public class BlankMask extends ImageByte
Constructor and Description |
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BlankMask(ImageHandler template) |
BlankMask(java.lang.String title,
int sizeX,
int sizeY,
int sizeZ) |
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) |
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
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
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
public BlankMask(java.lang.String title, int sizeX, int sizeY, int sizeZ)
public BlankMask(ImageHandler template)
public double getScaleXY()
getScaleXY
in class ImageHandler
public double getScaleZ()
getScaleZ
in class ImageHandler
public ImagePlus getImagePlus()
getImagePlus
in class ImageHandler
public int getPixelInt(int xy, int z)
getPixelInt
in class ImageByte
public int getPixelInt(int x, int y, int z)
getPixelInt
in class ImageByte
public int getPixelInt(int coord)
getPixelInt
in class ImageByte
public java.util.TreeMap<java.lang.Float,int[]> getBounds(boolean addBorder)
getBounds
in class ImageHandler
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)
crop3DBinary
in class ImageByte
public boolean shiftIndexes(java.util.TreeMap<java.lang.Integer,int[]> bounds)
shiftIndexes
in class ImageByte
public float getPixel(IntCoord3D vox)
public void setPixel(int x, int y, int z, float value)
public java.lang.Object getArray1D()
getArray1D
in class ImageByte
protected void getMinAndMax(ImageInt mask)
getMinAndMax
in class ImageByte
public void setMinAndMax(ImageInt mask)
setMinAndMax
in class ImageHandler
protected int[] getHisto(ImageInt mask, int nBins, double min, double max)
public ImageByte threshold(float thld, boolean keepUnderThld, boolean strict)
public void thresholdCut(float thld, boolean keepUnderThld, boolean strict)
thresholdCut
in class ImageByte
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)
public ImageByte[] crop3D(java.util.TreeMap<java.lang.Float,int[]> bounds)
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_)
crop3DMask
in class ImageByte
public ImageHandler resize(int dX, int dY, int dZ)
ImageHandler
public ImageByte resample(int newX, int newY, int newZ, int method)
ImageHandler
public ImageByte resample(int newZ, int method)
ImageByte
protected ImageFloat normalize_(ImageInt mask, double saturation)
normalize_
in class ImageByte
public boolean equals(java.lang.Object o)
equals
in class java.lang.Object
public int hashCode()
hashCode
in class java.lang.Object