Started manual pair matching by affine transform

src/main/java/com/elphel/imagej/correction/Eyesis_Correction.java

@@ -109,6 +109,7 @@ import com.elphel.imagej.ims.EventLogger;
 import com.elphel.imagej.ims.Imx5;
 import com.elphel.imagej.jp4.JP46_Reader_camera;
 import com.elphel.imagej.lwir.LwirReader;
+import com.elphel.imagej.orthomosaic.ComboMatch;
 import com.elphel.imagej.readers.ChangeImageResolution;
 import com.elphel.imagej.readers.DumpImageMetadata;
 import com.elphel.imagej.readers.EyesisTiff;
@@ -841,6 +842,8 @@ public class Eyesis_Correction implements PlugIn, ActionListener {
 			addButton("Build World", panelLWIRWorld, color_process);
 			addButton("Test IMX5", panelLWIRWorld, color_process);
 			addButton("Show mice", panelLWIRWorld, color_process);
+			addButton("Set pair",  panelLWIRWorld, color_process);
+			addButton("Warp pair",  panelLWIRWorld, color_process);
 			plugInFrame.add(panelLWIRWorld);
 			
 		}
@@ -5672,6 +5675,14 @@ public class Eyesis_Correction implements PlugIn, ActionListener {
 			ImagePlus imp_src = WindowManager.getCurrentImage();
 			ImagePlus imp_mice = subtractAverage(imp_src);
 			imp_mice.show();
+		} else if (label.equals("Set pair")) {
+			DEBUG_LEVEL = MASTER_DEBUG_LEVEL;
+			EYESIS_CORRECTIONS.setDebug(DEBUG_LEVEL);
+			ComboMatch.openTestPair();
+		} else if (label.equals("Warp pair")) {
+			DEBUG_LEVEL = MASTER_DEBUG_LEVEL;
+			EYESIS_CORRECTIONS.setDebug(DEBUG_LEVEL);
+			ComboMatch.testPair();
 		}
 	}
 

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

@@ -11624,6 +11624,10 @@ public class ImageDttCPU {
 	 * From Stephan Preibisch's Multithreading.java class. See:
 	 * http://repo.or.cz/w/trakem2.git?a=blob;f=mpi/fruitfly/general/MultiThreading.java;hb=HEAD
 	 */
+	public static Thread[] newThreadArray() {
+		return newThreadArray(THREADS_MAX);
+	}
+
 	public static Thread[] newThreadArray(int maxCPUs) { // USED in lwir
 		int n_cpus = Runtime.getRuntime().availableProcessors();
 		if (n_cpus>maxCPUs)n_cpus=maxCPUs;

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

@@ -2673,12 +2673,14 @@ public class TexturedModel {
 			}
 		}
 		// -------
+		boolean mixed_flat = false;
 		if (gsmth_enable && (!has_sfm || gsmth_sfm_gnd)) {
 			double [] smooth_ground = scenes[ref_index].getSmoothGround(
 					clt_parameters,
 					has_sfm, // boolean       sfm_mode,
 					debugLevel);
 			if (has_sfm && gsmth_sfm_deviate) {
+				mixed_flat = true;
 				// Change!
 				// Use FG for FG, and ground plane as BG?
 				TileNeibs tn = new TileNeibs(tilesX, smooth_ground.length/tilesX);
@@ -3189,7 +3191,7 @@ public class TexturedModel {
 					String suffix ="-RECT"; 
 					suffix +="-PIX"+pix_size * hdr_whs[2];
 					if (gsmth_enable) {
-						suffix +="-FLAT"; // flattened ground
+						suffix +=mixed_flat ? "-FLAT_MIX":"-FLAT_CLN"; // flattened ground - mixed or clean
 					}
 					scenes[ref_index].saveDoubleArrayInModelDirectory(
 							suffix+"-FULL", // String      suffix,