making grid calculation work for VNIR cameras and large cells (9f0c8d98) · Commits · Elphel / imagej-elphel

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

+30 −17

Original line number	Original line	Diff line number	Diff line
	@@ -375,11 +375,13 @@ public static MatchSimulatedPattern.DistortionParameters DISTORTION =new MatchSi
	8.0, // 3.0, // correlationMaxOffset, // maximal distance between predicted and actual pattern node		8.0, // 3.0, // correlationMaxOffset, // maximal distance between predicted and actual pattern node
	3.0, // 2.0, // increase back to .5? was needed with fisheye. 5.0, // double correlationMinContrast, // minimal contrast for the pattern to pass		3.0, // 2.0, // increase back to .5? was needed with fisheye. 5.0, // double correlationMinContrast, // minimal contrast for the pattern to pass
	3.5, // 2.5, // correlationMinInitialContrast, // minimal contrast for the pattern of the center (initial point)		3.5, // 2.5, // correlationMinInitialContrast, // minimal contrast for the pattern of the center (initial point)
	1.0, //this.correlationMinAbsoluteContrast, // minimal contrast for the pattern to pass, does not compensate for low ligt		// Absolute contrast is broken (05.29.2019), disabling it
			0.0, // 1.0, //this.correlationMinAbsoluteContrast, // minimal contrast for the pattern to pass, does not compensate for low ligt
	// TODO: adjust to a reasonable number		// TODO: adjust to a reasonable number
	1.0, //this.correlationMinAbsoluteInitialContrast, // minimal contrast for the pattern of the center (initial point)		0.0, // 1.0, //this.correlationMinAbsoluteInitialContrast, // minimal contrast for the pattern of the center (initial point)

	0.8, // scaleFirstPassContrast, // Decrease contrast of cells that are too close to the border to be processed in refinement pass		0.8, // scaleFirstPassContrast, // Decrease contrast of cells that are too close to the border to be processed in refinement pass
			2.0, // public double contrastSelectSigmaCenter; // Gaussian sigma to select correlation centers (fraction of UV period), 0.02 (center spot)
	0.1, // contrastSelectSigma, // Gaussian sigma to select correlation centers (fraction of UV period), 0.1		0.1, // contrastSelectSigma, // Gaussian sigma to select correlation centers (fraction of UV period), 0.1
	0.5, //contrastAverageSigma, // Gaussian sigma to average correlation variations (as contrast reference) 0.5		0.5, //contrastAverageSigma, // Gaussian sigma to average correlation variations (as contrast reference) 0.5

	@@ -9486,14 +9488,16 @@ if (MORE_BUTTONS) {
	for (int nfile = 0; nfile < sourceFilesList[nset].length; nfile++) if (sourceFilesList[nset][nfile] != null){		for (int nfile = 0; nfile < sourceFilesList[nset].length; nfile++) if (sourceFilesList[nset][nfile] != null){
	long startFileTime=System.nanoTime();		long startFileTime=System.nanoTime();
	if (DEBUG_LEVEL>0){		if (DEBUG_LEVEL>0){
	System.out.println(IJ.d2s(0.000000001*(System.nanoTime()-startTime),3)+"s: Processing file # "+(this_file+1)+		System.out.println(IJ.d2s(0.000000001*(System.nanoTime()-startTime),3)+"s: Processing set "+(nset+1) +" (of "+
	" (of "+ sourceFilesList.length+"): " + numFiles);		sourceFilesList.length+"), channel # "+(nfile + 1)+
			" (of "+ sourceFilesList[nset].length+"), file " +(this_file + 1)+" (of "+ numFiles+ ") - "+sourceFilesList[nset][nfile]);
	}		}
			String grid_path = null;
	if (saveGrids && !overwriteGrids){ // check if result already exists		if (saveGrids && !overwriteGrids){ // check if result already exists
	i = sourceFilesList[nset][nfile].lastIndexOf('/');		i = sourceFilesList[nset][nfile].lastIndexOf('/');
	if (i>0){		if (i>0){
	String grid_name = prefix+sourceFilesList[nset][nfile].substring(i+1);		String grid_name = prefix+sourceFilesList[nset][nfile].substring(i+1);
	String grid_path = gridSetPath + Prefs.getFileSeparator() + grid_name;		grid_path = gridSetPath + Prefs.getFileSeparator() + grid_name;
	if ((new File(grid_path)).exists()){		if ((new File(grid_path)).exists()){
	if (DEBUG_LEVEL>0) System.out.println("-->>> Skipping existing "+grid_path+" (as requested in \"Configure Process Distortions\")");		if (DEBUG_LEVEL>0) System.out.println("-->>> Skipping existing "+grid_path+" (as requested in \"Configure Process Distortions\")");
	continue;		continue;
	@@ -9543,6 +9547,10 @@ if (MORE_BUTTONS) {
	imp_sel, // image to process		imp_sel, // image to process
	THREADS_MAX);		THREADS_MAX);
	ImagePlus imp_calibrated=matchSimulatedPattern.getCalibratedPatternAsImage(imp_sel,prefix, numAbsolutePoints);		ImagePlus imp_calibrated=matchSimulatedPattern.getCalibratedPatternAsImage(imp_sel,prefix, numAbsolutePoints);
			if (imp_calibrated == null) {
			if (DEBUG_LEVEL> -1) System.out.println("Grid is empty !");
			continue;
			}
	if (DISTORTION_PROCESS_CONFIGURATION.showGridImages) imp_calibrated.show();		if (DISTORTION_PROCESS_CONFIGURATION.showGridImages) imp_calibrated.show();
	if (saveGrids){		if (saveGrids){
	FileSaver fs=new FileSaver(imp_calibrated);		FileSaver fs=new FileSaver(imp_calibrated);
	@@ -9550,10 +9558,11 @@ if (MORE_BUTTONS) {
	if (srcDir==null){		if (srcDir==null){
	saveGrids=false; // do not ask about the next ones too		saveGrids=false; // do not ask about the next ones too
	} else {		} else {
	String path=DISTORTION_PROCESS_CONFIGURATION.gridDirectory+Prefs.getFileSeparator()+imp_calibrated.getTitle();		// String path=DISTORTION_PROCESS_CONFIGURATION.gridDirectory+Prefs.getFileSeparator()+imp_calibrated.getTitle();
	if (UPDATE_STATUS) IJ.showStatus("Saving "+path);		// String path = gridDir + Prefs.getFileSeparator() + set_name+Prefs.getFileSeparator()+imp_calibrated.getTitle();
	if (DEBUG_LEVEL>0) System.out.println("-->>> Saving "+path+" - using "+numAbsolutePoints+" laser pointer references");		if (UPDATE_STATUS) IJ.showStatus("Saving "+grid_path);
	fs.saveAsTiffStack(path);		if (DEBUG_LEVEL>0) System.out.println("-->>> Saving "+grid_path+" - using "+numAbsolutePoints+" laser pointer references");
			fs.saveAsTiffStack(grid_path);
	}		}
	}		}
	}		}
	@@ -9657,7 +9666,7 @@ if (MORE_BUTTONS) {
	COMPONENTS.equalizeGreens,		COMPONENTS.equalizeGreens,
	imp_sel, // image to process		imp_sel, // image to process
	THREADS_MAX);		THREADS_MAX);
	ImagePlus imp_calibrated=matchSimulatedPattern.getCalibratedPatternAsImage(imp_sel,prefix, numAbsolutePoints);		ImagePlus imp_calibrated=matchSimulatedPattern.getCalibratedPatternAsImage(imp_sel,prefix, numAbsolutePoints); //----
	if (DISTORTION_PROCESS_CONFIGURATION.showGridImages) imp_calibrated.show();		if (DISTORTION_PROCESS_CONFIGURATION.showGridImages) imp_calibrated.show();
	if (saveGrids){		if (saveGrids){
	FileSaver fs=new FileSaver(imp_calibrated);		FileSaver fs=new FileSaver(imp_calibrated);
	@@ -17224,8 +17233,10 @@ private double [][] jacobianByJacobian(double [][] jacobian, boolean [] mask) {
	pixels[4],		pixels[4],
	WVgreens, // wave vectors (same units as the pixels array)		WVgreens, // wave vectors (same units as the pixels array)
	// patternDetectParameters.corrRingWidth, // ring (around r=0.5 dist to opposite corr) width		// patternDetectParameters.corrRingWidth, // ring (around r=0.5 dist to opposite corr) width
	0.1, // contrastSelectSigma		2.0, // distortionParameters.contrastSelectSigmaCenter, // Gaussian sigma to select correlation centers (fraction of UV period), 0.1
	0.5, // contrastAverageSigma		0.1, // distortionParameters.contrastSelectSigma, // Gaussian sigma to select correlation centers (fraction of UV period), 0.1
			// 0.1, // contrastSelectSigma
			// 0.5, // contrastAverageSigma
	0.0, // x0, // center coordinates		0.0, // x0, // center coordinates
	0.0, //y0,		0.0, //y0,
	title)[0]; // title base for optional plots names		title)[0]; // title base for optional plots names
	@@ -20320,7 +20331,8 @@ use the result to create a rejectiobn mask - if the energy was high, (multiplica
	gd.addNumericField("Correlation minimal contrast for initial search (absolute)", distortionParameters.correlationMinAbsoluteInitialContrast, 3);		gd.addNumericField("Correlation minimal contrast for initial search (absolute)", distortionParameters.correlationMinAbsoluteInitialContrast, 3);

	gd.addNumericField("Decrease contrast of cells that are too close to the border to be processed in refinement pass", distortionParameters.scaleFirstPassContrast, 3);		gd.addNumericField("Decrease contrast of cells that are too close to the border to be processed in refinement pass", distortionParameters.scaleFirstPassContrast, 3);
	gd.addNumericField("Gaussian sigma to select correlation centers (fraction of UV period), 0.1", distortionParameters.contrastSelectSigma, 3);		gd.addNumericField("Gaussian sigma to select correlation center in pixels, 2.0", distortionParameters.contrastSelectSigmaCenter, 3);
			gd.addNumericField("Gaussian sigma to select correlation off-centers (fraction of UV period), 0.1", distortionParameters.contrastSelectSigma, 3);
	gd.addNumericField("Gaussian sigma to average correlation variations (as contrast reference), 0.5", distortionParameters.contrastAverageSigma, 3);		gd.addNumericField("Gaussian sigma to average correlation variations (as contrast reference), 0.5", distortionParameters.contrastAverageSigma, 3);

	gd.addNumericField("Minimal initial pattern cluster size (0 - disable retries)", distortionParameters.minimalPatternCluster, 0);		gd.addNumericField("Minimal initial pattern cluster size (0 - disable retries)", distortionParameters.minimalPatternCluster, 0);
	@@ -20402,6 +20414,7 @@ use the result to create a rejectiobn mask - if the energy was high, (multiplica
	distortionParameters.correlationMinAbsoluteInitialContrast= gd.getNextNumber();		distortionParameters.correlationMinAbsoluteInitialContrast= gd.getNextNumber();

	distortionParameters.scaleFirstPassContrast= gd.getNextNumber();		distortionParameters.scaleFirstPassContrast= gd.getNextNumber();
			distortionParameters.contrastSelectSigmaCenter= gd.getNextNumber();
	distortionParameters.contrastSelectSigma= gd.getNextNumber();		distortionParameters.contrastSelectSigma= gd.getNextNumber();
	distortionParameters.contrastAverageSigma= gd.getNextNumber();		distortionParameters.contrastAverageSigma= gd.getNextNumber();

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