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ijp-localizej/src/main/java/EMCCD_Simulator.java
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EMCCD_Simulator.java
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import ij.IJ;
import ij.ImagePlus;
import ij.ImageStack;
import ij.measure.Calibration;
import ij.process.ImageProcessor;
public class EMCCD_Simulator extends CameraSimulator {
private boolean knownCamera=false;
public double gainfactor=1000;
public EMCCD_Simulator(double pixelSize, int exposureTime, double quantumEff, ImageProcessor ip){
super(pixelSize,exposureTime,quantumEff/2, ip);
}
public EMCCD_Simulator(ImagePlus imp, double gain){
super(imp,0.46,0.001,0.0018,0.105*gain,10);
this.gainfactor=gain;
}
public EMCCD_Simulator(ImagePlus imp, double quant, double dark, double cic, double read, double exp, double gain){
super(imp,quant/2,dark,cic,read*gain,exp);
this.gainfactor=gain;
}
public EMCCD_Simulator(ImagePlus imp, CameraDialog cd){
super(imp,cd.quant/2,cd.dark,cd.cic,cd.read*cd.emGain,cd.exp);
this.gainfactor=cd.emGain;
}
public EMCCD_Simulator(ImageProcessor ip, double quantumEff,Calibration cal){
super(ip,quantumEff,cal);
}
public ImagePlus run(){
int slice=super.getImagePlus().getStackSize();
super.setTitle("EM CCD Camera");
if (slice==1){
this.setImageProcessor(this.PoissonNoise());
this.setImageProcessor(this.Bimodal());
this.setImageProcessor(this.EMGain(gainfactor));
this.setImageProcessor(this.ReadNoise());
this.cam_imp.setProcessor(this.cam_ip);
}
else {
ImageStack stack=this.getImagePlus().createEmptyStack();
for (int i=1;i<=slice;i++){
IJ.showProgress(i/slice);
this.getImagePlus().setSliceWithoutUpdate(i);
EMCCD_Simulator ccd=new EMCCD_Simulator(this.getProcessor().duplicate(),this.getQuantumEff(),this.getCalibration());
ccd.run();
stack.addSlice(ccd.getProcessor());
}
this.setImagePlus(stack);
}
return this.getImagePlus();
}
ImagePlus resultStack(){
ImageStack stack=new ImageStack(super.getWidth(),super.getHeight());
stack.addSlice(this.getImagePlus().getProcessor().duplicate().convertToFloat());
stack.addSlice(this.PoissonNoise().duplicate().convertToFloat());
stack.addSlice(this.Bimodal().duplicate());
return new ImagePlus("Noise stack",stack);
}
}
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