ij.gui.HistogramPlot Maven / Gradle / Ivy
Go to download
Show more of this group Show more artifacts with this name
Show all versions of ij Show documentation
Show all versions of ij Show documentation
ImageJ is an open source Java image processing program inspired by NIH Image for the Macintosh.
package ij.gui;
import ij.*;
import ij.process.*;
import ij.plugin.filter.Analyzer;
import ij.measure.*;
import ij.macro.Interpreter;
import java.awt.*;
import java.awt.image.*;
public class HistogramPlot extends ImagePlus {
static final double SCALE = Prefs.getGuiScale();
static final int HIST_WIDTH = (int)(SCALE*256);
static final int HIST_HEIGHT = (int)(SCALE*128);
static final int XMARGIN = (int)(20*SCALE);
static final int YMARGIN = (int)(10*SCALE);
static final int WIN_WIDTH = HIST_WIDTH + (int)(44*SCALE);
static final int WIN_HEIGHT = HIST_HEIGHT + (int)(118*SCALE);
static final int BAR_HEIGHT = (int)(SCALE*12);
static final int INTENSITY1=0, INTENSITY2=1, RGB=2, RED=3, GREEN=4, BLUE=5;
static final Color frameColor = new Color(30,60,120);
int rgbMode = -1;
ImageStatistics stats;
boolean stackHistogram;
Calibration cal;
long[] histogram;
LookUpTable lut;
int decimalPlaces;
int digits;
long newMaxCount;
boolean logScale;
int yMax;
int srcImageID;
Rectangle frame;
Font font = new Font("SansSerif",Font.PLAIN,(int)(12*SCALE));
boolean showBins;
int col1, col2, row1, row2, row3, row4, row5;
public HistogramPlot() {
setImage(NewImage.createRGBImage("Histogram", WIN_WIDTH, WIN_HEIGHT, 1, NewImage.FILL_WHITE));
}
/** Plots a histogram using the specified title and number of bins.
Currently, the number of bins must be 256 expect for 32 bit images. */
public void draw(String title, ImagePlus imp, int bins) {
draw(imp, bins, 0.0, 0.0, 0);
}
/** Plots a histogram using the specified title, number of bins and histogram range.
Currently, the number of bins must be 256 and the histogram range range must be
the same as the image range expect for 32 bit images. */
public void draw(ImagePlus imp, int bins, double histMin, double histMax, int yMax) {
boolean limitToThreshold = (Analyzer.getMeasurements()&LIMIT)!=0;
ImageProcessor ip = imp.getProcessor();
if (ip.isThreshold() && ip.getLutUpdateMode()==ImageProcessor.NO_LUT_UPDATE)
limitToThreshold = false; // ignore invisible thresholds
if (imp.isRGB() && rgbMode maxCount2) && (i != stats.mode)) {
maxCount2 = histogram[i];
mode2 = i;
}
}
newMaxCount = histogram[stats.mode];
if ((newMaxCount>(maxCount2 * 2)) && (maxCount2 != 0))
newMaxCount = (int)(maxCount2 * 1.5);
if (logScale)
drawLogPlot(yMax>0?yMax:newMaxCount, ip);
drawPlot(yMax>0?yMax:newMaxCount, ip);
histogram[stats.mode] = saveModalCount;
x = XMARGIN + 1;
y = YMARGIN + HIST_HEIGHT + 2;
if (imp==null)
lut.drawUnscaledColorBar(ip, x-1, y, HIST_WIDTH, BAR_HEIGHT);
else
drawAlignedColorBar(imp, xMin, xMax, ip, x-1, y, HIST_WIDTH, BAR_HEIGHT);
y += BAR_HEIGHT+(int)(15*SCALE);
drawText(ip, x, y, fixedRange);
srcImageID = imp.getID();
}
void drawAlignedColorBar(ImagePlus imp, double xMin, double xMax, ImageProcessor ip, int x, int y, int width, int height) {
ImageProcessor ipSource = imp.getProcessor();
float[] pixels = null;
ImageProcessor ipRamp = null;
if (rgbMode>=INTENSITY1) {
ipRamp = new FloatProcessor(width, height);
if (rgbMode==RED)
ipRamp.setColorModel(LUT.createLutFromColor(Color.red));
else if (rgbMode==GREEN)
ipRamp.setColorModel(LUT.createLutFromColor(Color.green));
else if (rgbMode==BLUE)
ipRamp.setColorModel(LUT.createLutFromColor(Color.blue));
pixels = (float[])ipRamp.getPixels();
} else
pixels = new float[width*height];
for (int j=0; jipSource.getPixelCount()) { // stack histogram
cm = LUT.createLutFromColor(Color.white);
min = stats.min;
max = stats.max;
} else
cm = ((CompositeImage)imp).getChannelLut();
} else if (!ipSource.isThreshold())
cm = ipSource.getColorModel();
else
cm = ipSource.getCurrentColorModel();
ipRamp = new FloatProcessor(width, height, pixels, cm);
}
ipRamp.setMinAndMax(min,max);
ImageProcessor bar = null;
if (ip instanceof ColorProcessor)
bar = ipRamp.convertToRGB();
else
bar = ipRamp.convertToByte(true);
ip.insert(bar, x,y);
ip.setColor(Color.black);
ip.drawRect(x-1, y, width+2, height);
}
/** Scales a threshold level to the range 0-255. */
int scaleDown(ImageProcessor ip, double threshold) {
double min = ip.getMin();
double max = ip.getMax();
if (max>min)
return (int)(((threshold-min)/(max-min))*255.0);
else
return 0;
}
void drawPlot(long maxCount, ImageProcessor ip) {
if (maxCount==0) maxCount = 1;
frame = new Rectangle(XMARGIN, YMARGIN, HIST_WIDTH, HIST_HEIGHT);
if (histogram.length==256) {
double scale2 = HIST_WIDTH/256.0;
int barWidth = 1;
if (SCALE>1) barWidth=2;
if (SCALE>2) barWidth=3;
for (int i = 0; i < 256; i++) {
int x =(int)(i*scale2);
int y = (int)(((double)HIST_HEIGHT*(double)histogram[i])/maxCount);
if (y>HIST_HEIGHT) y = HIST_HEIGHT;
for (int j = 0; jHIST_HEIGHT) y = HIST_HEIGHT;
ip.drawLine(i+XMARGIN, YMARGIN+HIST_HEIGHT, i+XMARGIN, YMARGIN+HIST_HEIGHT-y);
}
} else {
double xscale = (double)HIST_WIDTH/histogram.length;
for (int i=0; i0L) {
int y = (int)(((double)HIST_HEIGHT*(double)value)/maxCount);
if (y>HIST_HEIGHT) y = HIST_HEIGHT;
int x = (int)(i*xscale)+XMARGIN;
ip.drawLine(x, YMARGIN+HIST_HEIGHT, x, YMARGIN+HIST_HEIGHT-y);
}
}
}
ip.setColor(frameColor);
ip.drawRect(frame.x-1, frame.y, frame.width+2, frame.height+1);
ip.setColor(Color.black);
}
void drawLogPlot (long maxCount, ImageProcessor ip) {
frame = new Rectangle(XMARGIN, YMARGIN, HIST_WIDTH, HIST_HEIGHT);
ip.drawRect(frame.x-1, frame.y, frame.width+2, frame.height+1);
double max = Math.log(maxCount);
ip.setColor(Color.gray);
if (histogram.length==256) {
double scale2 = HIST_WIDTH/256.0;
int barWidth = 1;
if (SCALE>1) barWidth=2;
if (SCALE>2) barWidth=3;
for (int i=0; i < 256; i++) {
int x =(int)(i*scale2);
int y = histogram[i]==0?0:(int)(HIST_HEIGHT*Math.log(histogram[i])/max);
if (y>HIST_HEIGHT) y = HIST_HEIGHT;
for (int j = 0; jHIST_HEIGHT) y = HIST_HEIGHT;
ip.drawLine(i+XMARGIN, YMARGIN+HIST_HEIGHT, i+XMARGIN, YMARGIN+HIST_HEIGHT-y);
}
} else {
double xscale = (double)HIST_WIDTH/histogram.length;
for (int i=0; i0L) {
int y = (int)(HIST_HEIGHT*Math.log(value)/max);
if (y>HIST_HEIGHT) y = HIST_HEIGHT;
int x = (int)(i*xscale)+XMARGIN;
ip.drawLine(x, YMARGIN+HIST_HEIGHT, x, YMARGIN+HIST_HEIGHT-y);
}
}
}
ip.setColor(Color.black);
}
void drawText(ImageProcessor ip, int x, int y, boolean fixedRange) {
ip.setFont(font);
ip.setAntialiasedText(true);
double hmin = cal.getCValue(stats.histMin);
double hmax = cal.getCValue(stats.histMax);
ip.drawString(d2s(hmin), x - 4, y);
ip.drawString(d2s(hmax), x + HIST_WIDTH - getWidth(hmax, ip) + 10, y);
if (rgbMode>=INTENSITY1) {
x += HIST_WIDTH/2;
y += 1;
ip.setJustification(ImageProcessor.CENTER_JUSTIFY);
boolean weighted = ((ColorProcessor)ip).weightedHistogram();
switch (rgbMode) {
case INTENSITY1: ip.drawString((weighted?"Intensity (weighted)":"Intensity (unweighted)"), x, y); break;
case INTENSITY2: ip.drawString((weighted?"Intensity (unweighted)":"Intensity (weighted)"), x, y); break;
case RGB: ip.drawString("R+G+B", x, y); break;
case RED: ip.drawString("Red", x, y); break;
case GREEN: ip.drawString("Green", x, y); break;
case BLUE: ip.drawString("Blue", x, y); break;
}
ip.setJustification(ImageProcessor.LEFT_JUSTIFY);
}
double binWidth = (hmax-hmin+1)/stats.nBins;
binWidth = Math.abs(binWidth);
showBins = binWidth!=1.0 || !fixedRange;
col1 = XMARGIN + 5;
col2 = XMARGIN + HIST_WIDTH/2;
row1 = y+(int)(25*SCALE);
if (showBins) row1 -= (int)(8*SCALE);
row2 = row1 + (int)(15*SCALE);
row3 = row2 + (int)(15*SCALE);
row4 = row3 + (int)(15*SCALE);
row5 = row4 + (int)(15*SCALE);
long count = stats.longPixelCount>0?stats.longPixelCount:stats.pixelCount;
String modeCount = " (" + stats.maxCount + ")";
if (histogram!=null) {// Add '*' if multi-modal histogram
int mcount = 0;;
for (int i=0; i1) break;
}
if (mcount>1) modeCount=modeCount+"*";
}
if (modeCount.length()>12) modeCount = "";
ip.drawString("N: " + count, col1, row1);
ip.drawString("Min: " + d2s(stats.min), col2, row1);
ip.drawString("Mean: " + d2s(stats.mean), col1, row2);
ip.drawString("Max: " + d2s(stats.max), col2, row2);
ip.drawString("StdDev: " + d2s(stats.stdDev), col1, row3);
ip.drawString("Mode: " + d2s(stats.dmode) + modeCount, col2, row3);
if (showBins) {
ip.drawString("Bins: " + d2s(stats.nBins), col1, row4);
ip.drawString("Bin Width: " + d2s(binWidth), col2, row4);
}
}
private String d2s(double d) {
if ((int)d==d)
return IJ.d2s(d, 0);
else
return IJ.d2s(d, 3, 8);
}
int getWidth(double d, ImageProcessor ip) {
return ip.getStringWidth(d2s(d));
}
public int[] getHistogram() {
int[] hist = new int[histogram.length];
for (int i=0; i © 2015 - 2025 Weber Informatics LLC | Privacy Policy