using 'interAxisAngle' to compensate for non-axial 'rotation' of the camera

pom.xml

@@ -8,19 +8,19 @@
 	<parent>
 		<groupId>org.scijava</groupId>
 		<artifactId>pom-scijava</artifactId>
-		<version>1.135</version>
-		<relativePath />
+		<version>3.1</version>
+		<relativePath/>
         </parent>
-<!-- 	
+ 	
 	<properties>
-		<imagej.app.directory>/data/ImageJ/ImageJ</imagej.app.directory>
+		<imagej.app.directory>/home/foxel/Desktop/Fiji.app</imagej.app.directory>
 	</properties>
- -->
+
 	<groupId>com.elphel</groupId>
  	<artifactId>imagej-elphel</artifactId>
 <!-- 	<artifactId>Aberration_Calibration</artifactId> -->
 	
-	<version>1.0.0</version>
+	<version>1.0.0-SNAPSHOT</version>
 
  	<name>plugins/imagej_elphel.jar</name>
 <!-- 	<name>plugins/Aberration_Calibration.jar</name> -->
@@ -31,8 +31,9 @@
 		<dependency>
                          <groupId>net.imagej</groupId>
                          <artifactId>ij</artifactId>
-			<version>${imagej1.version}</version>
+                         <version>1.49m</version>
                 </dependency>
+
 		<dependency>
 			<groupId>commons-configuration</groupId>
 			<artifactId>commons-configuration</artifactId>
@@ -94,8 +95,10 @@
 			<plugin>
 				<groupId>org.codehaus.mojo</groupId>
 				<artifactId>exec-maven-plugin</artifactId>
+                                <version>1.3.2</version>
 				<executions>
 					<execution>
+                                                <phase>package</phase>
 						<goals>
 							<goal>java</goal>
 						</goals>
@@ -106,7 +109,28 @@
 					<mainClass>Eyesis_Correction</mainClass>   
 				</configuration>
 			</plugin>
- 			
+ 			<plugin>
+				<groupId>org.codehaus.mojo</groupId>
+				<artifactId>buildnumber-maven-plugin</artifactId>
+				<version>1.3</version>
+				<executions>
+                                    <execution>
+                                    <phase>validate</phase>
+                                    <goals>
+                                        <goal>create</goal>
+                                    </goals>
+                                    </execution>
+				</executions>
+				<configuration>
+                                    <doCheck>true</doCheck>
+                                    <doUpdate>true</doUpdate>
+                                    <format>Build {0,date,yyyy-MM-dd} {0,time,HH:MM:SS} on host {1}</format>
+                                    <items>
+                                        <item>timestamp</item>
+                                        <item>foxel-MRHM7AP</item>
+                                    </items>
+				</configuration>
+                        </plugin>
 		</plugins>
 		
 	</build>
@@ -142,10 +166,22 @@
 
 	<scm>
 		<connection>scm:git:git://github.com/Elphel/imagej-elphel</connection>
-		<developerConnection>sscm:git:https://github.com/Elphel/imagej-elphel</developerConnection>
+		<developerConnection>scm:git:https://github.com/Elphel/imagej-elphel</developerConnection>
 		<tag>HEAD</tag>
 		<url>https://github.com/Elphel/imagej-elphel</url>
 	</scm>
 
 	<packaging>maven-plugin</packaging>
+    <reporting>
+        <plugins>
+            <plugin>
+                <groupId>org.apache.maven.plugins</groupId>
+                <artifactId>maven-checkstyle-plugin</artifactId>
+                 <version>2.14</version>
+                <configuration>
+                    <configLocation>config/sun_checks.xml</configLocation>
+                </configuration>
+            </plugin>
+        </plugins>
+    </reporting>
 </project>

src/main/java/Aberration_Calibration.java

@@ -6662,8 +6662,9 @@ if (MORE_BUTTONS) {
 	    		gd.addNumericField("Station number (0.."+(LENS_DISTORTIONS.fittingStrategy.distortionCalibrationData.eyesisCameraParameters.numStations-1), stationNumber, 0);
 			}
     		gd.addNumericField("Number of sub-camera (starting with 0)", 0, 0);
-    		gd.addNumericField("Camera tilt (0 - vertical, >0 looking above horizon on the target", 0.0, 1,6,"degrees");
-    		gd.addNumericField("Camera axial (0 - subcamera 0 looking to the target, >0 - rotated clockwise", 0.0, 1,6,"degrees");
+    		gd.addNumericField("Camera tilt (0 - vertical, >0 looking above horizon on the target)", 0.0, 1,6,"degrees");
+    		gd.addNumericField("Camera axial (0 - subcamera 0 looking to the target, >0 - rotated clockwise)", 0.0, 1,6,"degrees");
+    		gd.addNumericField("Inter-axis angle (from 90)", 0.0, 1,6,"degrees");
     		gd.showDialog();
     		if (gd.wasCanceled()) return;
 			if (LENS_DISTORTIONS.fittingStrategy.distortionCalibrationData.eyesisCameraParameters.numStations>1){
@@ -6672,11 +6673,13 @@ if (MORE_BUTTONS) {
     		int channelNumber=        (int) gd.getNextNumber();
     		double tilt=       gd.getNextNumber();
     		double axial=      gd.getNextNumber();
+    		double inter=      gd.getNextNumber();
     		ImagePlus imp_simulatePatternOnSensor=LENS_DISTORTIONS.simulatePatternOnSensor(
     				stationNumber,
     				channelNumber,
     				tilt,
     				axial,
+    				inter,
     				SIMUL,
     				THREADS_MAX,                 //int threadsMax,
     				UPDATE_STATUS,               // boolean updateStatus,

src/main/java/Distortions.java

@@ -716,10 +716,11 @@ public class Distortions {
 			if (this.debugLevel>2){
 				System.out.println("listImageSets() 1: ");
 				for (int is=0;is<this.fittingStrategy.distortionCalibrationData.gIS.length;is++){
-					System.out.println("listImageSets() 1: "+is+": tilt="+
-							this.fittingStrategy.distortionCalibrationData.gIS[is].goniometerTilt+" axial="+
-							this.fittingStrategy.distortionCalibrationData.gIS[is].goniometerAxial+" estimated="+
-							this.fittingStrategy.distortionCalibrationData.gIS[is].orientationEstimated);
+					System.out.println("listImageSets() 1: "+is+
+							": tilt="+    this.fittingStrategy.distortionCalibrationData.gIS[is].goniometerTilt+
+							" axial="+    this.fittingStrategy.distortionCalibrationData.gIS[is].goniometerAxial+
+							" interAxis="+this.fittingStrategy.distortionCalibrationData.gIS[is].interAxisAngle+
+							" estimated="+this.fittingStrategy.distortionCalibrationData.gIS[is].orientationEstimated);
 				}
 			}
 		}
@@ -731,10 +732,11 @@ public class Distortions {
 			if (this.debugLevel>2){
 				System.out.println("listImageSets() 2: ");
 				for (int is=0;is<this.fittingStrategy.distortionCalibrationData.gIS.length;is++){
-					System.out.println("listImageSets() 2: "+is+": tilt="+
-							this.fittingStrategy.distortionCalibrationData.gIS[is].goniometerTilt+" axial="+
-							this.fittingStrategy.distortionCalibrationData.gIS[is].goniometerAxial+" estimated="+
-							this.fittingStrategy.distortionCalibrationData.gIS[is].orientationEstimated);
+					System.out.println("listImageSets() 2: "+is+
+							": tilt="+    this.fittingStrategy.distortionCalibrationData.gIS[is].goniometerTilt+
+							" axial="+    this.fittingStrategy.distortionCalibrationData.gIS[is].goniometerAxial+
+							" interAxis="+this.fittingStrategy.distortionCalibrationData.gIS[is].interAxisAngle+
+							" estimated="+this.fittingStrategy.distortionCalibrationData.gIS[is].orientationEstimated);
 				}
 			}
 		}
@@ -2462,6 +2464,7 @@ For each point in the image
 			int subCam,
 			double goniometerTilt,
 			double goniometerAxial,
+			double goniometerInterAxis,
 			SimulationPattern.SimulParameters simulParametersDefault,
 			int threadsMax,
 			boolean updateStatus,
@@ -2481,6 +2484,7 @@ For each point in the image
 				subCam,
 				goniometerTilt, // Tilt, goniometerHorizontal
 				goniometerAxial,  // Axial,goniometerAxial
+				goniometerInterAxis, // inter-axis angle
 				-1, // use camera parameters, not imageSet
 				true // filter border
 		);
@@ -2662,6 +2666,7 @@ For each point in the image
 							dcd.gIP[numGridImage].channel,
 							goniometerTiltAxial[0], // Tilt, goniometerHorizontal
 							goniometerTiltAxial[1],  // Axial,goniometerAxial
+							goniometerTiltAxial[2],  // inter-axis angle
 							setNumber, // -1 or specific image set
 							true // filter border
 					);
@@ -2902,19 +2907,22 @@ For each point in the image
 			GenericDialog gd=new GenericDialog("Specify camera orientation (channel"+fittingStrategy.distortionCalibrationData.gIP[numGridImage].channel+")");
 			gd.addMessage("No goniometer orientation is available for image # "+numGridImage+" - "+fittingStrategy.distortionCalibrationData.gIP[numGridImage].path+
 			", please specify orientation manually");
-			gd.addNumericField("Camera tilt (0 - vertical, >0 looking above horizon on the target", 0.0, 1,6,"degrees");
-			gd.addNumericField("Camera axial (0 - subcamera 0 looking to the target, >0 - rotated clockwise", 0.0, 1,6,"degrees");
+			gd.addNumericField("Camera tilt (0 - vertical, >0 looking above horizon on the target)", 0.0, 1,6,"degrees");
+			gd.addNumericField("Camera axial (0 - subcamera 0 looking to the target, >0 - rotated clockwise)", 0.0, 1,6,"degrees");
+			gd.addNumericField("Camera inter-axis angle (from 90) ", 0.0, 1,6,"degrees");
 			gd.showDialog();
 			if (gd.wasCanceled()) return;
-			goniometerTiltAxial=new double[2];
+			goniometerTiltAxial=new double[3];
 			goniometerTiltAxial[0]=      gd.getNextNumber();
 			goniometerTiltAxial[1]=      gd.getNextNumber();
+			goniometerTiltAxial[2]=      gd.getNextNumber();
 		}
 		double [][][] hintGrid=estimateGridOnSensor(
 				fittingStrategy.distortionCalibrationData.getImageStation(numGridImage), // station number
 				fittingStrategy.distortionCalibrationData.gIP[numGridImage].channel,
 				goniometerTiltAxial[0], // Tilt, goniometerHorizontal
 				goniometerTiltAxial[1],  // Axial,goniometerAxial
+				goniometerTiltAxial[2],  // inter-axis angle
 				(useSetData?fittingStrategy.distortionCalibrationData.gIP[numGridImage].getSetNumber():-1),
 				true // filter border
 				);
@@ -3107,6 +3115,7 @@ For each point in the image
 			int subCamera,
 			double goniometerHorizontal, // Tilt 
 			double goniometerAxial,     // Axial
+			double goniometerInterAxis,     // interAxisAngle
 			int  imageSet,
 			boolean filterBorder){
 		double maxRelativeRadius=this.hintedMaxRelativeRadius; // make adjustable
@@ -3126,6 +3135,11 @@ For each point in the image
 			int goniometerAxialIndex=fittingStrategy.distortionCalibrationData.eyesisCameraParameters.getGoniometerAxialIndex();
 			parVector[goniometerAxialIndex]=     goniometerAxial;
 		}
+		if (!Double.isNaN(goniometerInterAxis)) {
+			int goniometerInterAxisAngleIndex=fittingStrategy.distortionCalibrationData.eyesisCameraParameters.getInterAxisAngleIndex();
+			parVector[goniometerInterAxisAngleIndex]=  goniometerInterAxis;
+		}
+//		/interAxis
 		int sensorWidth=fittingStrategy.distortionCalibrationData.eyesisCameraParameters.getSensorWidth(subCamera);
 		int sensorHeight=fittingStrategy.distortionCalibrationData.eyesisCameraParameters.getSensorHeight(subCamera);
 		System.out.println("estimateGridOnSensor(): subCamera="+subCamera+", goniometerHorizontal="+goniometerHorizontal+", goniometerAxial="+goniometerAxial);
@@ -9842,7 +9856,7 @@ M * V = B
 		distortionCalibrationData.gIS[numSet].goniometerAxial=Double.NaN;
 		distortionCalibrationData.gIS[numSet].goniometerTilt= Double.NaN;
 		// re-estimate orientation
-		double [] ta=distortionCalibrationData.getImagesetTiltAxial(distortionCalibrationData.gIS[numSet].timeStamp); // updates tilt/axial
+		double [] ta=distortionCalibrationData.getImagesetTiltAxial(distortionCalibrationData.gIS[numSet].timeStamp); // updates tilt/axial (now interAxis too!)
 	    if ((ta==null) || Double.isNaN(ta[0]) || Double.isNaN(ta[1])) return false;
 	    return true;
     }

src/main/java/EyesisAberrations.java

@@ -1254,6 +1254,7 @@ public class EyesisAberrations {
         						distortions.fittingStrategy.distortionCalibrationData.gIP[numGridImage].channel, // subCamera,
         						Double.NaN, // goniometerHorizontal, - not used
         						Double.NaN, // goniometerAxial, - not used
+        						Double.NaN, // inter-axis angle, - not used ?
         						distortions.fittingStrategy.distortionCalibrationData.gIP[numGridImage].getSetNumber(), //imageSet,
         						true); //filterBorder)
         				hintTolerance=5.0; // TODO:set from configurable parameter

src/main/java/EyesisCameraParameters.java

@@ -1136,6 +1136,7 @@ import org.apache.commons.configuration.XMLConfiguration;
  //       public int getNumSubCameras (){return (this.eyesisSubCameras==null)?0:this.eyesisSubCameras.length;}
         public int getGoniometerHorizontalIndex(){return 6;}
         public int getGoniometerAxialIndex(){return 7;}
+        public int getInterAxisAngleIndex(){return 9;}
         public int getSensorWidth() { return this.sensorWidth;}
         public int getSensorHeight() { return this.sensorHeight;}
         public int getSensorWidth(int subCam) { return this.sensorWidth;} // for the future? different sensors

src/main/java/Goniometer.java

@@ -598,6 +598,7 @@ horizontal axis:
 				subCam,
 				goniometerTiltAxial[0], // Tilt, goniometerHorizontal
 				goniometerTiltAxial[1],  // Axial,goniometerAxial
+				goniometerTiltAxial[2],  // inter-axis angle
 				-1, // use camera parameters, not imageSet
 				true // filter border
 				);