Importing EO+LWIR calibration to 3d program

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

@@ -38,7 +38,6 @@ import java.util.concurrent.atomic.AtomicInteger;
 
 import javax.swing.SwingUtilities;
 
-import com.elphel.imagej.calibration.CalibrationFileManagement.MultipleExtensionsFileFilter;
 import com.elphel.imagej.common.DoubleFHT;
 import com.elphel.imagej.common.DoubleGaussianBlur;
 import com.elphel.imagej.common.ShowDoubleFloatArrays;
@@ -109,15 +108,27 @@ public class PixelMapping {
        	}
     }
 
-    public PixelMapping (String [] calibFiles, int debugLevel){
+    public PixelMapping (
+    		String [] calibFiles,
+    		int first_channel, // 0 - old way
+    		int num_channels,  // 0 - any
+    		boolean update_channel, // false (replace file channel with effective channel (subtract first_channel)
+    		int debugLevel){
     	this.debugLevel=debugLevel;
     	if (calibFiles==null) calibFiles=new String[0];
-       	this.sensors=new SensorData[this.maxSensors];
+       	this.sensors=new SensorData[(num_channels > 0)? num_channels: this.maxSensors];
        	for (int i=0;i<this.sensors.length;i++) this.sensors[i]=null;
        	int maxChannel=0;
        	for (int i=0;i<calibFiles.length;i++){
        		SensorData sensorData=new SensorData (calibFiles[i],this.debugLevel);
-       		int channel=sensorData.getChannel();
+       		int channel=sensorData.getChannel(); // from Properties
+       		if ((channel < first_channel) || ((num_channels > 0) && (channel >= (first_channel + num_channels)))) {
+       			continue; // wrong channels
+       		}
+   			channel -= first_channel;
+       		if (update_channel) {
+       			sensorData.setChannel(channel);
+       		}
        		this.sensors[channel]=sensorData;
       		if (channel>maxChannel) maxChannel=channel;
        	}
@@ -16221,6 +16232,7 @@ public class PixelMapping {
 	    }
 	    public SensorData (){} // just to get parameter names
 
+	    public void setChannel(int chn){this.channel = chn;}
 	    public int getChannel(){return this.channel;}
 	    public int getSubChannel(){return this.subchannel;}
 	    public int getSubCamera(){return this.subcamera;}

src/main/java/com/elphel/imagej/correction/EyesisCorrections.java

@@ -98,17 +98,38 @@ public class EyesisCorrections {
 	// TODO: preserve some data when re-running with new source files
 	// FIXME: Make forgiving alien files
 	public void initSensorFiles(int debugLevel){
-		initSensorFiles(debugLevel, false);
-	}
-	public void initSensorFiles(int debugLevel, boolean missing_ok){
+		initSensorFiles(debugLevel,
+				false,
+				false,
+				false);
+	}
+	public void initSensorFiles(int debugLevel,
+			boolean missing_ok,
+			boolean all_sensors,
+			boolean no_vignetting
+			){
 		this.sharpKernelPaths=null;
 		this.smoothKernelPaths=null;
 		String [] sensorPaths=correctionsParameters.selectSensorFiles(this.debugLevel);
-		this.pixelMapping=new PixelMapping(sensorPaths,debugLevel);
+		this.pixelMapping=new PixelMapping(
+				sensorPaths,
+				correctionsParameters.firstSubCameraConfig, // 	int first_channel, // 0 - old way
+				correctionsParameters.numSubCameras,        // int num_channels,  // 0 - any
+	    		true, // boolean update_channel, // false (replace file channel with effective channel (subtract first_channel)
+				debugLevel);
+		if (all_sensors) {
+			this.usedChannels = new boolean [this.pixelMapping.sensors.length];
+			for (int i = 0; i < this.usedChannels.length; i++) {
+				this.usedChannels[i] = true;
+			}
+		} else {
 			this.usedChannels= usedChannels(correctionsParameters.getSourcePaths(),missing_ok);
+		}
 		// TODO: Combine with additional channel map to be able to select single image (of all 3)
 		if (correctionsParameters.removeUnusedSensorData){
-			for (int nChn=0;nChn< this.usedChannels.length; nChn++) if (!this.usedChannels[nChn]) this.pixelMapping.removeChannel(nChn);
+			for (int nChn=0;nChn< this.usedChannels.length; nChn++) {
+				if (!this.usedChannels[nChn]) this.pixelMapping.removeChannel(nChn);
+			}
 		}
 		int numUsedChannels=0;
 		for (int nChn=0;nChn< this.usedChannels.length; nChn++) if (this.usedChannels[nChn]) numUsedChannels++;
@@ -117,7 +138,9 @@ public class EyesisCorrections {
 			for (int nChn=0;nChn< this.usedChannels.length; nChn++) if (this.usedChannels[nChn]) sChannels+=" "+nChn;
 			System.out.println ("Number of used channels: "+numUsedChannels+" ("+sChannels+" )");
 		}
+		if (!no_vignetting) {
 			createChannelVignetting();
+		}
 		if ((this.debugLevel>101) && (correctionsParameters.sourcePaths!=null) && (correctionsParameters.sourcePaths.length>0)) {
 			testFF(correctionsParameters.sourcePaths[0]);
 		}
@@ -126,12 +149,32 @@ public class EyesisCorrections {
 		}
 	}
 
-	public void initSensorFilesAux(int debugLevel){
+	// Never used !
+	public void initSensorFilesAux(int debugLevel, // what is different from initSensorFiles()? Never used !
+			boolean missing_ok,
+			boolean all_sensors,
+			boolean no_vignetting
+			){
 //		this.sharpKernelPaths=null;
 //		this.smoothKernelPaths=null;
 		String [] sensorPaths=correctionsParameters.selectSensorFiles(this.debugLevel);
-		this.pixelMapping=new PixelMapping(sensorPaths,debugLevel);
-		this.usedChannels= usedChannels(correctionsParameters.getSourcePaths());
+
+//		this.pixelMapping=new PixelMapping(sensorPaths,debugLevel);
+
+		this.pixelMapping=new PixelMapping(
+				sensorPaths,
+				correctionsParameters.firstSubCameraConfig, // 	int first_channel, // 0 - old way
+				correctionsParameters.numSubCameras,        // int num_channels,  // 0 - any
+	    		true, // boolean update_channel, // false (replace file channel with effective channel (subtract first_channel)
+				debugLevel);
+		if (all_sensors) {
+			this.usedChannels = new boolean [this.pixelMapping.sensors.length];
+			for (int i = 0; i < this.usedChannels.length; i++) {
+				this.usedChannels[i] = true;
+			}
+		} else {
+			this.usedChannels= usedChannels(correctionsParameters.getSourcePaths(),missing_ok);
+		}
 		// TODO: Combine with additional channel map to be able to select single image (of all 3)
 		if (correctionsParameters.removeUnusedSensorData){
 			for (int nChn=0;nChn< this.usedChannels.length; nChn++) if (!this.usedChannels[nChn]) this.pixelMapping.removeChannel(nChn);
@@ -229,7 +272,12 @@ public class EyesisCorrections {
 //		boolean processPlaneProjection= equirectangularParameters.generateCommonPlane &&
 //			equirectangularParameters.selectChannelsToProcess("Select channels for plane projection", this.pixelMapping.sensors.length);
 
-		this.pixelMapping=new PixelMapping(sensorPaths,debugLevel);
+		this.pixelMapping=new PixelMapping(
+				sensorPaths,
+				0, // int first_channel, // 0 - old way
+				0, // int num_channels,  // 0 - any
+				false, // boolean update_channel, // false (replace file channel with effective channel (subtract first_channel)
+				debugLevel);
 		pixelMapping.generateAndSaveEquirectangularMaps(
 				correctionsParameters.equirectangularDirectory+
 				Prefs.getFileSeparator()+
@@ -356,12 +404,16 @@ public class EyesisCorrections {
 		}
 		this.sharpKernelPaths=correctionsParameters.selectKernelChannelFiles(
 				0,  // 0 - sharp, 1 - smooth
+				  correctionsParameters.firstSubCameraConfig,
+//				  correctionsParameters.numSubCameras,
 				numChannels, // number of channels
 				this.debugLevel);
 		if (this.sharpKernelPaths==null) return false;
 		if (nonlinParameters.useDiffNoiseGains) {
 			this.smoothKernelPaths=correctionsParameters.selectKernelChannelFiles(
 					1,  // 0 - sharp, 1 - smooth
+					  correctionsParameters.firstSubCameraConfig,
+//					  correctionsParameters.numSubCameras,
 					numChannels, // number of channels
 					this.debugLevel);
 			if (this.smoothKernelPaths==null) return false;
@@ -1024,7 +1076,9 @@ public class EyesisCorrections {
 			if (this.sharpKernelPaths==null){ // make sure the paths list is reset after changing parameters
 				this.sharpKernelPaths=correctionsParameters.selectKernelChannelFiles(
 						0,  // 0 - sharp, 1 - smooth
-						this.usedChannels.length, // number of channels
+						  correctionsParameters.firstSubCameraConfig,
+						  correctionsParameters.numSubCameras,
+//						this.usedChannels.length, // number of channels
 						this.debugLevel);
 			}
 			if ((this.sharpKernelPaths==null) || (this.sharpKernelPaths[channel]==null)){
@@ -1055,6 +1109,8 @@ public class EyesisCorrections {
 				if (this.smoothKernelPaths==null){ // make sure the paths list is reset after changing parameters
 					this.smoothKernelPaths=correctionsParameters.selectKernelChannelFiles(
 							1,  // 0 - sharp, 1 - smooth
+							  correctionsParameters.firstSubCameraConfig,
+//							  correctionsParameters.numSubCameras,
 							this.usedChannels.length, // number of channels
 							this.debugLevel);
 				}
@@ -1156,6 +1212,8 @@ public class EyesisCorrections {
 			if (this.smoothKernelPaths==null){ // make sure the paths list is reset after changing parameters
 				this.smoothKernelPaths=correctionsParameters.selectKernelChannelFiles(
 						1,  // 0 - sharp, 1 - smooth
+						  correctionsParameters.firstSubCameraConfig,
+//						  correctionsParameters.numSubCameras,
 						this.usedChannels.length, // number of channels
 						this.debugLevel);
 			}

src/main/java/com/elphel/imagej/correction/EyesisDCT.java

@@ -281,6 +281,8 @@ public class EyesisDCT {
 			){
 		String [] sharpKernelPaths= correctionsParameters.selectKernelChannelFiles(
 				0,  // 0 - sharp, 1 - smooth
+				  correctionsParameters.firstSubCameraConfig,
+//				  correctionsParameters.numSubCameras,
 				eyesisCorrections.usedChannels.length, // numChannels, // number of channels
 				eyesisCorrections.debugLevel);
 		if (sharpKernelPaths==null) return false;

src/main/java/com/elphel/imagej/correction/Eyesis_Correction.java

@@ -593,6 +593,7 @@ private Panel panel1,
 			addButton("Select second CLT image",   panelClt1, color_configure);
 			addButton("CLT correlate",             panelClt1, color_process);
 			addButton("Create CLT kernels",        panelClt1, color_process);
+			addButton("Create AUX CLT kernels",    panelClt1, color_process);
 			addButton("Read CLT kernels",          panelClt1, color_process);
 			addButton("Reset CLT kernels",         panelClt1, color_stop);
 			addButton("CLT process files",         panelClt1, color_process);
@@ -3902,7 +3903,11 @@ private Panel panel1,
 			return;
     	}
 
-        EYESIS_CORRECTIONS.initSensorFiles(DEBUG_LEVEL);
+        EYESIS_CORRECTIONS.initSensorFiles(DEBUG_LEVEL,
+        		true, // true - ignore missing files
+    			true, // boolean all_sensors,
+    			true); //boolean no_vignetting
+
 
         QUAD_CLT.createCLTKernels(
         		CLT_PARAMETERS,
@@ -3910,7 +3915,44 @@ private Panel panel1,
                 THREADS_MAX,
                 UPDATE_STATUS, // update status info
         		DEBUG_LEVEL);
+//==============================================================================
+    } else if (label.equals("Create AUX CLT kernels")) {
+        if (!CLT_PARAMETERS.showJDialog()) return;
+		if (EYESIS_CORRECTIONS_AUX == null) {
+			EYESIS_CORRECTIONS_AUX = new EyesisCorrections(SYNC_COMMAND.stopRequested,CORRECTION_PARAMETERS.getAux());
+		}
+        if ((QUAD_CLT_AUX == null) ||(QUAD_CLT_AUX.eyesisCorrections == null)){
+        	QUAD_CLT_AUX = new  QuadCLT (
+        			QuadCLT.PREFIX_AUX,
+        			PROPERTIES,
+        			EYESIS_CORRECTIONS_AUX,
+        			CORRECTION_PARAMETERS.getAux());
+        }
+    	String configPath=getSaveCongigPath();
+    	if (configPath.equals("ABORT")) return;
+    	String cltPath=EYESIS_CORRECTIONS.correctionsParameters.selectCLTKernelDirectory( // create if it does not exist
+				true,
+				true);
+    	if (cltPath==null) {
+			String msg="No CLT kernels (results) directory selected, command aborted";
+			System.out.println("Warning: "+msg);
+			IJ.showMessage("Warning",msg);
+			return;
+    	}
 
+
+        EYESIS_CORRECTIONS_AUX.initSensorFiles(DEBUG_LEVEL,
+        		true, // true - ignore missing files
+    			true, // boolean all_sensors,
+    			true); //boolean no_vignetting
+
+
+        QUAD_CLT_AUX.createCLTKernels(
+        		CLT_PARAMETERS,
+        		CONVOLVE_FFT_SIZE/2,
+                THREADS_MAX,
+                UPDATE_STATUS, // update status info
+        		DEBUG_LEVEL);
         //"Reset DCT kernels"
     } else if (label.equals("Reset CLT kernels")) {
         if (QUAD_CLT != null){
@@ -5013,11 +5055,11 @@ private Panel panel1,
     	if (DEBUG_LEVEL > -2){
     		System.out.println("++++++++++++++ Running initSensorFiles for the main camera ++++++++++++++");
     	}
-        EYESIS_CORRECTIONS.initSensorFiles(DEBUG_LEVEL+2, true); // missing_ok
+        EYESIS_CORRECTIONS.initSensorFiles(DEBUG_LEVEL+2, true, false, false); // missing_ok
     	if (DEBUG_LEVEL > -2){
     		System.out.println("++++++++++++++ Running initSensorFiles for the auxiliary camera ++++++++++++++");
     	}
-        EYESIS_CORRECTIONS_AUX.initSensorFiles(DEBUG_LEVEL+2, true); // some files belong to oher cameras\
+        EYESIS_CORRECTIONS_AUX.initSensorFiles(DEBUG_LEVEL+2, true, false, false); // some files belong to oher cameras\
 
 
         int numChannels=    EYESIS_CORRECTIONS.getNumChannels();
@@ -5147,11 +5189,11 @@ private Panel panel1,
     	if (DEBUG_LEVEL > -2){
     		System.out.println("++++++++++++++ Running initSensorFiles for the main camera ++++++++++++++");
     	}
-        EYESIS_CORRECTIONS.initSensorFiles(DEBUG_LEVEL+2, true); // missing_ok
+        EYESIS_CORRECTIONS.initSensorFiles(DEBUG_LEVEL+2, true, false, false); // missing_ok
     	if (DEBUG_LEVEL > -2){
     		System.out.println("++++++++++++++ Running initSensorFiles for the auxiliary camera ++++++++++++++");
     	}
-        EYESIS_CORRECTIONS_AUX.initSensorFiles(DEBUG_LEVEL+2, true); // some files belong to oher cameras\
+        EYESIS_CORRECTIONS_AUX.initSensorFiles(DEBUG_LEVEL+2, true, false, false); // some files belong to other cameras\
 
 
         int numChannels=    EYESIS_CORRECTIONS.getNumChannels();

src/main/java/com/elphel/imagej/tileprocessor/QuadCLT.java

@@ -867,7 +867,9 @@ public class QuadCLT {
 
 		  String [] sharpKernelPaths= correctionsParameters.selectKernelChannelFiles(
 				  0,  // 0 - sharp, 1 - smooth
-				  eyesisCorrections.usedChannels.length, // numChannels, // number of channels
+				  correctionsParameters.firstSubCameraConfig,
+				  correctionsParameters.numSubCameras,
+//				  eyesisCorrections.usedChannels.length, // numChannels, // number of channels
 				  eyesisCorrections.debugLevel);
 		  if (sharpKernelPaths==null) return false;
 		  for (int i=0;i<sharpKernelPaths.length;i++){
@@ -884,8 +886,8 @@ public class QuadCLT {
 		  for (int chn=0;chn<eyesisCorrections.usedChannels.length;chn++){
 			  if (eyesisCorrections.usedChannels[chn] && (sharpKernelPaths[chn]!=null) && (clt_kernels[chn]==null)){
 				  ImagePlus imp_kernel_sharp=new ImagePlus(sharpKernelPaths[chn]);
-				  if (imp_kernel_sharp.getStackSize()<3) {
-					  System.out.println("Need a 3-layer stack with kernels");
+				  if ((imp_kernel_sharp.getStackSize()<3) && (imp_kernel_sharp.getStackSize() != 1)) {
+					  System.out.println("Need a 3-layer stack with Bayer or single for mono kernels");
 					  sharpKernelPaths[chn]=null;
 					  continue;
 				  }
@@ -913,18 +915,20 @@ public class QuadCLT {
 				  int tileWidth =  2 * dtt_size;
 				  int width =  tileWidth *  kernelNumHor;
 				  int height = flat_kernels[0].length/width;
-
 				  String [] layerNames = {"red_clt_kernels","blue_clt_kernels","green_clt_kernels"};
+				  if (flat_kernels.length ==1){
+					  layerNames = new String[1];
+					  layerNames[0] = "mono_clt_kernels";
+				  }
 				  ImageStack cltStack = sdfa_instance.makeStack(
 						  flat_kernels,
 						  width,
 						  height,
 						  layerNames);
-
 				  String cltPath=correctionsParameters.cltKernelDirectory+
 						  Prefs.getFileSeparator()+
 						  correctionsParameters.cltKernelPrefix+
-						  String.format("%02d",chn)+
+						  String.format("%02d",chn + correctionsParameters.firstSubCameraConfig)+
 						  correctionsParameters.cltSuffix;
 				  String msg="Saving CLT convolution kernels to "+cltPath;
 				  IJ.showStatus(msg);
@@ -935,7 +939,8 @@ public class QuadCLT {
 					  imp_clt.show();
 				  }
 				  FileSaver fs=new FileSaver(imp_clt);
-				  fs.saveAsTiffStack(cltPath); // directory does not exist
+//				  fs.saveAsTiffStack(cltPath); // directory does not exist
+				  fs.saveAsTiff(cltPath); // directory does not exist
 			  }
 		  }
 		  return true;
@@ -951,6 +956,7 @@ public class QuadCLT {
 			  ){
 		  int dtt_size = clt_parameters.transform_size;
 		  String [] cltKernelPaths = correctionsParameters.selectCLTChannelFiles(
+				  correctionsParameters.firstSubCameraConfig,
 				  //					0,  // 0 - sharp, 1 - smooth
 				  eyesisCorrections.usedChannels.length, // numChannels, // number of channels
 				  eyesisCorrections.debugLevel);
@@ -974,8 +980,8 @@ public class QuadCLT {
 		  for (int chn=0;chn<eyesisCorrections.usedChannels.length;chn++){
 			  if (eyesisCorrections.usedChannels[chn] && (cltKernelPaths[chn]!=null)){
 				  ImagePlus imp_kernel_clt=new ImagePlus(cltKernelPaths[chn]);
-				  if (imp_kernel_clt.getStackSize()<3) {
-					  System.out.println("Need a 3-layer stack with symmetrical DCT kernels");
+				  if ((imp_kernel_clt.getStackSize()< 3) && (imp_kernel_clt.getStackSize()!= 1))   {
+					  System.out.println("Need a 3-layer stack or Bayer and 1-layer for mono with CLT kernels");
 					  cltKernelPaths[chn]=null;
 					  continue;
 				  }