public class ImageShort extends ImageInt
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Modifier and Type | Field and Description |
---|---|
short[][] |
pixels |
Constructor and Description |
---|
ImageShort(ImageHandler im,
boolean scaling)
Constructor from another generic ImageHandler
will convert to write format if necessary
|
ImageShort(ImagePlus img)
Constructor from ImagePlus
|
ImageShort(ImageStack img)
Constructor from ImageStack
|
ImageShort(short[][] pixels,
java.lang.String title,
int sizeX)
Generic constructor with array of pixels
|
ImageShort(java.lang.String title,
int sizeX,
int sizeY,
int sizeZ)
Generic consructor to generate a black image
|
Modifier and Type | Method and Description |
---|---|
void |
appendMasks(java.lang.Iterable<ImageInt> images,
int startLabel)
??
|
static short[] |
convert(byte[] input)
convert from byte array to short array
|
static short[] |
convert(float[] input,
boolean scaling)
convert from float array to short array
|
ImageByte |
convertToByte(boolean scaling)
Convert to byte image
|
ImageByte |
convertToByte(double saturation)
Convert to byte image using saturation of the values
|
ImageFloat |
convertToFloat(boolean scaling)
Convert to float 32 bit image
|
void |
copy(ImageShort destination)
Copy the pixels values into the parameter image
|
int |
countMaskVolume() |
ImageShort |
crop3D(java.lang.String title,
int x_min_,
int x_max_,
int y_min_,
int y_max_,
int z_min_,
int z_max_)
see ImageCropper
|
ImageShort[] |
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_) |
ImageShort |
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) |
ImageShort |
duplicate() |
void |
erase() |
void |
fill(double value,
int min,
int max) |
protected void |
flushPixels() |
java.lang.Object |
getArray1D()
get the 1D array as java Object
|
java.lang.Object |
getArray1D(int z)
get the 1D array as java Object for one slice
|
static short[] |
getArray1DShort(ImagePlus img)
(Should be somewhere else --> ImageJUtils ?)
Get the 1D array of a 3D image stored in ImagePlus
|
protected int[] |
getHisto(ImageInt mask) |
protected int[] |
getHisto(ImageInt mask,
int nBins,
double min,
double max) |
static ImagePlus |
getImagePlus(short[] pixels,
int sizeX,
int sizeY,
int sizeZ,
boolean setMinAndMax)
(Should be somewhere else --> ImageJUtils ?)
Get the ImagePlus from a 1D array of pixels
|
protected void |
getMinAndMax(ImageInt mask) |
float |
getPixel(int coord)
Deprecated.
|
float |
getPixel(int xy,
int z) |
float |
getPixel(int x,
int y,
int z) |
float |
getPixel(Point3D v) |
float |
getPixel(Point3DInt P) |
int |
getPixelInt(int coord)
Deprecated.
|
int |
getPixelInt(int xy,
int z) |
int |
getPixelInt(int x,
int y,
int z) |
int |
getPixelInt(Point3D v) |
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) |
ImageShort |
resample(int newZ,
int method)
Rescale the image to new dimension, only in Z
|
ImageShort |
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 |
setPixel(Point3DInt point,
float value) |
void |
setPixel(Voxel3D v,
short value)
Set the pixel value at a given Voxel3D position (position will be rounded)
|
void |
setPixelCross3D(int x,
int y,
int z,
int 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) |
ImageByte |
thresholdRangeExclusive(float min,
float max) |
ImageByte |
thresholdRangeInclusive(float min,
float max) |
ImageByte |
toMask() |
void |
trimSlices(int zmin,
int zmax) |
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, 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, 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, getNeighborhood3x3x3NoCenterListInt, 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, insertMask, invert, invertBackground, isBinary, isBinary, isVisible, maskContains, merge3D, merge3DBinary, merge3DRaw, multiplyByValue, multiplyImage, newBlankImageHandler, normaliseValue, normalize, openImage, powImage, radialDistribution, radialDistribution, radialDistribution, replacePixelsValueFloat, 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
public ImageShort(ImagePlus img)
img
- ImagePluspublic ImageShort(ImageStack img)
img
- ImageStackpublic ImageShort(short[][] pixels, java.lang.String title, int sizeX)
pixels
- 2D array of pixels, a slice being a 1D arraytitle
- the title *sizeX
- the size in X of the array, sizeY and sizeZ will be extracted from the array lengthpublic ImageShort(java.lang.String title, int sizeX, int sizeY, int sizeZ)
title
- title of the imagesizeX
- size in XsizeY
- size in YsizeZ
- size in Zpublic ImageShort(ImageHandler im, boolean scaling)
im
- the generic imagescaling
- do scaling if converting from other format (8 bits or 32 bit)public static short[] getArray1DShort(ImagePlus img)
img
- the imagePluspublic static ImagePlus getImagePlus(short[] pixels, int sizeX, int sizeY, int sizeZ, boolean setMinAndMax)
pixels
- the 1D array of shortsizeX
- the size XsizeY
- the size YsizeZ
- the size ZsetMinAndMax
- adjust the min and max valuespublic static short[] convert(float[] input, boolean scaling)
input
- the array of float valuesscaling
- scaling the valuespublic static short[] convert(byte[] input)
input
- the array of byte valuespublic java.lang.Object getArray1D()
getArray1D
in class ImageHandler
public java.lang.Object getArray1D(int z)
getArray1D
in class ImageHandler
z
- slice (starts at 0)public ImageByte convertToByte(boolean scaling)
scaling
- do scaling of valuespublic ImageByte convertToByte(double saturation)
saturation
- saturation value (0.0 - 1.0)public ImageFloat convertToFloat(boolean scaling)
scaling
- scalig the valuespublic void erase()
erase
in class ImageHandler
public void fill(double value, int min, int max)
fill
in class ImageHandler
public ImageShort duplicate()
public void copy(ImageShort destination)
destination
- the image where the values will be copied to@Deprecated public float getPixel(int coord)
getPixel
in class ImageHandler
public float getPixel(Point3DInt P)
getPixel
in class ImageHandler
public int getPixelInt(Point3D v)
getPixelInt
in class ImageInt
public float getPixel(int x, int y, int z)
getPixel
in class ImageHandler
public float getPixel(int xy, int z)
getPixel
in class ImageHandler
public int getPixelInt(int x, int y, int z)
getPixelInt
in class ImageInt
public int getPixelInt(int xy, int z)
getPixelInt
in class ImageInt
@Deprecated public int getPixelInt(int coord)
getPixelInt
in class ImageInt
@Deprecated public void setPixel(int coord, float value)
setPixel
in class ImageHandler
public void setPixel(Point3D point, float value)
setPixel
in class ImageHandler
public void setPixel(Point3DInt point, float value)
setPixel
in class ImageHandler
public void setPixel(int x, int y, int z, float value)
setPixel
in class ImageHandler
public void setPixel(int xy, int z, float value)
setPixel
in class ImageHandler
public void setPixel(int x, int y, int z, int value)
public void setPixelCross3D(int x, int y, int z, int value)
setPixelCross3D
in class ImageInt
public void setPixel(Voxel3D v, short value)
v
- the voxel positionvalue
- the valueprotected void getMinAndMax(ImageInt mask)
getMinAndMax
in class ImageHandler
protected int[] getHisto(ImageInt mask)
getHisto
in class ImageHandler
protected int[] getHisto(ImageInt mask, int nBins, double min, double max)
getHisto
in class ImageHandler
public ImageByte thresholdRangeInclusive(float min, float max)
thresholdRangeInclusive
in class ImageHandler
public ImageByte thresholdRangeExclusive(float min, float max)
thresholdRangeExclusive
in class ImageHandler
public ImageByte threshold(float thld, boolean keepUnderThld, boolean strict)
threshold
in class ImageHandler
public void thresholdCut(float thld, boolean keepUnderThld, boolean strict)
thresholdCut
in class ImageHandler
public ImageShort crop3D(java.lang.String title, int x_min_, int x_max_, int y_min_, int y_max_, int z_min_, int z_max_)
ImageHandler
public ImageShort[] crop3D(java.util.TreeMap<java.lang.Float,int[]> bounds)
public ImageShort 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 ImageInt
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 ImageInt
public void appendMasks(java.lang.Iterable<ImageInt> images, int startLabel)
images
- startLabel
- public boolean shiftIndexes(java.util.TreeMap<java.lang.Integer,int[]> bounds)
shiftIndexes
in class ImageInt
public ImageHandler resize(int dX, int dY, int dZ)
ImageHandler
resize
in class ImageHandler
dX
- the border to add in X, both on left and rightdY
- the border to add in Y, both on top and bottomdZ
- the border to add in Z, both above and belowpublic ImageShort resample(int newX, int newY, int newZ, int method)
ImageHandler
public ImageShort resample(int newZ, int method)
protected ImageFloat normalize_(ImageInt mask, double saturation)
normalize_
in class ImageHandler
public ImageFloat normalize(double min, double max)
normalize
in class ImageHandler
public void invert(ImageInt mask)
invert
in class ImageHandler
public void draw(Object3D o, float value)
draw
in class ImageHandler
protected void flushPixels()
flushPixels
in class ImageHandler
public boolean isOpened()
isOpened
in class ImageHandler
public float getPixelInterpolated(Point3D P)
getPixelInterpolated
in class ImageInt
public int getPixelIntInterpolated(Point3D P)
getPixelIntInterpolated
in class ImageInt
public ImageHandler deleteSlices(int zmin, int zmax)
deleteSlices
in class ImageHandler
public void trimSlices(int zmin, int zmax)
trimSlices
in class ImageHandler
@Deprecated public void intersectMask(ImageInt mask)
intersectMask
in class ImageHandler
public void intersectMask(ImageHandler mask)
intersectMask
in class ImageHandler
public double getSizeInMb()
getSizeInMb
in class ImageHandler
public int getType()
getType
in class ImageHandler
public int countMaskVolume()
countMaskVolume
in class ImageInt
public void intersectMask2D(ImageInt mask, int z)
intersectMask2D
in class ImageHandler