Grid matching for secondary (LWIR) sensors (5e90425c) · Commits · Elphel / imagej-elphel

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

+149 −20

Original line number	Diff line number	Diff line
		@@ -501,7 +501,7 @@ public static MatchSimulatedPattern.DistortionParameters DISTORTION =new MatchSi
		4, // int decimateMasks
		0.1, // double badNodeThreshold=0.1; // filter out grid nodes with difference from quadratically predicted from 8 neighbors in pixels
		1, // int maxBadNeighb; // maximal number of bad nodes around the corrected one to fix
		50, // int minimalValidNodes
		10, // int minimalValidNodes
		1, // int weightMultiImageMode=1; // increase weight for multi-image sets (0 - do not increase, 1 - multiply by number of images in a set)
		1.0, // public double weightMultiExponent= 1.0; // if( >0) use grid diameter to scale weights of this image
		1.0, // public double weightDiameterExponent=1.0;
		@@ -511,7 +511,8 @@ public static MatchSimulatedPattern.DistortionParameters DISTORTION =new MatchSi
		0.5, // public double shrinkBlurLevel = 0.5;
		-1.0, // double balanceChannelWeightsMode
		2.0, // public double removeOverRMS=2.0; // error is multiplied by weight function before comparison (more permissive on the borders
		4.0 //public double removeOverRMSNonweighted=4.0; // error is not multiplied (no more permissions on tyhe borders
		4.0, //public double removeOverRMSNonweighted=4.0; // error is not multiplied (no more permissions on tyhe borders
		true // boolean invertUnmarkedLwirGrid
		);

		//
		@@ -1020,6 +1021,7 @@ if (MORE_BUTTONS) {
		addButton("Import Subsystem", panelLWIR,color_configure);
		addButton("Select LWIR grids", panelLWIR,color_configure);
		addButton("Grid offset", panelLWIR,color_process);
		addButton("LWIR to EO", panelLWIR,color_process);
		addButton("Manual hint", panelLWIR,color_configure);

		add(panelLWIR);
		@@ -2080,6 +2082,8 @@ if (MORE_BUTTONS) {
		double[][] gridDisplay=LENS_DISTORTIONS.prepareDisplayGrid();
		SDFA_INSTANCE.showArrays(gridDisplay,LENS_DISTORTIONS.getGridWidth(),LENS_DISTORTIONS.getGridHeight(), true, "Grid",
		LENS_DISTORTIONS.displayGridTitles());

		// Does not update pixelSize and DistortionRadius !!
		LENS_DISTORTIONS.calcGridOnSensor(0.0);
		double[][] gridDisplayOnSensor=LENS_DISTORTIONS.prepareDisplayGridOnSensor(false);
		SDFA_INSTANCE.showArrays(gridDisplayOnSensor,LENS_DISTORTIONS.getGridWidth(),LENS_DISTORTIONS.getGridHeight(), true, "GridOnSensor",
		@@ -2297,7 +2301,9 @@ if (MORE_BUTTONS) {
		if (LENS_DISTORTIONS.fittingStrategy==null) return;
		LENS_DISTORTIONS.fittingStrategy.debugLevel=DEBUG_LEVEL;

		LENS_DISTORTIONS.LevenbergMarquardt(true); // open dialog
		LENS_DISTORTIONS.LevenbergMarquardt(true, // open dialog
		false); // dry_run

		return;
		}
		/* ======================================================================== */
		@@ -3610,7 +3616,9 @@ if (MORE_BUTTONS) {
		LENS_DISTORTIONS.thresholdFinish=FOCUS_MEASUREMENT_PARAMETERS.thresholdFinish;
		LENS_DISTORTIONS.numIterations=FOCUS_MEASUREMENT_PARAMETERS.numIterations;

		LENS_DISTORTIONS.LevenbergMarquardt(false); // skip dialog
		LENS_DISTORTIONS.LevenbergMarquardt(
		false, // skip dialog
		false); // new: dry_run use it here?
		if (DEBUG_LEVEL>0) System.out.println("Finished LMA at "+ IJ.d2s(0.000000001*(System.nanoTime()-startTime),3));
		int stationNumber=0;
		// Read camera parameters
		@@ -3635,7 +3643,9 @@ if (MORE_BUTTONS) {
		LENS_DISTORTIONS.thresholdFinish=FOCUS_MEASUREMENT_PARAMETERS.thresholdFinish;
		LENS_DISTORTIONS.numIterations=FOCUS_MEASUREMENT_PARAMETERS.numIterations;

		LENS_DISTORTIONS.LevenbergMarquardt(false); // skip dialog
		LENS_DISTORTIONS.LevenbergMarquardt(
		false, // skip dialog
		false); // new: dry_run use it here?
		if (DEBUG_LEVEL>0) System.out.println("Finished second LMA at "+ IJ.d2s(0.000000001*(System.nanoTime()-startTime),3));
		if (!FOCUS_MEASUREMENT_PARAMETERS.keepCircularMask) {
		DISTORTION_CALIBRATION_DATA.calculateSensorMasks(); // TODO: save/restore original mask for channel 0
		@@ -5922,7 +5932,7 @@ if (MORE_BUTTONS) {
		return;
		}
		GenericDialog gd=new GenericDialog ("Select list mode");
		gd.addNumericField("Mode 0 - pointers, 1 - shift/Rots, 2 - points/extra, 3 - rms", 0, 0);
		gd.addNumericField("Mode 0 - pointers, 1 - shift/Rots, 2 - points/extra, 3 - rms", 3, 0);
		gd.showDialog();
		if (gd.wasCanceled()) return;
		int listMode= (int) gd.getNextNumber();
		@@ -6100,7 +6110,9 @@ if (MORE_BUTTONS) {
		LENS_DISTORTIONS.stopEachSeries= false; // will not ask for confirmation after done
		LENS_DISTORTIONS.stopOnFailure=false;
		LENS_DISTORTIONS.lambda=LENS_DISTORTIONS.fittingStrategy.lambdas[0]; // 0.001; // why it does not use fitting series lambda?
		boolean LMA_OK=LENS_DISTORTIONS.LevenbergMarquardt(false); // skip dialog
		boolean LMA_OK=LENS_DISTORTIONS.LevenbergMarquardt(
		false, // skip dialog
		false); // new: dry_run use it here?
		if (LMA_OK) {
		finalTilt[tiltIndex][axialIndex]=LENS_DISTORTIONS.fittingStrategy.distortionCalibrationData.gIS[imageSetNumber].goniometerTilt;
		finalAxial[tiltIndex][axialIndex]=LENS_DISTORTIONS.fittingStrategy.distortionCalibrationData.gIS[imageSetNumber].goniometerAxial;
		@@ -6177,7 +6189,9 @@ if (MORE_BUTTONS) {
		LENS_DISTORTIONS.stopEachStep= false;
		LENS_DISTORTIONS.stopEachSeries= false; // will not ask for confirmation after done
		LENS_DISTORTIONS.lambda=LENS_DISTORTIONS.fittingStrategy.lambdas[0];
		LENS_DISTORTIONS.LevenbergMarquardt(false); // skip dialog
		LENS_DISTORTIONS.LevenbergMarquardt(
		false, // skip dialog
		false); // new: dry_run use it here?

		// save safe settings to run LMA manually
		LENS_DISTORTIONS.seriesNumber= 0; // start from 0;
		@@ -9435,16 +9449,17 @@ if (MORE_BUTTONS) {
		calculateLwirGrids();
		return;
		}

		/* ======================================================================== */
		if (label.equals("Import Subsystem")) {
		importSystem(null, "EYESIS_CAMERA_PARAMETERS.");
		return;
		}

		/* ======================================================================== */
		if (label.equals("Select LWIR grids")) {
		selectLwirGrids(LWIR_PARAMETERS);
		return;
		}
		/* ======================================================================== */
		if (label.equals("Manual hint")) {
		DEBUG_LEVEL=MASTER_DEBUG_LEVEL;
		if (LENS_DISTORTIONS==null) {
		@@ -9466,12 +9481,19 @@ if (MORE_BUTTONS) {
		LENS_DISTORTIONS.manualGridHint(numGridImage);
		return;
		}

		/* ======================================================================== */
		if (label.equals("Grid offset")) {
		DEBUG_LEVEL=MASTER_DEBUG_LEVEL;
		offsetGrids(0, 0, null);
		return;
		}
		/* ======================================================================== */
		if (label.equals("LWIR to EO")) {
		DEBUG_LEVEL=MASTER_DEBUG_LEVEL;
		lwirToEo();
		return;
		}

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

		IJ.showMessage("Not yet implemented");
		@@ -9480,6 +9502,108 @@ if (MORE_BUTTONS) {
		}

		/* ===== Other methods ==================================================== */

		public boolean lwirToEo() {
		if (LENS_DISTORTIONS == null) {
		System.out.println("LENS_DISTORTIONS is null");
		return false;
		}
		if (PATTERN_PARAMETERS == null) {
		System.out.println("PATTERN_PARAMETERS is null");
		return false;
		}
		DistortionCalibrationData dcd = LENS_DISTORTIONS.getDistortionCalibrationData();
		if (dcd == null) {
		dcd = DISTORTION_CALIBRATION_DATA;
		}
		if (dcd == null) {
		System.out.println("dcd is null");
		return false;
		}

		int min_set = 0;
		int max_set = dcd.getNumSets()-1;
		boolean adjust_eo = false;
		boolean adjust_lwir = true;
		boolean use_lma = true;

		GenericDialog gd = new GenericDialog("Initial alignment of the secondary camera to the reference one");
		gd.addMessage("This command used Fitting Strategy[0] that should be set with all parameters but\n"+
		"GXYZ0 and GXYZ1 are set to 'fixed', and GXYZ0 and GXYZ1 are set to 'individual'.\n"+
		"Each selected set should already have GXYZ set correctly (e.g. by reference cameras)");
		gd.addNumericField("Image set start", min_set, 0);
		gd.addNumericField("Image set last", max_set, 0);
		gd.addCheckbox("Adjust EO (reference) sensors", adjust_eo);
		gd.addCheckbox("Adjust LWIR (target) sensors", adjust_lwir);
		gd.addCheckbox("Use LMA (unchecked - initial approximate grid setum by correlation)", use_lma);
		gd.showDialog();
		if (gd.wasCanceled()) return false;
		min_set = (int) gd.getNextNumber();
		max_set = (int) gd.getNextNumber();
		adjust_eo = gd.getNextBoolean();
		adjust_lwir = gd.getNextBoolean();
		use_lma = gd.getNextBoolean();
		if (!dcd.hasSmallSensors()) {
		String msg="This system does not have any LWIR or other dependent sub-cameras";
		IJ.showMessage("Error",msg);
		return false;
		}

		if (use_lma) {
		for (int num_set = min_set; num_set <=max_set; num_set++) if
		((dcd.gIS[num_set] != null) && (dcd.gIS[num_set].imageSet != null)) {
		for (int nc = 0; nc < dcd.getNumChannels(); nc++) {
		if (dcd.gIS[num_set].imageSet[nc]!= null) {
		int num_img = dcd.gIS[num_set].imageSet[nc].imgNumber;
		if (dcd.isSmallSensor(num_img)) {
		if (!adjust_lwir) {
		continue;
		}
		} else {
		if (!adjust_eo) {
		continue;
		}
		}
		int [] uvr = LENS_DISTORTIONS. findImageGridOffset(
		num_img,
		true, // boolean even, For first time - use parameter and parity of uv_rot
		PATTERN_PARAMETERS);
		if ((uvr != null) && ((uvr[0] != 0) \|\| (uvr[1] != 0))) {
		int [] uv_shift_rot = {uvr[0],uvr[1],0};
		// int [] new_uv_shift_rots =
		dcd.offsetGrid(
		num_img, // int img_num,
		uv_shift_rot,
		PATTERN_PARAMETERS);
		if (DEBUG_LEVEL > 0) {
		System.out.println(num_img+ "("+num_set+"."+nc+"): uv_shift = "+uvr[0]+":"+uvr[1]);
		}
		}
		}
		}


		}

		} else {

		for (int num_set = min_set; num_set <=max_set; num_set++) {
		int extra_search =2;
		double sigma = 5;


		dcd.initialSetLwirFromEO( //
		num_set,
		EYESIS_CAMERA_PARAMETERS.invertUnmarkedLwirGrid, // boolean invert_unmarked_grid,
		extra_search, // 2
		sigma, //5.0
		PATTERN_PARAMETERS,
		true); // debug
		}
		}
		return true;
		}

		public boolean offsetGrids(int ichoice, int inum, int [] uv_shift_rot) {
		if (LENS_DISTORTIONS == null) {
		System.out.println("LENS_DISTORTIONS is null");
		@@ -9517,7 +9641,7 @@ if (MORE_BUTTONS) {
		gd.addNumericField("Image/set number", inum, 0);
		gd.addCheckbox ("Auto calculate UV", auto);
		if (has_lwir) {
		gd.addCheckbox ("Auto from EO grid", true);
		gd.addCheckbox ("Auto from EO grid (calculatre from EO even if the requested image is LWIR)", false); //true
		}
		gd.addNumericField("Grid offset U", uv_shift_rot[0], 0);
		gd.addNumericField("Grid offset V", uv_shift_rot[1], 0);
		@@ -9580,11 +9704,17 @@ if (MORE_BUTTONS) {
		// find first enabled image
		for (int n:img_nums) {
		if (n >= 0) {
		int [] auto_uvr = dcd. suggestOffset (
		n, // int num_img,
		true, // boolean non_estimated,

		int [] auto_uvr = LENS_DISTORTIONS.findImageGridOffset( // null for now
		n,
		true, // boolean even,
		PATTERN_PARAMETERS); // PatternParameters patternParameters)

		// int [] auto_uvr = dcd. suggestOffset (
		// n, // int num_img,
		// true, // boolean non_estimated,
		// true, // boolean even,
		// PATTERN_PARAMETERS); // PatternParameters patternParameters)
		return offsetGrids(ichoice, inum, auto_uvr);
		}
		}
		@@ -9616,14 +9746,14 @@ if (MORE_BUTTONS) {
		LENS_DISTORTIONS=new Distortions(LENS_DISTORTION_PARAMETERS,PATTERN_PARAMETERS,REFINE_PARAMETERS,this.SYNC_COMMAND.stopRequested);
		int min_files = 8; // use folders that have all 8 files
		int lwir_chn0 = lwirReaderParameters.getLwirChn0();
		int vnir_chn0 = lwirReaderParameters.getVnirChn0();
		int eo_chn0 = lwirReaderParameters.getEoChn0();
		int numStations = 3;
		GenericDialog gd = new GenericDialog("Setup Goniometer/Camera Stations");
		gd.addMessage("Setting up calibration that includes multiple camera tripod or goniometer positions.");
		gd.addMessage("File selection dialog will open for each station separateley.");
		gd.addNumericField("Number of goniometer/camera stations", numStations,0);
		gd.addMessage("lwir_chn0 = "+lwir_chn0);
		gd.addMessage("vnir_chn0 = "+vnir_chn0);
		gd.addMessage("eo_chn0 = "+eo_chn0);
		gd.addMessage("min_files = "+min_files);

		gd.showDialog();
		@@ -9757,7 +9887,6 @@ if (MORE_BUTTONS) {
		matchSimulatedPattern.debugLevel=MASTER_DEBUG_LEVEL;
		String [] sourceSetList = DISTORTION_PROCESS_CONFIGURATION.selectSourceSets();
		LWIR_PARAMETERS.selectSourceChannels();
		// boolean [] sel_chn = LWIR_PARAMETERS.getSelectedVnir(); // start with regular cameras only
		boolean [] sel_chn = LWIR_PARAMETERS.getSelected();
		int numFiles = LWIR_PARAMETERS.getSourceFilesFlat(sourceSetList, sel_chn).length; // just the number
		String [][] sourceFilesList=LWIR_PARAMETERS.getSourceFiles(sourceSetList, sel_chn);

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

+255 −62

File changed.

Preview size limit exceeded, changes collapsed.

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

+169 −52

File changed.

Preview size limit exceeded, changes collapsed.

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

+9 −8

Original line number	Diff line number	Diff line
		@@ -1520,9 +1520,10 @@ I* - special case when the subcamera is being adjusted/replaced. How to deal wit
		for (;(endIndex<enabled.length) && !allImages && !enabled[endIndex];endIndex++); // advance over disabled images
		GenericDialog gd=new GenericDialog("Select images "+startIndex+"..."+(endIndex-1));
		for (int i=startIndex;i<endIndex;i++) if (allImages \|\| enabled[i]){
		gd.addCheckbox (i+" - "+(this.distortionCalibrationData.gIP[i].enabled?"":"(disabled) ")+
		gd.addCheckbox (i+ " ("+this.distortionCalibrationData.gIP[i].getSetNumber()+
		"."+this.distortionCalibrationData.gIP[i].getChannel()+")"+
		" - "+(this.distortionCalibrationData.gIP[i].enabled?"":"(disabled) ")+
		IJ.d2s(this.distortionCalibrationData.gIP[i].timestamp,6)+
		": "+this.distortionCalibrationData.gIP[i].channel+
		" matched "+this.distortionCalibrationData.gIP[i].matchedPointers+" pointers"+
		", hinted state: "+((hintedMatch[i]<0)?"undefined":((hintedMatch[i]==0)?"failed":((hintedMatch[i]==1)?"orientation":"orientation and translation"))),
		selection[i]);
		@@ -1852,7 +1853,7 @@ I* - special case when the subcamera is being adjusted/replaced. How to deal wit
		// gd.addCheckbox("Select images with estimated orientation", selectEstimated);
		// gd.addCheckbox("Select new enabled images", selectNewEnabled);
		if (this.distortionCalibrationData.hasSmallSensors()) {
		gd.addMessage("=== Filter selection by High/Low resolution sensors (such as VNIR/LWIR)");
		gd.addMessage("=== Filter selection by High/Low resolution sensors (such as EO/LWIR)");
		gd.addCheckbox("Select high-res sensors", true);
		gd.addCheckbox("Select low-res sensors", true);
		}
		@@ -1977,7 +1978,7 @@ I* - special case when the subcamera is being adjusted/replaced. How to deal wit
		* @param useParameters Select parameters for this series
		* @param askNextSeries Ask for next series number
		* @param zeroAndOther use 2 channels 0 and "other", propagate settings for channel 1 to all the rest
		* For low/high res (LWIR/VNIR) - use first /other for each class
		* For low/high res (LWIR/EO) - use first /other for each class
		* @return -2 - cancel, -1, done, otherwise - number of step to edit
		*/

		@@ -2055,7 +2056,7 @@ I* - special case when the subcamera is being adjusted/replaced. How to deal wit
		// sub(other): their group number - no, 0 - later add this.definedModesAll.length to master subcamera
		// not zeroAndOther:
		// non-sub - -1:
		// sub(>0): subCam-1 (previous index) - will suggest any with smaller index - may be useless with lwir < vnir indices
		// sub(>0): subCam-1 (previous index) - will suggest any with smaller index - may be useless with lwir < eo indices
		// int subMaxNum = (this.distortionCalibrationData.isSubcameraParameter(parIndex) && (subCam > 0)) ? (zeroAndOther? 0 : (subCam-1)):-1;
		int subMaxNum = -1;
		if (this.distortionCalibrationData.isSubcameraParameter(parIndex)) { // only for subcamera parameters
		@@ -2120,7 +2121,7 @@ I* - special case when the subcamera is being adjusted/replaced. How to deal wit
		* @param useParameters Select parameters for this series
		* @param askNextSeries Ask for next series number
		* @param zeroAndOther use 2 channels 0 and "other", propagate settings for channel 1 to all the rest
		* Updated for more groups (up to 4 in LWIR/VNIR) - use 1 channel for each group, propagate to the rest of the group
		* Updated for more groups (up to 4 in LWIR/EO) - use 1 channel for each group, propagate to the rest of the group
		* @return -2 - cancel, -1, done, otherwise - number of step to edit
		*/
		public int selectStrategyStep(
		@@ -2187,7 +2188,7 @@ I* - special case when the subcamera is being adjusted/replaced. How to deal wit
		for (int i=0;i<this.distortionCalibrationData.eyesisCameraParameters.numStations;i++) gd.addCheckbox("Station "+i, constrainByStation[i]);
		}
		if (this.distortionCalibrationData.hasSmallSensors()) {
		gd.addMessage("Constrain (select/remove all) by High/Low resolution sensors (such as VNIR/LWIR)");
		gd.addMessage("Constrain (select/remove all) by High/Low resolution sensors (such as EO/LWIR)");
		gd.addCheckbox("Select high-res sensors", true);
		gd.addCheckbox("Select low-res sensors", true);
		}
		@@ -2272,7 +2273,7 @@ I* - special case when the subcamera is being adjusted/replaced. How to deal wit
		// sub(other): their group number - no, 0
		// not zeroAndOther:
		// non-sub - -1:
		// sub(>0): subCam-1 (previous index) - will suggest any with smaller index - may be useless with lwir < vnir indices
		// sub(>0): subCam-1 (previous index) - will suggest any with smaller index - may be useless with lwir < eo indices
		// int subMaxNum = (this.distortionCalibrationData.isSubcameraParameter(parIndex) && (subCam > 0)) ? (zeroAndOther? 0 : (subCam-1)):-1;
		int subMaxNum = -1;
		if (this.distortionCalibrationData.isSubcameraParameter(parIndex)) { // only for subcamera parameters

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

+3 −1

Original line number	Diff line number	Diff line
		@@ -989,7 +989,9 @@ horizontal axis:
		// TODO: Set initial values for the goniometer angles from the sensor
		// (channel) number, average them if there are several in the list

		lensDistortions.LevenbergMarquardt(false); // skip dialog
		lensDistortions.LevenbergMarquardt(
		false, // skip dialog
		false); // new: dry_run use it here?
		if (debug_level > 0)
		System.out.println("Finished LMA at "
		+ IJ.d2s(0.000000001 * (System.nanoTime() - startTime), 3));

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