Added GPU 2D phase correlation, related and debug functionality (84eeaf35) · Commits · Elphel / imagej-elphel

src/main/java/com/elphel/imagej/cameras/CLTParameters.java

+88 −5

Original line number	Diff line number	Diff line
		@@ -30,6 +30,7 @@ public class CLTParameters {
		public int dbg_mode = 0; // 0 - normal, +1 - no DCT/IDCT
		public int ishift_x = 0; // debug feature - shift source image by this pixels left
		public int ishift_y = 0; // debug feature - shift source image by this pixels down

		private double fat_zero = 0.05; // modify phase correlation to prevent division by very small numbers
		private double fat_zero_mono = 0.1; // modify phase correlation to prevent division by very small numbers
		private double corr_sigma = 0.8; // LPF correlation sigma
		@@ -763,7 +764,18 @@ public class CLTParameters {
		public boolean taEnFlaps = true; // Enable cost of using supertile "flaps" (not in the center 8x8 tiles area)
		public boolean taEnMismatch = false; // Enable cost of a measurement layer not having same layer in the same location or near


		// gpu processing parameters
		public int gpu_corr_rad = 7; // size of the correlation to save - initially only 15x15
		public double gpu_weight_r = 0.25;
		public double gpu_weight_b = 0.25; // weight g = 1.0 - gpu_weight_r - gpu_weight_b
		public double gpu_sigma_r = 1.1;
		public double gpu_sigma_b = 1.1;
		public double gpu_sigma_g = 0.7;
		public double gpu_sigma_m = 0.7;
		public double gpu_sigma_corr = 0.9;
		public double gpu_sigma_corr_m = 0.15;
		public double gpu_fatz = 30.0;
		public double gpu_fatz_m = 30.0;

		public boolean replaceWeakOutliers = true; // false;

		@@ -817,6 +829,15 @@ public class CLTParameters {
		return monochrome ? fat_zero_mono : fat_zero;
		}

		public double getGpuFatZero(boolean monochrome) {
		return monochrome ? gpu_fatz_m : gpu_fatz;
		}

		public double getGpuCorrSigma(boolean monochrome) {
		return monochrome ? gpu_sigma_corr_m : gpu_sigma_corr;
		}


		public double getScaleStrength(boolean aux) {
		return aux ? scale_strength_aux : scale_strength_main;
		}
		@@ -1512,6 +1533,18 @@ public class CLTParameters {
		properties.setProperty(prefix+"taEnMismatch", this.taEnMismatch +"");


		properties.setProperty(prefix+"gpu_corr_rad", this.gpu_corr_rad +"");
		properties.setProperty(prefix+"gpu_weight_r", this.gpu_weight_r +"");
		properties.setProperty(prefix+"gpu_weight_b", this.gpu_weight_b +"");
		properties.setProperty(prefix+"gpu_sigma_r", this.gpu_sigma_r +"");
		properties.setProperty(prefix+"gpu_sigma_b", this.gpu_sigma_b +"");
		properties.setProperty(prefix+"gpu_sigma_g", this.gpu_sigma_g +"");
		properties.setProperty(prefix+"gpu_sigma_m", this.gpu_sigma_m +"");
		properties.setProperty(prefix+"gpu_sigma_corr", this.gpu_sigma_corr +"");
		properties.setProperty(prefix+"gpu_sigma_corr_m", this.gpu_sigma_corr_m +"");
		properties.setProperty(prefix+"gpu_fatz", this.gpu_fatz +"");
		properties.setProperty(prefix+"gpu_fatz_m", this.gpu_fatz_m +"");

		properties.setProperty(prefix+"debug_initial_discriminate", this.debug_initial_discriminate+"");
		properties.setProperty(prefix+"dbg_migrate", this.dbg_migrate+"");

		@@ -2265,6 +2298,17 @@ public class CLTParameters {
		if (properties.getProperty(prefix+"taEnFlaps")!=null) this.taEnFlaps=Boolean.parseBoolean(properties.getProperty(prefix+"taEnFlaps"));
		if (properties.getProperty(prefix+"taEnMismatch")!=null) this.taEnMismatch=Boolean.parseBoolean(properties.getProperty(prefix+"taEnMismatch"));

		if (properties.getProperty(prefix+"gpu_corr_rad")!=null) this.gpu_corr_rad=Integer.parseInt(properties.getProperty(prefix+"gpu_corr_rad"));
		if (properties.getProperty(prefix+"gpu_weight_r")!=null) this.gpu_weight_r=Double.parseDouble(properties.getProperty(prefix+"gpu_weight_r"));
		if (properties.getProperty(prefix+"gpu_weight_b")!=null) this.gpu_weight_b=Double.parseDouble(properties.getProperty(prefix+"gpu_weight_b"));
		if (properties.getProperty(prefix+"gpu_sigma_r")!=null) this.gpu_sigma_r=Double.parseDouble(properties.getProperty(prefix+"gpu_sigma_r"));
		if (properties.getProperty(prefix+"gpu_sigma_b")!=null) this.gpu_sigma_b=Double.parseDouble(properties.getProperty(prefix+"gpu_sigma_b"));
		if (properties.getProperty(prefix+"gpu_sigma_g")!=null) this.gpu_sigma_g=Double.parseDouble(properties.getProperty(prefix+"gpu_sigma_g"));
		if (properties.getProperty(prefix+"gpu_sigma_m")!=null) this.gpu_sigma_m=Double.parseDouble(properties.getProperty(prefix+"gpu_sigma_m"));
		if (properties.getProperty(prefix+"gpu_sigma_corr")!=null) this.gpu_sigma_corr=Double.parseDouble(properties.getProperty(prefix+"gpu_sigma_corr"));
		if (properties.getProperty(prefix+"gpu_sigma_corr_m")!=null) this.gpu_sigma_corr_m=Double.parseDouble(properties.getProperty(prefix+"gpu_sigma_corr_m"));
		if (properties.getProperty(prefix+"gpu_fatz")!=null) this.gpu_fatz=Double.parseDouble(properties.getProperty(prefix+"gpu_fatz"));
		if (properties.getProperty(prefix+"gpu_fatz_m")!=null) this.gpu_fatz_m=Double.parseDouble(properties.getProperty(prefix+"gpu_fatz_m"));

		if (properties.getProperty(prefix+"debug_initial_discriminate")!=null) this.debug_initial_discriminate=Boolean.parseBoolean(properties.getProperty(prefix+"debug_initial_discriminate"));
		if (properties.getProperty(prefix+"dbg_migrate")!=null) this.dbg_migrate=Boolean.parseBoolean(properties.getProperty(prefix+"dbg_migrate"));
		@@ -3159,6 +3203,35 @@ public class CLTParameters {
		gd.addCheckbox ("Cost of using supertile \"flaps\" (not in the center 8x8 tiles area)", this.taEnFlaps);
		gd.addCheckbox ("Cost of a measurement layer not having same layer in the same location or near", this.taEnMismatch);

		gd.addTab ("GPU", "Parameters for GPU development");
		gd.addMessage ("--- GPU processing parameters ---");
		gd.addNumericField("Correlation radius", this.gpu_corr_rad, 0, 6,"pix",
		"Size of the 2D correlation - maximal radius = 7 corresponds to full 15x15 pixel tile");
		gd.addNumericField("Correlation weight R", this.gpu_weight_r, 4, 6,"",
		"Weight of R for composite 2D correlation (green weight is 1.0 -gpu_weight_r - gpu_weight_b");
		gd.addNumericField("Correlation weight B", this.gpu_weight_b, 4, 6,"",
		"Weight of R for composite 2D correlation (green weight is 1.0 -gpu_weight_r - gpu_weight_b");
		gd.addNumericField("Color LPF sigma R", this.gpu_sigma_r, 4, 6,"pix",
		"LPF sigma to process color components during aberration correction");
		gd.addNumericField("Color LPF sigma B", this.gpu_sigma_b, 4, 6,"pix",
		"LPF sigma to process color components during aberration correction");
		gd.addNumericField("Color LPF sigma G", this.gpu_sigma_g, 4, 6,"pix",
		"LPF sigma to process color components during aberration correction");
		gd.addNumericField("Monochrome LPF sigma", this.gpu_sigma_m, 4, 6,"pix",
		"LPF sigma to process monochrome (e.g.LWIR) during aberration correction");
		gd.addNumericField("LPF sigma for correlation, color", this.gpu_sigma_corr, 4, 6,"pix",
		"LPF sigma to apply to the composite 2D correlation for RGB images");
		gd.addNumericField("LPF sigma for correlation, mono", this.gpu_sigma_corr_m, 4, 6,"pix",
		"LPF sigma to apply to the composite 2D correlation for monochrome images");
		gd.addNumericField("Fat zero (absolute) for phase correlation of color images", this.gpu_fatz, 4, 6,"",
		"Add squared fat zero to the sum of squared amplitudes, color images");
		gd.addNumericField("Fat zero (absolute) for phase correlation of monochrome images", this.gpu_fatz_m, 4, 6,"",
		"Add squared fat zero to the sum of squared amplitudes, monochrome images");

		gd.addTab ("LWIR", "parameters for LWIR/EO 8-camera rig");
		this.lwir.dialogQuestions(gd);


		gd.addTab ("Debug", "Other debug images");
		gd.addMessage ("--- Other debug images ---");
		// clt_parameters.debug_initial_discriminate, // final boolean debug_initial_discriminate,
		@@ -3190,8 +3263,6 @@ public class CLTParameters {
		gd.addMessage ("Unity up vector in camera coordinate system (x - right, y - up, z - to camera): {"+
		this.vertical_xyz[0]+","+ this.vertical_xyz[1]+","+ this.vertical_xyz[2]+"}");

		gd.addTab ("LWIR", "parameters for LWIR/EO 8-camera rig");
		this.lwir.dialogQuestions(gd);

		// gd.buildDialog();
		gd.showDialog();
		@@ -3886,6 +3957,20 @@ public class CLTParameters {
		this.taEnFlaps= gd.getNextBoolean();
		this.taEnMismatch= gd.getNextBoolean();

		this.gpu_corr_rad = (int) gd.getNextNumber();
		this.gpu_weight_r = gd.getNextNumber();
		this.gpu_weight_b = gd.getNextNumber();
		this.gpu_sigma_r = gd.getNextNumber();
		this.gpu_sigma_b = gd.getNextNumber();
		this.gpu_sigma_g = gd.getNextNumber();
		this.gpu_sigma_m = gd.getNextNumber();
		this.gpu_sigma_corr = gd.getNextNumber();
		this.gpu_sigma_corr_m = gd.getNextNumber();
		this.gpu_fatz = gd.getNextNumber();
		this.gpu_fatz_m = gd.getNextNumber();

		this.lwir.dialogAnswers(gd);

		this.debug_initial_discriminate= gd.getNextBoolean();
		this.dbg_migrate= gd.getNextBoolean();

		@@ -3911,8 +3996,6 @@ public class CLTParameters {
		this.show_first_clusters= gd.getNextBoolean();
		this.show_planes= gd.getNextBoolean();

		this.lwir.dialogAnswers(gd);

		return true;
		}

src/main/java/com/elphel/imagej/cameras/EyesisCorrectionParameters.java

+4 −0

Original line number	Diff line number	Diff line
		@@ -231,6 +231,7 @@ public class EyesisCorrectionParameters {
		cp.zcorrect= this.zcorrect;
		cp.saveSettings= this.saveSettings;
		cp.sourceDirectory= this.sourceDirectory;
		cp.tile_processor_gpu = this.tile_processor_gpu;
		cp.use_set_dirs = this.use_set_dirs;
		// cp.sourcePrefix= this.sourcePrefix;
		// cp.sourceSuffix= this.sourceSuffix;
		@@ -388,6 +389,8 @@ public class EyesisCorrectionParameters {
		properties.setProperty(prefix+"saveSettings",this.saveSettings+"");

		properties.setProperty(prefix+"sourceDirectory",this.sourceDirectory);
		properties.setProperty(prefix+"tile_processor_gpu",this.tile_processor_gpu);

		properties.setProperty(prefix+"use_set_dirs", this.use_set_dirs+"");

		properties.setProperty(prefix+"sourcePrefix",this.sourcePrefix);
		@@ -543,6 +546,7 @@ public class EyesisCorrectionParameters {
		if (properties.getProperty(prefix+"zcorrect")!=null) this.zcorrect=Boolean.parseBoolean(properties.getProperty(prefix+"zcorrect"));
		if (properties.getProperty(prefix+"saveSettings")!=null) this.saveSettings=Boolean.parseBoolean(properties.getProperty(prefix+"saveSettings"));
		if (properties.getProperty(prefix+"sourceDirectory")!= null) this.sourceDirectory=properties.getProperty(prefix+"sourceDirectory");
		if (properties.getProperty(prefix+"tile_processor_gpu")!= null) this.tile_processor_gpu=properties.getProperty(prefix+"tile_processor_gpu");
		if (properties.getProperty(prefix+"firstSubCamera")!= null) this.firstSubCamera=Integer.parseInt(properties.getProperty(prefix+"firstSubCamera"));
		if (properties.getProperty(prefix+"firstSubCameraConfig")!= null) this.firstSubCameraConfig=Integer.parseInt(properties.getProperty(prefix+"firstSubCameraConfig"));
		if (properties.getProperty(prefix+"numSubCameras")!= null) this.numSubCameras=Integer.parseInt(properties.getProperty(prefix+"numSubCameras"));

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

+1 −1

Original line number	Diff line number	Diff line
		@@ -1220,7 +1220,7 @@ public class EyesisDCT {
		}

		if (this.correctionsParameters.deconvolve) { // process with DCT, otherwise use simple debayer
		ImageDtt image_dtt = new ImageDtt(false, 1.0); // Bayer( not monochrome), scale correlation strengths
		ImageDtt image_dtt = new ImageDtt(dctParameters.dct_size, false, 1.0); // Bayer( not monochrome), scale correlation strengths
		double [][][][] dct_data = image_dtt.mdctStack(
		stack,
		channel,

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

+17 −9

Original line number	Diff line number	Diff line
		@@ -3075,7 +3075,7 @@ private Panel panel1,
		}

		}
		ImageDtt image_dtt = new ImageDtt(false, 1.0); // Bayer( not monochrome), scale correlation strengths
		ImageDtt image_dtt = new ImageDtt(DCT_PARAMETERS.dct_size, false, 1.0); // Bayer( not monochrome), scale correlation strengths
		double [][][][] dctdc_data = image_dtt.mdctScale(
		DBG_IMP.getStack(),
		DCT_PARAMETERS.kernel_chn,
		@@ -3173,7 +3173,7 @@ private Panel panel1,
		}

		}
		ImageDtt image_dtt = new ImageDtt(false, 1.0); // Bayer( not monochrome), scale correlation strengths
		ImageDtt image_dtt = new ImageDtt(DCT_PARAMETERS.dct_size,false, 1.0); // Bayer( not monochrome), scale correlation strengths
		double [][][][] dctdc_data = image_dtt.mdctStack(
		DBG_IMP.getStack(),
		DCT_PARAMETERS.kernel_chn,
		@@ -5723,6 +5723,7 @@ private Panel panel1,
		if (!prepareRigImages()) return false;
		String configPath=getSaveCongigPath();
		if (configPath.equals("ABORT")) return false;
		// if ((CORRECTION_PARAMETERS.tile_processor_gpu != null) &&

		if (DEBUG_LEVEL > -2){
		System.out.println("++++++++++++++ Calculating combined correlations ++++++++++++++");
		@@ -5740,6 +5741,7 @@ private Panel panel1,

		try {
		TWO_QUAD_CLT.prepareFilesForGPUDebug(
		CORRECTION_PARAMETERS.tile_processor_gpu,// String save_prefix, // absolute path to the cuda project root
		QUAD_CLT, // QuadCLT quadCLT_main,
		QUAD_CLT_AUX, // QuadCLT quadCLT_aux,
		CLT_PARAMETERS, // EyesisCorrectionParameters.DCTParameters dct_parameters,
		@@ -7048,7 +7050,10 @@ private Panel panel1,
		}
		}

		ImageDtt image_dtt = new ImageDtt(false, 1.0); // Bayer( not monochrome), scale correlation strengths
		ImageDtt image_dtt = new ImageDtt(
		CLT_PARAMETERS.transform_size,
		false,
		1.0); // Bayer( not monochrome), scale correlation strengths
		double [][][][][] clt_data = image_dtt.cltStack(
		DBG_IMP.getStack(),
		0, // CLT_PARAMETERS.kernel_chn,
		@@ -7082,7 +7087,7 @@ private Panel panel1,
		for (int chn = 0; chn < clt_data.length; chn++) {
		clt_data[chn] = image_dtt.clt_shiftXY(
		clt_data[chn], // final double [][][][] dct_data, // array [tilesY][tilesX][4][dct_size*dct_size]
		CLT_PARAMETERS.transform_size, // final int dct_size,
		/// CLT_PARAMETERS.transform_size, // final int dct_size,
		CLT_PARAMETERS.shift_x, // final double shiftX,
		CLT_PARAMETERS.shift_y, // final double shiftY,
		(CLT_PARAMETERS.dbg_mode >> 2) & 3, // swap order hor/vert
		@@ -7095,7 +7100,7 @@ private Panel panel1,
		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.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
		@@ -7178,7 +7183,10 @@ private Panel panel1,

		}
		String suffix = "-dx_"+(CLT_PARAMETERS.ishift_x+CLT_PARAMETERS.shift_x)+"_dy_"+(CLT_PARAMETERS.ishift_y+CLT_PARAMETERS.shift_y);
		ImageDtt image_dtt = new ImageDtt(COLOR_PROC_PARAMETERS.isMonochrome(), CLT_PARAMETERS.getScaleStrength(false)); // Bayer, not monochrome
		ImageDtt image_dtt = new ImageDtt(
		CLT_PARAMETERS.transform_size,
		COLOR_PROC_PARAMETERS.isMonochrome(),
		CLT_PARAMETERS.getScaleStrength(false)); // Bayer, not monochrome
		String [] titles = {
		"redCC", "redSC", "redCS", "redSS",
		"blueCC", "blueSC", "blueCS", "blueSS",
		@@ -7235,7 +7243,7 @@ private Panel panel1,
		for (int chn = 0; chn < clt_data.length; chn++) {
		clt_data2[chn] = image_dtt.clt_shiftXY(
		clt_data2[chn], // final double [][][][] dct_data, // array [tilesY][tilesX][4][dct_size*dct_size]
		CLT_PARAMETERS.transform_size, // final int dct_size,
		/// CLT_PARAMETERS.transform_size, // final int dct_size,
		CLT_PARAMETERS.shift_x, // final double shiftX,
		CLT_PARAMETERS.shift_y, // final double shiftY,
		(CLT_PARAMETERS.dbg_mode >> 2) & 3, // swap order hor/vert
		@@ -7266,7 +7274,7 @@ private Panel panel1,
		clt_corr[chn] = image_dtt.clt_correlate(
		clt_data[chn], // final double [][][][] data1, // array [tilesY][tilesX][4][dct_size*dct_size]
		clt_data2[chn], // final double [][][][] data2, // array [tilesY][tilesX][4][dct_size*dct_size]
		CLT_PARAMETERS.transform_size, // final int dct_size,
		/// CLT_PARAMETERS.transform_size, // final int dct_size,
		CLT_PARAMETERS.getFatZero(image_dtt.isMonochrome()), // final double fat_zero, // add to denominator to modify phase correlation (same units as data1, data2)
		CLT_PARAMETERS.tileX, //final int debug_tileX
		CLT_PARAMETERS.tileY, //final int debug_tileY
		@@ -7297,7 +7305,7 @@ private Panel panel1,
		image_dtt.clt_lpf( // filter in-place
		CLT_PARAMETERS.getCorrSigma(image_dtt.isMonochrome()), // final double sigma,
		clt_corr[chn], // final double [][][][] clt_data,
		CLT_PARAMETERS.transform_size,
		/// CLT_PARAMETERS.transform_size,
		THREADS_MAX, // maximal number of threads to launch
		DEBUG_LEVEL); // globalDebugLevel)
		}

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

+286 −31

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