Commit ace015f7 authored by Luc Deschenaux's avatar Luc Deschenaux
Browse files

Fix Eyesis_Correction and JP46_Reader_camera 

Plugins must not extend or instantiate frames in order to be run in headless mode,
they must implement "PlugIn" and the entry point should be method run(); AFIK

- Eyesis_Correction can now be run from macro:
  run("Eyesis Correction","prefs=<path_to_xml>");

- or in headless mode from Fidji command line:
  ImageJ-linux64 --headless --run Eyesis_Correction prefs=<path_to_xml> ...
parent 3d9ac013

src/main/java/Eyesis_Correction.java

+114 −98
Original line number Diff line number Diff line
@@ -33,6 +33,7 @@ import ij.io.FileSaver; 
import ij.io.OpenDialog;

import ij.io.Opener;

import ij.plugin.frame.*;

import ij.plugin.PlugIn;



import java.awt.*;

import java.awt.event.*;
@@ -60,10 +61,14 @@ 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,panel3,panel4,panel5,panel5a, panel6,panel7,panelPostProcessing1,panelPostProcessing2,panelPostProcessing3;

   JP46_Reader_camera JP4_INSTANCE=null;
@@ -310,9 +315,9 @@ private Panel panel1,panel2,panel3,panel4,panel5,panel5a, panel6,panel7,panelPos 
	    public String  buttonLabel="";

	}



   

	public Eyesis_Correction() {

		super("Eyesis_Correction");

	public void run(String arg) {

		String options=Macro.getOptions();

		prefsPath=Macro.getValue(options, "prefs", Prefs.getPrefsDir()+Prefs.getFileSeparator()+"Eyesis_Correction.xml");

		if (IJ.versionLessThan("1.43q")) return;

		if (instance!=null) {

			instance.toFront();
@@ -322,21 +327,36 @@ private Panel panel1,panel2,panel3,panel4,panel5,panel5a, panel6,panel7,panelPos 
			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);

		



		instance = this;

		addKeyListener(IJ.getInstance());

		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=(Frame)plugInFrame;

		plugInFrame.addKeyListener(IJ.getInstance());

		int menuRows=4 + (ADVANCED_MODE?4:0) + (MODE_3D?3:0);

		setLayout(new GridLayout(menuRows, 1));



		plugInFrame.setLayout(new GridLayout(menuRows, 1));

		panel6 = new Panel();

		panel6.setLayout(new GridLayout(1, 0, 5, 5));

		addButton("Save",panel6);
@@ -344,13 +364,13 @@ private Panel panel1,panel2,panel3,panel4,panel5,panel5a, panel6,panel7,panelPos 
		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);
@@ -358,7 +378,7 @@ private Panel panel1,panel2,panel3,panel4,panel5,panel5a, panel6,panel7,panelPos 
		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
@@ -368,13 +388,13 @@ private Panel panel1,panel2,panel3,panel4,panel5,panel5a, panel6,panel7,panelPos 
			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));
@@ -382,14 +402,14 @@ private Panel panel1,panel2,panel3,panel4,panel5,panel5a, panel6,panel7,panelPos 
			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));
@@ -402,7 +422,7 @@ private Panel panel1,panel2,panel3,panel4,panel5,panel5a, panel6,panel7,panelPos 
			addButton("Tiff Writer", panel7);

			addButton("Tiff Properties", panel7);

		}

		add(panel7);

		plugInFrame.add(panel7);

		

		if (MODE_3D){

			panelPostProcessing1 = new Panel();
@@ -412,7 +432,7 @@ private Panel panel1,panel2,panel3,panel4,panel5,panel5a, panel6,panel7,panelPos 
			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));
@@ -423,19 +443,19 @@ private Panel panel1,panel2,panel3,panel4,panel5,panel5a, panel6,panel7,panelPos 
			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);

		}

		pack();

		plugInFrame.pack();



		GUI.center(this);

		setVisible(true);

		GUI.center(plugInFrame);

		plugInFrame.setVisible(true);

		FHT_INSTANCE=       new DoubleFHT();

		SDFA_INSTANCE=      new showDoubleFloatArrays();

		// main loop
@@ -464,7 +484,6 @@ private Panel panel1,panel2,panel3,panel4,panel5,panel5a, panel6,panel7,panelPos 
		}



	}

	private String prefsPath=Prefs.getPrefsDir()+Prefs.getFileSeparator()+"Eyesis_Correction.xml";

    private Properties prefsProperties=new Properties();



    public void loadPrefs() throws IOException{
@@ -478,6 +497,8 @@ private Panel panel1,panel2,panel3,panel4,panel5,panel5a, panel6,panel7,panelPos 
    	}

    	try {

    		prefsProperties.loadFromXML(is);

    		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;
@@ -536,13 +557,6 @@ private Panel panel1,panel2,panel3,panel4,panel5,panel5a, panel6,panel7,panelPos 
		b.addKeyListener(IJ.getInstance());

		panel.add(b);

	}

	public void processWindowEvent(WindowEvent e) {

		super.processWindowEvent(e);

		if (e.getID()==WindowEvent.WINDOW_CLOSING) {

			instance = null;	

		}

	}



	public void actionPerformed(ActionEvent e) {

		String label = e.getActionCommand();

		if        (label.equals("Abort")) {
@@ -569,6 +583,70 @@ private Panel panel1,panel2,panel3,panel4,panel5,panel5a, panel6,panel7,panelPos 
		}

		//		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();
@@ -982,69 +1060,7 @@ private Panel panel1,panel2,panel3,panel4,panel5,panel5a, panel6,panel7,panelPos 
    	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")) {

src/main/java/JP46_Reader_camera.java

+28 −39
Original line number Diff line number Diff line
@@ -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 +76,31 @@ 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) {

		initGui(showGui);

	}



	public JP46_Reader_camera() {

		initGui(true);

	}



		add(panel1);

	private void initGui(Boolean showGui) {

		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();
@@ -124,12 +112,14 @@ 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) {

		Button b = new Button(label);

		b.addActionListener(this);
@@ -1318,10 +1308,9 @@ Exception in thread "Thread-3564" java.lang.ArrayIndexOutOfBoundsException: 8970 
	 * image and calls the plugin, e.g. after setting breakpoints.

	 * Grabbed from https://github.com/imagej/minimal-ij1-plugin

	 * @param args unused

	 */

	public static void main(String[] args) {

		// set the plugins.dir property to make the plugin appear in the Plugins menu

		Class<?> clazz = Aberration_Calibration.class;

		Class<?> clazz = JP46_Reader_camera.class;

		String url = clazz.getResource("/" + clazz.getName().replace('.', '/') + ".class").toString();

		String pluginsDir = url.substring(5, url.length() - clazz.getName().length() - 6);

		System.setProperty("plugins.dir", pluginsDir);
@@ -1330,7 +1319,7 @@ Exception in thread "Thread-3564" java.lang.ArrayIndexOutOfBoundsException: 8970 
		// run the plugin

		IJ.runPlugIn(clazz.getName(), "");

	}

    

*/

}