next snapshot

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

@@ -840,6 +840,7 @@ public class Eyesis_Correction implements PlugIn, ActionListener {
 			addButton("Aux Build Series", panelLWIRWorld, color_stop);
 			addButton("Build World", panelLWIRWorld, color_process);
 			addButton("Test IMX5", panelLWIRWorld, color_process);
+			addButton("Show mice", panelLWIRWorld, color_process);
 			plugInFrame.add(panelLWIRWorld);
 			
 		}
@@ -5665,6 +5666,12 @@ public class Eyesis_Correction implements PlugIn, ActionListener {
 			return;
 //JTabbedTest
 // End of buttons code
+		} else if (label.equals("Show mice")) {
+			DEBUG_LEVEL = MASTER_DEBUG_LEVEL;
+			EYESIS_CORRECTIONS.setDebug(DEBUG_LEVEL);
+			ImagePlus imp_src = WindowManager.getCurrentImage();
+			ImagePlus imp_mice = subtractAverage(imp_src);
+			imp_mice.show();
 		}
 	}
 
@@ -8443,7 +8450,42 @@ public class Eyesis_Correction implements PlugIn, ActionListener {
 		}
 		return true;
 	}
-
+	public static ImagePlus subtractAverage(ImagePlus imp_src) {
+		ImagePlus imp_rslt = null;
+		int num_img = imp_src.getStackSize();
+		int width =  imp_src.getWidth();
+		int height = imp_src.getHeight();
+		ImageStack stack = imp_src.getStack();
+		// Simple version - global average
+		int [] num_pix = new int [width*height];
+		double [] sum_pix = new double [width*height];
+		double [][] out_pix = new double [num_img][sum_pix.length];
+		for (int nslice = 0; nslice < num_img; nslice++) {
+			float [] fpix =  (float[]) stack.getPixels(nslice + 1);
+			Arrays.fill(out_pix[nslice], Double.NaN);
+			for (int i = 0; i < fpix.length; i++) if (!Float.isNaN(fpix[i])) {
+				double d = fpix[i];
+				out_pix[nslice][i] = d;
+				sum_pix[i]+= d;
+				num_pix[i]++;
+			}
+		}
+		for (int i = 0; i < sum_pix.length; i++) {
+			if (num_pix[i] > 0) {
+				sum_pix[i] /= num_pix[i];
+			} else {
+				sum_pix[i] = Double.NaN;
+			}
+		}
+		for (int nslice = 0; nslice < num_img; nslice++) {
+			for (int i = 0; i < sum_pix.length; i++) {
+				out_pix[nslice][i] -= sum_pix[i]; 
+			}
+		}
+		ImageStack out_stack = ShowDoubleFloatArrays.makeStack(out_pix, width, height);
+		imp_rslt = new ImagePlus(imp_src.getTitle() + "-motion", out_stack);
+		return imp_rslt;
+	}
 	public ImagePlus selectCLTImage() {
 		if (!CLT_PARAMETERS.showJDialog())
 			return null;

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

@@ -114,11 +114,13 @@ public class IntersceneMatchParameters {
 	public  boolean run_ly =             false; // will return just after LY adjustments, skipping all output generation
 	public  int min_num_orient =         2; // make from parameters, should be >= 1
 	public  int min_num_interscene =     2; // make from parameters, should be >= 1
-	public  boolean adjust_imu_orient =  false;// adjust IMU misalignment to the camera
+	public  boolean adjust_imu_orient =  false; // adjust IMU misalignment to the camera
 	public  boolean apply_imu_orient =   true;  // apply  IMU misalignment to the camera if adjusted
-	public  boolean adjust_gyro =        false;// adjust qyro omegas offsets
+	public  boolean orient_by_move =     false; // use translation data to adjust IMU orientation  
+	public  boolean orient_by_rot =      true;  // use rotation data to adjust IMU orientation
+	public  boolean adjust_gyro =        false; // adjust qyro omegas offsets
 	public  boolean apply_gyro =         true;  // apply adjusted qyro omegas offsets
-	public  boolean adjust_accl =        false;// adjust IMU velocities scales
+	public  boolean adjust_accl =        false; // adjust IMU velocities scales
 	public  boolean apply_accl =         true;  // apply IMU velocities scales
 	
 	public  boolean calc_quat_corr =     true; // calculate camera orientation correction from predicted by IMS 
@@ -673,6 +675,10 @@ public class IntersceneMatchParameters {
 				"Adjust IMU misalignment to the camera.");
 		gd.addCheckbox ("Adjust IMU orientation",                    this.apply_imu_orient,
 				"Apply  IMU misalignment to the camera if adjusted.");
+		gd.addCheckbox ("Use translation for IMU orientation",       this.orient_by_move,
+				"Use translation data to adjust IMU orientation .");
+		gd.addCheckbox ("Use rotation for IMU orientation",          this.orient_by_rot,
+				"Use rotation data to adjust IMU orientation.");
 		gd.addCheckbox ("Adjust gyro offsets",                       this.adjust_gyro,
 				"Adjust qyro omegas offsets.");
 		gd.addCheckbox ("Apply gyro offsets",                        this.apply_gyro,
@@ -1480,6 +1486,8 @@ public class IntersceneMatchParameters {
 		this.min_num_interscene =       (int) gd.getNextNumber(); if (min_num_interscene < 1) min_num_interscene = 1;
 		this.adjust_imu_orient =              gd.getNextBoolean();
 		this.apply_imu_orient =               gd.getNextBoolean();
+		this.orient_by_move =                 gd.getNextBoolean();
+		this.orient_by_rot =                  gd.getNextBoolean();
 		this.adjust_gyro =                    gd.getNextBoolean();
 		this.apply_gyro =                     gd.getNextBoolean();
 		this.adjust_accl =                    gd.getNextBoolean();
@@ -1925,6 +1933,8 @@ public class IntersceneMatchParameters {
 		properties.setProperty(prefix+"min_num_interscene",            this.min_num_interscene+"");            // int
 		properties.setProperty(prefix+"adjust_imu_orient",             this.adjust_imu_orient+"");             // boolean
 		properties.setProperty(prefix+"apply_imu_orient",              this.apply_imu_orient+"");              // boolean
+		properties.setProperty(prefix+"orient_by_move",                this.orient_by_move+"");                // boolean
+		properties.setProperty(prefix+"orient_by_rot",                 this.orient_by_rot+"");                 // boolean
 		properties.setProperty(prefix+"adjust_gyro",                   this.adjust_gyro+"");                   // boolean
 		properties.setProperty(prefix+"apply_gyro",                    this.apply_gyro+"");                    // boolean
 		properties.setProperty(prefix+"adjust_accl",                   this.adjust_accl+"");                   // boolean
@@ -2333,13 +2343,12 @@ public class IntersceneMatchParameters {
 		if (properties.getProperty(prefix+"min_num_interscene")!=null)            this.min_num_interscene=Integer.parseInt(properties.getProperty(prefix+"min_num_interscene"));
 		if (properties.getProperty(prefix+"adjust_imu_orient")!=null)             this.adjust_imu_orient=Boolean.parseBoolean(properties.getProperty(prefix+"adjust_imu_orient"));
 		if (properties.getProperty(prefix+"apply_imu_orient")!=null)              this.apply_imu_orient=Boolean.parseBoolean(properties.getProperty(prefix+"apply_imu_orient"));
+		if (properties.getProperty(prefix+"orient_by_move")!=null)                this.orient_by_move=Boolean.parseBoolean(properties.getProperty(prefix+"orient_by_move"));
+		if (properties.getProperty(prefix+"orient_by_rot")!=null)                 this.orient_by_rot=Boolean.parseBoolean(properties.getProperty(prefix+"orient_by_rot"));
 		if (properties.getProperty(prefix+"adjust_gyro")!=null)                   this.adjust_gyro=Boolean.parseBoolean(properties.getProperty(prefix+"adjust_gyro"));
 		if (properties.getProperty(prefix+"apply_gyro")!=null)                    this.apply_gyro=Boolean.parseBoolean(properties.getProperty(prefix+"apply_gyro"));
-
 		if (properties.getProperty(prefix+"adjust_accl")!=null)                   this.adjust_accl=Boolean.parseBoolean(properties.getProperty(prefix+"adjust_accl"));
 		if (properties.getProperty(prefix+"apply_accl")!=null)                    this.apply_accl=Boolean.parseBoolean(properties.getProperty(prefix+"apply_accl"));
-		
-		
 		if (properties.getProperty(prefix+"calc_quat_corr")!=null)                this.calc_quat_corr=Boolean.parseBoolean(properties.getProperty(prefix+"calc_quat_corr"));
 		if (properties.getProperty(prefix+"apply_quat_corr")!=null)               this.apply_quat_corr=Boolean.parseBoolean(properties.getProperty(prefix+"apply_quat_corr"));
 		if (properties.getProperty(prefix+"use_quat_corr")!=null)                 this.use_quat_corr=Boolean.parseBoolean(properties.getProperty(prefix+"use_quat_corr"));
@@ -2771,6 +2780,8 @@ public class IntersceneMatchParameters {
 		imp.min_num_interscene            = this.min_num_interscene;
 		imp.adjust_imu_orient             = this.adjust_imu_orient;
 		imp.apply_imu_orient              = this.apply_imu_orient;
+		imp.orient_by_move                = this.orient_by_move;
+		imp.orient_by_rot                 = this.orient_by_rot;
 		imp.adjust_gyro                   = this.adjust_gyro;
 		imp.apply_gyro                    = this.apply_gyro;
 		imp.adjust_accl                   = this.adjust_accl;

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

@@ -414,7 +414,7 @@ public class QuadCLTCPU {
     		Rotation ims_atr = new Rotation(RotationOrder.YXZ, ErsCorrection.ROT_CONV,
     				ims_xyzatr[nscene][1][0],    ims_xyzatr[nscene][1][1],    ims_xyzatr[nscene][1][2]);
     		Rotation rotation_atr,rotation_atr2;
-    		if (use_inv) {
+    		if (use_inv) { // should not be used
         		rotation_atr = rot_invert.applyTo(ims_atr);
         		rotation_atr2 = rotation_atr.applyTo(rot); // applyInverseTo?
     		} else {
@@ -464,6 +464,12 @@ public class QuadCLTCPU {
     		int           last_index,
     		int debugLevel
     		) {
+		boolean orient_by_move =    clt_parameters.imp.orient_by_move; // use translation data to adjust IMU orientation
+		boolean orient_by_rot =     clt_parameters.imp.orient_by_rot; // use rotation data to adjust IMU orientation
+		if (!orient_by_move && !orient_by_rot) {
+			System.out.println("Neither translation nor rotation data are enabled to adjust IMU orientation relative to the camera");
+			return;
+		}
 		boolean apply_imu_orient =  clt_parameters.imp.apply_imu_orient; // apply  IMU misalignment to the camera if adjusted
 		boolean adjust_gyro =       clt_parameters.imp.adjust_gyro; // adjust qyro omegas offsets
 		boolean apply_gyro =        clt_parameters.imp.apply_gyro; // apply adjusted qyro omegas offsets
@@ -490,7 +496,12 @@ public class QuadCLTCPU {
     	int quat_lma_mode = QuaternionLma.MODE_XYZQ; // MODE_XYZ4Q3; // MODE_XYZQ; // MODE_XYZQ_LOCAL; // 4; // 3; //  2; // 1;
     	int debug_lev = debugLevel; // 3;
         double avg_z = quadCLTs[ref_index].getAverageZ(true); // in meters
-    	double  translation_weight =  0.0; //  1.0 / (avg_z + 1.0);
+    	double  translation_weight =  1.0 / (avg_z + 1.0);
+    	if (!orient_by_move) {
+    		translation_weight = 0.0;
+    	} else if (!orient_by_rot) {
+    		translation_weight = 1.0;
+    	}
     	double [][][] rotated_xyzatr = QuadCLT.rotateImsToCameraXYZ(
     			clt_parameters,     // CLTParameters clt_parameters,
     			quat_lma_mode,      // int quat_lma_mode,

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

@@ -224,7 +224,7 @@ public class QuaternionLma {
 		//MODE_XYZQ
 		N = vect_x.length;
 		this.mode = mode;
-		samples = 3+ quat0.length;
+		samples = 3 + quat0.length;
 		samples_x = 7;
 		pure_weight = 1.0 - reg_w;
 		int extra_samples = (reg_w > 0) ? quat0.length:0; // (quat0.length < 4)? 0:REGLEN;