Merge remote-tracking branch 'origin/dct'

src/main/java/Aberration_Calibration.java

@@ -12003,7 +12003,11 @@ if (MORE_BUTTONS) {
 			int       loopDebugLevel){
 		boolean noMove=false;
 		if (newMotorPos==null) {
-			newMotorPos=focusingMotors.readElphel10364Motors().clone();
+			try {
+				newMotorPos=focusingMotors.readElphel10364Motors().clone();
+			} catch (Exception e){
+				System.out.println("moveAndMaybeProbe(): Failed to read motors");
+			}
 			justMove=true;
 			noMove=true;
 		}
@@ -12098,7 +12102,11 @@ if (MORE_BUTTONS) {
 //		System.out.println(">"+focusingMotors.historySize()+": "+focusingMotors.curpos[0]+", "+focusingMotors.curpos[1]+", "+focusingMotors.curpos[2]);
 		boolean noMove=false;
 		if (newMotorPos==null) {
-			newMotorPos=focusingMotors.readElphel10364Motors().clone();
+			try {
+				newMotorPos=focusingMotors.readElphel10364Motors().clone();
+			} catch (Exception e){
+				System.out.println("moveMeasureAndSave(): motors unreachable.");
+			}
 			noMove=true;
 		}
 		if (!noMove)focusingMotors.moveElphel10364Motors(

src/main/java/CalibrationHardwareInterface.java

@@ -2671,7 +2671,7 @@ public class CalibrationHardwareInterface {
     		}
     		
     		boolean result=commandToDevice(command);
-    		updateCurrents();
+    		if (result)	updateCurrents();
     		return result;
 
     	}
@@ -2718,7 +2718,8 @@ public class CalibrationHardwareInterface {
     				String msg = e1.getMessage();
     				if (msg==null || msg.equals(""))  msg = ""+e1;
 					IJ.showMessage("Error",msg); 
-					throw new IllegalArgumentException (msg);
+					return false;
+//					throw new IllegalArgumentException (msg);
     			}catch(ParserConfigurationException pce) {
     				pce.printStackTrace();
     				return false;
@@ -3471,7 +3472,9 @@ public class CalibrationHardwareInterface {
     		IJ.showStatus("");
     		String error = e1.getMessage();
     		if (error==null || error.equals(""))  error = ""+e1;
-    		IJ.showMessage("commandElphel10364Motors ERRROR", ""+error);
+    		System.out.println("commandElphel10364Motors ERRROR: "+error);
+    		// *********** Temporary removed message box (usually "HOST UNREACHABLE") *************
+//    		IJ.showMessage("commandElphel10364Motors ERRROR", ""+error);
     		return null;
     	}catch(ParserConfigurationException pce) {
     		pce.printStackTrace();
@@ -6529,7 +6532,9 @@ if (debugLevel>=debugThreshold) System.out.println(i+" "+diff[0]+" "+diff[1]+" "
     	}
     	public double distFromProbed(int [] position){
     		double minDist=Double.NaN;
+    		if (this.history.size() <1) return Double.NaN;
     		if (position==null) position= this.history.get(this.history.size()-1).motorsPos;
+    		
     		if (this.history.size()>0){
     			for (int i=0;i<this.history.size();i++) if (this.history.get(i).isProbed) {
     				int [] probedPosition=this.history.get(i).motorsPos;

src/main/java/DistortionCalibrationData.java

@@ -1691,15 +1691,25 @@ import org.apache.commons.configuration.XMLConfiguration;
 			if (gridImages!=null) {
 //				this.pathName="";  // modified, keep the path anyway
 // overwrite saved paths with the provided images, number of images{ should match
-				if (this.gIP.length!=gridImages.length){
+				if (this.gIP.length == gridImages.length){
+					for (int i=0;i<this.gIP.length;i++){
+						this.gIP[i].gridImage=gridImages[i];
+						this.gIP[i].path=null; // not needed, just in case
+						this.gIP[i].enabled=true;// enable all (actually just one) acquired images
+					}
+				} else {
 					String msg="Number of provided images ("+gridImages.length+") does not match parameters restored from the "+pathname+" ("+this.gIP.length+")";
 		    		IJ.showMessage("Error",msg);
-		    		throw new IllegalArgumentException (msg);
-				}
-				for (int i=0;i<this.gIP.length;i++){
-					this.gIP[i].gridImage=gridImages[i];
-					this.gIP[i].path=null; // not needed, just in case
-					this.gIP[i].enabled=true;// enable all (actually just one) acquired images
+//		    		throw new IllegalArgumentException (msg);
+					for (int i=0; i<this.gIP.length ; i++){
+						this.gIP[i].path=null; // not needed, just in case
+						this.gIP[i].enabled=true;// enable all (actually just one) acquired images
+						if (i < gridImages.length) {
+							this.gIP[i].gridImage=gridImages[i];
+						} else {
+							this.gIP[i].gridImage=null;
+						}
+					}
 				}
 //				setGridImages(gridImages);
 			}
@@ -2080,7 +2090,7 @@ import org.apache.commons.configuration.XMLConfiguration;
         			imp_grid=this.gIP[numGridImg].gridImage;
         		} else {
         			if (this.updateStatus) IJ.showStatus("Reading grid file "+(fileNumber+1)+" (of "+(numImages)+"): "+this.gIP[fileNumber].path);
-        			if (this.debugLevel>1) System.out.print(fileNumber+" ("+this.gIP[fileNumber].getStationNumber()+"): "+this.gIP[fileNumber].path);
+        			if (this.debugLevel>-1) System.out.print(fileNumber+" ("+this.gIP[fileNumber].getStationNumber()+"): "+this.gIP[fileNumber].path);
         			imp_grid=opener.openImage("", this.gIP[fileNumber].path);  // or (path+filenames[nFile])
         			if (imp_grid==null) {
         				String msg="Failed to read grid file "+this.gIP[fileNumber].path;

src/main/java/EyesisCorrections.java

@@ -107,16 +107,6 @@ public class EyesisCorrections {
 		//if ((this.debugLevel>1) && (correctionsParameters.sourcePaths!=null) && (correctionsParameters.sourcePaths.length>0)) {
 		if ((this.debugLevel>101) && (correctionsParameters.sourcePaths!=null) && (correctionsParameters.sourcePaths.length>0)) {
 			testFF(correctionsParameters.sourcePaths[0]);
-//			this.channelVignettingCorrection[srcChannel]=this.pixelMapping.getBayerFlatFieldFloat(
-/*			
-			SDFA_INSTANCE.showArrays(
-					this.channelVignettingCorrection,
-					this.channelWidthHeight[srcChannel][0],
-					this.channelWidthHeight[srcChannel][1],
-					true,
-					"Flat-Field");
-					//LENS_DISTORTIONS.displayGridTitles());
-*/
 		}
 		
 	}

src/main/java/PixelMapping.java

@@ -151,23 +151,11 @@ public class PixelMapping {
     	return (this.sensors != null) && (channel>=0)  && (channel<this.sensors.length) && (this.sensors[channel]!=null);
     }
 
-/*
-    
-    public int [] channelsForSubCamera(int subCamera){
-    	if (this.sensors == null) return null;
-    	int numChannels=0;
-    	for (int i=0;i<this.sensors.length;i++) if ((this.sensors[i]!=null) &&(this.sensors[i].subcamera==subCamera)) numChannels++;
-    	int [] result=new int [numChannels];
-    	numChannels=0;
-    	for (int i=0;i<this.sensors.length;i++) if ((this.sensors[i]!=null) &&(this.sensors[i].subcamera==subCamera)) result[numChannels++]=i;
-    	return result;
-    }
-    
- */
     // Updating for nc393. subCamera here is 0..9 for Eyesis4pi393 - 0-based index of the file, so it combines physical camera (separate IP)
     // as stored in "subcamera" field of the calibration file and "sensor_port". sensor_port may start from non-0, so we need to count all combinations
-    
+    //removeUnusedSensorData xshould be off!
     public int [] channelsForSubCamera(int subCamera){
+		System.out.println("channelsForSubCamera("+subCamera+"),this.sensors.length="+this.sensors.length);
 //    	ArrayList<ArrayList<ArrayList<Integer>>> camera_IPs = new ArrayList<ArrayList<ArrayList<Integer>>>(); 
     	ArrayList<Point> cam_port = new ArrayList<Point>();
     	for (int i=0;i<this.sensors.length;i++)  if (this.sensors[i]!=null) {
@@ -175,6 +163,7 @@ public class PixelMapping {
     		if (!cam_port.contains(cp)){
     			cam_port.add(cp);
     		}
+//    		System.out.println("this.sensors["+i+"]!=null, this.sensors[i].subcamera="+this.sensors[i].subcamera+", this.sensors[i].sensor_port="+this.sensors[i].sensor_port);
     	}
     	Point [] cam_port_arr = cam_port.toArray(new Point[0]);
 		Arrays.sort(cam_port_arr, new Comparator<Point>() {
@@ -183,9 +172,7 @@ public class PixelMapping {
 				return (o1.x>o2.x)? 1:((o1.x < o2.x)?-1:(o1.y > o2.y)? 1:((o1.y < o2.y)?-1:0)); 
 			}
 		});
-//		for (int i=0; i<cam_port_arr.length;i++){
-//			System.out.println("----- physical camera #"+cam_port_arr[i].x+", sensor_port="+cam_port_arr[i].y);
-//		}
+		// debugging:
 		System.out.println("----- This filename subcamera "+subCamera+": physical camera "+cam_port_arr[subCamera].x+", sensor_port "+cam_port_arr[subCamera].y);
 		if (subCamera >= cam_port_arr.length) {
 			System.out.println("Error: Subcamera "+subCamera+" > that total namera of sensor ports in the system = "+cam_port_arr.length);