measureZ.bsh

/**
 * Micro-Manager script that measures the z position at all positions in the position list
 */

outputFile =  "D:\\Users\\Susana\\20150512\\posWholePlate3.txt";
nrColumns = 12;
nrRows = 8;
zDrive = "TIZDrive";


////////// Do NOT edit below this line
import org.micromanager.api.MultiStagePosition;

resultsFile = new File(outputFile);
resultsFile.createNewFile();
resultsWriter = new BufferedWriter(new FileWriter(resultsFile));

posList = gui.getPositionList();
positions = posList.getPositions();
currentWell = "";
count = 0;
sitesPerWell = 0;
wellCount = 0;

// first get out how many positions per well we have
for (int p = 0; p < positions.length; p++) {
	msp = positions[p];
	label = msp.getLabel();
	well = label.split("-")[0];
	if (!currentWell.equals(well)) {
		currentWell = well;
		wellCount++;
		sitesPerWell = 1;
	} else
	   sitesPerWell++;
}
nPerRow = Math.sqrt(sitesPerWell);
nPerRow = (int) nPerRow;
gui.message("" + sitesPerWell + " sites per well, " + wellCount + " wells, " + nPerRow + "rows/columns");

// this will only work with square sites per well

double[][][] zValues = new double[wellCount][nPerRow][nPerRow];

// now visit them all and record z positions after locking the PFS
wi = 0;
ri = 0;
ci = 0;
for (int p = 0; p < positions.length; p++) {
	msp = positions[p];
	label = msp.getLabel();
	well = label.split("-")[0];
	MultiStagePosition.goToPosition(msp, mmc);
	//gui.sleep(200);
	mmc.fullFocus();
	gui.message("well " + wi + ", " + ri + ", " + ci);
	zValues[wi][ri][ci] = mmc.getPosition(zDrive);
	ci++;
	if (ci == nPerRow) {
		ci = 0;
		ri++;
	}
	if (ri == nPerRow) {
		ri = 0;
		wi++;
	}
}

for (int r = 0; r < nrRows; r++) {
	for (int rr = 0; rr < nPerRow; rr++) {
		for (int sr = 0; sr < nPerRow * nrColumns; sr++) {
			wellIndex = r * nrColumns + sr / nPerRow;
			cci = sr % nPerRow;
			gui.message("" + wellIndex + ", " + rr + ", " + cci);
			resultsWriter.write("" + zValues[wellIndex][rr][cci]  + "\t" );
		}
	resultsWriter.newLine();	
	}
}
resultsWriter.close();