/* Wraps everything into a Cell Manager Class*/
private CellManager toCellManager(ImagePlus imp, ArrayList<PolygonRoi> rois, ImagePlus av_imp) {
CellManager cm = new CellManager(av_imp, imp, this.ovr);
Iterator itr = rois.iterator();
ArrayList<Double> av_sig = new ArrayList<>();
PolygonRoi roi;
while (itr.hasNext()) {
roi = (PolygonRoi) itr.next();
av_sig = Activity_Analysis.getAverageSignal(imp, roi);
CalciumSignal ca_sig = new CalciumSignal(av_sig, this.dt_r);
ovr.add(roi);
ca_sig.DeltaF();
cm.addCell(ca_sig, roi);
}
// catch(Exception e){
// IJ.showMessage(e.getMessage());
// }
// }
ovr.setLabelColor(Color.WHITE);
// ovr.setFillColor(Color.GREEN);
ovr.setStrokeColor(Color.getHSBColor(100, 30, 87));
av_imp.setOverlay(ovr);
av_imp.show();
IJ.run("In [+]", "");
IJ.run("In [+]", "");
return cm;
}
/* Replaces all sample index in imp with neighbor sample*/
public static ImagePlus ReplaceSlices(ImagePlus imp, ArrayList<Integer> samples) {
ImageStack ims = imp.getStack();
Iterator itr = samples.iterator();
while (itr.hasNext()) {
Integer k = (Integer) itr.next();
if (k == 0) {
continue;
}
ImageProcessor ip_slice = ims.getProcessor(k);
// double value_1 = getMeanOfSlice(ims.getProcessor(k-1));
// double value_2 = getMeanOfSlice(ims.getProcessor(k));
// double value_3 = getMeanOfSlice(ims.getProcessor(k+1));
// double value_4 = getMeanOfSlice(ims.getProcessor(k+2));
// System.out.print("Replacing "+ value_ori+"with " +value_re );
ims.addSlice("", ip_slice, k);
ims.deleteSlice(k + 2);
}
imp.setStack(ims);
return imp;
}