converting kernels (2e50bfb7) · Commits · Elphel / imagej-elphel

src/main/java/EyesisCorrectionParameters.java

+109 −5

Original line number	Diff line number	Diff line
		@@ -106,6 +106,10 @@ public class EyesisCorrectionParameters {
		public double referenceExposure=0.0003; // 3/10000 sec, used in absolute mode only
		public double relativeExposure=0.5; // 0.0 - use shortest (darken), 1.0 - use longest (brighten)

		public String cltKernelDirectory="";
		public String cltKernelPrefix="clt-";
		public String cltSuffix=".clt-tiff";


		public void setProperties(String prefix,Properties properties){
		properties.setProperty(prefix+"split",this.split+"");
		@@ -188,6 +192,10 @@ public class EyesisCorrectionParameters {
		properties.setProperty(prefix+"relativeExposure", this.relativeExposure+"");
		properties.setProperty(prefix+"swapSubchannels01", this.swapSubchannels01+"");

		properties.setProperty(prefix+"cltKernelDirectory", this.cltKernelDirectory);
		properties.setProperty(prefix+"cltKernelPrefix", this.cltKernelPrefix);
		properties.setProperty(prefix+"cltSuffix", this.cltSuffix);

		}

		public void getProperties(String prefix,Properties properties){
		@@ -273,6 +281,12 @@ public class EyesisCorrectionParameters {
		if (properties.getProperty(prefix+"referenceExposure") !=null) this.referenceExposure= Double.parseDouble(properties.getProperty(prefix+"referenceExposure"));
		if (properties.getProperty(prefix+"relativeExposure") !=null) this.relativeExposure= Double.parseDouble(properties.getProperty(prefix+"relativeExposure"));
		if (properties.getProperty(prefix+"swapSubchannels01")!=null) this.swapSubchannels01=Boolean.parseBoolean(properties.getProperty(prefix+"swapSubchannels01"));

		if (properties.getProperty(prefix+"cltKernelDirectory")!= null) this.cltKernelDirectory=properties.getProperty(prefix+"cltKernelDirectory");
		if (properties.getProperty(prefix+"cltKernelPrefix")!= null) this.cltKernelPrefix=properties.getProperty(prefix+"cltKernelPrefix");
		if (properties.getProperty(prefix+"cltSuffix")!= null) this.cltSuffix=properties.getProperty(prefix+"cltSuffix");


		}

		public boolean showDialog(String title) {
		@@ -338,6 +352,9 @@ public class EyesisCorrectionParameters {
		gd.addStringField ("Aberration kernels for DCT directory", this.dctKernelDirectory, 60);
		gd.addCheckbox ("Select aberration kernels for DCT directory", false);

		gd.addStringField ("Aberration kernels for CLT directory", this.cltKernelDirectory, 60);
		gd.addCheckbox ("Select aberration kernels for CLT directory", false);

		gd.addStringField("Equirectangular maps directory (may be empty)", this.equirectangularDirectory, 60);
		gd.addCheckbox("Select equirectangular maps directory", false);
		gd.addStringField("Results directory", this.resultsDirectory, 40);
		@@ -356,6 +373,8 @@ public class EyesisCorrectionParameters {
		gd.addStringField("DCT kernel files prefix", this.dctKernelPrefix, 40);
		gd.addStringField("DCT symmetical kernel files", this.dctSymSuffix, 40);
		gd.addStringField("DCT asymmetrical kernel files suffix", this.dctAsymSuffix, 40);
		gd.addStringField("CLT kernel files prefix", this.cltKernelPrefix, 40);
		gd.addStringField("CLT symmetical kernel files", this.cltSuffix, 40);

		gd.addStringField("Equirectangular maps prefix", this.equirectangularPrefix, 40);
		gd.addStringField("Equirectangular maps suffix", this.equirectangularSuffix, 40);
		@@ -417,6 +436,7 @@ public class EyesisCorrectionParameters {
		this.sharpKernelDirectory= gd.getNextString(); if (gd.getNextBoolean()) selectSharpKernelDirectory(false, false);
		this.smoothKernelDirectory= gd.getNextString(); if (gd.getNextBoolean()) selectSmoothKernelDirectory(false, true);
		this.dctKernelDirectory= gd.getNextString(); if (gd.getNextBoolean()) selectDCTKernelDirectory(false, true);
		this.cltKernelDirectory= gd.getNextString(); if (gd.getNextBoolean()) selectCLTKernelDirectory(false, true);
		this.equirectangularDirectory= gd.getNextString(); if (gd.getNextBoolean()) selectEquirectangularDirectory(false, false);
		this.resultsDirectory= gd.getNextString(); if (gd.getNextBoolean()) selectResultsDirectory(false, true);
		this.sourcePrefix= gd.getNextString();
		@@ -431,6 +451,8 @@ public class EyesisCorrectionParameters {
		this.dctKernelPrefix= gd.getNextString();
		this.dctSymSuffix= gd.getNextString();
		this.dctAsymSuffix= gd.getNextString();
		this.cltKernelPrefix= gd.getNextString();
		this.cltSuffix= gd.getNextString();
		this.equirectangularPrefix= gd.getNextString();
		this.equirectangularSuffix= gd.getNextString();
		this.equirectangularCut= gd.getNextBoolean();
		@@ -483,6 +505,8 @@ public class EyesisCorrectionParameters {
		public int getChannelFromDCTTiff(String path, int type){return getChannelFromTiff(path, (type==0)?this.dctSymSuffix:this.dctAsymSuffix);}
		public String getNameFromDCTTiff(String path, int type){return getNameFromTiff(path, (type==0)?this.dctSymSuffix:this.dctAsymSuffix);}

		public int getChannelFromCLTTiff(String path){return getChannelFromTiff(path, this.cltSuffix);}
		public String getNameFromCLTTiff(String path){return getNameFromTiff(path, this.cltSuffix);}

		public boolean selectSourceFiles(boolean allFiles) {
		return selectSourceFiles(allFiles, 1); // debug level 1 - modify here
		@@ -826,8 +850,74 @@ public class EyesisCorrectionParameters {



		public String [] selectCLTChannelFiles(
		int numChannels, // number of channels
		int debugLevel) { // will only open dialog if directory or files are not found
		String [] kernelFiles= selectCLTFiles(
		debugLevel);
		if (kernelFiles==null) return null;
		String [] channelPaths=new String[numChannels];
		for (int i=0;i<channelPaths.length;i++)channelPaths[i]=null;
		for (int fileNum=0;fileNum<kernelFiles.length;fileNum++){
		int chn=getChannelFromCLTTiff(kernelFiles[fileNum]);
		if ((chn>=0) && (chn<numChannels)){
		if (channelPaths[chn]==null){ // use first file for channel if there are multiple
		channelPaths[chn]=kernelFiles[fileNum];
		} else {
		if (debugLevel>0) System.out.println("Multiple kernel files for channel "+
		chn+": "+channelPaths[chn]+" and "+kernelFiles[fileNum]+". Using "+channelPaths[chn]);
		}
		}
		}
		return channelPaths;
		}

		public String [] selectCLTFiles(
		int debugLevel) { // will only open dialog if directory or files are not found
		String []defaultPaths = new String[1];
		String kernelDirectory=this.cltKernelDirectory;
		if ((kernelDirectory==null) \|\| (kernelDirectory.length()<=1)){ // empty or "/"
		defaultPaths[0]="";
		} else {
		defaultPaths[0]=kernelDirectory+Prefs.getFileSeparator();
		}
		String [] extensions={this.cltSuffix};
		String kernelPrefix= this.cltKernelPrefix;
		CalibrationFileManagement.MultipleExtensionsFileFilter kernelFilter =
		new CalibrationFileManagement.MultipleExtensionsFileFilter(kernelPrefix,extensions,kernelPrefix+
		"*"+extensions[0]+" CLT symmetrical kernel files");
		if (debugLevel>1) System.out.println("selectKernelFiles("+debugLevel+"): defaultPaths[0]="+defaultPaths[0]+" "+kernelPrefix+"*"+extensions[0]);

		String [] kernelFiles=null;
		// try reading all matching files
		File dir= new File (kernelDirectory);
		File [] fileList=null;
		if (dir.exists()) {
		fileList=dir.listFiles(kernelFilter);
		}
		if ((fileList==null) \|\| (fileList.length==0)){
		kernelFiles=CalibrationFileManagement.selectFiles(false,
		"Select CLT kernel files",
		"Select",
		kernelFilter,
		defaultPaths); // String [] defaultPaths); //this.sourceDirectory // null
		if ((kernelFiles!=null) && (kernelFiles.length>0)){
		kernelDirectory=kernelFiles[0].substring(0, kernelFiles[0].lastIndexOf(Prefs.getFileSeparator()));
		dir= new File (kernelDirectory);
		fileList=dir.listFiles(kernelFilter);
		this.cltKernelDirectory= kernelDirectory;
		}
		}
		if ((fileList==null) \|\| (fileList.length==0)) return null;
		if (debugLevel>1) System.out.println("CLT kernel directory "+kernelDirectory+" has "+fileList.length+" matching files.");
		kernelFiles = new String[fileList.length];
		for (int i=0;i<kernelFiles.length;i++) kernelFiles[i]=fileList[i].getPath();
		String directory=kernelFiles[0].substring(0, kernelFiles[0].lastIndexOf(Prefs.getFileSeparator()));
		String prefix=kernelFiles[0].substring(directory.length()+1, kernelFiles[0].length()-extensions[0].length()-2); // all but NN
		this.cltKernelDirectory=directory;
		this.cltKernelPrefix=prefix;
		return kernelFiles;
		}

		public String selectSourceDirectory(boolean smart, boolean newAllowed) { // normally newAllowed=false
		String dir= CalibrationFileManagement.selectDirectory(
		@@ -887,6 +977,18 @@ public class EyesisCorrectionParameters {
		return dir;
		}

		public String selectCLTKernelDirectory(boolean smart, boolean newAllowed) {
		String dir= CalibrationFileManagement.selectDirectory(
		smart,
		newAllowed, // save
		"CLT aberration kernels directory", // title
		"Select CLT aberration kernels directory", // button
		null, // filter
		this.cltKernelDirectory); //this.sourceDirectory);
		if (dir!=null) this.cltKernelDirectory=dir;
		return dir;
		}

		public String selectEquirectangularDirectory(boolean smart, boolean newAllowed) {
		String dir= CalibrationFileManagement.selectDirectory(
		smart,
		@@ -1780,6 +1882,8 @@ public class EyesisCorrectionParameters {
		public double fat_zero = 0.0; // modify phase correlation to prevent division by very small numbers
		public double corr_sigma =0.8; // LPF correlarion sigma

		public boolean norm_kern = true; // normalize kernels

		public CLTParameters(){}
		public void setProperties(String prefix,Properties properties){
		properties.setProperty(prefix+"transform_size",this.transform_size+"");
		@@ -1820,7 +1924,7 @@ public class EyesisCorrectionParameters {
		gd.addNumericField("Tile Y to extract (0..122)", this.tileY, 0);
		gd.addNumericField("dbg_mode: 0 - normal, +1 - no DCT/IDCT, just fold", this.dbg_mode, 0);
		gd.addNumericField("ishift_x: shift source image by this pixels left", this.ishift_x, 0);
		gd.addNumericField("ishift_x: shift source image by this pixels down", this.ishift_y, 0);
		gd.addNumericField("ishift_y: shift source image by this pixels down", this.ishift_y, 0);
		gd.addNumericField("Modify phase correlation to prevent division by very small numbers", this.fat_zero, 4);
		gd.addNumericField("LPF correlarion sigma ", this.corr_sigma, 3);
		WindowTools.addScrollBars(gd);

src/main/java/EyesisDCT.java

+644 −102

File changed.

Preview size limit exceeded, changes collapsed.

src/main/java/Eyesis_Correction.java

+101 −22

Original line number	Diff line number	Diff line
		@@ -490,9 +490,10 @@ private Panel panel1,
		addButton("CLT stack", panelClt1, color_process);
		addButton("Select second CLT image", panelClt1, color_configure);
		addButton("CLT correlate", panelClt1, color_process);
		addButton("CLT test 2", panelClt1, color_process);
		addButton("CLT test 3", panelClt1, color_process);
		addButton("CLT test 4", panelClt1, color_process);
		addButton("Create CLT kernels", panelClt1, color_process);
		addButton("Read CLT kernels", panelClt1, color_process);
		addButton("Reset CLT kernels", panelClt1, color_stop);
		addButton("CLT process files", panelClt1, color_process);
		add(panelClt1);
		}
		pack();
		@@ -4044,28 +4045,106 @@ private Panel panel1,
		DBG_IMP.getTitle()+"-C"+suffix, titles_rbg);
		}

		//==============================================================================

		} else if (label.equals("Create CLT kernels")) {
		if (!CLT_PARAMETERS.showDialog()) return;
		if (EYESIS_DCT == null){
		EYESIS_DCT = new EyesisDCT (
		EYESIS_CORRECTIONS,
		CORRECTION_PARAMETERS,
		DCT_PARAMETERS);
		}
		String configPath=null;
		if (EYESIS_CORRECTIONS.correctionsParameters.saveSettings) {
		configPath=EYESIS_CORRECTIONS.correctionsParameters.selectResultsDirectory(
		true,
		true);
		if (configPath==null){
		String msg="No results directory selected, command aborted";
		System.out.println("Warning: "+msg);
		IJ.showMessage("Warning",msg);
		return;
		}
		configPath+=Prefs.getFileSeparator()+"autoconfig";
		try {
		saveTimestampedProperties(
		configPath, // full path or null
		null, // use as default directory if path==null
		true,
		PROPERTIES);

		} catch (Exception e){
		String msg="Failed to save configuration to "+configPath+", command aborted";
		System.out.println("Error: "+msg);
		IJ.showMessage("Error",msg);
		return;
		}
		}

		EYESIS_CORRECTIONS.initSensorFiles(DEBUG_LEVEL);

		/*
		double [][] iclt_data = new double [clt_data.length][];
		for (int chn=0; chn<iclt_data.length;chn++){
		iclt_data[chn] = image_dtt.iclt_2d(
		clt_data[chn], // scanline representation of dcd data, organized as dct_size x dct_size tiles
		CLT_PARAMETERS.transform_size, // final int
		CLT_PARAMETERS.clt_window, //window_type
		CLT_PARAMETERS.iclt_mask, //which of 4 to transform back
		CLT_PARAMETERS.dbg_mode, //which of 4 to transform back
		THREADS_MAX, // maximal number of threads to launch
		DEBUG_LEVEL); // globalDebugLevel)
		EYESIS_DCT.createCLTKernels(
		CLT_PARAMETERS,
		CONVOLVE_FFT_SIZE/2,
		THREADS_MAX,
		UPDATE_STATUS, // update status info
		DEBUG_LEVEL);

		//"Reset DCT kernels"
		} else if (label.equals("Reset CLT kernels")) {
		if (EYESIS_DCT != null){
		EYESIS_DCT.resetCLTKernels();
		}
		SDFA_INSTANCE.showArrays(
		iclt_data,
		(tilesX + 1) * CLT_PARAMETERS.transform_size,
		(tilesY + 1) * CLT_PARAMETERS.transform_size,
		} else if (label.equals("Read CLT kernels")) {
		if (!CLT_PARAMETERS.showDialog()) return;
		if (EYESIS_DCT == null){
		EYESIS_DCT = new EyesisDCT (
		EYESIS_CORRECTIONS,
		CORRECTION_PARAMETERS,
		DCT_PARAMETERS);
		}
		String configPath=null;
		if (EYESIS_CORRECTIONS.correctionsParameters.saveSettings) {
		configPath=EYESIS_CORRECTIONS.correctionsParameters.selectResultsDirectory(
		true,
		DBG_IMP.getTitle()+"-ICLT-"+CLT_PARAMETERS.iclt_mask);
		*/
		true);
		if (configPath==null){
		String msg="No results directory selected, command aborted";
		System.out.println("Warning: "+msg);
		IJ.showMessage("Warning",msg);
		return;
		}
		configPath+=Prefs.getFileSeparator()+"autoconfig";
		try {
		saveTimestampedProperties(
		configPath, // full path or null
		null, // use as default directory if path==null
		true,
		PROPERTIES);

		} catch (Exception e){
		String msg="Failed to save configuration to "+configPath+", command aborted";
		System.out.println("Error: "+msg);
		IJ.showMessage("Error",msg);
		return;
		}
		}

		EYESIS_CORRECTIONS.initSensorFiles(DEBUG_LEVEL);

		EYESIS_DCT.readCLTKernels(
		CLT_PARAMETERS,
		THREADS_MAX,
		UPDATE_STATUS, // update status info
		DEBUG_LEVEL);
		if (DEBUG_LEVEL > -1){
		EYESIS_DCT.showCLTKernels(
		THREADS_MAX,
		UPDATE_STATUS, // update status info
		DEBUG_LEVEL);
		}

		return;

		// End of buttons code

src/main/java/ImageDtt.java

+108 −1

Original line number	Diff line number	Diff line
		@@ -929,7 +929,7 @@ public class ImageDtt {
		System.out.println("clt_shift():tilesX= "+tilesX);
		System.out.println("clt_shift():tilesY= "+tilesY);
		}
		/*
		/* Direct matrix Z1: X2 ~= Z1 * Shift
		* {{+cc -sc -cs +ss},
		* {+sc +cc -ss -cs},
		* {+cs -ss +cc -sc},
		@@ -1329,6 +1329,113 @@ public class ImageDtt {
		return dct_data_out;
		}

		void clt_convert_double_kernel( // converts double resolution kernel
		double [] src_kernel, //
		double [] dst_kernel, // should be (2dtt_size-1) (2*dtt_size-1) +2 size - kernel and dx, dy to the nearest 1/2 pixels
		int src_size, // 64
		int dtt_size) // 8
		{

		int [] indices = {0,-src_size,-1,1,src_size,-src_size-1,-src_size+1,src_size-1,src_size+1};
		double [] weights = {0.25,0.125,0.125,0.125,0.125,0.0625,0.0625,0.0625,0.0625};
		int src_center = src_size / 2; // 32
		// Find center
		double sx=0.0, sy = 0.0, s = 0.0;
		int indx = 0;
		for (int i= -src_center; i < src_center; i++){
		for (int j = -src_center; j < src_center; j++){
		double d = src_kernel[indx++];
		sx+= j*d;
		sy+= i*d;
		s += d;
		}
		}
		int src_x = (int) Math.round(sx / s) + src_center;
		int src_y = (int) Math.round(sy / s) + src_center;
		// make sure selected area (2dst_size-1) (2*dst_size-1) fits into src_kernel, move center if not
		if (src_x < 2 * dtt_size) src_x = 2 * dtt_size - 1; // 15
		else if (src_x > (src_size - 2* dtt_size)) src_x = src_size - 2* dtt_size;

		if (src_y < 2 * dtt_size) src_y = 2 * dtt_size - 1; // 15
		else if (src_y > (src_size - 2* dtt_size)) src_y = src_size - 2* dtt_size;
		indx = 0;
		// downscale, copy
		for (int i = -dtt_size + 1; i < dtt_size; i++){
		int src_i = (src_y + 2 * i) * src_size + src_x;
		for (int j = -dtt_size + 1; j < dtt_size; j++){
		double d = 0.0;
		for (int k = 0; k < indices.length; k++){
		d += weights[k]src_kernel[src_i + 2 j + indices[k]];
		}
		dst_kernel[indx++] = d;
		}
		}
		dst_kernel[indx++] = 0.5*(src_x - src_center);
		dst_kernel[indx++] = 0.5*(src_y - src_center);
		}

		void clt_normalize_kernel( //
		double [] kernel, // should be (2dtt_size-1) (2*dtt_size-1) +2 size (last 2 are not modified)
		double [] window, // normalizes result kernel * window to have sum of elements == 1.0
		final int dtt_size) // 8
		{
		double s = 0.0;
		int indx = 0;
		for (int i = -dtt_size + 1; i < dtt_size; i++){
		int ai = (i < 0)? -i: i;
		for (int j = -dtt_size + 1; j < dtt_size; j++){
		int aj = (j < 0)? -j: j;
		s += kernel[indx++] * window[ai*dtt_size+aj];
		}
		}
		s = 1.0/s;
		indx = 0;
		for (int i = 0; i < (dtt_size * dtt_size); i++) {
		kernel[indx++] *= s;
		}
		}

		void clt_symmetrize_kernel( //
		double [] kernel, // should be (2dtt_size-1) (2*dtt_size-1) +2 size (last 2 are not modified)
		double [][] sym_kernels, // set of 4 SS, AS, SA, AA kdernels, each dtt_size * dtt_size (may have 5-th with center shift
		final int dtt_size) // 8
		{
		int in_size = 2*dtt_size-1;
		int dtt_size_m1 = dtt_size - 1;
		int center = dtt_size_m1 * in_size + dtt_size_m1;

		for (int i = 0; i < dtt_size; i++){
		for (int j = 0; j < dtt_size; j++){
		int indx0 = center - i * in_size - j;
		int indx1 = center - i * in_size + j;
		int indx2 = center + i * in_size - j;
		int indx3 = center + i * in_size + j;
		sym_kernels[0][idtt_size+j] = 0.25( kernel[indx0] + kernel[indx1] + kernel[indx2] + kernel[indx3]);
		if (j > 0) sym_kernels[1][idtt_size+j-1] = 0.25(-kernel[indx0] + kernel[indx1] - kernel[indx2] + kernel[indx3]);
		if (i > 0) sym_kernels[2][(i-1)dtt_size+j] = 0.25(-kernel[indx0] - kernel[indx1] + kernel[indx2] + kernel[indx3]);
		if ((i > 0) && (j > 0)) sym_kernels[3][idtt_size+j] = 0.25(-kernel[indx0] + kernel[indx1] - kernel[indx2] + kernel[indx3]);
		}
		sym_kernels[1][i*dtt_size + dtt_size_m1] = 0.0;
		sym_kernels[2][dtt_size_m1*dtt_size + i] = 0.0;
		sym_kernels[3][i*dtt_size + dtt_size_m1] = 0.0;
		sym_kernels[3][dtt_size_m1*dtt_size + i] = 0.0;
		}
		}

		void clt_dtt3_kernel( //
		double [][] kernels, // set of 4 SS, AS, SA, AA kdernels, each dtt_size * dtt_size (may have 5-th with center shift
		final int dtt_size, // 8
		DttRad2 dtt)
		{
		if (dtt == null) dtt = new DttRad2(dtt_size);
		for (int quad = 0; quad < 4; quad ++){
		kernels[quad] = dtt.dttt_iiie(kernels[quad], quad, dtt_size);
		}
		}




		public double [][][][] mdctScale(
		final ImageStack imageStack,
		final int subcamera, //

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