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();
}
/**
* Splits the specified RGB stack into three 8-bit grayscale stacks. Deletes the source stack if
* keepSource is false.
*/
public static ImageStack[] splitRGB(ImageStack rgb, boolean keepSource) {
int w = rgb.getWidth();
int h = rgb.getHeight();
ImageStack[] channels = new ImageStack[3];
for (int i = 0; i < 3; i++) channels[i] = new ImageStack(w, h);
byte[] r, g, b;
ColorProcessor cp;
int slice = 1;
int inc = keepSource ? 1 : 0;
int n = rgb.getSize();
for (int i = 1; i <= n; i++) {
IJ.showStatus(i + "/" + n);
r = new byte[w * h];
g = new byte[w * h];
b = new byte[w * h];
cp = (ColorProcessor) rgb.getProcessor(slice);
slice += inc;
cp.getRGB(r, g, b);
if (!keepSource) rgb.deleteSlice(1);
channels[0].addSlice(null, r);
channels[1].addSlice(null, g);
channels[2].addSlice(null, b);
IJ.showProgress((double) i / n);
}
return channels;
}
/* 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;
}
/** Deletes the last slice in the stack. */
public void deleteLastSlice() {
if (nSlices > 0) deleteSlice(nSlices);
}
/* 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
}