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:

NameTypeDefaultDescription
imgboundaryfactorymirrorimage interpolation boundary conditions. For supported plug-ins see Plugin type: 1d/splinebc
imgkernelfactory[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:

NameTypeDefaultDescription
axis3dfvector(required)rotation axis
imgboundaryfactorymirrorimage interpolation boundary conditions. For supported plug-ins see Plugin type: 1d/splinebc
imgkernelfactory[bspline:d=3]image interpolator kernel. For supported plug-ins see Plugin type: 1d/splinekernel
origin3dfvector(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:

NameTypeDefaultDescription
axis3dfvector(required)rotation axis
imgboundaryfactorymirrorimage interpolation boundary conditions. For supported plug-ins see Plugin type: 1d/splinebc
imgkernelfactory[bspline:d=3]image interpolator kernel. For supported plug-ins see Plugin type: 1d/splinekernel
origin3dfvector(required)center of the transformation

rigid

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

NameTypeDefaultDescription
imgboundaryfactorymirrorimage interpolation boundary conditions. For supported plug-ins see Plugin type: 1d/splinebc
imgkernelfactory[bspline:d=3]image interpolator kernel. For supported plug-ins see Plugin type: 1d/splinekernel
origin3dfvector[[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:

NameTypeDefaultDescription
imgboundaryfactorymirrorimage interpolation boundary conditions. For supported plug-ins see Plugin type: 1d/splinebc
imgkernelfactory[bspline:d=3]image interpolator kernel. For supported plug-ins see Plugin type: 1d/splinekernel
origin3dfvector[[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:

NameTypeDefaultDescription
imgboundaryfactorymirrorimage interpolation boundary conditions. For supported plug-ins see Plugin type: 1d/splinebc
imgkernelfactory[bspline:d=3]image interpolator kernel. For supported plug-ins see Plugin type: 1d/splinekernel
norotbool0Don't optimize the rotation
origin3dfvector(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:

NameTypeDefaultDescription
anisorate3dfvector[[0,0,0]]anisotropic coefficient rate in pixels, nonpositive values will be overwritten by the 'rate' value.
debugbool0enable additional debuging output
imgboundaryfactorymirrorimage interpolation boundary conditions. For supported plug-ins see Plugin type: 1d/splinebc
imgkernelfactory[bspline:d=3]image interpolator kernel. For supported plug-ins see Plugin type: 1d/splinekernel
kernelfactory[bspline:d=3]transformation spline kernel. For supported plug-ins see Plugin type: 1d/splinekernel
penaltyfactory transformation penalty energy term. For supported plug-ins see Plugin type: 3dtransform/splinepenalty
ratefloat in [1, inf)10isotropic coefficient rate in pixels

translate

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

NameTypeDefaultDescription
imgboundaryfactorymirrorimage interpolation boundary conditions. For supported plug-ins see Plugin type: 1d/splinebc
imgkernelfactory[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:

NameTypeDefaultDescription
imgboundaryfactorymirrorimage interpolation boundary conditions. For supported plug-ins see Plugin type: 1d/splinebc
imgkernelfactory[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