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sample ¤

Used by:

Classes:

Name Description
LinearSampleAxisTransform
Sample

A dataset sample.
SampleBlock

A block of a dataset sample
SampleBlockBase

base class for SampleBlockMeta and SampleBlock
SampleBlockMeta

Meta data of a dataset sample block
SampleBlockWithOrigin

A SampleBlock with a reference (origin) to the whole Sample

Functions:

Name Description
sample_block_generator
sample_block_meta_generator

Attributes:

Name Type Description
BlockT

BlockT module-attribute ¤

BlockT = TypeVar('BlockT', Block, BlockMeta)
Subclassed by: Used by:

LinearSampleAxisTransform dataclass ¤

LinearSampleAxisTransform(axis: AxisId, scale: float, offset: int, member: MemberId)

Bases: LinearAxisTransform


              flowchart TD
              bioimageio.core.sample.LinearSampleAxisTransform[LinearSampleAxisTransform]
              bioimageio.core.block_meta.LinearAxisTransform[LinearAxisTransform]

                              bioimageio.core.block_meta.LinearAxisTransform --> bioimageio.core.sample.LinearSampleAxisTransform
                


              click bioimageio.core.sample.LinearSampleAxisTransform href "" "bioimageio.core.sample.LinearSampleAxisTransform"
              click bioimageio.core.block_meta.LinearAxisTransform href "" "bioimageio.core.block_meta.LinearAxisTransform"
Returned by:

Methods:

Name Description
compute

Attributes:

Name Type Description
axis AxisId
member MemberId
offset int
scale float

axis instance-attribute ¤

axis: AxisId

member instance-attribute ¤

member: MemberId

offset instance-attribute ¤

offset: int

scale instance-attribute ¤

scale: float

compute ¤

compute(s: int, round: Callable[[float], int] = floor) -> int
Source code in src/bioimageio/core/block_meta.py 
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def compute(self, s: int, round: Callable[[float], int] = floor) -> int:
    return round(s * self.scale) + self.offset

Sample dataclass ¤

Sample(members: Dict[MemberId, Tensor], stat: Stat, id: SampleId)

A dataset sample.

A Sample has members, which allows to combine multiple tensors into a single sample. For example a Sample from a dataset with masked images may contain a MemberId("raw") and MemberId("mask") image.

Returned by: Used by:

Methods:

Name Description
__getitem__
as_arrays

Return sample as dictionary of arrays.
as_single_block
from_blocks
pad

Convenience method to pad sample members.
split_into_blocks

Attributes:

Name Type Description
id SampleId

Identifies the Sample within the dataset -- typically a number or a string.
members Dict[MemberId, Tensor]

The sample's tensors
shape PerMember[PerAxis[int]]
stat Stat

Sample and dataset statistics

id instance-attribute ¤

id: SampleId

Identifies the Sample within the dataset -- typically a number or a string.

members instance-attribute ¤

members: Dict[MemberId, Tensor]

The sample's tensors

shape property ¤

shape: PerMember[PerAxis[int]]

stat instance-attribute ¤

stat: Stat

Sample and dataset statistics

__getitem__ ¤

__getitem__(key: PerMember[Union[SliceInfo, slice, int, PerAxis[Union[SliceInfo, slice, int]], Tensor, xr.DataArray]]) -> Self
Source code in src/bioimageio/core/sample.py 
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def __getitem__(
    self,
    key: PerMember[
        Union[
            SliceInfo,
            slice,
            int,
            PerAxis[Union[SliceInfo, slice, int]],
            Tensor,
            xr.DataArray,
        ]
    ],
) -> Self:
    return self.__class__(
        members={m: t[key[m]] for m, t in self.members.items() if m in key},
        stat=self.stat,
        id=self.id,
    )

as_arrays ¤

as_arrays() -> Dict[MemberId, NDArray[Any]]

Return sample as dictionary of arrays.

Source code in src/bioimageio/core/sample.py 
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def as_arrays(self) -> Dict[MemberId, NDArray[Any]]:
    """Return sample as dictionary of arrays."""
    return {m: t.to_numpy() for m, t in self.members.items()}

as_single_block ¤

as_single_block(halo: Optional[PerMember[PerAxis[Halo]]] = None)
Source code in src/bioimageio/core/sample.py 
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def as_single_block(self, halo: Optional[PerMember[PerAxis[Halo]]] = None):
    if halo is None:
        halo = {}
    return SampleBlockWithOrigin(
        sample_shape=self.shape,
        sample_id=self.id,
        blocks={
            m: Block(
                sample_shape=self.shape[m],
                data=data,
                inner_slice={
                    a: SliceInfo(0, s) for a, s in data.tagged_shape.items()
                },
                halo=halo.get(m, {}),
                block_index=0,
                blocks_in_sample=1,
            )
            for m, data in self.members.items()
        },
        stat=self.stat,
        origin=self,
        block_index=0,
        blocks_in_sample=1,
    )

from_blocks classmethod ¤

from_blocks(sample_blocks: Iterable[SampleBlock], *, fill_value: float = float('nan')) -> Self
Source code in src/bioimageio/core/sample.py 
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@classmethod
def from_blocks(
    cls,
    sample_blocks: Iterable[SampleBlock],
    *,
    fill_value: float = float("nan"),
) -> Self:
    members: PerMember[Tensor] = {}
    stat: Stat = {}
    sample_id = None
    for sample_block in sample_blocks:
        assert sample_id is None or sample_id == sample_block.sample_id
        sample_id = sample_block.sample_id
        stat = sample_block.stat
        for m, block in sample_block.blocks.items():
            if m not in members:
                if -1 in block.sample_shape.values():
                    raise NotImplementedError(
                        "merging blocks with data dependent axis not yet implemented"
                    )

                members[m] = Tensor(
                    np.full(
                        tuple(block.sample_shape[a] for a in block.data.dims),
                        fill_value,
                        dtype=block.data.dtype,
                    ),
                    dims=block.data.dims,
                )

            members[m][block.inner_slice] = block.inner_data

    return cls(members=members, stat=stat, id=sample_id)

pad ¤

pad(pad_width: PerMember[PerAxis[Union[int, PadWidthLike]]], mode: Union[PerMember[PadMode], PadMode]) -> Self

Convenience method to pad sample members.

Source code in src/bioimageio/core/sample.py 
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def pad(
    self,
    pad_width: PerMember[PerAxis[Union[int, PadWidthLike]]],
    mode: Union[PerMember[PadMode], PadMode],
) -> Self:
    """Convenience method to pad sample members."""
    default_mode = "symmetric"
    if isinstance(mode, collections.abc.Mapping):
        mode_per_member = mode
    else:
        mode_per_member: Mapping[MemberId, PadMode] = {}
        default_mode = mode

    return self.__class__(
        members={
            m: t.pad(
                pad_width=pad_width.get(m, {}),
                mode=mode_per_member.get(m, default_mode),
            )
            for m, t in self.members.items()
        },
        stat=self.stat,
        id=self.id,
    )

split_into_blocks ¤

split_into_blocks(block_shapes: PerMember[PerAxis[int]], halo: PerMember[PerAxis[HaloLike]], pad_mode: Union[PadMode, PerMember[PadMode]], broadcast: bool = False) -> Tuple[TotalNumberOfBlocks, Iterable[SampleBlockWithOrigin]]
Source code in src/bioimageio/core/sample.py 
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def split_into_blocks(
    self,
    block_shapes: PerMember[PerAxis[int]],
    halo: PerMember[PerAxis[HaloLike]],
    pad_mode: Union[PadMode, PerMember[PadMode]],
    broadcast: bool = False,
) -> Tuple[TotalNumberOfBlocks, Iterable[SampleBlockWithOrigin]]:
    assert not (missing := [m for m in block_shapes if m not in self.members]), (
        f"`block_shapes` specified for unknown members: {missing}"
    )
    assert not (missing := [m for m in halo if m not in block_shapes]), (
        f"`halo` specified for members without `block_shape`: {missing}"
    )

    n_blocks, blocks = split_multiple_shapes_into_blocks(
        shapes=self.shape,
        block_shapes=block_shapes,
        halo=halo,
        broadcast=broadcast,
    )
    return n_blocks, sample_block_generator(blocks, origin=self, pad_mode=pad_mode)

SampleBlock dataclass ¤

SampleBlock(sample_shape: PerMember[PerAxis[int]], sample_id: SampleId, blocks: Dict[MemberId, BlockT], block_index: BlockIndex, blocks_in_sample: TotalNumberOfBlocks, stat: Stat)

Bases: SampleBlockBase[Block]


              flowchart TD
              bioimageio.core.sample.SampleBlock[SampleBlock]
              bioimageio.core.sample.SampleBlockBase[SampleBlockBase]

                              bioimageio.core.sample.SampleBlockBase --> bioimageio.core.sample.SampleBlock
                


              click bioimageio.core.sample.SampleBlock href "" "bioimageio.core.sample.SampleBlock"
              click bioimageio.core.sample.SampleBlockBase href "" "bioimageio.core.sample.SampleBlockBase"

A block of a dataset sample

Subclassed by:

Methods:

Name Description
get_transformed_meta

Attributes:

Name Type Description
block_index BlockIndex

the n-th block of the sample
blocks Dict[MemberId, BlockT]

Individual tensor blocks comprising this sample block
blocks_in_sample TotalNumberOfBlocks

total number of blocks in the sample
inner_shape PerMember[PerAxis[int]]
members PerMember[Tensor]

the sample block's tensors
sample_id SampleId

identifier for the sample within its dataset
sample_shape PerMember[PerAxis[int]]

the sample shape this block represents a part of
shape PerMember[PerAxis[int]]
stat Stat

computed statistics

block_index instance-attribute ¤

block_index: BlockIndex

the n-th block of the sample

blocks instance-attribute ¤

blocks: Dict[MemberId, BlockT]

Individual tensor blocks comprising this sample block

blocks_in_sample instance-attribute ¤

blocks_in_sample: TotalNumberOfBlocks

total number of blocks in the sample

inner_shape property ¤

inner_shape: PerMember[PerAxis[int]]

members property ¤

members: PerMember[Tensor]

the sample block's tensors

sample_id instance-attribute ¤

sample_id: SampleId

identifier for the sample within its dataset

sample_shape instance-attribute ¤

sample_shape: PerMember[PerAxis[int]]

the sample shape this block represents a part of

shape property ¤

shape: PerMember[PerAxis[int]]

stat instance-attribute ¤

stat: Stat

computed statistics

get_transformed_meta ¤

get_transformed_meta(new_axes: PerMember[PerAxis[Union[LinearSampleAxisTransform, int]]]) -> SampleBlockMeta
Source code in src/bioimageio/core/sample.py 
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def get_transformed_meta(
    self, new_axes: PerMember[PerAxis[Union[LinearSampleAxisTransform, int]]]
) -> SampleBlockMeta:
    return SampleBlockMeta(
        sample_id=self.sample_id,
        blocks=dict(self.blocks),
        sample_shape=self.sample_shape,
        block_index=self.block_index,
        blocks_in_sample=self.blocks_in_sample,
    ).get_transformed(new_axes)

SampleBlockBase dataclass ¤

SampleBlockBase(sample_shape: PerMember[PerAxis[int]], sample_id: SampleId, blocks: Dict[MemberId, BlockT], block_index: BlockIndex, blocks_in_sample: TotalNumberOfBlocks)

Bases: Generic[BlockT]


              flowchart TD
              bioimageio.core.sample.SampleBlockBase[SampleBlockBase]

              

              click bioimageio.core.sample.SampleBlockBase href "" "bioimageio.core.sample.SampleBlockBase"

base class for SampleBlockMeta and SampleBlock

Subclassed by:

Attributes:

Name Type Description
block_index BlockIndex

the n-th block of the sample
blocks Dict[MemberId, BlockT]

Individual tensor blocks comprising this sample block
blocks_in_sample TotalNumberOfBlocks

total number of blocks in the sample
inner_shape PerMember[PerAxis[int]]
sample_id SampleId

identifier for the sample within its dataset
sample_shape PerMember[PerAxis[int]]

the sample shape this block represents a part of
shape PerMember[PerAxis[int]]

block_index instance-attribute ¤

block_index: BlockIndex

the n-th block of the sample

blocks instance-attribute ¤

blocks: Dict[MemberId, BlockT]

Individual tensor blocks comprising this sample block

blocks_in_sample instance-attribute ¤

blocks_in_sample: TotalNumberOfBlocks

total number of blocks in the sample

inner_shape property ¤

inner_shape: PerMember[PerAxis[int]]

sample_id instance-attribute ¤

sample_id: SampleId

identifier for the sample within its dataset

sample_shape instance-attribute ¤

sample_shape: PerMember[PerAxis[int]]

the sample shape this block represents a part of

shape property ¤

shape: PerMember[PerAxis[int]]

SampleBlockMeta dataclass ¤

SampleBlockMeta(sample_shape: PerMember[PerAxis[int]], sample_id: SampleId, blocks: Dict[MemberId, BlockT], block_index: BlockIndex, blocks_in_sample: TotalNumberOfBlocks)

Bases: SampleBlockBase[BlockMeta]


              flowchart TD
              bioimageio.core.sample.SampleBlockMeta[SampleBlockMeta]
              bioimageio.core.sample.SampleBlockBase[SampleBlockBase]

                              bioimageio.core.sample.SampleBlockBase --> bioimageio.core.sample.SampleBlockMeta
                


              click bioimageio.core.sample.SampleBlockMeta href "" "bioimageio.core.sample.SampleBlockMeta"
              click bioimageio.core.sample.SampleBlockBase href "" "bioimageio.core.sample.SampleBlockBase"

Meta data of a dataset sample block

Methods:

Name Description
get_transformed
with_data

Attributes:

Name Type Description
block_index BlockIndex

the n-th block of the sample
blocks Dict[MemberId, BlockT]

Individual tensor blocks comprising this sample block
blocks_in_sample TotalNumberOfBlocks

total number of blocks in the sample
inner_shape PerMember[PerAxis[int]]
sample_id SampleId

identifier for the sample within its dataset
sample_shape PerMember[PerAxis[int]]

the sample shape this block represents a part of
shape PerMember[PerAxis[int]]

block_index instance-attribute ¤

block_index: BlockIndex

the n-th block of the sample

blocks instance-attribute ¤

blocks: Dict[MemberId, BlockT]

Individual tensor blocks comprising this sample block

blocks_in_sample instance-attribute ¤

blocks_in_sample: TotalNumberOfBlocks

total number of blocks in the sample

inner_shape property ¤

inner_shape: PerMember[PerAxis[int]]

sample_id instance-attribute ¤

sample_id: SampleId

identifier for the sample within its dataset

sample_shape instance-attribute ¤

sample_shape: PerMember[PerAxis[int]]

the sample shape this block represents a part of

shape property ¤

shape: PerMember[PerAxis[int]]

get_transformed ¤

get_transformed(new_axes: PerMember[PerAxis[Union[LinearSampleAxisTransform, int]]]) -> Self
Source code in src/bioimageio/core/sample.py 
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def get_transformed(
    self, new_axes: PerMember[PerAxis[Union[LinearSampleAxisTransform, int]]]
) -> Self:
    sample_shape = {
        m: {
            a: (
                trf
                if isinstance(trf, int)
                else trf.compute(self.sample_shape[trf.member][trf.axis])
            )
            for a, trf in new_axes[m].items()
        }
        for m in new_axes
    }

    def get_member_halo(m: MemberId, round: Callable[[float], int]):
        return {
            a: (
                Halo(0, 0)
                if isinstance(trf, int)
                or trf.axis not in self.blocks[trf.member].halo
                else Halo(
                    round(self.blocks[trf.member].halo[trf.axis].left * trf.scale),
                    round(self.blocks[trf.member].halo[trf.axis].right * trf.scale),
                )
            )
            for a, trf in new_axes[m].items()
        }

    halo: Dict[MemberId, Dict[AxisId, Halo]] = {}
    for m in new_axes:
        halo[m] = get_member_halo(m, floor)
        if halo[m] != get_member_halo(m, ceil):
            raise ValueError(
                f"failed to unambiguously scale halo {halo[m]} with {new_axes[m]}"
                + f" for {m}."
            )

    inner_slice = {
        m: {
            a: (
                SliceInfo(0, trf)
                if isinstance(trf, int)
                else SliceInfo(
                    trf.compute(
                        self.blocks[trf.member].inner_slice[trf.axis].start
                    ),
                    trf.compute(self.blocks[trf.member].inner_slice[trf.axis].stop),
                )
            )
            for a, trf in new_axes[m].items()
        }
        for m in new_axes
    }
    return self.__class__(
        blocks={
            m: BlockMeta(
                sample_shape=sample_shape[m],
                inner_slice=inner_slice[m],
                halo=halo[m],
                block_index=self.block_index,
                blocks_in_sample=self.blocks_in_sample,
            )
            for m in new_axes
        },
        sample_shape=sample_shape,
        sample_id=self.sample_id,
        block_index=self.block_index,
        blocks_in_sample=self.blocks_in_sample,
    )

with_data ¤

with_data(data: PerMember[Tensor], *, stat: Stat) -> SampleBlock
Source code in src/bioimageio/core/sample.py 
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def with_data(self, data: PerMember[Tensor], *, stat: Stat) -> SampleBlock:
    return SampleBlock(
        sample_shape={
            m: {
                a: data[m].tagged_shape[a] if s == -1 else s
                for a, s in member_shape.items()
            }
            for m, member_shape in self.sample_shape.items()
        },
        sample_id=self.sample_id,
        blocks={
            m: Block.from_meta(b, data=data[m]) for m, b in self.blocks.items()
        },
        stat=stat,
        block_index=self.block_index,
        blocks_in_sample=self.blocks_in_sample,
    )

SampleBlockWithOrigin dataclass ¤

SampleBlockWithOrigin(sample_shape: PerMember[PerAxis[int]], sample_id: SampleId, blocks: Dict[MemberId, BlockT], block_index: BlockIndex, blocks_in_sample: TotalNumberOfBlocks, stat: Stat, origin: Sample)

Bases: SampleBlock


              flowchart TD
              bioimageio.core.sample.SampleBlockWithOrigin[SampleBlockWithOrigin]
              bioimageio.core.sample.SampleBlock[SampleBlock]
              bioimageio.core.sample.SampleBlockBase[SampleBlockBase]

                              bioimageio.core.sample.SampleBlock --> bioimageio.core.sample.SampleBlockWithOrigin
                                bioimageio.core.sample.SampleBlockBase --> bioimageio.core.sample.SampleBlock
                



              click bioimageio.core.sample.SampleBlockWithOrigin href "" "bioimageio.core.sample.SampleBlockWithOrigin"
              click bioimageio.core.sample.SampleBlock href "" "bioimageio.core.sample.SampleBlock"
              click bioimageio.core.sample.SampleBlockBase href "" "bioimageio.core.sample.SampleBlockBase"

A SampleBlock with a reference (origin) to the whole Sample

Returned by:

Methods:

Name Description
get_transformed_meta

Attributes:

Name Type Description
block_index BlockIndex

the n-th block of the sample
blocks Dict[MemberId, BlockT]

Individual tensor blocks comprising this sample block
blocks_in_sample TotalNumberOfBlocks

total number of blocks in the sample
inner_shape PerMember[PerAxis[int]]
members PerMember[Tensor]

the sample block's tensors
origin Sample

the sample this sample block was taken from
sample_id SampleId

identifier for the sample within its dataset
sample_shape PerMember[PerAxis[int]]

the sample shape this block represents a part of
shape PerMember[PerAxis[int]]
stat Stat

computed statistics

block_index instance-attribute ¤

block_index: BlockIndex

the n-th block of the sample

blocks instance-attribute ¤

blocks: Dict[MemberId, BlockT]

Individual tensor blocks comprising this sample block

blocks_in_sample instance-attribute ¤

blocks_in_sample: TotalNumberOfBlocks

total number of blocks in the sample

inner_shape property ¤

inner_shape: PerMember[PerAxis[int]]

members property ¤

members: PerMember[Tensor]

the sample block's tensors

origin instance-attribute ¤

origin: Sample

the sample this sample block was taken from

sample_id instance-attribute ¤

sample_id: SampleId

identifier for the sample within its dataset

sample_shape instance-attribute ¤

sample_shape: PerMember[PerAxis[int]]

the sample shape this block represents a part of

shape property ¤

shape: PerMember[PerAxis[int]]

stat instance-attribute ¤

stat: Stat

computed statistics

get_transformed_meta ¤

get_transformed_meta(new_axes: PerMember[PerAxis[Union[LinearSampleAxisTransform, int]]]) -> SampleBlockMeta
Source code in src/bioimageio/core/sample.py 
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def get_transformed_meta(
    self, new_axes: PerMember[PerAxis[Union[LinearSampleAxisTransform, int]]]
) -> SampleBlockMeta:
    return SampleBlockMeta(
        sample_id=self.sample_id,
        blocks=dict(self.blocks),
        sample_shape=self.sample_shape,
        block_index=self.block_index,
        blocks_in_sample=self.blocks_in_sample,
    ).get_transformed(new_axes)

sample_block_generator ¤

sample_block_generator(blocks: Iterable[PerMember[BlockMeta]], *, origin: Sample, pad_mode: Union[PadMode, PerMember[PadMode]]) -> Iterable[SampleBlockWithOrigin]
Source code in src/bioimageio/core/sample.py 
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def sample_block_generator(
    blocks: Iterable[PerMember[BlockMeta]],
    *,
    origin: Sample,
    pad_mode: Union[PadMode, PerMember[PadMode]],
) -> Iterable[SampleBlockWithOrigin]:
    for member_blocks in blocks:
        cons = _ConsolidatedMemberBlocks(member_blocks)
        yield SampleBlockWithOrigin(
            blocks={
                m: Block.from_sample_member(
                    origin.members[m],
                    block=member_blocks[m],
                    pad_mode=pad_mode.get(m, "symmetric")
                    if isinstance(pad_mode, collections.abc.Mapping)
                    else pad_mode,
                )
                for m in origin.members
            },
            sample_shape=origin.shape,
            origin=origin,
            stat=origin.stat,
            sample_id=origin.id,
            block_index=cons.block_index,
            blocks_in_sample=cons.blocks_in_sample,
        )

sample_block_meta_generator ¤

sample_block_meta_generator(blocks: Iterable[PerMember[BlockMeta]], *, sample_shape: PerMember[PerAxis[int]], sample_id: SampleId)
Source code in src/bioimageio/core/sample.py 
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def sample_block_meta_generator(
    blocks: Iterable[PerMember[BlockMeta]],
    *,
    sample_shape: PerMember[PerAxis[int]],
    sample_id: SampleId,
):
    for member_blocks in blocks:
        cons = _ConsolidatedMemberBlocks(member_blocks)
        yield SampleBlockMeta(
            blocks=dict(member_blocks),
            sample_shape=sample_shape,
            sample_id=sample_id,
            block_index=cons.block_index,
            blocks_in_sample=cons.blocks_in_sample,
        )