Implementing targets analysis

src/main/java/com/elphel/imagej/common/ShowDoubleFloatArrays.java

 package com.elphel.imagej.common;
 import java.awt.Rectangle;
 import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.HashMap;
 import java.util.Map;
 import java.util.Properties;
 
+import com.elphel.imagej.tileprocessor.QuadCLTCPU;
+
 import ij.IJ;
 import ij.ImagePlus;
 import ij.ImageStack;
@@ -1116,7 +1120,7 @@ G= Y  +Pr*(- 2*Kr*(1-Kr))/Kg + Pb*(-2*Kb*(1-Kb))/Kg
 		System.out.println("readDoubleHyperstack(): reading "+path);
 		ImagePlus imp = new ImagePlus(path);
 		if (imp.getWidth() == 0) {
-			System.out.println("testSynthetic(): Failed reading Vector field from: " + path);
+			System.out.println("readDoubleHyperstack(): Failed reading [][][] from: " + path);
 			return null;
 		}
 		int num_slices = imp.getStackSize();
@@ -1161,5 +1165,7 @@ G= Y  +Pr*(- 2*Kr*(1-Kr))/Kg + Pb*(-2*Kb*(1-Kb))/Kg
 		}
 		return out_data;
 	}
-}
+	
+  
 
+}
\ No newline at end of file

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

@@ -939,7 +939,8 @@ public class Eyesis_Correction implements PlugIn, ActionListener {
 					addJButton("Test LLT Cholesky",  jpanelOrange, color_process);
 					addJButton("UAS log",  jpanelOrange, color_process);
 					addJButton("DJI SRT",  jpanelOrange, color_process);
-					addJButton("SRT to KML",  jpanelOrange, color_process);
+					addJButton("SRT to KML",      jpanelOrange, color_process);
+					addJButton("Target Analyze",  jpanelOrange, color_process);
 //					addJButton("Motion_CUAS",  jpanelOrange, color_stop);
 //					addJButton("Motion_scan",  jpanelOrange, color_stop);
 					//
@@ -6142,33 +6143,15 @@ public class Eyesis_Correction implements PlugIn, ActionListener {
 				}
 			}
 			testUasLog();
+			return;
 		} else if (label.equals("DJI SRT")) {
 			testDjiSrt();
 		} else if (label.equals("SRT to KML")) {
 			djiSrtToKml();
-			
-		/*	
-		} else if (label.equals("Motion_CUAS")) {
-			DEBUG_LEVEL = MASTER_DEBUG_LEVEL;
-			ImagePlus imp_sel = WindowManager.getCurrentImage();
-			if (imp_sel != null) {
-				motion_cuas(
-						imp_sel,
-						0); // 						int       mode));
-			} else {
-				System.out.println("No image selected");
-			}
-		} else if (label.equals("Motion_scan")) {
-			DEBUG_LEVEL = MASTER_DEBUG_LEVEL;
-			ImagePlus imp_sel = WindowManager.getCurrentImage();
-			if (imp_sel != null) {
-				motion_cuas(
-						imp_sel,
-						1); // 						int       mode));
-			} else {
-				System.out.println("No image selected");
-			}
-			*/
+			return;
+		} else if (label.equals("Target Analyze")) {
+			CuasMotion.targetsAnalyze();
+			return;
 		}
 		} finally {
 			MCP_COMMAND_CONTEXT = false;

src/main/java/com/elphel/imagej/cuas/CuasRanging.java

@@ -57,6 +57,7 @@ public class CuasRanging {
 			boolean         batch_mode){
 		boolean save_linear_cuas = true;
 		boolean save_um_cuas = true;
+		boolean save_noise_map = true;
 		double  um_sigma =           clt_parameters.imp.um_sigma;
 		double  um_weight =          clt_parameters.imp.um_weight;
 		boolean mono_fixed =         clt_parameters.imp.mono_fixed;
@@ -207,6 +208,9 @@ public class CuasRanging {
             }
             scene_titles[nscene] = s;// imp_targets.getStack().getSliceLabel(nscene+first_corr+1);
         }
+        // get tile variations 
+       	float [] fpixels_avg = (float[]) imp_targets.getStack().getPixels(1); // here assuming first slice is average
+        
         boolean skip_targets = false;// true;
         if (skip_targets) {
         	return null;
@@ -218,9 +222,21 @@ public class CuasRanging {
 				clt_parameters, // CLTParameters     clt_parameters,
 				scene_titles,   // String []         scene_titles,
 				center_CLT,     // QuadCLT           parentCLT,
+				fpixels_avg,    // float []          fpixels_avg,
 				uasLogReader,   // UasLogReader      uasLogReader,
 				debugLevel);    // int               debugLevel)
-		double[][][] targets; //  = null;
+		if (save_noise_map) {
+			ImagePlus imp_noise_map = ShowDoubleFloatArrays.makeArrays(
+					cuasMotion.getNoiseMap(), // float[][] pixels,
+					cuasMotion.getTilesX(), // int width,
+					cuasMotion.getTilesY(), // int height,
+					center_CLT.getImageName()+"-NOISE-MAP"); //String [] titles)
+			center_CLT.saveImagePlusInModelDirectory(imp_noise_map);  // ImagePlus   imp)
+
+		}
+		
+		
+		double[][][] targets;   //  = null;
 
 		/*        
 		cuasMotion.processMovingTargetsMulti( // will remove rendering 
@@ -251,6 +267,7 @@ public class CuasRanging {
     		cuasMotion.processMovingTargetsMulti( // will remove rendering 
     				batch_mode,     // final boolean         batch_mode,
     				fpixels,        // final float [][]      fpixels,
+    				fpixels_avg,    // final float []        fpixels_avg,
     				debugLevel);    // final int             debugLevel) {
 //    		double[][][] 
     		targets = cuasMotion.getTargets();
@@ -470,7 +487,6 @@ public class CuasRanging {
 	}
 	
 	
-	
 	public double [][][] renderKeyFrames(
 			final double [][][] targets,   // centers
 			final double [][][] targets5x5,