public void calibrateCircularMask() {
this.setup(Layer.circular);
String filename = FileUtil.getcwd() + "/" + "Circular Mask Calibration" + ".dat";
MeasurementPlotter mPlot =
new MeasurementPlotter(
"Circular Mask Calibration",
numIDs,
filename,
new Range(0, 254),
new Rectangle(10, 10, 400, 300));
// minimize, i.e. find max. extinction
double[] targets = new double[] {0, 0};
double[] a = new double[numIDs];
double[] b = new double[numIDs];
for (int i = 0; i < a.length; i++) {
a[i] = (double) SLMModel.HuntRangeMasksMin_a;
b[i] = (double) SLMModel.HuntRangeMasksMin_b;
}
this.minimizeToTargets(a, b, slmModel.getTolCoarse(), targets, mPlot);
slmCtrl.setCircularExtinctSettings(this.getSettings());
// Maximize, i.e. fine max. transmission
targets = new double[] {254, 254};
for (int i = 0; i < a.length; i++) {
a[i] = (double) SLMModel.HuntRangeMasksMax_a;
b[i] = (double) SLMModel.HuntRangeMasksMax_b;
}
this.minimizeToTargets(a, b, slmModel.getTolCoarse(), targets, mPlot);
slmCtrl.setCircularTransmitSettings(this.getSettings());
}
public void setNominalSwing(int n) {
for (int sector = 0; sector < slmCtrl.settings.retardSetA[0].length; sector++) {
// setElement(0, extinctA, extinctB);
// setElement(1, extinctA + LC_Swing, extinctB);
// setElement(2, extinctA, extinctB + LC_Swing);
// setElement(3, extinctA, extinctB - LC_Swing);
// setElement(4, extinctA - LC_Swing, extinctB);
// swing of 0.01 = 0.0628 shift in retardance
// ??? Does swingEquivalent vary with Sector? Yes.
double swingeAngle = slmModel.getSwing() * slmModel.getWavelength() * 2 * Math.PI;
switch (n) {
case 0: // Extinction, nominal 0.25, 0.50
// ++ >>>>>>>> default extinction settings
// slmCtrl.settings.retardSetA[0][sector] = 1559;
// slmCtrl.settings.retardSetB[0][sector] = 1559;
slmCtrl.setRetA(sector, slmCtrl.settings.retardSetA[0][sector]);
slmCtrl.setRetB(sector, slmCtrl.settings.retardSetB[0][sector]);
break;
case 1:
slmCtrl.settings.retardSetA[1][sector] =
slmCtrl.settings.retardSetA[0][sector] + swingeAngle;
slmCtrl.settings.retardSetB[1][sector] = slmCtrl.settings.retardSetB[0][sector];
slmCtrl.setRetA(sector, slmCtrl.settings.retardSetA[1][sector]);
slmCtrl.setRetB(sector, slmCtrl.settings.retardSetB[1][sector]);
break;
case 2:
slmCtrl.settings.retardSetA[2][sector] = slmCtrl.settings.retardSetA[0][sector];
slmCtrl.settings.retardSetB[2][sector] =
slmCtrl.settings.retardSetB[0][sector] + swingeAngle;
slmCtrl.setRetA(sector, slmCtrl.settings.retardSetA[2][sector]);
slmCtrl.setRetB(sector, slmCtrl.settings.retardSetB[2][sector]);
break;
case 3:
slmCtrl.settings.retardSetA[3][sector] = slmCtrl.settings.retardSetA[0][sector];
slmCtrl.settings.retardSetB[3][sector] =
slmCtrl.settings.retardSetB[0][sector] - swingeAngle;
slmCtrl.setRetA(sector, slmCtrl.settings.retardSetA[3][sector]);
slmCtrl.setRetB(sector, slmCtrl.settings.retardSetB[3][sector]);
break;
case 4:
slmCtrl.settings.retardSetA[4][sector] =
slmCtrl.settings.retardSetA[0][sector] - swingeAngle;
slmCtrl.settings.retardSetB[4][sector] = slmCtrl.settings.retardSetB[0][sector];
slmCtrl.setRetA(sector, slmCtrl.settings.retardSetA[4][sector]);
slmCtrl.setRetB(sector, slmCtrl.settings.retardSetB[4][sector]);
break;
}
}
}
// class TaskMeasureSetting1
// extends SwingWorker {
//
// MeasurementPlotter mPlot;
//
//
// public TaskMeasureSetting1(MeasurementPlotter mPlot) {
// this.mPlot = mPlot;
// }
//
//
// final MultiSectorMeasurer acquireImageAndMeasure = new MultiSectorMeasurer();
//
//
// @Override
// public Object doInBackground() {
//
// System.out.println("measure setting 1");
// int step = (int) ((SLMConstants.startMax - SLMConstants.startMin) /
// SLMConstants.numPoints);
// for (int s = 0; s < SLMConstants.numPoints; s++) { // for each setting
// int setTo = (int) (SLMConstants.startMin + s * step);
// for (int i = 0; i < numIDs; i++) { //for each sector
// settings[i] = setTo;
// }
// acquireImageAndMeasure.run();
// for (int i = 0; i < numIDs; i++) {
// mPlot.recordData(i, s, measurements[i]);
// }
//
// }
// return null;
// }
//
//
// }
private void matchSettingN(int n, MeasurementPlotter mPlot) {
double[] a = new double[numIDs];
double[] b = new double[numIDs];
this.setup(Layer.retarderA);
for (int i = 0; i < a.length; i++) {
a[i] = slmCtrl.settings.retardSetA[n][i] - SLMModel.deltaExtinct;
b[i] = slmCtrl.settings.retardSetA[n][i] + SLMModel.deltaExtinct;
}
this.minimizeToTargets(a, b, slmModel.getTolCoarse(), measuredIntensity1, mPlot);
slmCtrl.setCalibratedRetarderASettings(n, this.getSettings());
this.setup(Layer.retarderB);
for (int i = 0; i < a.length; i++) {
a[i] = slmCtrl.settings.retardSetB[n][i] - SLMModel.deltaExtinct;
b[i] = slmCtrl.settings.retardSetB[n][i] + SLMModel.deltaExtinct;
}
this.minimizeToTargets(a, b, slmModel.getTolCoarse(), measuredIntensity1, mPlot);
slmCtrl.setCalibratedRetarderBSettings(n, this.getSettings());
// @todo repeat with tolFine
}
public void findExtinction(MeasurementPlotter mPlot) {
slmCtrl.setAllRetarderATo(SLMModel.extA);
slmCtrl.setAllRetarderBTo(SLMModel.extB);
double[] a = new double[numIDs];
double[] b = new double[numIDs];
System.out.println(">>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> findExtinction A coarse ...");
for (int i = 0; i < a.length; i++) {
a[i] = (double) SLMModel.HuntRangeRetarderA_a;
b[i] = (double) SLMModel.HuntRangeRetarderA_b;
}
findExtinctionA(mPlot, a, b, slmModel.getTolCoarse());
System.out.println(">>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> findExtinction B coarse ...");
for (int i = 0; i < a.length; i++) {
a[i] = (double) SLMModel.HuntRangeRetarderB_a;
b[i] = (double) SLMModel.HuntRangeRetarderB_b;
}
findExtinctionB(mPlot, a, b, slmModel.getTolCoarse());
System.out.println(">>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> findExtinction A fine ...");
for (int i = 0; i < a.length; i++) {
a[i] = (double) slmCtrl.settings.retardSetA[0][i] - SLMModel.deltaExtinct;
b[i] = (double) slmCtrl.settings.retardSetA[0][i] + SLMModel.deltaExtinct;
}
findExtinctionA(mPlot, a, b, slmModel.getTolFine());
System.out.println(">>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> findExtinction B fine ...");
for (int i = 0; i < a.length; i++) {
a[i] = (double) slmCtrl.settings.retardSetB[0][i] - SLMModel.deltaExtinct;
b[i] = (double) slmCtrl.settings.retardSetB[0][i] + SLMModel.deltaExtinct;
}
findExtinctionB(mPlot, a, b, slmModel.getTolFine());
measuredIntensity0 = this.getMeasuredValues().clone();
}
public void measureROIs() {
targets = new double[] {0, 0, 0, 0, 0, 0, 0, 0, 0};
// System.out.println("acquireImageAndMeasure");
byte[] data = acqCtrl.acquireSampleImage();
// measure intensity at ROIs
ImageStatistics[] iStats =
measureROIsIn(data, acqCtrl.getImageWidth(), acqCtrl.getImageHeight(), rois);
for (int i = 0; i < numIDs; i++) {
measurements[i] = Math.abs(iStats[i].meanInROI - slmModel.getZeroIntensity() - targets[i]);
}
IJ.log("\nMeasured ROIs:");
for (int i = 0; i < numIDs; i++) {
IJ.log(
" sector "
+ i
+ ": " // + settings[i]
+ " = "
+ measurements[i]);
}
}