filtering foreground selection for the rig

src/main/java/Eyesis_Correction.java

@@ -569,6 +569,7 @@ private Panel panel1,
 			addButton("Setup CLT Batch parameters", panelClt3, color_configure);
 			addButton("CLT batch process",          panelClt3, color_process);
 			addButton("CM Test",                    panelClt3, color_stop);
+			addButton("Show scan",                  panelClt3, color_configure);
 
 			add(panelClt3);
 		}
@@ -579,13 +580,16 @@ private Panel panel1,
 			addButton("Import Aux",                 panelClt4, color_restore);
 			addButton("Setup CLT Batch parameters", panelClt4, color_configure);
 			addButton("CLT rig edit",               panelClt4, color_configure);
-			addButton("CLT 2*4 images",             panelClt4, color_conf_process);
-			addButton("CLT 2*4 images - 2",         panelClt4, color_conf_process);
-			addButton("CLT 2*4 images - 3",         panelClt4, color_conf_process);
+//			addButton("CLT 2*4 images",             panelClt4, color_conf_process);
+//			addButton("CLT 2*4 images - 2",         panelClt4, color_conf_process);
+//			addButton("CLT 2*4 images - 3",         panelClt4, color_conf_process);
+			addButton("Rig8 images",                panelClt4, color_conf_process);
 			addButton("Rig infinity calibration",   panelClt4, color_conf_process);
 			addButton("AUX Extrinsics",             panelClt4, color_process);
 			addButton("AUX show fine",              panelClt4, color_configure);
-			addButton("Rig enhance",                panelClt4, color_conf_process);
+//			addButton("Rig enhance",                panelClt4, color_conf_process);
+			addButton("Ground truth",               panelClt4, color_conf_process);
+			addButton("ML export",                  panelClt4, color_conf_process);
 
 			add(panelClt4);
 		}
@@ -4519,10 +4523,15 @@ private Panel panel1,
         			PROPERTIES);
         }
         return;
+/* ======================================================================== */
     } else if (label.equals("CM Test")) {
     	cm_test();
         return;
 /* ======================================================================== */
+    } else if (label.equals("Show scan")) {
+    	showScan();
+        return;
+/* ======================================================================== */
 
     } else if (label.equals("Import Aux")) {
     	importAux();
@@ -4540,7 +4549,7 @@ private Panel panel1,
     	getPairImages2(false);
     	return;
 /* ======================================================================== */
-    } else if (label.equals("CLT 2*4 images - 3")) {
+    } else if (label.equals("Rig8 images")) {
         DEBUG_LEVEL=MASTER_DEBUG_LEVEL;
     	EYESIS_CORRECTIONS.setDebug(DEBUG_LEVEL);
     	getPairImages2(true);
@@ -4583,12 +4592,18 @@ private Panel panel1,
 
         return;
 /* ======================================================================== */
-    } else if (label.equals("Rig enhance")) {
+    } else if (label.equals("Ground truth")) {
         DEBUG_LEVEL=MASTER_DEBUG_LEVEL;
     	EYESIS_CORRECTIONS.setDebug(DEBUG_LEVEL);
     	enhanceByRig();
 
     	return;
+/* ======================================================================== */
+    } else if (label.equals("ML export")) {
+        DEBUG_LEVEL=MASTER_DEBUG_LEVEL;
+    	EYESIS_CORRECTIONS.setDebug(DEBUG_LEVEL);
+    	exportMLData();
+    	return;
 
 /* ======================================================================== */
     } else if (label.equals("CLT rig edit")) {
@@ -5007,6 +5022,12 @@ private Panel panel1,
 
 
 	public boolean enhanceByRig() {
+		if ((QUAD_CLT == null) || (QUAD_CLT.tp == null) || (QUAD_CLT.tp.clt_3d_passes == null)) {
+			String msg = "DSI data is not available. Please run \"CLT 3D\" first";
+			IJ.showMessage("Error",msg);
+			System.out.println(msg);
+			return false;
+		}
 		if (!prepareRigImages()) return false;
     	String configPath=getSaveCongigPath();
     	if (configPath.equals("ABORT")) return false;
@@ -5037,6 +5058,43 @@ private Panel panel1,
     	return true;
 	}
 
+	public boolean exportMLData() {
+		if ((QUAD_CLT == null) || (QUAD_CLT.tp == null) || (QUAD_CLT.tp.clt_3d_passes == null)) {
+			String msg = "DSI data is not available. Please run \"CLT 3D\" first";
+			IJ.showMessage("Error",msg);
+			System.out.println(msg);
+			return false;
+		}
+		if (!prepareRigImages()) return false;
+    	String configPath=getSaveCongigPath();
+    	if (configPath.equals("ABORT")) return false;
+
+    	if (DEBUG_LEVEL > -2){
+    		System.out.println("++++++++++++++ Generating ML datasets ++++++++++++++");
+    	}
+    	try {
+    		TWO_QUAD_CLT.outputMLData( // actually there is no sense to process multiple image sets. Combine with other processing?
+    				QUAD_CLT, // QuadCLT quadCLT_main,
+    				QUAD_CLT_AUX, // QuadCLT quadCLT_aux,
+    				CLT_PARAMETERS,  // EyesisCorrectionParameters.DCTParameters           dct_parameters,
+    				THREADS_MAX, //final int          threadsMax,  // maximal number of threads to launch
+    				UPDATE_STATUS, //final boolean    updateStatus,
+    				DEBUG_LEVEL);
+    	} catch (Exception e) {
+    		// TODO Auto-generated catch block
+    		e.printStackTrace();
+    	} //final int        debugLevel);
+
+    	if (configPath!=null) {
+    		saveTimestampedProperties( // save config again
+    				configPath,      // full path or null
+    				null, // use as default directory if path==null
+    				true,
+    				PROPERTIES);
+    	}
+    	return true;
+	}
+
 
 	public boolean infinityRig() {
 		if (!prepareRigImages()) return false;
@@ -5044,7 +5102,7 @@ private Panel panel1,
     	if (configPath.equals("ABORT")) return false;
 
     	if (DEBUG_LEVEL > -2){
-    		System.out.println("++++++++++++++ Processing Infinity rig calibration ++++++++++++++");
+    		System.out.println("++++++++++++++ Processing infinity rig calibration ++++++++++++++");
     	}
     	try {
     		TWO_QUAD_CLT.processInfinityRigs( // actually there is no sense to process multiple image sets. Combine with other processing?
@@ -5473,6 +5531,27 @@ private Panel panel1,
   			return true;
   		}
 
+ public boolean showScan() {
+		if ((QUAD_CLT == null) || (QUAD_CLT.tp == null) || (QUAD_CLT.tp.clt_3d_passes == null)) {
+			String msg = "DSI data is not available. Please run \"CLT 3D\" first";
+			IJ.showMessage("Error",msg);
+			System.out.println(msg);
+			return false;
+		}
+	    int scan_index = 0;
+		GenericJTabbedDialog gd = new GenericJTabbedDialog("Set CLT parameters",400,100);
+		gd.addNumericField("Scan index (0..."+(QUAD_CLT.tp.clt_3d_passes.size()-1),  scan_index, 0, 2, "",
+				"Display scan by index");
+
+		gd.showDialog();
+		if (gd.wasCanceled()) return false;
+
+		scan_index = (int) gd.getNextNumber();
+		QUAD_CLT.tp.showScan(QUAD_CLT.tp.clt_3d_passes.get(scan_index),"Scan-"+scan_index);
+		return true;
+
+ }
+
   public boolean cm_test() {
 	    double hsize_x = 1.5;
 	    double hsize_y = 1.5;

src/main/java/QuadCLT.java

@@ -73,7 +73,10 @@ public class QuadCLT {
 
 
 // magic scale should be set before using  TileProcessor (calculated disparities depend on it)
-
+    public double [][] getGroundTruthByRig(){
+    	if (tp == null) return null;
+    	return tp.rig_disparity_strength;
+    }
 	public void setTiles (ImagePlus imp, // set tp.tilesX, tp.tilesY
 			EyesisCorrectionParameters.CLTParameters    clt_parameters,
 			int threadsMax

src/main/java/TileProcessor.java

@@ -31,6 +31,7 @@ import java.util.concurrent.atomic.AtomicInteger;
 
 public class TileProcessor {
 	public ArrayList <CLTPass3d> clt_3d_passes = null;
+	public double [][] rig_disparity_strength =  null; // Disparity and strength created by a two-camera rig, with disparity scale and distortions of the main camera
 	public int       clt_3d_passes_size = 0; //clt_3d_passes size after initial processing
 	private int      tilesX;
 	private int      tilesY;
@@ -2218,11 +2219,11 @@ public class TileProcessor {
 				block_propagate[tindx] = (disparity_map[ImageDtt.IMG_DIFF0_INDEX + imax2][tindx] > sure_smth);
 			}
 		}
-		// TODO: check if minimal cluster strengh should be limited here
+		// TODO: check if minimal cluster strength should be limited here
 		if (min_clstr_seed > 1){
 			removeSmallClusters(
 					true,            // boolean    diag_en,   // enable diagonal directions, false only up, dowm, right,left
-					bgnd_tiles,      // boolean [] tiles_src,    // selected tiles, will modified
+					bgnd_tiles,      // boolean [] tiles_src,    // selected tiles, will be modified
 					null,            // double []   weights_src,   // or null
 					min_clstr_seed,  // int        min_area,  // minimal number of pixels
 					0.0, //clt_parameters.min_clstr_weight,  // double     min_weight // minimal total weight of the cluster