merged with lwir

src/main/java/JP46_Reader_camera0.java

@@ -55,6 +55,8 @@ import org.w3c.dom.NodeList;
 import org.xml.sax.InputSource;
 import org.xml.sax.SAXException;
 
+import com.elphel.imagej.readers.ImagejJp4Tiff;
+
 import ij.IJ;
 import ij.ImageJ;
 import ij.ImagePlus;
@@ -69,6 +71,7 @@ import ij.plugin.frame.PlugInFrame;
 import ij.process.ImageConverter;
 import ij.process.ImageProcessor;
 import ij.text.TextWindow;
+import loci.formats.FormatException;
 
 
 
@@ -87,6 +90,8 @@ public class JP46_Reader_camera0 extends PlugInFrame implements ActionListener {
 
 	static File dir;
 
+	ImagejJp4Tiff imagejJp4Tiff = new ImagejJp4Tiff();
+
 	public String camera_url = "http://192.168.0.236:8081/";
 	public String camera_img = "bimg";
 	public String camera_img_new = "towp/wait/bimg"; // will always wait for the next image (repetitive acquisitions get new images)
@@ -109,8 +114,9 @@ public class JP46_Reader_camera0 extends PlugInFrame implements ActionListener {
 
 		panel1 = new Panel();
 
-		panel1.setLayout(new GridLayout(6, 1, 50, 5));
+		panel1.setLayout(new GridLayout(8, 1, 50, 5));
 
+		addButton("Open JP4/Tiff...",panel1);
 		addButton("Open JP4/JP46...",panel1);
 		addButton("Open JP4/JP46 from camera",panel1);
 		addButton("Configure...",panel1);
@@ -137,8 +143,8 @@ public class JP46_Reader_camera0 extends PlugInFrame implements ActionListener {
 
 		panel1 = new Panel();
 
-		panel1.setLayout(new GridLayout(6, 1, 50, 5));
-
+		panel1.setLayout(new GridLayout(8, 1, 50, 5));
+		addButton("Open JP4/Tiff...",panel1);
 		addButton("Open JP4/JP46...",panel1);
 		addButton("Open JP4/JP46 from camera",panel1);
 		addButton("Configure...",panel1);
@@ -169,7 +175,11 @@ public class JP46_Reader_camera0 extends PlugInFrame implements ActionListener {
 		if (label==null) return;
 
 		/* button */
-		if (label.equals("Open JP4/JP46...")) {
+		if (label.equals("Open JP4/Tiff...")) {
+			read_jp4Tiff(arg,true);
+		}else if (label.equals("Open JP4/Tiff (no scale)...")) {
+			read_jp4Tiff(arg,false);
+		}else if (label.equals("Open JP4/JP46...")) {
 			read_jp46(arg,true);
 		}else if (label.equals("Open JP4/JP46 (no scale)...")) {
 			read_jp46(arg,false);
@@ -227,7 +237,54 @@ public class JP46_Reader_camera0 extends PlugInFrame implements ActionListener {
         imp_stack.getProcessor().resetMinAndMax();
         imp_stack.show();
     }
+	public void read_jp4Tiff(String arg, // not used?
+			boolean scale) {
+
+		String LOG_LEVEL = ABSOLUTELY_SILENT? "OFF" : (IS_SILENT?"ERROR":"INFO");
+    	boolean LOG_LEVEL_SET = loci.common.DebugTools.enableLogging(LOG_LEVEL);
+    	if (!LOG_LEVEL_SET) { // only first time true
+    		loci.common.DebugTools.setRootLevel(LOG_LEVEL);
+    	}
+
+		JFileChooser fc=null;
+		//try {fc = new JFileChooser();}
 
+		fc = new JFileChooser();
+
+		//catch (Throwable e) {IJ.error("This plugin requires Java 2 or Swing."); return;}
+		fc.setMultiSelectionEnabled(true);
+
+		if (dir==null) {
+			String sdir = OpenDialog.getDefaultDirectory();
+			if (sdir!=null)
+				dir = new File(sdir);
+		}
+		if (dir!=null)
+			fc.setCurrentDirectory(dir);
+
+		int returnVal = fc.showOpenDialog(IJ.getInstance());
+		if (returnVal!=JFileChooser.APPROVE_OPTION)
+			return;
+		File[] files = fc.getSelectedFiles();
+		if (files.length==0) { // getSelectedFiles does not work on some JVMs
+			files = new File[1];
+			files[0] = fc.getSelectedFile();
+		}
+		String path = fc.getCurrentDirectory().getPath()+Prefs.getFileSeparator();
+		dir = fc.getCurrentDirectory();
+		for (int i=0; i<files.length; i++) {
+			try {
+				ImagePlus imp = 	imagejJp4Tiff.readTiffJp4(path + files[i].getName(), scale);
+//				imp.updateAndDraw();
+				imp.show();
+			} catch (IOException | FormatException e) {
+				// TODO Auto-generated catch block
+				e.printStackTrace();
+			} // throws IOException, FormatException { // std - include non-elphel properties with prefix std
+//			open(path, files[i].getName(), arg, scale);
+		}
+
+	}
 	public void read_jp46(String arg, boolean scale) {
 		JFileChooser fc=null;
 		//try {fc = new JFileChooser();}
@@ -274,6 +331,7 @@ public class JP46_Reader_camera0 extends PlugInFrame implements ActionListener {
 
 		confpanel = new Panel();
 		gd.addPanel(confpanel);
+		addButton("Open JP4/Tiff (no scale)...", confpanel);
 		addButton("Open JP4/JP46 (no scale)...", confpanel);
 		addButton("Open JP4/JP46 from camera (no scale)", confpanel);
 
@@ -1413,9 +1471,13 @@ Exception in thread "Thread-3564" java.lang.ArrayIndexOutOfBoundsException: 8970
 	    NodeList allNodes=doc.getDocumentElement().getElementsByTagName("*");
 	    for (int i=0;i<allNodes.getLength();i++) {
 	        String name= allNodes.item(i).getNodeName();
-            String value=allNodes.item(i).getFirstChild().getNodeValue();
-    		imp.setProperty(name, value);
+	        String value="";
+	        try {
+	        	value=allNodes.item(i).getFirstChild().getNodeValue();
+	        } catch(Exception e) {
 
+	        }
+    		imp.setProperty(name, value);
 	    }
 
 		return true;

src/main/java/com/elphel/imagej/calibration/DistortionProcessConfiguration.java

@@ -6,7 +6,7 @@ package com.elphel.imagej.calibration;
  ** Copyright (C) 2011-2014 Elphel, Inc.
  **
  ** -----------------------------------------------------------------------------**
- **  
+ **
  **  DistortionProcessConfiguration.java is free software: you can redistribute it and/or modify
  **  it under the terms of the GNU General Public License as published by
  **  the Free Software Foundation, either version 3 of the License, or
@@ -23,16 +23,17 @@ package com.elphel.imagej.calibration;
  **
  */
 
-import ij.IJ;
-import ij.Prefs;
-import ij.gui.GenericDialog;
-
 import java.io.File;
+import java.io.FilenameFilter;
 import java.util.Properties;
 
 import com.elphel.imagej.common.WindowTools;
 
-    
+import ij.IJ;
+import ij.Prefs;
+import ij.gui.GenericDialog;
+
+
     public class DistortionProcessConfiguration{
     	public String  sourceDirectory="";
     	public String  gridDirectory=  "";
@@ -50,7 +51,7 @@ import com.elphel.imagej.common.WindowTools;
     	public String selectSourceDirectory(boolean smart, String defaultPath, boolean newAllowed) {
     		String dir= CalibrationFileManagement.selectDirectory(
     				smart,
-    				newAllowed, // save  
+    				newAllowed, // save
     				"Source (acquired from the camera) image directory", // title
     				"Select source directory", // button
     				null, // filter
@@ -61,7 +62,7 @@ import com.elphel.imagej.common.WindowTools;
     	public String selectGridFileDirectory(boolean smart, String defaultPath, boolean newAllowed) {
     		String dir= CalibrationFileManagement.selectDirectory(
     				smart,
-    				newAllowed, // save  
+    				newAllowed, // save
     				"Grid files directory (grid patterns extracted from the images)", // title
     				"Select grid files directory", // button
     				null, // filter
@@ -69,7 +70,7 @@ import com.elphel.imagej.common.WindowTools;
     		if (dir!=null) this.gridDirectory=dir;
     		return dir;
     	}
-    	
+
     	public void setProperties(String prefix,Properties properties){
     		properties.setProperty(prefix+"sourceDirectory",        this.sourceDirectory);
     		properties.setProperty(prefix+"gridDirectory",          this.gridDirectory);
@@ -123,9 +124,9 @@ import com.elphel.imagej.common.WindowTools;
     		gd.addCheckbox   ("Show grid files as images",            this.showGridImages);
     		gd.addCheckbox   ("Save grid files",                      this.saveGridImages);
     		gd.addCheckbox   ("Overwrite existing result files",      this.overwriteResultFiles);
-    		
-    		
-    		
+
+
+
     		gd.addNumericField("Debug level",                         this.debugLevel,0);
     	    WindowTools.addScrollBars(gd);
     	    gd.showDialog();
@@ -144,7 +145,7 @@ import com.elphel.imagej.common.WindowTools;
     	    this.debugLevel=       (int) gd.getNextNumber();
     	    System.out.println("1.newSourceDirectory = "+newSourceDirectory);
     	    System.out.println("1.newGridDirectory = "+  newGridDirectory);
-    	    if ((newSourceDirectory.length()==0) || (newSourceDirectory.indexOf('?')>=0)) 
+    	    if ((newSourceDirectory.length()==0) || (newSourceDirectory.indexOf('?')>=0))
     	    	newSourceDirectory= selectSourceDirectory(false, this.sourceDirectory, true);
     	    else
     	    	newSourceDirectory= selectSourceDirectory(true, newSourceDirectory, true); // if matches, no dialog
@@ -174,7 +175,7 @@ import com.elphel.imagej.common.WindowTools;
 			if (this.sourceDirectory.length()==0){
 				defaultPaths[0]="";
 			}
-			
+
 			CalibrationFileManagement.MultipleExtensionsFileFilter sourceFilter =
 				new CalibrationFileManagement.MultipleExtensionsFileFilter("",extensions,"Source files");
 			String [] sourceFiles=null;
@@ -206,5 +207,26 @@ import com.elphel.imagej.common.WindowTools;
     		}
 	       	return sourceFiles;
     	}
-    	
+
+        public String[] selectSourceSets() {
+			File dir= new File (this.sourceDirectory);
+			if (this.debugLevel>1) System.out.println("selectSourceSets, dir="+this.sourceDirectory);
+			if (!dir.exists()) {
+				String error="Source directory "+this.sourceDirectory+" does not exist.";
+        		IJ.showMessage("No files selected");
+				if (this.debugLevel>1) System.out.println("selectSourceFiles() ERROR:"+error);
+				return null;
+			}
+			File [] sourceFileSets = dir.listFiles(new FilenameFilter() {
+			  @Override
+			  public boolean accept(File current, String name) {
+			    return new File(current, name).isDirectory();
+			  }
+			});
+			String [] sourceSets = new String[sourceFileSets.length];
+			for (int i=0;i<sourceSets.length;i++) sourceSets[i]=sourceFileSets[i].getPath();
+			return sourceSets;
+        }
+
     }
+

src/main/java/com/elphel/imagej/calibration/Goniometer.java

@@ -665,9 +665,12 @@ horizontal axis:
 
 		boolean noMessageBoxes=true;
 		int numAbsolutePoints = matchSimulatedPattern.calculateDistortions(
+				        null, // LwirReaderParameters lwirReaderParameters, // null is OK
 						// allow more of grid around pointers?
 						distortionParameters, //
 						this.patternDetectParameters,
+//						this.patternDetectParameters.minGridPeriod/2,
+//						this.patternDetectParameters.maxGridPeriod/2,
 						simulParameters,
 						equalizeGreens, imp_eq,
 						this.laserPointers, // null, //LASER_POINTERS, //
@@ -838,23 +841,26 @@ horizontal axis:
 //	matchSimulatedPatterns[numSensor].getChannel(images[numSensor])+" ");
 
 				int numAbsolutePoints = this.matchSimulatedPatterns[numSensor].calculateDistortions(
-								// allow more of grid around pointers?
-								distortionParameters, //
-								this.patternDetectParameters,
-								simulParameters,
-								equalizeGreens, imp_eq,
-								this.laserPointers, // null, //LASER_POINTERS, //
-												// LaserPointer laserPointer, //
-												// LaserPointer object or null
-								true, // don't care -removeOutOfGridPointers
-								null, //   double [][][] hintGrid, // predicted grid array (or null)
-								0,    //   double  hintGridTolerance, // allowed mismatch (fraction of period) or 0 - orientation only
-
-								threadsMax,
-								updateStatus,
-								debug_level,
-								distortionParameters.loop_debug_level, // debug level
-								noMessageBoxes);
+						null, // LwirReaderParameters lwirReaderParameters, // null is OK
+						// allow more of grid around pointers?
+						distortionParameters, //
+						this.patternDetectParameters,
+//						this.patternDetectParameters.minGridPeriod/2,
+//						this.patternDetectParameters.maxGridPeriod/2,
+						simulParameters,
+						equalizeGreens, imp_eq,
+						this.laserPointers, // null, //LASER_POINTERS, //
+						// LaserPointer laserPointer, //
+						// LaserPointer object or null
+						true, // don't care -removeOutOfGridPointers
+						null, //   double [][][] hintGrid, // predicted grid array (or null)
+						0,    //   double  hintGridTolerance, // allowed mismatch (fraction of period) or 0 - orientation only
+
+						threadsMax,
+						updateStatus,
+						debug_level,
+						distortionParameters.loop_debug_level, // debug level
+						noMessageBoxes);
 				if (numAbsolutePoints <= 0) { // no pointers in this image
 					String msg = "*** No laser pointers matched for " + images[numSensor].getTitle() + " - they are needed for absolute grid positioning";
 					if (debug_level > 0) System.out.println("Warning: " + msg);

src/main/java/com/elphel/imagej/common/ShowDoubleFloatArrays.java

@@ -112,6 +112,30 @@ import ij.process.ImageProcessor;
 	      return;
 	    } else showArrays(pixels, width, height, titles);
 	  }
+  public void showComplex(double[][][] cpixels, String title) {
+	  int height = cpixels.length;
+	  int width =  cpixels[0].length;
+	  double [][]pixels = new double [height*width][];
+	  int indx = 0;
+	  for (int y = 0; y < height; y++) {
+		  for (int x = 0; x < width; x++) {
+			  pixels[indx++] = cpixels[y][x];
+		  }
+	  }
+	  showComplex(pixels, width, title);
+  }
+  public void showComplex(double[][] cpixels, int width, String title) {
+	  int height = cpixels.length/width;
+	  double [][]pixels = new double [2][cpixels.length];
+	  for (int i = 0; i< cpixels.length; i++) {
+		  pixels[0][i]= cpixels[i][0];
+		  pixels[1][i]= cpixels[i][1];
+	  }
+	  String [] titles = {"Re", "Im"};
+	  showArrays(pixels, width, height,  true, title, titles);
+  }
+
+
 
   public void showArrays(float[][] pixels, int width, int height,  boolean asStack, String title, String [] titles) {
 	    int i,j;

src/main/java/com/elphel/imagej/jp4/JP46_Reader_camera.java

@@ -1358,7 +1358,11 @@ Exception in thread "Thread-3564" java.lang.ArrayIndexOutOfBoundsException: 8970
 			itr=set.iterator();
 			while(itr.hasNext()) {
 				str = (String) itr.next();
-				imp_dst.setProperty(str,prop.getProperty(str));
+				try {
+					imp_dst.setProperty(str,prop.getProperty(str));
+				} catch (Exception e) {
+					imp_dst.setProperty(str,"");
+				}
 			}
 		}
 	}
@@ -1407,7 +1411,12 @@ Exception in thread "Thread-3564" java.lang.ArrayIndexOutOfBoundsException: 8970
 	    NodeList allNodes=doc.getDocumentElement().getElementsByTagName("*");
 	    for (int i=0;i<allNodes.getLength();i++) {
 	        String name= allNodes.item(i).getNodeName();
-            String value=allNodes.item(i).getFirstChild().getNodeValue();
+	        String value="";
+	        try {
+	        	value=allNodes.item(i).getFirstChild().getNodeValue();
+	        } catch(Exception e) {
+
+	        }
     		imp.setProperty(name, value);
 
 	    }

src/main/java/com/elphel/imagej/readers/EyesisTiff.java

@@ -640,7 +640,7 @@ the type of pixel data in this file 	getPixelType()
 	}
 
 // copied from JP46_Reader_camera.java
-	public ImagePlus encodeProperiesToInfo(ImagePlus imp){
+	public static ImagePlus encodeProperiesToInfo(ImagePlus imp){
 		String info="<?xml version=\"1.0\" encoding=\"UTF-8\"?><properties>";
 		Set<Object> jp4_set;
 		Properties jp4_prop;
@@ -661,7 +661,7 @@ the type of pixel data in this file 	getPixelType()
 		return imp;
 	}
 
-	public boolean decodeProperiesFromInfo(ImagePlus imp){
+	public static  boolean decodeProperiesFromInfo(ImagePlus imp){
 		if (imp.getProperty("Info")==null) return false;
 		String xml= (String) imp.getProperty("Info");
 
@@ -684,11 +684,15 @@ the type of pixel data in this file 	getPixelType()
 	    NodeList allNodes=doc.getDocumentElement().getElementsByTagName("*");
 	    for (int i=0;i<allNodes.getLength();i++) {
 	        String name= allNodes.item(i).getNodeName();
-            String value=allNodes.item(i).getFirstChild().getNodeValue();
-    		imp.setProperty(name, value);
-
+//            System.out.print(name+" -> ");
+            String value = "";
+            try {
+            	value=allNodes.item(i).getFirstChild().getNodeValue();
+            } catch (Exception e) {
+            }
+//            System.out.println(value);
+            imp.setProperty(name, value);
 	    }
-
 		return true;
 	}