package ij.plugin;
import ij.plugin.*;
import ij.*;
import ij.process.*;
import ij.gui.*;
import ij.measure.*;
import ij.plugin.filter.Analyzer;
import ij.util.Tools;
import java.awt.*;
public class ZAxisProfiler implements PlugIn, Measurements, PlotMaker {
private static String[] choices = {"time", "z-axis"};
private static String choice = choices[0];
private boolean showingDialog;
private ImagePlus imp;
private boolean isPlotMaker;
private boolean timeProfile;
private boolean firstTime = true;
private String options;
public static Plot getPlot(ImagePlus imp) {
return getPlot(imp, "time");
}
public static Plot getPlot(ImagePlus imp, String options) {
ZAxisProfiler zap = new ZAxisProfiler();
zap.imp = imp;
zap.options = options;
zap.isPlotMaker = true;
Plot plot = zap.getPlot();
return plot;
}
public void run(String arg) {
imp = IJ.getImage();
if (imp.getStackSize()<2) {
IJ.error("ZAxisProfiler", "This command requires a stack.");
return;
}
isPlotMaker = true;
Plot plot = getPlot();
if (plot!=null) {
if (isPlotMaker)
plot.setPlotMaker(this);
plot.show();
}
}
public Plot getPlot() {
Roi roi = imp.getRoi();
ImageProcessor ip = imp.getProcessor();
double minThreshold = ip.getMinThreshold();
double maxThreshold = ip.getMaxThreshold();
float[] y;
boolean hyperstack = imp.isHyperStack();
if (hyperstack)
y = getHyperstackProfile(roi, minThreshold, maxThreshold);
else
y = getZAxisProfile(roi, minThreshold, maxThreshold);
if (y==null)
return null;
float[] x = new float[y.length];
String xAxisLabel = showingDialog&&choice.equals(choices[0])?"Frame":"Slice";
Calibration cal = imp.getCalibration();
if (cal.scaled()) {
double c = 1.0f;
double origin = 0;
if (timeProfile) {
c = (float) cal.frameInterval;
boolean zeroInterval = c==0;
if (zeroInterval)
c = 1;
String timeUnit = zeroInterval?"Frame":"["+cal.getTimeUnit()+"]";
xAxisLabel = timeUnit;
} else {
c = (float) cal.pixelDepth;
boolean zeroDepth = c==0;
if (zeroDepth)
c = 1;
origin = cal.zOrigin;
String depthUnit = zeroDepth?"Slice":"["+cal.getZUnit()+"]";
xAxisLabel = depthUnit;
}
for (int i=0; i<x.length; i++)
x[i] = (float)((i-cal.zOrigin)*c);
} else {
for (int i=0; i<x.length; i++)
x[i] = i+1;
}
String title;
if (roi!=null) {
Rectangle r = roi.getBounds();
title = imp.getTitle()+"-"+r.x+"-"+r.y;
} else
title = imp.getTitle()+"-0-0";
Plot plot = new Plot(title, xAxisLabel, "Mean", x, y);
if (x.length<=60) {
plot.setColor(Color.red);
plot.addPoints(x, y, Plot.CIRCLE);
plot.setColor(Color.black);
}
double ymin = ProfilePlot.getFixedMin();
double ymax= ProfilePlot.getFixedMax();
if (!(ymin==0.0 && ymax==0.0)) {
double[] a = Tools.getMinMax(x);
double xmin=a[0]; double xmax=a[1];
plot.setLimits(xmin, xmax, ymin, ymax);
}
if (!firstTime) {
int pos = imp.getCurrentSlice();
int size = imp.getStackSize();
if (hyperstack) {
if (timeProfile) {
pos = imp.getT();
size = imp.getNFrames();
} else {
pos = imp.getZ();
size = imp.getNSlices();
}
}
double xx = (pos-1.0)/(size-1.0);
if (xx==0.0)
plot.setLineWidth(2);
plot.setColor(Color.blue);
plot.drawNormalizedLine(xx, 0, xx, 1.0);
plot.setColor(Color.black);
plot.setLineWidth(1);
}
firstTime = false;
return plot;
}
public ImagePlus getSourceImage() {
return imp;
}
private float[] getHyperstackProfile(Roi roi, double minThreshold, double maxThreshold) {
int slices = imp.getNSlices();
int frames = imp.getNFrames();
int c = imp.getC();
int z = imp.getZ();
int t = imp.getT();
int size = slices;
if (firstTime)
timeProfile = slices==1 && frames>1;
if (options==null && slices>1 && frames>1 && (!isPlotMaker ||firstTime)) {
showingDialog = true;
GenericDialog gd = new GenericDialog("Profiler");
gd.addChoice("Profile", choices, choice);
gd.showDialog();
if (gd.wasCanceled())
return null;
choice = gd.getNextChoice();
timeProfile = choice.equals(choices[0]);
}
if (options!=null)
timeProfile = frames>1 && !options.contains("z");
if (timeProfile)
size = frames;
else
size = slices;
float[] values = new float[size];
Calibration cal = imp.getCalibration();
ResultsTable rt = new ResultsTable();
Analyzer analyzer = new Analyzer(imp, rt);
int measurements = Analyzer.getMeasurements();
boolean showResults = !isPlotMaker && measurements!=0 && measurements!=LIMIT;
measurements |= MEAN;
if (showResults) {
if (!Analyzer.resetCounter())
return null;
}
ImageStack stack = imp.getStack();
boolean showProgress = size>400 || stack.isVirtual();
for (int i=1; i<=size; i++) {
if (showProgress)
IJ.showProgress(i,size);
int index = 1;
if (timeProfile)
index = imp.getStackIndex(c, z, i);
else
index = imp.getStackIndex(c, i, t);
ImageProcessor ip = stack.getProcessor(index);
if (minThreshold!=ImageProcessor.NO_THRESHOLD)
ip.setThreshold(minThreshold,maxThreshold,ImageProcessor.NO_LUT_UPDATE);
ip.setRoi(roi);
ImageStatistics stats = ImageStatistics.getStatistics(ip, measurements, cal);
analyzer.saveResults(stats, roi);
values[i-1] = (float)stats.mean;
}
if (showResults)
rt.show("Results");
return values;
}
private float[] getZAxisProfile(Roi roi, double minThreshold, double maxThreshold) {
ImageStack stack = imp.getStack();
if (firstTime) {
int slices = imp.getNSlices();
int frames = imp.getNFrames();
timeProfile = slices==1 && frames>1;
}
int size = stack.size();
boolean showProgress = size>400 || stack.isVirtual();
float[] values = new float[size];
Calibration cal = imp.getCalibration();
ResultsTable rt = new ResultsTable();
Analyzer analyzer = new Analyzer(imp, rt);
int measurements = Analyzer.getMeasurements();
boolean showResults = !isPlotMaker && measurements!=0 && measurements!=LIMIT;
boolean showingLabels = firstTime && showResults && ((measurements&LABELS)!=0 || (measurements&SLICE)!=0);
measurements |= MEAN;
if (showResults) {
if (!Analyzer.resetCounter())
return null;
}
boolean isLine = roi!=null && roi.isLine();
int current = imp.getCurrentSlice();
for (int i=1; i<=size; i++) {
if (showProgress)
IJ.showProgress(i,size);
if (showingLabels)
imp.setSlice(i);
ImageProcessor ip = stack.getProcessor(i);
if (minThreshold!=ImageProcessor.NO_THRESHOLD)
ip.setThreshold(minThreshold,maxThreshold,ImageProcessor.NO_LUT_UPDATE);
ip.setRoi(roi);
ImageStatistics stats = null;
if (isLine)
stats = getLineStatistics(roi, ip, measurements, cal);
else
stats = ImageStatistics.getStatistics(ip, measurements, cal);
analyzer.saveResults(stats, roi);
values[i-1] = (float)stats.mean;
}
if (showResults)
rt.show("Results");
if (showingLabels)
imp.setSlice(current);
return values;
}
private ImageStatistics getLineStatistics(Roi roi, ImageProcessor ip, int measurements, Calibration cal) {
ImagePlus imp = new ImagePlus("", ip);
imp.setRoi(roi);
ProfilePlot profile = new ProfilePlot(imp);
double[] values = profile.getProfile();
ImageProcessor ip2 = new FloatProcessor(values.length, 1, values);
return ImageStatistics.getStatistics(ip2, measurements, cal);
}
}