/**
* Builds dialog to query users for projection parameters.
*
* @param start starting slice to display
* @param stop last slice
*/
protected GenericDialog buildControlDialog(int start, int stop) {
GenericDialog gd = new GenericDialog("ZProjection", IJ.getInstance());
gd.addNumericField("Start slice:", startSlice, 0 /*digits*/);
gd.addNumericField("Stop slice:", stopSlice, 0 /*digits*/);
gd.addChoice("Projection type", METHODS, METHODS[method]);
if (isHyperstack && imp.getNFrames() > 1 && imp.getNSlices() > 1)
gd.addCheckbox("All time frames", allTimeFrames);
return gd;
}
public void doHyperStackProjection(boolean allTimeFrames) {
int start = startSlice;
int stop = stopSlice;
int firstFrame = 1;
int lastFrame = imp.getNFrames();
if (!allTimeFrames) firstFrame = lastFrame = imp.getFrame();
ImageStack stack = new ImageStack(imp.getWidth(), imp.getHeight());
int channels = imp.getNChannels();
int slices = imp.getNSlices();
if (slices == 1) {
slices = imp.getNFrames();
firstFrame = lastFrame = 1;
}
int frames = lastFrame - firstFrame + 1;
increment = channels;
boolean rgb = imp.getBitDepth() == 24;
for (int frame = firstFrame; frame <= lastFrame; frame++) {
for (int channel = 1; channel <= channels; channel++) {
startSlice = (frame - 1) * channels * slices + (start - 1) * channels + channel;
stopSlice = (frame - 1) * channels * slices + (stop - 1) * channels + channel;
if (rgb) doHSRGBProjection(imp);
else doProjection();
stack.addSlice(null, projImage.getProcessor());
}
}
projImage = new ImagePlus(makeTitle(), stack);
projImage.setDimensions(channels, 1, frames);
if (channels > 1) {
projImage = new CompositeImage(projImage, 0);
((CompositeImage) projImage).copyLuts(imp);
if (method == SUM_METHOD || method == SD_METHOD)
((CompositeImage) projImage).resetDisplayRanges();
}
if (frames > 1) projImage.setOpenAsHyperStack(true);
Overlay overlay = imp.getOverlay();
if (overlay != null) {
startSlice = start;
stopSlice = stop;
if (imp.getType() == ImagePlus.COLOR_RGB)
projImage.setOverlay(projectRGBHyperStackRois(overlay));
else projImage.setOverlay(projectHyperStackRois(overlay));
}
IJ.showProgress(1, 1);
}
public int setup(String arg, ImagePlus imp) {
// IJ.register(Average_Oversampled.class);
if (IJ.versionLessThan("1.32c")) return DONE;
if (this.pre) { // before finding means
imp.unlock();
this.imp = imp;
this.nslices = imp.getNSlices();
this.width = imp.getWidth();
this.height = imp.getHeight();
this.slicecols = new float[nslices][width];
this.pre = false;
return (DOES_ALL + DOES_STACKS + FINAL_PROCESSING);
} else { // find SD after finding means of columns
float sum; // sum of pixel values column
float avg; // average pixel value of a column
double devsum; // sum of deviations
double devavg; // standard deviation
double[] columns = new double[width]; // x-axis of plot
double[] sdevs = new double[width]; // y-axis of plot
for (int i = 0; i < width; i += 1) {
sum = 0; // reset with each column
avg = 0; // reset with each column
devsum = 0; // reset with each column
devavg = 0; // reset with each column
columns[i] = i; // building x-axis
for (int s = 0; s < nslices; s += 1) { // sum of column means
sum = sum + slicecols[s][i];
}
avg = sum / nslices; // mean of one column across all slices
for (int s = 0; s < nslices; s += 1) { // standard deviation
devsum = devsum + Math.pow((slicecols[s][i] - avg), 2); // square diff
}
devavg = Math.sqrt(devsum / nslices);
sdevs[i] = devavg; // building y-axis
}
Plot plot = new Plot("Average SD by Column", "Columns", "Standard Deviation", columns, sdevs);
plot.show();
// calculate CTN
double ctn;
double sdevssum = 0;
for (double sd : sdevs) {
sdevssum = sdevssum + sd;
}
ctn = sdevssum / width;
// display CTN on results table
ResultsTable rt = ResultsTable.getResultsTable();
// rt.incrementCounter();
rt.addValue("Column Temporal Noise", ctn);
rt.show("Results");
this.pre = false;
return DONE;
}
}
public void run(String arg) {
imp = IJ.getImage();
int stackSize = imp.getStackSize();
if (imp == null) {
IJ.noImage();
return;
}
// Make sure input image is a stack.
if (stackSize == 1) {
IJ.error("Z Project", "Stack required");
return;
}
// Check for inverting LUT.
if (imp.getProcessor().isInvertedLut()) {
if (!IJ.showMessageWithCancel("ZProjection", lutMessage)) return;
}
// Set default bounds.
int channels = imp.getNChannels();
int frames = imp.getNFrames();
int slices = imp.getNSlices();
isHyperstack =
imp.isHyperStack()
|| (ij.macro.Interpreter.isBatchMode()
&& ((frames > 1 && frames < stackSize) || (slices > 1 && slices < stackSize)));
boolean simpleComposite = channels == stackSize;
if (simpleComposite) isHyperstack = false;
startSlice = 1;
if (isHyperstack) {
int nSlices = imp.getNSlices();
if (nSlices > 1) stopSlice = nSlices;
else stopSlice = imp.getNFrames();
} else stopSlice = stackSize;
// Build control dialog
GenericDialog gd = buildControlDialog(startSlice, stopSlice);
gd.showDialog();
if (gd.wasCanceled()) return;
if (!imp.lock()) return; // exit if in use
long tstart = System.currentTimeMillis();
setStartSlice((int) gd.getNextNumber());
setStopSlice((int) gd.getNextNumber());
method = gd.getNextChoiceIndex();
Prefs.set(METHOD_KEY, method);
if (isHyperstack) {
allTimeFrames = imp.getNFrames() > 1 && imp.getNSlices() > 1 ? gd.getNextBoolean() : false;
doHyperStackProjection(allTimeFrames);
} else if (imp.getType() == ImagePlus.COLOR_RGB) doRGBProjection(true);
else doProjection(true);
if (arg.equals("") && projImage != null) {
long tstop = System.currentTimeMillis();
projImage.setCalibration(imp.getCalibration());
if (simpleComposite) IJ.run(projImage, "Grays", "");
projImage.show("ZProjector: " + IJ.d2s((tstop - tstart) / 1000.0, 2) + " seconds");
}
imp.unlock();
IJ.register(ZProjector.class);
return;
}