public abstract class ImageInt extends ImageHandler
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
| Modifier | Constructor and Description |
|---|---|
|
ImageInt(ImageHandler im,
boolean scaling) |
|
ImageInt(ImagePlus img) |
|
ImageInt(ImageStack img) |
|
ImageInt(java.lang.String title,
int sizeX,
int sizeY,
int sizeZ) |
protected |
ImageInt(java.lang.String title,
int sizeX,
int sizeY,
int sizeZ,
int offsetX,
int offsetY,
int offsetZ) |
| Modifier and Type | Method and Description |
|---|---|
ImageInt |
adaptiveFilter(float radx,
float rady,
float radz,
int nbcpus)
Deprecated.
|
void |
adaptiveFilter(ImageInt filtered,
float radx,
float rady,
float radz,
int zmin,
int zmax,
Chrono timer,
AbstractLog show) |
ImageInt |
addImage(ImageInt other) |
abstract int |
countMaskVolume() |
abstract ImageInt |
crop3D(java.lang.String title,
int x_min,
int x_max,
int y_min,
int y_max,
int z_min,
int z_max) |
abstract ImageInt[] |
crop3D(java.util.TreeMap<java.lang.Float,int[]> bounds) |
ImageByte[] |
crop3DBinary() |
abstract 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[] |
crop3DBinary(java.util.TreeMap<java.lang.Float,int[]> bounds) |
abstract ImageInt |
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_) |
ImageInt |
cropRadius(int xc,
int yc,
int zc,
int rx,
int ry,
int rz,
boolean mean,
boolean sphere)
Extract a 3D image from a specified location as the center of crop
|
ImageInt |
diffAbsImage(ImageHandler other) |
abstract void |
draw(Object3D o,
int value) |
abstract ImageInt |
duplicate() |
ImageByte |
erode(float erodeRadius,
int nbCPUs) |
void |
filterGeneric(ImageInt out,
float radx,
float rady,
float radz,
int zmin,
int zmax,
int filter)
3D filter using threads
|
void |
filterGeneric(ImageInt out,
float radx,
float rady,
float radz,
int zmin,
int zmax,
int filter,
Chrono timer,
AbstractLog log)
3D filter using threads
|
void |
filterGeneric(ImageInt out,
Object3DVoxels obj,
int zmin,
int zmax,
int filter) |
void |
filterGeneric(ImageInt out,
Object3DVoxels obj,
int zmin,
int zmax,
int filter,
Chrono timer,
AbstractLog log) |
void |
filterPooling(ImageInt out,
int stepx,
int stepy,
int stepz,
int zmin,
int zmax) |
void |
filterPooling(ImageInt out,
int stepx,
int stepy,
int stepz,
int zmin,
int zmax,
int filter,
Chrono timer,
AbstractLog log) |
Voxel3D |
firstVoxelValueInt(int f) |
ImageFloat |
getDistanceMapInsideMask(int nbCPUs) |
java.util.ArrayList<Voxel3DComparable> |
getListMaxima(float radx,
float rady,
float radz,
int zmin,
int zmax) |
java.util.ArrayList<Voxel3DComparable> |
getListMaxima(float radx,
float rady,
float radz,
int zmin,
int zmax,
Chrono timer,
AbstractLog log) |
Object3DVoxels |
getObject3DBackground(ImageInt mask) |
Object3DVoxels |
getObjectMask() |
Object3DVoxels[] |
getObjects3D() |
Object3DFuzzy[] |
getObjects3D(ImageFloat probaMap,
float contourProba)
Deprecated.
|
Objects3DPopulation |
getObjects3DPopulation() |
abstract float |
getPixel(Point3D P) |
abstract int |
getPixelInt(int coord)
Deprecated.
|
abstract int |
getPixelInt(int xy,
int z) |
abstract int |
getPixelInt(int x,
int y,
int z) |
abstract int |
getPixelInt(Point3D P) |
abstract float |
getPixelInterpolated(Point3D P) |
abstract int |
getPixelIntInterpolated(Point3D P) |
java.util.ArrayList<java.lang.Integer> |
getUniqueValues() |
java.util.ArrayList<java.lang.Integer> |
getUniqueValues(int th) |
boolean |
hasOneValueInt(int f) |
ImageInt |
invertMask(ImageInt mask) |
boolean |
isBinary() |
boolean |
isBinary(int background) |
void |
mathGeneric(ImageInt other,
ImageInt out,
int zmin,
int zmax,
int operation,
float par1,
float par2,
Chrono timer,
AbstractLog log)
Generic arithmetic between images
pixel1*parameter1 OPERATION pixel2*parameter2
|
void |
operationGeneric(ImageInt out,
int zmin,
int zmax,
int operation,
float par1,
float par2,
Chrono timer,
AbstractLog log) |
ImageHandler |
projectAVG(java.lang.String axis) |
void |
replacePixelsValue(int[] values,
int replace)
Replace a pixel values by another
|
void |
replacePixelsValue(int[] values,
int[] replace)
Replace pixel values by others
|
void |
replacePixelsValue(int val,
int rep)
Replace a pixel value by another
|
void |
replacePixelsValue(int val1,
int rep1,
int val2,
int rep2)
Replace a pixel value by another
|
abstract ImageInt |
resample(int newZ,
int method)
Rescale the image to new dimension, only in Z
|
abstract ImageInt |
resample(int newX,
int newY,
int newZ,
int method)
Rescale the image to new dimension, in X Y and Z
|
abstract void |
setPixel(int xy,
int z,
int value) |
abstract void |
setPixel(int x,
int y,
int z,
int value) |
abstract void |
setPixelCross3D(int x,
int y,
int z,
int value) |
abstract boolean |
shiftIndexes(java.util.TreeMap<java.lang.Integer,int[]> bounds) |
ImageInt |
sobelFilter()
Sobel-like filtering in 3D
|
ImageInt |
substractImage(ImageInt other)
Deprecated.
|
ImageInt |
subtractImage(ImageInt other) |
ImageInt |
subtractImageInt(ImageInt other) |
ImageByte |
toCenterMask() |
abstract ImageByte |
toMask() |
static ImageInt |
wrap(ImagePlus imp) |
static ImageInt |
wrap(ImageStack stack) |
addImage, addImage, addValue, closeImagePlus, contains, contains, contains, contains, convertToByte, convertToByte, createListVoxels, createSameDimensions, createSameType, deleteSlices, divideByValue, divideImage, draw, enlarge, erase, extractLine, fill, fill, flush, flushPixels, getArray1D, getArray1D, getBinaryData, getBounds, getCalibration, getDistanceMap, getHisto, getHisto, getHistogram, getHistogram, getHistogram, getHistogram, getHistogram, getHyperStack, getImagePlus, getImageStack, getImageStats, getLineX, getLineY, getLineZ, getMax, getMax, getMaxBelowValue, getMaxPosition, getMean, getMean, getMin, getMin, getMinAboveValue, getMinAndMax, 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, getPixel, getPixel, getPixel, getPixel, getScaleXY, getScaleZ, getSizeInMb, getThumbNail, getThumbNail, getThumbnailImage, getTitle, getType, getUnit, hasOneValue, hide, homogenizeBitDepth, insert, intersectMask, intersectMask, intersectMask2D, invert, invert, invertBackground, isOpened, isVisible, maskContains, merge3D, merge3DBinary, merge3DRaw, multiplyByValue, multiplyImage, newBlankImageHandler, normaliseValue, normalize_, normalize, normalize, openImage, powImage, radialDistribution, radialDistribution, radialDistribution, resetStats, resetStats, resize, sameDimensions, sameDimensions, sameDimentions, sameDimentions, save, save, saveThumbNail, set332RGBLut, setCalibration, setGraysLut, setLineX, setLineY, setLineZ, setMinAndMax, setMinAndMax, setOffset, setOffset, setPixel, setPixel, setPixel, setPixel, setPixelIncrement, setPixelIncrement, setScale, setScale, setTitle, show, show, showDuplicate, substractImage, subtractImage, threshold, thresholdAboveExclusive, thresholdAboveInclusive, thresholdCut, thresholdRangeExclusive, thresholdRangeInclusive, ToByte, touchBorders, transfertPixelValues, trimSlices, updateDisplay, zoompublic ImageInt(ImagePlus img)
public ImageInt(ImageStack img)
public ImageInt(java.lang.String title,
int sizeX,
int sizeY,
int sizeZ)
public ImageInt(ImageHandler im, boolean scaling)
protected ImageInt(java.lang.String title,
int sizeX,
int sizeY,
int sizeZ,
int offsetX,
int offsetY,
int offsetZ)
public static ImageInt wrap(ImagePlus imp)
public static ImageInt wrap(ImageStack stack)
public abstract void setPixel(int x,
int y,
int z,
int value)
public abstract void setPixel(int xy,
int z,
int value)
public abstract void setPixelCross3D(int x,
int y,
int z,
int value)
public abstract void draw(Object3D o, int value)
public abstract int getPixelInt(int xy,
int z)
public abstract int getPixelInt(int x,
int y,
int z)
@Deprecated public abstract int getPixelInt(int coord)
public abstract float getPixel(Point3D P)
getPixel in class ImageHandlerpublic abstract int getPixelInt(Point3D P)
public abstract float getPixelInterpolated(Point3D P)
getPixelInterpolated in class ImageHandlerpublic abstract int getPixelIntInterpolated(Point3D P)
public java.util.ArrayList<java.lang.Integer> getUniqueValues(int th)
public java.util.ArrayList<java.lang.Integer> getUniqueValues()
public abstract ImageInt crop3D(java.lang.String title, int x_min, int x_max, int y_min, int y_max, int z_min, int z_max)
crop3D in class ImageHandlerpublic abstract 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)
public abstract boolean shiftIndexes(java.util.TreeMap<java.lang.Integer,int[]> bounds)
public abstract ImageInt[] crop3D(java.util.TreeMap<java.lang.Float,int[]> bounds)
crop3D in class ImageHandlerpublic abstract ImageInt 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_)
crop3DMask in class ImageHandlerpublic ImageByte[] crop3DBinary(java.util.TreeMap<java.lang.Float,int[]> bounds)
public ImageByte[] crop3DBinary()
public ImageInt cropRadius(int xc, int yc, int zc, int rx, int ry, int rz, boolean mean, boolean sphere)
ImageHandlercropRadius in class ImageHandlerxc - the x coordinate of the center of the extractionyc - the y coordinate of the center of the extractionzc - the z coordinate of the center of the extractionrx - radius X of new imagery - radius Y of new imagerz - radius Z of new imagesphere - extract inside a sphere@Deprecated public Object3DFuzzy[] getObjects3D(ImageFloat probaMap, float contourProba)
public Object3DVoxels[] getObjects3D()
public Object3DVoxels getObjectMask()
public Objects3DPopulation getObjects3DPopulation()
public Object3DVoxels getObject3DBackground(ImageInt mask)
public ImageFloat getDistanceMapInsideMask(int nbCPUs)
public ImageByte erode(float erodeRadius, int nbCPUs)
public void replacePixelsValue(int val,
int rep)
replacePixelsValue in class ImageHandlerval - the value to be replacedrep - the new valuepublic void replacePixelsValue(int val1,
int rep1,
int val2,
int rep2)
replacePixelsValue in class ImageHandlerval1 - the value to be replacedrep1 - the new valuepublic void replacePixelsValue(int[] values,
int[] replace)
values - the values to be replacedreplace - the new valuespublic void replacePixelsValue(int[] values,
int replace)
values - the values to be replacedreplace - the new valuepublic ImageHandler projectAVG(java.lang.String axis)
public boolean isBinary(int background)
background - public boolean isBinary()
public abstract ImageInt resample(int newX, int newY, int newZ, int method)
ImageHandlerresample in class ImageHandlernewX - the new size in XnewY - the new size in YnewZ - the new size in Zmethod - the interpolation method, see ImageProcessorpublic abstract ImageInt resample(int newZ, int method)
resample in class ImageHandlernewZ - the new size in Zmethod - the method, see ImageProcessorpublic abstract ImageByte toMask()
public ImageByte toCenterMask()
public abstract int countMaskVolume()
public ImageInt diffAbsImage(ImageHandler other)
public abstract ImageInt duplicate()
duplicate in class ImageHandler@Deprecated public ImageInt substractImage(ImageInt other)
other - public ImageInt invertMask(ImageInt mask)
mask - reference maskpublic boolean hasOneValueInt(int f)
public Voxel3D firstVoxelValueInt(int f)
public void filterGeneric(ImageInt out, float radx, float rady, float radz, int zmin, int zmax, int filter)
out - radx - Radius of mean filter in xrady - Radius of mean filter in yradz - Radius of mean filter in zzmin - zmax - filter - public void filterGeneric(ImageInt out, float radx, float rady, float radz, int zmin, int zmax, int filter, Chrono timer, AbstractLog log)
out - radx - Radius of mean filter in xrady - Radius of mean filter in yradz - Radius of mean filter in zzmin - zmax - filter - public void filterPooling(ImageInt out, int stepx, int stepy, int stepz, int zmin, int zmax, int filter, Chrono timer, AbstractLog log)
public void filterPooling(ImageInt out, int stepx, int stepy, int stepz, int zmin, int zmax)
public void mathGeneric(ImageInt other, ImageInt out, int zmin, int zmax, int operation, float par1, float par2, Chrono timer, AbstractLog log)
other - other imageout - result imagezmin - minimum Zzmax - maximum Zoperation - filter ADD MULT ...par1 - parameter1par2 - parameter2timer - timer for timelog - logger for printpublic void operationGeneric(ImageInt out, int zmin, int zmax, int operation, float par1, float par2, Chrono timer, AbstractLog log)
public java.util.ArrayList<Voxel3DComparable> getListMaxima(float radx, float rady, float radz, int zmin, int zmax)
public java.util.ArrayList<Voxel3DComparable> getListMaxima(float radx, float rady, float radz, int zmin, int zmax, Chrono timer, AbstractLog log)
public void filterGeneric(ImageInt out, Object3DVoxels obj, int zmin, int zmax, int filter)
public void filterGeneric(ImageInt out, Object3DVoxels obj, int zmin, int zmax, int filter, Chrono timer, AbstractLog log)
public ImageInt sobelFilter()
public void adaptiveFilter(ImageInt filtered, float radx, float rady, float radz, int zmin, int zmax, Chrono timer, AbstractLog show)
@Deprecated public ImageInt adaptiveFilter(float radx, float rady, float radz, int nbcpus)
radx - radz - rady -