working on calculating grids for low frequency pattern

src/main/java/JP46_Reader_camera0.java

@@ -1413,9 +1413,13 @@ Exception in thread "Thread-3564" java.lang.ArrayIndexOutOfBoundsException: 8970
 	    NodeList allNodes=doc.getDocumentElement().getElementsByTagName("*");
 	    for (int i=0;i<allNodes.getLength();i++) {
 	        String name= allNodes.item(i).getNodeName();
-            String value=allNodes.item(i).getFirstChild().getNodeValue();
-    		imp.setProperty(name, value);
+	        String value="";
+	        try {
+	        	value=allNodes.item(i).getFirstChild().getNodeValue();
+	        } catch(Exception e) {
 
+	        }
+    		imp.setProperty(name, value);
 	    }
 
 		return true;

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

@@ -6,7 +6,7 @@ package com.elphel.imagej.calibration;
  ** Copyright (C) 2011-2014 Elphel, Inc.
  **
  ** -----------------------------------------------------------------------------**
- **  
+ **
  **  DistortionProcessConfiguration.java is free software: you can redistribute it and/or modify
  **  it under the terms of the GNU General Public License as published by
  **  the Free Software Foundation, either version 3 of the License, or
@@ -23,16 +23,17 @@ package com.elphel.imagej.calibration;
  **
  */
 
-import ij.IJ;
-import ij.Prefs;
-import ij.gui.GenericDialog;
-
 import java.io.File;
+import java.io.FilenameFilter;
 import java.util.Properties;
 
 import com.elphel.imagej.common.WindowTools;
 
-    
+import ij.IJ;
+import ij.Prefs;
+import ij.gui.GenericDialog;
+
+
     public class DistortionProcessConfiguration{
     	public String  sourceDirectory="";
     	public String  gridDirectory=  "";
@@ -50,7 +51,7 @@ import com.elphel.imagej.common.WindowTools;
     	public String selectSourceDirectory(boolean smart, String defaultPath, boolean newAllowed) {
     		String dir= CalibrationFileManagement.selectDirectory(
     				smart,
-    				newAllowed, // save  
+    				newAllowed, // save
     				"Source (acquired from the camera) image directory", // title
     				"Select source directory", // button
     				null, // filter
@@ -61,7 +62,7 @@ import com.elphel.imagej.common.WindowTools;
     	public String selectGridFileDirectory(boolean smart, String defaultPath, boolean newAllowed) {
     		String dir= CalibrationFileManagement.selectDirectory(
     				smart,
-    				newAllowed, // save  
+    				newAllowed, // save
     				"Grid files directory (grid patterns extracted from the images)", // title
     				"Select grid files directory", // button
     				null, // filter
@@ -69,7 +70,7 @@ import com.elphel.imagej.common.WindowTools;
     		if (dir!=null) this.gridDirectory=dir;
     		return dir;
     	}
-    	
+
     	public void setProperties(String prefix,Properties properties){
     		properties.setProperty(prefix+"sourceDirectory",        this.sourceDirectory);
     		properties.setProperty(prefix+"gridDirectory",          this.gridDirectory);
@@ -123,9 +124,9 @@ import com.elphel.imagej.common.WindowTools;
     		gd.addCheckbox   ("Show grid files as images",            this.showGridImages);
     		gd.addCheckbox   ("Save grid files",                      this.saveGridImages);
     		gd.addCheckbox   ("Overwrite existing result files",      this.overwriteResultFiles);
-    		
-    		
-    		
+
+
+
     		gd.addNumericField("Debug level",                         this.debugLevel,0);
     	    WindowTools.addScrollBars(gd);
     	    gd.showDialog();
@@ -144,7 +145,7 @@ import com.elphel.imagej.common.WindowTools;
     	    this.debugLevel=       (int) gd.getNextNumber();
     	    System.out.println("1.newSourceDirectory = "+newSourceDirectory);
     	    System.out.println("1.newGridDirectory = "+  newGridDirectory);
-    	    if ((newSourceDirectory.length()==0) || (newSourceDirectory.indexOf('?')>=0)) 
+    	    if ((newSourceDirectory.length()==0) || (newSourceDirectory.indexOf('?')>=0))
     	    	newSourceDirectory= selectSourceDirectory(false, this.sourceDirectory, true);
     	    else
     	    	newSourceDirectory= selectSourceDirectory(true, newSourceDirectory, true); // if matches, no dialog
@@ -174,7 +175,7 @@ import com.elphel.imagej.common.WindowTools;
 			if (this.sourceDirectory.length()==0){
 				defaultPaths[0]="";
 			}
-			
+
 			CalibrationFileManagement.MultipleExtensionsFileFilter sourceFilter =
 				new CalibrationFileManagement.MultipleExtensionsFileFilter("",extensions,"Source files");
 			String [] sourceFiles=null;
@@ -206,5 +207,26 @@ import com.elphel.imagej.common.WindowTools;
     		}
 	       	return sourceFiles;
     	}
-    	
+
+        public String[] selectSourceSets() {
+			File dir= new File (this.sourceDirectory);
+			if (this.debugLevel>1) System.out.println("selectSourceSets, dir="+this.sourceDirectory);
+			if (!dir.exists()) {
+				String error="Source directory "+this.sourceDirectory+" does not exist.";
+        		IJ.showMessage("No files selected");
+				if (this.debugLevel>1) System.out.println("selectSourceFiles() ERROR:"+error);
+				return null;
+			}
+			File [] sourceFileSets = dir.listFiles(new FilenameFilter() {
+			  @Override
+			  public boolean accept(File current, String name) {
+			    return new File(current, name).isDirectory();
+			  }
+			});
+			String [] sourceSets = new String[sourceFileSets.length];
+			for (int i=0;i<sourceSets.length;i++) sourceSets[i]=sourceFileSets[i].getPath();
+			return sourceSets;
+        }
+
     }
+

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

@@ -668,6 +668,8 @@ horizontal axis:
 						// allow more of grid around pointers?
 						distortionParameters, //
 						this.patternDetectParameters,
+						this.patternDetectParameters.minGridPeriod/2,
+						this.patternDetectParameters.maxGridPeriod/2,
 						simulParameters,
 						equalizeGreens, imp_eq,
 						this.laserPointers, // null, //LASER_POINTERS, //
@@ -841,6 +843,8 @@ horizontal axis:
 								// allow more of grid around pointers?
 								distortionParameters, //
 								this.patternDetectParameters,
+								this.patternDetectParameters.minGridPeriod/2,
+								this.patternDetectParameters.maxGridPeriod/2,
 								simulParameters,
 								equalizeGreens, imp_eq,
 								this.laserPointers, // null, //LASER_POINTERS, //

src/main/java/com/elphel/imagej/common/DoubleFHT.java

@@ -124,15 +124,7 @@ public class DoubleFHT  {
 	public boolean transform(double [] data, boolean inverse) {
 		//IJ.log("transform: "+maxN+" "+inverse);
 		updateMaxN(data);
-//		maxN = (int) Math.sqrt(data.length);
-//		if ((S==null) || (S.length!=(maxN/4))) {
-//			makeSinCosTables(maxN);
-//			makeBitReverseTable(maxN);
-//			tempArr = new double[maxN];
-//		}
-//		float[] fht = (float[])getPixels();
 	 	rc2DFHT(data, inverse, this.maxN);
-//		isFrequencyDomain = !inverse;
 		return true;
 	}
 
@@ -141,21 +133,15 @@ public class DoubleFHT  {
    		 double lowPass){
     	return createFrequencyFilter(null,highPass,lowPass);
     }
-/*    public double []createFrequencyFilter(
-    		double [] data,
-      		 double highPass,
-      		 double lowPass){
-       	return createFrequencyFilter(data.length,highPass,lowPass);
-       }
-*/
-	public double [] createFrequencyFilter(
+
+    public double [] createFrequencyFilter(
     		 double [] data, //int n,
     		 double highPass,
     		 double lowPass){
 		 if (data !=null) updateMaxN(data);
 //		 int n;
 
-		 if ((this.freqMask!=null) && (this.freqPass[0]==highPass)  && (this.freqPass[0]==lowPass)) return this.freqMask;
+		 if ((this.freqMask!=null) && (this.freqPass[0]==highPass)  && (this.freqPass[1]==lowPass)) return this.freqMask;
 		 this.freqMask= new double [(this.maxN+1)*this.maxN/2+1];
     	 double [] lo=new double[this.maxN];
     	 double [] hi=new double[this.maxN];
@@ -177,12 +163,9 @@ public class DoubleFHT  {
     		 if (j>this.maxN/2) j=this.maxN-j;
     		 this.freqMask[index]=(1.0-hi[i]*hi[j])*lo[i]*lo[j];
     	 }
-//    	 this.freqMaskN=n;
     	 this.freqPass=new double[2];
     	 this.freqPass[0]=highPass;
     	 this.freqPass[1]=lowPass;
-//    	 this.freqMask_cache[this.ln2]=this.freqMask;
-//    	 this.freqPass_cache[this.ln2]=this.freqPass;
     	 return this.freqMask;
      }
 	/**
@@ -195,49 +178,6 @@ public class DoubleFHT  {
 	 */
 	public double [] shift(double [] data, double dx, double dy){
 		return shift(data, 1, dx, dy);
-		/*
-		updateMaxN(data);
-		double sX=2*Math.PI*dx/this.maxN;
-		double sY=2*Math.PI*dy/this.maxN;
-		int halfN=this.maxN/2;
-		double [] cosDX = new double[this.maxN];
-		double [] sinDX = new double[this.maxN];
-		double [] cosDY = new double[halfN+1];
-		double [] sinDY = new double[halfN+1];
-		for (int i=0;i<=halfN;i++){ // need less?
-			cosDX[i]=Math.cos(sX*i);
-			sinDX[i]=Math.sin(sX*i);
-			cosDY[i]=Math.cos(sY*i);
-			sinDY[i]=Math.sin(sY*i);
-		}
-		for (int i=1;i<halfN;i++){ // need less?
-			cosDX[this.maxN-i]= cosDX[i];
-			sinDX[this.maxN-i]=-sinDX[i];
-		}
-		swapQuadrants(data);
-		if (!transform(data,false)) return null; // direct FHT
-		for (int row =0; row<=halfN; row++) {
-			int rowMod = (this.maxN - row) % this.maxN;
-			int maxCol=(row<halfN)?(this.maxN-1):halfN;
-			for (int col=0; col<=maxCol; col++) {
-				int colMod = (this.maxN - col) % this.maxN;
-				int index=   row * this.maxN + col;
-				int indexMod=rowMod * this.maxN + colMod;
-				double re=0.5*(data[index]+data[indexMod]);
-				double im=0.5*(data[index]-data[indexMod]);
-				if ((col==halfN) || (row==halfN)) im=0;
-				double cosDelta= cosDX[col]*cosDY[row] - sinDX[col]*sinDY[row]; // cos(deltaX)*cos(deltaY)-sin(deltaX)*sin(deltaY)
-				double sinDelta= sinDX[col]*cosDY[row] + cosDX[col]*sinDY[row]; // sin(deltaX)*cos(deltaY)+cos(deltaX)*sin(deltaY)
-				double reMod=re*cosDelta-im*sinDelta;
-				double imMod=re*sinDelta+im*cosDelta;
-				data[index]=   reMod+imMod;
-				data[indexMod]=reMod-imMod;
-			}
-		}
-		if (!transform(data,true)) return null; // inverse FHT
-		swapQuadrants(data);
-		return data;
-		*/
 	}
 	/**
 	 * Upsample input array by padding in the frequency domain
@@ -247,30 +187,6 @@ public class DoubleFHT  {
 	 */
 	public double [] upsample( double [] first, int scale){
 		return shift (first, scale, 0.0, 0.0);
-/*
-		 if (scale <=1) return first.clone();
-		 updateMaxN(first);
-    	 swapQuadrants(first);
-    	 if (!transform(first,false)) return null; // direct FHT
-    	 int halfN=this.maxN/2;
-    	 int shift=this.maxN*(scale-1);
-    	 int scaledN=this.maxN*scale;
-    	 double [] result =new double [first.length*scale*scale];
-    	 for (int i=0;i<result.length;i++) result [i]=0.0;
-    	 double scale2=scale*scale;
-    	 for (int i=0;i<first.length;i++){
-    		 int iy=i/this.maxN;
-    		 int ix=i%this.maxN;
-    		 if (ix>halfN) ix+=shift;
-    		 if (iy>halfN) iy+=shift;
-    		 result[scaledN*iy+ix]=scale2*first[i];
-    	 }
-		 updateMaxN(result);
-    	 if (!transform(result,true)) return null; // inverse FHT
-    	 swapQuadrants(result);
-    	 return result;
-    	 */
-
 	}
 
 	/**
@@ -408,6 +324,54 @@ public class DoubleFHT  {
  	    	 swapQuadrants(first);
  	    	 return first;
  	     }
+
+     public double [] phaseCorrelate (
+    		 double [] first,
+    		 double    phaseCoeff,
+    		 double    high_pass,
+    		 double    low_pass) { //  high/low pass filtering
+    	 return phaseCorrelate(first, phaseCoeff, high_pass, low_pass, null);
+     }
+
+     public double [] phaseCorrelate (
+    		 double [] first,
+    		 double    phaseCoeff,
+    		 double    high_pass,
+    		 double    low_pass, //  high/low pass filtering
+    		 double [] fht_save){ //null-OK
+    	 updateMaxN(first);
+    	 double [] filter = null;
+    	 if ((high_pass >0) || (low_pass > 0)) {
+    		 filter = createFrequencyFilter(high_pass, low_pass);
+    	 }
+    	 return phaseCorrelate(first, phaseCoeff, filter,fht_save);
+     }
+
+     public double [] phaseCorrelate (
+    		 double [] first,
+    		 double    phaseCoeff,
+    		 double [] filter) {     //  high/low pass filtering
+    	 return phaseCorrelate(first, phaseCoeff, filter, null);
+     }
+
+     public double [] phaseCorrelate (
+    		 double [] first,
+    		 double    phaseCoeff,
+    		 double [] filter,     //  high/low pass filtering
+    		 double [] fht_save){  //null-OK
+    	 updateMaxN(first);
+    	 swapQuadrants(first);
+    	 if (!transform(first,false)) return null; // direct FHT
+    	 if (fht_save != null) {
+    		 System.arraycopy(first, 0, fht_save, 0, first.length);
+    	 }
+    	 first= phaseMultiplyNorm(first, first, phaseCoeff); // correlation, not convolution
+    	 if (filter!=null) multiplyByReal(first, filter);
+    	 transform(first,true) ; // inverse transform
+    	 swapQuadrants(first);
+    	 return first;
+     }
+//
      public double [] applyFreqFilter(
     		 double [] first,
     		 double [] filter
@@ -2024,6 +1988,7 @@ public class DoubleFHT  {
 		return product;
 	}
 
+
 	public double [] phaseMultiply(double [] h1, double [] h2, double phaseCoeff) {
 		int rowMod, colMod;
 		double h2e, h2o,d;
@@ -2041,6 +2006,54 @@ public class DoubleFHT  {
 		return product;
 	}
 
+	public double [] phaseMultiplyNorm(double [] h1, double [] h2, double phaseCoeff) {
+		int size = maxN;
+		int size2 = size >> 1;
+		int size21 = size*size2;
+		int rowMod, colMod, base, baseMod;
+		double h2e, h2o;
+		double[] product = new double[size*size];
+		for (int r =0; r<size; r++) {
+			rowMod = (size - r) % size;
+			for (int c=0; c<size; c++) {
+				colMod = (size - c) % size;
+				h2e = (h2[r * size + c] + h2[rowMod * size + colMod]) / 2;
+				h2o = (h2[r * size + c] - h2[rowMod * size + colMod]) / 2;
+				product[r * size + c] = (h1[r * size + c] * h2e - h1[rowMod * size + colMod] * h2o);
+			}
+		}
+		double [] amplitude = calculateAmplitudeHalf(product);
+		double avg_ampl = 0.0;
+		for (int row = 1; row < size2; row++) {
+			base = row*size;
+			for (int col = 0; col < size; col++) {
+				avg_ampl += amplitude[col+base];
+			}
+		}
+		avg_ampl *= 2;
+		for (int col = 0; col < size; col++) {
+			avg_ampl += amplitude[col] + amplitude[col + size21];
+		}
+		avg_ampl /= size*size;
+		double aoffs = (1.0 - phaseCoeff) * avg_ampl;
+		double ampl;
+		for (int row = 0; row <= size2; row++) {
+			base = row*size;
+			rowMod = (size - row) % size;
+			baseMod = rowMod * size;
+			for (int col = 0; col < size; col++) {
+				ampl = phaseCoeff * amplitude[col+base] + aoffs;
+				product[col+base] /= ampl;
+				if ((row > 0) && (row < size2)) {
+					colMod = (size - col) % size;
+					product[colMod + baseMod] /= ampl;
+				}
+			}
+		}
+		return product;
+	}
+
+
 
 // Multiply by real array (i.e. filtering in frequency domain). Array m length should be at least maxN*maxN/2+1
 	public void multiplyByReal(double [] h, double [] m) {
@@ -2094,6 +2107,17 @@ public class DoubleFHT  {
     swapQuadrants(amp);
     return amp;
   }
+
+  public double [] calculateAmplitudeHalf(double [] fht) {
+	  int size=(int) Math.sqrt(fht.length);
+	  int size2 = (size >>1) +1;
+	  double[] amp = new double[size* size2];
+	  for (int row=0; row<size2; row++) {
+		  amplitude(row, size, fht, amp);
+	  }
+	  return amp;
+  }
+
   public double [] calculateAmplitude2(double [] fht) {
 	    int size=(int) Math.sqrt(fht.length);
 	    double[] amp = new double[size*size];
@@ -2133,8 +2157,6 @@ public class DoubleFHT  {
        row2=(fftsize-row1) %fftsize;
        for (col1=0;col1<fftsize;col1++) {
          col2=(fftsize-col1) %fftsize;
-//         fftHalf[row1][col1]=   complex( 0.5*(fht_pixels[row1*fftsize+col1] + fht_pixels[row2*fftsize+col2]),
-//                                         0.5*(fht_pixels[row2*fftsize+col2] - fht_pixels[row1*fftsize+col1]));
          fftHalf[row1][col1][0]=   0.5*(fht_pixels[row1*fftsize+col1] + fht_pixels[row2*fftsize+col2]);
          fftHalf[row1][col1][1]=   0.5*(fht_pixels[row2*fftsize+col2] - fht_pixels[row1*fftsize+col1]);
        }

src/main/java/com/elphel/imagej/common/ShowDoubleFloatArrays.java

@@ -112,6 +112,30 @@ import ij.process.ImageProcessor;
 	      return;
 	    } else showArrays(pixels, width, height, titles);
 	  }
+  public void showComplex(double[][][] cpixels, String title) {
+	  int height = cpixels.length;
+	  int width =  cpixels[0].length;
+	  double [][]pixels = new double [height*width][];
+	  int indx = 0;
+	  for (int y = 0; y < height; y++) {
+		  for (int x = 0; x < width; x++) {
+			  pixels[indx++] = cpixels[y][x];
+		  }
+	  }
+	  showComplex(pixels, width, title);
+  }
+  public void showComplex(double[][] cpixels, int width, String title) {
+	  int height = cpixels.length/width;
+	  double [][]pixels = new double [2][cpixels.length];
+	  for (int i = 0; i< cpixels.length; i++) {
+		  pixels[0][i]= cpixels[i][0];
+		  pixels[1][i]= cpixels[i][1];
+	  }
+	  String [] titles = {"Re", "Im"};
+	  showArrays(pixels, width, height,  true, title, titles);
+  }
+
+
 
   public void showArrays(float[][] pixels, int width, int height,  boolean asStack, String title, String [] titles) {
 	    int i,j;

src/main/java/com/elphel/imagej/jp4/JP46_Reader_camera.java

@@ -1407,7 +1407,12 @@ Exception in thread "Thread-3564" java.lang.ArrayIndexOutOfBoundsException: 8970
 	    NodeList allNodes=doc.getDocumentElement().getElementsByTagName("*");
 	    for (int i=0;i<allNodes.getLength();i++) {
 	        String name= allNodes.item(i).getNodeName();
-            String value=allNodes.item(i).getFirstChild().getNodeValue();
+	        String value="";
+	        try {
+	        	value=allNodes.item(i).getFirstChild().getNodeValue();
+	        } catch(Exception e) {
+
+	        }
     		imp.setProperty(name, value);
 
 	    }

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

@@ -26,10 +26,14 @@
  */
 package com.elphel.imagej.lwir;
 
+import java.io.File;
+import java.io.FilenameFilter;
 import java.util.Properties;
 
 import com.elphel.imagej.common.GenericJTabbedDialog;
 
+import ij.Prefs;
+
 public class LwirReaderParameters {
 	private boolean parameters_updated = false;
 	protected int     avg_number =            4; // number of measurements to average
@@ -49,6 +53,7 @@ public class LwirReaderParameters {
 	protected double  vnir_gain_g =           2.0;
 	protected double  vnir_gain_rg =          0.7705; // 1.116; halogen/fluorescent
 	protected double  vnir_gain_bg =          2.401;  // 1.476;
+	protected boolean [] selected_channels =  {true, true, true, true, true, true, true, true};
 
 /*
 	protected double [] vnir_exp_corr = {1.0, 1.0, 1.0, 1.0};
@@ -70,7 +75,7 @@ public class LwirReaderParameters {
 	protected int     vnir_lag   =          1; // frames
 	protected double  max_mismatch_ms =     0.05;
 	protected int     max_frame_diff =      1; // 2;
-	protected int     debug_level =           0;//-3: OFF, -2:Fatal, -1:ERROR, 0:WARN, 1:INFO,2:DEBUG
+	protected int     debug_level =         0;//-3: OFF, -2:Fatal, -1:ERROR, 0:WARN, 1:INFO,2:DEBUG
 
 
 	// --- interface methods
@@ -106,6 +111,7 @@ public class LwirReaderParameters {
 		properties.setProperty(prefix+"max_mismatch_ms",     this.max_mismatch_ms+"");
 		properties.setProperty(prefix+"max_frame_diff",      this.max_frame_diff+"");
 		properties.setProperty(prefix+"debug_level",         this.debug_level+"");
+		properties.setProperty(prefix+"selected_channels",   arr_to_str(this.selected_channels));
 
 	}
 
@@ -134,6 +140,7 @@ public class LwirReaderParameters {
 		if (properties.getProperty(prefix+"max_mismatch_ms")!=null)     this.max_mismatch_ms=Double.parseDouble(properties.getProperty(prefix+"max_mismatch_ms"));
 		if (properties.getProperty(prefix+"max_frame_diff")!=null)      this.max_frame_diff=Integer.parseInt(properties.getProperty(prefix+"max_frame_diff"));
 		if (properties.getProperty(prefix+"debug_level")!=null)         this.debug_level=Integer.parseInt(properties.getProperty(prefix+"debug_level"));
+		if (properties.getProperty(prefix+"selected_channels")!=null)   this.selected_channels=str_to_barr(properties.getProperty(prefix+"selected_channels"));
 		parameters_updated = true;
 	}
 	@Override
@@ -163,6 +170,7 @@ public class LwirReaderParameters {
 		lrp.max_mismatch_ms=           this.max_mismatch_ms;
 		lrp.max_frame_diff=            this.max_frame_diff;
 		lrp.debug_level=               this.debug_level;
+		lrp.selected_channels =        this.selected_channels.clone();
 		return lrp;
 	}
 
@@ -198,7 +206,8 @@ public class LwirReaderParameters {
 				(lrp.vnir_lag == this.vnir_lag) &&
 				(lrp.max_mismatch_ms == this.max_mismatch_ms) &&
 				(lrp.max_frame_diff == this.max_frame_diff) &&
-				(lrp.debug_level ==    this.debug_level);
+				(lrp.debug_level ==    this.debug_level) &&
+				(java.util.Arrays.equals(lrp.selected_channels, this.selected_channels));
 	}
 
 	@Override
@@ -225,6 +234,7 @@ public class LwirReaderParameters {
 		result = prime * result + arr_to_str(vnir_exp_corr).hashCode();
 		result = prime * result + arr_to_str(vnir_gcorr_rbgb).hashCode();
 		result = prime * result + (new Integer(lwir_trig_dly)).hashCode();
+		result = prime * result + arr_to_str(selected_channels).hashCode();
 		// next are not needed to be programmed to the cameras
 //		result = prime * result + (new Integer(vnir_lag)).hashCode();
 //		result = prime * result + (new Double(max_mismatch_ms)).hashCode();
@@ -241,7 +251,7 @@ public class LwirReaderParameters {
 		gd.addStringField ("LWIR channels", arr_to_str(this.lwir_channels), 20, "Space-separated list of used LWIR camera channels, such as '0 1 2 3'");
 		gd.addStringField ("VNIR channels", arr_to_str(this.vnir_channels), 20, "Space-separated list of used visible range camera channels, such as '0 1 2 3'");
 		gd.addCheckbox    ("LWIR telemetry",    this.lwir_telemetry, "Set LWIR sesnors to provide telemetry data in the last 2 lines (may become mandatory later)");
-		gd.addNumericField("VNIR quality",  this.vnir_quality,  3,6,"ms", "Visible range camera JPEG compression quality (all channels)");
+		gd.addNumericField("VNIR quality",  this.vnir_quality,  3,6,"%", "Visible range camera JPEG compression quality (all channels)");
 		gd.addCheckbox    ("VNIR undo white balance",    this.vnir_scale, "Undo in-camera white balancing");
 		gd.addCheckbox    ("VNIR autoexposure", this.vnir_autoexp, "Enable autoexposure for the visible range camera");
 		gd.addNumericField("VNIR vnir_max_autoexp_ms", this.vnir_max_autoexp_ms,  3,6,"ms", "Visible range camera maximal exposure in autoexposure mode");
@@ -256,12 +266,13 @@ public class LwirReaderParameters {
 		gd.addNumericField("VNIR lag",      this.vnir_lag,     0,3,"","Visible camera lag (in frames) relative to LWIR one");
 		gd.addNumericField("Max mismatch",  this.max_mismatch_ms,    3,6,"ms","Maximal mismatch between image timestamps. Larger mismatch requires LWIR sinsor reinitialization");
 		gd.addNumericField("Max frame diff",this.max_frame_diff,     0,3,"","Maximal difference in frames between simultaneously acquired channels as calculated from the timestamps");
-		gd.addNumericField("Debug level",   this.debug_level,         0,3,"","Image acquisition log level: -3: OFF, -2:FATAL, -1:ERROR, 0:WARN, 1:INFO, 2:DEBUG");
+		gd.addNumericField("Debug level",   this.debug_level,        0,3,"","Image acquisition log level: -3: OFF, -2:FATAL, -1:ERROR, 0:WARN, 1:INFO, 2:DEBUG");
+		gd.addStringField ("Selected channels", arr_to_str(this.selected_channels), 20, "Space-separated channel selection (1 - selected, 0 - unselected)");
 	}
 
 	public void dialogAnswers(GenericJTabbedDialog gd) {
 		this.avg_number =             (int) gd.getNextNumber();
-		this.lwir_ffc =                      gd.getNextBoolean();
+		this.lwir_ffc =                     gd.getNextBoolean();
 		this.avg_all =                      gd.getNextBoolean();
 		this.lwir_ip =                      gd.getNextString();
 		this.vnir_ip =                      gd.getNextString();
@@ -284,6 +295,7 @@ public class LwirReaderParameters {
 		this.max_mismatch_ms =              gd.getNextNumber();
 		this.max_frame_diff =         (int) gd.getNextNumber();
 		this.debug_level =            (int) gd.getNextNumber();
+		this.selected_channels =            str_to_barr(gd.getNextString());
 		parameters_updated = true;
 	}
 
@@ -307,6 +319,80 @@ public class LwirReaderParameters {
 		parameters_updated = false;
 	}
 
+	public boolean [] getSelected(){
+		return  selected_channels;
+	}
+
+	public boolean [] getSelectedLwir(){
+		boolean [] sel = selected_channels.clone();
+		for (int i = lwir_channels.length; i < sel.length; i++ ) {
+			sel[i] = false;
+		}
+		return  sel;
+	}
+
+	public boolean [] getSelectedVnir(){
+		boolean [] sel = selected_channels.clone();
+		for (int i = 0; i < lwir_channels.length; i++ ) {
+			sel[i] = false;
+		}
+		return  sel;
+	}
+
+	public String [] getSourceFilesFlat(String [] sets, boolean[] channels) {
+		int num_sel = 0;
+		for (boolean s: channels) if (s) num_sel++;
+		String [] files = new String [sets.length * num_sel];
+		int indx = 0;
+		for (String set:sets) {
+			for (int i = 0; i < channels.length; i++) if (channels[i]) {
+				String file_base = set;
+				if (set.indexOf(Prefs.getFileSeparator()) >=0) {
+					file_base = set.substring(set.lastIndexOf(Prefs.getFileSeparator())+1);
+				}
+			files[indx++] =set + Prefs.getFileSeparator()+ file_base+"_"+i+".tiff";
+			}
+		}
+		return files;
+	}
+
+
+	// Image set may have different timestamps, only lwir0 matches
+	public String [][] getSourceFiles(String [] sets, boolean[] channels) {
+		String [][] files = new String [sets.length][channels.length];
+		for (int nset= 0; nset < sets.length; nset++) {
+			// read all files in the directory
+			File  set_dir = new File(sets[nset]);
+			File [] channel_files = set_dir.listFiles(new FilenameFilter() {
+				@Override
+				public boolean accept(File current, String name) {
+					if (!(new File(current, name).isFile()) || !name.endsWith(".tiff")) return false;
+					String base = name.substring(0, name.lastIndexOf(".tiff"));
+					int undr = base.lastIndexOf("_");
+					if (undr < 0) return false;
+					int chn = -1;
+					try {
+						chn = Integer.parseInt(base.substring(undr + 1));
+					} catch (Exception e) {
+
+					}
+					return chn >= 0;
+				}
+			});
+			for (File f: channel_files) {
+				String base = f.getName().substring(0, f.getName().lastIndexOf(".tiff"));
+				int undr = base.lastIndexOf("_");
+				int chn =  Integer.parseInt(base.substring(undr + 1));
+				if ((chn >= 0) && (chn < channels.length) && channels[chn]) {
+					files[nset][chn] = f.getPath();
+				}
+			}
+		}
+		return files;
+	}
+
+
+
 	// --- internal methods
 
 	private String arr_to_str(int [] arr) {
@@ -321,6 +407,23 @@ public class LwirReaderParameters {
 		return s.trim();
 	}
 
+
+	private String arr_to_str(boolean [] arr) {
+		String s = "";
+		for (boolean c:arr) s+= (c?1:0)+" ";
+		return s.trim();
+	}
+
+	private boolean [] str_to_barr(String s) {
+		int [] iarr = str_to_iarr(s);
+		if (iarr == null) return null;
+		boolean [] barr = new boolean [iarr.length];
+		for (int i = 0; i < barr.length; i++) {
+			barr[i] = iarr[i] != 0;
+		}
+		return barr;
+	}
+
 	private int [] str_to_iarr(String s) {
 		String [] sa;
 		if (s.indexOf(",") >= 0) {
@@ -349,4 +452,22 @@ public class LwirReaderParameters {
 		return darr;
 	}
 
+
+	public boolean [] selectSourceChannels(){
+		return selectSourceChannels(selected_channels);
+	}
+
+	public boolean [] selectSourceChannels(boolean [] sel) {
+		GenericJTabbedDialog gd = new GenericJTabbedDialog("Set CLT parameters",300,500);
+		for (int i = 0; i < sel.length; i++) {
+			gd.addCheckbox    ("Channel "+i,       sel[i], "Enable processing camera channel "+i);
+		}
+		gd.showDialog();
+		if (gd.wasCanceled()) return null;
+		for (int i = 0; i < sel.length; i++) {
+			sel[i] = gd.getNextBoolean();
+		}
+    	return sel;
+    }
+
 }

src/main/java/com/elphel/imagej/readers/EyesisTiff.java

@@ -640,7 +640,7 @@ the type of pixel data in this file 	getPixelType()
 	}
 
 // copied from JP46_Reader_camera.java
-	public ImagePlus encodeProperiesToInfo(ImagePlus imp){
+	public static ImagePlus encodeProperiesToInfo(ImagePlus imp){
 		String info="<?xml version=\"1.0\" encoding=\"UTF-8\"?><properties>";
 		Set<Object> jp4_set;
 		Properties jp4_prop;
@@ -661,7 +661,7 @@ the type of pixel data in this file 	getPixelType()
 		return imp;
 	}
 
-	public boolean decodeProperiesFromInfo(ImagePlus imp){
+	public static  boolean decodeProperiesFromInfo(ImagePlus imp){
 		if (imp.getProperty("Info")==null) return false;
 		String xml= (String) imp.getProperty("Info");
 
@@ -684,11 +684,15 @@ the type of pixel data in this file 	getPixelType()
 	    NodeList allNodes=doc.getDocumentElement().getElementsByTagName("*");
 	    for (int i=0;i<allNodes.getLength();i++) {
 	        String name= allNodes.item(i).getNodeName();
-            String value=allNodes.item(i).getFirstChild().getNodeValue();
-    		imp.setProperty(name, value);
-
+//            System.out.print(name+" -> ");
+            String value = "";
+            try {
+            	value=allNodes.item(i).getFirstChild().getNodeValue();
+            } catch (Exception e) {
+            }
+//            System.out.println(value);
+            imp.setProperty(name, value);
 	    }
-
 		return true;
 	}