Adding goniometer motors initialization/control (80f959fc) · Commits · Elphel / imagej-elphel

src/main/java/Aberration_Calibration.java

+32 −0

Original line number	Original line	Diff line number	Diff line
	@@ -817,6 +817,7 @@ if (MORE_BUTTONS) {
	panelGoniometer = new Panel();		panelGoniometer = new Panel();
	panelGoniometer.setLayout(new GridLayout(1, 0, 5, 5));		panelGoniometer.setLayout(new GridLayout(1, 0, 5, 5));
	addButton("Configure Goniometer",panelGoniometer,color_configure);		addButton("Configure Goniometer",panelGoniometer,color_configure);
			addButton("Goniometer Move",panelGoniometer,color_debug);
	addButton("Goniometer Scan",panelGoniometer,color_conf_process);		addButton("Goniometer Scan",panelGoniometer,color_conf_process);
	addButton("Filter Grids",panelGoniometer,color_bundle);		addButton("Filter Grids",panelGoniometer,color_bundle);
	addButton("Update Image Set",panelGoniometer);		addButton("Update Image Set",panelGoniometer);
	@@ -5806,6 +5807,37 @@ if (MORE_BUTTONS) {
	return;		return;
	}		}
	/* ======================================================================== */		/* ======================================================================== */
			if (label.equals("Goniometer Move")) {
			DEBUG_LEVEL=MASTER_DEBUG_LEVEL;

			CAMERAS.setNumberOfThreads(THREADS_MAX);
			CAMERAS.debugLevel=DEBUG_LEVEL;

			if (GONIOMETER==null) {
			GONIOMETER= new Goniometer(
			CAMERAS, // CalibrationHardwareInterface.CamerasInterface cameras,
			DISTORTION, //MatchSimulatedPattern.DistortionParameters distortion,
			PATTERN_DETECT, //MatchSimulatedPattern.PatternDetectParameters patternDetectParameters,
			EYESIS_CAMERA_PARAMETERS, //Distortions.EyesisCameraParameters eyesisCameraParameters,
			LASER_POINTERS, // MatchSimulatedPattern.LaserPointer laserPointers
			SIMUL, //SimulationPattern.SimulParameters simulParametersDefault,
			GONIOMETER_PARAMETERS, //LensAdjustment.FocusMeasurementParameters focusMeasurementParameters,
			DISTORTION_PROCESS_CONFIGURATION
			);
			if (DEBUG_LEVEL>1){
			System.out.println("Initiaslizing Goniometer class");
			}
			} else if (DEBUG_LEVEL>1){
			System.out.println("GONIOMETER was initialized");
			}

			while (GONIOMETER.manualMove(
			this.SYNC_COMMAND.stopRequested,
			UPDATE_STATUS));

			return;
			}
			/* ======================================================================== */
	if (label.equals("Goniometer Scan")) {		if (label.equals("Goniometer Scan")) {
	DEBUG_LEVEL=MASTER_DEBUG_LEVEL;		DEBUG_LEVEL=MASTER_DEBUG_LEVEL;

src/main/java/CalibrationHardwareInterface.java

+87 −3

Original line number	Original line	Diff line number	Diff line
	@@ -2532,7 +2532,44 @@ public class CalibrationHardwareInterface {
	private long nanoReferenceTime; // last time the position was checked		private long nanoReferenceTime; // last time the position was checked
	private int []referencePosition=null;		private int []referencePosition=null;
	private double motorsStuckTestTime=5.0; // seconds		private double motorsStuckTestTime=5.0; // seconds
			private boolean motorsInitialized=false;
			public int tiltMotor=2; // 0-1-2
			public int axialMotor=1; // 0-1-2


			/**
			* Tries to initialize motors if needed. Assumes that non-initialized motors were not tried to be moved
			* @param force unconditionally try to initialize
			* @return
			*/
			public boolean tryInit(
			boolean force,
			boolean updateStatus){
			int delta=4;
			if (!force) {
			if (motorsInitialized) return true;
			updateMotorsPosition();
			if ((Math.abs(curpos[tiltMotor])>2) \|\| (Math.abs(curpos[axialMotor])>2)){
			motorsInitialized=true;
			return true;
			}
			System.out.println("Trying to move axial motor to see if it is initialized ...");
			motorsInitialized=true; // to avoid loop
			int newpos=curpos[axialMotor]+delta;
			if (moveMotorSetETA(axialMotor, newpos)) {
			if (waitMotor(axialMotor, null, true, updateStatus)) {// no interaction
			moveMotorSetETA(axialMotor, newpos-delta); // restore original
			if (waitMotor(axialMotor, null, true, updateStatus)) {// no interaction
			return true; // should be always true here
			}
			}
			}
			motorsInitialized=false;
			}
			initMotors();
			motorsInitialized=true;
			return true;
			}
	// TODO: Enable simultaneous motors		// TODO: Enable simultaneous motors

	public boolean moveMotorSetETA(int motorNumber, int position){		public boolean moveMotorSetETA(int motorNumber, int position){
	@@ -2550,6 +2587,17 @@ public class CalibrationHardwareInterface {
	return false;		return false;

	}		}
			if (!motorsInitialized) { // may be called from tryInit(), but with motorsInitialized set to true;
			if (!tryInit(false, true)){ // do not force, update status
			String msg="Motors failed to initialize";
			System.out.println("Error: "+msg);
			IJ.showMessage("Error",msg);
			//throw new RuntimeException(msg);
			return false;
			}
			}
			// TODO: check init is needed

	updateMotorsPosition();		updateMotorsPosition();
	this.targetPosition[motorNumber]=position;		this.targetPosition[motorNumber]=position;
	this.nanoReferenceTime=System.nanoTime();		this.nanoReferenceTime=System.nanoTime();
	@@ -2559,7 +2607,12 @@ public class CalibrationHardwareInterface {
	return true;		return true;
	}		}

	public boolean waitMotor(int motorNumber){		public boolean waitMotor(
			int motorNumber,
			AtomicInteger stopRequested, // or null
			boolean quiet,
			boolean updateStatus
			){
	if ((motorNumber<0) \|\|(motorNumber>=this.motorsRange.length) \|\| (this.motorsRange[motorNumber]==null)){		if ((motorNumber<0) \|\|(motorNumber>=this.motorsRange.length) \|\| (this.motorsRange[motorNumber]==null)){
	String msg="Motor "+motorNumber+" is undefined";		String msg="Motor "+motorNumber+" is undefined";
	IJ.showMessage("Error",msg);		IJ.showMessage("Error",msg);
	@@ -2568,6 +2621,10 @@ public class CalibrationHardwareInterface {
	while (true) {		while (true) {
	enableMotors(true); // just in case?		enableMotors(true); // just in case?
	updateMotorsPosition(1); // wait one second before testing to decrease re-test frequency		updateMotorsPosition(1); // wait one second before testing to decrease re-test frequency
			if (updateStatus) {
			IJ.showStatus("Goniometer: tilt="+curpos[tiltMotor]+" ("+this.targetPosition[tiltMotor]+") "+
			", axial="+curpos[axialMotor]+" ("+this.targetPosition[axialMotor]+")");
			}
	int positionError= Math.abs(this.targetPosition[motorNumber]-this.curpos[motorNumber]);		int positionError= Math.abs(this.targetPosition[motorNumber]-this.curpos[motorNumber]);
	if (positionError<this.motorTolerance){		if (positionError<this.motorTolerance){
	updateMotorsPosition(1); // re-test		updateMotorsPosition(1); // re-test
	@@ -2576,13 +2633,29 @@ public class CalibrationHardwareInterface {
	return true;		return true;
	}		}
	long nanoNow=System.nanoTime();		long nanoNow=System.nanoTime();
			if ((stopRequested!=null) && (stopRequested.get()>1)){
			enableMotors(false);
			if (this.debugLevel>0) System.out.println("User interrupt");
			stopRequested.set(0);
			updateMotorsPosition(1);
			String msg="Goniometer: tilt="+curpos[tiltMotor]+" ("+this.targetPosition[tiltMotor]+") "+
			", axial="+curpos[axialMotor]+" ("+this.targetPosition[axialMotor]+")\n"+
			"OK to continue, Cancel to abort movement";
			if (!IJ.showMessageWithCancel("Goniometer interrupted", msg)) {
			return false;
			}
			enableMotors(true);
			this.nanoETA += System.nanoTime()-nanoNow;
			}
	if (nanoNow>this.nanoETA) {		if (nanoNow>this.nanoETA) {
	enableMotors(false);		enableMotors(false);
			if (quiet) return false;
	String msg="Motor "+motorNumber+" failed to reach destination "+this.targetPosition[motorNumber]+		String msg="Motor "+motorNumber+" failed to reach destination "+this.targetPosition[motorNumber]+
	", current position is "+this.curpos[motorNumber]+		", current position is "+this.curpos[motorNumber]+
	"\nYou may try to manually fix the problem before hitting OK";		"\nYou may try to manually fix the problem before hitting OK";
	System.out.println ("Error:"+msg);		System.out.println ("Error:"+msg);
	IJ.showMessage("Error",msg);		IJ.showMessage("Error",msg);
			// if (IJ.showMessageWithCancel("Goniometer did not move", msg+"\n OK will try to initialize ");
	// Give chance to manually fix the problem		// Give chance to manually fix the problem
	updateMotorsPosition();		updateMotorsPosition();
	positionError= Math.abs(this.targetPosition[motorNumber]-this.curpos[motorNumber]);		positionError= Math.abs(this.targetPosition[motorNumber]-this.curpos[motorNumber]);
	@@ -2596,6 +2669,7 @@ public class CalibrationHardwareInterface {
	if ((nanoNow-this.nanoReferenceTime)> ((long) (this.motorsStuckTestTime*1E9))){		if ((nanoNow-this.nanoReferenceTime)> ((long) (this.motorsStuckTestTime*1E9))){
	if(Math.abs(this.referencePosition[motorNumber]-this.curpos[motorNumber]) < motorStuckTolerance){		if(Math.abs(this.referencePosition[motorNumber]-this.curpos[motorNumber]) < motorStuckTolerance){
	enableMotors(false);		enableMotors(false);
			if (quiet) return false;
	String msg="Motor "+motorNumber+" is stuck at "+this.curpos[motorNumber]+". "+		String msg="Motor "+motorNumber+" is stuck at "+this.curpos[motorNumber]+". "+
	this.motorsStuckTestTime+" seconds ago it was at "+this.referencePosition[motorNumber]+		this.motorsStuckTestTime+" seconds ago it was at "+this.referencePosition[motorNumber]+
	", target position is "+this.targetPosition[motorNumber]+		", target position is "+this.targetPosition[motorNumber]+
	@@ -2619,6 +2693,10 @@ public class CalibrationHardwareInterface {
	}		}

	// first check tolerance, then - if motor is stuck		// first check tolerance, then - if motor is stuck
			public int [] getCurrentPositions(){
			updateMotorsPosition();
			return this.curpos;
			}

	public int [] getTargetPositions(){		public int [] getTargetPositions(){
	return this.targetPosition;		return this.targetPosition;
	@@ -2626,6 +2704,12 @@ public class CalibrationHardwareInterface {
	public int[] enableMotors(boolean enable) {		public int[] enableMotors(boolean enable) {
	return commandElphel10364Motors("http://"+this.ipAddress+"/10364.php?"+(enable?"enable":"disable"));		return commandElphel10364Motors("http://"+this.ipAddress+"/10364.php?"+(enable?"enable":"disable"));
	}		}
			public int[] initMotors() {
			return commandElphel10364Motors("http://"+this.ipAddress+"/10364.php?init");
			}
			public int[] setHome() {
			return commandElphel10364Motors("http://"+this.ipAddress+"/10364.php?m1=0&m2=0&m3=0&reset");
			}

	public int[] updateMotorsPosition() {		public int[] updateMotorsPosition() {
	return commandElphel10364Motors("http://"+this.ipAddress+"/10364.php");		return commandElphel10364Motors("http://"+this.ipAddress+"/10364.php");

src/main/java/Distortions.java

+2 −2

Original line number	Original line	Diff line number	Diff line
	@@ -3851,9 +3851,9 @@ List calibration
	for (int i=0;i<imageSets.length;i++) availableSets[i]= !allNaNInSet[i]; //!Double.isNaN(rmsPerSet[i]);		for (int i=0;i<imageSets.length;i++) availableSets[i]= !allNaNInSet[i]; //!Double.isNaN(rmsPerSet[i]);
	if (removeEmptySets && (numNaN>0)){ //(this.debugLevel>0)		if (removeEmptySets && (numNaN>0)){ //(this.debugLevel>0)
	if (this.debugLevel>0) System.out.println("removeOutLayerSets(): Number of empty (rms=NaN) sets="+numNaN+":");		if (this.debugLevel>0) System.out.println("removeOutLayerSets(): Number of empty (rms=NaN) sets="+numNaN+":");
	int n=0;		// int n=0;
	for (int setNum=0;setNum<imageSets.length;setNum++) if (!availableSets[setNum]){		for (int setNum=0;setNum<imageSets.length;setNum++) if (!availableSets[setNum]){
	n++;		// n++;
	if (this.debugLevel>0) System.out.println("Set "+setNum);		if (this.debugLevel>0) System.out.println("Set "+setNum);
	for (int imgInSet=0;imgInSet<imageSets[setNum].length;imgInSet++){		for (int imgInSet=0;imgInSet<imageSets[setNum].length;imgInSet++){
	int numImg=imageSets[setNum][imgInSet];		int numImg=imageSets[setNum][imgInSet];

src/main/java/Goniometer.java

+123 −5

Original line number	Original line	Diff line number	Diff line
	@@ -94,7 +94,122 @@ horizontal axis:
	}		}

	//goniometerMotors		//goniometerMotors
			private enum MOT_ACT {
			MOVE_SPEC,
			HOME,
			TILT_P85,
			TILT_M85,
			RCW200,
			RCCW200,
			SET_HOME};
			private final String [] options={
			"Move to specified position",
			"Move home",
			"Tilt to target 85 degrees",
			"Tilt from target 85 degrees",
			"Rotate to clockwise 200 degrees",
			"Rotate to counter-clockwise 200 degrees",
			"set current position as new home"};


			public boolean manualMove(
			AtomicInteger stopRequested, // 1 - stop now, 2 - when convenient
			boolean updateStatus){
			int tiltMotor=2; // 0-1-2
			int axialMotor=1; // 0-1-2
			boolean needsInit=false;

			int [] currentMotors=this.goniometerParameters.goniometerMotors.getCurrentPositions();
			double currentTilt=currentMotors[tiltMotor]/this.goniometerParameters.goniometerMotors.stepsPerDegreeTilt;
			double currentAxial=currentMotors[axialMotor]/this.goniometerParameters.goniometerMotors.stepsPerDegreeAxial;
			currentTilt=0.1Math.round(10.0currentTilt);
			currentAxial=0.1Math.round(10.0currentAxial);
			this.goniometerParameters.goniometerMotors.debugLevel=this.debugLevel+1;
			System.out.println(
			"Current position:\n"+
			"Tilt: "+IJ.d2s(currentTilt,1)+" degrees ("+currentMotors[tiltMotor]+" steps)\n"+
			"Axial: "+IJ.d2s(currentAxial,1)+" degrees ("+currentMotors[axialMotor]+" steps)\n");

			GenericDialog gd = new GenericDialog("User interrupt");

			gd.addRadioButtonGroup("Select action", options, 7, 1, options[0]);
			gd.addNumericField("Goniometer tilt angle", currentTilt, 1,5,"degrees");
			gd.addNumericField("Goniometer axial angle", currentAxial, 1,5,"degrees");
			gd.addCheckbox("Initialize goniometer motor driver",needsInit);
			gd.showDialog();
			if (gd.wasCanceled()) return false;
			String selectedAction=gd.getNextRadioButton();
			currentTilt= gd.getNextNumber();
			currentAxial= gd.getNextNumber();
			needsInit= gd.getNextBoolean();
			if (needsInit){
			if (!this.goniometerParameters.goniometerMotors.tryInit(true,updateStatus)){
			String msg="Failed to initialize goniometer motor driver";
			System.out.println("Error: "+msg);
			IJ.showMessage("Error",msg);
			return false; // failed initialization
			}
			}
			if (selectedAction.equals(options[MOT_ACT.SET_HOME.ordinal()])){
			if (this.goniometerParameters.goniometerMotors.setHome()==null){
			String msg="Failed to set new home position";
			System.out.println("Error: "+msg);
			IJ.showMessage("Error",msg);
			return false; // failed set home
			}
			return true;
			}
			MOT_ACT act=MOT_ACT.MOVE_SPEC;
			for (MOT_ACT a: MOT_ACT.values()){
			if (selectedAction.equals(options[a.ordinal()])){
			act=a;
			break;
			}
			}
			double targetTilt=currentTilt;
			double targetAxial=currentAxial;
			switch (act) {
			case HOME:
			targetTilt=0;
			targetAxial=0;
			act=MOT_ACT.MOVE_SPEC;
			break;
			case TILT_P85:
			targetTilt=85.0;
			act=MOT_ACT.MOVE_SPEC;
			break;
			case TILT_M85:
			targetTilt=-85.0;
			act=MOT_ACT.MOVE_SPEC;
			break;
			case RCW200:
			targetAxial=200.0;
			act=MOT_ACT.MOVE_SPEC;
			break;
			case RCCW200:
			targetAxial=-200.0;
			act=MOT_ACT.MOVE_SPEC;
			break;
			default:
			break;
			}
			if (act!=MOT_ACT.MOVE_SPEC){
			String msg="Program BUG, action "+selectedAction+" can not be processed";
			System.out.println("Error: "+msg);
			IJ.showMessage("Error",msg);
			return false;
			}
			int tiltMotorPosition= (int) Math.round(targetTilt*this.goniometerParameters.goniometerMotors.stepsPerDegreeTilt);
			int axialMotorPosition= (int) Math.round(targetAxial*this.goniometerParameters.goniometerMotors.stepsPerDegreeAxial);
			boolean OK= motorsMove(
			tiltMotor,
			axialMotor,
			tiltMotorPosition,
			axialMotorPosition,
			stopRequested,
			updateStatus);
			return OK;
			}
	public boolean scanAndAcquire(		public boolean scanAndAcquire(
	double targetAngleHorizontal,		double targetAngleHorizontal,
	double targetAngleVertical,		double targetAngleVertical,
	@@ -270,7 +385,7 @@ horizontal axis:
	IJ.showMessage("Error",msg);		IJ.showMessage("Error",msg);
	return false;		return false;
	}		}
	OK=this.goniometerParameters.goniometerMotors.waitMotor(tiltMotor);		OK=this.goniometerParameters.goniometerMotors.waitMotor(tiltMotor, null, false,updateStatus); // no interrupts during movement
	if (!OK) {		if (!OK) {
	String msg="Motor "+(tiltMotor+1)+" failed to reach "+tiltMotorPosition+".";		String msg="Motor "+(tiltMotor+1)+" failed to reach "+tiltMotorPosition+".";
	System.out.println("Error: "+msg);		System.out.println("Error: "+msg);
	@@ -297,7 +412,7 @@ horizontal axis:
	IJ.showMessage("Error",msg);		IJ.showMessage("Error",msg);
	return false;		return false;
	}		}
	OK=this.goniometerParameters.goniometerMotors.waitMotor(axialMotor);		OK=this.goniometerParameters.goniometerMotors.waitMotor(axialMotor, null, false,updateStatus);
	if (!OK) {		if (!OK) {
	String msg="Motor "+(axialMotor+1)+" failed to reach "+axialMotorPosition+".";		String msg="Motor "+(axialMotor+1)+" failed to reach "+axialMotorPosition+".";
	System.out.println("Error: "+msg);		System.out.println("Error: "+msg);
	@@ -328,6 +443,7 @@ horizontal axis:
	axialMotor,		axialMotor,
	0, //tiltMotorPosition,		0, //tiltMotorPosition,
	0, //axialMotorPosition,		0, //axialMotorPosition,
			null, // no interrupts
	updateStatus);		updateStatus);
	return false;		return false;
	}		}
	@@ -341,6 +457,7 @@ horizontal axis:
	axialMotor,		axialMotor,
	0, //tiltMotorPosition,		0, //tiltMotorPosition,
	0, //axialMotorPosition,		0, //axialMotorPosition,
			null, // no interrupts
	updateStatus);		updateStatus);
	if (this.debugLevel>0) System.out.println("Scan finished in "+IJ.d2s(1E-9*(System.nanoTime()-startTime),3)+" seconds.");		if (this.debugLevel>0) System.out.println("Scan finished in "+IJ.d2s(1E-9*(System.nanoTime()-startTime),3)+" seconds.");

	@@ -352,8 +469,9 @@ horizontal axis:
	int axialMotor,		int axialMotor,
	int tiltMotorPosition,		int tiltMotorPosition,
	int axialMotorPosition,		int axialMotorPosition,
			AtomicInteger stopRequested, // or null
	boolean updateStatus){		boolean updateStatus){
	String status="Movin axial motor to "+axialMotorPosition+"...";		String status="Moving axial motor to "+axialMotorPosition+"...";
	if (updateStatus) IJ.showStatus(status);		if (updateStatus) IJ.showStatus(status);
	boolean OK= this.goniometerParameters.goniometerMotors.moveMotorSetETA(axialMotor, axialMotorPosition);		boolean OK= this.goniometerParameters.goniometerMotors.moveMotorSetETA(axialMotor, axialMotorPosition);
	if (!OK) {		if (!OK) {
	@@ -362,7 +480,7 @@ horizontal axis:
	IJ.showMessage("Error",msg);		IJ.showMessage("Error",msg);
	return false;		return false;
	}		}
	OK=this.goniometerParameters.goniometerMotors.waitMotor(axialMotor);		OK=this.goniometerParameters.goniometerMotors.waitMotor(axialMotor, stopRequested, false,updateStatus);
	if (!OK) {		if (!OK) {
	String msg="Motor "+(axialMotor+1)+" failed to reach "+axialMotorPosition+".";		String msg="Motor "+(axialMotor+1)+" failed to reach "+axialMotorPosition+".";
	System.out.println("Error: "+msg);		System.out.println("Error: "+msg);
	@@ -376,7 +494,7 @@ horizontal axis:
	IJ.showMessage("Error",msg);		IJ.showMessage("Error",msg);
	return false;		return false;
	}		}
	OK=this.goniometerParameters.goniometerMotors.waitMotor(tiltMotor);		OK=this.goniometerParameters.goniometerMotors.waitMotor(tiltMotor,stopRequested, false, updateStatus);
	if (!OK) {		if (!OK) {
	String msg="Motor "+(tiltMotor+1)+" failed to reach "+tiltMotorPosition+".";		String msg="Motor "+(tiltMotor+1)+" failed to reach "+tiltMotorPosition+".";
	System.out.println("Error: "+msg);		System.out.println("Error: "+msg);

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