mcib3d.image3d

Class ImageByte

java.lang.Object

mcib3d.image3d.ImageHandler

mcib3d.image3d.ImageInt

mcib3d.image3d.ImageByte

Direct Known Subclasses:

BlankMask

public class ImageByte
extends ImageInt

Copyright (C) 2012 Jean Ollion

This file is part of tango

tango is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 3 of the License, or (at your option) any later version.

This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.

You should have received a copy of the GNU General Public License along with this program. If not, see .

Field Summary

Fields

Modifier and Type	Field and Description
byte[][]	pixels

Fields inherited from class mcib3d.image3d.ImageHandler

defZoomFactor, img, offsetX, offsetY, offsetZ, sizeX, sizeXY, sizeXYZ, sizeY, sizeZ, title

Constructor Summary

Constructors

Modifier	Constructor and Description
	ImageByte(byte[][] pixels, java.lang.String title, int sizeX)
	ImageByte(ImageHandler im, boolean scaling)
	ImageByte(ImagePlus img)
	ImageByte(ImageStack stack)
protected	ImageByte(int sizeX, int sizeY, int sizeZ)
	ImageByte(java.lang.String title, int sizeX, int sizeY, int sizeZ)

Method Summary

Modifier and Type	Method and Description
void	addMask(ImageInt mask)
static byte[]	convert(float[] input, boolean scaling)
static byte[]	convert(short[] input, boolean scaling)
ImageFloat	convertToFloat(boolean scaling)
ImageShort	convertToShort(boolean scaling)
void	copy(ImageByte destination)
int	countMaskVolume()
ImageByte	crop3D(java.lang.String title, int x_min_, int x_max_, int y_min_, int y_max_, int z_min_, int z_max_)
ImageByte[]	crop3D(java.util.TreeMap<java.lang.Float,int[]> bounds)
ImageByte	crop3DBinary(java.lang.String title, float label, int x_min_, int x_max_, int y_min_, int y_max_, int z_min_, int z_max_)
ImageByte	crop3DMask(java.lang.String title, ImageInt mask, float label, int x_min_, int x_max_, int y_min_, int y_max_, int z_min_, int z_max_)
ImageHandler	deleteSlices(int zmin, int zmax)
void	draw(Object3D o, float value)
void	draw(Object3D o, int value)
ImageByte	duplicate()
void	erase()
void	fill(double value, int min, int max)
protected void	flushPixels()
java.lang.Object	getArray1D()
java.lang.Object	getArray1D(int z)
static byte[]	getArray1DByte(ImagePlus img)
protected int[]	getHisto(ImageInt mask)
protected int[]	getHisto(ImageInt mask, int nBins, double min, double max)
static ImagePlus	getImagePlus(byte[] pixels, int sizeX, int sizeY, int sizeZ, boolean setMinAndMax)
protected void	getMinAndMax(ImageInt mask)
float	getPixel(int coord) Deprecated.
float	getPixel(IntCoord3D vox)
float	getPixel(int xy, int z)
float	getPixel(int x, int y, int z)
float	getPixel(Point3D P)
float	getPixel(Point3DInt P)
float	getPixel(Voxel3D vox, boolean approx)
int	getPixelInt(int coord) Deprecated.
int	getPixelInt(IntCoord3D vox)
int	getPixelInt(int xy, int z)
int	getPixelInt(int x, int y, int z)
int	getPixelInt(Point3D P)
float	getPixelInterpolated(Point3D P)
int	getPixelIntInterpolated(Point3D P)
double	getSizeInMb()
int	getType()
void	intersectMask(ImageHandler mask)
void	intersectMask(ImageInt mask) Deprecated.
void	intersectMask2D(ImageInt mask, int z)
void	invert(ImageInt mask)
boolean	isOpened()
protected ImageFloat	normalize_(ImageInt mask, double saturation)
ImageFloat	normalize(double min, double max)
ImageByte	resample(int newZ, int method) Rescale the image to new dimension, only in Z
ImageByte	resample(int newX, int newY, int newZ, int method) Rescale the image to new dimension, in X Y and Z
ImageHandler	resize(int dX, int dY, int dZ) Enlarge the canvas size of the image in X, Y and Z .
void	setPixel(int coord, float value) Deprecated.
void	setPixel(int xy, int z, float value)
void	setPixel(int xy, int z, int value)
void	setPixel(int x, int y, int z, float value)
void	setPixel(int x, int y, int z, int value)
void	setPixel(Point3D point, float value)
void	setPixelCross3D(int x, int y, int z, int value)
boolean	shiftIndexes(java.util.TreeMap<java.lang.Integer,int[]> bounds)
void	substractMask(ImageInt mask)
ImageByte	threshold(float thld, boolean keepUnderThld, boolean strict)
void	thresholdCut(float thld, boolean keepUnderThld, boolean strict)
ImageByte	thresholdRangeExclusive(float min, float max)
ImageByte	thresholdRangeInclusive(float min, float max)
ImageByte	toMask()
void	trimSlices(int zmin, int zmax)

Methods inherited from class mcib3d.image3d.ImageInt

adaptiveFilter, adaptiveFilter, addImage, crop3DBinary, crop3DBinary, cropRadius, diffAbsImage, erode, filterGeneric, filterGeneric, filterGeneric, filterGeneric, filterPooling, filterPooling, firstVoxelValueInt, getDistanceMapInsideMask, getListMaxima, getListMaxima, getObject3DBackground, getObjectMask, getObjects3D, getObjects3D, getObjects3DPopulation, getUniqueValues, getUniqueValues, hasOneValueInt, invertMask, isBinary, isBinary, mathGeneric, operationGeneric, projectAVG, replacePixelsValue, replacePixelsValue, replacePixelsValue, replacePixelsValue, sobelFilter, substractImage, subtractImage, subtractImageInt, toCenterMask, wrap, wrap

Methods inherited from class mcib3d.image3d.ImageHandler

addImage, addImage, addValue, closeImagePlus, contains, contains, contains, contains, convertToByte, convertToByte, createListVoxels, createSameDimensions, createSameType, divideByValue, divideImage, enlarge, extractLine, fill, flush, getBinaryData, getBounds, getCalibration, getDistanceMap, getHistogram, getHistogram, getHistogram, getHistogram, getHistogram, getHyperStack, getImagePlus, getImageStack, getImageStats, getLineX, getLineY, getLineZ, getMax, getMax, getMaxBelowValue, getMaxPosition, getMean, getMean, getMin, getMin, getMinAboveValue, getMinAndMaxArray, getMinAndMaxArray, getMoments, getNeighborhood, getNeighborhood3x3x3, getNeighborhood3x3x3CenterList, getNeighborhood3x3x3ListCenter, getNeighborhood3x3x3ListNoCenter, getNeighborhood3x3x3NoCenterList, getNeighborhoodBrick, getNeighborhoodCross3D, getNeighborhoodCross3DList, getNeighborhoodKernel, getNeighborhoodKernel, getNeighborhoodKernelAdd, getNeighborhoodKernelSubstract, getNeighborhoodLayer, getNeighborhoodLayer, getNeighborhoodLayerAngle, getNeighborhoodLayerList, getNeighborhoodLayerList, getNeighborhoodSphere, getNeighborhoodXY3x3, getPercentile, getPixel, getPixel, getScaleXY, getScaleZ, getThumbNail, getThumbNail, getThumbnailImage, getTitle, getUnit, hasOneValue, hide, homogenizeBitDepth, insert, invert, invertBackground, isVisible, maskContains, merge3D, merge3DBinary, merge3DRaw, multiplyByValue, multiplyImage, newBlankImageHandler, normaliseValue, normalize, openImage, powImage, radialDistribution, radialDistribution, radialDistribution, resetStats, resetStats, sameDimensions, sameDimensions, sameDimentions, sameDimentions, save, save, saveThumbNail, set332RGBLut, setCalibration, setGraysLut, setLineX, setLineY, setLineZ, setMinAndMax, setMinAndMax, setOffset, setOffset, setPixelIncrement, setPixelIncrement, setScale, setScale, setTitle, show, show, showDuplicate, substractImage, subtractImage, thresholdAboveExclusive, thresholdAboveInclusive, ToByte, touchBorders, transfertPixelValues, updateDisplay, zoom

Methods inherited from class java.lang.Object

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

Field Detail

pixels

public byte[][] pixels

Constructor Detail

ImageByte

public ImageByte(ImagePlus img)

ImageByte

public ImageByte(ImageStack stack)

ImageByte

public ImageByte(byte[][] pixels,
                 java.lang.String title,
                 int sizeX)

ImageByte

public ImageByte(java.lang.String title,
                 int sizeX,
                 int sizeY,
                 int sizeZ)

ImageByte

protected ImageByte(int sizeX,
                    int sizeY,
                    int sizeZ)

ImageByte

public ImageByte(ImageHandler im,
                 boolean scaling)

Method Detail

getArray1DByte

public static byte[] getArray1DByte(ImagePlus img)

getImagePlus

public static ImagePlus getImagePlus(byte[] pixels,
                                     int sizeX,
                                     int sizeY,
                                     int sizeZ,
                                     boolean setMinAndMax)

convert

public static byte[] convert(float[] input,
                             boolean scaling)

convert

public static byte[] convert(short[] input,
                             boolean scaling)

getArray1D

public java.lang.Object getArray1D()

Specified by:

getArray1D in class ImageHandler

getArray1D

public java.lang.Object getArray1D(int z)

Specified by:

getArray1D in class ImageHandler

convertToShort

public ImageShort convertToShort(boolean scaling)

convertToFloat

public ImageFloat convertToFloat(boolean scaling)

erase

public void erase()

Specified by:

erase in class ImageHandler

fill

public void fill(double value,
                 int min,
                 int max)

Specified by:

fill in class ImageHandler

duplicate

public ImageByte duplicate()

Specified by:

duplicate in class ImageInt

copy

public void copy(ImageByte destination)

getPixel

public float getPixel(int xy,
                      int z)

Specified by:

getPixel in class ImageHandler

getPixel

@Deprecated
public float getPixel(int coord)

Deprecated.

Specified by:

getPixel in class ImageHandler

getPixel

public float getPixel(Voxel3D vox,
                      boolean approx)

getPixel

public float getPixel(int x,
                      int y,
                      int z)

Specified by:

getPixel in class ImageHandler

getPixelInt

public int getPixelInt(int xy,
                       int z)

Specified by:

getPixelInt in class ImageInt

getPixelInt

@Deprecated
public int getPixelInt(int coord)

Deprecated.

Specified by:

getPixelInt in class ImageInt

getPixelInt

public int getPixelInt(int x,
                       int y,
                       int z)

Specified by:

getPixelInt in class ImageInt

getPixel

public float getPixel(IntCoord3D vox)

getPixelInt

public int getPixelInt(IntCoord3D vox)

setPixel

@Deprecated
public void setPixel(int coord,
                                 float value)

Deprecated.

Specified by:

setPixel in class ImageHandler

setPixel

public void setPixel(Point3D point,
                     float value)

Specified by:

setPixel in class ImageHandler

setPixel

public void setPixel(int x,
                     int y,
                     int z,
                     float value)

Specified by:

setPixel in class ImageHandler

setPixel

public void setPixel(int xy,
                     int z,
                     float value)

Specified by:

setPixel in class ImageHandler

setPixel

public void setPixel(int x,
                     int y,
                     int z,
                     int value)

Specified by:

setPixel in class ImageInt

setPixelCross3D

public void setPixelCross3D(int x,
                            int y,
                            int z,
                            int value)

Specified by:

setPixelCross3D in class ImageInt

setPixel

public void setPixel(int xy,
                     int z,
                     int value)

Specified by:

setPixel in class ImageInt

getMinAndMax

protected void getMinAndMax(ImageInt mask)

Specified by:

getMinAndMax in class ImageHandler

getHisto

protected int[] getHisto(ImageInt mask)

Specified by:

getHisto in class ImageHandler

getHisto

protected int[] getHisto(ImageInt mask,
                         int nBins,
                         double min,
                         double max)

Specified by:

getHisto in class ImageHandler

thresholdRangeInclusive

public ImageByte thresholdRangeInclusive(float min,
                                         float max)

Specified by:

thresholdRangeInclusive in class ImageHandler

thresholdRangeExclusive

public ImageByte thresholdRangeExclusive(float min,
                                         float max)

Specified by:

thresholdRangeExclusive in class ImageHandler

threshold

public ImageByte threshold(float thld,
                           boolean keepUnderThld,
                           boolean strict)

Specified by:

threshold in class ImageHandler

thresholdCut

public void thresholdCut(float thld,
                         boolean keepUnderThld,
                         boolean strict)

Specified by:

thresholdCut in class ImageHandler

crop3D

public ImageByte crop3D(java.lang.String title,
                        int x_min_,
                        int x_max_,
                        int y_min_,
                        int y_max_,
                        int z_min_,
                        int z_max_)

Specified by:

crop3D in class ImageInt

shiftIndexes

public boolean shiftIndexes(java.util.TreeMap<java.lang.Integer,int[]> bounds)

Specified by:

shiftIndexes in class ImageInt

crop3D

public ImageByte[] crop3D(java.util.TreeMap<java.lang.Float,int[]> bounds)

Specified by:

crop3D in class ImageInt

crop3DMask

public ImageByte crop3DMask(java.lang.String title,
                            ImageInt mask,
                            float label,
                            int x_min_,
                            int x_max_,
                            int y_min_,
                            int y_max_,
                            int z_min_,
                            int z_max_)

Specified by:

crop3DMask in class ImageInt

crop3DBinary

public ImageByte crop3DBinary(java.lang.String title,
                              float label,
                              int x_min_,
                              int x_max_,
                              int y_min_,
                              int y_max_,
                              int z_min_,
                              int z_max_)

Specified by:

crop3DBinary in class ImageInt

resize

public ImageHandler resize(int dX,
                           int dY,
                           int dZ)

Description copied from class: ImageHandler

Enlarge the canvas size of the image in X, Y and Z . New size is then increased by 2*border

Specified by:

resize in class ImageHandler

Parameters:

dX - the border to add in X, both on left and right

dY - the border to add in Y, both on top and bottom

dZ - the border to add in Z, both above and below

Returns:

the resized enlarged image

resample

public ImageByte resample(int newX,
                          int newY,
                          int newZ,
                          int method)

Description copied from class: ImageHandler

Rescale the image to new dimension, in X Y and Z

Specified by:

resample in class ImageInt

Parameters:

newX - the new size in X

newY - the new size in Y

newZ - the new size in Z

method - the interpolation method, see ImageProcessor

Returns:

the rescaled image

resample

public ImageByte resample(int newZ,
                          int method)

Rescale the image to new dimension, only in Z

Specified by:

resample in class ImageInt

Parameters:

newZ - the new size in Z

method - the method, see ImageProcessor

Returns:

the rescaled image

normalize_

protected ImageFloat normalize_(ImageInt mask,
                                double saturation)

Specified by:

normalize_ in class ImageHandler

normalize

public ImageFloat normalize(double min,
                            double max)

Specified by:

normalize in class ImageHandler

invert

public void invert(ImageInt mask)

Specified by:

invert in class ImageHandler

draw

public void draw(Object3D o,
                 float value)

Specified by:

draw in class ImageHandler

draw

public void draw(Object3D o,
                 int value)

Specified by:

draw in class ImageInt

flushPixels

protected void flushPixels()

Specified by:

flushPixels in class ImageHandler

isOpened

public boolean isOpened()

Specified by:

isOpened in class ImageHandler

getPixel

public float getPixel(Point3D P)

Specified by:

getPixel in class ImageInt

getPixel

public float getPixel(Point3DInt P)

Specified by:

getPixel in class ImageHandler

getPixelInt

public int getPixelInt(Point3D P)

Specified by:

getPixelInt in class ImageInt

getPixelInterpolated

public float getPixelInterpolated(Point3D P)

Specified by:

getPixelInterpolated in class ImageInt

getPixelIntInterpolated

public int getPixelIntInterpolated(Point3D P)

Specified by:

getPixelIntInterpolated in class ImageInt

deleteSlices

public ImageHandler deleteSlices(int zmin,
                                 int zmax)

Specified by:

deleteSlices in class ImageHandler

trimSlices

public void trimSlices(int zmin,
                       int zmax)

Specified by:

trimSlices in class ImageHandler

intersectMask

@Deprecated
public void intersectMask(ImageInt mask)

Deprecated.

Specified by:

intersectMask in class ImageHandler

intersectMask

public void intersectMask(ImageHandler mask)

Specified by:

intersectMask in class ImageHandler

intersectMask2D

public void intersectMask2D(ImageInt mask,
                            int z)

Specified by:

intersectMask2D in class ImageHandler

substractMask

public void substractMask(ImageInt mask)

addMask

public void addMask(ImageInt mask)

getSizeInMb

public double getSizeInMb()

Specified by:

getSizeInMb in class ImageHandler

getType

public int getType()

Specified by:

getType in class ImageHandler

toMask

public ImageByte toMask()

Specified by:

toMask in class ImageInt

countMaskVolume

public int countMaskVolume()

Specified by:

countMaskVolume in class ImageInt