cornucopia.fov

This module contains transforms that operate on the field of view (FOV) of the image.

FlipTransform

FlipTransform(axis=None, **kwargs)

Bases: FinalTransform

Flip one or more axes.

Parameters:

Name	Type	Description	Default
`axis`	`[list of] int`	Axes to flip. By default, flip all spatial axes.	`None`

Other Parameters:

Name	Type	Description
`returns`		See `Transform` for details.
`append`		See `Transform` for details.
`prefix`		See `Transform` for details.
`include`		See `Transform` for details.
`exclude`		See `Transform` for details.
`consume`		See `Transform` for details.

RandomFlipTransform

RandomFlipTransform(axes=None, *, shared=True, **kwargs)

Bases: NonFinalTransform

Randomly flip one or more axes.

Parameters:

Name	Type	Description	Default
`axes`	`Sampler \| [list of] int`	Axes that can be flipped (default: all spatial axes)	`None`

Other Parameters:

Name	Type	Description
`shared`	`bool`	See `NonFinalTransform` for details.
`returns`		See `Transform` for details.
`append`		See `Transform` for details.
`prefix`		See `Transform` for details.
`include`		See `Transform` for details.
`exclude`		See `Transform` for details.
`consume`		See `Transform` for details.

Final `class-attribute` `instance-attribute`

Final = FlipTransform

The transform type returned by unroll, next and final.

Next `class-attribute` `instance-attribute`

Next = FlipTransform

The transform type returned by unroll, next and final.

PermuteAxesTransform

PermuteAxesTransform(permutation=None, **kwargs)

Bases: FinalTransform

Permute axes

Parameters:

Name	Type	Description	Default
`permutation`	`[list of] int`	Axes permutation. By default, reverse axes. Only applies to spatial axes, so axes are numbered [C, 0, 1, 2]	`None`

Other Parameters:

Name	Type	Description
`returns`		See `Transform` for details.
`append`		See `Transform` for details.
`prefix`		See `Transform` for details.
`include`		See `Transform` for details.
`exclude`		See `Transform` for details.
`consume`		See `Transform` for details.

RandomPermuteAxesTransform

RandomPermuteAxesTransform(axes=None, *, shared=True, **kwargs)

Bases: NonFinalTransform

Randomly permute axes.

Parameters:

Name	Type	Description	Default
`axes`	`[list of] int`	Axes that can be permuted (default: all)	`None`

Other Parameters:

Name	Type	Description
`shared`	`bool`	See `NonFinalTransform` for details.
`returns`		See `Transform` for details.
`append`		See `Transform` for details.
`prefix`		See `Transform` for details.
`include`		See `Transform` for details.
`exclude`		See `Transform` for details.
`consume`		See `Transform` for details.

Final `class-attribute` `instance-attribute`

Final = PermuteAxesTransform

The transform type returned by unroll, next and final.

Next `class-attribute` `instance-attribute`

Next = PermuteAxesTransform

The transform type returned by unroll, next and final.

Rot90Transform

Rot90Transform(axis=0, negative=False, double=False, **kwargs)

Bases: FinalTransform

Apply a 90 (or 180) rotation along one or several axes.

Parameters:

Name	Type	Description	Default
`axis`	`[list of] int`	Rotation axis (indexing does not account for the channel axis)	`0`
`negative`	`[list of] bool`	Rotate by -90 deg instead of 90 deg	`False`
`double`	`[list of] bool`	Rotate be 180 instead of 90 (`negative` is then unused)	`False`

Other Parameters:

Name	Type	Description
`returns`		See `Transform` for details.
`append`		See `Transform` for details.
`prefix`		See `Transform` for details.
`include`		See `Transform` for details.
`exclude`		See `Transform` for details.
`consume`		See `Transform` for details.

Rot180Transform

Rot180Transform(axis=0, **kwargs)

Bases: Rot90Transform

Apply a 180 deg rotation along one or several axes

Parameters:

Name	Type	Description	Default
`axis`	`[list of] int`	Rotation axis (indexing does not account for the channel axis)	`0`

Other Parameters:

Name	Type	Description
`returns`		See `Transform` for details.
`append`		See `Transform` for details.
`prefix`		See `Transform` for details.
`include`		See `Transform` for details.
`exclude`		See `Transform` for details.
`consume`		See `Transform` for details.

RandomRot90Transform

RandomRot90Transform(axes=None, max_rot=2, negative=True, *, shared=True, **kwargs)

Bases: NonFinalTransform

Random set of 90 transforms.

Parameters:

Name	Type	Description	Default
`axes`	`[list of] int`	Axes along which rotations can happen. If `None`, all axes.	`None`
`max_rot`	`Sampler \| int`	Maximum number of consecutive rotations.	`2`
`negative`	`bool`	Whether to authorize negative rotations.	`True`

Other Parameters:

Name	Type	Description
`shared`	`SharedT`	See `NonFinalTransform` for details.
`returns`		See `Transform` for details.
`append`		See `Transform` for details.
`prefix`		See `Transform` for details.
`include`		See `Transform` for details.
`exclude`		See `Transform` for details.
`consume`		See `Transform` for details.

Final `class-attribute` `instance-attribute`

Final = Rot90Transform

The transform type returned by unroll, next and final.

Next `class-attribute` `instance-attribute`

Next = Rot90Transform

The transform type returned by unroll, next and final.

CropPadTransform

CropPadTransform(crop=(), pad=(), bound='zero', value=0, **kwargs)

Bases: FinalTransform

Crop and/or pad a tensor.

Parameters:

Name	Type	Description	Default
`crop`	`list[slice]`	Slicing operator per dimension.	`()`
`pad`	`list[int]`	Left and right padding per dimensions	`()`
`bound`	`[list of] str`	Boundary condition for padding	`'zero'`
`value`	`number`	Padding value in case `bound='constant`	`0`

Other Parameters:

Name	Type	Description
`returns`		See `Transform` for details.
`append`		See `Transform` for details.
`prefix`		See `Transform` for details.
`include`		See `Transform` for details.
`exclude`		See `Transform` for details.
`consume`		See `Transform` for details.

PatchTransform

PatchTransform(shape=64, center=0, bound='zero', *, shared=True, **kwargs)

Bases: NonFinalTransform

Extract a patch from the volume

Parameters:

Name	Type	Description	Default
`shape`	`[list of] int`	Patch shape	`64`
`center`	`[list of] float`	Patch center, in relative coordinates -1..1	`0`
`bound`	`[list of]str`	Boundary condition in case padding is needed	`'zero'`

Other Parameters:

Name	Type	Description
`shared`	`SharedT`	See `NonFinalTransform` for details. Default for `shared` changed from `"channels"` to `True`
`returns`		See `Transform` for details.
`append`		See `Transform` for details.
`prefix`		See `Transform` for details.
`include`		See `Transform` for details.
`exclude`		See `Transform` for details.
`consume`		See `Transform` for details.

Final `class-attribute` `instance-attribute`

Final = CropPadTransform

The transform type returned by unroll, next and final.

Next `class-attribute` `instance-attribute`

Next = CropPadTransform

The transform type returned by unroll, next and final.

RandomPatchTransform

RandomPatchTransform(shape, bound='zero', *, shared=True, **kwargs)

Bases: NonFinalTransform

Extract a (randomly located) patch from the volume.

This transform ensures that the patch is fully contained within the original field of view (unless the patch size is larger than the input shape).

Parameters:

Name	Type	Description	Default
`shape`	`[list of] int`	Patch shape	required
`bound`	`[list of] str`	Boundary condition in case padding is needed	`'zero'`

Other Parameters:

Name	Type	Description
`shared`	`SharedT`	See `NonFinalTransform` for details. Default for `shared` changed from `"channels"` to `True`
`returns`		See `Transform` for details.
`append`		See `Transform` for details.
`prefix`		See `Transform` for details.
`include`		See `Transform` for details.
`exclude`		See `Transform` for details.
`consume`		See `Transform` for details.

Next `class-attribute` `instance-attribute`

Next = PatchTransform

The transform type returned by next.

Final `class-attribute` `instance-attribute`

Final = CropPadTransform

The transform type returned by final.

CropTransform

CropTransform(cropping, unit='vox', side='both', **kwargs)

Bases: NonFinalTransform

Crop a tensor by some amount

Parameters:

Name	Type	Description	Default
`cropping`	`[list of] int or float`	Amount of cropping. If `side` is `None`, pre and post cropping must be provided in turn.	required
`unit`	`(vox, pct)`	Padding unit	`'vox'`
`side`	`(pre, post, both, None)`	Side to crop	`'pre'`

Other Parameters:

Name	Type	Description
`shared`		See `NonFinalTransform` for details. Default for `shared` changed from `"channels"` to `True`
`returns`		See `Transform` for details.
`append`		See `Transform` for details.
`prefix`		See `Transform` for details.
`include`		See `Transform` for details.
`exclude`		See `Transform` for details.
`consume`		See `Transform` for details.

PadTransform

PadTransform(padding, unit='vox', side='both', bound='zero', value=0, **kwargs)

Bases: NonFinalTransform

Pad a tensor by some amount

Parameters:

Name	Type	Description	Default
`padding`	`[list of] int or float`	Amount of padding. If `side` is `None`, pre and post padding must be provided in turn.	required
`unit`	`(vox, pct)`	Padding unit	`'vox'`
`side`	`(pre, post, both, None)`	Side to pad	`'pre'`
`bound`	`str`	Boundary condition	`'zero'`
`value`	`float`	Value for case `bound='constant'`	`0`

Other Parameters:

Name	Type	Description
`shared`		See `NonFinalTransform` for details. Default for `shared` changed from `"channels"` to `True`
`returns`		See `Transform` for details.
`append`		See `Transform` for details.
`prefix`		See `Transform` for details.
`include`		See `Transform` for details.
`exclude`		See `Transform` for details.
`consume`		See `Transform` for details.

Final `class-attribute` `instance-attribute`

Final = CropPadTransform

The transform type returned by unroll, next and final.

Next `class-attribute` `instance-attribute`

Next = CropPadTransform

The transform type returned by unroll, next and final.

PowerTwoTransform

PowerTwoTransform(exponent=1, bound='zero', **kwargs)

Bases: NonFinalTransform

Pad the volume such that the tensor shape can be divided by 2**x

Parameters:

Name	Type	Description	Default
`exponent`	`[list of] int`	Ensure that the shape can be divided by 2 ** exponent	`1`
`bound`	`[list of] str`	Boundary condition for padding	`'zero'`

Other Parameters:

Name	Type	Description
`shared`		See `NonFinalTransform` for details. Default for `shared` changed from `"channels"` to `True`
`returns`		See `Transform` for details.
`append`		See `Transform` for details.
`prefix`		See `Transform` for details.
`include`		See `Transform` for details.
`exclude`		See `Transform` for details.
`consume`		See `Transform` for details.

Next `class-attribute` `instance-attribute`

Next = PatchTransform

The transform type returned by next.

Final `class-attribute` `instance-attribute`

Final = CropPadTransform

The transform type returned by final.

cornucopia.fov

FlipTransform

RandomFlipTransform

Final class-attribute instance-attribute

Next class-attribute instance-attribute

PermuteAxesTransform

RandomPermuteAxesTransform

Final class-attribute instance-attribute

Next class-attribute instance-attribute

Rot90Transform

Rot180Transform

RandomRot90Transform

Final class-attribute instance-attribute

Next class-attribute instance-attribute

CropPadTransform

PatchTransform

Final class-attribute instance-attribute

Next class-attribute instance-attribute

RandomPatchTransform

Next class-attribute instance-attribute

Final class-attribute instance-attribute

CropTransform

PadTransform

Final class-attribute instance-attribute

Next class-attribute instance-attribute

PowerTwoTransform

Next class-attribute instance-attribute

Final class-attribute instance-attribute

Final `class-attribute` `instance-attribute`

Next `class-attribute` `instance-attribute`

Final `class-attribute` `instance-attribute`

Next `class-attribute` `instance-attribute`

Final `class-attribute` `instance-attribute`

Next `class-attribute` `instance-attribute`

Final `class-attribute` `instance-attribute`

Next `class-attribute` `instance-attribute`

Next `class-attribute` `instance-attribute`

Final `class-attribute` `instance-attribute`

Final `class-attribute` `instance-attribute`

Next `class-attribute` `instance-attribute`

Next `class-attribute` `instance-attribute`

Final `class-attribute` `instance-attribute`