updating correction

src/main/java/com/elphel/imagej/calibration/Aberration_Calibration.java

@@ -2081,7 +2081,7 @@ if (MORE_BUTTONS) {
 		if (label.equals("List Eyesis4pi") || label.equals("List X-cam")) {
 			DEBUG_LEVEL=MASTER_DEBUG_LEVEL;
 			DistortionCalibrationData dcd=(DISTORTION_CALIBRATION_DATA!=null)?DISTORTION_CALIBRATION_DATA:
-				new DistortionCalibrationData(EYESIS_CAMERA_PARAMETERS);
+				new DistortionCalibrationData(EYESIS_CAMERA_PARAMETERS,GONIOMETER_PARAMETERS);
 			dcd.listCameraParameters(label.equals("List X-cam"));
 			return;
 		}
@@ -2137,11 +2137,27 @@ if (MORE_BUTTONS) {
 			PATTERN_PARAMETERS.debugLevel=MASTER_DEBUG_LEVEL;
 			EYESIS_CAMERA_PARAMETERS.updateNumstations (numStations);
 //if (MASTER_DEBUG_LEVEL==0) return; //TODO: Remove - just debugging
+
+			if (GONIOMETER==null) {
+				GONIOMETER= new Goniometer(
+						CAMERAS, // CalibrationHardwareInterface.CamerasInterface cameras,
+						DISTORTION, //MatchSimulatedPattern.DistortionParameters distortion,
+						PATTERN_DETECT, //MatchSimulatedPattern.PatternDetectParameters patternDetectParameters,
+						EYESIS_CAMERA_PARAMETERS, //EyesisCameraParameters eyesisCameraParameters,
+						LASER_POINTERS, // MatchSimulatedPattern.LaserPointer laserPointers
+						SIMUL,                       //SimulationPattern.SimulParameters  simulParametersDefault,
+						GONIOMETER_PARAMETERS, //LensAdjustment.FocusMeasurementParameters focusMeasurementParameters,
+						DISTORTION_PROCESS_CONFIGURATION
+				);
+			}
+
+
 			DISTORTION_CALIBRATION_DATA=new DistortionCalibrationData(
 					gridFiles,
 					PATTERN_PARAMETERS,
 					EYESIS_CAMERA_PARAMETERS,
 					LASER_POINTERS,
+					GONIOMETER_PARAMETERS,
 					MASTER_DEBUG_LEVEL);
 			LENS_DISTORTIONS.initImageSet(
  					DISTORTION_CALIBRATION_DATA,
@@ -2178,7 +2194,6 @@ if (MORE_BUTTONS) {
 		if       (label.equals("Restore Calibration")) {
 			DEBUG_LEVEL=MASTER_DEBUG_LEVEL;
 			String defaultPath= (DISTORTION_CALIBRATION_DATA!=null)?DISTORTION_CALIBRATION_DATA.pathName:"";
-//    public static DistortionCalibrationData DISTORTION_CALIBRATION_DATA=null;
 			DistortionCalibrationData oldDISTORTION_CALIBRATION_DATA=DISTORTION_CALIBRATION_DATA;
 			DISTORTION_CALIBRATION_DATA=new DistortionCalibrationData(
 					false,
@@ -2187,6 +2202,7 @@ if (MORE_BUTTONS) {
 					EYESIS_CAMERA_PARAMETERS,
 					ABERRATIONS_PARAMETERS,
 					LASER_POINTERS,
+					GONIOMETER_PARAMETERS,
 					null); // gridImages null - use specified files
 			if (DISTORTION_CALIBRATION_DATA.pathName== null){ // failed to select/open the file
 				DISTORTION_CALIBRATION_DATA=oldDISTORTION_CALIBRATION_DATA;
@@ -3563,6 +3579,7 @@ if (MORE_BUTTONS) {
 						EYESIS_CAMERA_PARAMETERS, // is it null or 1?
 						ABERRATIONS_PARAMETERS,
 						LASER_POINTERS,
+						GONIOMETER_PARAMETERS,
 						imp_calibrated); // gridImages null - use specified files - single image
 				if (DISTORTION_CALIBRATION_DATA.pathName== null){ // failed to select/open the file
 					DISTORTION_CALIBRATION_DATA=null;
@@ -6262,7 +6279,8 @@ if (MORE_BUTTONS) {
 			}
 			// initialize needed classes
 			DISTORTION_CALIBRATION_DATA=new DistortionCalibrationData( // images are not setup yet
-	        		EYESIS_CAMERA_PARAMETERS); //EyesisCameraParameters eyesisCameraParameters
+	        		EYESIS_CAMERA_PARAMETERS, //EyesisCameraParameters eyesisCameraParameters
+	        		GONIOMETER_PARAMETERS);
 			if ((LENS_DISTORTIONS!=null) && (LENS_DISTORTIONS.fittingStrategy!=null)) {
 				LENS_DISTORTIONS.fittingStrategy.distortionCalibrationData=DISTORTION_CALIBRATION_DATA;
 			}
@@ -9860,7 +9878,8 @@ if (MORE_BUTTONS) {
         		sourceFilter,
 				PATTERN_PARAMETERS,
 				EYESIS_CAMERA_PARAMETERS,
-				LASER_POINTERS, //LaserPointer                                           laserPointers
+				LASER_POINTERS,          //LaserPointer                                           laserPointers
+				GONIOMETER_PARAMETERS,   //
 				true,                    // boolean read_grids
 				MASTER_DEBUG_LEVEL);
 
@@ -9868,7 +9887,7 @@ if (MORE_BUTTONS) {
 					DISTORTION_CALIBRATION_DATA,
 				EYESIS_CAMERA_PARAMETERS
 				);
-		// set initial orientation of the cameras from the sensors that see mpst of the matching pointers
+		// set initial orientation of the cameras from the sensors that see most of the matching pointers
 		// just for the LMA to start
 		DISTORTION_CALIBRATION_DATA.setInitialOrientation(true);
 		return true;
@@ -9899,6 +9918,7 @@ if (MORE_BUTTONS) {
 				null,
 				LENS_DISTORTIONS,
 				DISTORTION_CALIBRATION_DATA, // may be null, then it will not be updated, obviously (sensor masks)
+				GONIOMETER_PARAMETERS, // for motor sensitivity
 				ABERRATIONS_PARAMETERS.calibrationDirectory);//String calibration_directory
 //getProperties(String prefix,Properties properties)
 //EyesisCameraParameters
@@ -9951,6 +9971,7 @@ if (MORE_BUTTONS) {
         					" (of "+ sourceFilesList[nset].length+"), file "+in_file+" (of "+ numFiles+ ") success in "+saved_file+" - "+sourceFilesList[nset][nfile]);
         		}
         		String grid_path = null;
+        		/*
         		if (saveGrids && !overwriteGrids){ // check if result already exists
         			i = sourceFilesList[nset][nfile].lastIndexOf('/');
         			if (i>0){
@@ -9961,6 +9982,19 @@ if (MORE_BUTTONS) {
     						continue;
     					}
         			}
+        		}
+        		 */
+
+        		if (saveGrids){ // check if result already exists
+        			i = sourceFilesList[nset][nfile].lastIndexOf('/');
+        			if (i>0){
+        				String grid_name = prefix+sourceFilesList[nset][nfile].substring(i+1);
+        				grid_path = gridSetPath + Prefs.getFileSeparator() + grid_name;
+        				if (!overwriteGrids && ((new File(grid_path)).exists())){ // check if result already exists
+    						if (DEBUG_LEVEL>0) System.out.println("-->>> Skipping existing "+grid_path+" (as requested in \"Configure Process Distortions\")");
+    						continue;
+    					}
+        			}
         		}
         		imp_sel=new ImagePlus(sourceFilesList[nset][nfile]); // read source file
         		EyesisTiff.decodeProperiesFromInfo(imp_sel);
@@ -11260,6 +11294,7 @@ if (MORE_BUTTONS) {
 				eyesisCameraParameters,
 				aberrationParameters,
 				laserPointers,
+				GONIOMETER_PARAMETERS,
 				null); // gridImages null - use specified files
 		if (distortions.fittingStrategy!=null) {
 			distortions.fittingStrategy.distortionCalibrationData=dcd;
@@ -11291,7 +11326,7 @@ if (MORE_BUTTONS) {
 		if (configPaths[2] !=null){ // load grid file
 			patternParameters.debugLevel=debugLevel;
 			patternParameters.updateStatus=updateStstus;
-			if (DEBUG_LEVEL>0) System.out.println("Autolading grid file "+configPaths[2]);
+			if (DEBUG_LEVEL>0) System.out.println("Autoloading grid file "+configPaths[2]);
 			patternParameters.selectAndRestore(true,configPaths[2],dcd.eyesisCameraParameters.numStations); // returns path or null on failure
 		} else {
 			System.out.println("No pattern grid file (ground gtruth) is provided");

src/main/java/com/elphel/imagej/calibration/Distortions.java

@@ -3026,6 +3026,7 @@ For each point in the image
 			if (imp.getRoi() instanceof PointRoi) {
 				pointRoi =  (PointRoi) imp.getRoi();
 			} else {
+				System.out.println("This image does not have point marks - please mark it in "+source_path);
 				IJ.showMessage("This image does not have point marks - please mark it in "+source_path);
 				return null;
 			}
@@ -3123,7 +3124,7 @@ For each point in the image
 				xyuv[i][3]=0.5;
 			}
 			GenericDialog gd=new GenericDialog("Specify U,V coordinates of the marker(s)");
-			gd.addMessage("Center white cell U=0.5, V=0.5");
+			gd.addMessage("Center white (LWIR black) cell U=0.5, V=0.5");
 			for (int n = 0; n < markers.length; n++) {
 				String label = "Marker "+(n+1)+" (x="+markers[n][0]+", y="+markers[n][1];
 				gd.addNumericField(label+" U", xyuv[n][2], 1, 5, "");

src/main/java/com/elphel/imagej/calibration/MatchSimulatedPattern.java

@@ -24,6 +24,7 @@ package com.elphel.imagej.calibration;
  **
  */
 
+import java.awt.Point;
 import java.awt.Rectangle;
 import java.util.ArrayList;
 import java.util.Arrays;
@@ -49,6 +50,7 @@ import Jama.Matrix;  // Download here: http://math.nist.gov/javanumerics/jama/
 import ij.IJ;
 import ij.ImagePlus;
 import ij.ImageStack;
+import ij.gui.PointRoi;
 import ij.gui.Roi;
 import ij.process.FHT; // get rid, change to double
 import ij.process.FloatProcessor;
@@ -3133,7 +3135,7 @@ public class MatchSimulatedPattern {
 		if (roi==null){
 			selection=new Rectangle(0, 0, imp.getWidth(), imp.getHeight());
 		} else {
-			selection=roi.getBounds();
+			selection= (roi instanceof PointRoi) ? (new Rectangle(0, 0, imp.getWidth(), imp.getHeight())) : roi.getBounds();
 		}
 		MatchSimulatedPattern matchSimulatedPattern=new MatchSimulatedPattern(distortionParameters.FFTSize);
 		matchSimulatedPattern.debugLevel=debugLevel;
@@ -3299,7 +3301,7 @@ public class MatchSimulatedPattern {
 		if (roi==null){
 			selection=new Rectangle(0, 0, imp.getWidth(), imp.getHeight());
 		} else {
-			selection=roi.getBounds();
+			selection= (roi instanceof PointRoi) ? (new Rectangle(0, 0, imp.getWidth(), imp.getHeight())) : roi.getBounds();
 		}
 		Rectangle initialPatternCell=new Rectangle(xc-fft_size,
 				yc-fft_size,
@@ -3626,7 +3628,7 @@ public class MatchSimulatedPattern {
 			if (roi==null){
 				selection=new Rectangle(0, 0, imp.getWidth(), imp.getHeight());
 			} else {
-				selection=roi.getBounds();
+				selection= (roi instanceof PointRoi) ? (new Rectangle(0, 0, imp.getWidth(), imp.getHeight())) : roi.getBounds();
 			}
 		} else {
 			if ((getImageHeight()!=imp.getHeight()) || (getImageWidth()!=imp.getWidth())){
@@ -6193,8 +6195,32 @@ public class MatchSimulatedPattern {
 			setWOI(0, 0, imp.getWidth(), imp.getHeight());
 			selection=new Rectangle(0, 0, imp.getWidth(), imp.getHeight());
 		} else {
-			setWOI(roi.getBounds());
-			selection=roi.getBounds();
+			if (roi instanceof PointRoi) {
+				PointRoi pointRoi =  (PointRoi) roi;
+				Point [] points = pointRoi.getContainedPoints();
+				int [][] ipoints = new int [points.length][2];
+				for (int n = 0; n < ipoints.length; n++) {
+					ipoints[n][0] = points[n].x;
+					ipoints[n][1] = points[n].y;
+				}
+				// as if they a laser pointers
+				double [][] xyuv = new double [points.length][4];
+				for (int i =0; i < ipoints.length; i++) {
+					xyuv[i][0]=ipoints[i][0];
+					xyuv[i][1]=ipoints[i][1];
+					xyuv[i][2]=0.5;
+					xyuv[i][3]=0.5;
+				}
+				System.out.println("Setting first marker (of "+ipoints.length+") as pointer 0.5/0.5 - use use multiple?");
+				System.out.println("**** Not yet implemented, use 'Manual hint' command for each of the annotated files ****");
+//				setPointersXYUV(imp, xyuv);
+
+				setWOI(0, 0, imp.getWidth(), imp.getHeight());
+				selection=new Rectangle(0, 0, imp.getWidth(), imp.getHeight());
+			} else {
+				setWOI(roi.getBounds());
+				selection=roi.getBounds();
+			}
 		}
 		this.debugLevel=global_debug_level;
 		int patternCells=0;
@@ -6377,6 +6403,8 @@ public class MatchSimulatedPattern {
 
 		int numPointers=(laserPointer!=null)?laserPointer.laserUVMap.length:0;
 		double [][] pointersXY=(numPointers>0)?getPointersXYUV(imp, laserPointer):null;
+
+
 		if (global_debug_level > (debugThreshold+1)){
 			if (pointersXY!=null){
 				System.out.println("calculateDistortions() numPointers="+numPointers+" pointersXY.length="+pointersXY.length);

src/main/java/com/elphel/imagej/cameras/EyesisCameraParameters.java

@@ -7,6 +7,7 @@ import com.elphel.imagej.calibration.CalibrationFileManagement;
 import com.elphel.imagej.calibration.DistortionCalibrationData;
 import com.elphel.imagej.calibration.Distortions;
 import com.elphel.imagej.calibration.EyesisAberrations;
+import com.elphel.imagej.calibration.Goniometer;
 import com.elphel.imagej.calibration.LensDistortionParameters;
 import com.elphel.imagej.calibration.MultipleExtensionsFileFilter;
 import com.elphel.imagej.common.GenericJTabbedDialog;
@@ -2705,6 +2706,7 @@ import ij.gui.GenericDialog;
     			SubsystemOffsets subsystemOffsets,
     			Distortions systemDistortions,
     			DistortionCalibrationData system_distortionCalibrationData,
+    			Goniometer.GoniometerParameters goniometerParameters,
     			String calibration_directory) {
     		EyesisCameraParameters sub_system = new EyesisCameraParameters();
     		sub_system.getProperties(prefix, properties);
@@ -2745,7 +2747,8 @@ import ij.gui.GenericDialog;
     			System.out.println("sensors_path = "+sensors_path);
 ///    			String [][] stationFilenames = new String[sub_system.numStations][0];
     			sub_distortionCalibrationData = new DistortionCalibrationData(
-    	        		sub_system // EyesisCameraParameters eyesisCameraParameters
+    	        		sub_system, // EyesisCameraParameters eyesisCameraParameters
+    	        		goniometerParameters
     					);
     			// now read all sensor files
     			if ((sensors_path !=null) && (sensors_path != "")){ // load sensor
@@ -2827,7 +2830,7 @@ import ij.gui.GenericDialog;
     				for (int i = 0; i < tmpPixelCorrection.length; i++ ) systemDistortions.pixelCorrection[i] = tmpPixelCorrection[i];
     			}
     			if (system_distortionCalibrationData == null) {
-    				system_distortionCalibrationData = new DistortionCalibrationData (this);
+    				system_distortionCalibrationData = new DistortionCalibrationData (this, goniometerParameters);
     			}
     			if (system_distortionCalibrationData.sensorMasks == null) {
     				system_distortionCalibrationData.sensorMasks = new double [new_channels][];