public void measureSetting1(MeasurementPlotter mPlot) {
// switch (layer) {
// case retarderA:
// targets = new double[]{0, 0, 0, 0, 0, 0, 0, 0, 0};
// break;
// case retarderB:
// targets = new double[]{0, 0, 0, 0, 0, 0, 0, 0, 0};
// break;
// case elliptical:
// targets = new double[]{0, 0, 0, 0, 0, 0, 0, 0};
// break;
// case circular:
// targets = new double[]{0, 0};
// break;
// }
final MultiSectorMeasurer acquireImageAndMeasure = new MultiSectorMeasurer();
System.out.println("measure setting 1");
int step = (int) ((SLMModel.startMax - SLMModel.startMin) / SLMModel.numPoints);
for (int s = 0; s < SLMModel.numPoints; s++) { // for each setting
int setTo = (int) (SLMModel.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]);
}
}
// TaskMeasureSetting1 task = new TaskMeasureSetting1(mPlot);
// task.execute();
}
// <editor-fold defaultstate="collapsed" desc=">>>--- Minimizations... ---<<<" >
public void minimizeToTargets(
double[] startMin,
double[] startMax,
double tol,
double[] targets,
MeasurementPlotter mPlot) {
// AcquireAndMeasure waits for all minimizers to send next setting,
// using CyclicBarrier, then aquires an image, measures all the roi's,
// then returns measurement to each minimizer.
//
// This is where the target retarder is indicated...
// For balancing intensity (settings 2-4), pass in the setting1 intensities
// in targets[]
acqCtrl.start();
MultiSectorMeasurer acquireImageAndMeasure = new MultiSectorMeasurer(mPlot);
this.targets = targets;
barrier = new CyclicBarrier(numIDs, acquireImageAndMeasure);
final MinimizeFunction function = new MinimizeFunction();
stopSignal = new CountDownLatch(numIDs);
// create and launch minimizations
minimizations = new BrentsMethod_IntDouble[numIDs];
for (int i = 0; i < numIDs; i++) {
minimizations[i] = new BrentsMethod_IntDouble(function, stopSignal);
}
for (int i = 0; i < numIDs; i++) {
createMinimizationThread(i, startMin[i], startMax[i], tol);
}
// Await completion of all of the minimizations- CountDownLatch is released...
System.out.println("* Waiting for stopSignal...");
try {
stopSignal.await();
} catch (InterruptedException ex) {
ex.printStackTrace();
}
System.out.println(">>>>> All minimizations done <<<<<");
for (int i = 0; i < numIDs; i++) {
// measurements[i] = minimizations[i].getMinX();
System.out.println(" " + i + " setting: " + settings[i] + ", measure: " + measurements[i]);
}
mPlot.closeTextFile();
acqCtrl.finish();
}
public void run() {
try {
System.out.println("acquireImageAndMeasure");
for (int i = 0; i < numIDs; i++) {
// for testing using MockRetarders
switch (layer) {
case retarderA:
slmCtrl.setRetA(i, (int) settings[i]);
break;
case retarderB:
slmCtrl.setRetB(i, (int) settings[i]);
break;
case elliptical:
slmCtrl.setElliptical(i, (int) settings[i]);
break;
case circular:
slmCtrl.setCircular(i, (int) settings[i]);
break;
}
}
if (!SLMModel.useMockRetarders) {
Thread.currentThread().sleep(slmModel.getSettlingtime());
// byte[] data = acqCtrl.acquireSampleImage();
acqCtrl.acquireImage(data);
// test
// BufferedImage img =
// ImageFactoryGrayScale.createImage(acqCtrl.getImageWidth(), acqCtrl.getImageHeight(), 8,
// (byte[]) data);
// edu.mbl.jif.gui.imaging.FrameImageDisplay id = new
// edu.mbl.jif.gui.imaging.FrameImageDisplay(img, "Sample");
// id.setVisible(true);
// measure intensity at ROIs
ImageStatistics[] iStats =
measureROIsIn(data, acqCtrl.getImageWidth(), acqCtrl.getImageHeight(), rois);
iteration++;
for (int i = 0; i < numIDs; i++) {
measurements[i] =
Math.abs(iStats[i].meanInROI - slmModel.getZeroIntensity() - targets[i]);
if (mPlot != null) {
mPlot.recordData(i, iteration, measurements[i]);
}
}
} else { // useMockRetarders
for (int i = 0; i < numIDs; i++) {
// for testing using MockRetarders
switch (layer) {
case retarderA:
measurements[i] = mockRet[i].calcA(settings[i]);
break;
case retarderB:
measurements[i] = mockRet[i].calcB(settings[i]);
break;
case elliptical:
measurements[i] = mockRet[i].calc(settings[i]);
break;
case circular:
measurements[i] = mockRet[i].calc(settings[i]);
break;
}
if (mPlot != null) {
mPlot.recordData(i, iteration, measurements[i]);
}
}
}
} catch (InterruptedException ex) {
Logger.getLogger(SLM_Calibrator.class.getName()).log(Level.SEVERE, null, ex);
}
}
private void normalize(DataSet[] dataSets) {
double[] max = new double[numIDs];
// find max
for (int i = 0; i < numIDs; i++) {
for (int j = 0; j < SLMModel.numPoints; j++) {
if (max[i] < dataSets[i].getMeasurement(j)) {
max[i] = dataSets[i].getMeasurement(j);
}
}
}
// normalize
for (int i = 0; i < numIDs; i++) {
for (int j = 0; j < SLMModel.numPoints; j++) {
dataSets[i].measurement[j] = dataSets[i].measurement[j] / max[i];
}
}
// dumpDataSet();
// Plot & record Normalized Intensity
for (int i = 0; i < numIDs; i++) {
System.out.println("\n" + ">>>>>>> ID: " + i);
for (int j = 0; j < SLMModel.numPoints; j++) {
System.out.println(dataSets[i].setting[j] + " => " + dataSets[i].measurement[j]);
double s = dataSets[i].getSetting(j);
double m = dataSets[i].getMeasurement(j);
mNPlot.recordData(i, j, s, m);
}
}
mNPlot.closeTextFile();
writeOutMatrix(dataSets, "Normalized");
// Plot & record RetardanceCurve
for (int i = 0; i < numIDs; i++) {
System.out.println("\n" + ">>>>>>> ID: " + i);
double lastValue = 0;
boolean inSection1 = true;
boolean inSection2 = false;
boolean inSection3 = false;
for (int j = 0; j < SLMModel.numPoints; j++) {
System.out.println(dataSets[i].setting[j] + " => " + dataSets[i].measurement[j]);
double s = dataSets[i].getSetting(j);
double m = dataSets[i].getMeasurement(j);
if (inSection1 && (lastValue > m)) {
inSection1 = false;
inSection2 = true;
}
if (inSection2 && (lastValue < m)) {
inSection2 = false;
inSection3 = true;
}
lastValue = m;
double ret = 0;
if (inSection1) {
ret = 3.0 * Math.PI - 2 * Math.asin(Math.sqrt(m));
}
if (inSection2) {
ret = Math.PI + 2 * Math.asin(Math.sqrt(m));
}
if (inSection3) {
ret = Math.PI - 2 * Math.asin(Math.sqrt(m));
}
mNPlot.recordData(i, j, s, ret);
dataSets[i].measurement[j] = ret;
}
}
mNPlot.closeTextFile();
writeOutMatrix(dataSets, "Retardance");
}
