Implemented saving parameters with the model version, fixed bugs

src/main/java/com/elphel/imagej/cameras/CLTParameters.java

@@ -504,7 +504,7 @@ public class CLTParameters {
 	public double     gmap_discard_rdisp =   0.02;  // discard above/below this fraction of average height
 	public double     gmap_pix_size =        0.005; // hdr_x0y0,       // in meters
 	public int        gmap_max_image_width = 4000;  // 3200;  // increase pixel size as a power of 2 until image fits
-	public double     gmap_min_sfm =         10.0;  // minimal SfM gain to keep ground map
+	public double     gmap_min_sfm =         2.0;   //10.0;  // minimal SfM gain to keep ground map
 	public double     gmap_frac_sfm =        0.25;  // Disregard SfM mask if lower good SfM area
 	public boolean    gmap_crop_empty =      true;
 	public int        gmap_crop_extra =      20;

src/main/java/com/elphel/imagej/correction/Eyesis_Correction.java

@@ -436,7 +436,8 @@ public class Eyesis_Correction implements PlugIn, ActionListener {
 	public static int CONVOLVE_FFT_SIZE = 128; // FFT size for sliding convolution with kernel
 	public static int THREADS_MAX = 100; // testing multi-threading, limit maximal number of threads
 
-	public double GAUSS_WIDTH = 0.4; // 0 - use Hamming window
+///	public double GAUSS_WIDTH = 0.4; // 0 - use Hamming window
+	public static double GAUSS_WIDTH = 0.4; // 0 - use Hamming window
 
 	/* replace */
 	public static int PSF_SUBPIXEL_SHOULD_BE_4 = 4; // sub-pixel decimation
@@ -1595,7 +1596,12 @@ public class Eyesis_Correction implements PlugIn, ActionListener {
 			if (label.equals("Save Clean")) {
 				PROPERTIES = new Properties();
 			}
-			saveProperties(null, CORRECTION_PARAMETERS.resultsDirectory, true, PROPERTIES, DEBUG_LEVEL);
+			saveProperties(
+					null,
+					CORRECTION_PARAMETERS.resultsDirectory,
+					true,
+					PROPERTIES,
+					DEBUG_LEVEL);
 			return;
 			/* ======================================================================== */
 		} else if (label.equals("Save offset")) {
@@ -9273,15 +9279,26 @@ public class Eyesis_Correction implements PlugIn, ActionListener {
 		return selectDirectoryOrFile(save, false, title, button, filter, defaultPath);
 	}
 
-	public String selectFile(boolean save, String title, String button, FileFilter filter, String defaultPath) {
-		return selectDirectoryOrFile(save, false, title, button, filter, defaultPath);
+	public static String selectFile(
+			boolean save,
+			String title,
+			String button,
+			FileFilter filter,
+			String defaultPath) {
+		return selectDirectoryOrFile(
+				save,
+				false,
+				title,
+				button,
+				filter,
+				defaultPath);
 	}
 
-	public String[] selectFiles(boolean save, String title, String button, FileFilter filter, String[] defaultPaths) {
+	public static String[] selectFiles(boolean save, String title, String button, FileFilter filter, String[] defaultPaths) {
 		return selectDirectoriesOrFiles(save, false, title, button, filter, defaultPaths);
 	}
 
-	public String[] selectDirectoriesOrFiles(boolean save, boolean directory, String title, String button,
+	public static String[] selectDirectoriesOrFiles(boolean save, boolean directory, String title, String button,
 			FileFilter filter, String[] defaultPaths) {
 		File dir = null;
 		String defaultPath = null;
@@ -9352,7 +9369,7 @@ public class Eyesis_Correction implements PlugIn, ActionListener {
 		return filenames;
 	}
 
-	public String selectDirectoryOrFile(boolean save, boolean directory, String title, String button, FileFilter filter,
+	public static String selectDirectoryOrFile(boolean save, boolean directory, String title, String button, FileFilter filter,
 			String defaultPath) {
 		File dir = null;
 		if ((defaultPath != null) && (!defaultPath.equals(""))) {
@@ -9392,7 +9409,7 @@ public class Eyesis_Correction implements PlugIn, ActionListener {
 		DEFAULT_DIRECTORY = fc.getCurrentDirectory().getPath();
 		return fc.getSelectedFile().getPath();
 	}
-
+/*
 	class MultipleExtensionsFileFilter extends FileFilter {
 		protected String[] patterns;
 		protected String description = "JP4 files";
@@ -9424,10 +9441,10 @@ public class Eyesis_Correction implements PlugIn, ActionListener {
 			return description;
 		}
 	}
-
+*/
 	/* ======================================================================== */
 
-	private boolean fixSliceSequence(ImageStack stack) {
+	private static boolean fixSliceSequence(ImageStack stack) {
 		int i, j;
 		int[] rgbNumbers = { 0, 0, 0 };
 		for (j = 0; j < 3; j++) {
@@ -9474,7 +9491,7 @@ public class Eyesis_Correction implements PlugIn, ActionListener {
 	}
 
 	/* ======================================================================== */
-	public void swapStackSlices(ImageStack stack, int slice1, int slice2) {
+	public static void swapStackSlices(ImageStack stack, int slice1, int slice2) {
 		String label = stack.getSliceLabel(slice1);
 		stack.setSliceLabel(stack.getSliceLabel(slice2), slice1);
 		stack.setSliceLabel(label, slice2);
@@ -9484,7 +9501,7 @@ public class Eyesis_Correction implements PlugIn, ActionListener {
 	}
 
 	/* ======================================================================== */
-	public ImageStack cropStack32(ImageStack stack, EyesisCorrectionParameters.SplitParameters splitParameters) {
+	public static ImageStack cropStack32(ImageStack stack, EyesisCorrectionParameters.SplitParameters splitParameters) {
 		int size = stack.getSize();
 		int iWidth = stack.getWidth();
 		int height = stack.getHeight() - splitParameters.addTop - splitParameters.addBottom;
@@ -9509,7 +9526,7 @@ public class Eyesis_Correction implements PlugIn, ActionListener {
 	}
 
 	/* ======================================================================== */
-	public ImageStack rotateStack32CW(ImageStack stack) {
+	public static ImageStack rotateStack32CW(ImageStack stack) {
 		int size = stack.getSize();
 		int height = stack.getHeight();
 		int width = stack.getWidth();
@@ -9532,7 +9549,7 @@ public class Eyesis_Correction implements PlugIn, ActionListener {
 	}
 
 	/* ======================================================================== */
-	public ImagePlus cropImage32(ImagePlus imp, EyesisCorrectionParameters.SplitParameters splitParameters) {
+	public static ImagePlus cropImage32(ImagePlus imp, EyesisCorrectionParameters.SplitParameters splitParameters) {
 		int iWidth = imp.getWidth();
 		int height = imp.getHeight() - splitParameters.addTop - splitParameters.addBottom;
 		int width = imp.getWidth() - splitParameters.addLeft - splitParameters.addRight;
@@ -9552,7 +9569,7 @@ public class Eyesis_Correction implements PlugIn, ActionListener {
 	}
 
 	/* ======================================================================== */
-	public ImagePlus rotateImage32CW(ImagePlus imp) {
+	public static ImagePlus rotateImage32CW(ImagePlus imp) {
 		int width = imp.getWidth();
 		int height = imp.getHeight();
 		int length = width * height;
@@ -9569,7 +9586,7 @@ public class Eyesis_Correction implements PlugIn, ActionListener {
 	}
 
 	/* ======================================================================== */
-	public CompositeImage convertToComposite(ImagePlus imp) {
+	public static CompositeImage convertToComposite(ImagePlus imp) {
 //	  if (imp.isComposite()) return imp;
 		if (imp.isComposite())
 			return null;
@@ -9585,7 +9602,7 @@ public class Eyesis_Correction implements PlugIn, ActionListener {
 	}
 
 	/* ======================================================================== */
-	public ImageStack convertRGB32toRGB16Stack(ImageStack stack32,
+	public static ImageStack convertRGB32toRGB16Stack(ImageStack stack32,
 			EyesisCorrectionParameters.RGBParameters rgbParameters) {
 		ImageStack stack16 = new ImageStack(stack32.getWidth(), stack32.getHeight());
 		int length = stack32.getWidth() * stack32.getHeight();
@@ -9619,7 +9636,7 @@ public class Eyesis_Correction implements PlugIn, ActionListener {
 
 	}
 
-	public ImagePlus convertRGB48toRGB24(ImageStack stack16, String title, int r_min, int r_max, int g_min, int g_max,
+	public static ImagePlus convertRGB48toRGB24(ImageStack stack16, String title, int r_min, int r_max, int g_min, int g_max,
 			int b_min, int b_max, int alpha_min, int alpha_max) {
 		int[] mins = { r_min, g_min, b_min, alpha_min };
 		int[] maxs = { r_max, g_max, b_max, alpha_max };
@@ -9655,7 +9672,7 @@ public class Eyesis_Correction implements PlugIn, ActionListener {
 	}
 
 	/* ======================================================================== */
-	public ImagePlus Image32toGreyRGB24(ImagePlus imp) {
+	public static ImagePlus Image32toGreyRGB24(ImagePlus imp) {
 		int width = imp.getWidth();
 		int height = imp.getHeight();
 		int length = width * height;
@@ -9684,7 +9701,7 @@ public class Eyesis_Correction implements PlugIn, ActionListener {
 	}
 
 	/* ======================================================================== */
-	public void saveTimestampedProperties(String path, // full path or null
+	public static void saveTimestampedProperties(String path, // full path or null
 			String directory, // use as default directory if path==null
 			boolean useXML, Properties properties) {
 		if (path == null) {
@@ -9701,7 +9718,8 @@ public class Eyesis_Correction implements PlugIn, ActionListener {
 
 	}
 
-	public void saveProperties(String path, // full path or null
+	public static void saveProperties(
+			String path, // full path or null
 			String     directory, // use as default directory if path==null
 			boolean    useXML,
 			Properties properties,
@@ -9709,13 +9727,15 @@ public class Eyesis_Correction implements PlugIn, ActionListener {
 		String[] XMLPatterns = { ".corr-xml", ".xml" };
 		String[] confPatterns = { ".conf" };
 		String[] patterns = useXML ? XMLPatterns : confPatterns;
+		String ext = (useXML ? "XML " : "") + "Configuration files (" + (useXML ? "*.corr-xml" : "*.conf")
+				+ ")";
+		MultipleExtensionsFileFilter filter = new MultipleExtensionsFileFilter(patterns, ext); // filter
+
 		if (path == null) {
 			path = selectFile(true, // save
 					"Save configuration selection", // title
 					"Select configuration file", // button
-					new MultipleExtensionsFileFilter(patterns,
-							(useXML ? "XML " : "") + "Configuration files (" + (useXML ? "*.corr-xml" : "*.conf")
-									+ ")"), // filter
+					filter, // filter
 					directory); // may be ""
 		} else
 			path += patterns[0];
@@ -9898,7 +9918,7 @@ public class Eyesis_Correction implements PlugIn, ActionListener {
 	
 	
 	/* ======================================================================== */
-	public void setAllProperties(Properties properties) {
+	public static void setAllProperties(Properties properties) {
 		properties.setProperty("MASTER_DEBUG_LEVEL", MASTER_DEBUG_LEVEL + "");
 		properties.setProperty("UPDATE_STATUS", UPDATE_STATUS + "");
 		SPLIT_PARAMETERS.setProperties("SPLIT_PARAMETERS.", properties);
@@ -9937,7 +9957,7 @@ public class Eyesis_Correction implements PlugIn, ActionListener {
 	}
 
 	/* ======================================================================== */
-	public void getAllProperties(Properties properties) {
+	public static void getAllProperties(Properties properties) {
 		MASTER_DEBUG_LEVEL = Integer.parseInt(properties.getProperty("MASTER_DEBUG_LEVEL"));
 		UPDATE_STATUS = Boolean.parseBoolean(properties.getProperty("UPDATE_STATUS"));
 		SPLIT_PARAMETERS.getProperties("SPLIT_PARAMETERS.", properties);

src/main/java/com/elphel/imagej/correction/MultipleExtensionsFileFilter.java

+package com.elphel.imagej.correction;
+
+import java.io.File;
+
+import javax.swing.filechooser.FileFilter;
+
+public class MultipleExtensionsFileFilter extends FileFilter {
+	protected String[] patterns;
+	protected String description = "JP4 files";
+
+	public MultipleExtensionsFileFilter(String[] patterns, String description) {
+		this.description = description;
+		this.patterns = patterns.clone();
+	}
+
+	public MultipleExtensionsFileFilter(String[] patterns) {
+		this.patterns = patterns.clone();
+	}
+
+	@Override
+	public boolean accept(File file) {
+		int i;
+		String name = file.getName();
+		if (file.isDirectory())
+			return true;
+		for (i = 0; i < patterns.length; i++) {
+			if (name.toLowerCase().endsWith(patterns[i].toLowerCase()))
+				return true;
+		}
+		return false;
+	}
+
+	@Override
+	public String getDescription() {
+		return description;
+	}
+}
+

src/main/java/com/elphel/imagej/tileprocessor/ErsCorrection.java

@@ -1075,7 +1075,7 @@ public class ErsCorrection extends GeometryCorrection {
 		System.arraycopy(deltas0, 0, deltas, 0,              deltas0.length);
 		System.arraycopy(deltas0, 3, deltas, deltas0.length, deltas0.length - 3);
 		for (int i = 0; i < deltas.length; i++) deltas[i] *= scale_delta;
-	    int dbg_tile = 7508; // 56:23 // 16629;
+	    int dbg_tile = -7508; // 56:23 // 16629;
 	    ErsCorrection scene_ers = scene_QuadClt.getErsCorrection();
 		TileProcessor tp = reference_QuadClt.getTileProcessor();
 		int tilesX = tp.getTilesX();

src/main/java/com/elphel/imagej/tileprocessor/IntersceneMatchParameters.java

@@ -65,7 +65,7 @@ public class IntersceneMatchParameters {
 	
 	public  boolean sfm_use =            true;   // use SfM to improve depth map
 	public  double  sfm_min_base =       0.6;    // 2.0;    // use SfM if baseline exceeds this
-	public  double  sfm_min_gain =       3.0;    // 5.0;    // Minimal SfM gain to apply SfM to the depth map
+	public  double  sfm_min_gain =       2.0;    // 5.0;    // Minimal SfM gain to apply SfM to the depth map
 	public  double  sfm_min_frac =       0.5;    // Minimal fraction of defined tiles to have SfM correction
 	
     public  int     sfm_num_pairs =     32;      // desired number of SfM pairs to average

src/main/java/com/elphel/imagej/tileprocessor/OpticalFlow.java

@@ -6492,6 +6492,17 @@ public class OpticalFlow {
 			start_ref_pointers[0] = earliest_scene;
 			start_ref_pointers[1] = ref_index;
 		}
+		// temporary fix save/restore linkedModels, sourceDirectory, sourcePaths
+		// that are copied main-> aux in EyesisCorrectionParameters.updateAuxFromMain()
+		// quadCLT_main.correctionsParameters
+		String bkp_linkedModels = quadCLT_main.correctionsParameters.linkedModels;
+		String bkp_sourceDirectory =  quadCLT_main.correctionsParameters.sourceDirectory;
+		String [] bkp_sourcePaths =   quadCLT_main.correctionsParameters.sourcePaths;
+		quadCLTs[ref_index].saveConfInModelDirectory(); // save all (global) configurations in model/version directory
+		quadCLT_main.correctionsParameters.linkedModels =    bkp_linkedModels;
+		quadCLT_main.correctionsParameters.sourceDirectory = bkp_sourceDirectory;
+		quadCLT_main.correctionsParameters.sourcePaths =     bkp_sourcePaths;
+		
 		System.out.println("buildSeries(): DONE"); //
 		return quadCLTs[ref_index].getX3dTopDirectory();
     }

src/main/java/com/elphel/imagej/tileprocessor/QuadCLTCPU.java

@@ -4979,6 +4979,21 @@ public class QuadCLTCPU {
 		return file_path;
 	}
 
+	public String saveConfInModelDirectory()
+	{
+		String x3d_path = getX3dDirectory();
+		String file_name = image_name + "-SETTINGS";
+		String file_path = x3d_path + Prefs.getFileSeparator() + file_name;
+		Properties properties=new Properties();
+		Eyesis_Correction.saveProperties(
+				file_path,
+				null,
+				true,
+				properties,
+				0); // DEBUG_LEVEL >-3);
+		return file_path;
+	}
+	
 	
 	public String saveAVIInModelDirectory(
 			boolean     dry_run,