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imagej-elphel
Commit ace015f7 authored by Luc Deschenaux's avatar Luc Deschenaux
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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
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Showing with 142 additions and 137 deletions
src/main/java/Eyesis_Correction.java
View file @ ace015f7
......@@ -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;
......@@ -309,10 +314,10 @@ private Panel panel1,panel2,panel3,panel4,panel5,panel5a, panel6,panel7,panelPos
public AtomicInteger stopRequested= new AtomicInteger(0); // 0 - not requested, 1 - ASAP, 2 - gracefully
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;
......@@ -490,7 +511,7 @@ private Panel panel1,panel2,panel3,panel4,panel5,panel5a, panel6,panel7,panelPos
// 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);
......@@ -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
View file @ ace015f7
......@@ -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;
......@@ -72,47 +73,34 @@ public class JP46_Reader_camera extends PlugInFrame implements ActionListener {
public String camera_jp46settings = "";
public boolean IS_SILENT=true;
public boolean ABSOLUTELY_SILENT=false;
public boolean demux=true;
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;
}
instance = this;
addKeyListener(IJ.getInstance());
panel1 = new Panel();
public void run(String arg) {
}
panel1.setLayout(new GridLayout(6, 1, 50, 5));
public JP46_Reader_camera(Boolean showGui) {
initGui(showGui);
}
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() {
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(), "");
}
*/
}
......
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