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]);
}
}
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");
}
