BSplineModel (Fiji Javadocs 0-SNAPSHOT API)

java.lang.Object
- bunwarpj.BSplineModel

All Implemented Interfaces:

Runnable
```
public class BSplineModel
extends Object
implements Runnable
```
Class for representing the images and the deformations by cubic B-splines:
- Both, images and deformations, are stored in multi-resolution pyramids.
- The pyramids are not calculated in the constructors but in the method startPyramids.
- For images, even if they are set to be scaled, the original image information is stored.
- The information corresponding to the output window size is also stored at any time.

Field Summary

Fields
Modifier and Type	Field and Description
`static int`	`MAX_OUTPUT_SIZE` maximum output window dimensions
`int[][]`	`prec_xIndex` precomputed x index
`int[][]`	`prec_yIndex` precomputed y index
`int[]`	`xIndex` x index
`int[]`	`yIndex` y index

Constructor Summary

Constructors
Constructor and Description
`BSplineModel(double[][] c)` Initialize the B-spline model from a set of coefficients.
`BSplineModel(double[][] img, boolean isTarget)` The same as before, but take the image from an array.
`BSplineModel(double[] c, int Ydim, int Xdim, int offset)` Initialize the B-spline model from a set of coefficients.
`BSplineModel(ij.process.ImageProcessor ip, boolean isTarget, int maxImageSubsamplingFactor)` Create image model for image processor: image and coefficient pyramid.
`BSplineModel(int width, int height, int maxImageSubsamplingFactor)` Create image model without image pixel information (for landmark only registration): empty image and full coefficient pyramid.

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`void`	`clearPyramids()` Clear the pyramid.
`double[]`	`getCoefficients()` Get b-spline coefficients.
`int`	`getCurrentDepth()` Get current depth.
`int`	`getCurrentHeight()` Get current height.
`double[]`	`getCurrentImage()` Get current image.
`int`	`getCurrentWidth()` Get current width.
`double`	`getFactorHeight()` Get factor height.
`double`	`getFactorWidth()` Get fact or width.
`int`	`getHeight()` Get height.
`double[]`	`getImage()` Get image (at the maximum resolution size determined by the scaling).
`double[]`	`getOriginalImage()` Get original image.
`int`	`getOriginalImageHeight()` Get original image height.
`int`	`getOriginalImageWidth()` Get original image width.
`double`	`getPixelValFromPyramid(int x, int y)` Get the pixel value from the image pyramid.
`int`	`getPyramidDepth()` Get pyramid depth.
`int`	`getSmallestHeight()` Get smallest height.
`int`	`getSmallestWidth()` Get smallest width.
`double[]`	`getSubImage()` Get subsampled output image.
`int`	`getSubsamplingFactor()` Get sub-sampling factor at highest resolution
`Thread`	`getThread()` Get thread.
`double`	`getWeightDx(int l, int m)` Get weight dx.
`double`	`getWeightDxDx(int l, int m)` Get weight dxdx.
`double`	`getWeightDxDy(int l, int m)` Get weight dxdy.
`double`	`getWeightDy(int l, int m)` Get weight dy.
`double`	`getWeightDyDy(int l, int m)` Get weight dydy.
`double`	`getWeightI(int l, int m)` Get image coefficient weight.
`int`	`getWidth()` Get width.
`void`	`interpolateD(double[] D)` Interpolate the X and Y derivatives of the image at a given point.
`void`	`interpolateD2(double[] D2)` Interpolate the XY, XX and YY derivatives of the image at a given point.
`double`	`interpolateDx()` Interpolate the X derivative of the image at a given point.
`double`	`interpolateDxDx()` Interpolate the X derivative of the image at a given point.
`double`	`interpolateDxDy()` Interpolate the X derivative of the image at a given point.
`double`	`interpolateDy()` Interpolate the Y derivative of the image at a given point.
`double`	`interpolateDyDy()` Interpolate the X derivative of the image at a given point.
`double`	`interpolateI()` Interpolate the image at a given point.
`boolean`	`isFinest()` Check if the coefficients pyramid is empty.
`void`	`popFromPyramid()` Pop one element from the coefficients and image pyramids.
`double`	`precomputed_getWeightDx(int l, int m, int u, int v)` Get precomputed weight dx.
`double`	`precomputed_getWeightDxDx(int l, int m, int u, int v)` Get precomputed weight dxdx
`double`	`precomputed_getWeightDxDy(int l, int m, int u, int v)` Get precomputed weight dxdy
`double`	`precomputed_getWeightDy(int l, int m, int u, int v)` Get precomputed weight dy
`double`	`precomputed_getWeightDyDy(int l, int m, int u, int v)` Get precomputed weight dydy
`double`	`precomputed_getWeightI(int l, int m, int u, int v)` Get precomputed weight of coefficient l,m
`int`	`precomputed_getWidth()` Get width of precomputed vectors.
`void`	`precomputed_interpolateD(double[] D, int u, int v)` Interpolate the X and Y derivatives of the image at a given point.
`void`	`precomputed_interpolateD2(double[] D2, int u, int v)` Interpolate the XY, XX and YY derivatives of the image at a given point.
`double`	`precomputed_interpolateI(int u, int v)` Interpolate the image (or deformation) at a given point using the precomputed weights.
`void`	`precomputed_prepareForInterpolation(int Ydim, int Xdim, int intervals)` Prepare precomputations for a given image size.
`void`	`prepareForInterpolation(double x, double y, boolean fromCurrent)` If `fromCurrent` is true, the interpolation is prepared to be done from the current image in the pyramid.
`double`	`prepareForInterpolationAndInterpolateI(double x, double y, boolean fromSub, boolean fromCurrent)` Prepare for interpolation and interpolate fromSub = true: The interpolation is done from the subsampled version of the image
`double`	`prepareForInterpolationAndInterpolateIAndD(double x, double y, double[] D, boolean fromSub, boolean fromCurrent)` Prepare for interpolation and interpolate the image value and its derivatives fromSub = true: The interpolation is done from the subsampled version of the image
`double[]`	`reduceCoeffsBy2(double[] c, int width, int height)` Reduce coefficients by a factor of 2 (beta)
`void`	`run()` Start the image pre-computations.
`void`	`setCoefficients(double[] c, int Ydim, int Xdim, int offset)` Set spline coefficients.
`void`	`setPyramidDepth(int pyramidDepth)` Sets the depth up to which the pyramids should be computed.
`void`	`setSubsamplingFactor(int maxImageSubsamplingFactor)` Set maximum sub-sampling factor
`void`	`startPyramids()` Start coefficient and image pyramids

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

- Field Detail
  - MAX_OUTPUT_SIZE
```
public static final int MAX_OUTPUT_SIZE
```
    maximum output window dimensions
    
    See Also:
    
    Constant Field Values
  - xIndex
```
public int[] xIndex
```
    x index
  - yIndex
```
public int[] yIndex
```
    y index
  - prec_xIndex
```
public int[][] prec_xIndex
```
    precomputed x index
  - prec_yIndex
```
public int[][] prec_yIndex
```
    precomputed y index
- Constructor Detail
  - BSplineModel
```
public BSplineModel(ij.process.ImageProcessor ip,
                    boolean isTarget,
                    int maxImageSubsamplingFactor)
```
    Create image model for image processor: image and coefficient pyramid. When calling this constructor, the thread is not started, to do so, startPyramids needs to be called.
    
    Parameters:
    
    ip - image pointer (ImageProcessor)
    
    isTarget - enables the computation of the derivative or not
    
    maxImageSubsamplingFactor - sub-sampling factor at highest resolution level
  - BSplineModel
```
public BSplineModel(int width,
                    int height,
                    int maxImageSubsamplingFactor)
```
    Create image model without image pixel information (for landmark only registration): empty image and full coefficient pyramid. When calling this constructor, the thread is not started, to do so, startPyramids needs to be called.
    
    Parameters:
    
    width - image width
    
    height - image height
    
    maxImageSubsamplingFactor - sub-sampling factor at highest resolution level
  - BSplineModel
```
public BSplineModel(double[][] img,
                    boolean isTarget)
```
    The same as before, but take the image from an array.
    
    Parameters:
    
    img - image in a double array
    
    isTarget - enables the computation of the derivative or not
  - BSplineModel
```
public BSplineModel(double[][] c)
```
    Initialize the B-spline model from a set of coefficients.
    
    Parameters:
    
    c - Set of B-spline coefficients
  - BSplineModel
```
public BSplineModel(double[] c,
                    int Ydim,
                    int Xdim,
                    int offset)
```
    Initialize the B-spline model from a set of coefficients. The same as the previous function but now the coefficients are in a single row.
    
    Parameters:
    
    c - Set of B-spline coefficients
    
    Ydim - Y-dimension of the set of coefficients
    
    Xdim - X-dimension of the set of coefficients
    
    offset - Offset of the beginning of the array with respect to the origin of c
- Method Detail
  - startPyramids
```
public void startPyramids()
```
    Start coefficient and image pyramids
  - clearPyramids
```
public void clearPyramids()
```
    Clear the pyramid.
  - getCurrentHeight
```
public int getCurrentHeight()
```
    Get current height.
    
    Returns:
    
    the current height of the image/coefficients
  - getCurrentImage
```
public double[] getCurrentImage()
```
    Get current image.
    
    Returns:
    
    the current image of the image/coefficients
  - getCurrentWidth
```
public int getCurrentWidth()
```
    Get current width.
    
    Returns:
    
    the current width of the image/coefficients
  - getFactorHeight
```
public double getFactorHeight()
```
    Get factor height.
    
    Returns:
    
    the relationship between the current size of the image and the original size
  - getFactorWidth
```
public double getFactorWidth()
```
    Get fact or width.
    
    Returns:
    
    the relationship between the current size of the image and the original size.
  - getCurrentDepth
```
public int getCurrentDepth()
```
    Get current depth.
    
    Returns:
    
    the current depth of the image/coefficients
  - getHeight
```
public int getHeight()
```
    Get height.
    
    Returns:
    
    the full-size image height.
  - getImage
```
public double[] getImage()
```
    Get image (at the maximum resolution size determined by the scaling).
    
    Returns:
    
    the less scaled image.
  - getOriginalImage
```
public double[] getOriginalImage()
```
    Get original image.
    
    Returns:
    
    the original full-size image.
  - getOriginalImageWidth
```
public int getOriginalImageWidth()
```
    Get original image width.
    
    Returns:
    
    the original full-size image width.
  - getOriginalImageHeight
```
public int getOriginalImageHeight()
```
    Get original image height.
    
    Returns:
    
    the original full-size image height.
  - getSubImage
```
public double[] getSubImage()
```
    Get subsampled output image.
    
    Returns:
    
    the subsumpled (to show) output image.
  - getCoefficients
```
public double[] getCoefficients()
```
    Get b-spline coefficients.
    
    Returns:
    
    the full-size B-spline coefficients
  - getPixelValFromPyramid
```
public double getPixelValFromPyramid(int x,
                                     int y)
```
    Get the pixel value from the image pyramid.
    
    Parameters:
    
    x - x-coordinate of the pixel
    
    y - y-coordinate of the pixel
    
    Returns:
    
    pixel value
  - getPyramidDepth
```
public int getPyramidDepth()
```
    Get pyramid depth.
    
    Returns:
    
    the depth of the image pyramid. A depth 1 means that one coarse resolution level is present in the stack. The full-size level is not placed on the stack
  - getSmallestHeight
```
public int getSmallestHeight()
```
    Get smallest height.
    
    Returns:
    
    the height of the smallest image in the pyramid
  - getSmallestWidth
```
public int getSmallestWidth()
```
    Get smallest width.
    
    Returns:
    
    the width of the smallest image in the pyramid
  - getThread
```
public Thread getThread()
```
    Get thread.
    
    Returns:
    
    the thread associated
  - getWidth
```
public int getWidth()
```
    Get width.
    
    Returns:
    
    the full-size image width
  - getWeightDx
```
public double getWeightDx(int l,
                          int m)
```
    Get weight dx.
    
    Returns:
    
    the weight of the coefficient l,m (yWeight, dxWeight) in the image interpolation
  - getWeightDxDx
```
public double getWeightDxDx(int l,
                            int m)
```
    Get weight dxdx.
    
    Returns:
    
    the weight of the coefficient l,m (yWeight, d2xWeight) in the image interpolation
  - getWeightDxDy
```
public double getWeightDxDy(int l,
                            int m)
```
    Get weight dxdy.
    
    Returns:
    
    the weight of the coefficient l,m (dyWeight, dxWeight) in the image interpolation
  - getWeightDy
```
public double getWeightDy(int l,
                          int m)
```
    Get weight dy.
    
    Returns:
    
    the weight of the coefficient l,m (dyWeight, xWeight) in the image interpolation
  - getWeightDyDy
```
public double getWeightDyDy(int l,
                            int m)
```
    Get weight dydy.
    
    Returns:
    
    the weight of the coefficient l,m (d2yWeight, xWeight) in the image interpolation
  - getWeightI
```
public double getWeightI(int l,
                         int m)
```
    Get image coefficient weight.
    
    Returns:
    
    the weight of the coefficient l,m (yWeight, xWeight) in the image interpolation
  - interpolateD
```
public void interpolateD(double[] D)
```
    Interpolate the X and Y derivatives of the image at a given point.
    
    Parameters:
    
    D - output, interpolation the X and Y derivatives of the image
  - interpolateD2
```
public void interpolateD2(double[] D2)
```
    Interpolate the XY, XX and YY derivatives of the image at a given point.
    
    Parameters:
    
    D2 - output, interpolation of the XY, XX and YY derivatives of the image
  - interpolateDx
```
public double interpolateDx()
```
    Interpolate the X derivative of the image at a given point.
    
    Returns:
    
    dx interpolation
  - interpolateDxDx
```
public double interpolateDxDx()
```
    Interpolate the X derivative of the image at a given point.
    
    Returns:
    
    dxdx interpolation
  - interpolateDxDy
```
public double interpolateDxDy()
```
    Interpolate the X derivative of the image at a given point.
    
    Returns:
    
    dxdy interpolation
  - interpolateDy
```
public double interpolateDy()
```
    Interpolate the Y derivative of the image at a given point.
    
    Returns:
    
    dy interpolation
  - interpolateDyDy
```
public double interpolateDyDy()
```
    Interpolate the X derivative of the image at a given point.
    
    Returns:
    
    dydy interpolation
  - interpolateI
```
public double interpolateI()
```
    Interpolate the image at a given point.
    
    Returns:
    
    image interpolation
  - isFinest
```
public boolean isFinest()
```
    Check if the coefficients pyramid is empty.
    
    Returns:
    
    true when the coefficients pyramid is empty false if not
  - popFromPyramid
```
public void popFromPyramid()
```
    Pop one element from the coefficients and image pyramids.
  - prepareForInterpolation
```
public void prepareForInterpolation(double x,
                                    double y,
                                    boolean fromCurrent)
```
    If fromCurrent is true, the interpolation is prepared to be done from the current image in the pyramid. Otherwise, the interpolation is prepared to be done from the original image.
    
    Parameters:
    
    x - x- point coordinate
    
    y - y- point coordinate
    
    fromCurrent - flag to determine the image to do the interpolation from
  - prepareForInterpolationAndInterpolateI
```
public double prepareForInterpolationAndInterpolateI(double x,
                                                     double y,
                                                     boolean fromSub,
                                                     boolean fromCurrent)
```
    Prepare for interpolation and interpolate
    - fromSub = true: The interpolation is done from the subsampled version of the image
    else:
    - fromCurrent=true: The interpolation is done from the current image in the pyramid.
    - fromCurrent=false: The interpolation is done from the original image.
    Parameters:
    
    x - x- point coordinate
    
    y - y- point coordinate
    
    fromSub - flat to determine to do the interpolation from the subsampled version of the image
    
    fromCurrent - flag to determine the image to do the interpolation from interpolated value
  - prepareForInterpolationAndInterpolateIAndD
```
public double prepareForInterpolationAndInterpolateIAndD(double x,
                                                         double y,
                                                         double[] D,
                                                         boolean fromSub,
                                                         boolean fromCurrent)
```
    Prepare for interpolation and interpolate the image value and its derivatives
    - fromSub = true: The interpolation is done from the subsampled version of the image
    else:
    - fromCurrent=true: The interpolation is done from the current image in the pyramid.
    - fromCurrent=false: The interpolation is done from the original image.
    Parameters:
    
    x - x- point coordinate
    
    y - y- point coordinate
    
    D - output, interpolation the X and Y derivatives of the image
    
    fromSub - flat to determine to do the interpolation from the subsampled version of the image
    
    fromCurrent - flag to determine the image to do the interpolation from interpolated value
  - precomputed_getWidth
```
public int precomputed_getWidth()
```
    Get width of precomputed vectors.
    
    Returns:
    
    the width of the precomputed vectors
  - precomputed_getWeightDx
```
public double precomputed_getWeightDx(int l,
                                      int m,
                                      int u,
                                      int v)
```
    Get precomputed weight dx.
    
    Parameters:
    
    l -
    
    m -
    
    u -
    
    v -
    
    Returns:
    
    the weight of the coefficient l,m (yIndex, xIndex) in the image interpolation
  - precomputed_getWeightDxDx
```
public double precomputed_getWeightDxDx(int l,
                                        int m,
                                        int u,
                                        int v)
```
    Get precomputed weight dxdx
    
    Parameters:
    
    l -
    
    m -
    
    u -
    
    v -
    
    Returns:
    
    the weight of the coefficient l,m (prec_yWeight, prec_d2xWeight) in the image interpolation
  - precomputed_getWeightDxDy
```
public double precomputed_getWeightDxDy(int l,
                                        int m,
                                        int u,
                                        int v)
```
    Get precomputed weight dxdy
    
    Parameters:
    
    l -
    
    m -
    
    u -
    
    v -
    
    Returns:
    
    the weight of the coefficient l,m (prec_dyWeight, prec_dxWeight) in the image interpolation
  - precomputed_getWeightDy
```
public double precomputed_getWeightDy(int l,
                                      int m,
                                      int u,
                                      int v)
```
    Get precomputed weight dy
    
    Parameters:
    
    l -
    
    m -
    
    u -
    
    v -
    
    Returns:
    
    the weight of the coefficient l,m (prec_dyWeight, prec_xWeight) in the image interpolation
  - precomputed_getWeightDyDy
```
public double precomputed_getWeightDyDy(int l,
                                        int m,
                                        int u,
                                        int v)
```
    Get precomputed weight dydy
    
    Parameters:
    
    l -
    
    m -
    
    u -
    
    v -
    
    Returns:
    
    the weight of the coefficient l,m (prec_d2yWeight, prec_xWeight) in the image interpolation
  - precomputed_getWeightI
```
public double precomputed_getWeightI(int l,
                                     int m,
                                     int u,
                                     int v)
```
    Get precomputed weight of coefficient l,m
    
    Parameters:
    
    l -
    
    m -
    
    u -
    
    v -
    
    Returns:
    
    the weight of the coefficient l,m (prec_yWeight, prec_xWeight) in the image interpolation
  - precomputed_interpolateD
```
public void precomputed_interpolateD(double[] D,
                                     int u,
                                     int v)
```
    Interpolate the X and Y derivatives of the image at a given point.
    
    Parameters:
    
    D - output, X and Y derivatives of the image
    
    u - x- point coordinate
    
    v - y- point coordinate
  - precomputed_interpolateD2
```
public void precomputed_interpolateD2(double[] D2,
                                      int u,
                                      int v)
```
    Interpolate the XY, XX and YY derivatives of the image at a given point.
    
    Parameters:
    
    D2 - output, XY, XX and YY derivatives of the image
    
    u - x- point coordinate
    
    v - y- point coordinate
  - precomputed_interpolateI
```
public double precomputed_interpolateI(int u,
                                       int v)
```
    Interpolate the image (or deformation) at a given point using the precomputed weights.
    
    Parameters:
    
    u - x- point coordinate
    
    v - y- point coordinate
  - precomputed_prepareForInterpolation
```
public void precomputed_prepareForInterpolation(int Ydim,
                                                int Xdim,
                                                int intervals)
```
    Prepare precomputations for a given image size. It calls prepareForInterpolation with ORIGINAL flag.
    
    Parameters:
    
    Ydim - y- image dimension
    
    Xdim - x- image dimension
    
    intervals - intervals in the deformation
  - run
```
public void run()
```
    Start the image pre-computations. The computation of the B-spline coefficients of the full-size image is not interruptible; all other methods are.
    
    Specified by:
    
    run in interface Runnable
  - setCoefficients
```
public void setCoefficients(double[] c,
                            int Ydim,
                            int Xdim,
                            int offset)
```
    Set spline coefficients. Copy coefficients to the model array.
    
    Parameters:
    
    c - Set of B-spline coefficients
    
    Ydim - Y-dimension of the set of coefficients
    
    Xdim - X-dimension of the set of coefficients
    
    offset - Offset of the beginning of the array with respect to the origin of c
  - setPyramidDepth
```
public void setPyramidDepth(int pyramidDepth)
```
    Sets the depth up to which the pyramids should be computed.
    
    Parameters:
    
    pyramidDepth - pyramid depth to be set
  - reduceCoeffsBy2
```
public double[] reduceCoeffsBy2(double[] c,
                                int width,
                                int height)
```
    Reduce coefficients by a factor of 2 (beta)
    
    Parameters:
    
    c -
    
    width -
    
    height -
  - setSubsamplingFactor
```
public void setSubsamplingFactor(int maxImageSubsamplingFactor)
```
    Set maximum sub-sampling factor
    
    Parameters:
    
    maxImageSubsamplingFactor -
  - getSubsamplingFactor
```
public int getSubsamplingFactor()
```
    Get sub-sampling factor at highest resolution
    
    Returns:
    
    maxImageSubsamplingFactor

Class BSplineModel

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

MAX_OUTPUT_SIZE

xIndex

yIndex

prec_xIndex

prec_yIndex

Constructor Detail

BSplineModel

BSplineModel

BSplineModel

BSplineModel

BSplineModel

Method Detail

startPyramids

clearPyramids

getCurrentHeight

getCurrentImage

getCurrentWidth

getFactorHeight

getFactorWidth

getCurrentDepth

getHeight

getImage

getOriginalImage

getOriginalImageWidth

getOriginalImageHeight

getSubImage

getCoefficients

getPixelValFromPyramid

getPyramidDepth

getSmallestHeight

getSmallestWidth

getThread

getWidth

getWeightDx

getWeightDxDx

getWeightDxDy

getWeightDy

getWeightDyDy

getWeightI

interpolateD

interpolateD2

interpolateDx

interpolateDxDx

interpolateDxDy

interpolateDy

interpolateDyDy

interpolateI

isFinest

popFromPyramid

prepareForInterpolation

prepareForInterpolationAndInterpolateI

prepareForInterpolationAndInterpolateIAndD

precomputed_getWidth

precomputed_getWeightDx

precomputed_getWeightDxDx

precomputed_getWeightDxDy

precomputed_getWeightDy

precomputed_getWeightDyDy

precomputed_getWeightI

precomputed_interpolateD

precomputed_interpolateD2

precomputed_interpolateI

precomputed_prepareForInterpolation

run

setCoefficients

setPyramidDepth

reduceCoeffsBy2

setSubsamplingFactor

getSubsamplingFactor