Package stitching

Class CommonFunctions

java.lang.Object

stitching.CommonFunctions

public class CommonFunctions
extends Object

Field Summary

Fields

Modifier and Type	Field	Description
static final int	AVG
static String[]	colorList
static String[]	cpuMemSelect
static String[]	fusionMethodList
static String[]	fusionMethodListGrid
static String[]	fusionMethodListSimple
static final int	LIN_BLEND
static final int	MAX
static String[]	methodList
static String[]	methodListCollection
static final int	MIN
static final int	NONE
static final int	RED_CYAN
static String[]	rgbTypes
static String[]	timeSelect

Constructor Summary

Constructors

Constructor	Description
CommonFunctions()

Method Summary

Modifier and Type	Method	Description
static final void	addHyperLinkListener(ij.gui.MultiLineLabel text, String myURL)
static void	complexConjugate(float[] complex)
static FloatArray2D	computeFFT(FloatArray2D img)
static FloatArray3D	computeFFT(FloatArray3D img)
static float[]	computePhaseCorrelationMatrix(float[] fft1, float[] fft2, boolean inPlace)
static FloatArray2D	computePhaseCorrelationMatrix(FloatArray2D fft1, FloatArray2D fft2, int width)
static FloatArray3D	computePhaseCorrelationMatrix(FloatArray3D fft1, FloatArray3D fft2, int width)
static final float	getPixelMin(int imageType, Object[] imageStack, int width, int height, int depth, int x, int y, int z, double min)
static final int[]	getPixelMinRGB(Object[] imageStack, int width, int height, int depth, int x, int y, int z, double min)
static float	getPixelValueRGB(int rgb, int rgbType)
static final double[]	getPlanePosition(loci.formats.IFormatReader r, loci.formats.meta.MetadataRetrieve retrieve, int series, int t)
static final double[]	getPlanePosition(loci.formats.IFormatReader r, loci.formats.meta.MetadataRetrieve retrieve, int series, int t, boolean invertX, boolean invertY, boolean ignoreZStage)
static ij.ImagePlus	loadImage(String directory, String file, int seriesNumber)
static ij.ImagePlus	loadImage(String directory, String file, int seriesNumber, String rgb)
static float[]	multiply(float[] complexA, float[] complexB, boolean overwriteA)
static float	multiplyComplexImg(float a, float b, float c, float d)
static float	multiplyComplexReal(float a, float b, float c, float d)
static Thread[]	newThreads()
static Thread[]	newThreads(int numThreads)
static void	normalizeComplexVectorsToUnitVectors(float[] complex)
static ij.ImagePlus	openLOCIImagePlus(String path, String fileName, int seriesNumber)
static ij.ImagePlus	openLOCIImagePlus(String path, String fileName, int seriesNumber, String rgb)
static ij.ImagePlus	openLOCIImagePlus(String path, String fileName, int seriesNumber, String rgb, int from, int to)
static FloatArray2D	pffft2D(FloatArray2D values, boolean scale)
static FloatArray3D	pffft3DMT(FloatArray3D values, boolean scale)
static FloatArray2D	pffftInv2D(FloatArray2D values, int nfft)
static FloatArray3D	pffftInv3DMT(FloatArray3D values, int nfft)
static void	quicksort(Quicksortable[] data, int left, int right)
static void	startAndJoin(Thread[] threads)
static void	startTask(Runnable run, int numThreads)
static FloatArray2D	zeroPad(FloatArray2D ip, int width, int height)
static FloatArray3D	zeroPad(FloatArray3D ip, int width, int height, int depth)
static FloatArray2D[]	zeroPadImages(FloatArray2D img1, FloatArray2D img2)
static FloatArray3D[]	zeroPadImages(FloatArray3D img1, FloatArray3D img2)

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Details

methodList

public static String[] methodList

AVG

public static final int AVG

See Also:

• Constant Field Values

LIN_BLEND

public static final int LIN_BLEND

See Also:

• Constant Field Values

MAX

public static final int MAX

See Also:

• Constant Field Values

MIN

public static final int MIN

See Also:

• Constant Field Values

RED_CYAN

public static final int RED_CYAN

See Also:

• Constant Field Values

NONE

public static final int NONE

See Also:

• Constant Field Values

methodListCollection

public static String[] methodListCollection

rgbTypes

public static String[] rgbTypes

colorList

public static String[] colorList

fusionMethodList

public static String[] fusionMethodList

fusionMethodListSimple

public static String[] fusionMethodListSimple

fusionMethodListGrid

public static String[] fusionMethodListGrid

timeSelect

public static String[] timeSelect

cpuMemSelect

public static String[] cpuMemSelect

Constructor Details

CommonFunctions

public CommonFunctions()

Method Details

loadImage

public static ij.ImagePlus loadImage(String directory,
 String file,
 int seriesNumber)

loadImage

public static ij.ImagePlus loadImage(String directory,
 String file,
 int seriesNumber,
 String rgb)

addHyperLinkListener

public static final void addHyperLinkListener(ij.gui.MultiLineLabel text,
 String myURL)

openLOCIImagePlus

public static ij.ImagePlus openLOCIImagePlus(String path,
 String fileName,
 int seriesNumber,
 String rgb)

openLOCIImagePlus

public static ij.ImagePlus openLOCIImagePlus(String path,
 String fileName,
 int seriesNumber)

openLOCIImagePlus

public static ij.ImagePlus openLOCIImagePlus(String path,
 String fileName,
 int seriesNumber,
 String rgb,
 int from,
 int to)

getPixelValueRGB

public static float getPixelValueRGB(int rgb,
 int rgbType)

zeroPad

public static FloatArray3D zeroPad(FloatArray3D ip,
 int width,
 int height,
 int depth)

zeroPadImages

public static FloatArray3D[] zeroPadImages(FloatArray3D img1,
 FloatArray3D img2)

zeroPad

public static FloatArray2D zeroPad(FloatArray2D ip,
 int width,
 int height)

zeroPadImages

public static FloatArray2D[] zeroPadImages(FloatArray2D img1,
 FloatArray2D img2)

quicksort

public static void quicksort(Quicksortable[] data,
 int left,
 int right)

pffft2D

public static FloatArray2D pffft2D(FloatArray2D values,
 boolean scale)

pffftInv2D

public static FloatArray2D pffftInv2D(FloatArray2D values,
 int nfft)

pffft3DMT

public static FloatArray3D pffft3DMT(FloatArray3D values,
 boolean scale)

computePhaseCorrelationMatrix

public static FloatArray2D computePhaseCorrelationMatrix(FloatArray2D fft1,
 FloatArray2D fft2,
 int width)

computeFFT

public static FloatArray2D computeFFT(FloatArray2D img)

computePhaseCorrelationMatrix

public static FloatArray3D computePhaseCorrelationMatrix(FloatArray3D fft1,
 FloatArray3D fft2,
 int width)

computeFFT

public static FloatArray3D computeFFT(FloatArray3D img)

computePhaseCorrelationMatrix

public static float[] computePhaseCorrelationMatrix(float[] fft1,
 float[] fft2,
 boolean inPlace)

normalizeComplexVectorsToUnitVectors

public static void normalizeComplexVectorsToUnitVectors(float[] complex)

complexConjugate

public static void complexConjugate(float[] complex)

multiplyComplexReal

public static float multiplyComplexReal(float a,
 float b,
 float c,
 float d)

multiplyComplexImg

public static float multiplyComplexImg(float a,
 float b,
 float c,
 float d)

multiply

public static float[] multiply(float[] complexA,
 float[] complexB,
 boolean overwriteA)

pffftInv3DMT

public static FloatArray3D pffftInv3DMT(FloatArray3D values,
 int nfft)

startTask

public static void startTask(Runnable run,
 int numThreads)

newThreads

public static Thread[] newThreads()

newThreads

public static Thread[] newThreads(int numThreads)

startAndJoin

public static void startAndJoin(Thread[] threads)

getPixelMinRGB

public static final int[] getPixelMinRGB(Object[] imageStack,
 int width,
 int height,
 int depth,
 int x,
 int y,
 int z,
 double min)

getPixelMin

public static final float getPixelMin(int imageType,
 Object[] imageStack,
 int width,
 int height,
 int depth,
 int x,
 int y,
 int z,
 double min)

getPlanePosition

public static final double[] getPlanePosition(loci.formats.IFormatReader r,
 loci.formats.meta.MetadataRetrieve retrieve,
 int series,
 int t)

getPlanePosition

public static final double[] getPlanePosition(loci.formats.IFormatReader r,
 loci.formats.meta.MetadataRetrieve retrieve,
 int series,
 int t,
 boolean invertX,
 boolean invertY,
 boolean ignoreZStage)