More work on low-textured areas with bi-quad camera

src/main/java/BiCamDSI.java

@@ -5,7 +5,7 @@
  **
  ** -----------------------------------------------------------------------------**
  **
- **  TwoQuadCLT.java is free software: you can redistribute it and/or modify
+ **  BiCamDSI.java is free software: you can redistribute it and/or modify
  **  it under the terms of the GNU General Public License as published by
  **  the Free Software Foundation, either version 3 of the License, or
  **  (at your option) any later version.
@@ -25,13 +25,52 @@ import java.util.ArrayList;
 
 
 public class BiCamDSI {
-//	public int tilesX;
-//	public int tilesY;
-	TileNeibs tnImage; //  = new TileNeibs(tilesX, tilesY)
+	TileNeibs         tnImage; //  = new TileNeibs(tilesX, tilesY)
+	int               threadsMax;
+	ArrayList<BiScan> biScans;
+
+
+
+	public int addBiScan(
+			double [] disparity,
+			double [] strength,
+			boolean [] trusted,
+			boolean [] disabled) {
+
+		if (biScans == null) biScans = new ArrayList<BiScan>();
+		biScans.add(new BiScan(this, biScans.size(), disparity, strength, trusted, disabled));
+		return biScans.size()-1;
+
+	}
+
+	public int addBiScan(
+			double [][] disparity_bimap) {
+		return addBiScan(
+				disparity_bimap[ImageDtt.BI_TARGET_INDEX], // double [] disparity,
+				disparity_bimap[ImageDtt.BI_STR_CROSS_INDEX], // double [] strength,
+				null, // boolean [] trusted,
+				null); // boolean [] disabled)
+	}
+
+	public BiScan getLastBiScan() {
+		return getBiScan(-1);
+	}
+	public BiScan getBiScan(int indx) {
+		if (biScans.isEmpty()) return null;
+		return biScans.get((indx>=0)? indx: (biScans.size() - 1));
+	}
+
+	public double [] getTargetDisparity(int indx) {
+		BiScan biScan = getBiScan(indx);
+		if (biScan == null) return null;
+		return biScan.target_disparity;
+	}
 
 	public BiCamDSI(
 			int tilesX,
-			int tilesY) {
+			int tilesY,
+			int threadsMax) {
+		this.threadsMax = threadsMax;
 		tnImage  = new TileNeibs(tilesX, tilesY);
 	}
 

src/main/java/Eyesis_Correction.java

@@ -588,6 +588,9 @@ private Panel panel1,
 			addButton("AUX Extrinsics",             panelClt4, color_process);
 			addButton("AUX show fine",              panelClt4, color_configure);
 //			addButton("Rig enhance",                panelClt4, color_conf_process);
+//			/"Reset GT"
+			addButton("Reset GT",                   panelClt4, color_stop);
+			addButton("Ground truth 0",             panelClt4, color_configure);
 			addButton("Ground truth",               panelClt4, color_conf_process);
 			addButton("ML export",                  panelClt4, color_conf_process);
 			addButton("Rig planes",                 panelClt4, color_conf_process);
@@ -4593,14 +4596,28 @@ private Panel panel1,
         QuadCLT dbg_QUAD_CLT_AUX = QUAD_CLT_AUX;
 
         return;
+/* ======================================================================== */
+    } else if (label.equals("Reset GT")) {
+        DEBUG_LEVEL=MASTER_DEBUG_LEVEL;
+    	EYESIS_CORRECTIONS.setDebug(DEBUG_LEVEL);
+    	resetGroundTruth();
+
+    	return;
+/* ======================================================================== */
+    } else if (label.equals("Ground truth 0")) {
+        DEBUG_LEVEL=MASTER_DEBUG_LEVEL;
+    	EYESIS_CORRECTIONS.setDebug(DEBUG_LEVEL);
+    	enhanceByRig(false);
+
+    	return;
 /* ======================================================================== */
     } else if (label.equals("Ground truth")) {
         DEBUG_LEVEL=MASTER_DEBUG_LEVEL;
     	EYESIS_CORRECTIONS.setDebug(DEBUG_LEVEL);
-    	enhanceByRig();
+    	enhanceByRig(true);
 
     	return;
-    	/* ======================================================================== */
+/* ======================================================================== */
     } else if (label.equals("CLT planes")) {
     	DEBUG_LEVEL=MASTER_DEBUG_LEVEL;
     	EYESIS_CORRECTIONS.setDebug(DEBUG_LEVEL);
@@ -5052,10 +5069,14 @@ private Panel panel1,
 		return true;
 
 	}
-
-	public boolean enhanceByRig() {
+//resetGroundTruthByRig()
+	public boolean resetGroundTruth() {
+		if ((QUAD_CLT == null) || (QUAD_CLT.tp == null)) return false;
+		QUAD_CLT.resetGroundTruthByRig();
+		return true;
+	}
+	public boolean enhanceByRig( boolean use_planes) {
 		long startTime=System.nanoTime();
-
 		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);
@@ -5066,22 +5087,17 @@ private Panel panel1,
     	String configPath=getSaveCongigPath();
     	if (configPath.equals("ABORT")) return false;
 
-    	if (DEBUG_LEVEL > -2){
-    		System.out.println("++++++++++++++ Enhancing single-camera DSI by the dual-camera rig++++++++++++++");
-    	}
-    	try {
+        	if (DEBUG_LEVEL > -2){
+        		System.out.println("++++++++++++++ Enhancing single-camera DSI by the dual-camera rig using planes ++++++++++++++");
+        	}
     		TWO_QUAD_CLT.enhanceByRig( // 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,
+    				use_planes, //   final boolean                                  use_planes,
     				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

src/main/java/ImageDtt.java

@@ -2711,7 +2711,7 @@ public class ImageDtt {
 								for (int chn = 0; chn < numcol; chn++){
 
 									tiles_debayered[i][chn] =  tile_debayer_shot_corr(
-											(chn != 2), // red or blue (flase - green)
+											(chn != 2), // red or blue (false - green)
 											iclt_tile[i][chn],
 											2 * transform_size,
 											lt_window2, // squared lapping window
@@ -7098,12 +7098,12 @@ public class ImageDtt {
 							for (int i =0; i<quad; i++){
 								for (int chn = 0; chn < numcol; chn++){
 									//								tiles_debayered[i][chn] =  tile_debayer(
-									//										(chn != 2), // red or blue (flase - green)
+									//										(chn != 2), // red or blue (false - green)
 									//										iclt_tile[i][chn],
 									//										2 * transform_size);
 
 									tiles_debayered[i][chn] =  tile_debayer_shot_corr(
-											(chn != 2), // red or blue (flase - green)
+											(chn != 2), // red or blue (false - green)
 											iclt_tile[i][chn],
 											2 * transform_size,
 											lt_window2, // squared lapping window
@@ -7642,7 +7642,7 @@ public class ImageDtt {
 			for (int chn = 0; chn < numcol; chn++){
 
 				tiles_debayered[i][chn] =  tile_debayer_shot_corr(
-						(chn != 2),                 // red or blue (flase - green)
+						(chn != 2),                 // red or blue (false - green)
 						iclt_tile[i][chn],
 						2 * clt_parameters.transform_size,
 						lt_window2,                 // squared lapping window

src/main/java/QuadCLT.java

@@ -73,6 +73,9 @@ public class QuadCLT {
 
 
 // magic scale should be set before using  TileProcessor (calculated disparities depend on it)
+    public void resetGroundTruthByRig() {
+    	tp.rig_disparity_strength = null;
+    }
     public double [][] getGroundTruthByRig(){
     	if (tp == null) return null;
     	return tp.rig_disparity_strength;
@@ -118,6 +121,57 @@ public class QuadCLT {
 		}
 	}
 
+// used for aux camera
+	public boolean setupImageData(
+			String image_name,
+			String [] sourceFiles,
+			EyesisCorrectionParameters.CLTParameters       clt_parameters,
+			int threadsMax,
+			int debugLevel) {
+		  QuadCLT.SetChannels [] set_channels_aux =  setChannels(image_name, debugLevel);
+		  if ((set_channels_aux == null) || (set_channels_aux.length==0)) {
+			  System.out.println("No files for the auxiliary camera match series "+image_name);
+			  return false;
+		  }
+		  double [] referenceExposures_aux =  eyesisCorrections.calcReferenceExposures(debugLevel); // multiply each image by this and divide by individual (if not NaN)
+		  int [] channelFiles_aux =  set_channels_aux[0].fileNumber();
+		  // make single
+		  boolean [][] saturation_aux =  (clt_parameters.sat_level > 0.0)? new boolean[channelFiles_aux.length][] : null;
+		  double [] scaleExposures_aux =  new double[channelFiles_aux.length];
+		  ImagePlus [] imp_srcs_aux = conditionImageSet(
+				  clt_parameters,               // EyesisCorrectionParameters.CLTParameters  clt_parameters,
+				  sourceFiles,                  // String []                                 sourceFiles,
+				  image_name,      // set_channels_aux[0].name(), // String                                    set_name,
+				  referenceExposures_aux,       // double []                                 referenceExposures,
+				  channelFiles_aux,             // int []                                    channelFiles,
+				  scaleExposures_aux,           //output  // double [] scaleExposures
+				  saturation_aux,               //output  // boolean [][]                              saturation_imp,
+				  debugLevel); // int                                       debugLevel);
+
+		  double [][][] double_stacks_aux = new double [imp_srcs_aux.length][][];
+		  for (int i = 0; i < double_stacks_aux.length; i++){
+			  double_stacks_aux[i] = eyesisCorrections.bayerToDoubleStack(
+					  imp_srcs_aux[i], // source Bayer image, linearized, 32-bit (float))
+					  null); // no margins, no oversample
+		  }
+
+		  for (int i = 0; i < double_stacks_aux.length; i++){
+			  for (int j =0 ; j < double_stacks_aux[i][0].length; j++){
+				  double_stacks_aux[i][2][j]*=0.5; // Scale green 0.5 to compensate more pixels than R,B
+			  }
+		  }
+		  setTiles (imp_srcs_aux[0], // set global tp.tilesX, tp.tilesY
+				  clt_parameters,
+				  threadsMax);
+		  this.image_name =      image_name;
+		  image_data =      double_stacks_aux;
+		  saturation_imp =  saturation_aux;
+		  tp.setTrustedCorrelation(clt_parameters.grow_disp_trust);
+		  tp.resetCLTPasses();
+		  return true;
+
+	}
+
 
 	public QuadCLT(
 			String                                          prefix,

src/main/java/TileNeibs.java

@@ -59,6 +59,12 @@ public class TileNeibs{
 		int [] xy = {indx % sizeX ,indx / sizeX};
 		return xy;
 	}
+	int getSizeX() {
+		return sizeX;
+	}
+	int getSizeY() {
+		return sizeY;
+	}
 
 	/**
 	 * Get element index from x and y