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Histogram2D.java
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Histogram2D.java
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/*-
* #%L
* Fiji's plugin for colocalization analysis.
* %%
* Copyright (C) 2009 - 2017 Fiji developers.
* %%
* This program 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
* <http://www.gnu.org/licenses/gpl-3.0.html>.
* #L%
*/
package sc.fiji.coloc.algorithms;
import ij.measure.ResultsTable;
import java.util.EnumSet;
import net.imglib2.RandomAccess;
import net.imglib2.RandomAccessibleInterval;
import net.imglib2.TwinCursor;
import net.imglib2.img.ImgFactory;
import net.imglib2.img.array.ArrayImgFactory;
import net.imglib2.type.logic.BitType;
import net.imglib2.type.numeric.RealType;
import net.imglib2.type.numeric.integer.LongType;
import net.imglib2.view.Views;
import sc.fiji.coloc.gadgets.DataContainer;
import sc.fiji.coloc.results.ResultHandler;
/**
* Represents the creation of a 2D histogram between two images.
* Channel 1 is set out in x direction, while channel 2 in y direction.
* @param <T> The source images value type
*/
public class Histogram2D<T extends RealType< T >> extends Algorithm<T> {
// An enumeration of possible drawings
public enum DrawingFlags { Plot, RegressionLine, Axes }
// the drawing configuration
EnumSet<DrawingFlags> drawingSettings;
// The width of the scatter-plot
protected int xBins = 256;
// The height of the scatter-plot
protected int yBins = 256;
// The name of the result 2D histogram to pass elsewhere
protected String title = "";
// Swap or not swap ch1 and ch2
protected boolean swapChannels = false;
// member variables for labeling
protected String ch1Label = "Channel 1";
protected String ch2Label = "Channel 2";
// Result keeping members
// the generated plot image
private RandomAccessibleInterval<LongType> plotImage;
// the bin widths for each channel
private double xBinWidth = 0.0, yBinWidth = 0.0;
// labels for the axes
private String xLabel = "", yLabel = "";
// ranges for the axes
private double xMin = 0.0, xMax = 0.0, yMin = 0.0, yMax = 0.0;
public Histogram2D(){
this("2D Histogram");
}
public Histogram2D(String title){
this(title, false);
}
public Histogram2D(String title, boolean swapChannels){
this(title, swapChannels, EnumSet.of( DrawingFlags.Plot, DrawingFlags.RegressionLine ));
}
public Histogram2D(String title, boolean swapChannels, EnumSet<DrawingFlags> drawingSettings){
super(title);
this.title = title;
this.swapChannels = swapChannels;
if (swapChannels) {
int xBins = this.xBins;
this.xBins = this.yBins;
this.yBins = xBins;
}
this.drawingSettings = drawingSettings;
}
/**
* Gets the minimum of channel one. Takes channel
* swapping into consideration and will return min
* of channel two if swapped.
*
* @return The minimum of what is seen as channel one.
*/
protected double getMinCh1(DataContainer<T> container) {
return swapChannels ? container.getMinCh2() : container.getMinCh1();
}
/**
* Gets the minimum of channel two. Takes channel
* swapping into consideration and will return min
* of channel one if swapped.
*
* @return The minimum of what is seen as channel two.
*/
protected double getMinCh2(DataContainer<T> container) {
return swapChannels ? container.getMinCh1() : container.getMinCh2();
}
/**
* Gets the maximum of channel one. Takes channel
* swapping into consideration and will return max
* of channel two if swapped.
*
* @return The maximum of what is seen as channel one.
*/
protected double getMaxCh1(DataContainer<T> container) {
return swapChannels ? container.getMaxCh2() : container.getMaxCh1();
}
/**
* Gets the maximum of channel two. Takes channel
* swapping into consideration and will return max
* of channel one if swapped.
*
* @return The maximum of what is seen as channel two.
*/
protected double getMaxCh2(DataContainer<T> container) {
return swapChannels ? container.getMaxCh1() : container.getMaxCh2();
}
/**
* Gets the image of channel one. Takes channel
* swapping into consideration and will return image
* of channel two if swapped.
*
* @return The image of what is seen as channel one.
*/
protected RandomAccessibleInterval<T> getImageCh1(DataContainer<T> container) {
return swapChannels ? container.getSourceImage2() : container.getSourceImage1();
}
/**
* Gets the image of channel two. Takes channel
* swapping into consideration and will return image
* of channel one if swapped.
*
* @return The image of what is seen as channel two.
*/
protected RandomAccessibleInterval<T> getImageCh2(DataContainer<T> container) {
return swapChannels ? container.getSourceImage1() : container.getSourceImage2();
}
/**
* Gets the label of channel one. Takes channel
* swapping into consideration and will return label
* of channel two if swapped.
*
* @return The label of what is seen as channel one.
*/
protected String getLabelCh1() {
return swapChannels ? ch2Label : ch1Label;
}
/**
* Gets the label of channel two. Takes channel
* swapping into consideration and will return label
* of channel one if swapped.
*
* @return The label of what is seen as channel two.
*/
protected String getLabelCh2() {
return swapChannels ? ch1Label : ch2Label;
}
@Override
public void execute(DataContainer<T> container) throws MissingPreconditionException {
generateHistogramData(container);
}
protected void generateHistogramData(DataContainer<T> container) {
double ch1BinWidth = getXBinWidth(container);
double ch2BinWidth = getYBinWidth(container);
// get the 2 images for the calculation of Pearson's
final RandomAccessibleInterval<T> img1 = getImageCh1(container);
final RandomAccessibleInterval<T> img2 = getImageCh2(container);
final RandomAccessibleInterval<BitType> mask = container.getMask();
// get the cursors for iterating through pixels in images
TwinCursor<T> cursor = new TwinCursor<T>(img1.randomAccess(),
img2.randomAccess(), Views.iterable(mask).localizingCursor());
// create new image to put the scatter-plot in
final ImgFactory<LongType> scatterFactory = new ArrayImgFactory< LongType >();
plotImage = scatterFactory.create(new int[] {xBins, yBins}, new LongType() );
// create access cursors
final RandomAccess<LongType> histogram2DCursor =
plotImage.randomAccess();
long ignoredPixelCount = 0;
// iterate over images
long[] pos = new long[ plotImage.numDimensions() ];
while (cursor.hasNext()) {
cursor.fwd();
double ch1 = cursor.getFirst().getRealDouble();
double ch2 = cursor.getSecond().getRealDouble();
/* Scale values for both channels to fit in the range.
* Moreover mirror the y value on the x axis.
*/
pos[0] = getXValue(ch1, ch1BinWidth, ch2, ch2BinWidth);
pos[1] = getYValue(ch1, ch1BinWidth, ch2, ch2BinWidth);
if (pos[0] >= 0 && pos[1] >=0 && pos[0] < xBins && pos[1] < yBins) {
// set position of input/output cursor
histogram2DCursor.setPosition( pos );
// get current value at position and increment it
long count = histogram2DCursor.get().getIntegerLong();
count++;
histogram2DCursor.get().set(count);
} else {
ignoredPixelCount ++;
}
}
if (ignoredPixelCount > 0) {
addWarning("Ignored pixels while generating histogram.",
"" + ignoredPixelCount + " pixels were ignored while generating the 2D histogram \"" + title +
"\" because the grey values were out of range." +
"This may happen, if an image contains negative pixel values.");
}
xBinWidth = ch1BinWidth;
yBinWidth = ch2BinWidth;
xLabel = getLabelCh1();
yLabel = getLabelCh2();
xMin = getXMin(container);
xMax = getXMax(container);
yMin = getYMin(container);
yMax = getYMax(container);
}
/**
* A table of x-values, y-values and the counts is generated and
* returned as a string. The single fields in one row (X Y Count)
* are separated by tabs.
*
* @return A String representation of the histogram data.
*/
public String getData() {
StringBuffer sb = new StringBuffer();
double xBinWidth = 1.0 / getXBinWidth();
double yBinWidth = 1.0 / getYBinWidth();
double xMin = getXMin();
double yMin = getYMin();
// check if we have bins of size one or other ones
boolean xBinWidthIsOne = Math.abs(xBinWidth - 1.0) < 0.00001;
boolean yBinWidthIsOne = Math.abs(yBinWidth - 1.0) < 0.00001;
// configure decimal places accordingly
int xDecimalPlaces = xBinWidthIsOne ? 0 : 3;
int yDecimalPlaces = yBinWidthIsOne ? 0 : 3;
// create a cursor to access the histogram data
RandomAccess<LongType> cursor = plotImage.randomAccess();
// loop over 2D histogram
for (int i=0; i < plotImage.dimension(0); ++i) {
for (int j=0; j < plotImage.dimension(1); ++j) {
cursor.setPosition(i, 0);
cursor.setPosition(j, 1);
sb.append(
ResultsTable.d2s(xMin + (i * xBinWidth), xDecimalPlaces) + "\t" +
ResultsTable.d2s(yMin + (j * yBinWidth), yDecimalPlaces) + "\t" +
ResultsTable.d2s(cursor.get().getRealDouble(), 0) + "\n");
}
}
return sb.toString();
}
@Override
public void processResults(ResultHandler<T> handler) {
super.processResults(handler);
handler.handleHistogram( this, title );
}
/**
* Calculates the bin width of one bin in x/ch1 direction.
* @param container The container with images to work on
* @return The width of one bin in x direction
*/
protected double getXBinWidth(DataContainer<T> container) {
double ch1Max = getMaxCh1(container);
if (ch1Max < yBins) {
// bin widths must not exceed 1
return 1;
}
// we need (ch1Max * width + 0.5) < yBins, but just so, i.e.
// ch1Max * width + 0.5 == yBins - eps
// width = (yBins - 0.5 - eps) / ch1Max
return (yBins - 0.50001) / ch1Max;
}
/**
* Calculates the bin width of one bin in y/ch2 direction.
* @param container The container with images to work on
* @return The width of one bin in y direction
*/
protected double getYBinWidth(DataContainer<T> container) {
double ch2Max = getMaxCh2(container);
if (ch2Max < yBins) {
// bin widths must not exceed 1
return 1;
}
return (yBins - 0.50001) / ch2Max;
}
/**
* Calculates the locations x value.
* @param ch1Val The intensity of channel one
* @param ch1BinWidth The bin width for channel one
* @return The x value of the data point location
*/
protected int getXValue(double ch1Val, double ch1BinWidth, double ch2Val, double ch2BinWidth) {
return (int)(ch1Val * ch1BinWidth + 0.5);
}
/**
* Calculates the locations y value.
* @param ch2Val The intensity of channel one
* @param ch2BinWidth The bin width for channel one
* @return The x value of the data point location
*/
protected int getYValue(double ch1Val, double ch1BinWidth, double ch2Val, double ch2BinWidth) {
return (yBins - 1) - (int)(ch2Val * ch2BinWidth + 0.5);
}
protected double getXMin(DataContainer<T> container) {
return 0;
}
protected double getXMax(DataContainer<T> container) {
return swapChannels ? getMaxCh2(container) : getMaxCh1(container);
}
protected double getYMin(DataContainer<T> container) {
return 0;
}
protected double getYMax(DataContainer<T> container) {
return swapChannels ? getMaxCh1(container) : getMaxCh2(container);
}
// Result access methods
public RandomAccessibleInterval<LongType> getPlotImage() {
return plotImage;
}
public double getXBinWidth() {
return xBinWidth;
}
public double getYBinWidth() {
return yBinWidth;
}
public String getXLabel() {
return xLabel;
}
public String getYLabel() {
return yLabel;
}
public double getXMin() {
return xMin;
}
public double getXMax() {
return xMax;
}
public double getYMin() {
return yMin;
}
public double getYMax() {
return yMax;
}
public String getTitle() {
return title;
}
public EnumSet<DrawingFlags> getDrawingSettings() {
return drawingSettings;
}
}

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