preparing for the goniometer with LWIR (50de1233) · Commits · Elphel / imagej-elphel

src/main/java/com/elphel/imagej/calibration/Aberration_Calibration.java

+492 −338

File changed.

Preview size limit exceeded, changes collapsed.

src/main/java/com/elphel/imagej/calibration/Goniometer.java

+144 −119

Original line number	Diff line number	Diff line
		@@ -29,12 +29,10 @@ package com.elphel.imagej.calibration;
		import java.util.Properties;
		import java.util.concurrent.atomic.AtomicInteger;

		import com.elphel.imagej.calibration.CalibrationHardwareInterface.CamerasInterface;
		import com.elphel.imagej.calibration.CalibrationHardwareInterface.GoniometerMotors;
		import com.elphel.imagej.calibration.SimulationPattern.SimulParameters;
		import com.elphel.imagej.cameras.EyesisCameraParameters;
		import com.elphel.imagej.common.ShowDoubleFloatArrays;
		import com.elphel.imagej.common.WindowTools;
		import com.elphel.imagej.lwir.LwirReader;

		import ij.IJ;
		import ij.ImagePlus;
		@@ -53,6 +51,7 @@ horizontal axis:
		// for
		// debugging
		public CalibrationHardwareInterface.CamerasInterface cameras = null;
		LwirReader lwirReader = null;
		// public CalibrationHardwareInterface.LaserPointers lasers = null;
		// public static CalibrationHardwareInterface.FocusingMotors motorsS=null;
		// public DistortionProcessConfiguration
		@@ -81,7 +80,6 @@ horizontal axis:

		public Goniometer(CalibrationHardwareInterface.CamerasInterface cameras,
		MatchSimulatedPattern.DistortionParameters distortionParametersDefault,
		// MatchSimulatedPattern.DistortionParameters distortion,
		MatchSimulatedPattern.PatternDetectParameters patternDetectParameters,
		EyesisCameraParameters eyesisCameraParameters,
		MatchSimulatedPattern.LaserPointer laserPointers,
		@@ -98,9 +96,34 @@ horizontal axis:
		this.simulParametersDefault=simulParametersDefault;
		this.goniometerParameters=goniometerParameters;
		this.distortionProcessConfiguration=distortionProcessConfiguration;
		}

		public Goniometer(
		LwirReader lwirReader,
		// CalibrationHardwareInterface.CamerasInterface cameras,
		MatchSimulatedPattern.DistortionParameters distortionParametersDefault,
		MatchSimulatedPattern.PatternDetectParameters patternDetectParameters,
		EyesisCameraParameters eyesisCameraParameters,
		MatchSimulatedPattern.LaserPointer laserPointers,
		SimulationPattern.SimulParameters simulParametersDefault,
		Goniometer.GoniometerParameters goniometerParameters,
		DistortionProcessConfiguration distortionProcessConfiguration
		) {
		this.lwirReader= lwirReader;
		// this.cameras = cameras;
		this.distortionParametersDefault = distortionParametersDefault;
		// this.distortion = distortion;
		this.patternDetectParameters=patternDetectParameters;
		this.eyesisCameraParameters = eyesisCameraParameters;
		this.laserPointers = laserPointers;
		this.simulParametersDefault=simulParametersDefault;
		this.goniometerParameters=goniometerParameters;
		this.distortionProcessConfiguration=distortionProcessConfiguration;
		}




		//goniometerMotors
		private enum MOT_ACT {
		MOVE_SPEC,
		@@ -222,6 +245,8 @@ horizontal axis:
		if (!OK) System.out.println("motorsMove()->false");
		return true; // OK; // So will re-open dialog even after abort
		}


		public boolean scanAndAcquire(
		double targetAngleHorizontal,
		double targetAngleVertical,
		@@ -276,7 +301,6 @@ horizontal axis:
		double cosMinAbsTilt=Math.cos(minAbsTilt*Math.PI/180.0);
		if (this.debugLevel>2) System.out.println("tilt="+IJ.d2s(tilt,2)+"tiltL="+IJ.d2s(tiltL,2)+", tiltH="+IJ.d2s(tiltH,2)+
		", minAbsTilt="+IJ.d2s(minAbsTilt,2)+", cosMinAbsTilt="+IJ.d2s(cosMinAbsTilt,2));
		// double axialRange=
		double scanStep=scanStepAxial;
		double overlap=scanOverlapHorizontal;
		int numAxialSteps=(int) Math.ceil((scanLimitAxialHigh-scanLimitAxialLow)*cosMinAbsTilt/scanStepAxial);
		@@ -296,8 +320,6 @@ horizontal axis:

		// spread evenly
		if (numAxialSteps>0){ // increase vertical overlap to make it same for all images
		// scanStep=(scanLimitAxialHigh-scanLimitAxialLow)*cosMinAbsTilt/numAxialSteps;
		// overlap=1.0-(scanStep/targetAngleHorizontal);
		scanStep=(scanLimitAxialHigh-scanLimitAxialLow)/numAxialSteps;
		overlap=1.0-(scanStep*cosMinAbsTilt/targetAngleHorizontal);
		}
		@@ -322,14 +344,8 @@ horizontal axis:
		System.out.println();
		}
		}
		// return true;

		// motorsSimultaneous
		// show current tilt/axial
		// double absTiltRange=Math.abs(this.goniometerParameters.scanLimitTiltStart-this.goniometerParameters.scanLimitTiltStart);

		GenericDialog gd = new GenericDialog("Start scanning");
		// this.serialNumber, // camera serial number string
		gd.addMessage("About to start scanning and recording images, parameters are set in the \"Configure Goniometer\" dialog");
		gd.addMessage("Please make sure goniometer motors are set that 0,0 corresponds to the camera in the initial position -");
		gd.addMessage("vertical and cables are not entangled, camera exposure is set correctly.");
		@@ -389,7 +405,6 @@ horizontal axis:
		if (this.debugLevel>0) System.out.println(status);
		if (updateStatus) IJ.showStatus(status);
		this.goniometerParameters.motorsSimultaneous=false; // not yet implemented
		// if (!this.goniometerParameters.motorsSimultaneous){
		OK= this.goniometerParameters.goniometerMotors.moveMotorSetETA(tiltMotor, tiltMotorPosition);
		if (!OK) {
		String msg="Could not set motor "+(tiltMotor+1)+" to move to "+tiltMotorPosition+" - may be out of limit";
		@@ -433,10 +448,19 @@ horizontal axis:
		}
		// update motor positions in the image properties, acquire and save images.
		// TODO: Make acquisition/decoding/laser identification multi-threaded

		if (cameras != null) {
		this.cameras.setMotorsPosition(this.goniometerParameters.goniometerMotors.getTargetPositions()); // Used target, not current to prevent minor variations
		this.cameras.reportTiming=debugTiming;

		this.cameras.acquire(this.distortionProcessConfiguration.sourceDirectory,true, updateStatus); // true - use lasers, updateStatus - make false?
		} else if (lwirReader != null) {
		this.lwirReader.setMotorsPosition(this.goniometerParameters.goniometerMotors.getTargetPositions()); // Used target, not current to prevent minor variations
		this.lwirReader.reportTiming=debugTiming;
		this.lwirReader.acquire(this.distortionProcessConfiguration.sourceDirectory); // true - use lasers, updateStatus - make false?
		} else {
		System.out.println("Neignter traditional camera/rig, no LWIR rig are initialized, dry run");
		}

		this.lastScanStep++;
		if (stopRequested.get()>1){
		if (this.debugLevel>0) System.out.println("User interrupt");
		@@ -1185,6 +1209,7 @@ horizontal axis:
		this.scanBidirectional=scanBidirectional;
		this.motorsSimultaneous=motorsSimultaneous;
		}
		@Override
		public GoniometerParameters clone(){
		return new GoniometerParameters(
		this.goniometerMotors,

src/main/java/com/elphel/imagej/correction/Eyesis_Correction.java

+2 −2

Original line number	Diff line number	Diff line
		@@ -4873,10 +4873,10 @@ private Panel panel1,
		if (LWIR_READER == null) {
		LWIR_READER = new LwirReader(CLT_PARAMETERS.lwir);
		}
		ImagePlus [] imps = LWIR_READER.acquire();
		ImagePlus [] imps = LWIR_READER.acquire("/data_ssd/imagej-elphel/attic/camera_img/test"); // directory to save
		if (imps != null) {
		for (ImagePlus imp: imps) {
		imp.show();
		// imp.show();
		}
		}

src/main/java/com/elphel/imagej/lwir/LwirReader.java

+64 −5

Original line number	Diff line number	Diff line
		@@ -26,6 +26,7 @@
		*/
		package com.elphel.imagej.lwir;

		import java.io.File;
		import java.io.IOException;
		import java.net.MalformedURLException;
		import java.util.Properties;
		@@ -40,9 +41,13 @@ import org.slf4j.LoggerFactory;
		import org.w3c.dom.Document;
		import org.xml.sax.SAXException;

		import com.elphel.imagej.readers.ImagejJp4Tiff;
		import com.elphel.imagej.readers.ImagejJp4TiffMulti;

		import ij.IJ;
		import ij.ImagePlus;
		import ij.Prefs;
		import ij.io.FileSaver;
		import ij.process.FloatProcessor;
		import ij.process.ImageProcessor;
		import loci.formats.FormatException;
		@@ -68,7 +73,7 @@ public class LwirReader {
		public static final int LWIR_HEIGHT = 120;
		public static final int LWIR_TELEMETRY_LINES = 2;

		public static final int FRAMES_SKIP = 3;
		public static final int FRAMES_SKIP = 4;
		public static final int MAX_THREADS = 100; // combine from all classes?

		/** Logger for this class. */
		@@ -82,6 +87,10 @@ public class LwirReader {
		private LwirReaderParameters lwirReaderParameters = null;
		private LwirReaderParameters last_programmed = null;


		private int [] motorsPosition = null;
		public boolean reportTiming=false;

		// -- constructors

		public LwirReader() {
		@@ -99,6 +108,15 @@ public class LwirReader {
		}


		public void setMotorsPosition (int [] position) {
		this.motorsPosition=position;
		}

		public int [] getMotorsPosition() {
		return this.motorsPosition; // may be null
		}


		// TODO: create
		public boolean reSyncNeeded() {
		return out_of_sync;
		@@ -220,6 +238,10 @@ public class LwirReader {
		imps_avg[chn].setProperty(key, properties0.getProperty(key));
		}
		imps_avg[chn].setProperty("average", ""+num_frames);
		if (motorsPosition!=null) for (int m=0;m<motorsPosition.length;m++ ) {
		imps_avg[chn].setProperty("MOTOR"+(m+1), ""+motorsPosition[m]);
		}
		ImagejJp4Tiff.encodeProperiesToInfo(imps_avg[chn]);
		// TODO: Overwrite some properties?
		}

		@@ -333,10 +355,12 @@ public class LwirReader {
		for (int c : lrp.lwir_channels) {
		channels \|= 1 << c;
		}
		String hex_chan = String.format("%x", channels);
		String hex_chan = String.format("0x%x", channels);

		String url = "http://"+lrp.lwir_ip+"/parsedit.php?immediate&sensor_port="+chn+
		"&SENSOR_REGS67=0!"+hex_chan;
		// String url = "http://"+lrp.lwir_ip+"/parsedit.php?immediate&sensor_port="+chn+
		// "&SENSOR_REGS67=0&*SENSOR_REGS67="+hex_chan;
		Document dom=null;
		LOGGER.warn("calibrate(): Perform calibration (instead of 15 frames), url="+url);
		try {
		@@ -415,12 +439,12 @@ public class LwirReader {
		return true;
		}

		public ImagePlus [] acquire() {
		return acquire(lwirReaderParameters);
		public ImagePlus [] acquire(String dirpath) {
		return acquire(lwirReaderParameters, dirpath);
		}


		public ImagePlus [] acquire(LwirReaderParameters lrp) {
		public ImagePlus [] acquire(LwirReaderParameters lrp, String dirpath) {
		if (!condProgramLWIRCamera(lrp)) {
		LOGGER.error("acquire(): failed to program cameras");
		return null;
		@@ -439,6 +463,20 @@ public class LwirReader {
		return null;
		}
		LOGGER.debug("LWIR_ACQUIRE: got "+imps.length+" image sets");
		// Verify fresh FFC for all channels
		double [] after_ffc = new double [lrp.lwir_channels.length];
		for (int chn = 0; chn < after_ffc.length; chn++) {
		double uptime = Double.NaN, ffctime = Double.NaN;
		try {
		uptime = Double.parseDouble(((String) imps[0][chn].getProperty("TLM_UPTIME")));
		ffctime = Double.parseDouble(((String) imps[0][chn].getProperty("TLM_FFC_TIME")));
		after_ffc[chn] = uptime-ffctime;
		} catch (Exception e) {
		LOGGER.warn("acquire(): TLM_UPTIME and/or TLM_FFC_TIME properties are not available for"+imps[0][chn].getTitle());
		}
		LOGGER.warn(String.format("LWIR channel %d time from FFC: %.3f", chn, after_ffc[chn]));
		}

		int [] lags = new int [lrp.lwir_channels.length + lrp.vnir_channels.length];
		for (int i = 0; i < lags.length; i++) {
		lags[i] = (i >= lrp.lwir_channels.length) ? lrp.vnir_lag : 0;
		@@ -464,6 +502,27 @@ public class LwirReader {
		}
		}
		ImagePlus [] imps_avg = averageMultiFrames(imps_sync);



		if (dirpath != null) {
		File f_dir = new File(dirpath);
		// get series path from the first channel file title
		String first_name = imps_sync[0][0].getTitle();
		String set_name = first_name.substring(0, first_name.lastIndexOf('_'));
		String set_path = dirpath+Prefs.getFileSeparator()+set_name;
		File set_dir = new File(set_path);
		set_dir.mkdirs(); // including parent
		for (ImagePlus imp:imps_avg) {
		String fname = imp.getTitle();
		fname = fname.substring(0, fname.lastIndexOf('_')) + ".tiff"; // remove _average
		FileSaver fs=new FileSaver(imp);
		String path=set_path+Prefs.getFileSeparator()+fname;
		IJ.showStatus("Saving "+path);
		LOGGER.debug("LWIR_ACQUIRE: 'Saving "+path+ " (and other with the same timestamp)" );
		fs.saveAsTiff(path);
		}
		}
		return imps_avg;
		}

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