added per-set infinity offset

src/main/java/EyesisCorrectionParameters.java

@@ -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+"");
@@ -3324,7 +3334,13 @@ 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"));
   			if (properties.getProperty(prefix+"clt_window")!=null)     this.clt_window=Integer.parseInt(properties.getProperty(prefix+"clt_window"));
@@ -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

@@ -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

@@ -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

@@ -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