Bug fixes, added super-batch run (multiple configs) (64394dd7) · Commits · Elphel / imagej-elphel

src/main/java/com/elphel/imagej/correction/Eyesis_Correction.java

+59 −2

Original line number	Diff line number	Diff line
		@@ -815,6 +815,7 @@ public class Eyesis_Correction implements PlugIn, ActionListener {
		addButton("Image Properties", panelLWIR16, color_conf_process);
		addButton("Illustrations Configure", panelLWIR16, color_conf_process);
		addButton("Footage Organize", panelLWIR16, color_conf_process);
		addButton("Super batch", panelLWIR16, color_process);

		plugInFrame.add(panelLWIR16);

		@@ -5433,6 +5434,41 @@ public class Eyesis_Correction implements PlugIn, ActionListener {
		FOOTAGE_ORGANIZE.OrganizeSeries(
		CLT_PARAMETERS,
		CALIBRATION_ILLUSTRATION);
		} else if (label.equals("Super batch")) {
		DEBUG_LEVEL = MASTER_DEBUG_LEVEL;
		EYESIS_CORRECTIONS.setDebug(DEBUG_LEVEL);
		CLT_PARAMETERS.batch_run = true;
		String [] configs = loadMultiProperties(
		CORRECTION_PARAMETERS.resultsDirectory, // String directory,
		true);// boolean useXML,
		if (configs == null) {
		return;
		}
		long startTime = System.nanoTime();
		for (int nc = 0; nc < configs.length; nc++) {
		long startTimeRun = System.nanoTime();
		String config = configs[nc];
		String path = loadProperties(config, CORRECTION_PARAMETERS.resultsDirectory, true, PROPERTIES);
		System.out.println(path);
		if (path != null) {
		getAllProperties(PROPERTIES);
		if (DEBUG_LEVEL > -3)
		System.out.println("Configuration parameters are restored from " + path);
		} else {
		if (DEBUG_LEVEL > -10)
		System.out.println("Failed to restore configuration parameters");
		return;
		}
		batchLwir();
		System.out.println("Super batch: processing of run "+ nc+" (of "+configs.length+"): "+config+ " finished in "
		+ IJ.d2s(0.000000001 * (System.nanoTime() - startTimeRun), 3) + " sec, --- Free memory="
		+ Runtime.getRuntime().freeMemory() + " (of " + Runtime.getRuntime().totalMemory() + ")");
		}
		System.out.println("Super batch: all (of "+configs.length+"): finished at "
		+ IJ.d2s(0.000000001 * (System.nanoTime() - startTime), 3) + " sec, --- Free memory="
		+ Runtime.getRuntime().freeMemory() + " (of " + Runtime.getRuntime().totalMemory() + ")");
		return;


		} else if (label.equals("Image Properties")) {
		DEBUG_LEVEL = MASTER_DEBUG_LEVEL;
		@@ -9136,7 +9172,9 @@ public class Eyesis_Correction implements PlugIn, ActionListener {
		+ ")"), // filter
		directory); // may be ""
		} else
		path += patterns[0];
		if (!path.endsWith(patterns[0])) {
		path += patterns[0]; // where was it used???
		}
		if (path == null)
		return null;
		InputStream is;
		@@ -9172,6 +9210,25 @@ public class Eyesis_Correction implements PlugIn, ActionListener {
		return path;
		}


		public String [] loadMultiProperties(
		String directory,
		boolean useXML) {
		String[] XMLPatterns = { ".corr-xml", ".xml" };
		String[] confPatterns = { ".conf" };
		String[] patterns = useXML ? XMLPatterns : confPatterns;
		String [] paths = selectFiles(
		false, // boolean save,
		"Multiple configuration file selection", // title
		"Read configuration files", // button
		new MultipleExtensionsFileFilter(patterns,
		(useXML ? "XML " : "") + "Configuration files (" + (useXML ? ".corr-xml" : ".conf")
		+ ")"), // filter
		new String[] {directory}); // String[] defaultPaths)
		return paths;
		}


		/* ======================================================================== */
		public void setAllProperties(Properties properties) {
		properties.setProperty("MASTER_DEBUG_LEVEL", MASTER_DEBUG_LEVEL + "");

src/main/java/com/elphel/imagej/gpu/GpuQuad.java

+3 −1

Original line number	Diff line number	Diff line
		@@ -201,7 +201,9 @@ public class GpuQuad{ // quad camera description
		resetGeometryCorrectionVector();
		this.gpuTileProcessor.bayer_set = false;
		}

		public void resetBayer() {
		this.gpuTileProcessor.bayer_set = false;
		}
		public QuadCLT getQuadCLT( ) {
		return this.quadCLT;
		}

src/main/java/com/elphel/imagej/tileprocessor/ErsCorrection.java

+15 −0

Original line number	Diff line number	Diff line
		@@ -1972,6 +1972,21 @@ public class ErsCorrection extends GeometryCorrection {

		}

		public static double [][] invertXYZATR(
		double [] source_xyz,
		double [] source_atr)
		{
		Rotation scene_rotation= new Rotation(RotationOrder.YXZ, ROT_CONV, source_atr[0], source_atr[1], source_atr[2]);
		Vector3D scene_offset = new Vector3D(-source_xyz[0], -source_xyz[1], -source_xyz[2]);
		Rotation rotation = scene_rotation.revert(); //
		Vector3D offset = rotation.applyTo(scene_offset); // junk
		double [] angles = rotation.getAngles(RotationOrder.YXZ, ROT_CONV);
		double [] xyz = offset.toArray();
		return new double[][] {xyz,angles};
		}



		public double [] getImageCoordinatesERS(
		double [] xyzw,
		boolean correctDistortions, // correct distortion (will need corrected background too !)

src/main/java/com/elphel/imagej/tileprocessor/OpticalFlow.java

+141 −0

Original line number	Diff line number	Diff line
		@@ -3090,6 +3090,141 @@ public class OpticalFlow {
		double [] new_from_last_xyz = ers_scene_last_known.getSceneXYZ(scene_ts);
		double [] new_from_last_atr = ers_scene_last_known.getSceneATR(scene_ts);

		double [][] last_from_new = ErsCorrection.invertXYZATR(new_from_last_xyz, new_from_last_atr);
		double [][] vfy_new_from_last = ErsCorrection.invertXYZATR(last_from_new[0], last_from_new[1]);
		System.out.println(new_from_last_xyz[0]+","+new_from_last_xyz[1]+","+new_from_last_xyz[2]+","+
		new_from_last_atr[0]+","+new_from_last_atr[1]+","+new_from_last_atr[2]);
		System.out.println(last_from_new[0][0]+","+last_from_new[0][1]+","+last_from_new[0][2]+","+
		last_from_new[1][0]+","+last_from_new[1][1]+","+last_from_new[1][2]);
		System.out.println(vfy_new_from_last[0][0]+","+vfy_new_from_last[0][1]+","+vfy_new_from_last[0][2]+","+
		vfy_new_from_last[1][0]+","+vfy_new_from_last[1][1]+","+vfy_new_from_last[1][2]);
		/*
		double [][] last_from_new1 = ErsCorrection.invertXYZATR(vfy_new_from_last[0],vfy_new_from_last[1]);
		double [][] vfy_new_from_last1 = ErsCorrection.invertXYZATR(last_from_new1[0], last_from_new1[1]);

		System.out.println(last_from_new1[0][0]+","+last_from_new1[0][1]+","+last_from_new1[0][2]+","+
		last_from_new1[1][0]+","+last_from_new1[1][1]+","+last_from_new1[1][2]);
		System.out.println(vfy_new_from_last1[0][0]+","+vfy_new_from_last1[0][1]+","+vfy_new_from_last1[0][2]+","+
		vfy_new_from_last1[1][0]+","+vfy_new_from_last1[1][1]+","+vfy_new_from_last1[1][2]);
		*/



		// combine two rotations and two translations
		System.out.println("Processing scene "+i+": "+scene_QuadClt.getImageName());
		double [][] combo_XYZATR = ErsCorrection.combineXYZATR(
		last_known_xyz, // double [] reference_xyz,
		last_known_atr, // double [] reference_atr, // null?
		new_from_last_xyz, // double [] scene_xyz,
		new_from_last_atr); // double [] scene_atr)

		// before adjusting - save original ERS, restart afterwards
		double [] ers_scene_original_xyz_dt = ers_scene.getErsXYZ_dt();
		double [] ers_scene_original_atr_dt = ers_scene.getErsATR_dt();

		// ers should be correct for both

		scenes_xyzatr[i] = adjustPairsLMA(
		clt_parameters, // CLTParameters clt_parameters,
		reference_QuadClt, // QuadCLT reference_QuadCLT,
		scene_QuadClt, // QuadCLT scene_QuadCLT,
		combo_XYZATR[0], // xyz
		combo_XYZATR[1], // atr
		param_select2, // final boolean[] param_select,
		param_regweights2, // final double [] param_regweights,
		debug_level); // int debug_level)
		ers_reference.addScene(scene_QuadClt.getImageName(),
		scenes_xyzatr[i][0],
		scenes_xyzatr[i][1],
		ers_scene.getErsXYZ_dt(),
		ers_scene.getErsATR_dt()
		);

		// restore original ers data
		ers_scene.setErsDt(
		ers_scene_original_xyz_dt, // double [] ers_xyz_dt,
		ers_scene_original_atr_dt); // double [] ers_atr_dt)(ers_scene_original_xyz_dt);
		ers_scene.setupERS();
		if (debug_level > -1) {
		System.out.println("Pass multi scene "+i+" (of "+ scenes.length+") "+
		reference_QuadClt.getImageName() + "/" + scene_QuadClt.getImageName()+" Done.");
		}
		if (delete_scene_asap) {
		scenes[i+1] = null;
		}
		// Runtime.getRuntime().gc();
		// System.out.println("Scene "+i+", --- Free memory="+Runtime.getRuntime().freeMemory()+" (of "+Runtime.getRuntime().totalMemory()+")");

		}
		reference_QuadClt.saveInterProperties( // save properties for interscene processing (extrinsics, ers, ...)
		null, // String path, // full name with extension or w/o path to use x3d directory
		debug_level+1);
		if (!delete_scene_asap && (debug_level > -1)) {
		System.out.println("adjustSeries(): preparing image set...");
		int nscenes = scenes.length;
		int indx_ref = nscenes - 1;
		double [][][] all_scenes_xyzatr = new double [scenes.length][][]; // includes reference (last)
		double [][][] all_scenes_ers_dt = new double [scenes.length][][]; // includes reference (last)
		all_scenes_xyzatr[indx_ref] = new double [][] {ZERO3,ZERO3};
		all_scenes_ers_dt[indx_ref] = new double [][] {
		ers_reference.getErsXYZ_dt(),
		ers_reference.getErsATR_dt()};
		for (int i = 0; i < nscenes; i++) if (i != indx_ref) {
		String ts = scenes[i].getImageName();
		all_scenes_xyzatr[i] = new double[][] {ers_reference.getSceneXYZ(ts), ers_reference.getSceneATR(ts)};
		all_scenes_ers_dt[i] = new double[][] {ers_reference.getSceneErsXYZ_dt(ts), ers_reference.getSceneErsATR_dt(ts)};
		}
		compareRefSceneTiles(
		"" , // String suffix,
		false, // boolean blur_reference,
		all_scenes_xyzatr, // double [][][] scene_xyzatr, // does not include reference
		all_scenes_ers_dt, // double [][][] scene_ers_dt, // does not include reference
		scenes, // QuadCLT [] scenes,
		8); // int iscale) // 8
		}
		if (debug_level > -1) {
		System.out.println("adjustSeries() Done.");
		}
		}

		public void adjustSeries(
		CLTParameters clt_parameters,
		double k_prev,
		QuadCLT [] scenes, // ordered by increasing timestamps
		int ref_index,
		int debug_level
		)
		{
		double [][][] scenes_xyzatr = new double [scenes.length][][]; // previous scene relative to the next one
		QuadCLT reference_QuadClt = scenes[ref_index]; // scenes.length-1]; // last acquired
		ErsCorrection ers_reference = reference_QuadClt.getErsCorrection();
		// modify LMA parameters to freeze reference ERS, remove pull on scene ERS
		boolean[] param_select2 = clt_parameters.ilp.ilma_lma_select.clone(); // final boolean[] param_select,
		double [] param_regweights2 = clt_parameters.ilp.ilma_regularization_weights; // final double [] param_regweights,
		boolean delete_scene_asap = (debug_level < 10); // to save memory
		// freeze reference ERS, free scene ERS
		for (int j = 0; j <3; j++) {
		param_select2[ErsCorrection.DP_DVX + j] = false;
		param_select2[ErsCorrection.DP_DVAZ + j] = false;
		param_regweights2[ErsCorrection.DP_DSVX + j] = 0.0;
		param_regweights2[ErsCorrection.DP_DSVAZ + j] = 0.0;
		}

		// process scenes before reference
		if (ref_index > 1) {
		for (int i = ref_index - 2; i >=0 ; i--) {
		QuadCLT scene_QuadClt = scenes[i];
		String last_known_ts = scenes[i+1].getImageName(); // it should be present in the reference scene scenes
		String scene_ts = scenes[i].getImageName(); // it should be present in the scenes[i+1] scenes
		ErsCorrection ers_scene_last_known = scenes[i+1].getErsCorrection();
		ErsCorrection ers_scene = scene_QuadClt.getErsCorrection();

		double [] last_known_xyz = ers_reference.getSceneXYZ(last_known_ts);
		double [] last_known_atr = ers_reference.getSceneATR(last_known_ts);

		double [] new_from_last_xyz = ers_scene_last_known.getSceneXYZ(scene_ts);
		double [] new_from_last_atr = ers_scene_last_known.getSceneATR(scene_ts);

		// combine two rotations and two translations
		System.out.println("Processing scene "+i+": "+scene_QuadClt.getImageName());
		double [][] combo_XYZATR = ErsCorrection.combineXYZATR(
		@@ -3136,6 +3271,12 @@ public class OpticalFlow {
		// System.out.println("Scene "+i+", --- Free memory="+Runtime.getRuntime().freeMemory()+" (of "+Runtime.getRuntime().totalMemory()+")");

		}
		}
		// process scenes after reference (if it is not the last
		if (ref_index < (scenes.length - 1)) {
		}


		reference_QuadClt.saveInterProperties( // save properties for interscene processing (extrinsics, ers, ...)
		null, // String path, // full name with extension or w/o path to use x3d directory
		debug_level+1);

src/main/java/com/elphel/imagej/tileprocessor/QuadCLT.java

+6 −0

Original line number	Diff line number	Diff line
		@@ -5532,6 +5532,12 @@ if (debugLevel < -100) {
		}
		}

		public void resetBayer() {
		if (getGPU() != null) {
		getGPU().resetBayer();
		}
		}

		public QuadCLT spawnQuadCLT(
		String set_name,
		CLTParameters clt_parameters,

Admin message