverted_cdf" for sample quantiles and "linear" (numpy's default) for dataset quantiles. - bioimageio.spec.model.v0_5.ScaleRangeKwargs implies "linear" (numpy's default)

Used by:

• API Reference  stat_calculators  SampleQuantilesCalculator

SampleId module-attribute

SampleId = Hashable

ID of a sample, see bioimageio.core.sample.Sample

Used by:

• API Reference
  •  digest_spec
    •  create_sample_for_model
    •  load_sample_for_model
  •  sample
    •  Sample
    •  SampleBlock
    •  SampleBlockBase
    •  SampleBlockMeta
    •  SampleBlockWithOrigin
    •  sample_block_meta_generator

SupportedWeightsFormat module-attribute

SupportedWeightsFormat = Literal['keras_hdf5', 'onnx', 'pytorch_state_dict', 'tensorflow_saved_model_bundle', 'torchscript']

Used by:

• API Reference  core
  •  create_prediction_pipeline
  •  enable_determinism
  •  load_description_and_test
  •  test_description
  •  test_model

T module-attribute

T = TypeVar('T')

Used by:

• API Reference  common  PerMember

TotalNumberOfBlocks module-attribute

TotalNumberOfBlocks = int

Returned by:

• API Reference
  •  block  split_tensor_into_blocks
  •  block_meta
    •  split_multiple_shapes_into_blocks
    •  split_shape_into_blocks
  •  digest_spec  get_io_sample_block_metas

Used by:

• API Reference
  •  block  Block
  •  block_meta  BlockMeta
  •  sample
    •  SampleBlock
    •  SampleBlockBase
    •  SampleBlockMeta
    •  SampleBlockWithOrigin

V module-attribute

V = TypeVar('V')

CropWidth

Bases: _LeftRight

              flowchart TD
              bioimageio.core.common.CropWidth[CropWidth]
              bioimageio.core.common._LeftRight[_LeftRight]

                              bioimageio.core.common._LeftRight --> bioimageio.core.common.CropWidth
                


              click bioimageio.core.common.CropWidth href "" "bioimageio.core.common.CropWidth"
              click bioimageio.core.common._LeftRight href "" "bioimageio.core.common._LeftRight"
            

Used by:

• API Reference  common  CropWidthLike

Methods:

Name	Description
create

Attributes:

Name	Type	Description
left	int
right	int

left instance-attribute

left: int

right instance-attribute

right: int

create classmethod

create(like: _LeftRightLike[Self]) -> Self

Source code in src/bioimageio/core/common.py

@classmethod
def create(cls, like: _LeftRightLike[Self]) -> Self:
    if isinstance(like, cls):
        return like
    elif isinstance(like, tuple):
        return cls(*like)
    elif isinstance(like, int):
        return cls(like, like)
    else:
        assert_never(like)

Halo

Bases: _LeftRight

              flowchart TD
              bioimageio.core.common.Halo[Halo]
              bioimageio.core.common._LeftRight[_LeftRight]

                              bioimageio.core.common._LeftRight --> bioimageio.core.common.Halo
                


              click bioimageio.core.common.Halo href "" "bioimageio.core.common.Halo"
              click bioimageio.core.common._LeftRight href "" "bioimageio.core.common._LeftRight"
            

Used by:

• API Reference
  •  block  Block
  •  block_meta  BlockMeta
  •  common  HaloLike
  •  digest_spec  get_input_halo

Methods:

Name	Description
create

Attributes:

Name	Type	Description
left	int
right	int

left instance-attribute

left: int

right instance-attribute

right: int

create classmethod

create(like: _LeftRightLike[Self]) -> Self

Source code in src/bioimageio/core/common.py

@classmethod
def create(cls, like: _LeftRightLike[Self]) -> Self:
    if isinstance(like, cls):
        return like
    elif isinstance(like, tuple):
        return cls(*like)
    elif isinstance(like, int):
        return cls(like, like)
    else:
        assert_never(like)

OverlapWidth

Bases: _LeftRight

              flowchart TD
              bioimageio.core.common.OverlapWidth[OverlapWidth]
              bioimageio.core.common._LeftRight[_LeftRight]

                              bioimageio.core.common._LeftRight --> bioimageio.core.common.OverlapWidth
                


              click bioimageio.core.common.OverlapWidth href "" "bioimageio.core.common.OverlapWidth"
              click bioimageio.core.common._LeftRight href "" "bioimageio.core.common._LeftRight"
            

Methods:

Name	Description
create

Attributes:

Name	Type	Description
left	int
right	int

left instance-attribute

left: int

right instance-attribute

right: int

create classmethod

create(like: _LeftRightLike[Self]) -> Self

Source code in src/bioimageio/core/common.py

@classmethod
def create(cls, like: _LeftRightLike[Self]) -> Self:
    if isinstance(like, cls):
        return like
    elif isinstance(like, tuple):
        return cls(*like)
    elif isinstance(like, int):
        return cls(like, like)
    else:
        assert_never(like)

PadWidth

Bases: _LeftRight

              flowchart TD
              bioimageio.core.common.PadWidth[PadWidth]
              bioimageio.core.common._LeftRight[_LeftRight]

                              bioimageio.core.common._LeftRight --> bioimageio.core.common.PadWidth
                


              click bioimageio.core.common.PadWidth href "" "bioimageio.core.common.PadWidth"
              click bioimageio.core.common._LeftRight href "" "bioimageio.core.common._LeftRight"
            

Used by:

• API Reference  common  PadWidthLike

Methods:

Name	Description
create

Attributes:

Name	Type	Description
left	int
right	int

left instance-attribute

left: int

right instance-attribute

right: int

create classmethod

create(like: _LeftRightLike[Self]) -> Self

Source code in src/bioimageio/core/common.py

@classmethod
def create(cls, like: _LeftRightLike[Self]) -> Self:
    if isinstance(like, cls):
        return like
    elif isinstance(like, tuple):
        return cls(*like)
    elif isinstance(like, int):
        return cls(like, like)
    else:
        assert_never(like)

SliceInfo

Bases: NamedTuple

              flowchart TD
              bioimageio.core.common.SliceInfo[SliceInfo]

              

              click bioimageio.core.common.SliceInfo href "" "bioimageio.core.common.SliceInfo"
            

Used by:

• API Reference
  •  block  Block
  •  block_meta  BlockMeta

Attributes:

Name	Type	Description
start	int
stop	int

start instance-attribute

start: int

stop instance-attribute

stop: int