Class SlicingTransform
- java.lang.Object
-
- net.imglib2.transform.integer.AbstractMixedTransform
-
- net.imglib2.transform.integer.SlicingTransform
-
- All Implemented Interfaces:
Concatenable<Slicing>
,PreConcatenable<Slicing>
,BoundingBoxTransform
,Mixed
,Slicing
,Transform
public class SlicingTransform extends AbstractMixedTransform implements Slicing, Concatenable<Slicing>, PreConcatenable<Slicing>
Map the components of the source vector to a slice of the target space, for instance transform (x,y) to (x,C,y) where C is a constant.A
SlicingTransform
transform a n-dimensional source vector to a m-dimensional target vector, where m ≥ n. It can be represented as a m+1 × n+1 homogeneous matrix. TheSlicingTransform
can be decomposed as follows:- component permutation
- project up and position (add constant components in the target vector)
The component permutation step is implemented by the
component mapping
. This is a lookup array that specifies for each target dimension from which source dimension it is taken. Note, that it is not allowed to set this array such that a source component is mapped to several target components!- Author:
- Tobias Pietzsch
-
-
Field Summary
Fields Modifier and Type Field Description protected int[]
component
specifies for each component of the target vector from which source vector component should it be taken.protected int
numSourceDimensions
dimension of source vector.protected long[]
translation
translation is added to the target vector after applying the permutation and project-up operations.protected boolean[]
zero
for each component of the target vector (before translation).-
Fields inherited from class net.imglib2.transform.integer.AbstractMixedTransform
numTargetDimensions
-
-
Constructor Summary
Constructors Constructor Description SlicingTransform(int sourceDim, int targetDim)
-
Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description void
apply(int[] source, int[] target)
Apply theTransform
to a source vector to obtain a target vector.void
apply(long[] source, long[] target)
Apply theTransform
to a source vector to obtain a target vector.void
apply(Localizable source, Positionable target)
SlicingTransform
concatenate(Slicing t)
Concatenate this object with a.int
getComponentMapping(int d)
Get the source dimension which is mapped to the d-th target dimension (seeMixed.getComponentMapping(int[])
).void
getComponentMapping(int[] component)
Get an array indicating for each target dimensions from which source dimension it is taken.void
getComponentZero(boolean[] zero)
Get a boolean array indicating which target dimensions are _not_ taken from source dimensions.boolean
getComponentZero(int d)
Get the d-th component of zeroing vector (seeMixed.getComponentZero(boolean[])
).java.lang.Class<Slicing>
getConcatenableClass()
double[][]
getMatrix()
Get the matrix that transforms homogeneous source points to homogeneous target points.java.lang.Class<Slicing>
getPreConcatenableClass()
long
getTranslation(int d)
Get the d-th component of translation (seeMixed.getTranslation(long[])
).void
getTranslation(long[] t)
Get the translation.boolean
hasFullSourceMapping()
Check whether the transforms has a full mapping of source to target components (no source component is discarded).int
numSourceDimensions()
Returns n, the dimension of the source vector.SlicingTransform
preConcatenate(Slicing t)
Pre-concatenate this object with a.void
set(Slicing transform)
set parameters totransform
.void
setComponentMapping(int[] component)
Set for each target dimensions from which source dimension it is taken.void
setComponentZero(boolean[] zero)
Set which target dimensions are _not_ taken from source dimensions.void
setTranslation(long[] t)
-
Methods inherited from class net.imglib2.transform.integer.AbstractMixedTransform
getComponentInversion, getComponentInversion, numTargetDimensions, transform
-
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
-
Methods inherited from interface net.imglib2.transform.integer.BoundingBoxTransform
transform
-
Methods inherited from interface net.imglib2.transform.integer.Mixed
getComponentInversion, getComponentInversion
-
Methods inherited from interface net.imglib2.transform.Transform
numTargetDimensions
-
-
-
-
Field Detail
-
numSourceDimensions
protected final int numSourceDimensions
dimension of source vector.
-
zero
protected final boolean[] zero
for each component of the target vector (before translation). should the value be taken from a source vector component (false) or should it be zero (true).
-
translation
protected final long[] translation
translation is added to the target vector after applying the permutation and project-up operations. Only translation values for dimensions that have not been assigned a source vector component are used. For instance, if you project (x,y) to (x,y,z) only the translation value for z is used.
-
component
protected final int[] component
specifies for each component of the target vector from which source vector component should it be taken.
-
-
Method Detail
-
numSourceDimensions
public int numSourceDimensions()
Description copied from interface:Transform
Returns n, the dimension of the source vector.- Specified by:
numSourceDimensions
in interfaceTransform
- Overrides:
numSourceDimensions
in classAbstractMixedTransform
- Returns:
- the dimension of the source vector.
-
getTranslation
public void getTranslation(long[] t)
Description copied from interface:Mixed
Get the translation. Translation is added to the target vector after applying permutation, projection, inversion operations.- Specified by:
getTranslation
in interfaceMixed
- Overrides:
getTranslation
in classAbstractMixedTransform
- Parameters:
t
- array of size at least the target dimension to store the result.
-
getTranslation
public long getTranslation(int d)
Description copied from interface:Mixed
Get the d-th component of translation (seeMixed.getTranslation(long[])
).- Specified by:
getTranslation
in interfaceMixed
- Overrides:
getTranslation
in classAbstractMixedTransform
-
setTranslation
public void setTranslation(long[] t)
-
getComponentZero
public void getComponentZero(boolean[] zero)
Description copied from interface:Mixed
Get a boolean array indicating which target dimensions are _not_ taken from source dimensions.For instance, if the transform maps 2D (x,y) coordinates to the first two components of a 3D (x,y,z) coordinate, the result will be [false, false, true]
- Specified by:
getComponentZero
in interfaceMixed
- Overrides:
getComponentZero
in classAbstractMixedTransform
- Parameters:
zero
- array of size at least the target dimension to store the result.
-
getComponentZero
public boolean getComponentZero(int d)
Description copied from interface:Mixed
Get the d-th component of zeroing vector (seeMixed.getComponentZero(boolean[])
).- Specified by:
getComponentZero
in interfaceMixed
- Overrides:
getComponentZero
in classAbstractMixedTransform
-
setComponentZero
public void setComponentZero(boolean[] zero)
Set which target dimensions are _not_ taken from source dimensions.For instance, if the transform maps 2D (x,y) coordinates to the first two components of a 3D (x,y,z) coordinate, this will be [false, false, true]
- Parameters:
zero
- array that says for each component of the target vector (before translation) whether the value should be taken from a source vector component (false) or should be set to zero (true).
-
getComponentMapping
public void getComponentMapping(int[] component)
Description copied from interface:Mixed
Get an array indicating for each target dimensions from which source dimension it is taken.For instance, if the transform maps 2D (x,y) coordinates to the first two components of a 3D (x,y,z) coordinate, the result will be [0, 1, x]. Here, the value of x is undefined because the third target dimension does not correspond to any source dimension. See
Mixed.getComponentZero(boolean[])
.- Specified by:
getComponentMapping
in interfaceMixed
- Overrides:
getComponentMapping
in classAbstractMixedTransform
- Parameters:
component
- array of size at least the target dimension to store the result.
-
getComponentMapping
public int getComponentMapping(int d)
Description copied from interface:Mixed
Get the source dimension which is mapped to the d-th target dimension (seeMixed.getComponentMapping(int[])
).- Specified by:
getComponentMapping
in interfaceMixed
- Overrides:
getComponentMapping
in classAbstractMixedTransform
-
setComponentMapping
public void setComponentMapping(int[] component)
Set for each target dimensions from which source dimension it is taken.For instance, if the transform maps 2D (x,y) coordinates to the first two components of a 3D (x,y,z) coordinate, this will be [0, 1, x]. Here, x can be any value because the third target dimension does not correspond to any source dimension, which can be realized using
setComponentZero(boolean[])
.Note, that it is not allowed to set the
component
array such that a source component is mapped to several target components!- Parameters:
component
- array that says for each component of the target vector (before translation) from which source vector component it should be taken.
-
apply
public void apply(long[] source, long[] target)
Description copied from interface:Transform
Apply theTransform
to a source vector to obtain a target vector.
-
apply
public void apply(int[] source, int[] target)
Description copied from interface:Transform
Apply theTransform
to a source vector to obtain a target vector.
-
apply
public void apply(Localizable source, Positionable target)
Description copied from interface:Transform
-
concatenate
public SlicingTransform concatenate(Slicing t)
Description copied from interface:Concatenable
Concatenate this object with a. The result will be an object that can be concatenated with another A. The conventional meaning for concatenating transformations is the following: Let ba = b.concatenate(a). Applying ba to x is equivalent to first applying a to x and then applying b to the result.- Specified by:
concatenate
in interfaceConcatenable<Slicing>
-
getConcatenableClass
public java.lang.Class<Slicing> getConcatenableClass()
- Specified by:
getConcatenableClass
in interfaceConcatenable<Slicing>
-
preConcatenate
public SlicingTransform preConcatenate(Slicing t)
Description copied from interface:PreConcatenable
Pre-concatenate this object with a. The result will be an object that can be pre-concatenated with another A. The conventional meaning for concatenating transformations is the following: Let ba = a.preConcatenate(b). Applying ba to x is equivalent to first applying a to x and then applying b to the result.- Specified by:
preConcatenate
in interfacePreConcatenable<Slicing>
-
getPreConcatenableClass
public java.lang.Class<Slicing> getPreConcatenableClass()
- Specified by:
getPreConcatenableClass
in interfacePreConcatenable<Slicing>
-
set
public void set(Slicing transform)
set parameters totransform
.- Parameters:
transform
-
-
getMatrix
public double[][] getMatrix()
Get the matrix that transforms homogeneous source points to homogeneous target points. For testing purposes.
-
hasFullSourceMapping
public boolean hasFullSourceMapping()
Check whether the transforms has a full mapping of source to target components (no source component is discarded).- Returns:
- whether there is a full mapping of source to target components.
-
-