fixing bugs for variable images per set (e.g. eo only)

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

@@ -92,6 +92,18 @@ import ij.text.TextWindow;
     	public boolean updateStatus=true;
     	public int     debugLevel=2;
     	private ShowDoubleFloatArrays SDFA_INSTANCE=null; // just for debugging
+    	
+    	public static int pathToChannel(String path) {
+    		int last_dash = path.lastIndexOf('-');
+    		int last =      path.lastIndexOf('_');
+    		if (last_dash >last) last = last_dash;
+    		int last_dot = path.lastIndexOf('.');
+    		if (last_dot < 0) {
+    			last_dot = path.length();
+    		}
+    		return Integer.parseInt(path.substring(last+1, last_dot));
+    	}
+    	
     	public int getNumStations(){
     		return (eyesisCameraParameters==null)?0:eyesisCameraParameters.getNumStations();
     	}
@@ -839,6 +851,8 @@ import ij.text.TextWindow;
 
         public DistortionCalibrationData (
         		String [][]                      stationFilenames,
+        		boolean [][][]                   gridUseChn,   // per station, per set - a bmask of permitted channels
+//        		int    [][]                      gridUseTypes, // per station, per set - a bitbmask of channels to use (+1 - eo, +2 - lwir)                          
         		String []                        source_dirs,      // directories of the source files per station
         		MultipleExtensionsFileFilter     gridFilter,
         		MultipleExtensionsFileFilter     sourceFilter,
@@ -852,6 +866,8 @@ import ij.text.TextWindow;
         	    this.debugLevel=debugLevel;
         	    setupDirDistortionCalibrationData(
         			stationFilenames,
+            		gridUseChn,   // per station, per set - a bmask of permitted channels
+//            		gridUseTypes, // per station, per set - a bitbmask of channels to use (+1 - eo, +2 - lwir)                          
             		source_dirs,      // directories of the source files per station
         			gridFilter,
         			sourceFilter,
@@ -933,6 +949,7 @@ import ij.text.TextWindow;
 // from data organized as image sets
         public static int getChannelFromPath(String path) {
 //        		int indexSuffix=path.length()-suffix.length();
+        	if (path == null) return -1;
         	int indexSuffix = path.lastIndexOf(".");
         	int indexLastDash=indexSuffix-1;
         	while ((indexLastDash>0) &&
@@ -951,6 +968,8 @@ import ij.text.TextWindow;
         
         public void setupDirDistortionCalibrationData (
         		String [][]                     stationFilenames, // per-station List of image set directories
+        		boolean [][][]                  gridUseChn,   // per station, per set - a bmask of permitted channels
+//        		int    [][]                     gridUseTypes, // per station, per set - a bitbmask of channels to use (+1 - eo, +2 - lwir)                          
         		String []                       source_dirs,      // directories of the source files per station
         		MultipleExtensionsFileFilter    gridFilter,
         		MultipleExtensionsFileFilter    sourceFilter,
@@ -971,6 +990,7 @@ import ij.text.TextWindow;
         		String [] getSourcePaths() {return spaths;} // may not be null
         		DirTs(int station,
         			  String dir,  // grid image set directory that contains channel files (may be different timestamps)
+        			  boolean [] permitted_channels, // bitmask of permitted channels (lwir/eo), or null - use nay
         			  String sdir, // source super directory that contains image set directories with files
         			  int num_chn,
         			  MultipleExtensionsFileFilter gridFilter,
@@ -993,6 +1013,7 @@ import ij.text.TextWindow;
         			String [] files = (new File(dir)).list(gridFilter); // are these full files?
         			paths = new String[num_chn];
         			for (String path:files) {
+        				/*
         				int last_dash = path.lastIndexOf('-');
         				int last =      path.lastIndexOf('_');
         				if (last_dash >last) last = last_dash;
@@ -1001,7 +1022,11 @@ import ij.text.TextWindow;
         					last_dot = path.length();
         				}
         				int chn = Integer.parseInt(path.substring(last+1, last_dot));
+        				*/
+        				int chn = pathToChannel(path);
+        				if ((permitted_channels == null) || (permitted_channels[chn])) {
         					paths[chn] = (new File(dir,path)).getPath();
+        				}
         				//grid-elphelimg_1559195695_507621_4.tiff
         			}
     				spaths = new String[num_chn];
@@ -1014,6 +1039,7 @@ import ij.text.TextWindow;
         					System.out.println("sfiles == null");
         				}
         				for (String spath:sfiles) {
+        					/*
         					int last_dash = spath.lastIndexOf('-');
         					int last =      spath.lastIndexOf('_');
         					if (last_dash >last) last = last_dash;
@@ -1022,6 +1048,8 @@ import ij.text.TextWindow;
         						last_dot = spath.length();
         					}
         					int chn = Integer.parseInt(spath.substring(last+1, last_dot));
+        					*/
+            				int chn = pathToChannel(spath);
         					spaths[chn] = (new File(set_dir,spath)).getPath();
         				}
         			}
@@ -1040,6 +1068,7 @@ import ij.text.TextWindow;
         			dirTsList.add(new DirTs(
         					numStation,
         					stationFilenames[numStation][is], // 	String dir,
+        					gridUseChn[numStation][is], //
         					source_dirs[numStation],
         					numSubCameras, // int num_chn,
         					gridFilter,
@@ -1297,7 +1326,8 @@ import ij.text.TextWindow;
 //        				boolean invert_color = ((base_channel ^ nc) & 4) != 0;
         				boolean invert_color = invertColor(base_channel) ^ invertColor(nc); // eyesisCameraParameters.isLWIR(main_channel);
 
-        				if ((this.gIS[nis].imageSet[nc].matchedPointers <= 0) && (nc != base_channel)) { // Later add non-laser conditions
+        				if ( (this.gIS[nis].imageSet[nc] != null) &&
+        						(this.gIS[nis].imageSet[nc].matchedPointers <= 0) && (nc != base_channel)) { // Later add non-laser conditions
         					int imgNum =  this.gIS[nis].imageSet[nc].imgNumber; // with_pointers - base_channel + nc;
     						if (this.updateStatus) IJ.showStatus("Re-reading grid file "+(imgNum+1)+" (of "+(numFiles)+"): "+this.gIP[imgNum].path);
     						if (this.debugLevel>-1) System.out.print(imgNum+"*("+this.gIP[imgNum].getStationNumber()+
@@ -2442,16 +2472,36 @@ import ij.text.TextWindow;
          * create list of image indices per image set
          * @return array of image indices for each image set
          */
-        public int [][] listImages(boolean enabledOnly){
+        public int [][] listImages(
+        		boolean enabledOnly,
+        		//int type_mask // 0 - all, otherwise +1 - eo, +2 - lwir
+        		boolean [] chn_sel // selected channels or null
+        		){
         	int [][] imageSets = new int [this.gIS.length][];
     		for (int i=0;i<this.gIS.length;i++){
     			int setSize=0;
-    			for (int n=0;n<this.gIS[i].imageSet.length;n++) if ((this.gIS[i].imageSet[n]!=null) && (this.gIS[i].imageSet[n].imgNumber>=0) && (!enabledOnly || this.gIS[i].imageSet[n].enabled)) setSize++;
+    			for (int n=0;n<this.gIS[i].imageSet.length;n++) {
+    				if (    (this.gIS[i].imageSet[n]!=null) &&
+    						(this.gIS[i].imageSet[n].imgNumber>=0) &&
+    						(!enabledOnly || this.gIS[i].imageSet[n].enabled)) {
+    					if ((chn_sel == null) || (chn_sel[this.gIS[i].imageSet[n].getChannel()])){
+    						setSize++;
+    					}
+    				}
+    			}
     			imageSets[i]=new int [setSize];
     		}
     		for (int i=0;i<this.gIS.length;i++){
     			int index=0;
-    			for (int n=0;n<this.gIS[i].imageSet.length;n++) if ((this.gIS[i].imageSet[n]!=null) && (this.gIS[i].imageSet[n].imgNumber>=0) && (!enabledOnly || this.gIS[i].imageSet[n].enabled)) imageSets[i][index++]=this.gIS[i].imageSet[n].imgNumber;
+    			for (int n=0;n<this.gIS[i].imageSet.length;n++) {
+    				if (    (this.gIS[i].imageSet[n]!=null) && 
+    						(this.gIS[i].imageSet[n].imgNumber>=0) &&
+    						(!enabledOnly || this.gIS[i].imageSet[n].enabled)) {
+    					if ((chn_sel == null) || (chn_sel[this.gIS[i].imageSet[n].getChannel()])){
+    						imageSets[i][index++]=this.gIS[i].imageSet[n].imgNumber;
+    					}
+    				}
+    			}
     		}
         	return imageSets;
         }
@@ -4466,7 +4516,7 @@ import ij.text.TextWindow;
     		}
     		return small_sensors;
     	}
-    	public boolean isSmallSensor(int numImg) {
+    	public boolean isSmallSensor(int numImg) { // number of image, not a channel!!!
     		boolean [] ss = getSmallSensors();
     		if ((this.gIP != null) && (numImg >= 0) &&   (numImg < this.gIP.length)){
     			return ss[this.gIP[numImg].getChannel()];

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

@@ -1583,7 +1583,10 @@ I* - special case when the subcamera is being adjusted/replaced. How to deal wit
     			System.out.println("BUG: selectIndividualImages(): selection.length!=enabled.length!");
     			return false;
     		}
-    	    int [][] imageSets=this.distortionCalibrationData.listImages(!allImages); // true - only enabled images
+    	    int [][] imageSets=this.distortionCalibrationData.listImages(
+    	    		!allImages, // true - only enabled images
+    	    		null); // do not filter by eo/lwir?
+    	    
     	    boolean [] enabledSets=new boolean [imageSets.length];
     	    boolean [] selectedSets=new boolean [imageSets.length]; // at least one image selected in the series
     	    for (int i=0;i<imageSets.length;i++){
@@ -2483,7 +2486,7 @@ I* - special case when the subcamera is being adjusted/replaced. How to deal wit
 					this.selectedImages[numSeries][i]=selectAllImages || ((i==0) && removeAllImages); // invalidate - all, regardless of .enabled
 					this.selectedImages[numSeries][i] &= constrainByStation[this.distortionCalibrationData.gIP[i].getStationNumber()];
 					if (selectHiLowRes != null) {
-						int small_01 = this.distortionCalibrationData.isSmallSensor(i)?1:0;
+						int small_01 = this.distortionCalibrationData.isSmallSensor(i)?1:0;  //OK, i here is image number, not channel number
 //						System.out.println(i+":"+small_01);
 						this.selectedImages[numSeries][i] &= selectHiLowRes[small_01];
 					}

src/main/java/com/elphel/imagej/lwir/LwirReaderParameters.java

@@ -142,7 +142,15 @@ public class LwirReaderParameters {
 	}
 	
 	public int getNumChannels() {
-		return 20;
+		return isLwir16()?20:8;
+	}
+	
+	public int [] getTypeMap() { // eo - 0, lwir - 1
+		int [] types = new int [getNumChannels()];
+		for (int i = 0; i < types.length; i++) {
+			types[i] = (i >= getEoChn0())? 0 : 1;
+		}
+		return types;
 	}
 	
 	public static boolean is_LWIR(int width) {