batch mode for multiple image sets (770a8d96) · Commits · Elphel / imagej-elphel

src/main/java/EyesisCorrectionParameters.java

+94 −19

Original line number	Diff line number	Diff line
		@@ -110,6 +110,19 @@ public class EyesisCorrectionParameters {
		public String cltKernelDirectory="";
		public String cltKernelPrefix="clt-";
		public String cltSuffix=".clt-tiff";
		public boolean use_x3d_subdirs = true;

		// CLT 3d batch parameters

		public boolean clt_batch_4img = true; // Create a set of 4 images, usually for disparity = 0
		public boolean clt_batch_extrinsic = false; // Calibrate extrinsic parameters for each set
		public boolean clt_batch_poly = false; // Calculate fine polynomial correction for each set
		public boolean clt_batch_explore = true; // 1-st step of 3d reconstruction - explore disparities for each tile
		public boolean clt_batch_surf = true; // Create super-tile 2.5d surfaces
		public boolean clt_batch_assign = true; // Assign tiles to surfaces
		public boolean clt_batch_gen3d = true; // Generate 3d output: x3d and/or obj+mtl



		public String x3dDirectory="";

		@@ -200,7 +213,15 @@ public class EyesisCorrectionParameters {
		properties.setProperty(prefix+"cltSuffix", this.cltSuffix);

		properties.setProperty(prefix+"x3dDirectory", this.x3dDirectory);
		properties.setProperty(prefix+"use_x3d_subdirs", this.use_x3d_subdirs+"");

		properties.setProperty(prefix+"clt_batch_4img", this.clt_batch_4img+"");
		properties.setProperty(prefix+"clt_batch_extrinsic", this.clt_batch_extrinsic+"");
		properties.setProperty(prefix+"clt_batch_poly", this.clt_batch_poly+"");
		properties.setProperty(prefix+"clt_batch_explore", this.clt_batch_explore+"");
		properties.setProperty(prefix+"clt_batch_surf", this.clt_batch_surf+"");
		properties.setProperty(prefix+"clt_batch_assign", this.clt_batch_assign+"");
		properties.setProperty(prefix+"clt_batch_gen3d", this.clt_batch_gen3d+"");
		}

		public void getProperties(String prefix,Properties properties){
		@@ -294,6 +315,15 @@ public class EyesisCorrectionParameters {

		if (properties.getProperty(prefix+"x3dDirectory")!= null) this.x3dDirectory=properties.getProperty(prefix+"x3dDirectory");

		if (properties.getProperty(prefix+"use_x3d_subdirs")!= null) this.use_x3d_subdirs=Boolean.parseBoolean((String) properties.getProperty(prefix+"use_x3d_subdirs"));

		if (properties.getProperty(prefix+"clt_batch_4img")!= null) this.clt_batch_4img=Boolean.parseBoolean((String) properties.getProperty(prefix+"clt_batch_4img"));
		if (properties.getProperty(prefix+"clt_batch_extrinsic")!= null) this.clt_batch_extrinsic=Boolean.parseBoolean((String) properties.getProperty(prefix+"clt_batch_extrinsic"));
		if (properties.getProperty(prefix+"clt_batch_poly")!= null) this.clt_batch_poly=Boolean.parseBoolean((String) properties.getProperty(prefix+"clt_batch_poly"));
		if (properties.getProperty(prefix+"clt_batch_explore")!= null) this.clt_batch_explore=Boolean.parseBoolean((String) properties.getProperty(prefix+"clt_batch_explore"));
		if (properties.getProperty(prefix+"clt_batch_surf")!= null) this.clt_batch_surf=Boolean.parseBoolean((String) properties.getProperty(prefix+"clt_batch_surf"));
		if (properties.getProperty(prefix+"clt_batch_assign")!= null) this.clt_batch_assign=Boolean.parseBoolean((String) properties.getProperty(prefix+"clt_batch_assign"));
		if (properties.getProperty(prefix+"clt_batch_gen3d")!= null) this.clt_batch_gen3d=Boolean.parseBoolean((String) properties.getProperty(prefix+"clt_batch_gen3d"));
		}

		public boolean showDialog(String title) {
		@@ -365,6 +395,7 @@ public class EyesisCorrectionParameters {

		gd.addStringField ("x3d output directory", this.x3dDirectory, 60);
		gd.addCheckbox ("Select x3d output directory", false);
		gd.addCheckbox ("Use individual subdirectory for each 3d model (timestamp as name)", this.use_x3d_subdirs);

		gd.addStringField("Equirectangular maps directory (may be empty)", this.equirectangularDirectory, 60);
		gd.addCheckbox("Select equirectangular maps directory", false);
		@@ -450,6 +481,7 @@ public class EyesisCorrectionParameters {
		this.dctKernelDirectory= gd.getNextString(); if (gd.getNextBoolean()) selectDCTKernelDirectory(false, true);
		this.cltKernelDirectory= gd.getNextString(); if (gd.getNextBoolean()) selectCLTKernelDirectory(false, true);
		this.x3dDirectory= gd.getNextString(); if (gd.getNextBoolean()) selectX3dDirectory(false, true);
		this.use_x3d_subdirs= gd.getNextBoolean();
		this.equirectangularDirectory= gd.getNextString(); if (gd.getNextBoolean()) selectEquirectangularDirectory(false, false);
		this.resultsDirectory= gd.getNextString(); if (gd.getNextBoolean()) selectResultsDirectory(false, true);
		this.sourcePrefix= gd.getNextString();
		@@ -488,20 +520,29 @@ public class EyesisCorrectionParameters {
		gd.addStringField ("x3d output directory", this.x3dDirectory, 60); // 8
		gd.addCheckbox ("Select x3d output directory", false); // 9

		gd.addStringField("Results directory", this.resultsDirectory, 60); // 10
		gd.addCheckbox("Select results directory", false); // 11
		gd.addCheckbox ("Use individual subdirectory for each 3d model (timestamp as name)", this.use_x3d_subdirs); //10

		gd.addStringField("Results directory", this.resultsDirectory, 60); // 11
		gd.addCheckbox("Select results directory", false); // 12

		gd.addStringField("Source files prefix", this.sourcePrefix, 60); // 12
		gd.addStringField("Source files suffix", this.sourceSuffix, 60); // 13
		gd.addNumericField("First subcamera (in the source filename)", this.firstSubCamera, 0); // 14
		gd.addStringField("Source files prefix", this.sourcePrefix, 60); // 13
		gd.addStringField("Source files suffix", this.sourceSuffix, 60); // 14
		gd.addNumericField("First subcamera (in the source filename)", this.firstSubCamera, 0); // 15

		gd.addStringField("Sensor files prefix", this.sensorPrefix, 40); // 15
		gd.addStringField("Sensor files suffix", this.sensorSuffix, 40); // 16
		gd.addStringField("Sensor files prefix", this.sensorPrefix, 40); // 16
		gd.addStringField("Sensor files suffix", this.sensorSuffix, 40); // 17

		gd.addStringField("CLT kernel files prefix", this.cltKernelPrefix, 40); // 17
		gd.addStringField("CLT symmetical kernel files", this.cltSuffix, 40); // 18
		gd.addStringField("CLT kernel files prefix", this.cltKernelPrefix, 40); // 18
		gd.addStringField("CLT symmetical kernel files", this.cltSuffix, 40); // 19

		gd.addMessage("============ batch parameters ============");
		gd.addCheckbox ("Create a set of 4 images, usually for disparity = 0", this.clt_batch_4img); // 20
		gd.addCheckbox ("Calibrate extrinsic parameters for each set", this.clt_batch_extrinsic); // 21
		gd.addCheckbox ("Calculate fine polynomial correction for each set", this.clt_batch_poly); // 22
		gd.addCheckbox ("1-st step of 3d reconstruction - explore disparities for each tile", this.clt_batch_explore); // 23
		gd.addCheckbox ("Create super-tile 2.5d surfaces", this.clt_batch_surf); // 24
		gd.addCheckbox ("Assign tiles to surfaces", this.clt_batch_assign); // 25
		gd.addCheckbox ("Generate 3d output: x3d and/or obj+mtl", this.clt_batch_gen3d); // 26


		WindowTools.addScrollBars(gd);
		@@ -516,14 +557,23 @@ public class EyesisCorrectionParameters {
		this.sensorDirectory= gd.getNextString(); if (gd.getNextBoolean()) selectSensorDirectory(false, false); // 5
		this.cltKernelDirectory= gd.getNextString(); if (gd.getNextBoolean()) selectCLTKernelDirectory(false, true); // 7
		this.x3dDirectory= gd.getNextString(); if (gd.getNextBoolean()) selectX3dDirectory(false, true); // 9
		this.resultsDirectory= gd.getNextString(); if (gd.getNextBoolean()) selectResultsDirectory(false, true); // 11
		this.sourcePrefix= gd.getNextString(); // 12
		this.sourceSuffix= gd.getNextString(); // 13
		this.firstSubCamera= (int) gd.getNextNumber(); // 14
		this.sensorPrefix= gd.getNextString(); // 15
		this.sensorSuffix= gd.getNextString(); // 16
		this.cltKernelPrefix= gd.getNextString(); // 17
		this.cltSuffix= gd.getNextString(); // 18
		this.use_x3d_subdirs= gd.getNextBoolean(); // 10
		this.resultsDirectory= gd.getNextString(); if (gd.getNextBoolean()) selectResultsDirectory(false, true); // 12
		this.sourcePrefix= gd.getNextString(); // 13
		this.sourceSuffix= gd.getNextString(); // 14
		this.firstSubCamera= (int) gd.getNextNumber(); // 15
		this.sensorPrefix= gd.getNextString(); // 16
		this.sensorSuffix= gd.getNextString(); // 17
		this.cltKernelPrefix= gd.getNextString(); // 18
		this.cltSuffix= gd.getNextString(); // 19

		this.clt_batch_4img= gd.getNextBoolean(); // 20
		this.clt_batch_extrinsic= gd.getNextBoolean(); // 21
		this.clt_batch_poly= gd.getNextBoolean(); // 22
		this.clt_batch_explore= gd.getNextBoolean(); // 23
		this.clt_batch_surf= gd.getNextBoolean(); // 24
		this.clt_batch_assign= gd.getNextBoolean(); // 25
		this.clt_batch_gen3d= gd.getNextBoolean(); // 26
		return true;
		}

		@@ -1061,6 +1111,31 @@ public class EyesisCorrectionParameters {
		return dir;
		}

		// select qualified (by 'name' - quad timestamp) x3d subdirectory
		public String selectX3dDirectory(String name, boolean smart, boolean newAllowed) {

		String dir= CalibrationFileManagement.selectDirectory(
		smart,
		newAllowed, // save
		"x3d output directory", // title
		"Select x3d output directory", // button
		null, // filter
		this.x3dDirectory); //this.sourceDirectory);
		if (dir!=null) {
		this.x3dDirectory=dir;
		if (this.use_x3d_subdirs &&(name != null) && !name.equals("")) {
		dir= CalibrationFileManagement.selectDirectory(
		smart,
		newAllowed, // save
		"x3d output sub-directory", // title
		"Select x3d output sub-directory", // button
		null, // filter
		this.x3dDirectory + Prefs.getFileSeparator()+name); //this.sourceDirectory);
		}
		}
		return dir;
		}

		public String selectEquirectangularDirectory(boolean smart, boolean newAllowed) {
		String dir= CalibrationFileManagement.selectDirectory(
		smart,

src/main/java/Eyesis_Correction.java

+96 −14

Original line number	Diff line number	Diff line
		@@ -544,7 +544,7 @@ private Panel panel1,
		panelClt3.setLayout(new GridLayout(1, 0, 5, 5)); // rows, columns, vgap, hgap
		addButton("Setup CLT Batch parameters", panelClt3, color_configure);
		addButton("Setup CLT parameters", panelClt3, color_configure);
		addButton("CLT Batch process", panelClt3, color_process);
		addButton("CLT batch process", panelClt3, color_process);
		add(panelClt3);
		}
		pack();
		@@ -4937,22 +4937,13 @@ private Panel panel1,
		return;
		}
		}
		/*
		public boolean output3d(
		EyesisCorrectionParameters.CLTParameters clt_parameters,
		EyesisCorrectionParameters.ColorProcParameters colorProcParameters,
		EyesisCorrectionParameters.RGBParameters rgbParameters,
		final int threadsMax, // maximal number of threads to launch
		final boolean updateStatus,
		final int debugLevel)

		*/
		boolean OK = QUAD_CLT.output3d(
		CLT_PARAMETERS, // EyesisCorrectionParameters.DCTParameters dct_parameters,
		COLOR_PROC_PARAMETERS, //EyesisCorrectionParameters.ColorProcParameters colorProcParameters,
		RGB_PARAMETERS, // EyesisCorrectionParameters.RGBParameters rgbParameters,
		THREADS_MAX, // final int threadsMax, // maximal number of threads to launch
		UPDATE_STATUS, // final boolean updateStatus,
		false, // final boolean batch_mode,
		DEBUG_LEVEL); //final int debugLevel);
		if (!OK) {
		String msg="Image data not initialized, run 'CLT 3D' command first";
		@@ -4970,7 +4961,98 @@ private Panel panel1,
		}

		*/
		} else if (label.equals("CLT batch process")) {
		DEBUG_LEVEL=MASTER_DEBUG_LEVEL;
		EYESIS_CORRECTIONS.setDebug(DEBUG_LEVEL);
		if (QUAD_CLT == null){
		QUAD_CLT = new QuadCLT (
		PROPERTIES,
		EYESIS_CORRECTIONS,
		CORRECTION_PARAMETERS);
		if (DEBUG_LEVEL > 0){
		System.out.println("Created new QuadCLT instance, will need to read CLT kernels");
		}
		}
		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"+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);
		int numChannels=EYESIS_CORRECTIONS.getNumChannels();
		NONLIN_PARAMETERS.modifyNumChannels(numChannels);
		CHANNEL_GAINS_PARAMETERS.modifyNumChannels(numChannels);

		if (!QUAD_CLT.CLTKernelsAvailable()){
		if (DEBUG_LEVEL > 0){
		System.out.println("Reading CLT kernels");
		}
		QUAD_CLT.readCLTKernels(
		CLT_PARAMETERS,
		THREADS_MAX,
		UPDATE_STATUS, // update status info
		DEBUG_LEVEL);

		if (DEBUG_LEVEL > 1){
		QUAD_CLT.showCLTKernels(
		THREADS_MAX,
		UPDATE_STATUS, // update status info
		DEBUG_LEVEL);
		}
		}

		if (!QUAD_CLT.geometryCorrectionAvailable()){
		if (DEBUG_LEVEL > 0){
		System.out.println("Calculating geometryCorrection");
		}
		if (!QUAD_CLT.initGeometryCorrection(DEBUG_LEVEL+2)){
		return;
		}
		}

		///========================================
		QUAD_CLT.batchCLT3d(
		CLT_PARAMETERS, // EyesisCorrectionParameters.DCTParameters dct_parameters,
		DEBAYER_PARAMETERS, //EyesisCorrectionParameters.DebayerParameters debayerParameters,
		NONLIN_PARAMETERS, //EyesisCorrectionParameters.NonlinParameters nonlinParameters,
		COLOR_PROC_PARAMETERS, //EyesisCorrectionParameters.ColorProcParameters colorProcParameters,
		CHANNEL_GAINS_PARAMETERS, //CorrectionColorProc.ColorGainsParameters channelGainParameters,
		RGB_PARAMETERS, //EyesisCorrectionParameters.RGBParameters rgbParameters,
		EQUIRECTANGULAR_PARAMETERS, // EyesisCorrectionParameters.EquirectangularParameters equirectangularParameters,
		CONVOLVE_FFT_SIZE, //int convolveFFTSize, // 128 - fft size, kernel size should be size/2
		THREADS_MAX, //final int threadsMax, // maximal number of threads to launch
		UPDATE_STATUS, //final boolean updateStatus,
		DEBUG_LEVEL); //final int debugLevel);

		if (configPath!=null) {
		saveTimestampedProperties( // save config again
		configPath, // full path or null
		null, // use as default directory if path==null
		true,
		PROPERTIES);
		}
		return;

src/main/java/ImageDtt.java

+1 −1

Original line number	Diff line number	Diff line
		@@ -1042,7 +1042,7 @@ public class ImageDtt {
		final int corr_size = transform_size * 2 -1;
		final int [][] transpose_indices = new int [corr_size*(corr_size-1)/2][2];
		int indx = 0;
		if (disparity_corr != 0.0){
		if ((globalDebugLevel > -1) && (disparity_corr != 0.0)){
		System.out.println(String.format("Using manual infinity disparity correction of %8.5f pixels",disparity_corr));
		}
		for (int i =0; i < corr_size-1; i++){

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