mcib3d.image3d

Class ImageFloat

java.lang.Object

mcib3d.image3d.ImageHandler

mcib3d.image3d.ImageFloat

public class ImageFloat
extends ImageHandler

* /** 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
float[][]	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
ImageFloat(float[][] pixels, java.lang.String title, int sizeX)
ImageFloat(ImagePlus img)
ImageFloat(ImageStack img)
ImageFloat(java.lang.String title, int sizeX, int sizeY, int sizeZ)

Method Summary

Modifier and Type	Method and Description
ImageFloat	adaptiveFilter(float radx, float rady, float radz, int nbcpus) Deprecated.
void	adaptiveFilter(ImageFloat filtered, float radx, float rady, float radz, int zmin, int zmax, Chrono timer, AbstractLog show)
static float[]	convert(byte[] input)
static float[]	convert(short[] input)
ImageByte	convertToByte(boolean scaling)
ImageShort	convertToShort(boolean scaling)
void	copy(ImageFloat destination)
ImageFloat	crop3D(java.lang.String title, int x_min_, int x_max_, int y_min_, int y_max_, int z_min_, int z_max_)
ImageFloat[]	crop3D(java.util.TreeMap<java.lang.Float,int[]> bounds)
ImageFloat	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	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
ImageHandler	deleteSlices(int zmin, int zmax)
void	draw(Object3D o, float value)
ImageFloat	duplicate()
void	erase()
void	fill(double value, int min, int max)
void	filterGeneric(ImageFloat out, float radx, float rady, float radz, int zmin, int zmax, int filter) 3D filter using threads
void	filterGeneric(ImageFloat out, float radx, float rady, float radz, int zmin, int zmax, int filter, Chrono timer, AbstractLog log) 3D filter using threads
void	filterGeneric(ImageFloat out, Object3DVoxels obj, int zmin, int zmax, int filter)
void	filterGeneric(ImageFloat out, Object3DVoxels obj, int zmin, int zmax, int filter, Chrono timer, AbstractLog log)
protected void	flushPixels()
java.lang.Object	getArray1D()
java.lang.Object	getArray1D(int z)
static float[]	getArray1DFloat(ImagePlus img)
protected int[]	getHisto(ImageInt mask)
protected int[]	getHisto(ImageInt mask, int nBins, double min, double max)
static ImagePlus	getImagePlus(float[] pixels, int sizeX, int sizeY, int sizeZ, boolean setMinAndMax)
static ImagePlus	getImagePlus(int[] pixels, int sizeX, int sizeY, int sizeZ, boolean setMinAndMax)
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)
protected void	getMinAndMax(ImageInt mask)
float	getPixel(Coordinate3D coord)
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	getPixelInterpolated(Point3D P)
double	getSizeInMb()
int	getType()
void	intersectMask(ImageFloat mask) Deprecated.
void	intersectMask(ImageHandler mask)
void	intersectMask(ImageInt mask) Deprecated.
void	intersectMask2D(ImageInt mask, int z)
void	invert(ImageInt mask)
boolean	isOpened()
void	mathGeneric(ImageFloat other, ImageFloat out, int zmin, int zmax, int operation, float par1, float par2, Chrono timer, AbstractLog log) Generic arithmetic between images pixel1*parameter1 OPERATION pixel2*parameter2
static ImageFloat	newBlankImageFloat(java.lang.String title, ImageHandler ih)
protected ImageFloat	normalize_(ImageInt mask, double saturation)
ImageFloat	normalize(double min, double max)
void	operationGeneric(ImageFloat out, int zmin, int zmax, int operation, float par1, float par2, Chrono timer, AbstractLog log)
void	opposite()
ImageHandler	resample(int newZ, int method) Rescale the image to new dimension, only in Z
ImageHandler	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 x, int y, int z, float value)
void	setPixel(Point3D point, float value)
ImageFloat	sobelFilter() Sobel-like filtering in 3D
void	subtract(ImageFloat other)
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)
void	trimSlices(int zmin, int zmax)

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, replacePixelsValue, replacePixelsValue, 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, wrap, wrap, zoom

Methods inherited from class java.lang.Object

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

Field Detail

pixels

public float[][] pixels

Constructor Detail

ImageFloat

public ImageFloat(ImagePlus img)

ImageFloat

public ImageFloat(ImageStack img)

ImageFloat

public ImageFloat(float[][] pixels,
                  java.lang.String title,
                  int sizeX)

ImageFloat

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

Method Detail

newBlankImageFloat

public static ImageFloat newBlankImageFloat(java.lang.String title,
                                            ImageHandler ih)

getArray1DFloat

public static float[] getArray1DFloat(ImagePlus img)

getImagePlus

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

getImagePlus

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

convert

public static float[] convert(short[] input)

convert

public static float[] convert(byte[] input)

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)

convertToByte

public ImageByte convertToByte(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 ImageFloat duplicate()

Overrides:

duplicate in class ImageHandler

copy

public void copy(ImageFloat destination)

getPixel

@Deprecated
public float getPixel(int coord)

Deprecated.

Specified by:

getPixel in class ImageHandler

getPixel

public float getPixel(IntCoord3D vox)

getPixel

public float getPixel(Coordinate3D coord)

getPixel

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

Specified by:

getPixel in class ImageHandler

getPixel

public float getPixel(int xy,
                      int z)

Specified by:

getPixel in class ImageHandler

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

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

draw

public void draw(Object3D o,
                 float value)

Specified by:

draw 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 ImageFloat 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 ImageHandler

crop3D

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

Specified by:

crop3D in class ImageHandler

crop3DMask

public ImageFloat 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 ImageHandler

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 ImageHandler 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 ImageHandler

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 ImageHandler resample(int newZ,
                             int method)

Description copied from class: ImageHandler

Rescale the image to new dimension, only in Z

Specified by:

resample in class ImageHandler

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

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

intersectMask

@Deprecated
public void intersectMask(ImageFloat mask)

Deprecated.

invert

public void invert(ImageInt mask)

Specified by:

invert in class ImageHandler

opposite

public void opposite()

subtract

public void subtract(ImageFloat other)

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 ImageHandler

getPixel

public float getPixel(Point3DInt P)

Specified by:

getPixel in class ImageHandler

getPixelInterpolated

public float getPixelInterpolated(Point3D P)

Specified by:

getPixelInterpolated in class ImageHandler

cropRadius

public ImageHandler cropRadius(int xc,
                               int yc,
                               int zc,
                               int rx,
                               int ry,
                               int rz,
                               boolean mean,
                               boolean sphere)

Description copied from class: ImageHandler

Extract a 3D image from a specified location as the center of crop

Specified by:

cropRadius in class ImageHandler

Parameters:

xc - the x coordinate of the center of the extraction

yc - the y coordinate of the center of the extraction

zc - the z coordinate of the center of the extraction

rx - radius X of new image

ry - radius Y of new image

rz - radius Z of new image

sphere - extract inside a sphere

Returns:

the cropped image

filterGeneric

public void filterGeneric(ImageFloat out,
                          float radx,
                          float rady,
                          float radz,
                          int zmin,
                          int zmax,
                          int filter)

3D filter using threads

Parameters:

out -

radx - Radius of mean filter in x

rady - Radius of mean filter in y

radz - Radius of mean filter in z

zmin -

zmax -

filter -

filterGeneric

public void filterGeneric(ImageFloat out,
                          float radx,
                          float rady,
                          float radz,
                          int zmin,
                          int zmax,
                          int filter,
                          Chrono timer,
                          AbstractLog log)

3D filter using threads

Parameters:

out -

radx - Radius of mean filter in x

rady - Radius of mean filter in y

radz - Radius of mean filter in z

zmin -

zmax -

filter -

filterGeneric

public void filterGeneric(ImageFloat out,
                          Object3DVoxels obj,
                          int zmin,
                          int zmax,
                          int filter)

filterGeneric

public void filterGeneric(ImageFloat out,
                          Object3DVoxels obj,
                          int zmin,
                          int zmax,
                          int filter,
                          Chrono timer,
                          AbstractLog log)

mathGeneric

public void mathGeneric(ImageFloat other,
                        ImageFloat out,
                        int zmin,
                        int zmax,
                        int operation,
                        float par1,
                        float par2,
                        Chrono timer,
                        AbstractLog log)

Generic arithmetic between images pixel1*parameter1 OPERATION pixel2*parameter2

Parameters:

other - other image

out - result image

zmin - minimum Z

zmax - maximum Z

operation - filter ADD MULT ...

par1 - parameter1

par2 - parameter2

timer - timer for time

log - logger for print

operationGeneric

public void operationGeneric(ImageFloat out,
                             int zmin,
                             int zmax,
                             int operation,
                             float par1,
                             float par2,
                             Chrono timer,
                             AbstractLog log)

sobelFilter

public ImageFloat sobelFilter()

Sobel-like filtering in 3D

Returns:

The 3D filtered image

adaptiveFilter

public void adaptiveFilter(ImageFloat filtered,
                           float radx,
                           float rady,
                           float radz,
                           int zmin,
                           int zmax,
                           Chrono timer,
                           AbstractLog show)

adaptiveFilter

@Deprecated
public ImageFloat adaptiveFilter(float radx,
                                             float rady,
                                             float radz,
                                             int nbcpus)

Deprecated.

Adaptive Filter in 3D (expermimental) Take 7 neighborhood, compute mean and std dev Assign mean of neighborhood with lowest std dev

Parameters:

radx -

radz -

rady -

Returns:

3D filtered image

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

getSizeInMb

public double getSizeInMb()

Specified by:

getSizeInMb in class ImageHandler

getType

public int getType()

Specified by:

getType in class ImageHandler

getListMaxima

public java.util.ArrayList<Voxel3DComparable> getListMaxima(float radx,
                                                            float rady,
                                                            float radz,
                                                            int zmin,
                                                            int zmax)

getListMaxima

public java.util.ArrayList<Voxel3DComparable> getListMaxima(float radx,
                                                            float rady,
                                                            float radz,
                                                            int zmin,
                                                            int zmax,
                                                            Chrono timer,
                                                            AbstractLog log)