fixing configuration and missing clt directory creation (484ec936) · Commits · Elphel / imagej-elphel

src/main/java/EyesisCorrectionParameters.java

+555 −550

src/main/java/Eyesis_Correction.java

+611 −577

Original line number	Original line	Diff line number	Diff line
	@@ -25,17 +25,15 @@
	**		**
	*/		*/

	import ij.*;		import java.awt.Button;
	import ij.process.*;		import java.awt.Color;
	import ij.gui.*;		import java.awt.Frame;
	import ij.io.FileInfo;		import java.awt.GridLayout;
	import ij.io.FileSaver;		import java.awt.Panel;
	import ij.io.OpenDialog;		import java.awt.Rectangle;
	import ij.io.Opener;		import java.awt.event.ActionEvent;
	import ij.plugin.frame.*;		import java.awt.event.ActionListener;
			import java.awt.event.WindowEvent;
	import java.awt.*;
	import java.awt.event.*;
	import java.io.File;		import java.io.File;
	import java.io.FileInputStream;		import java.io.FileInputStream;
	import java.io.FileNotFoundException;		import java.io.FileNotFoundException;
	@@ -53,6 +51,26 @@ import java.util.concurrent.atomic.AtomicInteger;
	import javax.swing.JFileChooser;		import javax.swing.JFileChooser;
	import javax.swing.filechooser.FileFilter;		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.DependencyException;
	import loci.common.services.ServiceException;		import loci.common.services.ServiceException;
	import loci.formats.FormatException;		import loci.formats.FormatException;
	@@ -662,6 +680,7 @@ private Panel panel1,
	b.addKeyListener(IJ.getInstance());		b.addKeyListener(IJ.getInstance());
	panel.add(b);		panel.add(b);
	}		}
			@Override
	public void processWindowEvent(WindowEvent e) {		public void processWindowEvent(WindowEvent e) {
	super.processWindowEvent(e);		super.processWindowEvent(e);
	if (e.getID()==WindowEvent.WINDOW_CLOSING) {		if (e.getID()==WindowEvent.WINDOW_CLOSING) {
	@@ -669,6 +688,7 @@ private Panel panel1,
	}		}
	}		}

			@Override
	public void actionPerformed(ActionEvent e) {		public void actionPerformed(ActionEvent e) {
	String label = e.getActionCommand();		String label = e.getActionCommand();
	if (label.equals("Abort")) {		if (label.equals("Abort")) {
	@@ -2633,7 +2653,7 @@ private Panel panel1,


	for (int ii = 0; ii<n; ii++) {		for (int ii = 0; ii<n; ii++) {
	dindex[ii] = (double) ii;		dindex[ii] = ii;
	x[ii] = 0.0;		x[ii] = 0.0;
	}		}
	// x[1] = 1.0;		// x[1] = 1.0;
	@@ -4146,6 +4166,15 @@ private Panel panel1,
	return;		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);		EYESIS_CORRECTIONS.initSensorFiles(DEBUG_LEVEL);

	@@ -5288,6 +5317,7 @@ private Panel panel1,
	public MultipleExtensionsFileFilter (String [] patterns) {		public MultipleExtensionsFileFilter (String [] patterns) {
	this.patterns=patterns.clone();		this.patterns=patterns.clone();
	}		}
			@Override
	public boolean accept (File file) {		public boolean accept (File file) {
	int i;		int i;
	String name=file.getName();		String name=file.getName();
	@@ -5297,6 +5327,7 @@ private Panel panel1,
	}		}
	return false;		return false;
	}		}
			@Override
	public String getDescription() {		public String getDescription() {
	return description;		return description;
	}		}
	@@ -6617,6 +6648,7 @@ private Panel panel1,
	final long startTime = System.nanoTime();		final long startTime = System.nanoTime();
	for (int ithread = 0; ithread < threads.length; ithread++) {		for (int ithread = 0; ithread < threads.length; ithread++) {
	threads[ithread] = new Thread() {		threads[ithread] = new Thread() {
			@Override
	public void run() {		public void run() {
	float [] pixels=null; // will be initialized at first use		float [] pixels=null; // will be initialized at first use
	float [] kernelPixels=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();		final long startTime = System.nanoTime();
	for (int ithread = 0; ithread < threads.length; ithread++) {		for (int ithread = 0; ithread < threads.length; ithread++) {
	threads[ithread] = new Thread() {		threads[ithread] = new Thread() {
			@Override
	public void run() {		public void run() {
	double [][] tile= new double[nChn][debayerParameters.size * debayerParameters.size ];		double [][] tile= new double[nChn][debayerParameters.size * debayerParameters.size ];
	double [][] both_masks;		double [][] both_masks;
	@@ -7006,6 +7039,7 @@ private Panel panel1,
	final long startTime = System.nanoTime();		final long startTime = System.nanoTime();
	for (int ithread = 0; ithread < threads.length; ithread++) {		for (int ithread = 0; ithread < threads.length; ithread++) {
	threads[ithread] = new Thread() {		threads[ithread] = new Thread() {
			@Override
	public void run() {		public void run() {
	double [] tile= new double[size * size ];		double [] tile= new double[size * size ];
	int tileY,tileX;		int tileY,tileX;

src/main/java/QuadCLT.java

+1 −1

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

Original line number	Original line	Diff line number	Diff line
	@@ -25,17 +25,15 @@
	**		**
	*/		*/

	import ij.IJ;
	import ij.Prefs;
	import ij.gui.GenericDialog;

	import java.io.File;		import java.io.File;
	import java.util.ArrayList;
	import java.util.Enumeration;
	import java.util.HashMap;		import java.util.HashMap;
	import java.util.Properties;		import java.util.Properties;
	import java.util.Set;		import java.util.Set;

			import ij.IJ;
			import ij.Prefs;
			import ij.gui.GenericDialog;


	public class EyesisCorrectionParameters {		public class EyesisCorrectionParameters {
	public static class CorrectionParameters{		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+"equirectangularSuffix")!=null) this.equirectangularSuffix=properties.getProperty(prefix+"equirectangularSuffix");

	if (properties.getProperty(prefix+"equirectangularCut")!=null)		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+"equirectangularSuffixA")!=null) this.equirectangularSuffixA=properties.getProperty(prefix+"equirectangularSuffixA");

	if (properties.getProperty(prefix+"planeMapPrefix")!=null) this.planeMapPrefix=properties.getProperty(prefix+"planeMapPrefix");		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+"planeMapSuffix")!=null) this.planeMapSuffix=properties.getProperty(prefix+"planeMapSuffix");
	if (properties.getProperty(prefix+"usePlaneProjection")!=null)		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)		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+"resultsDirectory")!= null) this.resultsDirectory=properties.getProperty(prefix+"resultsDirectory");
	if (properties.getProperty(prefix+"removeUnusedSensorData")!= null)		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){		if (properties.getProperty(prefix+"sourcePaths")!= null){
	int numFiles=Integer.parseInt(properties.getProperty(prefix+"sourcePaths"));		int numFiles=Integer.parseInt(properties.getProperty(prefix+"sourcePaths"));

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