Plugin type: 3dimage/transform
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## Plugin type: 3dimage/transform

These plug-ins define creators for 3D transformations.

#### Plugins:

affine axisrot raffine rigid rotation rotbend spline translate vf

##### affine

Affine transformation (12 degrees of freedom). Supported parameters are:

Name | Type | Default | Description
--- | --- | --- | ---
imgboundary | factory | mirror | image interpolation boundary conditions. For supported plug-ins see Plugin type: 1d/splinebc
imgkernel | factory | [bspline:d=3] | image interpolator kernel. For supported plug-ins see Plugin type: 1d/splinekernel

##### axisrot

Restricted rotation transformation (1 degrees of freedom). The transformation is restricted to the rotation around the given axis about the given rotation center. Supported parameters are:

Name | Type | Default | Description
--- | --- | --- | ---
axis | 3dfvector | (required) | rotation axis
imgboundary | factory | mirror | image interpolation boundary conditions. For supported plug-ins see Plugin type: 1d/splinebc
imgkernel | factory | [bspline:d=3] | image interpolator kernel. For supported plug-ins see Plugin type: 1d/splinekernel
origin | 3dfvector | (required) | center of the transformation

##### raffine

Restricted affine transformation (3 degrees of freedom). The transformation is restricted to the rotation around the given axis and shearing along the two axis perpendicular to the given one. Supported parameters are:

Name | Type | Default | Description
--- | --- | --- | ---
axis | 3dfvector | (required) | rotation axis
imgboundary | factory | mirror | image interpolation boundary conditions. For supported plug-ins see Plugin type: 1d/splinebc
imgkernel | factory | [bspline:d=3] | image interpolator kernel. For supported plug-ins see Plugin type: 1d/splinekernel
origin | 3dfvector | (required) | center of the transformation

##### rigid

Rigid transformation, i.e. rotation and translation (six degrees of freedom).. Supported parameters are:

Name | Type | Default | Description
--- | --- | --- | ---
imgboundary | factory | mirror | image interpolation boundary conditions. For supported plug-ins see Plugin type: 1d/splinebc
imgkernel | factory | [bspline:d=3] | image interpolator kernel. For supported plug-ins see Plugin type: 1d/splinekernel
origin | 3dfvector | [[0,0,0]] | Relative rotation center, i.e. <0.5,0.5,0.5> corresponds to the center of the volume

##### rotation

Rotation transformation (three degrees of freedom).. Supported parameters are:

Name | Type | Default | Description
--- | --- | --- | ---
imgboundary | factory | mirror | image interpolation boundary conditions. For supported plug-ins see Plugin type: 1d/splinebc
imgkernel | factory | [bspline:d=3] | image interpolator kernel. For supported plug-ins see Plugin type: 1d/splinekernel
origin | 3dfvector | [[0,0,0]] | Relative rotation center, i.e. <0.5,0.5,0.5> corresponds to the center of the volume

##### rotbend

Restricted transformation (4 degrees of freedom). The transformation is restricted to the rotation around the x and y axis and a bending along the x axis, independedn in each direction, with the bending increasing with the squared distance from the rotation axis.. Supported parameters are:

Name | Type | Default | Description
--- | --- | --- | ---
imgboundary | factory | mirror | image interpolation boundary conditions. For supported plug-ins see Plugin type: 1d/splinebc
imgkernel | factory | [bspline:d=3] | image interpolator kernel. For supported plug-ins see Plugin type: 1d/splinekernel
norot | bool | 0 | Don't optimize the rotation
origin | 3dfvector | (required) | center of the transformation

##### spline

Free-form transformation that can be described by a set of B-spline coefficients and an underlying B-spline kernel.. Supported parameters are:

Name | Type | Default | Description
--- | --- | --- | ---
anisorate | 3dfvector | [[0,0,0]] | anisotropic coefficient rate in pixels, nonpositive values will be overwritten by the 'rate' value.
debug | bool | 0 | enable additional debugging output
imgboundary | factory | mirror | image interpolation boundary conditions. For supported plug-ins see Plugin type: 1d/splinebc
imgkernel | factory | [bspline:d=3] | image interpolator kernel. For supported plug-ins see Plugin type: 1d/splinekernel
kernel | factory | [bspline:d=3] | transformation spline kernel. For supported plug-ins see Plugin type: 1d/splinekernel
penalty | factory |  | transformation penalty energy term. For supported plug-ins see Plugin type: 3dtransform/splinepenalty
rate | float in [1, inf) | 10 | isotropic coefficient rate in pixels

##### translate

Translation (three degrees of freedom). Supported parameters are:

Name | Type | Default | Description
--- | --- | --- | ---
imgboundary | factory | mirror | image interpolation boundary conditions. For supported plug-ins see Plugin type: 1d/splinebc
imgkernel | factory | [bspline:d=3] | image interpolator kernel. For supported plug-ins see Plugin type: 1d/splinekernel

##### vf

This plug-in implements a transformation that defines a translation for each point of the grid defining the domain of the transformation.. Supported parameters are:

Name | Type | Default | Description
--- | --- | --- | ---
imgboundary | factory | mirror | image interpolation boundary conditions. For supported plug-ins see Plugin type: 1d/splinebc
imgkernel | factory | [bspline:d=3] | image interpolator kernel. For supported plug-ins see Plugin type: 1d/splinekernel

#### Plugin consumers:

mia-3dcost-translatedgrad mia-3dmany2one-nonrigid mia-3dnonrigidreg mia-3dnonrigidreg-alt mia-3dprealign-nonrigid mia-3drigidreg mia-3dserial-nonrigid

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