BSplineModel

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bunwarpj
Class BSplineModel

java.lang.Object
  bunwarpj.BSplineModel

All Implemented Interfaces:: java.lang.Runnable

public class BSplineModel
extends java.lang.Object
implements java.lang.Runnable
extends java.lang.Object
implements java.lang.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
`private boolean`	`bSubsampledOutput` flag for using subsampled output image
`private double[]`	`coefficient` image spline coefficients
`private boolean`	`coefficientsAreMirrored` flag to check if the coefficients are mirrored
`private java.util.Stack`	`cpyramid` stack of coefficients pyramid
`private double[]`	`currentCoefficient` current image spline coefficients
`private int`	`currentDepth` current pyramid depth
`private int`	`currentHeight` current image height
`private double[]`	`currentImage` current image (at the current resolution level)
`private int`	`currentWidth` current image width
`private double[]`	`d2xWeight` x component of the weight of second derivative spline
`private double[]`	`d2yWeight` y component of the weight of second derivative spline
`private double[]`	`dxWeight` x component of the weight of derivative spline
`private double[]`	`dyWeight` y component of the weight of derivative spline
`private boolean`	`fromCurrent` Interpolation source (current or original)
`private int`	`height` working image height (after scaling)
`private int`	`heightToUse` height of the image used for the interpolation
`private double[]`	`image` working image at maximum resolution (after scaling)
`private java.util.Stack`	`imgpyramid` stack of image pyramid
`private ij.process.ImageProcessor`	`ip` image information (after corresponding scaling)
`private boolean`	`isTarget` flag to check target image
`static int`	`MAX_OUTPUT_SIZE` maximum output window dimensions
`private int`	`maxImageSubsamplingFactor` sub-sampling factor at highest image resolution level (always a power of 2)
`private static int`	`min_image_size` minimum image size
`private double[]`	`original_image` original image, full-size without scaling
`private int`	`originalHeight` original image height (at full-resolution, without scaling)
`private int`	`originalWidth` original image width (at full-resolution, without scaling)
`private double[][]`	`prec_d2xWeight` precomputed x component of the weight of second derivative spline
`private double[][]`	`prec_d2yWeight` precomputed y component of the weight of second derivative spline
`private double[][]`	`prec_dxWeight` precomputed x component of the weight of derivative spline
`private double[][]`	`prec_dyWeight` precomputed y component of the weight of derivative spline
`int[][]`	`prec_xIndex` precomputed x index
`private double[][]`	`prec_xWeight` precomputed x component of the weight of the spline
`int[][]`	`prec_yIndex` precomputed y index
`private double[][]`	`prec_yWeight` precomputed y component of the weight of the spline
`private int`	`pyramidDepth` resolution pyramid depth
`private int`	`smallestHeight` smallest image height
`private int`	`smallestWidth` smallest image width
`private double[]`	`subCoeffs` subsampled output image B-spline coefficients
`private int`	`subHeight` height of the subsampled output image
`private double[]`	`subImage` subsampled output image
`private int`	`subWidth` width of the subsampled output image
`private java.lang.Thread`	`t` thread to create the model
`private int`	`width` working image width (after scaling)
`private int`	`widthToUse` width of the image used for the interpolation
`int[]`	`xIndex` x index
`private double[]`	`xWeight` x component of the weight of the spline
`int[]`	`yIndex` y index
`private double[]`	`yWeight` y component of the weight of the spline

Constructor Summary
`BSplineModel(double[][] c)` Initialize the 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 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.

Method Summary
`private void`	`antiSymmetricFirMirrorOffBounds1D(double[] h, double[] c, double[] s)`
`private void`	`basicToCardinal2D(double[] basic, double[] cardinal, int width, int height, int degree)` Pass from basic to cardinal.
`private void`	`buildCoefficientPyramid()` Build the coefficients pyramid.
`private void`	`buildImagePyramid()` Build the image pyramid.
`private void`	`cardinalToDual2D(double[] cardinal, double[] dual, int width, int height, int degree)` Passes from cardinal to dual (2D).
`void`	`clearPyramids()` Clear the pyramid.
`private void`	`coefficientToGradient1D(double[] c)` Pass coefficients to gradient (1D).
`private void`	`coefficientToSamples1D(double[] c)` Pass coefficients to samples.
`private void`	`coefficientToXYGradient2D(double[] basic, double[] xGradient, double[] yGradient, int width, int height)` Pass coefficients to x,y gradient 2D
`private void`	`dualToCardinal2D(double[] dual, double[] cardinal, int width, int height, int degree)` Pass from dual to cardinal (2D).
`private void`	`extractColumn(double[] array, int width, int x, double[] column)` Extract a column from the array.
`private void`	`extractRow(double[] array, int y, double[] row)` Extract a row from the array .
`private double[]`	`getBasicFromCardinal2D()` Get basic from cardinal: convert the 2D image from regular samples to standard B-spline coefficients.
`private double[]`	`getBasicFromCardinal2D(double[] cardinal, int width, int height, int degree)` Get basic from cardinal (2D): convert a 2D signal from regular samples to standard B-spline coefficients.
`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.
`private double[]`	`getHalfDual2D(double[] fullDual, int fullWidth, int fullHeight)` Get half dual (2D).
`int`	`getHeight()` Get height.
`double[]`	`getImage()` Get image (at the maximum resolution size determined by the scaling).
`private double`	`getInitialAntiCausalCoefficientMirrorOffBounds(double[] c, double z, double tolerance)` Get initial anti-causal coefficients mirror of bounds.
`private double`	`getInitialCausalCoefficientMirrorOffBounds(double[] c, double z, double tolerance)` Get initial causal coefficients mirror of bounds.
`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.
`(package private) int`	`getSubHeight()` Get subsampled output height
`double[]`	`getSubImage()` Get subsampled output image.
`(package private) int`	`getSubWidth()` Get subsampled output width
`java.lang.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.
`(package private) boolean`	`isSubOutput()` Get subsampled output flag
`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)` fromCurrent=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 else: fromCurrent=true --> The interpolation is done from the current image in the pyramid.
`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.
`private void`	`putColumn(double[] array, int width, int x, double[] column)` Put a column in the array.
`private void`	`putRow(double[] array, int y, double[] row)` Put a row in the array.
`double[]`	`reduceCoeffsBy2(double[] c, int width, int height)` Reduce coefficients by a factor of 2 (beta)
`private void`	`reduceDual1D(double[] c, double[] s)` Reduce dual (1D).
`void`	`run()` Start the image pre-computations.
`private void`	`samplesToInterpolationCoefficient1D(double[] c, int degree, double tolerance)` Samples to interpolation coefficient (1D).
`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.
`(package private) void`	`setSubOutput(boolean b)` Set subsampled output flag
`void`	`setSubsamplingFactor(int maxImageSubsamplingFactor)` Set maximum sub-sampling factor
`void`	`startPyramids()` Start coefficient and image pyramids
`private void`	`symmetricFirMirrorOffBounds1D(double[] h, double[] c, double[] s)` Symmetric FIR filter with mirror off bounds (1D) conditions.

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 int MAX_OUTPUT_SIZE

maximum output window dimensions

min_image_size

private static int min_image_size

minimum image size

ip

private ij.process.ImageProcessor ip

image information (after corresponding scaling)

t

private java.lang.Thread t

thread to create the model

cpyramid

private final java.util.Stack cpyramid

stack of coefficients pyramid

imgpyramid

private final java.util.Stack imgpyramid

stack of image pyramid

original_image

private double[] original_image

original image, full-size without scaling

image

private double[] image

working image at maximum resolution (after scaling)

coefficient

private double[] coefficient

image spline coefficients

currentImage

private double[] currentImage

current image (at the current resolution level)

currentCoefficient

private double[] currentCoefficient

current image spline coefficients

currentWidth

private int currentWidth

current image width

currentHeight

private int currentHeight

current image height

width

private int width

working image width (after scaling)

height

private int height

working image height (after scaling)

pyramidDepth

private int pyramidDepth

resolution pyramid depth

currentDepth

private int currentDepth

current pyramid depth

smallestWidth

private int smallestWidth

smallest image width

smallestHeight

private int smallestHeight

smallest image height

isTarget

private boolean isTarget

flag to check target image

coefficientsAreMirrored

private boolean coefficientsAreMirrored

flag to check if the coefficients are mirrored

maxImageSubsamplingFactor

private int maxImageSubsamplingFactor

sub-sampling factor at highest image resolution level (always a power of 2)

xIndex

public int[] xIndex

x index

yIndex

public int[] yIndex

y index

xWeight

private double[] xWeight

x component of the weight of the spline

yWeight

private double[] yWeight

y component of the weight of the spline

dxWeight

private double[] dxWeight

x component of the weight of derivative spline

dyWeight

private double[] dyWeight

y component of the weight of derivative spline

d2xWeight

private double[] d2xWeight

x component of the weight of second derivative spline

d2yWeight

private double[] d2yWeight

y component of the weight of second derivative spline

fromCurrent

private boolean fromCurrent

Interpolation source (current or original)

widthToUse

private int widthToUse

width of the image used for the interpolation

heightToUse

private int heightToUse

height of the image used for the interpolation

bSubsampledOutput

private boolean bSubsampledOutput

flag for using subsampled output image

subWidth

private int subWidth

width of the subsampled output image

subHeight

private int subHeight

height of the subsampled output image

subCoeffs

private double[] subCoeffs

subsampled output image B-spline coefficients

subImage

private double[] subImage

subsampled output image

prec_xIndex

public int[][] prec_xIndex

precomputed x index

prec_yIndex

public int[][] prec_yIndex

precomputed y index

prec_xWeight

private double[][] prec_xWeight

precomputed x component of the weight of the spline

prec_yWeight

private double[][] prec_yWeight

precomputed y component of the weight of the spline

prec_dxWeight

private double[][] prec_dxWeight

precomputed x component of the weight of derivative spline

prec_dyWeight

private double[][] prec_dyWeight

precomputed y component of the weight of derivative spline

prec_d2xWeight

private double[][] prec_d2xWeight

precomputed x component of the weight of second derivative spline

prec_d2yWeight

private double[][] prec_d2yWeight

precomputed y component of the weight of second derivative spline

originalWidth

private int originalWidth

original image width (at full-resolution, without scaling)

originalHeight

private int originalHeight

original image height (at full-resolution, without scaling)

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 in pixel array; isTarget - enables the computation of the derivative or not; maxImageSubsamplingFactor - subsampling 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 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 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 java.lang.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)

fromCurrent=true --> The interpolation is prepared to be done from the current image in the pyramid. fromCurrent=false --> 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 java.lang.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

isSubOutput

boolean isSubOutput()

Get subsampled output flag

Returns:: true if the output needs to be subsampled

setSubOutput

void setSubOutput(boolean b)

Set subsampled output flag

Parameters:: b - new subsampled output flag

getSubHeight

int getSubHeight()

Get subsampled output height

Returns:: subsampled output height

getSubWidth

int getSubWidth()

Get subsampled output width

Returns:: subsampled output width

antiSymmetricFirMirrorOffBounds1D

private void antiSymmetricFirMirrorOffBounds1D(double[] h,
                                               double[] c,
                                               double[] s)

Parameters:: h -; c -; s -

basicToCardinal2D

private void basicToCardinal2D(double[] basic,
                               double[] cardinal,
                               int width,
                               int height,
                               int degree)

Pass from basic to cardinal.

Parameters:: basic - basic (standard B-splines) 2D array; cardinal - cardinal (sampled signal) 2D array; width - 2D signal width; height - 2D signal height; degree - B-splines degree

buildCoefficientPyramid

private void buildCoefficientPyramid()

Build the coefficients pyramid.

buildImagePyramid

private void buildImagePyramid()

Build the image pyramid.

cardinalToDual2D

private void cardinalToDual2D(double[] cardinal,
                              double[] dual,
                              int width,
                              int height,
                              int degree)

Passes from cardinal to dual (2D).

Parameters:: cardinal -; dual -; width -; height -; degree -

coefficientToGradient1D

private void coefficientToGradient1D(double[] c)

Pass coefficients to gradient (1D).

Parameters:: c - coefficients

coefficientToSamples1D

private void coefficientToSamples1D(double[] c)

Pass coefficients to samples.

Parameters:: c - coefficients

coefficientToXYGradient2D

private void coefficientToXYGradient2D(double[] basic,
                                       double[] xGradient,
                                       double[] yGradient,
                                       int width,
                                       int height)

Pass coefficients to x,y gradient 2D

Parameters:: basic -; xGradient -; yGradient -; width -; height -

dualToCardinal2D

private void dualToCardinal2D(double[] dual,
                              double[] cardinal,
                              int width,
                              int height,
                              int degree)

Pass from dual to cardinal (2D).

Parameters:: dual -; cardinal -; width -; height -; degree -

extractColumn

private void extractColumn(double[] array,
                           int width,
                           int x,
                           double[] column)

Extract a column from the array.

Parameters:: array -; width - of the position of the column in the array; x - column position in the array; column - output, extracted column

extractRow

private void extractRow(double[] array,
                        int y,
                        double[] row)

Extract a row from the array .

Parameters:: array -; y - row position in the array; row - output, extracted row

getBasicFromCardinal2D

private double[] getBasicFromCardinal2D()

Get basic from cardinal: convert the 2D image from regular samples to standard B-spline coefficients.

Returns:: array of standard B-spline coefficients

getBasicFromCardinal2D

private double[] getBasicFromCardinal2D(double[] cardinal,
                                        int width,
                                        int height,
                                        int degree)

Get basic from cardinal (2D): convert a 2D signal from regular samples to standard B-spline coefficients.

Parameters:: cardinal - sampled 2D signal; width - signal width; height - signal height; degree - B-spline degree
Returns:: array of standard B-spline coefficients

getHalfDual2D

private double[] getHalfDual2D(double[] fullDual,
                               int fullWidth,
                               int fullHeight)

Get half dual (2D).

Parameters:: fullDual - full coefficients; fullWidth - full coefficients width; fullHeight - full coefficients height

getInitialAntiCausalCoefficientMirrorOffBounds

private double getInitialAntiCausalCoefficientMirrorOffBounds(double[] c,
                                                              double z,
                                                              double tolerance)

Get initial anti-causal coefficients mirror of bounds.

Parameters:: c - coefficients; z -; tolerance -

getInitialCausalCoefficientMirrorOffBounds

private double getInitialCausalCoefficientMirrorOffBounds(double[] c,
                                                          double z,
                                                          double tolerance)

Get initial causal coefficients mirror of bounds.

Parameters:: c - coefficients; z -; tolerance -

putColumn

private void putColumn(double[] array,
                       int width,
                       int x,
                       double[] column)

Put a column in the array.

Parameters:: array -; width - of the position of the column in the array; x - column position in the array; column - column to be put

putRow

private void putRow(double[] array,
                    int y,
                    double[] row)

Put a row in the array.

Parameters:: array -; y - row position in the array; row - row to be put

reduceDual1D

private void reduceDual1D(double[] c,
                          double[] s)

Reduce dual (1D).

Parameters:: c -; s -

samplesToInterpolationCoefficient1D

private void samplesToInterpolationCoefficient1D(double[] c,
                                                 int degree,
                                                 double tolerance)

Samples to interpolation coefficient (1D).

Parameters:: c - coefficients; degree -; tolerance -

symmetricFirMirrorOffBounds1D

private void symmetricFirMirrorOffBounds1D(double[] h,
                                           double[] c,
                                           double[] s)

Symmetric FIR filter with mirror off bounds (1D) conditions.

Parameters:: h -; c -; s -

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 -

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bunwarpj Class BSplineModel

MAX_OUTPUT_SIZE

min_image_size

ip

t

cpyramid

imgpyramid

original_image

image

coefficient

currentImage

currentCoefficient

currentWidth

currentHeight

width

height

pyramidDepth

currentDepth

smallestWidth

smallestHeight

isTarget

coefficientsAreMirrored

maxImageSubsamplingFactor

xIndex

yIndex

xWeight

yWeight

dxWeight

dyWeight

d2xWeight

d2yWeight

fromCurrent

widthToUse

heightToUse

bSubsampledOutput

subWidth

subHeight

subCoeffs

subImage

prec_xIndex

prec_yIndex

prec_xWeight

prec_yWeight

prec_dxWeight

prec_dyWeight

prec_d2xWeight

prec_d2yWeight

originalWidth

originalHeight

BSplineModel

BSplineModel

BSplineModel

BSplineModel

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

bunwarpj
Class BSplineModel