next snapshot (238bf728) · Commits · Elphel / imagej-elphel

src/main/java/EyesisCorrectionParameters.java

+56 −4

Original line number	Diff line number	Diff line
		@@ -1914,12 +1914,20 @@ public class EyesisCorrectionParameters {

		public int tile_task_op = 0xff; // bitmask of operation modes applied to tiles (0 - nothing), bits TBD later
		// +(0..f) - images, +(00.f0) - process pairs +256 - force disparity when combining images
		// window to process tiles;
		// window to process tiles (later arbitrary masks will be generated to follow particular stages);
		public int tile_task_wl = 0; //
		public int tile_task_wt = 0; //
		public int tile_task_ww = 324; //
		public int tile_task_wh = 242; //

		public double diff_thershold = 5.0; // RMS difference from average to discard channel (~ 1.0 - 1/255 full scale image)
		public boolean diff_gauss = true; // when averaging images, use gaussian around average as weight (false - sharp all/nothing)

		public boolean sharp_alpha = false; // combining mode for alpha channel: false - treat as RGB, true - apply center 8x8 only
		public boolean gen_chn_img = false; // generate shifted channel images
		public boolean show_nonoverlap = true; // show result RGBA before overlap combined (first channels, then RGBA combined?)
		public boolean show_overlap = true; // show result RGBA (first channels, then RGBA combined?)




		@@ -1943,7 +1951,6 @@ public class EyesisCorrectionParameters {
		properties.setProperty(prefix+"novignetting_r", this.novignetting_r+"");
		properties.setProperty(prefix+"novignetting_g", this.novignetting_g+"");
		properties.setProperty(prefix+"novignetting_b", this.novignetting_b+"");

		properties.setProperty(prefix+"scale_r", this.scale_r+"");
		properties.setProperty(prefix+"scale_g", this.scale_g+"");
		properties.setProperty(prefix+"scale_b", this.scale_b+"");
		@@ -1964,6 +1971,17 @@ public class EyesisCorrectionParameters {
		properties.setProperty(prefix+"max_corr_sigma", this.max_corr_sigma +"");
		properties.setProperty(prefix+"max_corr_radius", this.max_corr_radius +"");
		properties.setProperty(prefix+"corr_border_contrast", this.corr_border_contrast +"");
		properties.setProperty(prefix+"tile_task_op", this.tile_task_op+"");
		properties.setProperty(prefix+"tile_task_wl", this.tile_task_wl+"");
		properties.setProperty(prefix+"tile_task_wt", this.tile_task_wt+"");
		properties.setProperty(prefix+"tile_task_ww", this.tile_task_ww+"");
		properties.setProperty(prefix+"tile_task_wh", this.tile_task_wh+"");
		properties.setProperty(prefix+"diff_thershold", this.diff_thershold +"");
		properties.setProperty(prefix+"diff_gauss", this.diff_gauss+"");
		properties.setProperty(prefix+"sharp_alpha", this.sharp_alpha+"");
		properties.setProperty(prefix+"gen_chn_img", this.gen_chn_img+"");
		properties.setProperty(prefix+"show_nonoverlap", this.show_nonoverlap+"");
		properties.setProperty(prefix+"show_overlap", this.show_overlap+"");

		}
		public void getProperties(String prefix,Properties properties){
		@@ -2005,6 +2023,18 @@ public class EyesisCorrectionParameters {
		if (properties.getProperty(prefix+"max_corr_sigma")!=null) this.max_corr_sigma=Double.parseDouble(properties.getProperty(prefix+"max_corr_sigma"));
		if (properties.getProperty(prefix+"max_corr_radius")!=null) this.max_corr_radius=Double.parseDouble(properties.getProperty(prefix+"max_corr_radius"));
		if (properties.getProperty(prefix+"corr_border_contrast")!=null) this.corr_border_contrast=Double.parseDouble(properties.getProperty(prefix+"corr_border_contrast"));
		if (properties.getProperty(prefix+"tile_task_op")!=null) this.tile_task_op=Integer.parseInt(properties.getProperty(prefix+"tile_task_op"));
		if (properties.getProperty(prefix+"tile_task_wl")!=null) this.tile_task_wl=Integer.parseInt(properties.getProperty(prefix+"tile_task_wl"));
		if (properties.getProperty(prefix+"tile_task_wt")!=null) this.tile_task_wt=Integer.parseInt(properties.getProperty(prefix+"tile_task_wt"));
		if (properties.getProperty(prefix+"tile_task_ww")!=null) this.tile_task_ww=Integer.parseInt(properties.getProperty(prefix+"tile_task_ww"));
		if (properties.getProperty(prefix+"tile_task_wh")!=null) this.tile_task_wh=Integer.parseInt(properties.getProperty(prefix+"tile_task_wh"));
		if (properties.getProperty(prefix+"diff_thershold")!=null) this.diff_thershold=Double.parseDouble(properties.getProperty(prefix+"diff_thershold"));
		if (properties.getProperty(prefix+"diff_gauss")!=null) this.diff_gauss=Boolean.parseBoolean(properties.getProperty(prefix+"v"));
		if (properties.getProperty(prefix+"sharp_alpha")!=null) this.sharp_alpha=Boolean.parseBoolean(properties.getProperty(prefix+"sharp_alpha"));
		if (properties.getProperty(prefix+"gen_chn_img")!=null) this.gen_chn_img=Boolean.parseBoolean(properties.getProperty(prefix+"gen_chn_img"));
		if (properties.getProperty(prefix+"show_nonoverlap")!=null)this.show_nonoverlap=Boolean.parseBoolean(properties.getProperty(prefix+"show_nonoverlap"));
		if (properties.getProperty(prefix+"show_overlap")!=null) this.show_overlap=Boolean.parseBoolean(properties.getProperty(prefix+"show_overlap"));

		}

		public boolean showDialog() {
		@@ -2047,6 +2077,18 @@ public class EyesisCorrectionParameters {
		gd.addNumericField("Sigma for weights of points around global max to find fractional", this.max_corr_sigma, 3);
		gd.addNumericField("Maximal distance from int max to consider", this.max_corr_radius, 3);
		gd.addNumericField("Contrast of dotted border on correlation results", this.corr_border_contrast, 6);
		gd.addMessage("--- tiles tasks ---");
		gd.addNumericField("Tile operations bits: +(0..f) - images, +(00.f0) - process pairs +256, ... ", this.tile_task_op, 0);
		gd.addNumericField("Tile operations window left (in 8x8 tiles)", this.tile_task_wl, 0);
		gd.addNumericField("Tile operations window top", this.tile_task_wt, 0);
		gd.addNumericField("Tile operations window width", this.tile_task_ww, 0);
		gd.addNumericField("Tile operations window height", this.tile_task_wh, 0);
		gd.addNumericField("RMS difference from average to discard channel (255 full scale image)", this.diff_thershold, 4);
		gd.addCheckbox ("Gaussian as weight when averaging images (false - sharp all/nothing)", this.diff_gauss);
		gd.addCheckbox ("Alpha channel: use center 8x8 (unchecked - treat same as RGB)", this.sharp_alpha);
		gd.addCheckbox ("Generate shifted channel images", this.gen_chn_img);
		gd.addCheckbox ("Show result RGBA before overlap combined", this.show_nonoverlap);
		gd.addCheckbox ("Show result RGBA ", this.show_overlap);

		WindowTools.addScrollBars(gd);
		gd.showDialog();
		@@ -2090,7 +2132,17 @@ public class EyesisCorrectionParameters {
		this.max_corr_sigma= gd.getNextNumber();
		this.max_corr_radius= gd.getNextNumber();
		this.corr_border_contrast= gd.getNextNumber();

		this.tile_task_op= (int) gd.getNextNumber();
		this.tile_task_wl= (int) gd.getNextNumber();
		this.tile_task_wt= (int) gd.getNextNumber();
		this.tile_task_ww= (int) gd.getNextNumber();
		this.tile_task_wh= (int) gd.getNextNumber();
		this.diff_thershold= gd.getNextNumber();
		this.diff_gauss= gd.getNextBoolean();
		this.sharp_alpha= gd.getNextBoolean();
		this.gen_chn_img= gd.getNextBoolean();
		this.show_nonoverlap= gd.getNextBoolean();
		this.show_overlap= gd.getNextBoolean();
		return true;
		}
		}

src/main/java/EyesisDCT.java

+344 −243

Original line number	Diff line number	Diff line
		@@ -2920,6 +2920,7 @@ public class EyesisDCT {
		image_dtt.clt_lpf(
		clt_parameters.corr_sigma,
		clt_data[chn],
		clt_parameters.transform_size,
		threadsMax,
		debugLevel);
		}
		@@ -3612,6 +3613,7 @@ public class EyesisDCT {
		image_dtt.clt_lpf(
		clt_parameters.corr_sigma,
		clt_data[chn],
		clt_parameters.transform_size,
		threadsMax,
		debugLevel);
		}
		@@ -4237,6 +4239,7 @@ public class EyesisDCT {
		image_dtt.clt_lpf(
		clt_parameters.corr_sigma,
		clt_data[iQuad][chn],
		clt_parameters.transform_size,
		threadsMax,
		debugLevel);
		}
		@@ -4814,22 +4817,65 @@ public class EyesisDCT {

		int tilesY = imp_quad[0].getHeight()/clt_parameters.transform_size;
		int tilesX = imp_quad[0].getWidth()/clt_parameters.transform_size;
		// temporary setting up tile task file (one integer per tile, bitmask
		// for testing defined for a window, later the tiles to process will be calculated based on previous passes results
		int [][] tile_op = new int [tilesY][tilesX]; // all zero
		int txl = clt_parameters.tile_task_wl;
		int txr = txl + clt_parameters.tile_task_wl;
		int tyt = clt_parameters.tile_task_wl;
		int tyb = tyt + clt_parameters.tile_task_wh;
		if (txl < 0) txl = 0;
		else if (txl >= tilesX) txl = tilesX - 1;

		if (txr <= txl) txr = txl + 1;
		else if (txr > tilesX) txr = tilesX;

		if (tyt < 0) tyt = 0;
		else if (tyt >= tilesY) tyt = tilesY - 1;

		if (tyb <= tyt) tyb = tyt + 1;
		else if (tyb > tilesY) tyb = tilesY;

		for (int i = tyt; i < tyb; i++) {
		for (int j = txl; j < txr; j++) {
		tile_op[i][j] = clt_parameters.tile_task_op;
		}
		}
		//TODO: Add array of default disparity - use for combining images in force disparity mode (no correlation), when disparity is predicted from other tiles

		double [][][][] clt_corr_combo = null;
		double [][][][][] clt_corr_partial = null;
		double [][][][] texture_tiles = null; // [tilesY][tilesX]["RGBA".length()][]; // tiles will be 16x16, 2 visualizaion mode full 16 or overlapped
		// undecided, so 2 modes of combining alpha - same as rgb, or use center tile only
		if (clt_parameters.correlate){
		clt_corr_combo = new double [2][tilesY][tilesX][];
		texture_tiles = new double [tilesY][tilesX]["RGBA".length()][];
		for (int i = 0; i < tilesY; i++){
		for (int j = 0; j < tilesX; j++){
		clt_corr_combo[0][i][j] = null;
		clt_corr_combo[1][i][j] = null;
		texture_tiles[i][j] = null;
		}
		}
		if (clt_parameters.corr_keep){
		clt_corr_partial = new double [tilesY][tilesX][][][];
		for (int i = 0; i < tilesY; i++){
		for (int j = 0; j < tilesX; j++){
		clt_corr_partial[i][j] = null;
		}
		}
		}
		}
		double [][] disparity_map = new double [8][]; //[0] -residual disparity, [1] - orthogonal (just for debugging)
		double [][][][][][] clt_data = image_dtt.clt_aberrations_quad_corr(
		tile_op, // per-tile operation bit codes
		clt_parameters.disparity, // final double disparity,
		double_stacks, // final double [][][] imade_data, // first index - number of image in a quad
		// correlation results - final and partial
		clt_corr_combo, // [tilesY][tilesX][(2transform_size-1)(2*transform_size-1)] // if null - will not calculate
		clt_corr_partial, // [tilesY][tilesX][quad]color][(2transform_size-1)(2*transform_size-1)] // if null - will not calculate
		disparity_map, // [2][tilesY * tilesX]
		texture_tiles, // [tilesY][tilesX]["RGBA".length()][];
		imp_quad[0].getWidth(), // final int width,
		clt_parameters.fat_zero, // add to denominator to modify phase correlation (same units as data1, data2). <0 - pure sum
		clt_parameters.corr_sym,
		@@ -4859,8 +4905,50 @@ public class EyesisDCT {

		System.out.println("clt_data.length="+clt_data.length+" clt_data[0].length="+clt_data[0].length
		+" clt_data[0][0].length="+clt_data[0][0].length+" clt_data[0][0][0].length="+
		clt_data[0][0][0].length+" clt_data[0][0][0][0].length="+clt_data[0][0][0][0].length+
		" clt_data[0][0][0][0][0].length="+clt_data[0][0][0][0][0].length);
		clt_data[0][0][0].length);
		// +" clt_data[0][0][0][0].length="+clt_data[0][0][0][0].length+
		// " clt_data[0][0][0][0][0].length="+clt_data[0][0][0][0][0].length);
		// visualize texture tiles as RGBA slices
		double [][] texture_nonoverlap = null;
		double [][] texture_overlap = null;
		String [] rgba_titles = {"red","green","blue","alpha"};
		if (texture_tiles != null){
		if (clt_parameters.show_nonoverlap){
		texture_nonoverlap = image_dtt.combineRGBATiles(
		texture_tiles, // array [tilesY][tilesX][4][4*transform_size] or [tilesY][tilesX]{null}
		clt_parameters.transform_size,
		false, // when false - output each tile as 16x16, true - overlap to make 8x8
		clt_parameters.sharp_alpha, // combining mode for alpha channel: false - treat as RGB, true - apply center 8x8 only
		threadsMax, // maximal number of threads to launch
		debugLevel);
		sdfa_instance.showArrays(
		texture_nonoverlap,
		tilesX * (2 * clt_parameters.transform_size),
		tilesY * (2 * clt_parameters.transform_size),
		true,
		name + "-TXTNOL-D"+clt_parameters.disparity,
		rgba_titles );

		}
		if (clt_parameters.show_overlap){
		texture_overlap = image_dtt.combineRGBATiles(
		texture_tiles, // array [tilesY][tilesX][4][4*transform_size] or [tilesY][tilesX]{null}
		clt_parameters.transform_size,
		true, // when false - output each tile as 16x16, true - overlap to make 8x8
		clt_parameters.sharp_alpha, // combining mode for alpha channel: false - treat as RGB, true - apply center 8x8 only
		threadsMax, // maximal number of threads to launch
		debugLevel);
		sdfa_instance.showArrays(
		texture_overlap,
		tilesX * clt_parameters.transform_size,
		tilesY * clt_parameters.transform_size,
		true,
		name + "-TXTOL-D"+clt_parameters.disparity,
		rgba_titles );

		}

		}
		// visualize correlation results
		if (clt_corr_combo!=null){
		if (disparity_map != null){
		@@ -4884,6 +4972,7 @@ public class EyesisDCT {
		for (int i = 0; i<corr_rslt.length; i++) {
		corr_rslt[i] = image_dtt.corr_dbg(
		clt_corr_combo[i],
		2*clt_parameters.transform_size - 1,
		clt_parameters.corr_border_contrast,
		threadsMax,
		debugLevel);
		@@ -4898,7 +4987,7 @@ public class EyesisDCT {
		titles );
		}

		if (debugLevel > -1){
		if (debugLevel > 0){ // -1
		if (clt_corr_partial!=null){
		String [] allColorNames = {"red","blue","green","combo"};
		String [] titles = new String[clt_corr_partial.length];
		@@ -4907,6 +4996,9 @@ public class EyesisDCT {
		}
		double [][] corr_rslt_partial = image_dtt.corr_partial_dbg(
		clt_corr_partial,
		2*clt_parameters.transform_size - 1, //final int corr_size,
		4, // final int pairs,
		4, // final int colors,
		clt_parameters.corr_border_contrast,
		threadsMax,
		debugLevel);
		@@ -4921,7 +5013,8 @@ public class EyesisDCT {
		}
		}


		if (clt_parameters.gen_chn_img) {
		ImagePlus [] imps_RGB = new ImagePlus[clt_data.length];
		for (int iQuad = 0; iQuad < clt_data.length; iQuad++){

		String title=name+"-"+String.format("%02d", iQuad);
		@@ -4932,6 +5025,7 @@ public class EyesisDCT {
		image_dtt.clt_lpf(
		clt_parameters.corr_sigma,
		clt_data[iQuad][chn],
		clt_parameters.transform_size,
		threadsMax,
		debugLevel);
		}
		@@ -4973,7 +5067,7 @@ public class EyesisDCT {
		debugLevel);

		}
		if (debugLevel > 0) sdfa_instance.showArrays(
		if (debugLevel > 0) sdfa_instance.showArrays( // -1
		iclt_data,
		(tilesX + 0) * clt_parameters.transform_size,
		(tilesY + 0) * clt_parameters.transform_size,
		@@ -5108,7 +5202,7 @@ public class EyesisDCT {
		eyesisCorrections.correctionsParameters.JPEG_quality); // save, no show
		}
		// convert to RGB48 (16 bits per color component)
		ImagePlus imp_RGB;
		// ImagePlus imp_RGB;
		stack=eyesisCorrections.convertRGB32toRGB16Stack(
		stack,
		rgbParameters);
		@@ -5132,33 +5226,40 @@ public class EyesisDCT {
		// eyesisCorrections.saveAndShow(compositeImage, this.correctionsParameters, this.correctionsParameters.save16, true); // save, no show
		}

		imp_RGB=eyesisCorrections.convertRGB48toRGB24(
		imps_RGB[iQuad]=eyesisCorrections.convertRGB48toRGB24(
		stack,
		title+"-RGB24-D"+clt_parameters.disparity,
		0, 65536, // r range 0->0, 65536->256
		0, 65536, // g range
		0, 65536);// b range
		if (JPEG_scale!=1.0){
		ImageProcessor ip=imp_RGB.getProcessor();
		ImageProcessor ip=imps_RGB[iQuad].getProcessor();
		ip.setInterpolationMethod(ImageProcessor.BICUBIC);
		ip=ip.resize((int)(ip.getWidth()JPEG_scale),(int) (ip.getHeight()JPEG_scale));
		imp_RGB= new ImagePlus(imp_RGB.getTitle(),ip);
		imp_RGB.updateAndDraw();
		imps_RGB[iQuad]= new ImagePlus(imps_RGB[iQuad].getTitle(),ip);
		imps_RGB[iQuad].updateAndDraw();
		}
		if (iQuad <0) eyesisCorrections.saveAndShow(imps_RGB[iQuad], this.correctionsParameters); // individual images (just commented out)
		} // and generating shifted channle images
		// combine to a sliced color image
		int [] slice_seq = {0,1,3,2}; //clockwise
		int width = imps_RGB[0].getWidth();
		int height = imps_RGB[0].getHeight();
		ImageStack array_stack=new ImageStack(width,height);
		for (int i = 0; i<slice_seq.length; i++){
		if (imps_RGB[slice_seq[i]] != null) {
		array_stack.addSlice("port_"+slice_seq[i], imps_RGB[slice_seq[i]].getProcessor().getPixels());
		} else {
		array_stack.addSlice("port_"+slice_seq[i], results[slice_seq[i]].getProcessor().getPixels());
		}
		eyesisCorrections.saveAndShow(imp_RGB, this.correctionsParameters);
		}
		ImagePlus imp_stack = new ImagePlus(name+"-SHIFTED-D"+clt_parameters.disparity, array_stack);
		imp_stack.getProcessor().resetMinAndMax();
		imp_stack.updateAndDraw();
		//imp_stack.getProcessor().resetMinAndMax();
		//imp_stack.show();
		eyesisCorrections.saveAndShow(imp_stack, this.correctionsParameters);
		}
		return results;
		}












		}

src/main/java/Eyesis_Correction.java

+3 −1

Original line number	Diff line number	Diff line
		@@ -3968,6 +3968,7 @@ private Panel panel1,
		image_dtt.clt_lpf( // filter in-place
		CLT_PARAMETERS.corr_sigma, // final double sigma,
		clt_corr[chn], // final double [][][][] clt_data,
		CLT_PARAMETERS.transform_size,
		THREADS_MAX, // maximal number of threads to launch
		DEBUG_LEVEL); // globalDebugLevel)
		}
		@@ -4018,11 +4019,12 @@ private Panel panel1,
		THREADS_MAX,
		DEBUG_LEVEL);
		}
		if (DEBUG_LEVEL > -1){
		if (DEBUG_LEVEL > 0){ //============== -1 =================
		double [][] corr_rslt = new double [clt_corr.length][];
		for (int chn = 0; chn < clt_corr.length; chn++) {
		corr_rslt[chn] = image_dtt.corr_dbg(
		corr_tiles[chn],
		2*CLT_PARAMETERS.transform_size - 1,
		CLT_PARAMETERS.corr_border_contrast,
		THREADS_MAX,
		DEBUG_LEVEL);

src/main/java/ImageDtt.java

+209 −57

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