Tweaking software to handle more precise disparity measurements

src/main/java/Eyesis_Correction.java

@@ -572,6 +572,7 @@ private Panel panel1,
 			addButton("Infinity offset",            panelClt3, color_configure);
 			addButton("Setup CLT Batch parameters", panelClt3, color_configure);
 			addButton("CLT batch process",          panelClt3, color_process);
+			addButton("CM Test",                    panelClt3, color_stop);
 //			addButton("JTabbed",                    panelClt3, color_stop);
 //			addButton("Demo",                       panelClt3, color_process);
 
@@ -3752,7 +3753,7 @@ private Panel panel1,
 
 /* ======================================================================== */
     } else if (label.equals("Setup CLT parameters")) {
-    	CLT_PARAMETERS.showDialog();
+    	CLT_PARAMETERS.showJDialog();
         return;
 /* ======================================================================== */
     } else if (label.equals("Setup CLT")) {
@@ -3769,7 +3770,7 @@ private Panel panel1,
     } else if (label.equals("Select CLT image")) {
     	DEBUG_LEVEL=MASTER_DEBUG_LEVEL;
     	//            	IJ.showMessage("DCT test 1");
-    	if (!CLT_PARAMETERS.showDialog()) return;
+    	if (!CLT_PARAMETERS.showJDialog()) return;
     	// process selected image stack
     	ImagePlus imp_src = WindowManager.getCurrentImage();
     	if (imp_src==null){
@@ -3802,7 +3803,7 @@ private Panel panel1,
     } else if (label.equals("Select second CLT image")) {
     	DEBUG_LEVEL=MASTER_DEBUG_LEVEL;
     	//            	IJ.showMessage("DCT test 1");
-    	if (!CLT_PARAMETERS.showDialog()) return;
+    	if (!CLT_PARAMETERS.showJDialog()) return;
     	// process selected image stack
     	ImagePlus imp_src = WindowManager.getCurrentImage();
     	if (imp_src==null){
@@ -3837,7 +3838,7 @@ private Panel panel1,
     } else if (label.equals("CLT stack")) {
     	DEBUG_LEVEL=MASTER_DEBUG_LEVEL;
 //    	IJ.showMessage("DCT test 1");
-        if (!CLT_PARAMETERS.showDialog()) return;
+        if (!CLT_PARAMETERS.showJDialog()) return;
 // process selected image stack
         if (DBG_IMP == null) {
         	ImagePlus imp_src = WindowManager.getCurrentImage();
@@ -3937,7 +3938,7 @@ private Panel panel1,
 		System.out.println("--- Free memory="+runtime.freeMemory()+" (of "+runtime.totalMemory()+")");
 
 //    	IJ.showMessage("DCT test 1");
-        if (!CLT_PARAMETERS.showDialog()) return;
+        if (!CLT_PARAMETERS.showJDialog()) return;
 // process selected image stack
         if (DBG_IMP == null) {
         	ImagePlus imp_src = WindowManager.getCurrentImage();
@@ -4191,7 +4192,7 @@ private Panel panel1,
 //==============================================================================
 
     } else if (label.equals("Create CLT kernels")) {
-        if (!CLT_PARAMETERS.showDialog()) return;
+        if (!CLT_PARAMETERS.showJDialog()) return;
         if (QUAD_CLT == null){
         	QUAD_CLT = new  QuadCLT (
         			PROPERTIES,
@@ -4250,7 +4251,7 @@ private Panel panel1,
         }
 
     } else if (label.equals("Read CLT kernels")) {
-        if (!CLT_PARAMETERS.showDialog()) return;
+        if (!CLT_PARAMETERS.showJDialog()) return;
         if (QUAD_CLT == null){
         	QUAD_CLT = new  QuadCLT (
         			PROPERTIES,
@@ -5161,6 +5162,9 @@ private Panel panel1,
         			PROPERTIES);
         }
         return;
+    } else if (label.equals("CM Test")) {
+    	cm_test();
+        return;
 
 //JTabbedTest
 // End of buttons code
@@ -5185,7 +5189,136 @@ private Panel panel1,
   			return true;
   		}
 
+  public boolean cm_test() {
+	    double hsize_x = 1.5;
+	    double hsize_y = 1.5;
+	    int    steps =  20;
+	    double sigma =   0.0;
+	    boolean separable = true; // false;
+	    double pwr = 1.0;
+		GenericJTabbedDialog gd = new GenericJTabbedDialog("Set CLT parameters",400,300);
+		gd.addNumericField("Half size X",                                              hsize_x,            6, 8, "pix",
+				"Correlation maximum half width in disparity direction");
+		gd.addNumericField("Half size Y",                                              hsize_y,            6, 8, "pix",
+				"Correlation maximum half width in orthogonal direction");
+		gd.addNumericField("Number of steps",                                          steps,              0, 6, "",
+				"Number of steps to subdivide [0,1) half-interval");
+		gd.addNumericField("Low pass sigma",                                           sigma,              3, 6, "pix",
+				"Correlation maximum half width in orthogonal direction");
+		gd.addCheckbox    ("X/Y separable",                                                                 separable);
+		gd.addNumericField("Value power",                                              pwr,                6, 8, "",
+				"Raise values to this power before calculating CM");
+
+		gd.showDialog();
+		if (gd.wasCanceled()) return false;
+		DoubleGaussianBlur gb=new DoubleGaussianBlur();
+
+		hsize_x =              gd.getNextNumber();
+		hsize_y =              gd.getNextNumber();
+
+		steps =          (int) gd.getNextNumber();
+		sigma =                gd.getNextNumber();
+		separable =            gd.getNextBoolean();
+		pwr =                  gd.getNextNumber();
+
+		int size_x = 2*((int) Math.round(hsize_x+ 2*sigma+1)) + 1;
+		int size_y = 2*((int) Math.round(hsize_y+ 2*sigma+1)) + 1;
+
+		System.out.println("size_x="+size_x+", size_y="+size_y+" sigma = "+sigma+" separable "+separable+" pwr=" + pwr);
+		String [] titles = new String[steps];
+		double [][] data = new double [steps][size_x*size_y];
+		for (int i = 0;i<steps; i++) {
+			double dx = 1.0*i/steps;
+			titles[i] = IJ.d2s(dx,3);
+			for (int iy = 0; iy < size_y; iy++) {
+				double y =  (iy - (size_y - 1)/2)/hsize_y;
+				if ((y >= -1.0) && (y <= 1.0)) {
+					double ay = separable ? (0.5*(Math.cos(y * Math.PI) + 1.0)):1.0;
+					for (int ix = 0; ix < size_x; ix++) {
+
+						double x = (ix - (size_x - 1)/2 - dx)/hsize_x;
+						double r = separable? Math.abs(x) : Math.sqrt(x*x+y*y);
+//						if ((r >= -hsize_x) && (x <= hsize_x)) {
+						if (r <= 1.0) {
+							double ax = 0.5*(Math.cos(r  * Math.PI) + 1.0);
+							data[i][iy*size_x+ix] = ax*ay;
+						}
+					}
+				}
+			}
+		}
+		(new showDoubleFloatArrays()) .showArrays(data,  size_x, size_y, true, "pre-gauss", titles);
+		if (sigma > 0.0) {
+			for (int i = 0; i < steps; i++) {
+				gb.blurDouble(
+						data[i],
+						size_x,
+						size_y,
+						sigma,
+						sigma,
+						0.01);
+			}
+			(new showDoubleFloatArrays()) .showArrays(data,  size_x, size_y, true, "blured", titles);
+		}
+
+		double [] cm_x = new double [steps];
+		for (int i = 0;i<steps; i++) {
+			double s0=0,sx=0;
+			for (int iy = 0; iy < size_y; iy++ ) {
+				for (int ix = 0; ix < size_x; ix++ ) {
+					double d = Math.pow(data[i][iy*size_y+ix], pwr);
+					s0+=d;
+					sx+=ix*d;
+				}
+			}
+			cm_x[i] = sx/s0 - (size_x - 1)/2;
+		}
+		for (int i = 0;i <= steps/2; i++) {
+			double dx = 1.0*i/steps;
+			System.out.println(String.format("%3d %8.5f %8.5f %8.5f %8.5f %8.5f", i, dx, cm_x[i],cm_x[i]-dx, cm_x[i]/(dx+0.00000001), dx/(cm_x[i]+0.00000001)));
+		}
+
+
 
+		return true;
+/*
+		double s0 = 0, sx=0,sy = 0;
+		for (int y = - iradius ; y <= iradius; y++){
+			int dataY = icenter[1] +y;
+			if ((dataY >= 0) && (dataY < data_size)){
+				int y2 = y*y;
+				for (int x = - iradius ; x <= iradius; x++){
+					int dataX = icenter[0] +x;
+					double r2 = y2 + x * x;
+//					if ((dataX >= 0) && (dataX < data_size) && (square || ((y2 + x * x) <= ir2))){
+					if ((dataX >= 0) && (dataX < data_size) && (square || (r2 <= ir2))){
+//						double w = max_corr_double? (1.0 - r2/ir2):1.0;
+//						double d =  w* data[dataY * data_size + dataX];
+						double d =  data[dataY * data_size + dataX];
+						s0 += d;
+						sx += d * dataX;
+						sy += d * dataY;
+					}
+				}
+			}
+		}
+		double [] rslt = {sx / s0, sy / s0};
+ *
+ * 		  showDoubleFloatArrays sdfa_instance = new showDoubleFloatArrays(); // just for debugging?
+
+			  sdfa_instance.showArrays(double_stack,  imp_src.getWidth(), imp_src.getHeight(), true, "BEFORE_CLT_PROC", rbg_titles);
+ *
+			        	   gb.blurDouble(
+			        			   results[indexVar],
+			        			   size,
+			        			   size,
+			        			   blurVarianceSigma,
+			        			   blurVarianceSigma,
+			        			   0.01);
+
+ */
+
+  }
 
   private boolean loadCorrelations(){
     	String []patterns={".corr-tiff",".tiff",".tif"};

src/main/java/GenericJTabbedDialog.java

@@ -5,6 +5,7 @@
 
 import java.awt.BorderLayout;
 import java.awt.Color;
+import java.awt.Component;
 import java.awt.FlowLayout;
 import java.awt.Font;
 import java.awt.GridBagConstraints;
@@ -109,7 +110,13 @@ public class GenericJTabbedDialog implements ActionListener {
    		}
 		if (tooltip != null) {
 			label.setToolTipText(tooltip);
-			if (component != null) component.setToolTipText(tooltip);
+			if (component != null) {
+				component.setToolTipText(tooltip);
+				Component [] comps = component.getComponents();
+				if ((comps != null) && (comps.length >0)) {
+					((JComponent) comps[0]).setToolTipText(tooltip);
+				}
+			}
 		}
 		labels.get(labels.size()-1).add(label);
 		components.get(components.size()-1).add(component);
@@ -148,6 +155,7 @@ public class GenericJTabbedDialog implements ActionListener {
 		inp_units.putClientProperty("type",  "String");
 		inp_units.setLayout(new FlowLayout(FlowLayout.LEFT));
 		addLine(label, inp_units, tooltip);
+
 	}
 
 	public void addNumericField(String label, double defaultValue, int digits) { // as in IJ

src/main/java/QuadCLT.java

@@ -3572,7 +3572,7 @@ public class QuadCLT {
 		  showDoubleFloatArrays sdfa_instance = new showDoubleFloatArrays(); // just for debugging?
 
 		  // may use this.StartTime to report intermediate steps execution times
-		  String name=(String) imp_quad[0].getProperty("name");
+		  String name=this.correctionsParameters.getModelName((String) imp_quad[0].getProperty("name"));
 		  //		int channel= Integer.parseInt((String) imp_src.getProperty("channel"));
 //		  int channel= (Integer) imp_quad[0].getProperty("channel");
 		  String path= (String) imp_quad[0].getProperty("path");
@@ -3666,6 +3666,7 @@ public class QuadCLT {
 		  }
 		  final double disparity_corr = (z_correction == 0) ? 0.0 : geometryCorrection.getDisparityFromZ(1.0/z_correction);
 		  double [][][][][][] clt_data = image_dtt.clt_aberrations_quad_corr(
+				  clt_parameters.img_dtt,       // final ImageDttParameters  imgdtt_params,   // Now just extra correlation parameters, later will include, most others
 				  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
 				  disparity_array,              // final double            disparity,
@@ -4740,6 +4741,7 @@ public class QuadCLT {
 			  final double disparity_corr = (z_correction == 0) ? 0.0 : geometryCorrection.getDisparityFromZ(1.0/z_correction);
 
 			  image_dtt.clt_aberrations_quad_corr(
+					  clt_parameters.img_dtt,       // final ImageDttParameters  imgdtt_params,   // Now just extra correlation parameters, later will include, most others
 					  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
 					  disparity_array,              // clt_parameters.disparity,     // final double            disparity,
@@ -5632,13 +5634,13 @@ public class QuadCLT {
 				  debugLevel);
 		  tp.clt_3d_passes.add(bgnd_data);
 		  //    	  if (show_init_refine)
-		  if (debugLevel > -1) {
+		  if ((debugLevel > -2) && clt_parameters.show_first_bg) {
 			  tp.showScan(
 					  tp.clt_3d_passes.get(0), // CLTPass3d   scan,
 					  "bgnd_data-"+tp.clt_3d_passes.size());
 		  }
 
-		  //TODO: Move away form here?
+		  //TODO: Move away from here?
     	  ImagePlus imp_bgnd = getBackgroundImage(
     			  clt_parameters,
     			  colorProcParameters,
@@ -5827,7 +5829,8 @@ public class QuadCLT {
     			  tp.clt_3d_passes.add(refined);
 
     			  ///    		  if (debugLevel > 1)
-    			  if (debugLevel > 0)
+//    			  if (debugLevel > 0)
+       			  if ((debugLevel > -2) && clt_parameters.show_first_bg)
     				  tp.showScan(
     						  tp.clt_3d_passes.get(refine_pass), // CLTPass3d   scan,
     						  "before_makeUnique-"+refine_pass);
@@ -5973,8 +5976,9 @@ public class QuadCLT {
 					  threadsMax,  // maximal number of threads to launch
 					  updateStatus,
 					  debugLevel);
-			  if (debugLevel > -1){
-				  System.out.println("CLTMeasure("+refine_pass+")");
+//			  if (debugLevel > -1){
+			  if (debugLevel > -2){
+				  System.out.println("?.CLTMeasure("+refine_pass+")");
 			  }
 			  if (show_init_refine) tp.showScan(
 					  tp.clt_3d_passes.get(refine_pass), // CLTPass3d   scan,
@@ -7041,7 +7045,7 @@ public class QuadCLT {
 					  "after_pass3-"+(next_pass-1)); //String title)
 		  }
  		  String x3d_path= correctionsParameters.selectX3dDirectory( // for x3d and obj
- 				  this.image_name, // quad timestamp. Will be ignored if correctionsParameters.use_x3d_subdirs is false
+ 				 correctionsParameters.getModelName(this.image_name), // quad timestamp. Will be ignored if correctionsParameters.use_x3d_subdirs is false
  				  correctionsParameters.x3dModelVersion,
 				  true,  // smart,
 				  true);  //newAllowed, // save
@@ -7058,7 +7062,7 @@ public class QuadCLT {
 			  try {
 				wfOutput = new WavefrontExport(
 						  x3d_path,
-						  this.image_name,
+						  correctionsParameters.getModelName(this.image_name),
 						  clt_parameters,
 						  correctionsParameters,
 						  geometryCorrection,
@@ -7117,7 +7121,7 @@ public class QuadCLT {
 						  clt_parameters,
 						  colorProcParameters,
 						  rgbParameters,
-						  this.image_name+"-img_infinity", // +scanIndex,
+						  correctionsParameters.getModelName(this.image_name)+"-img_infinity", // +scanIndex,
 						  bgndIndex,
 						  threadsMax,  // maximal number of threads to launch
 						  updateStatus,
@@ -7198,7 +7202,7 @@ public class QuadCLT {
 					  clt_parameters,
 					  colorProcParameters,
 					  rgbParameters,
-					  this.image_name+"-img"+scanIndex,
+					  correctionsParameters.getModelName(this.image_name)+"-img"+scanIndex,
 					  scanIndex,
 					  threadsMax,  // maximal number of threads to launch
 					  updateStatus,
@@ -7275,9 +7279,9 @@ public class QuadCLT {
 
 
 		  if ((x3d_path != null) && (x3dOutput != null)){
-//			  x3d_path+=Prefs.getFileSeparator()+this.image_name+".x3d";
+//			  x3d_path+=Prefs.getFileSeparator()+correctionsParameters.getModelName(this.image_name)+".x3d";
 //			  x3dOutput.generateX3D(x3d_path);
-			  x3dOutput.generateX3D(x3d_path+Prefs.getFileSeparator()+this.image_name+".x3d");
+			  x3dOutput.generateX3D(x3d_path+Prefs.getFileSeparator()+correctionsParameters.getModelName(this.image_name)+".x3d");
 		  }
 		  if (wfOutput != null){
 			  wfOutput.close();
@@ -7562,7 +7566,7 @@ public class QuadCLT {
 				  debugLevel);
 		  String path= correctionsParameters.selectX3dDirectory(
 				  //TODO: Which one to use - name or this.image_name ?
- 				  this.image_name, // quad timestamp. Will be ignored if correctionsParameters.use_x3d_subdirs is false
+ 				  correctionsParameters.getModelName(this.image_name), // quad timestamp. Will be ignored if correctionsParameters.use_x3d_subdirs is false
  				  correctionsParameters.x3dModelVersion,
 // 				  name, // quad timestamp. Will be ignored if correctionsParameters.use_x3d_subdirs is false
 				  true,  // smart,
@@ -7711,7 +7715,7 @@ public class QuadCLT {
 
 		  String path= correctionsParameters.selectX3dDirectory(
 				  //TODO: Which one to use - name or this.image_name ?
- 				  this.image_name, // quad timestamp. Will be ignored if correctionsParameters.use_x3d_subdirs is false
+ 				  correctionsParameters.getModelName(this.image_name), // quad timestamp. Will be ignored if correctionsParameters.use_x3d_subdirs is false
  				  correctionsParameters.x3dModelVersion,
 // 				  name, // quad timestamp. Will be ignored if correctionsParameters.use_x3d_subdirs is false
 				  true,  // smart,
@@ -7841,6 +7845,7 @@ public class QuadCLT {
 		  final double disparity_corr = (z_correction == 0) ? 0.0 : geometryCorrection.getDisparityFromZ(1.0/z_correction);
 
 		  image_dtt.clt_aberrations_quad_corr(
+				  clt_parameters.img_dtt,       // final ImageDttParameters  imgdtt_params,   // Now just extra correlation parameters, later will include, most others
 				  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
 				  disparity_array,              // clt_parameters.disparity,     // final double            disparity,
@@ -8054,6 +8059,7 @@ public class QuadCLT {
 		  final double disparity_corr = (z_correction == 0) ? 0.0 : geometryCorrection.getDisparityFromZ(1.0/z_correction);
 
 		  image_dtt.clt_aberrations_quad_corr(
+				  clt_parameters.img_dtt,       // final ImageDttParameters  imgdtt_params,   // Now just extra correlation parameters, later will include, most others
 				  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
 				  disparity_array,              // clt_parameters.disparity,     // final double            disparity,