/** Set display range for each channel to min-max. */
private static void displayMinToMax(ImagePlus imp) {
if (imp.isComposite()) {
for (int c = 1; c <= imp.getNChannels(); c++) {
double min = I1l.getStatsForChannel(imp, c).min;
double max = I1l.getStatsForChannel(imp, c).max;
imp.setC(c);
IJ.setMinAndMax(imp, min, max);
}
imp.setC(1);
} else {
double min = imp.getStatistics().min;
double max = imp.getStatistics().max;
IJ.setMinAndMax(imp, min, max);
}
}
/**
* Execute plugin functionality: stack FFT with window function, max projection over all slices
* (phase, Z angle), blank out central 1/8 circle (set to min value), display min-max.
*/
public ResultSet exec(ImagePlus... imps) {
ImagePlus imp = imps[0];
Util_StackFFT2D stackFFT2D = new Util_StackFFT2D();
stackFFT2D.resultTypeChoice = Util_StackFFT2D.resultType[1];
ImagePlus impF = stackFFT2D.exec(imp);
IJ.run(impF, "Z Project...", "projection=[Max Intensity]");
ImagePlus impProjF = ij.WindowManager.getCurrentImage();
maskCentralRegion(impProjF);
if (impProjF.isComposite()) {
// display grayscale, not colored composite
CompositeImage ci = (CompositeImage) impProjF;
ci.setMode(IJ.GRAYSCALE);
impProjF.updateAndDraw();
}
displayMinToMax(impProjF);
impProjF.setTitle(I1l.makeTitle(imps[0], TLA));
String shortInfo =
"Maximum intensity projection of log"
+ " (amplitude^2) 2D FFT stack, central region masked,"
+ " rescaled (min-max) to improve contrast of the relevant"
+ " frequency range.";
results.addImp(shortInfo, impProjF);
results.addInfo(
"How to interpret",
"look for clean 1st & 2nd"
+ " order spots, similar across angles. Note that spot"
+ " intensity depends on image content.");
return results;
}
/** Mask central offset / low freq spike to better use display range. */
private void maskCentralRegion(ImagePlus imp) {
int w = imp.getWidth();
double d = this.maskDiameter * w;
if (w % 2 == 0) {
d += 1; // tweak to centre the mask about zero freq stripes
}
// N.B. we assume the image is square! (FFT result)
OvalRoi mask = new OvalRoi(w / 2 - d / 2 + 1, w / 2 - d / 2 + 1, d, d);
imp.setRoi(mask);
for (int c = 1; c <= imp.getNChannels(); c++) {
imp.setC(c);
double min = I1l.getStatsForChannel(imp, c).min;
IJ.run(imp, "Set...", "value=" + min + " slice");
}
imp.setC(1);
imp.deleteRoi();
}
@Override
public void run(String arg) {
ImagePlus imp = IJ.getImage();
GenericDialog gd = new GenericDialog(name);
gd.addMessage("Requires SI raw data in OMX (CPZAT) order.");
gd.addNumericField("angles", angles, 0);
gd.addNumericField("phases", phases, 0);
gd.showDialog();
if (gd.wasCanceled()) return;
if (gd.wasOKed()) {
angles = (int) gd.getNextNumber();
phases = (int) gd.getNextNumber();
}
if (!I1l.stackDivisibleBy(imp, phases * angles)) {
IJ.showMessage(name, "Error: stack size not consistent with phases/angles.");
return;
}
results = exec(imp);
results.report();
}
