Acquiring images sets with LWIR16 (016b8b7c) · Commits · Elphel / imagej-elphel

pom.xml

+8 −0

Original line number	Original line	Diff line number	Diff line
	@@ -27,6 +27,14 @@
	<description>A Maven project implementing imagej-elphel plugin</description>		<description>A Maven project implementing imagej-elphel plugin</description>

	<dependencies>		<dependencies>
			<!-- ssh support - see https://www.baeldung.com/java-ssh-connection -->
			<!-- https://mvnrepository.com/artifact/org.apache.sshd/sshd-core -->
			<dependency>
			<groupId>org.apache.sshd</groupId>
			<artifactId>sshd-core</artifactId>
			<version>2.6.0</version>
			</dependency>

	<dependency>		<dependency>
	<groupId>net.imagej</groupId>		<groupId>net.imagej</groupId>
	<artifactId>ij</artifactId>		<artifactId>ij</artifactId>

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

+132 −42

Original line number	Original line	Diff line number	Diff line
	@@ -73,6 +73,7 @@ import com.elphel.imagej.common.PolynomialApproximation;
	import com.elphel.imagej.common.ShowDoubleFloatArrays;		import com.elphel.imagej.common.ShowDoubleFloatArrays;
	import com.elphel.imagej.common.WindowTools;		import com.elphel.imagej.common.WindowTools;
	import com.elphel.imagej.jp4.JP46_Reader_camera;		import com.elphel.imagej.jp4.JP46_Reader_camera;
			import com.elphel.imagej.lwir.Lwir16Reader;
	import com.elphel.imagej.lwir.LwirReader;		import com.elphel.imagej.lwir.LwirReader;
	import com.elphel.imagej.lwir.LwirReaderParameters;		import com.elphel.imagej.lwir.LwirReaderParameters;
	import com.elphel.imagej.readers.EyesisTiff;		import com.elphel.imagej.readers.EyesisTiff;
	@@ -108,6 +109,7 @@ public class Aberration_Calibration extends PlugInFrame implements ActionListene
	private Panel panelGoniometer;		private Panel panelGoniometer;
	private Panel panelPixelMapping, panelStereo,panelStereo1;		private Panel panelPixelMapping, panelStereo,panelStereo1;
	private Panel panelLWIR;		private Panel panelLWIR;
			private Panel panelLWIR16;

	private ShowDoubleFloatArrays SDFA_INSTANCE; // just for debugging?		private ShowDoubleFloatArrays SDFA_INSTANCE; // just for debugging?
	JP46_Reader_camera JP4_INSTANCE;		JP46_Reader_camera JP4_INSTANCE;
	@@ -289,6 +291,7 @@ public class Aberration_Calibration extends PlugInFrame implements ActionListene
	);		);

	public static LwirReader LWIR_READER = null;		public static LwirReader LWIR_READER = null;
			public static Lwir16Reader LWIR16_READER = null;


	public static ProcessCalibrationFilesParameters PROCESS_PARAMETERS = new ProcessCalibrationFilesParameters(		public static ProcessCalibrationFilesParameters PROCESS_PARAMETERS = new ProcessCalibrationFilesParameters(
	@@ -652,8 +655,6 @@ public static MatchSimulatedPattern.DistortionParameters DISTORTION =new MatchSi

	public static LwirReaderParameters LWIR_PARAMETERS = new LwirReaderParameters();		public static LwirReaderParameters LWIR_PARAMETERS = new LwirReaderParameters();



	// new CalibrationHardwareInterface.LaserPointers();		// new CalibrationHardwareInterface.LaserPointers();
	public class SyncCommand{		public class SyncCommand{
	public boolean isRunning= false;		public boolean isRunning= false;
	@@ -1030,6 +1031,11 @@ if (MORE_BUTTONS) {
	panelLWIR.setLayout(new GridLayout(1, 0, 5, 5)); // rows, columns, vgap, hgap		panelLWIR.setLayout(new GridLayout(1, 0, 5, 5)); // rows, columns, vgap, hgap
	addButton("LWIR Configure", panelLWIR,color_configure);		addButton("LWIR Configure", panelLWIR,color_configure);
	addButton("LWIR_TEST", panelLWIR, color_conf_process);		addButton("LWIR_TEST", panelLWIR, color_conf_process);
			addButton("CMPRS_STOP", panelLWIR, color_stop);
			addButton("CMPRS_START", panelLWIR, color_process);
			addButton("LWIR_FFC", panelLWIR, color_conf_process);
			addButton("RST BUFs", panelLWIR, color_stop);

	addButton("LWIR_ACQUIRE", panelLWIR, color_conf_process);		addButton("LWIR_ACQUIRE", panelLWIR, color_conf_process);
	addButton("Configure Goniometer", panelLWIR,color_configure);		addButton("Configure Goniometer", panelLWIR,color_configure);
	addButton("Goniometer Move", panelLWIR,color_debug);		addButton("Goniometer Move", panelLWIR,color_debug);
	@@ -1041,8 +1047,8 @@ if (MORE_BUTTONS) {
	addButton("EO Offsets", panelLWIR,color_process);		addButton("EO Offsets", panelLWIR,color_process);
	addButton("LWIR to EO", panelLWIR,color_process);		addButton("LWIR to EO", panelLWIR,color_process);
	addButton("Manual hint", panelLWIR,color_configure);		addButton("Manual hint", panelLWIR,color_configure);

	add(panelLWIR);		add(panelLWIR);

	pack();		pack();
	GUI.center(this);		GUI.center(this);
	setVisible(true);		setVisible(true);
	@@ -9284,25 +9290,90 @@ if (MORE_BUTTONS) {
	LWIR_PARAMETERS.showJDialog();		LWIR_PARAMETERS.showJDialog();
	return;		return;
	}		}
			//startStopCompressor(LwirReaderParameters lrp, boolean start, double delay)
			//condProgramLWIRCamera()
			/* ======================================================================== */
			if (label.equals("CMPRS_START") \|\| label.equals("CMPRS_STOP")) {
			boolean start = label.equals("CMPRS_START");
			if (LWIR_PARAMETERS.isLwir16()) {
			if (LWIR16_READER == null) {
			LWIR16_READER = new Lwir16Reader(LWIR_PARAMETERS);
			}
			LWIR16_READER.condProgramLWIRCamera();
			double delay = 3.0;
			LWIR16_READER.startStopCompressor(LWIR_PARAMETERS, start, delay);
			}
			return;
			}
			/* ======================================================================== */
			if (label.equals("LWIR_FFC")) {
			if (LWIR_PARAMETERS.isLwir16()) {
			if (LWIR16_READER == null) {
			LWIR16_READER = new Lwir16Reader(LWIR_PARAMETERS);
			}
			LWIR16_READER.condProgramLWIRCamera();
			int skip_frames = 0; // 300; // 5 second to come to the camera, remove later
			if (skip_frames > 0) {
			LWIR16_READER.skipMasterFrames(new String[] {LWIR_PARAMETERS.getLwirIP(0)}, skip_frames);
			}
			LWIR16_READER.runFFC(LWIR_PARAMETERS);
			}
			return;
			}
			/* ======================================================================== */
			if (label.equals("RST BUFs")) {
			if (LWIR_PARAMETERS.isLwir16()) {
			if (LWIR16_READER == null) {
			LWIR16_READER = new Lwir16Reader(LWIR_PARAMETERS);
			}
			LWIR16_READER.condProgramLWIRCamera();
			LWIR16_READER.resetFrameBuffers(LWIR_PARAMETERS);
			}
			return;
			}
	/* ======================================================================== */		/* ======================================================================== */
	//
	if (label.equals("LWIR_TEST")) {		if (label.equals("LWIR_TEST")) {
	DEBUG_LEVEL=MASTER_DEBUG_LEVEL;		DEBUG_LEVEL=MASTER_DEBUG_LEVEL;
	// public static LwirReader LWIR_READER = null;		// public static LwirReader LWIR_READER = null;
			ImagePlus [][] imps;
			if (LWIR_PARAMETERS.isLwir16()) {
			if (LWIR16_READER == null) {
			LWIR16_READER = new Lwir16Reader(LWIR_PARAMETERS);
			}
			LWIR16_READER.programLWIRCamera(LWIR_PARAMETERS);
			if (DEBUG_LEVEL <1000) {
			return;
			}
			imps = LWIR16_READER.readAllMultiple(
			LWIR_PARAMETERS.getNumFrames(), // 10, // final int num_frames,
			// true, // use LWIR telemetry
			true, // final boolean show,
			false); // true); // final boolean scale)
			} else {
	if (LWIR_READER == null) {		if (LWIR_READER == null) {
	LWIR_READER = new LwirReader(LWIR_PARAMETERS);		LWIR_READER = new LwirReader(LWIR_PARAMETERS);
	}		}
	ImagePlus [][] imps = LWIR_READER.readAllMultiple(		imps = LWIR_READER.readAllMultiple(
	LWIR_PARAMETERS.getNumFrames(), // 10, // final int num_frames,		LWIR_PARAMETERS.getNumFrames(), // 10, // final int num_frames,
	// true, // use LWIR telemetry		// true, // use LWIR telemetry
	true, // final boolean show,		true, // final boolean show,
	false); // true); // final boolean scale)		false); // true); // final boolean scale)
			}
	for (ImagePlus imp: imps[0]) {		for (ImagePlus imp: imps[0]) {
	imp.show();		imp.show();
	}		}

	System.out.println("LWIR_TEST: got "+imps.length+" image sets");		System.out.println("LWIR_TEST: got "+imps.length+" image sets");
			if (LWIR_PARAMETERS.isLwir16()) {
			// will probably not needed for Bosons
			ImagePlus [][] imps_sync = LWIR16_READER.matchSets(imps, 0.001, 3); // double max_mismatch)
			if (imps_sync != null) {
			ImagePlus [] imps_avg = LWIR16_READER.averageMultiFrames(imps_sync);
			for (ImagePlus imp: imps_avg) {
			imp.show();
			}
			}
			} else {
	ImagePlus [][] imps_sync = LWIR_READER.matchSets(imps, 0.001, 3); // double max_mismatch)		ImagePlus [][] imps_sync = LWIR_READER.matchSets(imps, 0.001, 3); // double max_mismatch)
	if (imps_sync != null) {		if (imps_sync != null) {
	ImagePlus [] imps_avg = LWIR_READER.averageMultiFrames(imps_sync);		ImagePlus [] imps_avg = LWIR_READER.averageMultiFrames(imps_sync);
	@@ -9310,48 +9381,68 @@ if (MORE_BUTTONS) {
	imp.show();		imp.show();
	}		}
	}		}
			}
	return;		return;
	}		}
	/* ======================================================================== */		/* ======================================================================== */
	if (label.equals("LWIR_ACQUIRE")) {		if (label.equals("LWIR_ACQUIRE")) {
	DEBUG_LEVEL=MASTER_DEBUG_LEVEL;		DEBUG_LEVEL=MASTER_DEBUG_LEVEL;
	// public static LwirReader LWIR_READER = null;		ImagePlus [][] imps;
			if (LWIR_PARAMETERS.isLwir16()) {
			if (LWIR16_READER == null) {
			LWIR16_READER = new Lwir16Reader(LWIR_PARAMETERS);
			}
			// ImagePlus [] imps =
			LWIR16_READER.acquire(DISTORTION_PROCESS_CONFIGURATION.sourceDirectory); // directory to save
			// ImagePlus [] imps = LWIR_READER.acquire("attic/lwir_test_images"); // directory to save
			} else {
	if (LWIR_READER == null) {		if (LWIR_READER == null) {
	LWIR_READER = new LwirReader(LWIR_PARAMETERS);		LWIR_READER = new LwirReader(LWIR_PARAMETERS);
	}		}
	// ImagePlus [] imps =		// ImagePlus [] imps =
	LWIR_READER.acquire(DISTORTION_PROCESS_CONFIGURATION.sourceDirectory); // directory to save		LWIR_READER.acquire(DISTORTION_PROCESS_CONFIGURATION.sourceDirectory); // directory to save
	// ImagePlus [] imps = LWIR_READER.acquire("attic/lwir_test_images"); // directory to save		// ImagePlus [] imps = LWIR_READER.acquire("attic/lwir_test_images"); // directory to save
			}
	return;		return;
	}		}

	/* ======================================================================== */		/* ======================================================================== */
	if (label.equals("LWIR Goniometer")) {		if (label.equals("LWIR Goniometer")) {
	DEBUG_LEVEL=MASTER_DEBUG_LEVEL;		DEBUG_LEVEL=MASTER_DEBUG_LEVEL;
			if ((GONIOMETER==null) \|\| (LWIR_PARAMETERS.isLwir16()?(GONIOMETER.lwir16Reader == null):(GONIOMETER.lwirReader == null))) {
	// CAMERAS.setNumberOfThreads(THREADS_MAX);		if (LWIR_PARAMETERS.isLwir16()) {
	// CAMERAS.debugLevel=DEBUG_LEVEL;		if (LWIR16_READER == null) {
			LWIR16_READER = new Lwir16Reader(LWIR_PARAMETERS);
	if ((GONIOMETER==null) \|\| (GONIOMETER.lwirReader == null)) {		}
			GONIOMETER= new Goniometer(
			LWIR16_READER,
			DISTORTION, //MatchSimulatedPattern.DistortionParameters distortion,
			PATTERN_DETECT, //MatchSimulatedPattern.PatternDetectParameters patternDetectParameters,
			EYESIS_CAMERA_PARAMETERS, //EyesisCameraParameters eyesisCameraParameters,
			LASER_POINTERS, // MatchSimulatedPattern.LaserPointer laserPointers
			SIMUL, //SimulationPattern.SimulParameters simulParametersDefault,
			GONIOMETER_PARAMETERS, //LensAdjustment.FocusMeasurementParameters focusMeasurementParameters,
			DISTORTION_PROCESS_CONFIGURATION);
			} else {
	if (LWIR_READER == null) {		if (LWIR_READER == null) {
	LWIR_READER = new LwirReader(LWIR_PARAMETERS);		LWIR_READER = new LwirReader(LWIR_PARAMETERS);
	}		}
	GONIOMETER= new Goniometer(		GONIOMETER= new Goniometer(
	LWIR_READER,		LWIR_READER,
	// CAMERAS, // CalibrationHardwareInterface.CamerasInterface cameras,
	DISTORTION, //MatchSimulatedPattern.DistortionParameters distortion,		DISTORTION, //MatchSimulatedPattern.DistortionParameters distortion,
	PATTERN_DETECT, //MatchSimulatedPattern.PatternDetectParameters patternDetectParameters,		PATTERN_DETECT, //MatchSimulatedPattern.PatternDetectParameters patternDetectParameters,
	EYESIS_CAMERA_PARAMETERS, //EyesisCameraParameters eyesisCameraParameters,		EYESIS_CAMERA_PARAMETERS, //EyesisCameraParameters eyesisCameraParameters,
	LASER_POINTERS, // MatchSimulatedPattern.LaserPointer laserPointers		LASER_POINTERS, // MatchSimulatedPattern.LaserPointer laserPointers
	SIMUL, //SimulationPattern.SimulParameters simulParametersDefault,		SIMUL, //SimulationPattern.SimulParameters simulParametersDefault,
	GONIOMETER_PARAMETERS, //LensAdjustment.FocusMeasurementParameters focusMeasurementParameters,		GONIOMETER_PARAMETERS, //LensAdjustment.FocusMeasurementParameters focusMeasurementParameters,
	DISTORTION_PROCESS_CONFIGURATION		DISTORTION_PROCESS_CONFIGURATION);
	);
			}
	if (DEBUG_LEVEL>1){		if (DEBUG_LEVEL>1){
	System.out.println("Initiaslizing Goniometer class");		System.out.println("Initialized Goniometer class for "+LWIR_PARAMETERS.getCameraName());
	}		}
	} else if (DEBUG_LEVEL>1){		} else if (DEBUG_LEVEL>1){
	System.out.println("GONIOMETER was initialized");		System.out.println("GONIOMETER was initialized for "+LWIR_PARAMETERS.getCameraName());
	}		}

	// calculate angular size of the target as visible from the camera		// calculate angular size of the target as visible from the camera
	@@ -9437,7 +9528,6 @@ if (MORE_BUTTONS) {
	}		}

	/* ======================================================================== */		/* ======================================================================== */

	IJ.showMessage("Not yet implemented");		IJ.showMessage("Not yet implemented");
	DEBUG_LEVEL=MASTER_DEBUG_LEVEL;		DEBUG_LEVEL=MASTER_DEBUG_LEVEL;
	return;		return;

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

+29 −1

Original line number	Original line	Diff line number	Diff line
	@@ -34,6 +34,7 @@ import com.elphel.imagej.calibration.hardware.GoniometerMotors;
	import com.elphel.imagej.cameras.EyesisCameraParameters;		import com.elphel.imagej.cameras.EyesisCameraParameters;
	import com.elphel.imagej.common.ShowDoubleFloatArrays;		import com.elphel.imagej.common.ShowDoubleFloatArrays;
	import com.elphel.imagej.common.WindowTools;		import com.elphel.imagej.common.WindowTools;
			import com.elphel.imagej.lwir.Lwir16Reader;
	import com.elphel.imagej.lwir.LwirReader;		import com.elphel.imagej.lwir.LwirReader;

	import ij.IJ;		import ij.IJ;
	@@ -54,6 +55,7 @@ horizontal axis:
	// debugging		// debugging
	public CamerasInterface cameras = null;		public CamerasInterface cameras = null;
	public LwirReader lwirReader = null;		public LwirReader lwirReader = null;
			public Lwir16Reader lwir16Reader = null;
	// public CalibrationHardwareInterface.LaserPointers lasers = null;		// public CalibrationHardwareInterface.LaserPointers lasers = null;
	// public static CalibrationHardwareInterface.FocusingMotors motorsS=null;		// public static CalibrationHardwareInterface.FocusingMotors motorsS=null;
	// public DistortionProcessConfiguration		// public DistortionProcessConfiguration
	@@ -123,6 +125,28 @@ horizontal axis:
	this.distortionProcessConfiguration=distortionProcessConfiguration;		this.distortionProcessConfiguration=distortionProcessConfiguration;
	}		}

			public Goniometer(
			Lwir16Reader lwir16Reader,
			// CalibrationHardwareInterface.CamerasInterface cameras,
			MatchSimulatedPattern.DistortionParameters distortionParametersDefault,
			MatchSimulatedPattern.PatternDetectParameters patternDetectParameters,
			EyesisCameraParameters eyesisCameraParameters,
			LaserPointer laserPointers,
			SimulationPattern.SimulParameters simulParametersDefault,
			Goniometer.GoniometerParameters goniometerParameters,
			DistortionProcessConfiguration distortionProcessConfiguration
			) {
			this.lwir16Reader= lwir16Reader;
			// 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;
			}



	@@ -459,6 +483,10 @@ horizontal axis:
	this.lwirReader.setMotorsPosition(this.goniometerParameters.goniometerMotors.getTargetPositions()); // Used target, not current to prevent minor variations		this.lwirReader.setMotorsPosition(this.goniometerParameters.goniometerMotors.getTargetPositions()); // Used target, not current to prevent minor variations
	this.lwirReader.reportTiming=debugTiming;		this.lwirReader.reportTiming=debugTiming;
	this.lwirReader.acquire(this.distortionProcessConfiguration.sourceDirectory); // true - use lasers, updateStatus - make false?		this.lwirReader.acquire(this.distortionProcessConfiguration.sourceDirectory); // true - use lasers, updateStatus - make false?
			} else if (lwir16Reader != null) {
			this.lwir16Reader.setMotorsPosition(this.goniometerParameters.goniometerMotors.getTargetPositions()); // Used target, not current to prevent minor variations
			this.lwir16Reader.reportTiming=debugTiming;
			this.lwir16Reader.acquire(this.distortionProcessConfiguration.sourceDirectory); // true - use lasers, updateStatus - make false?
	} else {		} else {
	System.out.println("Neignter traditional camera/rig, no LWIR rig are initialized, dry run");		System.out.println("Neignter traditional camera/rig, no LWIR rig are initialized, dry run");
	}		}

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

+3 −1

Original line number	Original line	Diff line number	Diff line
	@@ -4793,7 +4793,7 @@ public class MatchSimulatedPattern {
	// process		// process
	final double[] bPattern, final double[] windowFunction, final double[] windowFunctionCorr,		final double[] bPattern, final double[] windowFunction, final double[] windowFunctionCorr,
	final double[] windowFunctionCorr2, final double[] windowFunctionCorr4, final double[][] locsNeib, // which		final double[] windowFunctionCorr2, final double[] windowFunctionCorr4, final double[][] locsNeib, // which
	// neibors		// neighbors
	// to		// to
	// try		// try
	// (here		// (here
	@@ -6919,6 +6919,8 @@ public class MatchSimulatedPattern {
	noMessageBoxes);		noMessageBoxes);
	}		}



	// ====== end of calculateDistortions()		// ====== end of calculateDistortions()
	// ==============================================		// ==============================================
	/**		/**

src/main/java/com/elphel/imagej/common/GenericJTabbedDialog.java

+2 −2

Original line number	Original line	Diff line number	Diff line
	@@ -318,7 +318,7 @@ public class GenericJTabbedDialog implements ActionListener {

	@Override		@Override
	public void actionPerformed(ActionEvent e) {		public void actionPerformed(ActionEvent e) {
	System.out.println(e.getActionCommand());		// System.out.println(e.getActionCommand());
	if (e.getActionCommand().equals("Cancel")) {		if (e.getActionCommand().equals("Cancel")) {
	result = e.getActionCommand();		result = e.getActionCommand();
	jd.dispose();		jd.dispose();
	@@ -409,7 +409,7 @@ public class GenericJTabbedDialog implements ActionListener {
	}		}


	System.out.println(combo.getSelectedItem());		// System.out.println(combo.getSelectedItem());
	// for (int i = 0; i < selectedItem.length; i++){		// for (int i = 0; i < selectedItem.length; i++){
	// System.out.println(String.format("item %s = %s", i, selectedItem[i]));		// System.out.println(String.format("item %s = %s", i, selectedItem[i]));
	// }		// }

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