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();
}
public boolean beadCalibration3d() {
imp = IJ.getImage();
if (imp == null) {
IJ.noImage();
return false;
} else if (imp.getStackSize() == 1) {
IJ.error("Stack required");
return false;
} else if (imp.getType() != ImagePlus.GRAY8 && imp.getType() != ImagePlus.GRAY16) {
// In order to support 32bit images, pict[] must be changed to float[], and getPixel(x, y);
// requires a Float.intBitsToFloat() conversion
IJ.error("8 or 16 bit greyscale image required");
return false;
}
width = imp.getWidth();
height = imp.getHeight();
nslices = imp.getStackSize();
imtitle = imp.getTitle();
models[0] = "*None*";
models[1] = "line";
models[2] = "2nd degree polynomial";
models[3] = "3rd degree polynomial";
models[4] = "4th degree polynomial";
GenericDialog gd = new GenericDialog("3D PALM calibration");
gd.addNumericField("Maximum FWHM (in px)", prefs.get("QuickPALM.3Dcal_fwhm", 20), 0);
gd.addNumericField(
"Particle local threshold (% maximum intensity)", prefs.get("QuickPALM.pthrsh", 20), 0);
gd.addNumericField("Z-spacing (nm)", prefs.get("QuickPALM.z-step", 10), 2);
gd.addNumericField("Calibration Z-smoothing (radius)", prefs.get("QuickPALM.window", 1), 0);
gd.addChoice("Model", models, prefs.get("QuickPALM.model", models[3]));
gd.addCheckbox(
"Show divergence of bead positions against model",
prefs.get("QuickPALM.3Dcal_showDivergence", false));
gd.addCheckbox("Show extra particle info", prefs.get("QuickPALM.3Dcal_showExtraInfo", false));
gd.addMessage("\n\nDon't forget to save the table in the end...");
gd.showDialog();
if (gd.wasCanceled()) return false;
fwhm = gd.getNextNumber();
prefs.set("QuickPALM.QuickPALM.3Dcal_fwhm", fwhm);
pthrsh = gd.getNextNumber() / 100;
prefs.set("QuickPALM.pthrsh", pthrsh * 100);
cal_z = gd.getNextNumber();
prefs.set("QuickPALM.z-step", cal_z);
window = (int) gd.getNextNumber();
prefs.set("QuickPALM.window", window);
model = gd.getNextChoice();
prefs.set("QuickPALM.model", model);
part_divergence = gd.getNextBoolean();
prefs.set("QuickPALM.3Dcal_showDivergence", part_divergence);
part_extrainfo = gd.getNextBoolean();
prefs.set("QuickPALM.3Dcal_showExtraInfo", part_extrainfo);
return true;
}
public void run(String arg) {
ImagePlus imp = WindowManager.getCurrentImage();
if (imp == null) {
IJ.noImage();
return;
}
if (imp.getStackSize() > 1) {
IJ.error("This command requires a montage");
return;
}
GenericDialog gd = new GenericDialog("Stack Maker");
gd.addNumericField("Images_per_row: ", w, 0);
gd.addNumericField("Images_per_column: ", h, 0);
gd.addNumericField("Border width: ", b, 0);
gd.showDialog();
if (gd.wasCanceled()) return;
w = (int) gd.getNextNumber();
h = (int) gd.getNextNumber();
b = (int) gd.getNextNumber();
ImageStack stack = makeStack(imp.getProcessor(), w, h, b);
new ImagePlus("Stack", stack).show();
}
public boolean showDialog() {
String bgChoice = "NoBg";
int[] wList = WindowManager.getIDList();
if (wList == null) {
IJ.noImage();
return false;
}
String[] sampleTitles = new String[wList.length];
for (int i = 0; i < wList.length; i++) {
ImagePlus imp = WindowManager.getImage(wList[i]);
sampleTitles[i] = imp != null ? imp.getTitle() : "";
}
String[] bgTitles = new String[wList.length + 1];
bgTitles[0] = "NoBg";
for (int i = 1; i < wList.length + 1; i++) {
bgTitles[i] = sampleTitles[i - 1];
}
for (int i = 1; i < (wList.length + 1); i++) {
if (bgTitles[i] == bgStackTitle) bgChoice = bgStackTitle;
}
String sampleChoice = sampleTitles[0];
for (int i = 1; i < (wList.length); i++) {
if (sampleTitles[i] == sampleStackTitle) sampleChoice = sampleStackTitle;
}
String[] mirrors = new String[2];
mirrors[0] = "No";
mirrors[1] = "Yes";
GenericDialog gd = new GenericDialog("PolScope 5Frame Calc");
gd.addChoice("Sample:", sampleTitles, sampleChoice);
gd.addChoice("Background:", bgTitles, bgChoice);
gd.addChoice("Mirror:", mirrors, mirror);
gd.addNumericField("Wavelength: ", wavelength, 1, 8, " nm");
gd.addNumericField("Swing: ", swing, 3, 8, " wavelength");
gd.addNumericField("Ret. Ceiling: ", retCeiling, 1, 8, " nm");
gd.addNumericField("Orient. Ref.: ", azimRef, 1, 8, " degree");
gd.showDialog();
if (gd.wasCanceled()) return false;
int index1 = gd.getNextChoiceIndex();
int index2 = gd.getNextChoiceIndex();
int index3 = gd.getNextChoiceIndex();
wavelength = (float) gd.getNextNumber();
swing = (float) gd.getNextNumber();
retCeiling = (float) gd.getNextNumber();
azimRef = (float) gd.getNextNumber();
imp1 = WindowManager.getImage(wList[index1]);
sampleStackTitle = sampleTitles[index1];
bgStackTitle = bgTitles[index2];
if (bgStackTitle == "NoBg") {
imp2 =
WindowManager.getImage(
wList[
index1]); // only to assign a valid ImagePlus to imp2 which is not used when NoBg
} else {
imp2 = WindowManager.getImage(wList[index2 - 1]);
}
mirror = mirrors[index3];
return true;
}