mcib3d.image3d

Class BlankMask

java.lang.Object

mcib3d.image3d.ImageHandler

mcib3d.image3d.ImageInt

mcib3d.image3d.ImageByte

mcib3d.image3d.BlankMask

public class BlankMask
extends ImageByte

/** 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 inherited from class mcib3d.image3d.ImageByte

pixels

Fields inherited from class mcib3d.image3d.ImageHandler

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

Constructor Summary

Constructors

Constructor and Description
BlankMask(ImageHandler template)
BlankMask(java.lang.String title, int sizeX, int sizeY, int sizeZ)

Method Summary

Modifier and Type	Method and Description
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_)
void	draw(Object3D o, int value)
boolean	equals(java.lang.Object o)
void	erase()
java.lang.Object	getArray1D()
java.util.TreeMap<java.lang.Float,int[]>	getBounds(boolean addBorder)
int[]	getHisto(ImageInt mask)
protected int[]	getHisto(ImageInt mask, int nBins, double min, double max)
ImagePlus	getImagePlus()
protected void	getMinAndMax(ImageInt mask)
float	getPixel(int coord)
float	getPixel(IntCoord3D vox)
float	getPixel(int xy, int z)
float	getPixel(int x, int y, int z)
int	getPixelInt(int coord)
int	getPixelInt(int xy, int z)
int	getPixelInt(int x, int y, int z)
double	getScaleXY()
double	getScaleZ()
int	hashCode()
protected ImageFloat	normalize_(ImageInt mask, double saturation)
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	setMinAndMax(ImageInt mask)
void	setPixel(int coord, float value)
void	setPixel(int xy, int z, float value)
void	setPixel(int x, int y, int z, float value)
boolean	shiftIndexes(java.util.TreeMap<java.lang.Integer,int[]> bounds)
ImageByte	threshold(float thld, boolean keepUnderThld, boolean strict)
void	thresholdCut(float thld, boolean keepUnderThld, boolean strict)

Methods inherited from class mcib3d.image3d.ImageByte

addMask, convert, convert, convertToFloat, convertToShort, copy, countMaskVolume, deleteSlices, draw, duplicate, fill, flushPixels, getArray1D, getArray1DByte, getImagePlus, getPixel, getPixel, getPixel, getPixelInt, getPixelInt, getPixelInterpolated, getPixelIntInterpolated, getSizeInMb, getType, intersectMask, intersectMask, intersectMask2D, invert, isOpened, normalize, setPixel, setPixel, setPixel, setPixelCross3D, substractMask, thresholdRangeExclusive, thresholdRangeInclusive, toMask, trimSlices

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, getCalibration, getDistanceMap, getHistogram, getHistogram, getHistogram, getHistogram, getHistogram, getHyperStack, 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, 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, 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, finalize, getClass, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

BlankMask

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

BlankMask

public BlankMask(ImageHandler template)

Method Detail

getScaleXY

public double getScaleXY()

Overrides:

getScaleXY in class ImageHandler

getScaleZ

public double getScaleZ()

Overrides:

getScaleZ in class ImageHandler

getImagePlus

public ImagePlus getImagePlus()

Overrides:

getImagePlus in class ImageHandler

draw

public void draw(Object3D o,
                 int value)

Overrides:

draw in class ImageByte

getPixelInt

public int getPixelInt(int xy,
                       int z)

Overrides:

getPixelInt in class ImageByte

getPixelInt

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

Overrides:

getPixelInt in class ImageByte

getPixelInt

public int getPixelInt(int coord)

Overrides:

getPixelInt in class ImageByte

getBounds

public java.util.TreeMap<java.lang.Float,int[]> getBounds(boolean addBorder)

Overrides:

getBounds in class ImageHandler

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)

Overrides:

crop3DBinary in class ImageByte

shiftIndexes

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

Overrides:

shiftIndexes in class ImageByte

getPixel

public float getPixel(int coord)

Overrides:

getPixel in class ImageByte

getPixel

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

Overrides:

getPixel in class ImageByte

getPixel

public float getPixel(int xy,
                      int z)

Overrides:

getPixel in class ImageByte

getPixel

public float getPixel(IntCoord3D vox)

Overrides:

getPixel in class ImageByte

setPixel

public void setPixel(int coord,
                     float value)

Overrides:

setPixel in class ImageByte

setPixel

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

Overrides:

setPixel in class ImageByte

setPixel

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

Overrides:

setPixel in class ImageByte

getArray1D

public java.lang.Object getArray1D()

Overrides:

getArray1D in class ImageByte

erase

public void erase()

Overrides:

erase in class ImageByte

getMinAndMax

protected void getMinAndMax(ImageInt mask)

Overrides:

getMinAndMax in class ImageByte

setMinAndMax

public void setMinAndMax(ImageInt mask)

Overrides:

setMinAndMax in class ImageHandler

getHisto

public int[] getHisto(ImageInt mask)

Overrides:

getHisto in class ImageByte

getHisto

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

Overrides:

getHisto in class ImageByte

threshold

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

Overrides:

threshold in class ImageByte

thresholdCut

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

Overrides:

thresholdCut in class ImageByte

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)

Overrides:

crop3D in class ImageByte

crop3D

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

Overrides:

crop3D in class ImageByte

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_)

Overrides:

crop3DMask in class ImageByte

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

Overrides:

resize in class ImageByte

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

Overrides:

resample in class ImageByte

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)

Description copied from class: ImageByte

Rescale the image to new dimension, only in Z

Overrides:

resample in class ImageByte

Parameters:

newZ - the new size in Z

method - the method, see ImageProcessor

Returns:

the rescaled image

normalize_

protected ImageFloat normalize_(ImageInt mask,
                                double saturation)

Overrides:

normalize_ in class ImageByte

equals

public boolean equals(java.lang.Object o)

Overrides:

equals in class java.lang.Object

hashCode

public int hashCode()

Overrides:

hashCode in class java.lang.Object