Merge branch 'master' of https://github.com/Elphel/imagej-elphel

pom.xml

@@ -11,14 +11,18 @@
 		<version>1.135</version>
 		<relativePath />
 	</parent>
-
+<!-- 	
+	<properties>
+		<imagej.app.directory>/data/ImageJ/ImageJ</imagej.app.directory>
+	</properties>
+ -->
 	<groupId>com.elphel</groupId>
  	<artifactId>imagej-elphel</artifactId>
 <!-- 	<artifactId>Aberration_Calibration</artifactId> -->
 	
 	<version>1.0.0</version>
 
- 	<name>plugins/ImageJ_Elphel.jar</name>
+ 	<name>plugins/imagej_elphel.jar</name>
 <!-- 	<name>plugins/Aberration_Calibration.jar</name> -->
     <description>A Maven project implementing imagej-elphel plugin</description>
 
@@ -74,9 +78,8 @@
                 <artifactId>maven-plugin-plugin</artifactId>
                 <configuration>
                     <!-- see http://jira.codehaus.org/browse/MNG-5346 -->
-                    <skipErrorNoDescriptorsFound>true</skipErrorNoDescriptorsFound>
+                   <skipErrorNoDescriptorsFound>true</skipErrorNoDescriptorsFound>
                 </configuration>
-
                 <executions>
                     <execution>
                         <id>mojo-descriptor</id>
@@ -85,6 +88,7 @@
                         </goals>
                     </execution>
                 </executions>
+	
             </plugin>
   			
 			<plugin>

src/main/java/Distortions.java

@@ -12398,7 +12398,7 @@ Which parameters affect which matrices
         public int getGoniometerHorizontalIndex(){return 6;}
         public int getGoniometerAxialIndex(){return 7;}
         public int getSensorWidth() { return this.sensorWidth;}
-        public int getSensorHeight() { return this.sensorWidth;}
+        public int getSensorHeight() { return this.sensorHeight;}
         public int getSensorWidth(int subCam) { return this.sensorWidth;} // for the future? different sensors
         public int getSensorHeight(int subCam) { return this.sensorHeight;}// for the future? different sensors
         public double getPixelSize(int subCamNumber){return  this.eyesisSubCameras[0][subCamNumber].pixelSize;} // use station 0's pixel size
@@ -13952,6 +13952,33 @@ Which parameters affect which matrices
 			this.flipVertical=flipVertical;
 			recalcCommons();
 		}
+		public void setIntrincicFromSubcamera(EyesisSubCameraParameters pars){
+			setLensDistortionParameters(
+					pars.focalLength,
+					pars.pixelSize,  //um
+					pars.distortionRadius, // mm
+					pars.distortionA8, // r^7
+					pars.distortionA7, // r^6
+					pars.distortionA6, // r^5
+					pars.distortionA5, // r^4
+					pars.distortionA,  // r^4
+					pars.distortionB,  // r^3
+					pars.distortionC,  // r^2
+					// orientation/position parameters
+					this.yaw,          // (keep) angle in degrees from perpendicular to the pattern, 0 - towards wall, positive - clockwise from top
+					this.pitch,        // (keep) angle in degrees from perpendicular to the pattern, 0 - towards wall, positive - up
+					this.roll,         // (keep) angle in degrees rotation around camera optical axis (perpendicular to pattern if yaw==0, pitch==0), positive - clockwise
+					this.x0,           // (keep) lens axis from pattern center, mm (to the right)
+					this.y0,           // (keep) lens axis from pattern center, mm (down)
+					this.z0,           // (keep) lens axis from pattern center, mm (away)
+					this.distance,     // (keep) distance from the lens input pupil to the pattern plane along the camera axis, mm
+					pars.px0,          //        center of the lens on the sensor, pixels
+					pars.py0,          // center of the lens on the sensor, pixels
+					this.flipVertical  // (keep)  acquired image is mirrored vertically (mirror used)
+			);
+		}
+		
+		
 		public void setLensDistortionParameters(LensDistortionParameters ldp
 		){
 			this.focalLength=ldp.focalLength;

src/main/java/MatchSimulatedPattern.java

@@ -5332,6 +5332,7 @@ java.lang.ArrayIndexOutOfBoundsException: -3566
 				   if (mask[i]<maskCutOff) mask[i]=0.0;
 			   int size = (int) Math.sqrt(psf.length);
 			   int hsize=size/2;
+//			   int nn=0;
 			   double S0=0.0, SR=0.0, ST=0.0,SR2=0.0,ST2=0.0; //,SRT=0.0;
 			   for (int i=0;i<mask.length;i++)  if (mask[i]>0.0) {
 				   double x=(i % size) - hsize;
@@ -5344,13 +5345,62 @@ java.lang.ArrayIndexOutOfBoundsException: -3566
 				   ST+=d*tc;
 				   SR2+=d*rc*rc;
 				   ST2+=d*tc*tc;
-//				   SRT+=d*rc*tc;
+//				   nn++;
 			   }
 			   if (S0==0.0) return null; // make sure it is OK
 			   double  [] result={ Math.sqrt(ST2*S0 - ST*ST)/S0, Math.sqrt(SR2*S0 - SR*SR)/S0};
+//			   System.out.println(" mask.length="+mask.length+" nn="+nn+" S0="+S0+" SR="+SR+" ST="+ST+" SR2="+SR2+" ST2="+ST2+
+//					   " result={"+result[0]+","+result[1]+"}");
 			   return result;
 		   }
 
+		 //====================================================
+		   public double [] x2y2xySizes(
+				   double []       psf,     // PSF function, square array, nominally positive
+				   double cutoffEnergy,     // fraction of energy in the pixels to be used
+				   double cutoffLevel,      // minimal level as a fraction of maximal
+				   int         minArea,      // minimal selected area in pixels
+				   double      blurSigma,    // optionally blur the selection
+				   double      maskCutOff,
+				   int           debugLevel, // debug level
+				   String        title) {    // prefix used for debug images
+			   double [] mask=findClusterOnPSF(
+					   psf,
+					   cutoffEnergy,
+					   cutoffLevel,
+					   minArea,
+					   blurSigma,
+					   debugLevel,
+					   title);
+			   for (int i=0;i<mask.length;i++)
+				   if (mask[i]<maskCutOff) mask[i]=0.0;
+			   int size = (int) Math.sqrt(psf.length);
+			   int hsize=size/2;
+//			   int nn=0;
+			   double S0=0.0, SX=0.0, SY=0.0,SX2=0.0,SY2=0.0,SXY=0.0;
+			   for (int i=0;i<mask.length;i++)  if (mask[i]>0.0) {
+				   double x=(i % size) - hsize;
+				   double y=(i / size) - hsize;
+				   double d=psf[i]*mask[i];
+				   S0+=d;
+				   SX+=d*x;
+				   SY+=d*y;
+				   SX2+=d*x*x;
+				   SY2+=d*y*y;
+				   SXY+=d*x*y;
+//				   nn++;
+			   }
+			   if (S0==0.0) return null; // make sure it is OK
+			   double  [] result={
+					   (SX2*S0 - SX*SX)/S0/S0,
+					   (SY2*S0 - SY*SY)/S0/S0,
+					   (SXY*S0 - SX*SY)/S0/S0}; // this may be negative
+//			   System.out.println(" mask.length="+mask.length+" nn="+nn+" S0="+S0+" SX="+SX+" SY="+SY+" SX2="+SXR2+" SY2="+SY2+" SXY="+SXY+
+//					   " result={"+result[0]+","+result[1]+","+result[2]+"}");
+			   return result;
+		   }
+		   
+		   
 //====================================================
 		   
 			public double [] findClusterOnPSF(
@@ -5382,7 +5432,8 @@ java.lang.ArrayIndexOutOfBoundsException: -3566
 				}
 				if (maxValue<=0.0){
 	    		  String msg="psf array does not contain any positive values";
-	    		  IJ.showMessage("Error",msg);
+//	    		  IJ.showMessage("Error",msg);
+	    		  System.out.println("Error "+msg);
 	    		  throw new IllegalArgumentException (msg);
 				}
 				ix=Index % size;
@@ -8506,6 +8557,7 @@ d()/dy=C*x+2*B*y+E=0
 				IJ.showMessage("Error",msg);
 				throw new IllegalArgumentException (msg);
 			}
+			if (this.PATTERN_GRID.length==0) return null;
 			double x1=x0,y1=y0;
 			double x2=x1+size;
 			double y2=y1+size;

src/main/resources/plugins.config

@@ -8,9 +8,9 @@
 #
 # If something like ("<arg>") is appended to the class name, the setup() method
 # will get that as arg parameter; otherwise arg is simply the empty string.
-Process, "Process Pixels", Process_Pixels
+#Process, "Process Pixels", Process_Pixels
 Process, "Aberration Calibration", Aberration_Calibration
 #Plugins, "Aberration Calibration", Aberration_Calibration
 #Process, "Aberration Correction", Aberration_Correction
 Process, "Eyesis Correction", Eyesis_Correction
-#Process, "JP46 Reader camera", JP46_Reader_camera
+Process, "JP46 Reader camera", JP46_Reader_camera