fixing configuration and missing clt directory creation

src/main/java/EyesisCorrectionParameters.java

@@ -25,17 +25,15 @@
 **
 */
 
-import ij.IJ;
-import ij.Prefs;
-import ij.gui.GenericDialog;
-
 import java.io.File;
-import java.util.ArrayList;
-import java.util.Enumeration;
 import java.util.HashMap;
 import java.util.Properties;
 import java.util.Set;
 
+import ij.IJ;
+import ij.Prefs;
+import ij.gui.GenericDialog;
+
 
 public class EyesisCorrectionParameters {
     public static class CorrectionParameters{
@@ -293,18 +291,18 @@ public class EyesisCorrectionParameters {
 			if (properties.getProperty(prefix+"equirectangularSuffix")!=null) this.equirectangularSuffix=properties.getProperty(prefix+"equirectangularSuffix");
 
 			if (properties.getProperty(prefix+"equirectangularCut")!=null)
-				this.equirectangularCut=Boolean.parseBoolean((String)properties.getProperty(prefix+"equirectangularCut"));
+				this.equirectangularCut=Boolean.parseBoolean(properties.getProperty(prefix+"equirectangularCut"));
 //			if (properties.getProperty(prefix+"equirectangularSuffixA")!=null) this.equirectangularSuffixA=properties.getProperty(prefix+"equirectangularSuffixA");
 
 			if (properties.getProperty(prefix+"planeMapPrefix")!=null) this.planeMapPrefix=properties.getProperty(prefix+"planeMapPrefix");
 			if (properties.getProperty(prefix+"planeMapSuffix")!=null) this.planeMapSuffix=properties.getProperty(prefix+"planeMapSuffix");
 			if (properties.getProperty(prefix+"usePlaneProjection")!=null)
-				this.usePlaneProjection=Boolean.parseBoolean((String)properties.getProperty(prefix+"usePlaneProjection"));
+				this.usePlaneProjection=Boolean.parseBoolean(properties.getProperty(prefix+"usePlaneProjection"));
 			if (properties.getProperty(prefix+"planeAsJPEG")!=null)
-				this.planeAsJPEG=Boolean.parseBoolean((String)properties.getProperty(prefix+"planeAsJPEG"));
+				this.planeAsJPEG=Boolean.parseBoolean(properties.getProperty(prefix+"planeAsJPEG"));
 			if (properties.getProperty(prefix+"resultsDirectory")!=     null) this.resultsDirectory=properties.getProperty(prefix+"resultsDirectory");
 			if (properties.getProperty(prefix+"removeUnusedSensorData")!= null)
-				this.removeUnusedSensorData=Boolean.parseBoolean((String) properties.getProperty(prefix+"removeUnusedSensorData"));
+				this.removeUnusedSensorData=Boolean.parseBoolean(properties.getProperty(prefix+"removeUnusedSensorData"));
 			if (properties.getProperty(prefix+"sourcePaths")!=   null){
 				int numFiles=Integer.parseInt(properties.getProperty(prefix+"sourcePaths"));
 				this.sourcePaths=new String[numFiles];
@@ -323,17 +321,17 @@ public class EyesisCorrectionParameters {
 
 			if (properties.getProperty(prefix+"x3dDirectory")!=         null) this.x3dDirectory=properties.getProperty(prefix+"x3dDirectory");
 
-			if (properties.getProperty(prefix+"use_x3d_subdirs")!= null) this.use_x3d_subdirs=Boolean.parseBoolean((String) properties.getProperty(prefix+"use_x3d_subdirs"));
+			if (properties.getProperty(prefix+"use_x3d_subdirs")!= null) this.use_x3d_subdirs=Boolean.parseBoolean(properties.getProperty(prefix+"use_x3d_subdirs"));
 
-			if (properties.getProperty(prefix+"clt_batch_apply_man")!= null) this.clt_batch_apply_man=Boolean.parseBoolean((String) properties.getProperty(prefix+"clt_batch_apply_man"));
-			if (properties.getProperty(prefix+"clt_batch_extrinsic")!= null) this.clt_batch_extrinsic=Boolean.parseBoolean((String) properties.getProperty(prefix+"clt_batch_extrinsic"));
-			if (properties.getProperty(prefix+"clt_batch_poly")!= null)      this.clt_batch_poly=Boolean.parseBoolean((String) properties.getProperty(prefix+"clt_batch_poly"));
-			if (properties.getProperty(prefix+"clt_batch_4img")!= null)      this.clt_batch_4img=Boolean.parseBoolean((String) properties.getProperty(prefix+"clt_batch_4img"));
-			if (properties.getProperty(prefix+"clt_batch_explore")!= null)   this.clt_batch_explore=Boolean.parseBoolean((String) properties.getProperty(prefix+"clt_batch_explore"));
-			if (properties.getProperty(prefix+"clt_batch_surf")!= null)      this.clt_batch_surf=Boolean.parseBoolean((String) properties.getProperty(prefix+"clt_batch_surf"));
-			if (properties.getProperty(prefix+"clt_batch_assign")!= null)    this.clt_batch_assign=Boolean.parseBoolean((String) properties.getProperty(prefix+"clt_batch_assign"));
-			if (properties.getProperty(prefix+"clt_batch_gen3d")!= null)     this.clt_batch_gen3d=Boolean.parseBoolean((String) properties.getProperty(prefix+"clt_batch_gen3d"));
-			if (properties.getProperty(prefix+"clt_batch_dbg1")!= null)      this.clt_batch_dbg1=Boolean.parseBoolean((String) properties.getProperty(prefix+"clt_batch_dbg1"));
+			if (properties.getProperty(prefix+"clt_batch_apply_man")!= null) this.clt_batch_apply_man=Boolean.parseBoolean(properties.getProperty(prefix+"clt_batch_apply_man"));
+			if (properties.getProperty(prefix+"clt_batch_extrinsic")!= null) this.clt_batch_extrinsic=Boolean.parseBoolean(properties.getProperty(prefix+"clt_batch_extrinsic"));
+			if (properties.getProperty(prefix+"clt_batch_poly")!= null)      this.clt_batch_poly=Boolean.parseBoolean(properties.getProperty(prefix+"clt_batch_poly"));
+			if (properties.getProperty(prefix+"clt_batch_4img")!= null)      this.clt_batch_4img=Boolean.parseBoolean(properties.getProperty(prefix+"clt_batch_4img"));
+			if (properties.getProperty(prefix+"clt_batch_explore")!= null)   this.clt_batch_explore=Boolean.parseBoolean(properties.getProperty(prefix+"clt_batch_explore"));
+			if (properties.getProperty(prefix+"clt_batch_surf")!= null)      this.clt_batch_surf=Boolean.parseBoolean(properties.getProperty(prefix+"clt_batch_surf"));
+			if (properties.getProperty(prefix+"clt_batch_assign")!= null)    this.clt_batch_assign=Boolean.parseBoolean(properties.getProperty(prefix+"clt_batch_assign"));
+			if (properties.getProperty(prefix+"clt_batch_gen3d")!= null)     this.clt_batch_gen3d=Boolean.parseBoolean(properties.getProperty(prefix+"clt_batch_gen3d"));
+			if (properties.getProperty(prefix+"clt_batch_dbg1")!= null)      this.clt_batch_dbg1=Boolean.parseBoolean(properties.getProperty(prefix+"clt_batch_dbg1"));
     	}
 
     	public boolean showDialog(String title) {
@@ -426,7 +424,7 @@ public class EyesisCorrectionParameters {
     		gd.addStringField("DCT symmetical kernel files",                       this.dctSymSuffix, 40);
     		gd.addStringField("DCT asymmetrical kernel files suffix",              this.dctAsymSuffix, 40);
     		gd.addStringField("CLT kernel files prefix",                           this.cltKernelPrefix, 40);
-    		gd.addStringField("CLT symmetical kernel files",                       this.cltSuffix, 40);
+    		gd.addStringField("CLT kernel files suffix",                           this.cltSuffix, 40);
 
     		gd.addStringField("Equirectangular maps prefix",     this.equirectangularPrefix, 40);
     		gd.addStringField("Equirectangular maps suffix",     this.equirectangularSuffix, 40);
@@ -499,6 +497,13 @@ public class EyesisCorrectionParameters {
     		this.firstSubCamera=   (int) gd.getNextNumber();
     		this.sensorPrefix=           gd.getNextString();
     		this.sensorSuffix=           gd.getNextString();
+    		this.sharpKernelPrefix=      gd.getNextString();
+    		this.sharpKernelSuffix=      gd.getNextString();
+    		this.smoothKernelPrefix=     gd.getNextString();
+    		this.smoothKernelSuffix=     gd.getNextString();
+    		this.dctKernelPrefix=        gd.getNextString();
+    		this.dctSymSuffix=           gd.getNextString();
+    		this.dctAsymSuffix=          gd.getNextString();
     		this.cltKernelPrefix=        gd.getNextString();
     		this.cltSuffix=              gd.getNextString();
     		this.equirectangularPrefix=  gd.getNextString();
@@ -544,7 +549,7 @@ public class EyesisCorrectionParameters {
     		gd.addStringField("Sensor files suffix",                               this.sensorSuffix, 40);       // 17
 
     		gd.addStringField("CLT kernel files prefix",                           this.cltKernelPrefix, 40);    // 18
-    		gd.addStringField("CLT symmetical kernel files",                       this.cltSuffix, 40);          // 19
+    		gd.addStringField("CLT kernel files suffix",                           this.cltSuffix, 40);          // 19
 
     		gd.addMessage     ("============ batch parameters ============");
     		gd.addCheckbox    ("Apply (and disable) manual pixel shift",                             this.clt_batch_apply_man); // 20
@@ -1026,7 +1031,7 @@ public class EyesisCorrectionParameters {
     		String  kernelPrefix= this.cltKernelPrefix;
 			CalibrationFileManagement.MultipleExtensionsFileFilter kernelFilter =
 				new CalibrationFileManagement.MultipleExtensionsFileFilter(kernelPrefix,extensions,kernelPrefix+
-						"*"+extensions[0]+" CLT symmetrical kernel files");
+						"*"+extensions[0]+" CLT kernel files");
 			if (debugLevel>1) System.out.println("selectKernelFiles("+debugLevel+"): defaultPaths[0]="+defaultPaths[0]+" "+kernelPrefix+"*"+extensions[0]);
 
 			String [] kernelFiles=null;
@@ -2025,8 +2030,8 @@ public class EyesisCorrectionParameters {
   		this.ringIR=Double.parseDouble(properties.getProperty(prefix+"ringIR"));
   		this.ringOR=Double.parseDouble(properties.getProperty(prefix+"ringOR"));
   		if (properties.getProperty(prefix+"thresholdCorr")!=null){
-  			this.thresholdCorr=new double [Integer.parseInt((String) properties.getProperty(prefix+"thresholdCorr"))];
-  			for (int i=0;i<this.thresholdCorr.length;i++) this.thresholdCorr[i]=Double.parseDouble((String)properties.getProperty(prefix+"thresholdCorr_"+i));
+  			this.thresholdCorr=new double [Integer.parseInt(properties.getProperty(prefix+"thresholdCorr"))];
+  			for (int i=0;i<this.thresholdCorr.length;i++) this.thresholdCorr[i]=Double.parseDouble(properties.getProperty(prefix+"thresholdCorr_"+i));
   		}
   	}
 

src/main/java/Eyesis_Correction.java

@@ -25,17 +25,15 @@
 **
 */
 
-import ij.*;
-import ij.process.*;
-import ij.gui.*;
-import ij.io.FileInfo;
-import ij.io.FileSaver;
-import ij.io.OpenDialog;
-import ij.io.Opener;
-import ij.plugin.frame.*;
-
-import java.awt.*;
-import java.awt.event.*;
+import java.awt.Button;
+import java.awt.Color;
+import java.awt.Frame;
+import java.awt.GridLayout;
+import java.awt.Panel;
+import java.awt.Rectangle;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.awt.event.WindowEvent;
 import java.io.File;
 import java.io.FileInputStream;
 import java.io.FileNotFoundException;
@@ -53,6 +51,26 @@ import java.util.concurrent.atomic.AtomicInteger;
 import javax.swing.JFileChooser;
 import javax.swing.filechooser.FileFilter;
 
+import ij.CompositeImage;
+import ij.IJ;
+import ij.ImageJ;
+import ij.ImagePlus;
+import ij.ImageStack;
+import ij.Prefs;
+import ij.WindowManager;
+import ij.gui.GUI;
+import ij.gui.GenericDialog;
+import ij.gui.Plot;
+import ij.gui.PlotWindow;
+import ij.gui.Roi;
+import ij.io.FileInfo;
+import ij.io.FileSaver;
+import ij.io.OpenDialog;
+import ij.io.Opener;
+import ij.plugin.frame.PlugInFrame;
+import ij.process.ColorProcessor;
+import ij.process.FloatProcessor;
+import ij.process.ImageProcessor;
 import loci.common.services.DependencyException;
 import loci.common.services.ServiceException;
 import loci.formats.FormatException;
@@ -662,6 +680,7 @@ private Panel panel1,
 		b.addKeyListener(IJ.getInstance());
 		panel.add(b);
 	}
+	@Override
 	public void processWindowEvent(WindowEvent e) {
 		super.processWindowEvent(e);
 		if (e.getID()==WindowEvent.WINDOW_CLOSING) {
@@ -669,6 +688,7 @@ private Panel panel1,
 		}
 	}
 
+	@Override
 	public void actionPerformed(ActionEvent e) {
 		String label = e.getActionCommand();
 		if        (label.equals("Abort")) {
@@ -2633,7 +2653,7 @@ private Panel panel1,
 
 
     	for (int ii = 0; ii<n; ii++) {
-    		dindex[ii] = (double) ii;
+    		dindex[ii] = ii;
     		x[ii] = 0.0;
     	}
 //    	x[1] = 1.0;
@@ -4146,6 +4166,15 @@ private Panel panel1,
     			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.initSensorFiles(DEBUG_LEVEL);
 
@@ -5288,6 +5317,7 @@ private Panel panel1,
 	  public MultipleExtensionsFileFilter (String [] patterns) {
 		  this.patterns=patterns.clone();
 	  }
+	  @Override
 	public boolean accept (File file) {
 		  int i;
 		  String name=file.getName();
@@ -5297,6 +5327,7 @@ private Panel panel1,
 		  }
 		  return false;
 	  }
+	  @Override
 	public String getDescription() {
 		  return description;
 	  }
@@ -6617,6 +6648,7 @@ private Panel panel1,
 	  final long startTime = System.nanoTime();
 	  for (int ithread = 0; ithread < threads.length; ithread++) {
 		  threads[ithread] = new Thread() {
+			  @Override
 			public void run() {
 				  float [] pixels=null;       // will be initialized at first use
 				  float [] kernelPixels=null; // will be initialized at first use
@@ -6759,6 +6791,7 @@ private Panel panel1,
 	  final long startTime = System.nanoTime();
 	  for (int ithread = 0; ithread < threads.length; ithread++) {
 		  threads[ithread] = new Thread() {
+			  @Override
 			public void run() {
 				  double [][] tile=        new double[nChn][debayerParameters.size * debayerParameters.size ];
 				  double [][] both_masks;
@@ -7006,6 +7039,7 @@ private Panel panel1,
 	  final long startTime = System.nanoTime();
 	  for (int ithread = 0; ithread < threads.length; ithread++) {
 		  threads[ithread] = new Thread() {
+			  @Override
 			public void run() {
 				  double [] tile=        new double[size * size ];
 				  int tileY,tileX;

src/main/java/QuadCLT.java

@@ -711,7 +711,7 @@ public class QuadCLT {
 					  imp_clt.show();
 				  }
 				  FileSaver fs=new FileSaver(imp_clt);
-				  fs.saveAsTiffStack(cltPath);
+				  fs.saveAsTiffStack(cltPath); // directory does not exist
 			  }
 		  }
 		  return true;