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Reshape Array

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Utilities for reshaping arrays between original and transformed space.

AxesTransform dataclass

Transformation between original and transformed space axes.

All transformation decisions are derived from the original axes string, shape.

Attributes:

Name Type Description
original_axes str

User defined attribute. Axes string of the input data (e.g. "YXC", "STCZYX").
original_shape tuple[int, ...]

User defined attribute. Shape corresponding to original_axes.
sample_dims list[str]

Computed property. Original dimensions merged into S. Spatial (Y, X and Z), as well as channels, are never considered sample dimensions.
c_added bool

Computed property. Whether C is added as a singleton.
has_z bool

Computed property. Whether original data contains a Z axis.
dim_sizes dict[str, int]

Computed property. Map from axis name to original size.
transformed_axes str

Computed property. Transformed axes string: "SC(Z)YX".
transformed_shape tuple[int, ...]

Computed property. Expected shape after forward transformation.
order_permutation list[int]

Computed property. Permutation to reorder original axes to STCZYX reference order in SC(Z)YX space.

c_added property

C is added as a singleton dimension.

Returns:

Type Description
bool

True if C is not in original axes, False otherwise.

dim_sizes property

Map from axis name to original size.

Returns:

Type Description
dict[str, int]

Dictionary mapping axis name to its size in the original shape.

has_z property

Original data contains a Z axis.

Returns:

Type Description
bool

True if Z is in original axes, False otherwise.

order_permutation property

Permutation to reorder original axes to STCZYX reference order.

Returns:

Type Description
list[int]

List of indices representing the permutation to reorder original axes to STCZYX reference order. Only includes axes present in the original axes.

sample_dims property

Original dimensions merged into S.

Spatial (Y, X and Z), as well as channels, are never considered sample dimensions.

Returns:

Type Description
list[str]

List of original axes that are considered sample dimensions and merged into S. Will be in the order they appear in the reference STCZYX.

transformed_axes property

Transformed axes string, SC(Z)YX or SCYX.

Returns:

Type Description
str

Transformed axes string. Will be SCZYX if original data has Z axis, otherwise SCYX.

transformed_shape property

Expected shape in transformed space.

Returns:

Type Description
tuple[int, ...]

Expected shape after forward transformation, in the order of transformed_axes.

get_original_stitch_slices(original_axes, original_shape, sample_idx, stitch_coords, crop_size)

Get slices to stitch tile back into original array.

sample_idx andstitch_coords` are expressed with respect to the transformed space (SCZYX or SCYX). The returned slices will index into the original array for stitching the tile back in place.

Parameters:

Name Type Description Default
original_axes str

Original axes string of the full data.

 required
original_shape Sequence[int]

Original shape of the full data.

 required
sample_idx int

Index of the sample in transformed space (S axis) to stitch back.

 required
stitch_coords Sequence[int]

Starting coordinates of the tile in the original spatial axes (Y, X and Z if present).

 required
crop_size Sequence[int]

Size of the tile in the original spatial axes (Y, X and Z if present).

 required

Returns:

Type Description
tuple[slice | int, ...]

Slices to index into the original array for stitching the tile back in place.

reshape_array(array, original_axes)

Reshape array from arbitrary axes order to SC(Z)YX.

Parameters:

Name Type Description Default
array ndarray

Input array.

 required
original_axes str

Original axes string describing current dimension order (e.g. YXC).

 required

Returns:

Type Description
ndarray

Array reshaped to SC(Z)YX.

restore_array(array, original_axes, original_shape)

Restore array from SC(Z)YX space back to original axes and shape.

Parameters:

Name Type Description Default
array ndarray

Array in SC(Z)YX format.

 required
original_axes str

Original axes string (e.g. YXC).

 required
original_shape Sequence[int]

Original shape of the data.

 required

Returns:

Type Description
ndarray

Array with original axes order and shape restored.

Raises:

Type Description
ValueError

If input array is not 4D (SCYX) or 5D (SCZYX), or if restoring shape is not supported for the given original axes (e.g. T as Z with CZI format).

restore_tile(tile, original_axes, original_shape)

Restore single tile from C(Z)YX space back to original axes and shape.

Parameters:

Name Type Description Default
tile ndarray

Tile in C(Z)YX format.

 required
original_axes str

Original axes string of the full data.

 required
original_shape Sequence[int]

Original shape of the full data.

 required

Returns:

Type Description
ndarray

Tile with original spatial axes order restored.