added per-set infinity offset (c500f3ad) · Commits · Elphel / imagej-elphel

src/main/java/EyesisCorrectionParameters.java

+62 −1

Original line number	Diff line number	Diff line
		@@ -30,7 +30,11 @@ import ij.Prefs;
		import ij.gui.GenericDialog;

		import java.io.File;
		import java.util.ArrayList;
		import java.util.Enumeration;
		import java.util.HashMap;
		import java.util.Properties;
		import java.util.Set;


		public class EyesisCorrectionParameters {
		@@ -602,6 +606,8 @@ public class EyesisCorrectionParameters {
		return true;
		}



		// TODO: extract timestamnp from JP4 or, at least combine movie timestamp+frame into a single filename string
		public String [] getSourcePaths(){
		String [] empty={};
		@@ -2720,6 +2726,10 @@ public class EyesisCorrectionParameters {
		public boolean show_planes = false; // show planes
		public double [] vertical_xyz = {0.0,1.0,0.0}; // real world up unit vector in camera CS (x - right, y - up, z - to camera};

		public HashMap<String,Double> z_corr_map = new HashMap<String,Double>();
		public static String Z_CORR_PREFIX = "z_corr.";


		public CLTParameters(){}
		public void setProperties(String prefix,Properties properties){
		properties.setProperty(prefix+"transform_size", this.transform_size+"");
		@@ -3324,6 +3334,12 @@ public class EyesisCorrectionParameters {
		properties.setProperty(prefix+"vertical_xyz.x", this.vertical_xyz[0]+"");
		properties.setProperty(prefix+"vertical_xyz.y", this.vertical_xyz[1]+"");
		properties.setProperty(prefix+"vertical_xyz.z", this.vertical_xyz[2]+"");

		if (z_corr_map != null) {
		for (HashMap.Entry<String,Double> entry : z_corr_map.entrySet()){
		properties.setProperty(prefix+Z_CORR_PREFIX+entry.getKey(), entry.getValue().toString());
		}
		}
		}
		public void getProperties(String prefix,Properties properties){
		if (properties.getProperty(prefix+"transform_size")!=null) this.transform_size=Integer.parseInt(properties.getProperty(prefix+"transform_size"));
		@@ -3929,6 +3945,14 @@ public class EyesisCorrectionParameters {
		if (properties.getProperty(prefix+"vertical_xyz.y")!=null) this.vertical_xyz[1]=Double.parseDouble(properties.getProperty(prefix+"vertical_xyz.y"));
		if (properties.getProperty(prefix+"vertical_xyz.z")!=null) this.vertical_xyz[2]=Double.parseDouble(properties.getProperty(prefix+"vertical_xyz.z"));

		Set<String> ss = properties.stringPropertyNames();
		String full_prefix = prefix+Z_CORR_PREFIX;
		int li = full_prefix.length();
		for (String s:ss){
		if (s.indexOf(full_prefix) == 0){
		z_corr_map.put(s.substring(li), Double.parseDouble(properties.getProperty(s)));
		}
		}
		}

		public boolean showDialog() {
		@@ -5353,6 +5377,43 @@ public class EyesisCorrectionParameters {

		return true;
		}
		public boolean modifyZCorr (String title) {
		if (z_corr_map == null){
		z_corr_map = new HashMap<String,Double>();
		}
		GenericDialog gd = new GenericDialog(title);
		if (z_corr_map.size() > 0) {
		gd.addMessage("Edit infinity disparity correction (in 1/m), set >= 1.0 to remove for the following");
		for (HashMap.Entry<String,Double> entry : z_corr_map.entrySet()){
		gd.addNumericField(entry.getKey(), entry.getValue(), 8);
		}
		}
		gd.addMessage("Add new infinity correction");
		gd.addStringField ("Timestamp string (seconds_microseconds):", "", 40);
		gd.addNumericField("Infinity correction (in 1/m)", 0, 8);
		gd.addCheckbox ("Clear list", false);
		WindowTools.addScrollBars(gd);
		gd.showDialog();
		if (gd.wasCanceled()) return false;
		HashMap<String,Double> new_map = new HashMap<String,Double>();
		for (HashMap.Entry<String,Double> entry : z_corr_map.entrySet()){
		double d = gd.getNextNumber();
		if (d < 1.0) {
		new_map.put(entry.getKey(),d);
		}
		}
		String new_ts = gd.getNextString();
		double d = gd.getNextNumber();
		if (gd.getNextBoolean()){
		z_corr_map = new HashMap<String,Double>();
		} else {
		z_corr_map = new_map;
		}
		if(new_ts.length() > 0){
		z_corr_map.put(new_ts, d);
		}
		return true;
		}
		}

		public static class DCTParameters {

src/main/java/Eyesis_Correction.java

+7 −0

Original line number	Diff line number	Diff line
		@@ -543,6 +543,7 @@ private Panel panel1,
		panelClt3 = new Panel();
		panelClt3.setLayout(new GridLayout(1, 0, 5, 5)); // rows, columns, vgap, hgap
		addButton("Setup CLT parameters", panelClt3, color_configure);
		addButton("Infinity offset", panelClt3, color_configure);
		addButton("Setup CLT Batch parameters", panelClt3, color_configure);
		addButton("CLT batch process", panelClt3, color_process);
		add(panelClt3);
		@@ -3678,6 +3679,12 @@ private Panel panel1,
		} else if (label.equals("Setup CLT parameters")) {
		CLT_PARAMETERS.showDialog();
		return;
		/* ======================================================================== */
		} else if (label.equals("Infinity offset")) {
		while (true) {
		if (!CLT_PARAMETERS.modifyZCorr("Modify infinity per image set disparity corrections")) break;
		}
		return;
		/* ======================================================================== */
		// public ImagePlus DBG_IMP = null;
		} else if (label.equals("Select CLT image")) {

src/main/java/ImageDtt.java

+1 −1

Original line number	Diff line number	Diff line
		@@ -1053,7 +1053,7 @@ 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 ((globalDebugLevel > -1) && (disparity_corr != 0.0)){
		if ((globalDebugLevel > -10) && (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++){

src/main/java/QuadCLT.java

+36 −13

Original line number	Diff line number	Diff line
		@@ -3606,8 +3606,12 @@ public class QuadCLT {
		{clt_parameters.fine_corr_x_3,clt_parameters.fine_corr_y_3}};
		shiftXY = shiftXY0;
		}

		final double disparity_corr = (clt_parameters.z_correction == 0) ? 0.0 : geometryCorrection.getDisparityFromZ(1.0/clt_parameters.z_correction);
		// final double disparity_corr = (clt_parameters.z_correction == 0) ? 0.0 : geometryCorrection.getDisparityFromZ(1.0/clt_parameters.z_correction);
		double z_correction = clt_parameters.z_correction;
		if (clt_parameters.z_corr_map.containsKey(name)){
		z_correction +=clt_parameters.z_corr_map.get(name);
		}
		final double disparity_corr = (z_correction == 0) ? 0.0 : geometryCorrection.getDisparityFromZ(1.0/z_correction);
		double [][][][][][] clt_data = image_dtt.clt_aberrations_quad_corr(
		1, // final int macro_scale, // to correlate tile data instead of the pixel data: 1 - pixels, 8 - tiles
		tile_op, // per-tile operation bit codes
		@@ -4672,7 +4676,12 @@ public class QuadCLT {
		shiftXY = shiftXY0;
		}

		final double disparity_corr = (clt_parameters.z_correction == 0) ? 0.0 : geometryCorrection.getDisparityFromZ(1.0/clt_parameters.z_correction);
		// final double disparity_corr = (clt_parameters.z_correction == 0) ? 0.0 : geometryCorrection.getDisparityFromZ(1.0/clt_parameters.z_correction);
		double z_correction = clt_parameters.z_correction;
		if (clt_parameters.z_corr_map.containsKey(image_name)){
		z_correction +=clt_parameters.z_corr_map.get(image_name);
		}
		final double disparity_corr = (z_correction == 0) ? 0.0 : geometryCorrection.getDisparityFromZ(1.0/z_correction);

		image_dtt.clt_aberrations_quad_corr(
		1, // final int macro_scale, // to correlate tile data instead of the pixel data: 1 - pixels, 8 - tiles
		@@ -6272,7 +6281,7 @@ public class QuadCLT {
		final boolean batch_mode,
		final int debugLevel)
		{
		final int debugLevelInner = batch_mode ? -5: debugLevel;
		final int debugLevelInner = batch_mode ? -3: debugLevel;

		// final int tilesX = tp.getTilesX();
		// final int tilesY = tp.getTilesY();
		@@ -6440,7 +6449,7 @@ public class QuadCLT {

		dbg_x,
		dbg_y, // final int dbg_y,
		debugLevelInner+1); // final int debugLevel)
		debugLevelInner + 2); // final int debugLevel)

		if (last_pass) {
		break;
		@@ -7728,6 +7737,7 @@ public class QuadCLT {
		//linearStackToColor

		public CLTPass3d CLTBackgroundMeas( // measure background
		// final String image_name,
		final double [][][] image_data, // first index - number of image in a quad
		final boolean [][] saturation_imp, // (near) saturated pixels or null
		EyesisCorrectionParameters.CLTParameters clt_parameters,
		@@ -7764,7 +7774,13 @@ public class QuadCLT {

		double [][][][] texture_tiles = new double [tilesY][tilesX][][]; // ["RGBA".length()][];
		ImageDtt image_dtt = new ImageDtt();
		final double disparity_corr = (clt_parameters.z_correction == 0) ? 0.0 : geometryCorrection.getDisparityFromZ(1.0/clt_parameters.z_correction);
		// final double disparity_corr = (clt_parameters.z_correction == 0) ? 0.0 : geometryCorrection.getDisparityFromZ(1.0/clt_parameters.z_correction);
		double z_correction = clt_parameters.z_correction;
		if (clt_parameters.z_corr_map.containsKey(image_name)){
		z_correction +=clt_parameters.z_corr_map.get(image_name);
		}
		final double disparity_corr = (z_correction == 0) ? 0.0 : geometryCorrection.getDisparityFromZ(1.0/z_correction);

		image_dtt.clt_aberrations_quad_corr(
		1, // final int macro_scale, // to correlate tile data instead of the pixel data: 1 - pixels, 8 - tiles
		tile_op, // per-tile operation bit codes
		@@ -7922,6 +7938,7 @@ public class QuadCLT {
		}

		public CLTPass3d CLTMeasure( // perform single pass according to prepared tiles operations and disparity
		// final String image_name,
		final double [][][] image_data, // first index - number of image in a quad
		final boolean [][] saturation_imp, // (near) saturated pixels or null
		final EyesisCorrectionParameters.CLTParameters clt_parameters,
		@@ -7970,7 +7987,13 @@ public class QuadCLT {

		double [][][][] texture_tiles = save_textures ? new double [tilesY][tilesX][][] : null; // ["RGBA".length()][];
		ImageDtt image_dtt = new ImageDtt();
		final double disparity_corr = (clt_parameters.z_correction == 0) ? 0.0 : geometryCorrection.getDisparityFromZ(1.0/clt_parameters.z_correction);
		// final double disparity_corr = (clt_parameters.z_correction == 0) ? 0.0 : geometryCorrection.getDisparityFromZ(1.0/clt_parameters.z_correction);
		double z_correction = clt_parameters.z_correction;
		if (clt_parameters.z_corr_map.containsKey(image_name)){
		z_correction +=clt_parameters.z_corr_map.get(image_name);
		}
		final double disparity_corr = (z_correction == 0) ? 0.0 : geometryCorrection.getDisparityFromZ(1.0/z_correction);

		image_dtt.clt_aberrations_quad_corr(
		1, // final int macro_scale, // to correlate tile data instead of the pixel data: 1 - pixels, 8 - tiles
		tile_op, // per-tile operation bit codes

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