merged with nc393 branch

src/main/java/Aberration_Correction.java

@@ -2514,8 +2514,8 @@ if (PROCESS_PARAMETERS.saveSettings) saveProperties(FILE_PARAMETERS.resultsDirec
 					  tileY = nTile /tilesX;
 					  tileX = nTile % tilesX;
 					  if (tileX==0) {
-						  if (updateStatus) IJ.showStatus("Reducing sampling aliases, row "+(tileY+1)+" of "+tilesY);
-						  if (MASTER_DEBUG_LEVEL>2) System.out.println("Reducing sampling aliases, row "+(tileY+1)+" of "+tilesY+" : "+IJ.d2s(0.000000001*(System.nanoTime()-startTime),3));
+						  if (updateStatus) IJ.showStatus("(3)Reducing sampling aliases, row "+(tileY+1)+" of "+tilesY);
+						  if (MASTER_DEBUG_LEVEL>2) System.out.println("(3)Reducing sampling aliases, row "+(tileY+1)+" of "+tilesY+" : "+IJ.d2s(0.000000001*(System.nanoTime()-startTime),3));
 					  }
 				  
 					  if ((tileY==yTileDebug) && (tileX==xTileDebug)) DEBUG_LEVEL=4;

src/main/java/DenseCorrespondence.java

@@ -39,7 +39,7 @@ public class DenseCorrespondence {
 
 
 
-	private void disparitySweepTile (
+	public void disparitySweepTile ( // never used so far
 			int tileX,
 			int tileY,
 			CyclopeanTile [][] allCyclopeanMap,

src/main/java/Distortions.java

@@ -5989,6 +5989,8 @@ List calibration
     	imp.setProperty("channel",  ""+numSensor);
     	imp.setProperty("comment_subcamera", "number of the subcamera with individual IP, starting with 0");
     	imp.setProperty("subcamera",  ""+camerasInterface.getSubCamera(numSensor));
+		imp.setProperty("sensor_port",""+camerasInterface.getSensorPort(numSensor)); 
+    	
     	imp.setProperty("comment_subchannel", "number of the sensor port on a subcamera (0..2)");
     	imp.setProperty("subchannel",  ""+camerasInterface.getSubChannel(numSensor));
     	imp.setProperty("comment_entrancePupilForward",  "entrance pupil distance from the azimuth/radius/height, outwards in mm");

src/main/java/EyesisAberrations.java

@@ -2213,7 +2213,7 @@ public class EyesisAberrations {
 
 	public double [][][][] createPSFMap(
 			final MatchSimulatedPattern commonMatchSimulatedPattern, // to be cloned in threads, using common data
-			final ImagePlus          imp_sel, // linearized Bayer mosaic image form the camera, GR/BG
+			final ImagePlus          imp_sel, // linearized Bayer mosaic image from the camera, GR/BG
 			final int [][][]        sampleList, // optional (or null) 2-d array: list of coordinate pairs (2d - to match existent  pdfKernelMap structure)  
 			final double  overexposedAllowed, // fraction of pixels OK to be overexposed
 			final SimulationPattern.SimulParameters simulParameters,
@@ -2400,7 +2400,7 @@ public class EyesisAberrations {
 			};
 		}
 		startAndJoin(threads);
-		 if (globalDebugLevel>1) System.out.println("Threads done at "+IJ.d2s(0.000000001*(System.nanoTime()-startTime),3));
+		if (globalDebugLevel>1) System.out.println("Threads done at "+IJ.d2s(0.000000001*(System.nanoTime()-startTime),3));
 //		globalDebugLevel=saved_globalDebugLevel;
 		if (debugLateralShifts) {
 		    boolean [] debugUsedColors=new boolean [debugNumColors];

src/main/java/Eyesis_Correction.java

@@ -3464,7 +3464,7 @@ private Panel panel1,panel2,panel3,panel4,panel5,panel5a, panel6,panel7,panelPos
 						  continue;
 					  }
 					  convolutionKernelStack=imp_kernels.getStack();
-					  if (DEBUG_LEVEL>1) System.out.println("Using kernel stack "+kernelPath+" for convolution with "+result[nFile][nChn][nSubChn].getTitle());
+					  if (DEBUG_LEVEL>1) System.out.println("(1)Using kernel stack "+kernelPath+" for convolution with "+result[nFile][nChn][nSubChn].getTitle());
 					  stack_d= convolveStackWithKernelStack(
 							  stack,  // stack with 3 colors/slices with the image
 							  convolutionKernelStack, // stack with 3 colors/slices convolution kernels
@@ -3492,7 +3492,7 @@ private Panel panel1,panel2,panel3,panel4,panel5,panel5a, panel6,panel7,panelPos
 							  continue;
 						  }
 						  convolutionKernelStack=imp_kernels.getStack();
-						  if (DEBUG_LEVEL>1) System.out.println("Using Gaussian stack "+kernelPath+" for convolution with "+result[nFile][nChn][nSubChn].getTitle());
+						  if (DEBUG_LEVEL>1) System.out.println("(2)Using Gaussian stack "+kernelPath+" for convolution with "+result[nFile][nChn][nSubChn].getTitle());
 						  stack_g= convolveStackWithKernelStack(
 								  stack,  // stack with 3 colors/slices with the image
 								  convolutionKernelStack, // stack with 3 colors/slices convolution kernels
@@ -3592,7 +3592,7 @@ private Panel panel1,panel2,panel3,panel4,panel5,panel5a, panel6,panel7,panelPos
 						  continue;
 					  }
 					  convolutionKernelStack=imp_kernels.getStack();
-					  if (DEBUG_LEVEL>1) System.out.println("Using Gaussian stack "+kernelPath+" for convolution with "+result[nFile][nChn][nSubChn].getTitle());
+					  if (DEBUG_LEVEL>1) System.out.println("(3)Using Gaussian stack "+kernelPath+" for convolution with "+result[nFile][nChn][nSubChn].getTitle());
 					  stack_g= convolveStackWithKernelStack(
 							  stack,  // stack with 3 colors/slices with the image
 							  convolutionKernelStack, // stack with 3 colors/slices convolution kernels
@@ -3977,7 +3977,6 @@ private Panel panel1,panel2,panel3,panel4,panel5,panel5a, panel6,panel7,panelPos
 	  final int tilesY=imgHeight/step-1; // vertical number of overlapping tiles in the source image (should be expanded from the registerd one by "step" in each direction)
 	  final int kernelWidth=kernelStack.getWidth();
 	  final int kernelNumHor=kernelWidth/(size/2);
-
 	  final int nChn=imageStack.getSize();
 	  final float [][] outPixels=new float[nChn][length]; // GLOBAL same as input
 	  //	   float [][] outPixels=new float[nChn][length]; // same as input
@@ -3988,6 +3987,21 @@ private Panel panel1,panel2,panel3,panel4,panel5,panel5a, panel6,panel7,panelPos
 	  final AtomicInteger ai = new AtomicInteger(0);
 	  final int numberOfKernels=     tilesY*tilesX*nChn;
 	  final int numberOfKernelsInChn=tilesY*tilesX;
+	  if (MASTER_DEBUG_LEVEL>1) 
+		  System.out.println("Eyesis_Correction:convolveStackWithKernelStack :\n"+
+			  "MASTER_DEBUG_LEVEL="+MASTER_DEBUG_LEVEL+"\n"+
+			  "imgWidth="+imgWidth+"\n"+
+			  "imgHeight="+imgHeight+"\n"+
+			  "tilesX="+tilesX+"\n"+
+			  "tilesY="+tilesY+"\n"+
+			  "step="+step+"\n"+
+			  "kernelSize="+kernelSize+"\n"+
+			  "tilesX="+tilesX+"\n"+
+			  "tilesY="+tilesY+"\n"+
+			  "kernelWidth="+kernelWidth+"\n"+
+			  "kernelNumHor="+kernelNumHor+"\n"+
+			  "numberOfKernelsInChn="+numberOfKernelsInChn+"\n");
+	  
 	  final long startTime = System.nanoTime();
 	  for (int ithread = 0; ithread < threads.length; ithread++) {
 		  threads[ithread] = new Thread() {
@@ -4153,8 +4167,8 @@ private Panel panel1,panel2,panel3,panel4,panel5,panel5a, panel6,panel7,panelPos
 					  tileY = nTile /tilesX;
 					  tileX = nTile % tilesX;
 					  if (tileX==0) {
-						  if (updateStatus) IJ.showStatus("Reducing sampling aliases, row "+(tileY+1)+" of "+tilesY);
-						  if (MASTER_DEBUG_LEVEL>2) System.out.println("Reducing sampling aliases, row "+(tileY+1)+" of "+tilesY+" : "+IJ.d2s(0.000000001*(System.nanoTime()-startTime),3));
+						  if (updateStatus) IJ.showStatus("(2)Reducing sampling aliases, row "+(tileY+1)+" of "+tilesY);
+						  if (MASTER_DEBUG_LEVEL>1) System.out.println("(2)Reducing sampling aliases, row "+(tileY+1)+" of "+tilesY+" : "+IJ.d2s(0.000000001*(System.nanoTime()-startTime),3));
 					  }
 				  
 					  if ((tileY==yTileDebug) && (tileX==xTileDebug)) DEBUG_LEVEL=4;

src/main/java/JP46_Reader_camera.java

@@ -346,6 +346,7 @@ public class JP46_Reader_camera implements PlugIn, ActionListener {
 		boolean showDemux=showImage && demux;
 		if (demux) showImage=false;
 		double [] xtraExif=new double[1]; // ExposureTime
+		
 
 //		System.out.println("imp_src is "+((imp_src!=null)?"not ":"")+"null");
 		try {

src/main/java/PixelMapping.java

@@ -25,10 +25,14 @@
 **
 */
 
+import java.awt.Point;
 import java.awt.Rectangle;
 import java.io.IOException;
 import java.util.ArrayList;
+import java.util.Arrays;
 import java.util.BitSet;
+import java.util.Collections;
+import java.util.Comparator;
 import java.util.List;
 import java.util.concurrent.atomic.AtomicInteger;
 
@@ -135,10 +139,19 @@ public class PixelMapping {
     	if ((channel<0) || (channel>=this.sensors.length)) return -1;
     	return this.sensors[channel].getSubCamera();
     }
+/*    
+    public int getSensorPort(int channel ){
+    	if ((channel<0) || (channel>=this.sensors.length)) return -1;
+    	return this.sensors[channel].getSensorPort();
+    }
+    */
+    
     
     public boolean isChannelAvailable(int channel){
     	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;
@@ -149,6 +162,50 @@ public class PixelMapping {
     	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
+    
+    public int [] channelsForSubCamera(int subCamera){
+//    	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) {
+    		Point cp = new Point(this.sensors[i].subcamera, this.sensors[i].sensor_port);
+    		if (!cam_port.contains(cp)){
+    			cam_port.add(cp);
+    		}
+    	}
+    	Point [] cam_port_arr = cam_port.toArray(new Point[0]);
+		Arrays.sort(cam_port_arr, new Comparator<Point>() {
+			@Override
+			public int compare(Point o1, Point o2) {
+				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);
+//		}
+		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);
+			return null; 
+		}
+    	if (this.sensors == null) return null;
+    	int numChannels=0;
+    	for (int i=0;i<this.sensors.length;i++) if (this.sensors[i]!=null) {
+    		if (new Point(this.sensors[i].subcamera, this.sensors[i].sensor_port).equals(cam_port_arr[subCamera])) numChannels++;
+    	}
+    	int [] result=new int [numChannels];
+    	numChannels=0;
+    	for (int i=0;i<this.sensors.length;i++) if (this.sensors[i]!=null){
+    		if (new Point(this.sensors[i].subcamera, this.sensors[i].sensor_port).equals(cam_port_arr[subCamera])) result[numChannels++]=i;
+    	}
+    	return result;
+    }
+    
+    
+    
     public void removeChannel(int channel){
     	if ((this.sensors != null) && (channel>=0)  && (channel<this.sensors.length)) this.sensors[channel]=null;
     }
@@ -9403,7 +9460,8 @@ public class PixelMapping {
         		private BitSet innerMask=null;
         		private int []borderMask=null;
         		public int getNumberOfPlanes(){return this.maximums.length;}
-        		public int getForegroundPlane(){return this.foregroundIndex;}
+        		@SuppressWarnings("unused")
+				public int getForegroundPlane(){return this.foregroundIndex;}
         		public double getPlaneDisparity (int plane){return this.maximums[plane][0];}
         		public void setPlaneDisparity (double disparity, int plane){this.maximums[plane][0]=disparity;}
         		public double getPlaneStrength (int plane){return this.maximums[plane][1];}
@@ -9441,14 +9499,16 @@ public class PixelMapping {
         			this.auxData=new float[n][];
         			for (int i=0;i<n;i++) this.auxData[i]=null;
         		}
-        		public void resetAux(){
+        		@SuppressWarnings("unused")
+				public void resetAux(){
         			this.auxData=null;
         		}
         		public void setAux(int n, float [] data){
         			if (this.auxData==null) initAux(n+1);
         			this.auxData[n]=data;
         		}
-        		public float [][] getAux (){
+        		@SuppressWarnings("unused")
+				public float [][] getAux (){
         			return this.auxData;
         		}
         		public float [] getAux (int n){
@@ -9460,17 +9520,21 @@ public class PixelMapping {
         			this.likely=new float[this.numPlanes][];
         			for (int i=0;i<this.numPlanes;i++) this.likely[i]=null;
         		}
-        		public void resetLikely(){
+        		@SuppressWarnings("unused")
+				public void resetLikely(){
         			this.likely=null;
         		}
-        		public void setLikely(int n, float [] data){
+        		@SuppressWarnings("unused")
+				public void setLikely(int n, float [] data){
         			if (this.likely==null) initLikely();
         			this.likely[n]=data;
         		}
-        		public float [][] getLikely (){
+        		@SuppressWarnings("unused")
+				public float [][] getLikely (){
         			return this.likely;
         		}
-        		public float [] getLikely (int n){
+        		@SuppressWarnings("unused")
+				public float [] getLikely (int n){
         			if ((this.likely==null) || (this.likely.length<=n)) return null;
         			return this.likely[n];
         		}
@@ -9479,17 +9543,21 @@ public class PixelMapping {
         			this.unlikely=new float[this.numPlanes][];
         			for (int i=0;i<this.numPlanes;i++) this.unlikely[i]=null;
         		}
-        		public void resetUnlikely(){
+        		@SuppressWarnings("unused")
+				public void resetUnlikely(){
         			this.unlikely=null;
         		}
-        		public void setUnlikely(int n, float [] data){
+        		@SuppressWarnings("unused")
+				public void setUnlikely(int n, float [] data){
         			if (this.unlikely==null) initUnlikely();
         			this.unlikely[n]=data;
         		}
-        		public float [][] getUnlikely(){
+        		@SuppressWarnings("unused")
+				public float [][] getUnlikely(){
         			return this.unlikely;
         		}
-        		public float [] getUnlikely(int n){
+        		@SuppressWarnings("unused")
+				public float [] getUnlikely(int n){
         			if ((this.unlikely==null) || (this.unlikely.length<=n)) return null;
         			return this.unlikely[n];
         		}
@@ -9577,7 +9645,8 @@ public class PixelMapping {
         		 * @param disparityTolerance - consider "this" as being withing disparityTolerance of disparity. NaN - do not filter by this
         		 * @return
         		 */
-        		public boolean [] getEnabledNonOccluded(
+        		@SuppressWarnings("unused")
+				public boolean [] getEnabledNonOccluded(
         				double disparityFG,
         				double disparity,
         				double disparityTolerance){
@@ -15527,6 +15596,7 @@ public class PixelMapping {
 		public int    channel=   -1;
 	    public int    subcamera= -1;
 	    public int    subchannel=-1;
+	    public int    sensor_port=-1;
 	    // TODO: add serial# (and temperature?)
     	public double azimuth; // azimuth of the lens entrance pupil center, degrees, clockwise looking from top
     	public double radius;  // mm, distance from the rotation axis
@@ -16094,6 +16164,9 @@ public class PixelMapping {
 	    public int getChannel(){return this.channel;}
 	    public int getSubChannel(){return this.subchannel;}
 	    public int getSubCamera(){return this.subcamera;}
+	    public int getSensorPort(){return this.sensor_port;}
+	    
+	    
 	    public void setSensorDataFromImageStack(ImagePlus imp){
 //	    	int corrX=0,corrY=1,corrMask=2;
 	    	if (imp == null){
@@ -16170,6 +16243,9 @@ public class PixelMapping {
 // older files do not have these properties	        
 	        if (imp.getProperty("subcamera")!=null)  this.subcamera= Integer.parseInt((String) imp.getProperty("subcamera"));
 	        if (imp.getProperty("subchannel")!=null) this.subchannel=Integer.parseInt((String) imp.getProperty("subchannel"));
+	        if (imp.getProperty("sensor_port")!=null) this.sensor_port=Integer.parseInt((String) imp.getProperty("sensor_port"));
+	        
+	        
 	        
 	        // now read the calibration data and mask
 	        	this.pixelCorrection=null;