Adding arbitrary reference frame (not just the last), debugging 'Super (91f2ace8) · Commits · Elphel / imagej-elphel

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

+1 −1

Original line number	Original line	Diff line number	Diff line
	@@ -2705,7 +2705,7 @@ public class EyesisCorrections {
	png,		png,
	show,		show,
	jpegQuality,// <0 - keep current, 0 - force Tiff, >0 use for JPEG		jpegQuality,// <0 - keep current, 0 - force Tiff, >0 use for JPEG
	this.debugLevel);		this.debugLevel+3);
	}		}

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

+3 −1

Original line number	Original line	Diff line number	Diff line
	@@ -7141,7 +7141,9 @@ public class Eyesis_Correction implements PlugIn, ActionListener {
	QuadCLT quadCLT = use_aux ? QUAD_CLT_AUX : QUAD_CLT;		QuadCLT quadCLT = use_aux ? QUAD_CLT_AUX : QUAD_CLT;
	ColorProcParameters colorProcParameters = use_aux ? COLOR_PROC_PARAMETERS_AUX : COLOR_PROC_PARAMETERS;		ColorProcParameters colorProcParameters = use_aux ? COLOR_PROC_PARAMETERS_AUX : COLOR_PROC_PARAMETERS;
	try {		try {
	TWO_QUAD_CLT.interIntraExportML(quadCLT, // QuadCLT quadCLT_main,		TWO_QUAD_CLT.interIntraExportML(
			quadCLT, // QuadCLT quadCLT_main,
			-1, // use last // int indx_ref, // = num_scenes - 1;
	CLT_PARAMETERS, // EyesisCorrectionParameters.DCTParameters dct_parameters,		CLT_PARAMETERS, // EyesisCorrectionParameters.DCTParameters dct_parameters,
	DEBAYER_PARAMETERS, // EyesisCorrectionParameters.DebayerParameters debayerParameters,		DEBAYER_PARAMETERS, // EyesisCorrectionParameters.DebayerParameters debayerParameters,
	colorProcParameters, // EyesisCorrectionParameters.ColorProcParameters colorProcParameters,		colorProcParameters, // EyesisCorrectionParameters.ColorProcParameters colorProcParameters,

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

+35 −30

Original line number	Original line	Diff line number	Diff line
	@@ -1526,7 +1526,8 @@ public class OpticalFlow {
	}		}
	int iwidth = imax_tX - imin_tX + 1;		int iwidth = imax_tX - imin_tX + 1;
	int iheight = imax_tY - imin_tY + 1;		int iheight = imax_tY - imin_tY + 1;
	if ((iwidth <= 0) \|\| (iheight <= 0)) {		//// if ((iwidth <= 0) \|\| (iheight <= 0)) {
			if ((iwidth <= 1) \|\| (iheight <= 1)) {
	System.out.println ("prepareSceneTiles(): iwidth ="+iwidth+", iheight ="+iheight+", min_tX="+min_tX+", imin_tY="+imin_tY+", max_tX="+max_tX+", imax_tY="+imax_tY);		System.out.println ("prepareSceneTiles(): iwidth ="+iwidth+", iheight ="+iheight+", min_tX="+min_tX+", imin_tY="+imin_tY+", max_tX="+max_tX+", imax_tY="+imax_tY);
	continue;		continue;
	}		}
	@@ -3480,8 +3481,8 @@ public class OpticalFlow {
	}		}
	double [][] disparity_map = null;		double [][] disparity_map = null;
	for (int nrefine = 0; nrefine < max_refines; nrefine++) {		for (int nrefine = 0; nrefine < max_refines; nrefine++) {
	Runtime.getRuntime().gc();		/// Runtime.getRuntime().gc();
	System.out.println("--- Free memory="+Runtime.getRuntime().freeMemory()+" (of "+Runtime.getRuntime().totalMemory()+")");		/// System.out.println("--- Free memory="+Runtime.getRuntime().freeMemory()+" (of "+Runtime.getRuntime().totalMemory()+")");
	int mcorr_sel = Correlation2d.corrSelEncode(clt_parameters.img_dtt,scenes[indx_ref].getNumSensors());		int mcorr_sel = Correlation2d.corrSelEncode(clt_parameters.img_dtt,scenes[indx_ref].getNumSensors());
	disparity_map = correlateInterscene(		disparity_map = correlateInterscene(
	clt_parameters, // final CLTParameters clt_parameters,		clt_parameters, // final CLTParameters clt_parameters,
	@@ -3496,8 +3497,8 @@ public class OpticalFlow {
	false, // final boolean no_map, // do not generate disparity_map (time-consuming LMA)		false, // final boolean no_map, // do not generate disparity_map (time-consuming LMA)
	debug_level-5); // final int debug_level)		debug_level-5); // final int debug_level)

	Runtime.getRuntime().gc();		/// Runtime.getRuntime().gc();
	System.out.println("--- Free memory="+Runtime.getRuntime().freeMemory()+" (of "+Runtime.getRuntime().totalMemory()+")");		/// System.out.println("--- Free memory="+Runtime.getRuntime().freeMemory()+" (of "+Runtime.getRuntime().totalMemory()+")");

	(new ShowDoubleFloatArrays()).showArrays(		(new ShowDoubleFloatArrays()).showArrays(
	disparity_map,		disparity_map,
	@@ -3699,8 +3700,8 @@ public class OpticalFlow {
	}		}
	}		}
	for (int nrefine = 0; nrefine < max_refines; nrefine++) {		for (int nrefine = 0; nrefine < max_refines; nrefine++) {
	Runtime.getRuntime().gc();		/// Runtime.getRuntime().gc();
	System.out.println("--- Free memory="+Runtime.getRuntime().freeMemory()+" (of "+Runtime.getRuntime().totalMemory()+")");		/// System.out.println("--- Free memory="+Runtime.getRuntime().freeMemory()+" (of "+Runtime.getRuntime().totalMemory()+")");

	double [][] disparity_map =		double [][] disparity_map =
	// double [][][][][] clt_corr_partial =		// double [][][][][] clt_corr_partial =
	@@ -3713,8 +3714,8 @@ public class OpticalFlow {
	nrefine, // final int nrefine, // just for debug title		nrefine, // final int nrefine, // just for debug title
	debug_level-5); // final int debug_level)		debug_level-5); // final int debug_level)

	Runtime.getRuntime().gc();		/// Runtime.getRuntime().gc();
	System.out.println("--- Free memory="+Runtime.getRuntime().freeMemory()+" (of "+Runtime.getRuntime().totalMemory()+")");		/// System.out.println("--- Free memory="+Runtime.getRuntime().freeMemory()+" (of "+Runtime.getRuntime().totalMemory()+")");
	if (debug_level > 0) {		if (debug_level > 0) {
	(new ShowDoubleFloatArrays()).showArrays(		(new ShowDoubleFloatArrays()).showArrays(
	disparity_map,		disparity_map,
	@@ -3972,8 +3973,8 @@ public class OpticalFlow {
	}		}

	ImagePlus imp_stack = new ImagePlus("scene_outlines", stack);		ImagePlus imp_stack = new ImagePlus("scene_outlines", stack);
	imp_stack.getProcessor().resetMinAndMax();		// imp_stack.getProcessor().resetMinAndMax();
	imp_stack.show();		// imp_stack.show();
	return imp_stack;		return imp_stack;
	}		}

	@@ -3987,6 +3988,7 @@ public class OpticalFlow {
	int debug_level		int debug_level
	)		)
	{		{
			boolean generate_outlines = true; // TODO: move to configs
	System.out.println("intersceneExport(), scene timestamp="+ref_scene.getImageName());		System.out.println("intersceneExport(), scene timestamp="+ref_scene.getImageName());
	int num_scenes = scenes.length;		int num_scenes = scenes.length;
	String [] combo_dsn_titles = {"disp", "strength","disp_lma","num_valid","change"};		String [] combo_dsn_titles = {"disp", "strength","disp_lma","num_valid","change"};
	@@ -4023,7 +4025,7 @@ public class OpticalFlow {
	final int tilesX = ref_scene.getTileProcessor().getTilesX();		final int tilesX = ref_scene.getTileProcessor().getTilesX();
	final int tilesY = ref_scene.getTileProcessor().getTilesY();		final int tilesY = ref_scene.getTileProcessor().getTilesY();
	final int tiles = tilesX * tilesY;		final int tiles = tilesX * tilesY;
	if (debug_level > 100) { // add parameter?		if (generate_outlines) { // debug_level > 100) { // add parameter?
	int extra = 10; // pixels around largest outline		int extra = 10; // pixels around largest outline
	int scale = 4;		int scale = 4;

	@@ -4043,7 +4045,10 @@ public class OpticalFlow {
	line_color_outline, // Color line_color_outline,		line_color_outline, // Color line_color_outline,
	line_color_corners // Color line_color_corners		line_color_corners // Color line_color_corners
	);		);
	imp_outlines.show();		ref_scene.saveImagePlusInModelDirectory(
			"scene_outlines", // String suffix,
			imp_outlines); // ImagePlus imp)
			// imp_outlines.show();
	}		}
	final double [][] combo_dsn_change = new double [combo_dsn_titles.length] [tiles];		final double [][] combo_dsn_change = new double [combo_dsn_titles.length] [tiles];
	for (int i = 0; i < combo_dsn.length; i++) { // 4 elements: "disp", "strength","disp_lma","num_valid"		for (int i = 0; i < combo_dsn.length; i++) { // 4 elements: "disp", "strength","disp_lma","num_valid"
	@@ -4792,8 +4797,8 @@ public class OpticalFlow {
	}		}
	}		}
	for (int nrefine = 0; nrefine < max_refines; nrefine++) {		for (int nrefine = 0; nrefine < max_refines; nrefine++) {
	Runtime.getRuntime().gc();		/// Runtime.getRuntime().gc();
	System.out.println("--- Free memory="+Runtime.getRuntime().freeMemory()+" (of "+Runtime.getRuntime().totalMemory()+")");		/// System.out.println("--- Free memory="+Runtime.getRuntime().freeMemory()+" (of "+Runtime.getRuntime().totalMemory()+")");
	int mcorr_sel = Correlation2d.corrSelEncode(clt_parameters.img_dtt,scenes[indx_ref].getNumSensors());		int mcorr_sel = Correlation2d.corrSelEncode(clt_parameters.img_dtt,scenes[indx_ref].getNumSensors());
	double [][] disparity_map =		double [][] disparity_map =
	correlateInterscene(		correlateInterscene(
	@@ -4809,8 +4814,8 @@ public class OpticalFlow {
	false, // final boolean no_map, // do not generate disparity_map (time-consuming LMA)		false, // final boolean no_map, // do not generate disparity_map (time-consuming LMA)
	debug_level-5); // final int debug_level)		debug_level-5); // final int debug_level)

	Runtime.getRuntime().gc();		/// Runtime.getRuntime().gc();
	System.out.println("--- Free memory="+Runtime.getRuntime().freeMemory()+" (of "+Runtime.getRuntime().totalMemory()+")");		/// System.out.println("--- Free memory="+Runtime.getRuntime().freeMemory()+" (of "+Runtime.getRuntime().totalMemory()+")");

	if (debug_level > 0) {		if (debug_level > 0) {
	(new ShowDoubleFloatArrays()).showArrays(		(new ShowDoubleFloatArrays()).showArrays(
	@@ -5228,8 +5233,8 @@ public double[][] correlateIntersceneDebug( // only uses GPU and quad
	wis_wh, // final int [] wh,		wis_wh, // final int [] wh,
	image_dtt.transform_size, // final int transform_size,		image_dtt.transform_size, // final int transform_size,
	threadsMax); // final int threadsMax) // maximal number of threads to launch		threadsMax); // final int threadsMax) // maximal number of threads to launch
	Runtime.getRuntime().gc();		/// Runtime.getRuntime().gc();
	System.out.println("--- Free memory="+Runtime.getRuntime().freeMemory()+" (of "+Runtime.getRuntime().totalMemory()+")");		/// System.out.println("--- Free memory="+Runtime.getRuntime().freeMemory()+" (of "+Runtime.getRuntime().totalMemory()+")");
	}		}
	if ((vis_corr_pd != null) \|\| (fclt_corrs != null)) { // calculate and extract correlation		if ((vis_corr_pd != null) \|\| (fclt_corrs != null)) { // calculate and extract correlation
	image_dtt.clt_process_tl_correlations_GPU( // convert to pixel domain and process correlations already prepared in fcorr_td and/or fcorr_combo_td		image_dtt.clt_process_tl_correlations_GPU( // convert to pixel domain and process correlations already prepared in fcorr_td and/or fcorr_combo_td
	@@ -5276,8 +5281,8 @@ public double[][] correlateIntersceneDebug( // only uses GPU and quad
	threadsMax); // final int threadsMax) // maximal number of threads to launch		threadsMax); // final int threadsMax) // maximal number of threads to launch

	}		}
	Runtime.getRuntime().gc();		/// Runtime.getRuntime().gc();
	System.out.println("--- Free memory="+Runtime.getRuntime().freeMemory()+" (of "+Runtime.getRuntime().totalMemory()+")");		/// System.out.println("--- Free memory="+Runtime.getRuntime().freeMemory()+" (of "+Runtime.getRuntime().totalMemory()+")");
	//nscene		//nscene
	if (debug_dhv != null) {		if (debug_dhv != null) {
	debug_dhv[3 * nscene + 0] = disparity_map[ImageDtt.DISPARITY_INDEX_CM];		debug_dhv[3 * nscene + 0] = disparity_map[ImageDtt.DISPARITY_INDEX_CM];
	@@ -5450,8 +5455,8 @@ public double[][] correlateIntersceneDebug( // only uses GPU and quad
	dbg_titles);		dbg_titles);
	}		}

	Runtime.getRuntime().gc();		/// Runtime.getRuntime().gc();
	System.out.println("--- Free memory="+Runtime.getRuntime().freeMemory()+" (of "+Runtime.getRuntime().totalMemory()+")");		/// System.out.println("--- Free memory="+Runtime.getRuntime().freeMemory()+" (of "+Runtime.getRuntime().totalMemory()+")");
	final float [][][] fclt_corr = new float [tilesX * tilesY][][];		final float [][][] fclt_corr = new float [tilesX * tilesY][][];
	image_dtt.clt_process_tl_correlations_GPU( // convert to pixel domain and process correlations already prepared in fcorr_td and/or fcorr_combo_td		image_dtt.clt_process_tl_correlations_GPU( // convert to pixel domain and process correlations already prepared in fcorr_td and/or fcorr_combo_td
	clt_parameters.img_dtt, // final ImageDttParameters imgdtt_params, // Now just extra correlation parameters, later will include, most others		clt_parameters.img_dtt, // final ImageDttParameters imgdtt_params, // Now just extra correlation parameters, later will include, most others
	@@ -5914,8 +5919,8 @@ public double[][] correlateIntersceneDebug( // only uses GPU and quad
	}		}


	Runtime.getRuntime().gc();		/// Runtime.getRuntime().gc();
	System.out.println("--- Free memory="+Runtime.getRuntime().freeMemory()+" (of "+Runtime.getRuntime().totalMemory()+")");		/// System.out.println("--- Free memory="+Runtime.getRuntime().freeMemory()+" (of "+Runtime.getRuntime().totalMemory()+")");

	if (vis_corr_td != null) { // add combined data as the last slice		if (vis_corr_td != null) { // add combined data as the last slice
	vis_corr_td[num_scenes] = ImageDtt.corr_td_wnd(		vis_corr_td[num_scenes] = ImageDtt.corr_td_wnd(
	@@ -6281,8 +6286,8 @@ public double[][] correlateIntersceneDebug( // only uses GPU and quad


	}		}
	Runtime.getRuntime().gc();		/// Runtime.getRuntime().gc();
	System.out.println("--- Free memory="+Runtime.getRuntime().freeMemory()+" (of "+Runtime.getRuntime().totalMemory()+")");		/// System.out.println("--- Free memory="+Runtime.getRuntime().freeMemory()+" (of "+Runtime.getRuntime().totalMemory()+")");
	// Normalize accumulated corelations		// Normalize accumulated corelations
	if (ref_scene.hasGPU()) {		if (ref_scene.hasGPU()) {
	accumulateCorrelationsAcOnly(		accumulateCorrelationsAcOnly(
	@@ -6385,8 +6390,8 @@ public double[][] correlateIntersceneDebug( // only uses GPU and quad

	}		}

	Runtime.getRuntime().gc();		/// Runtime.getRuntime().gc();
	System.out.println("--- Free memory="+Runtime.getRuntime().freeMemory()+" (of "+Runtime.getRuntime().totalMemory()+")");		/// System.out.println("--- Free memory="+Runtime.getRuntime().freeMemory()+" (of "+Runtime.getRuntime().totalMemory()+")");
	if (show_accumulated_correlations \|\| (accum_2d_corr != null)){ // -1		if (show_accumulated_correlations \|\| (accum_2d_corr != null)){ // -1
	float [][] accum_2d_img = ImageDtt.corr_partial_dbg( // not used in lwir		float [][] accum_2d_img = ImageDtt.corr_partial_dbg( // not used in lwir
	fclt_corr, // final float [][][] fcorr_data, // [tile][pair][(2transform_size-1)(2*transform_size-1)] // if null - will not calculate		fclt_corr, // final float [][][] fcorr_data, // [tile][pair][(2transform_size-1)(2*transform_size-1)] // if null - will not calculate

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

+5 −0

Original line number	Original line	Diff line number	Diff line
	@@ -109,6 +109,11 @@ public class QuadCLT extends QuadCLTCPU {
	}		}
	}		}

			void setQuadClt() {
			if (gpuQuad != null) {
			gpuQuad.updateQuadCLT(this); // to re-load new set of Bayer images to the GPU
			}
			}

	public QuadCLT(QuadCLTCPU pq, String name) {		public QuadCLT(QuadCLTCPU pq, String name) {
	super (pq, name);		super (pq, name);

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

+18 −5

Original line number	Original line	Diff line number	Diff line
	@@ -222,7 +222,10 @@ public class QuadCLTCPU {
	return null;		return null;
	}		}

	void restoreQuadClt(QuadCLT savedQuadClt) {		void restoreQuadClt(QuadCLT savedQuadClt) { // do nothing
			}

			void setQuadClt() { // do nothing
	}		}

	double [][][][][][] getCltKernels() {		double [][][][][][] getCltKernels() {
	@@ -937,10 +940,6 @@ public class QuadCLTCPU {
	}		}






	public ImagePlus saveDoubleArrayInModelDirectory(		public ImagePlus saveDoubleArrayInModelDirectory(
	String suffix,		String suffix,
	String [] labels, // or null		String [] labels, // or null
	@@ -959,6 +958,20 @@ public class QuadCLTCPU {
	return imp;		return imp;
	}		}

			public void saveImagePlusInModelDirectory(
			String suffix,
			ImagePlus imp)
			{
			String x3d_path = getX3dDirectory();
			String file_name = image_name + suffix;
			String file_path = x3d_path + Prefs.getFileSeparator() + file_name + ".tiff";
			FileSaver fs=new FileSaver(imp);
			fs.saveAsTiff(file_path);
			System.out.println("saveDoubleArrayInModelDirectory(): saved "+file_path);
			}



	public double [][] readDoubleArrayFromModelDirectory(		public double [][] readDoubleArrayFromModelDirectory(
	String suffix,		String suffix,
	int num_slices, // (0 - all)		int num_slices, // (0 - all)

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