/* 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;
}
/* Methods */
public void run(String argv) {
if (this.setup()) { // validates conditions
IJ.showStatus(" Dark noise removal...");
imp_r = DarkNoiseRemoval(imp_r, NOISE_ROI);
if (removeFirst) {
ImageStack t_stack = imp_r.getStack(); // deletes first slice
t_stack.deleteSlice(1);
imp_r.setStack(t_stack);
} else {
// if first slice wasn't removed we must move the first index of the stim in binSize
this.imp_s_index[0] -= Math.round((float) (this.dt_r / this.DT_S));
}
// imp_r.show();
// get Cells by segmentation;
IJ.showStatus(" Cell Segmentation...");
ImagePlus avr_imp = AApSegmetator.getAverageIm(imp_r);
AApSegmetator segmentator = new AApSegmetator(avr_imp);
this.cells_roi = segmentator.SegmentCellsCWT();
// this.cells_roi = segmentator.SegmentCellsML();
// Resample stimulus
ArrayList<Double> stim_vector = new ArrayList<>();
if (!this.useArtifact) {
IJ.showStatus(" Stimulus srtifact removal....");
Stimulus_API sapi = new Stimulus_API();
sapi.setup("", this.imp_s, this.cells_roi, 0);
stim_vector =
sapi.ResampleStimulus(
this.dt_r, imp_r.getStackSize(), this.imp_s_index[0], this.imp_s_index[1]);
} else {
double[] var1 = Activity_Analysis.getAverageSignal(imp_r);
Object[] var2 = Extract_Stimulus.getPeaks(var1, 1);
TimeSeries var3 = Extract_Stimulus.getStimulusArray(var2, imp_r.getStackSize());
for (int i = 0; i < var3.Signal.length; i++) {
stim_vector.add(var3.Signal[i]);
}
}
// Remove stimulus slices
ArrayList<Integer> stim_sampels = new ArrayList<>();
for (int i = 0; i < stim_vector.size(); i++) {
if (stim_vector.get(i) > 0) stim_sampels.add(i);
}
this.imp_r = ReplaceSlices(this.imp_r, stim_sampels);
// this.imp_r.show();
// IJ.run("In [+]", "");
// IJ.run("In [+]", "");
// Kalman filter
ImageStack ims = imp_r.getStack();
Kalman_Stack_Filter kl = new Kalman_Stack_Filter();
kl.filter(ims, this.KL_PRECVAR, this.KM_GAIN);
imp_r.setStack(ims);
// wrap everything with the Cell manager
this.cm = toCellManager(this.imp_r, this.cells_roi, avr_imp);
System.out.print("Success!!");
}
// run local method
}
/* Setup GUI */
protected final boolean setup() {
if (IJ.versionLessThan("1.40c")) {
return false;
} else {
int[] ids = WindowManager.getIDList();
if (ids != null && ids.length >= 2) {
ArrayList titlesList = new ArrayList();
ArrayList idsList = new ArrayList();
String currentTitle = null;
for (int titles = 0; titles < ids.length; ++titles) {
ImagePlus var1 = WindowManager.getImage(ids[titles]);
titlesList.add(var1.getTitle());
idsList.add(Integer.valueOf(ids[titles]));
if (var1 == WindowManager.getCurrentImage()) {
currentTitle = var1.getTitle();
}
}
if (titlesList.size() < 2) {
IJ.showMessage("You should have at least two stacks - stimulus and response.");
return false;
} else {
String[] var8 = new String[titlesList.size()];
titlesList.toArray(var8);
if (currentTitle == null) {
currentTitle = var8[0];
}
SubstackMaker sm = new SubstackMaker();
GenericDialog gd = new GenericDialog("AAP - 1.1.0");
// gd.setInsets(10, 45, 0);
gd.addChoice("Stimulus stack", var8, currentTitle);
gd.addChoice("Response stack", var8, currentTitle.equals(var8[0]) ? var8[1] : var8[0]);
String defautltSlices =
"1-" + WindowManager.getImage(((Integer) idsList.get(0)).intValue()).getStackSize();
gd.addMessage("Enter a range (e.g. 2-14)...", null, Color.darkGray);
gd.addStringField("Slices of Response:", defautltSlices, 40);
gd.addCheckbox("Remove first slice", true);
gd.addCheckbox("Use Artifact from response", true);
gd.showDialog();
if (gd.wasCanceled()) {
return false;
} else {
this.imp_s =
WindowManager.getImage(((Integer) idsList.get(gd.getNextChoiceIndex())).intValue());
this.imp_r =
WindowManager.getImage(((Integer) idsList.get(gd.getNextChoiceIndex())).intValue());
String userInput = gd.getNextString();
this.dt_r = Activity_Analysis.findSignalDt(this.imp_r.getTitle());
if (userInput == null) {
return false;
}
IJ.showStatus(" Making substack copy of selection...");
this.imp_r = sm.makeSubstack(this.imp_r, userInput);
this.imp_s_index = getFirstNLast(this.imp_r, userInput);
if (this.imp_s_index[0] != 1 | !gd.getNextBoolean()) this.removeFirst = false;
if (gd.getNextBoolean()) this.useArtifact = true;
// this.imp_s = makeStimSubstack(this.imp_s , userInput);
return true;
}
}
} else {
IJ.showMessage("You should have at least two stacks open.");
return false;
}
}
}