public boolean checkBeads() {
rmanager = RoiManager.getInstance();
if (IJ.versionLessThan("1.26i")) return false;
else if (rmanager == null) {
IJ.error("Add bead ROIs to the RoiManager first (select region then press [t]).");
return false;
}
nrois = rmanager.getCount();
if (nrois == 0) {
IJ.error("Add bead ROIs to the RoiManager first (select region then press [t]).");
return false;
}
rois = rmanager.getRoisAsArray();
return true;
}
public void run(String arg) {
String[] labels = {
"Masked_Chromosomes", "Unmixed_Image", "Spectral_Image(optional)", "Spectra(optional)"
};
ImagePlus[] imps = jutils.selectImages(true, 4, labels);
if (imps == null) {
return;
}
if (imps[0] == null) {
return;
}
float[] mask = (float[]) imps[0].getStack().getPixels(2);
findblobs3 fb = new findblobs3(imps[0].getWidth(), imps[0].getHeight());
float[] objects = fb.dofindblobs(mask, 0.5f);
WaitForUserDialog dg =
new WaitForUserDialog(
"Optional Input", "Place RoiManager Points on Chromosome Segments (if desired)");
dg.show();
if (!dg.escPressed()) {
RoiManager rman = RoiManager.getInstance();
while (rman != null && rman.getCount() > 1) {
Roi[] rois = rman.getRoisAsArray();
int[] ids = new int[rois.length];
for (int i = 0; i < rois.length; i++) {
Rectangle r = rois[i].getBounds();
ids[i] = (int) objects[r.x + fb.width * r.y];
}
objects = fb.link_objects(objects, ids);
rman.reset();
dg =
new WaitForUserDialog(
"Optional Input",
"Place More RoiManager Points on Chromosome Segments (if desired)");
dg.show();
if (dg.escPressed()) break;
}
}
int[] areas = fb.get_areas(objects);
int[] temprank = jsort.get_javasort_order(areas);
int[] arearank = jsort.get_javasort_order(temprank);
for (int i = 0; i < fb.nobjects; i++) {
arearank[i] = fb.nobjects - arearank[i] - 1;
}
// if the spectra are available, get them
float[][][] spectra = null;
Object[] data = null;
if (imps[1] != null && imps[2] != null && imps[3] != null) {
ImageWindow iw = imps[3].getWindow();
if (iw.getClass().getName().equals("jguis.PlotWindow4")) {
float[][] yvals = (float[][]) jutils.runPW4VoidMethod(iw, "getYValues");
data = jutils.stack2array(imps[2].getStack());
Object[] coef = jutils.stack2array(imps[1].getStack());
spectra = new float[fb.nobjects][2][];
for (int i = 0; i < fb.nobjects; i++) {
spectra[i][0] = fb.get_object_spectrum(objects, (i + 1), data, "Sum");
spectra[i][1] = new float[yvals[0].length];
float[] tempcoef = fb.get_object_spectrum(objects, (i + 1), coef, "Sum");
for (int j = 0; j < yvals[0].length; j++) {
for (int k = 0; k < 5; k++) {
spectra[i][1][j] += tempcoef[k] * yvals[k][j];
}
}
}
}
}
CompositeImage imp = (CompositeImage) imps[0];
imp.setPosition(1, 1, 1);
LUT graylut = jutils.get_lut_for_color(Color.white);
imp.setChannelColorModel(graylut);
imp.setPosition(2, 1, 1);
LUT redlut = jutils.get_lut_for_color(Color.red);
imp.setChannelColorModel(redlut);
imp.setPosition(1, 1, 1);
imp.updateAndRepaintWindow();
SkyPanel_v3 sp = new SkyPanel_v3();
int skychan = 6;
if (imps[1] != null) skychan = imps[1].getNChannels();
// assume that the sky image has 6 channels and that the second is the unknown green
// shift the unknown green to the end
ImagePlus skyimp = null;
if (imps[1] != null) {
Object[] skystack = jutils.stack2array(imps[1].getStack());
// Object[]
// skystack2={skystack[0],skystack[2],skystack[3],skystack[4],skystack[5],skystack[1]};
Object[] skystack2 = null;
if (skychan == 6)
skystack2 = new Object[] {skystack[0], skystack[2], skystack[3], skystack[4], skystack[5]};
else
skystack2 = new Object[] {skystack[0], skystack[1], skystack[2], skystack[3], skystack[4]};
skyimp =
new ImagePlus(
"rearranged", jutils.array2stack(skystack2, imps[1].getWidth(), imps[1].getHeight()));
}
int nch = 5;
if (skyimp != null) nch = skyimp.getStack().getSize();
GenericDialog gd2 = new GenericDialog("Options");
gd2.addNumericField("Area Accuracy (percent)", 30, 0);
for (int i = 0; i < nch; i++) {
gd2.addNumericField("Ch_" + (i + 1) + "_Contr_Thresh", 0.35, 5, 15, null);
}
// gd2.addNumericField("Contribution Threshold",0.35,5,15,null);
gd2.addCheckbox("Mouse?", false);
gd2.addNumericField("Box_Width", 150, 0);
gd2.addNumericField("Box_Height", 100, 0);
gd2.showDialog();
if (gd2.wasCanceled()) {
return;
}
sp.areathresh = (float) gd2.getNextNumber();
sp.objthresh2 = new float[nch];
for (int i = 0; i < nch; i++) sp.objthresh2[i] = (float) gd2.getNextNumber();
// sp.objthresh=(float)gd2.getNextNumber();
boolean mouse = gd2.getNextBoolean();
int bwidth = (int) gd2.getNextNumber();
int bheight = (int) gd2.getNextNumber();
int[] colorindices = {4, 1, 2, 6, 3};
GenericDialog gd3 = new GenericDialog("Color Options");
for (int i = 0; i < 5; i++)
gd3.addChoice(
"Ch" + (i + 1) + " Color",
SkyPanel_v3.colornames,
SkyPanel_v3.colornames[colorindices[i]]);
gd3.showDialog();
if (gd3.wasCanceled()) return;
for (int i = 0; i < 5; i++) colorindices[i] = gd3.getNextChoiceIndex();
sp.colorindices = colorindices;
sp.nch = 5;
sp.dapilast = false;
sp.cellwidth = bwidth;
sp.cellheight = bheight;
sp.init(imps[0], skyimp, objects, areas, arearank, fb, true, spectra, data, mouse);
SkyPanel_v3.launch_frame(sp);
}
