SlicingTransform (ImgLib2 Javadocs 0-SNAPSHOT API)

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. The SlicingTransform can be decomposed as follows:
1. component permutation
2. 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 and 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 and Description

SlicingTransform(int sourceDim, int targetDim)

Constructors
Constructor and Description
`SlicingTransform(int sourceDim, int targetDim)`

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`void`	`apply(int[] source, int[] target)` Apply the `Transform` to a source vector to obtain a target vector.
`void`	`apply(Localizable source, Positionable target)` Apply the `Transform` to a source `Localizable` to obtain a target `Positionable`.
`void`	`apply(long[] source, long[] target)` Apply the `Transform` to a source vector to obtain a target vector.
`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 (see `Mixed.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 (see `Mixed.getComponentZero(boolean[])`).
`Class<Slicing>`	`getConcatenableClass()`
`double[][]`	`getMatrix()` Get the matrix that transforms homogeneous source points to homogeneous target points.
`Class<Slicing>`	`getPreConcatenableClass()`
`long`	`getTranslation(int d)` Get the d-th component of translation (see `Mixed.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 to `transform`.
`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.Mixed
getComponentInversion, getComponentInversion

Methods inherited from interface net.imglib2.transform.Transform
numTargetDimensions

Methods inherited from interface net.imglib2.transform.integer.BoundingBoxTransform
transform

- 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.
- Constructor Detail
  - SlicingTransform
```
public SlicingTransform(int sourceDim,
                        int targetDim)
```
- Method Detail
  - numSourceDimensions
```
public int numSourceDimensions()
```
    Description copied from interface: Transform
    
    Returns n, the dimension of the source vector.
    
    Specified by:
    
    numSourceDimensions in interface Transform
    
    Overrides:
    
    numSourceDimensions in class AbstractMixedTransform
    
    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 interface Mixed
    
    Overrides:
    
    getTranslation in class AbstractMixedTransform
    
    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 (see Mixed.getTranslation(long[])).
    
    Specified by:
    
    getTranslation in interface Mixed
    
    Overrides:
    
    getTranslation in class AbstractMixedTransform
  - 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 interface Mixed
    
    Overrides:
    
    getComponentZero in class AbstractMixedTransform
    
    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 (see Mixed.getComponentZero(boolean[])).
    
    Specified by:
    
    getComponentZero in interface Mixed
    
    Overrides:
    
    getComponentZero in class AbstractMixedTransform
  - 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 interface Mixed
    
    Overrides:
    
    getComponentMapping in class AbstractMixedTransform
    
    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 (see Mixed.getComponentMapping(int[])).
    
    Specified by:
    
    getComponentMapping in interface Mixed
    
    Overrides:
    
    getComponentMapping in class AbstractMixedTransform
  - 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 the Transform to a source vector to obtain a target vector.
    
    Specified by:
    
    apply in interface Transform
    
    Parameters:
    
    source - source coordinates.
    
    target - set this to the target coordinates.
  - apply
```
public void apply(int[] source,
                  int[] target)
```
    Description copied from interface: Transform
    
    Apply the Transform to a source vector to obtain a target vector.
    
    Specified by:
    
    apply in interface Transform
    
    Parameters:
    
    source - source coordinates.
    
    target - set this to the target coordinates.
  - apply
```
public void apply(Localizable source,
                  Positionable target)
```
    Description copied from interface: Transform
    
    Apply the Transform to a source Localizable to obtain a target Positionable.
    
    Specified by:
    
    apply in interface Transform
    
    Parameters:
    
    source - source coordinates.
    
    target - set this to the target coordinates.
  - 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 interface Concatenable<Slicing>
  - getConcatenableClass
```
public Class<Slicing> getConcatenableClass()
```
    Specified by:
    
    getConcatenableClass in interface Concatenable<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 interface PreConcatenable<Slicing>
  - getPreConcatenableClass
```
public Class<Slicing> getPreConcatenableClass()
```
    Specified by:
    
    getPreConcatenableClass in interface PreConcatenable<Slicing>
  - set
```
public void set(Slicing transform)
```
    set parameters to transform.
    
    Parameters:
    
    transform -
  - getMatrix
```
public double[][] getMatrix()
```
    Get the matrix that transforms homogeneous source points to homogeneous target points. For testing purposes.
    
    Specified by:
    
    getMatrix in interface Mixed
  - 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.

Class SlicingTransform

Field Summary

Fields inherited from class net.imglib2.transform.integer.AbstractMixedTransform

Constructor Summary

Method Summary

Methods inherited from class net.imglib2.transform.integer.AbstractMixedTransform

Methods inherited from class java.lang.Object

Methods inherited from interface net.imglib2.transform.integer.Mixed

Methods inherited from interface net.imglib2.transform.Transform

Methods inherited from interface net.imglib2.transform.integer.BoundingBoxTransform

Field Detail

numSourceDimensions

zero

translation

component

Constructor Detail

SlicingTransform

Method Detail

numSourceDimensions

getTranslation

getTranslation

setTranslation

getComponentZero

getComponentZero

setComponentZero

getComponentMapping

getComponentMapping

setComponentMapping

apply

apply

apply

concatenate

getConcatenableClass

preConcatenate

getPreConcatenableClass

set

getMatrix

hasFullSourceMapping