JacobianDeterminantSource (Fiji Javadocs 0-SNAPSHOT API)

java.lang.Object
- bigwarp.source.JacobianDeterminantSource<T>

All Implemented Interfaces:: Source<T>

public class JacobianDeterminantSource<T extends RealType<T>>
extends Object
implements Source<T>

Field Summary

Fields
Modifier and Type	Field and Description
`protected Interval`	`interval`
`protected JacobianDeterminantRandomAccess.JacobianDeterminantRandomAccessibleInterval<T>`	`jacDetImg`
`protected String`	`name`
`protected BigWarp.BigWarpData<?>`	`sourceData`
`protected T`	`type`
`protected VoxelDimensions`	`voxDims`

Constructor Summary

Constructors
Constructor and Description

JacobianDeterminantSource(String name, BigWarp.BigWarpData<?> data, T t)

Constructors
Constructor and Description
`JacobianDeterminantSource(String name, BigWarp.BigWarpData<?> data, T t)`

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`void`	`debug(double[] pt)`
`RealRandomAccessible<T>`	`getInterpolatedSource(int t, int level, Interpolation method)` Get the 3D stack at timepoint index t, extended to infinity and interpolated.
`double`	`getMax(LandmarkTableModel lm)`
`String`	`getName()` Get the name of the source.
`int`	`getNumMipmapLevels()`
`RandomAccessibleInterval<T>`	`getSource(int t, int level)` Get the 3D stack at timepoint index t.
`void`	`getSourceTransform(int t, int level, AffineTransform3D transform)` Get the transform from the `source` at the given timepoint index and mipmap level into the global coordinate system.
`T`	`getType()` Get an instance of the pixel type.
`VoxelDimensions`	`getVoxelDimensions()` Get voxel size and unit for this source.
`boolean`	`isPresent(int t)` Is there a stack at timepoint index t?
`double[]`	`minMax()`
`void`	`setTransform(DifferentiableRealTransform transform)`

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Methods inherited from interface bdv.viewer.Source
doBoundingBoxCulling

- Field Detail
  - name
```
protected final String name
```
  - sourceData
```
protected final BigWarp.BigWarpData<?> sourceData
```
  - interval
```
protected final Interval interval
```
  - jacDetImg
```
protected final JacobianDeterminantRandomAccess.JacobianDeterminantRandomAccessibleInterval<T extends RealType<T>> jacDetImg
```
  - voxDims
```
protected final VoxelDimensions voxDims
```
  - type
```
protected T extends RealType<T> type
```
- Constructor Detail
  - JacobianDeterminantSource
```
public JacobianDeterminantSource(String name,
                                 BigWarp.BigWarpData<?> data,
                                 T t)
```
- Method Detail
  - getMax
```
public double getMax(LandmarkTableModel lm)
```
  - setTransform
```
public void setTransform(DifferentiableRealTransform transform)
```
  - debug
```
public void debug(double[] pt)
```
  - minMax
```
public double[] minMax()
```
  - isPresent
```
public boolean isPresent(int t)
```
    Description copied from interface: Source
    
    Is there a stack at timepoint index t?
    
    Specified by:
    
    isPresent in interface Source<T extends RealType<T>>
    
    Parameters:
    
    t - timepoint index
    
    Returns:
    
    true, if there is data for timepoint index t.
  - getSource
```
public RandomAccessibleInterval<T> getSource(int t,
                                             int level)
```
    Description copied from interface: Source
    
    Get the 3D stack at timepoint index t.
    
    Specified by:
    
    getSource in interface Source<T extends RealType<T>>
    
    Parameters:
    
    t - timepoint index
    
    level - mipmap level
    
    Returns:
    
    the stack.
  - getInterpolatedSource
```
public RealRandomAccessible<T> getInterpolatedSource(int t,
                                                     int level,
                                                     Interpolation method)
```
    Description copied from interface: Source
    
    Get the 3D stack at timepoint index t, extended to infinity and interpolated.
    
    Specified by:
    
    getInterpolatedSource in interface Source<T extends RealType<T>>
    
    Parameters:
    
    t - timepoint index
    
    level - mipmap level
    
    method - interpolation method to use
    
    Returns:
    
    the extended and interpolated stack.
  - getSourceTransform
```
public void getSourceTransform(int t,
                               int level,
                               AffineTransform3D transform)
```
    Description copied from interface: Source
    
    Get the transform from the source at the given timepoint index and mipmap level into the global coordinate system.
    
    Specified by:
    
    getSourceTransform in interface Source<T extends RealType<T>>
    
    Parameters:
    
    t - timepoint index
    
    level - mipmap level
    
    transform - is set to the source-to-global transform, that transforms source coordinates into the global coordinates
  - getType
```
public T getType()
```
    Description copied from interface: Source
    
    Get an instance of the pixel type.
    
    Specified by:
    
    getType in interface Source<T extends RealType<T>>
    
    Returns:
    
    instance of pixel type.
  - getName
```
public String getName()
```
    Description copied from interface: Source
    
    Get the name of the source.
    
    Specified by:
    
    getName in interface Source<T extends RealType<T>>
    
    Returns:
    
    the name of the source.
  - getVoxelDimensions
```
public VoxelDimensions getVoxelDimensions()
```
    Description copied from interface: Source
    
    Get voxel size and unit for this source. May return null.
    
    Specified by:
    
    getVoxelDimensions in interface Source<T extends RealType<T>>
    
    Returns:
    
    voxel size and unit or null.
  - getNumMipmapLevels
```
public int getNumMipmapLevels()
```
    Specified by:
    
    getNumMipmapLevels in interface Source<T extends RealType<T>>

Class JacobianDeterminantSource<T extends RealType<T>>

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Methods inherited from interface bdv.viewer.Source

Field Detail

name

sourceData

interval

jacDetImg

voxDims

type

Constructor Detail

JacobianDeterminantSource

Method Detail

getMax

setTransform

debug

minMax

isPresent

getSource

getInterpolatedSource

getSourceTransform

getType

getName

getVoxelDimensions

getNumMipmapLevels