fixing headless run

src/main/java/EyesisCorrectionParameters.java

@@ -573,7 +573,7 @@ public class EyesisCorrectionParameters {
 			String [] sensorFiles=null;
 // try reading all matching files
 			File dir= new File (this.sensorDirectory);
-//			if (debugLevel>1) System.out.println("selectSensorFiles, dir="+this.sensorDirectory);
+			if (debugLevel>1) System.out.println("selectSensorFiles, dir="+this.sensorDirectory);
 			File [] fileList=null;
 			if (dir.exists()) {
 				fileList=dir.listFiles(sensorFilter);

src/main/java/Eyesis_Correction.java

@@ -25,17 +25,16 @@
 **
 */
 
-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.GraphicsEnvironment;
+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 +52,28 @@ 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.Macro;
+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.PlugIn;
+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;
@@ -60,10 +81,14 @@ import loci.formats.FormatException;
 //import javax.swing.SwingUtilities;
 //import javax.swing.UIManager;
 
-public class Eyesis_Correction extends PlugInFrame implements ActionListener {
+public class Eyesis_Correction implements PlugIn, ActionListener {
    /**
 	 *
 	 */
+	private Boolean headless=GraphicsEnvironment.getLocalGraphicsEnvironment().isHeadlessInstance();
+	private PlugInFrame plugInFrame;
+	String prefsPath;
+
 	private static final long serialVersionUID = -1507307664341265263L;
 private Panel panel1,
          panel2,
@@ -341,9 +366,14 @@ private Panel panel1,
 	    public String  buttonLabel="";
 	}
 
-   
-	public Eyesis_Correction() {
-		super("Eyesis_Correction");
+	@Override
+	public void run(String arg) {
+		String options=Macro.getOptions();
+		try {
+			prefsPath=Macro.getValue(options, "prefs", Prefs.getPrefsDir()+Prefs.getFileSeparator()+"Eyesis_Correction.xml");
+		} catch(Exception e) {
+			prefsPath=Prefs.getPrefsDir()+Prefs.getFileSeparator()+"Eyesis_Correction.xml";
+		}
 		if (IJ.versionLessThan("1.43q")) return;
 		if (instance!=null) {
 			instance.toFront();
@@ -353,14 +383,38 @@ private Panel panel1,
 			loadPrefs();
 		} catch (IOException e1) {
 			System.out.println("failed to load preferences");
-//			e1.printStackTrace();
+			e1.printStackTrace();
 		}
 		EYESIS_CORRECTIONS =       new EyesisCorrections(SYNC_COMMAND.stopRequested,CORRECTION_PARAMETERS);
+		if (options!=null || headless) {
+			processFiles();
+		} else {
+			initGui();
+		}
+	}
+
+	public void initGui()  {
 		Color color_configure=     new Color(200, 200,160);
 		Color color_process=       new Color(180, 180, 240);
 		Color color_conf_process=  new Color(180, 240, 240);
 		Color color_restore=       new Color(180, 240, 180);
 		Color color_stop=          new Color(255, 160, 160);
+//<<<<<<< HEAD
+		plugInFrame=new PlugInFrame("Eyesis_Correction") {
+			private static final long serialVersionUID = -4138832568507690332L;
+			@Override
+			public void processWindowEvent(WindowEvent e) {
+				super.processWindowEvent(e);
+				if (e.getID()==WindowEvent.WINDOW_CLOSING) {
+					instance = null;
+				}
+			}
+		};
+		instance=plugInFrame;
+		plugInFrame.addKeyListener(IJ.getInstance());
+		int menuRows=4 + (ADVANCED_MODE?4:0) + (MODE_3D?3:0);
+		plugInFrame.setLayout(new GridLayout(menuRows, 1));
+/*=======
 
 
 		instance = this;
@@ -368,6 +422,8 @@ private Panel panel1,
 		int menuRows=4 + (ADVANCED_MODE?4:0) + (MODE_3D?3:0) + (DCT_MODE?2:0);
 		setLayout(new GridLayout(menuRows, 1));
 
+>>>>>>> origin/dct
+*/
 		panel6 = new Panel();
 		panel6.setLayout(new GridLayout(1, 0, 5, 5));
 		addButton("Save",panel6);
@@ -375,13 +431,13 @@ private Panel panel1,
 		addButton("Stop",panel6,color_stop);
 		addButton("Abort",panel6,color_stop);
 
-		add(panel6);
+		plugInFrame.add(panel6);
 
 		panel5 = new Panel();
 		panel5.setLayout(new GridLayout(1, 0, 5, 5));
 		addButton("Configure spilt",    panel5, color_configure);
 		addButton("Configure demosaic", panel5, color_configure);
-		add(panel5);
+		plugInFrame.add(panel5);
 		panel5a = new Panel();
 		panel5a.setLayout(new GridLayout(1, 0, 5, 5));
 		addButton("Configure convolution", panel5a, color_configure);
@@ -389,7 +445,7 @@ private Panel panel1,
 		addButton("Configure color", panel5a, color_configure);
 		addButton("Channel gains", panel5a, color_configure);
 		addButton("Configure RGB", panel5a, color_configure);
-		add(panel5a);
+		plugInFrame.add(panel5a);
 
 
 		// Debug/development options
@@ -399,13 +455,13 @@ private Panel panel1,
 			panel1.setLayout(new GridLayout(1, 0, 5, 5)); // rows, columns, vgap, hgap
 			addButton("Split Image",panel1);
 			addButton("Debayer Image",panel1);
-			add(panel1);
+			plugInFrame.add(panel1);
 
 			panel2 = new Panel();
 			panel2.setLayout(new GridLayout(1, 0, 5, 5));
 			addButton("Select kernel stack",panel2);
 			addButton("Convolve with stack",panel2);
-			add(panel2);
+			plugInFrame.add(panel2);
 
 			panel3 = new Panel();
 			panel3.setLayout(new GridLayout(1, 0, 5, 5));
@@ -413,14 +469,14 @@ private Panel panel1,
 			addButton("Combine pair",panel3);
 			addButton("Colors",panel3);
 			addButton("RGB",panel3);
-			add(panel3);
+			plugInFrame.add(panel3);
 
 
 			panel4 = new Panel();
 			panel4.setLayout(new GridLayout(1, 0, 5, 5));
 			addButton("Test",panel4);
 			addButton("Test Debayer",panel4);
-			add(panel4);
+			plugInFrame.add(panel4);
 		}
 		panel7 = new Panel();
 		panel7.setLayout(new GridLayout(1, 0, 5, 5));
@@ -433,7 +489,7 @@ private Panel panel1,
 			addButton("Tiff Writer", panel7);
 			addButton("Tiff Properties", panel7);
 		}
-		add(panel7);
+		plugInFrame.add(panel7);
 
 		if (MODE_3D){
 			panelPostProcessing1 = new Panel();
@@ -443,7 +499,7 @@ private Panel panel1,
 			addButton("ConvertPP", panelPostProcessing1,color_process);
 			addButton("Linear Features", panelPostProcessing1);
 			addButton("Intercam correlations", panelPostProcessing1);
-			add(panelPostProcessing1);
+			plugInFrame.add(panelPostProcessing1);
 
 			panelPostProcessing2 = new Panel();
 			panelPostProcessing2.setLayout(new GridLayout(1, 0, 5, 5));
@@ -454,15 +510,18 @@ private Panel panel1,
 			addButton("Fill FG gaps", panelPostProcessing2);
 			addButton("Filter Z-map", panelPostProcessing2);
 			addButton("Occluding FG", panelPostProcessing2);
-			add(panelPostProcessing2);
+			plugInFrame.add(panelPostProcessing2);
 
 			panelPostProcessing3 = new Panel();
 			panelPostProcessing3.setLayout(new GridLayout(1, 0, 5, 5));
 			addButton("Refine Disparities", panelPostProcessing3);
 			addButton("Init Photometry", panelPostProcessing3);
 			addButton("Plane Likely", panelPostProcessing3);
-			add(panelPostProcessing3);
+			plugInFrame.add(panelPostProcessing3);
 		}
+// <<<<<<< HEAD
+		plugInFrame.pack();
+/* =======
 		if (DCT_MODE) {
 			panelDct1 = new Panel();
 			panelDct1.setLayout(new GridLayout(1, 0, 5, 5)); // rows, columns, vgap, hgap
@@ -490,16 +549,16 @@ private Panel panel1,
 			addButton("CLT stack",                 panelClt1, color_process);
 			addButton("Select second CLT image",   panelClt1, color_configure);
 			addButton("CLT correlate",             panelClt1, color_process);
-			addButton("Create 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);
+			addButton("CLT test 2",                panelClt1, color_process);
+			addButton("CLT test 3",                panelClt1, color_process);
+			addButton("CLT test 4",                panelClt1, color_process);
 			add(panelClt1);
 		}
 		pack();
-
-		GUI.center(this);
-		setVisible(true);
+>>>>>>> origin/dct
+*/
+		GUI.center(plugInFrame);
+		plugInFrame.setVisible(true);
 		FHT_INSTANCE=       new DoubleFHT();
 		SDFA_INSTANCE=      new showDoubleFloatArrays();
 		// main loop
@@ -528,7 +587,6 @@ private Panel panel1,
 		}
 
 	}
-	private String prefsPath=Prefs.getPrefsDir()+Prefs.getFileSeparator()+"Eyesis_Correction.xml";
     private Properties prefsProperties=new Properties();
 
     public void loadPrefs() throws IOException{
@@ -543,6 +601,13 @@ private Panel panel1,
     	try {
     		prefsProperties.loadFromXML(is);
 
+    		if (!headless){
+                  System.out.println("Skipping getAllProperties(prefsProperties)");
+                }else{
+                  getAllProperties(prefsProperties);
+                  if (DEBUG_LEVEL>0) System.out.println("Configuration parameters are restored from "+this.prefsPath);
+                }
+
     	} catch (IOException e) {
     		String msg="Failed to read XML configuration file: "+this.prefsPath;
     		IJ.showMessage("Error",msg);
@@ -554,7 +619,7 @@ private Panel panel1,
     		// TODO Auto-generated catch block
     		e.printStackTrace();
     	}
-		String sValue=	this.prefsProperties.getProperty("ADVANCED_MODE");
+		String sValue = this.prefsProperties.getProperty("ADVANCED_MODE");
 		if (sValue!=null) {
 			ADVANCED_MODE=Boolean.parseBoolean(sValue);
 			System.out.println("Read ADVANCED_MODE="+ADVANCED_MODE);
@@ -609,13 +674,7 @@ private Panel panel1,
 		b.addKeyListener(IJ.getInstance());
 		panel.add(b);
 	}
-	public void processWindowEvent(WindowEvent e) {
-		super.processWindowEvent(e);
-		if (e.getID()==WindowEvent.WINDOW_CLOSING) {
-			instance = null;	
-		}
-	}
-
+	@Override
 	public void actionPerformed(ActionEvent e) {
 		String label = e.getActionCommand();
 		if        (label.equals("Abort")) {
@@ -642,6 +701,70 @@ private Panel panel1,
 		}
 		//		matchSimulatedPattern.FFT_SIZE=FFT_SIZE;
 	}
+
+	public void processFiles() {
+		DEBUG_LEVEL=MASTER_DEBUG_LEVEL;
+		EYESIS_CORRECTIONS.setDebug(DEBUG_LEVEL);
+		String configPath=null;
+		if (!headless && EYESIS_CORRECTIONS.correctionsParameters.saveSettings) {
+			configPath=EYESIS_CORRECTIONS.correctionsParameters.selectResultsDirectory(
+					true,
+					true);
+			if (configPath==null){
+				String msg="No results directory selected, command aborted";
+				System.out.println("Warning: "+msg);
+				IJ.showMessage("Warning",msg);
+				return;
+			}
+			configPath+=Prefs.getFileSeparator()+"autoconfig";
+			try {
+				saveTimestampedProperties(
+						configPath,      // full path or null
+						null, // use as default directory if path==null
+						true,
+						PROPERTIES);
+			} catch (Exception e){
+				String msg="Failed to save configuration to "+configPath+", command aborted";
+				System.out.println("Error: "+msg);
+				IJ.showMessage("Error",msg);
+				return;
+			}
+		}
+	    EYESIS_CORRECTIONS.initSensorFiles(DEBUG_LEVEL);
+	    int numChannels=EYESIS_CORRECTIONS.getNumChannels();
+	    NONLIN_PARAMETERS.modifyNumChannels(numChannels);
+	    CHANNEL_GAINS_PARAMETERS.modifyNumChannels(numChannels);
+
+	    if (CORRECTION_PARAMETERS.deconvolve && (NONLIN_PARAMETERS.noiseGainPower!=0)) {
+	    EYESIS_CORRECTIONS.updateImageNoiseGains(
+	    		NONLIN_PARAMETERS,     //EyesisCorrectionParameters.NonlinParameters nonlinParameters,
+	    		CONVOLVE_FFT_SIZE,     //int          fftSize, // 128 - fft size, kernel size should be size/2
+				THREADS_MAX,           // int          threadsMax,  // maximal number of threads to launch
+				UPDATE_STATUS,         // boolean    updateStatus,
+				DEBUG_LEVEL);           //int        globalDebugLevel){
+	    }
+
+	    EYESIS_CORRECTIONS.processChannelImages(
+	    		SPLIT_PARAMETERS, // EyesisCorrectionParameters.SplitParameters         splitParameters,
+	    		DEBAYER_PARAMETERS, //EyesisCorrectionParameters.DebayerParameters     debayerParameters,
+	    		NONLIN_PARAMETERS, //EyesisCorrectionParameters.NonlinParameters       nonlinParameters,
+	    		COLOR_PROC_PARAMETERS, //EyesisCorrectionParameters.ColorProcParameters colorProcParameters,
+	    		CHANNEL_GAINS_PARAMETERS, //CorrectionColorProc.ColorGainsParameters     channelGainParameters,
+	    		RGB_PARAMETERS, //EyesisCorrectionParameters.RGBParameters             rgbParameters,
+	    		EQUIRECTANGULAR_PARAMETERS, // EyesisCorrectionParameters.EquirectangularParameters equirectangularParameters,
+	    		CONVOLVE_FFT_SIZE, //int          convolveFFTSize, // 128 - fft size, kernel size should be size/2
+	    		THREADS_MAX, //final int          threadsMax,  // maximal number of threads to launch
+	    		UPDATE_STATUS, //final boolean    updateStatus,
+	    		DEBUG_LEVEL); //final int        debugLevel);
+	    if (configPath!=null) {
+	    	saveTimestampedProperties( // save config again
+	    			configPath,      // full path or null
+	    			null, // use as default directory if path==null
+	    			true,
+	    			PROPERTIES);
+	    }
+	}
+
 	public void runMenuCommand(String label){
     int i, j; //,l,iq;
 //    String label = e.getActionCommand();
@@ -1055,69 +1178,7 @@ private Panel panel1,
     	return;
 /* ======================================================================== */
     } else if (label.equals("Process files")) {
-    	DEBUG_LEVEL=MASTER_DEBUG_LEVEL;
-    	EYESIS_CORRECTIONS.setDebug(DEBUG_LEVEL);
-    	String configPath=null;
-    	if (EYESIS_CORRECTIONS.correctionsParameters.saveSettings) {
-    		configPath=EYESIS_CORRECTIONS.correctionsParameters.selectResultsDirectory(
-    				true,
-    				true);
-    		if (configPath==null){
-    			String msg="No results directory selected, command aborted";
-    			System.out.println("Warning: "+msg);
-    			IJ.showMessage("Warning",msg);
-    			return;
-    		}
-    		configPath+=Prefs.getFileSeparator()+"autoconfig";
-    		try {
-    			saveTimestampedProperties(
-    					configPath,      // full path or null
-    					null, // use as default directory if path==null 
-    					true,
-    					PROPERTIES);
-
-    		} catch (Exception e){
-    			String msg="Failed to save configuration to "+configPath+", command aborted";
-    			System.out.println("Error: "+msg);
-    			IJ.showMessage("Error",msg);
-    			return;
-    		}
-    	}      
-        
-        EYESIS_CORRECTIONS.initSensorFiles(DEBUG_LEVEL);
-        int numChannels=EYESIS_CORRECTIONS.getNumChannels();
-        NONLIN_PARAMETERS.modifyNumChannels(numChannels);
-        CHANNEL_GAINS_PARAMETERS.modifyNumChannels(numChannels);
-        
-        if (CORRECTION_PARAMETERS.deconvolve && (NONLIN_PARAMETERS.noiseGainPower!=0)) {
-        EYESIS_CORRECTIONS.updateImageNoiseGains(
-        		NONLIN_PARAMETERS,     //EyesisCorrectionParameters.NonlinParameters nonlinParameters,
-        		CONVOLVE_FFT_SIZE,     //int          fftSize, // 128 - fft size, kernel size should be size/2
-    			THREADS_MAX,           // int          threadsMax,  // maximal number of threads to launch                         
-    			UPDATE_STATUS,         // boolean    updateStatus,
-    			DEBUG_LEVEL);           //int        globalDebugLevel){
-        }
-       
-        EYESIS_CORRECTIONS.processChannelImages(
-        		SPLIT_PARAMETERS, // EyesisCorrectionParameters.SplitParameters         splitParameters,
-        		DEBAYER_PARAMETERS, //EyesisCorrectionParameters.DebayerParameters     debayerParameters,
-        		NONLIN_PARAMETERS, //EyesisCorrectionParameters.NonlinParameters       nonlinParameters,
-        		COLOR_PROC_PARAMETERS, //EyesisCorrectionParameters.ColorProcParameters colorProcParameters,
-        		CHANNEL_GAINS_PARAMETERS, //CorrectionColorProc.ColorGainsParameters     channelGainParameters,
-        		RGB_PARAMETERS, //EyesisCorrectionParameters.RGBParameters             rgbParameters,
-        		EQUIRECTANGULAR_PARAMETERS, // EyesisCorrectionParameters.EquirectangularParameters equirectangularParameters,
-        		CONVOLVE_FFT_SIZE, //int          convolveFFTSize, // 128 - fft size, kernel size should be size/2
-        		THREADS_MAX, //final int          threadsMax,  // maximal number of threads to launch                         
-        		UPDATE_STATUS, //final boolean    updateStatus,
-        		DEBUG_LEVEL); //final int        debugLevel);
-        if (configPath!=null) {
-        	saveTimestampedProperties( // save config again
-        			configPath,      // full path or null
-        			null, // use as default directory if path==null 
-        			true,
-        			PROPERTIES);
-        }
-
+    	processFiles();
         return;
 /* ======================================================================== */
     } else if (label.equals("Tiff Writer")) {
@@ -2579,7 +2640,7 @@ 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;
@@ -2890,7 +2951,16 @@ private Panel panel1,
         int numChannels=EYESIS_CORRECTIONS.getNumChannels();
         NONLIN_PARAMETERS.modifyNumChannels(numChannels);
         CHANNEL_GAINS_PARAMETERS.modifyNumChannels(numChannels);
-
+/*
+        if (CORRECTION_PARAMETERS.deconvolve && (NONLIN_PARAMETERS.noiseGainPower!=0)) {
+        EYESIS_CORRECTIONS.updateImageNoiseGains(
+        		NONLIN_PARAMETERS,     //EyesisCorrectionParameters.NonlinParameters nonlinParameters,
+        		CONVOLVE_FFT_SIZE,     //int          fftSize, // 128 - fft size, kernel size should be size/2
+    			THREADS_MAX,           // int          threadsMax,  // maximal number of threads to launch
+    			UPDATE_STATUS,         // boolean    updateStatus,
+    			DEBUG_LEVEL);           //int        globalDebugLevel){
+        }
+*/
         if (!EYESIS_DCT.DCTKernelsAvailable()){
         	if (DEBUG_LEVEL > 0){
         		System.out.println("Reading/converting DCT kernels");
@@ -2905,7 +2975,11 @@ private Panel panel1,
         		EYESIS_DCT.showKernels(); // show restored kernels
         	}
         }
+
+
+//        EYESIS_CORRECTIONS.processChannelImages(
         EYESIS_DCT.processDCTChannelImages(
+//        		SPLIT_PARAMETERS, // EyesisCorrectionParameters.SplitParameters         splitParameters,
         		DCT_PARAMETERS,  // EyesisCorrectionParameters.DCTParameters           dct_parameters,
         		DEBAYER_PARAMETERS, //EyesisCorrectionParameters.DebayerParameters     debayerParameters,
         		NONLIN_PARAMETERS, //EyesisCorrectionParameters.NonlinParameters       nonlinParameters,
@@ -3780,9 +3854,6 @@ private Panel panel1,
 /* ======================================================================== */
     } else if (label.equals("CLT correlate")) {
     	DEBUG_LEVEL=MASTER_DEBUG_LEVEL;
-	    runtime.gc();
-		System.out.println("--- Free memory="+runtime.freeMemory()+" (of "+runtime.totalMemory()+")");
-
 //    	IJ.showMessage("DCT test 1");
         if (!CLT_PARAMETERS.showDialog()) return;
 // process selected image stack
@@ -3988,7 +4059,6 @@ private Panel panel1,
     	for (int chn = 0; chn < clt_corr.length; chn++) {
     		image_dtt.clt_dtt2( // DCCT2, DSCT2, DCST2, DSST2 - in-place
     				clt_corr[chn],                        // final double [][][][] clt_data,
-    				true,                                 // final boolean transpose, // when doing inverse transform, the data comes in transposed form, so CS <->SC
     				THREADS_MAX,                          // maximal number of threads to launch
     				DEBUG_LEVEL);                        // globalDebugLevel)
     	}
@@ -4032,193 +4102,28 @@ private Panel panel1,
         			DBG_IMP.getTitle()+"-C"+suffix, titles_rbg);
         }
 
-//==============================================================================
-        
-    } else if (label.equals("Create CLT kernels")) {
-        if (!CLT_PARAMETERS.showDialog()) return;
-        if (EYESIS_DCT == null){
-        	EYESIS_DCT = new  EyesisDCT (
-        			EYESIS_CORRECTIONS,
-        			CORRECTION_PARAMETERS,
-        			DCT_PARAMETERS);
-        }
-    	String configPath=null;
-    	if (EYESIS_CORRECTIONS.correctionsParameters.saveSettings) {
-    		configPath=EYESIS_CORRECTIONS.correctionsParameters.selectResultsDirectory(
-    				true,
-    				true);
-    		if (configPath==null){
-    			String msg="No results directory selected, command aborted";
-    			System.out.println("Warning: "+msg);
-    			IJ.showMessage("Warning",msg);
-    			return;
-    		}
-    		configPath+=Prefs.getFileSeparator()+"autoconfig";
-    		try {
-    			saveTimestampedProperties(
-    					configPath,      // full path or null
-    					null, // use as default directory if path==null 
-    					true,
-    					PROPERTIES);
-
-    		} catch (Exception e){
-    			String msg="Failed to save configuration to "+configPath+", command aborted";
-    			System.out.println("Error: "+msg);
-    			IJ.showMessage("Error",msg);
-    			return;
-    		}
-    	}      
-        
-        EYESIS_CORRECTIONS.initSensorFiles(DEBUG_LEVEL);
-
-        EYESIS_DCT.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 (EYESIS_DCT != null){
-        	EYESIS_DCT.resetCLTKernels();
-        }
-        
-    } else if (label.equals("Read CLT kernels")) {
-        if (!CLT_PARAMETERS.showDialog()) return;
-        if (EYESIS_DCT == null){
-        	EYESIS_DCT = new  EyesisDCT (
-        			EYESIS_CORRECTIONS,
-        			CORRECTION_PARAMETERS,
-        			DCT_PARAMETERS);
-        }
-    	String configPath=null;
-    	if (EYESIS_CORRECTIONS.correctionsParameters.saveSettings) {
-    		configPath=EYESIS_CORRECTIONS.correctionsParameters.selectResultsDirectory(
-    				true,
-    				true);
-    		if (configPath==null){
-    			String msg="No results directory selected, command aborted";
-    			System.out.println("Warning: "+msg);
-    			IJ.showMessage("Warning",msg);
-    			return;
-    		}
-    		configPath+=Prefs.getFileSeparator()+"autoconfig";
-    		try {
-    			saveTimestampedProperties(
-    					configPath,      // full path or null
-    					null, // use as default directory if path==null 
-    					true,
-    					PROPERTIES);
-
-    		} catch (Exception e){
-    			String msg="Failed to save configuration to "+configPath+", command aborted";
-    			System.out.println("Error: "+msg);
-    			IJ.showMessage("Error",msg);
-    			return;
-    		}
-    	}      
 
-        EYESIS_CORRECTIONS.initSensorFiles(DEBUG_LEVEL);
 
-        EYESIS_DCT.readCLTKernels(
-        		CLT_PARAMETERS,
-                THREADS_MAX,
-                UPDATE_STATUS, // update status info
-        		DEBUG_LEVEL);
-        if (DEBUG_LEVEL > -1){
-        	EYESIS_DCT.showCLTKernels(
-        			THREADS_MAX,
-        			UPDATE_STATUS, // update status info
-        			DEBUG_LEVEL);
-        }
 
-        return;
-    } else if (label.equals("CLT process files")) {
-    	DEBUG_LEVEL=MASTER_DEBUG_LEVEL;
-    	EYESIS_CORRECTIONS.setDebug(DEBUG_LEVEL);
-        if (EYESIS_DCT == null){
-        	EYESIS_DCT = new  EyesisDCT (
-        			EYESIS_CORRECTIONS,
-        			CORRECTION_PARAMETERS,
-        			DCT_PARAMETERS);
-        	if (DEBUG_LEVEL > 0){
-        		System.out.println("Created new EyesisDCT instance, will need to read CLT kernels");
-        	}
-        }
-    	String configPath=null;
-    	if (EYESIS_CORRECTIONS.correctionsParameters.saveSettings) {
-    		configPath=EYESIS_CORRECTIONS.correctionsParameters.selectResultsDirectory(
-    				true,
-    				true);
-    		if (configPath==null){
-    			String msg="No results directory selected, command aborted";
-    			System.out.println("Warning: "+msg);
-    			IJ.showMessage("Warning",msg);
-    			return;
-    		}
-    		configPath+=Prefs.getFileSeparator()+"autoconfig";
-    		try {
-    			saveTimestampedProperties(
-    					configPath,      // full path or null
-    					null, // use as default directory if path==null 
-    					true,
-    					PROPERTIES);
-
-    		} catch (Exception e){
-    			String msg="Failed to save configuration to "+configPath+", command aborted";
-    			System.out.println("Error: "+msg);
-    			IJ.showMessage("Error",msg);
-    			return;
-    		}
-    	}      
-        
-        EYESIS_CORRECTIONS.initSensorFiles(DEBUG_LEVEL);
-        int numChannels=EYESIS_CORRECTIONS.getNumChannels();
-        NONLIN_PARAMETERS.modifyNumChannels(numChannels);
-        CHANNEL_GAINS_PARAMETERS.modifyNumChannels(numChannels);
-
-        if (!EYESIS_DCT.CLTKernelsAvailable()){
-        	if (DEBUG_LEVEL > 0){
-        		System.out.println("Reading CLT kernels");
-        	}
-            EYESIS_DCT.readCLTKernels(
-            		CLT_PARAMETERS,
-                    THREADS_MAX,
-                    UPDATE_STATUS, // update status info
-            		DEBUG_LEVEL);
-
-            if (DEBUG_LEVEL > 1){
-            	EYESIS_DCT.showCLTKernels(
-            			THREADS_MAX,
-            			UPDATE_STATUS, // update status info
-            			DEBUG_LEVEL);
-        	}
+/*
+        double [][] iclt_data = new double [clt_data.length][];
+        for (int chn=0; chn<iclt_data.length;chn++){
+        	iclt_data[chn] = image_dtt.iclt_2d(
+        			clt_data[chn],                  // scanline representation of dcd data, organized as dct_size x dct_size tiles
+        			CLT_PARAMETERS.transform_size,  // final int
+        			CLT_PARAMETERS.clt_window,      //window_type
+        			CLT_PARAMETERS.iclt_mask,       //which of 4 to transform back
+        			CLT_PARAMETERS.dbg_mode,       //which of 4 to transform back
+        			THREADS_MAX,                    // maximal number of threads to launch
+        			DEBUG_LEVEL);                   //        globalDebugLevel)
         }
-        
-///========================================        
-        
-        EYESIS_DCT.processCLTChannelImages(
-        		CLT_PARAMETERS,  // EyesisCorrectionParameters.DCTParameters           dct_parameters,
-        		DEBAYER_PARAMETERS, //EyesisCorrectionParameters.DebayerParameters     debayerParameters,
-        		NONLIN_PARAMETERS, //EyesisCorrectionParameters.NonlinParameters       nonlinParameters,
-        		COLOR_PROC_PARAMETERS, //EyesisCorrectionParameters.ColorProcParameters colorProcParameters,
-        		CHANNEL_GAINS_PARAMETERS, //CorrectionColorProc.ColorGainsParameters     channelGainParameters,
-        		RGB_PARAMETERS, //EyesisCorrectionParameters.RGBParameters             rgbParameters,
-        		EQUIRECTANGULAR_PARAMETERS, // EyesisCorrectionParameters.EquirectangularParameters equirectangularParameters,
-        		CONVOLVE_FFT_SIZE, //int          convolveFFTSize, // 128 - fft size, kernel size should be size/2
-        		THREADS_MAX, //final int          threadsMax,  // maximal number of threads to launch                         
-        		UPDATE_STATUS, //final boolean    updateStatus,
-        		DEBUG_LEVEL); //final int        debugLevel);
-        
-        if (configPath!=null) {
-        	saveTimestampedProperties( // save config again
-        			configPath,      // full path or null
-        			null, // use as default directory if path==null 
+        SDFA_INSTANCE.showArrays(
+        		iclt_data,
+        		(tilesX + 1) * CLT_PARAMETERS.transform_size,
+        		(tilesY + 1) * CLT_PARAMETERS.transform_size,
         		true,
-        			PROPERTIES);
-        }
-
+        		DBG_IMP.getTitle()+"-ICLT-"+CLT_PARAMETERS.iclt_mask);
+*/
     	return;
 
 // End of buttons code
@@ -4429,6 +4334,7 @@ private Panel panel1,
 	  public MultipleExtensionsFileFilter (String [] patterns) {
 		  this.patterns=patterns.clone();
 	  }
+	  @Override
 	public boolean accept (File file) {
 		  int i;
 		  String name=file.getName();
@@ -4438,6 +4344,7 @@ private Panel panel1,
 		  }
 		  return false;
 	  }
+	  @Override
 	public String getDescription() {
 		  return description;
 	  }
@@ -5736,6 +5643,7 @@ 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
@@ -5878,6 +5786,7 @@ 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;
@@ -6125,6 +6034,7 @@ 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;
@@ -7449,4 +7359,3 @@ G= Y  +Pr*(- 2*Kr*(1-Kr))/Kg + Pb*(-2*Kb*(1-Kb))/Kg
 	}
 
 }
-

src/main/java/JP46_Reader_camera.java

@@ -30,6 +30,7 @@ import ij.process.*;
 import ij.gui.*;
 import ij.plugin.frame.*;
 import ij.text.*;
+import ij.plugin.PlugIn;
 
 import java.awt.*;
 import java.awt.event.*;
@@ -50,9 +51,8 @@ import org.xml.sax.InputSource;
 import org.xml.sax.SAXException;
 
 
-
 /* This plugin opens images in Elphel JP4/JP46 format (opens as JPEG, reads MakerNote and converts). */
-public class JP46_Reader_camera extends PlugInFrame implements ActionListener {
+public class JP46_Reader_camera implements PlugIn,ActionListener {
 
 	/**
 	 *
@@ -61,6 +61,7 @@ public class JP46_Reader_camera extends PlugInFrame implements ActionListener {
 	Panel panel1;
 	Panel confpanel;
 	Frame instance;
+	PlugInFrame plugInFrame;
 
 	String arg;
 
@@ -75,44 +76,33 @@ public class JP46_Reader_camera extends PlugInFrame implements ActionListener {
         public boolean demux=true;
 	public String imageTitle="cameraImage";
 	private int ExifOffset=0x0c;
+	private Boolean headless=GraphicsEnvironment.getLocalGraphicsEnvironment().isHeadlessInstance();
 
-	public JP46_Reader_camera() {
-		super("JP46 Reader Camera");
-		if (IJ.versionLessThan("1.39t")) return;
-		if (instance!=null) {
-			instance.toFront();
-			return;
+	public void run(String arg) {
 	}
-		instance = this;
-		addKeyListener(IJ.getInstance());
 
-		panel1 = new Panel();
-
-		panel1.setLayout(new GridLayout(6, 1, 50, 5));
-
-		addButton("Open JP4/JP46...",panel1);    
-		addButton("Open JP4/JP46 from camera",panel1);
-		addButton("Configure...",panel1);
-		addButton("Show image properties",panel1);
-		addButton("Decode image info to properties",panel1);
-		addButton("Split Bayer",panel1);
+	public JP46_Reader_camera(Boolean showGui) {
+		if (showGui) initGui();
+	}
 
+	public JP46_Reader_camera() {
+		initGui();
+	}
 
-		add(panel1);
+	public void initGui() {
+		//super("JP46 Reader Camera");
+		if (headless) return;
 
-		pack();
-		GUI.center(this);
-		setVisible(true);
-	}
-	public JP46_Reader_camera(boolean showGUI) {
-		super("JP46 Reader Camera");
 		if (IJ.versionLessThan("1.39t")) return;
 		if (instance!=null) {
 			instance.toFront();
 			return;
 		}
-		instance = this;
-		addKeyListener(IJ.getInstance());
+
+		plugInFrame=new PlugInFrame("JP46 Reader Camera");
+		instance = (Frame)plugInFrame;
+
+		plugInFrame.addKeyListener(IJ.getInstance());
 
 		panel1 = new Panel();
 
@@ -124,10 +114,10 @@ public class JP46_Reader_camera extends PlugInFrame implements ActionListener {
 		addButton("Show image properties",panel1);
 		addButton("Decode image info to properties",panel1);
 		addButton("Split Bayer",panel1);
-		add(panel1);
-		pack();
-		GUI.center(this);
-		setVisible(showGUI);
+		plugInFrame.add(panel1);
+		plugInFrame.pack();
+		GUI.center(plugInFrame);
+		plugInFrame.setVisible(true);
 	}
 
 	void addButton(String label, Panel panel) {