public void run(String arg) {
ImagePlus imp = WindowManager.getCurrentImage();
if (imp == null) {
IJ.noImage();
return;
}
ImageStack stack1 = imp.getStack();
String fileName = imp.getTitle();
int endslice = stack1.getSize();
ImagePlus imp2 = duplicateStack(imp);
imp2.show();
String duplicateName = imp2.getTitle();
// IJ.showMessage("Box",fileName);
ImageStack stack2 = imp2.getStack();
stack1.deleteSlice(1);
stack2.deleteSlice(endslice);
String calculatorstring =
("image1='"
+ fileName
+ "' operation=Subtract image2="
+ imp2.getTitle()
+ " create stack");
IJ.run("Image Calculator...", calculatorstring);
ImagePlus imp3 = WindowManager.getCurrentImage();
imp3.setTitle(fileName + " DeltaF up");
imp2.getWindow().close();
imp.getWindow().close();
}
/**
* 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;
}