Saving center CLT and weights

src/main/java/com/elphel/imagej/tileprocessor/OpticalFlow.java

@@ -5915,11 +5915,12 @@ public class OpticalFlow {
 			cuas_atr = new double [] { center_ATR[0][0], center_ATR[0][1], center_ATR[0][2]};
 		}
 		
-		boolean combine_clt = true;
+		boolean combine_clt = (cuas_atr[0] != 0) || (cuas_atr[1] != 0) || (cuas_atr[2] != 0);
 		if (combine_clt) {
 			boolean apply_clt = true; // set GPU with data
 			boolean show_clt =  true;
 			boolean merge_clt = true;
+			boolean save_clt = true;
 			QuadCLT ref_clt = quadCLTs[ref_index];
 			int sensor_mask_clt = -1; // all
 			
@@ -5937,9 +5938,10 @@ public class OpticalFlow {
         			dls,                 // double [][]    dls
         			quadCLTs[ref_index], // QuadCLT        scene,
         			debugLevel);			
-			
-			float [][] combo_seq_clt = getTDComboSceneSequence(
+        	boolean save_weights = true;
+			float [][] combo_seq_clt_w = getTDComboSceneSequence(
 					clt_parameters,      // CLTParameters  clt_parameters,
+					save_weights,        // boolean        save_weights, // output corresponding weights for each data
 					merge_clt,           // boolean        merge_all,
 					sensor_mask_clt,     // int            sensor_mask,
 		    		null,                // Rectangle      fov_tiles,
@@ -5949,6 +5951,36 @@ public class OpticalFlow {
 		    		quadCLTs,            // QuadCLT []     quadCLTs,
 		    		ref_clt,             // QuadCLT        refCLT, // should be the same instance if one of quadCLTs
 		    		debugLevel);         // int            debugLevel)
+			float [][] combo_seq_clt = save_weights? new float [combo_seq_clt_w.length/2][]: combo_seq_clt_w;
+			if (save_weights) { // remove second half (weights as integer numbers)
+				for (int i = 0; i< combo_seq_clt.length; i++) {
+					combo_seq_clt[i] = combo_seq_clt_w[i];
+				}
+			}
+			if (save_clt) {
+				int [] wh_c = ref_clt.getWHC(false);
+				//final int tile_size_td = 4 * GPUTileProcessor.DTT_SIZE * GPUTileProcessor.DTT_SIZE;
+				final int width_clt = wh_c[0] * 2; // to make image dimensions similar
+				final int height_clt = combo_seq_clt[0].length/width_clt;
+				String [] clt_titles = new String [combo_seq_clt_w.length];
+				for (int i = 0; i < combo_seq_clt.length; i++) {
+					clt_titles[i] = "chn-"+i;
+					if (save_weights) {
+						clt_titles[i+combo_seq_clt.length] = "weight-"+i;
+					}
+				}
+				String suffix_clt = "-clt_combo";
+				if (save_weights) {
+					suffix_clt+="_weights";
+				}
+				ref_clt.saveFloatArrayInModelDirectory( // error
+						suffix_clt,     // String      suffix,
+						clt_titles,       // combo_dsn_titles_full, // null,          // String []   labels, // or null
+						combo_seq_clt_w,    // dbg_data,         // float [][] data,
+						width_clt,        // int         width,
+						height_clt);      // int         height)
+			}
+
 			int [] whc = new int[3];
 			if (apply_clt) { // set GPU with data
 				quadCLTs[ref_index].setComboToTD(
@@ -8169,8 +8201,9 @@ public class OpticalFlow {
     
     public static float [][] getTDComboSceneSequence(
     		CLTParameters  clt_parameters,
-    		boolean        merge_all,
-    		int            sensor_mask,
+    		final boolean  save_weights, // output corresponding weights for each data
+    		final boolean  merge_all,
+    		final int      sensor_mask,
     		Rectangle      fov_tiles,
     		double []      stereo_xyz, // offset reference camera {x,y,z}
     		double []      stereo_atr_in, // offset reference orientation (cuas)
@@ -8222,12 +8255,14 @@ public class OpticalFlow {
 			sc0 = nscene;
 			break;
 		}
-        final float [][] sumFclt = new float [merge_all? 1 : quadCLTs[sc0].getNumSensors()][quadCLTs[sc0].getCltSize(false)];
-        final int [][] numAcc = new int [sumFclt.length][sumFclt[0].length];
+		
+		final int num_slices = merge_all? 1 : quadCLTs[sc0].getNumSensors();
+        final float [][] sumFclt = new float [num_slices * (save_weights? 2:1)][quadCLTs[sc0].getCltSize(false)];
+        final int [][] numAcc = new int [num_slices][sumFclt[0].length];
         // next two to improve multithreading performance
         final int tile_size_td = 4 * GPUTileProcessor.DTT_SIZE * GPUTileProcessor.DTT_SIZE;
         final int tiles_td = sumFclt[0].length/tile_size_td;
-        final int tiles_td_all = tiles_td * sumFclt.length; // usually sumFclt.length==1
+        final int tiles_td_all = tiles_td * num_slices; // usually sumFclt.length==1
         
 		final Thread[] threads = ImageDtt.newThreadArray(THREADS_MAX);
 		final AtomicInteger ai = new AtomicInteger(0);
@@ -8363,6 +8398,9 @@ public class OpticalFlow {
 							} else {
 								sumFclt[nsens][indx] = Float.NaN;
 							}
+							if (save_weights) {
+								sumFclt[nsens + num_slices][indx] = numAcc[nsens][indx];
+							}
 						}
 					}
 				}

src/main/java/com/elphel/imagej/tileprocessor/QuadCLT.java

@@ -2616,6 +2616,7 @@ public class QuadCLT extends QuadCLTCPU {
 	public int getCltSize(boolean use_ref) {// per sensor, in floats
 		return gpuQuad.getCltSize(use_ref);
 	}
+
 	public int getNumSensors() { // Use QCC - this one may be null
 		if (gpuQuad != null) {
 			return gpuQuad.getNumSensors();
@@ -2623,6 +2624,12 @@ public class QuadCLT extends QuadCLTCPU {
 		return super.getNumSensors();
 	}
 	
+	public int [] getWHC(boolean use_reference) {
+		final int [] width_height = gpuQuad.getWH(use_reference);
+		final int num_colors = gpuQuad.getNumColors();
+		return new int [] {width_height[0],width_height[1],num_colors};
+	}
+	
 	/**
 	 * Get individual or combined transform domain data from the GPU
 	 * @param sensor_mask bitmask of the sensors to use

src/main/java/com/elphel/imagej/tileprocessor/QuadCLTCPU.java

@@ -5117,6 +5117,26 @@ public class QuadCLTCPU {
 		return imp;
 	}
 
+	public ImagePlus saveFloatArrayInModelDirectory(
+			String      suffix,
+			String []   labels, // or null
+			float [][]  data,
+			int         width,
+			int         height)
+	{
+		String x3d_path = getX3dDirectory();
+		String file_name = image_name + suffix;
+		String file_path = x3d_path + Prefs.getFileSeparator() + file_name + ".tiff";
+		ImageStack imageStack = ShowDoubleFloatArrays.makeStack(data, width, height, labels, false);
+		ImagePlus imp = new ImagePlus( file_name, imageStack);
+		FileSaver fs=new FileSaver(imp);
+		fs.saveAsTiff(file_path);
+		System.out.println("saveFloatArrayInModelDirectory(): saved "+file_path);
+		return imp;
+	}
+	
+	
+	
 	public ImagePlus saveDoubleArrayInTopModelDirectory(
 			String      suffix,
 			String []   labels, // or null