Tuning classifier

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

@@ -268,6 +268,22 @@ import ij.process.ImageProcessor;
       return array_stack;
   }
 
+  public static ImageStack makeStack(byte[][] pixels, int width, int height, String [] titles) {
+      ImageStack array_stack=new ImageStack(width,height);
+      for (int i=0;i<pixels.length;i++) if (pixels[i]!=null) {
+          if (pixels[i].length!=(width*height)){
+        	  System.out.println("showArrays(): pixels["+i+"].length="+pixels[i].length+" != width (+"+width+") * height("+height+")="+(width*height));
+        	  return null;
+          }
+        if (titles!=null){
+            array_stack.addSlice(titles[i],    pixels[i]);
+        } else {
+        	array_stack.addSlice("chn-"+i,    pixels[i]);
+        }
+      }
+      return array_stack;
+  }
+  
 
   public static ImagePlus [] makeArrays(double[][] pixels, int width, int height, String title) {
 	  int i,j;

src/main/java/com/elphel/imagej/orthomosaic/ComboMatch.java

@@ -103,7 +103,8 @@ public class ComboMatch {
 				"/media/elphel/SSD3-4GB/lwir16-proc/ortho_videos/maps_sep12-13_50-25-50-75-100m",
 				"/media/elphel/SSD3-4GB/lwir16-proc/ortho_videos/maps_19_sep13_25-50-75-100m",
 				"/media/elphel/SSD3-4GB/lwir16-proc/ortho_videos/maps_nov3_50-75",
-				"/media/elphel/SSD3-4GB/lwir16-proc/ortho_videos/maps_sep12-50m"};
+				"/media/elphel/SSD3-4GB/lwir16-proc/ortho_videos/maps_sep12-50m",
+				"/media/elphel/SSD3-4GB/lwir16-proc/ortho_videos/maps_sep12-13_50-25-50-75-100m-SUBSET"};
 		int default_list_choice = 0; // files_lists_paths.length-1;
 //		String files_list_path =          "/media/elphel/SSD3-4GB/lwir16-proc/ortho_videos/maps_nov3_50-75.list";
 //		String orthoMapsCollection_path = "/media/elphel/SSD3-4GB/lwir16-proc/ortho_videos/maps_nov3_50-75.data";
@@ -142,7 +143,9 @@ public class ComboMatch {
 		int gpu_width=  clt_parameters.imp.rln_gpu_width; // 3008;
 		int gpu_height= clt_parameters.imp.rln_gpu_height; // 3008;
 		int zoom_lev = -3; // 0; // +1 - zoom in twice, -1 - zoom out twice
+		boolean show_map_stats =      false;      
 		boolean show_combo_map =      false; // true;
+		boolean show_combo_mask =     false; // generate image mas (where it is defined)_
 		boolean use_alt =             false;
 		boolean show_centers =        true;
 		boolean use_saved_collection = true; // false;
@@ -164,6 +167,10 @@ public class ComboMatch {
 		if (!use_marked_image) {
 			process_correlation=false; // use already adjusted by default
 		}
+		if (process_correlation) {
+			render_match = true; // default
+			pattern_match = false;
+		}
 		
 		
 		GenericJTabbedDialog gd = new GenericJTabbedDialog("Set image pair",1200,900);
@@ -201,7 +208,9 @@ public class ComboMatch {
 		gd.addNumericField("GPU image height",             gpu_height,  0,4,"",
 				"GPU image height");
 		gd.addCheckbox    ("Show transformation centers",      show_centers, "Mark verticals from the UAS on the ground.");
+		gd.addCheckbox    ("Show statistics for ortho images", show_map_stats, "Generate and show statistics for ortho maps.");
 		gd.addCheckbox    ("Show combo image map",             show_combo_map, "Load and process altitude maps.");
+		gd.addCheckbox    ("Show combo image mask",            show_combo_mask, "Display combo binary image.");
 		gd.addCheckbox    ("Show altitude combo image", use_alt, "Load and process altitude maps.");
 		gd.addNumericField("Remove fraction of worst matches",   frac_remove,  3,7,"",	"When fitting scenes remove this fraction of worst match.");
 		gd.addNumericField("Maximal metric error",      metric_error,  3,7,"m",	"Maximal tolerable fitting error caused by elevation variations.");
@@ -244,7 +253,9 @@ public class ComboMatch {
 		OrthoMap.setGPUWidthHeight(gpu_width,gpu_height);
 		
 		show_centers =              gd.getNextBoolean();
+		show_map_stats =            gd.getNextBoolean();
 		show_combo_map =            gd.getNextBoolean();
+		show_combo_mask =           gd.getNextBoolean();
 		use_alt =                   gd.getNextBoolean();
 
 //		gpu_spair[0] =              gd.getNextString();
@@ -271,8 +282,10 @@ public class ComboMatch {
 			}
 		} else {
 			maps_collection = new OrthoMapsCollection(files_list_path); // should have ".list" extension
+			maps_collection.updateNumberScenes();
+			maps_collection.updateSfmGain();
 		}
-		String [] names = maps_collection.getNames();
+		String [] names = maps_collection.getNames(); // null
 		if (object_list != null) {
 			int       corr_size =                128;
 			int       extr_size =     200; // 256;
@@ -300,7 +313,6 @@ public class ComboMatch {
 			double    inv_blur_rate =    0.2; // blur increase outside of blur_radius
 			
 			
-			
 //			String pattern_dir= "/media/elphel/SSD3-4GB/lwir16-proc/ortho_videos/debug/mines/pattern_25m_zoom1/synthetic/";
 			String pattern_dir= "/media/elphel/NVME/lwir16-proc/ortho_videos/mines_extract/evening_50m_sept12/debug_cross/new_synth/";
 			String [] pattern_files={
@@ -392,8 +404,6 @@ public class ComboMatch {
 			if (gdo.wasCanceled()) return false;
 			corr_size =                (int) gdo.getNextNumber();
 			extr_size =           (int) gdo.getNextNumber();
-//			OrthoMap.pattern_dir=       gdo.getNextString();		
-//			String pattern_file = OrthoMap.pattern_files[gdo.getNextChoiceIndex()];
 			pattern_dir=                gdo.getNextString();		
 			String pattern_file =       pattern_files[gdo.getNextChoiceIndex()];
 			zoomout=              (int) gdo.getNextNumber();
@@ -718,16 +728,27 @@ public class ComboMatch {
 		if (update_lla) {
 			System.out.println("Updating map files metadata");
 			maps_collection.updateLLa();
+			maps_collection.updateNumberScenes();
+			maps_collection.updateSfmGain();
 		}
 		
         // which pair to compare
 //		String [] gpu_spair = {names[gpu_ipair[0]],names[gpu_ipair[1]]}; 
 		int [] origin = new int[2];
 		ImagePlus imp_img = null;
+		if (show_map_stats) {
+			boolean ok = maps_collection.showScenesStats(false); // boolean select_all)
+			if (!ok) {
+				return false;
+			}
+			
+//			System.out.println("Exiting after generating stats");
+//			return true; // do not process anything else
+		}
 		if (show_combo_map) {
 			imp_img = 	maps_collection.renderMulti (
 					"multi_zoom"+zoom_lev, // String      title,
-					false,             // boolean     use_alt,
+					OrthoMapsCollection.MODE_IMAGE,  // int           mode,    // 0 - regular image, 1 - altitudes, 2 - black/white mask       // boolean     use_alt,
 					show_centers,      // boolean     show_centers,
 					zoom_lev,          // int         zoom_level,
 					temp_mode,         // int         temp_mode, // 0 - do nothing, 1 - equalize average,2 - try to correct
@@ -738,7 +759,19 @@ public class ComboMatch {
 		if (use_alt) {
 			imp_alt =maps_collection.renderMulti (
 					"multi_alt_zoom"+zoom_lev, // String      title,
-					true,              // boolean     use_alt,
+//					true,              // boolean     use_alt,
+					OrthoMapsCollection.MODE_ALT,  // int           mode,    // 0 - regular image, 1 - altitudes, 2 - black/white mask       // boolean     use_alt,
+					show_centers,      // boolean     show_centers,
+					zoom_lev,          // int         zoom_level,
+					0,                 // int         temp_mode, // 0 - do nothing, 1 - equalize average,2 - try to correct
+					origin);           // int []      origin){
+			imp_alt.show();
+		}
+		if (show_combo_mask) {
+			imp_alt =maps_collection.renderMulti (
+					"multi_alt_zoom"+zoom_lev, // String      title,
+//					true,              // boolean     use_alt,
+					OrthoMapsCollection.MODE_MASK,  // int           mode,    // 0 - regular image, 1 - altitudes, 2 - black/white mask       // boolean     use_alt,
 					show_centers,      // boolean     show_centers,
 					zoom_lev,          // int         zoom_level,
 					0,                 // int         temp_mode, // 0 - do nothing, 1 - equalize average,2 - try to correct
@@ -886,7 +919,8 @@ public class ComboMatch {
 						ImagePlus imp_img_pair = 	maps_collection.renderMulti (
 								//_zoom<integer> is needed for opening with "Extract Objects" command
 								"multi_"+gpu_spair[0]+"-"+gpu_spair[1]+"_zoom"+min_zoom_lev+"_"+zoom_lev, // String      title,
-								false,             // boolean     use_alt,
+//								false,             // boolean     use_alt,
+								OrthoMapsCollection.MODE_IMAGE,  // int           mode,    // 0 - regular image, 1 - altitudes, 2 - black/white mask       // boolean     use_alt,
 								gpu_pair,          // int []        indices, // null or which indices to use (normally just 2 for pairwise comparison)
 								bounds_to_indices, // boolean       bounds_to_indices,
 								temp_mode,         // int           temp_mode, // 0 - do nothing, 1 - equalize average,2 - try to correct
@@ -910,10 +944,6 @@ public class ComboMatch {
         	System.out.println("Saved data to "+ orthoMapsCollection_path);
         }
         return true;
-	}
-	
-	public void printSceneStats() {
-		
 	}
 	
 	

src/main/java/com/elphel/imagej/orthomosaic/OrthoMap.java

@@ -34,6 +34,7 @@ import com.elphel.imagej.readers.ElphelTiffReader;
 import com.elphel.imagej.readers.ImagejJp4Tiff;
 import com.elphel.imagej.tileprocessor.ImageDtt;
 import com.elphel.imagej.tileprocessor.IntersceneMatchParameters;
+import com.elphel.imagej.tileprocessor.OpticalFlow;
 import com.elphel.imagej.tileprocessor.QuadCLT;
 import com.elphel.imagej.tileprocessor.TileNeibs;
 
@@ -54,6 +55,8 @@ import loci.formats.FormatException;
 
 public class OrthoMap implements Comparable <OrthoMap>, Serializable{
 	private static final long serialVersionUID = 1L;
+	public static final String DSI_SUFFIX =    "-INTER-INTRA-LMA.tiff";
+	public static final String MERGED_SUFFIX = "-MERGED.tiff";
 	public static boolean FIX_VERT_Y = false; // true; // temporarily fix vertical Y coordinate bug (use -GCORR in the filename?)
 	public static int gpu_width =  4096;
 	public static int gpu_height =  4096;
@@ -84,12 +87,9 @@ public class OrthoMap implements Comparable <OrthoMap>, Serializable{
 	
 	
 	public static final String ALT_SUFFIX = "-ALT";
-//	public transient final String               name;  // timestamp
-//	public transient final double               ts;
 	public transient String                     name;  // timestamp
 	public transient double                     ts;
 	public transient String                     path;        // full path to the model directory (including /vXX?)
-//	public transient String                     scenes_path; // full path to the model directory (including /vXX?)
 	public double []                            lla;      // lat/long/alt
 	public LocalDateTime                        dt;
 	// affine convert (input) rectified coordinates (meters) relative to vert_meters to source image
@@ -110,6 +110,8 @@ public class OrthoMap implements Comparable <OrthoMap>, Serializable{
 	HashMap <String, PairwiseOrthoMatch>        pairwise_matches;
 	public transient SensorTemperatureData[]    temp_data;
 	public transient double                     agl = Double.NaN;
+	public transient int                        num_scenes = -1;;   // number of scenes that made up this image
+	public transient double                     sfm_gain = Double.NaN;     // maximal SfM gain of this map
 	private void writeObject(ObjectOutputStream oos) throws IOException {
 		oos.defaultWriteObject();
 		oos.writeObject(path);
@@ -130,9 +132,13 @@ public class OrthoMap implements Comparable <OrthoMap>, Serializable{
 		// pairwise_matches is not transient
 		oos.writeObject(temp_data); // temporary, while transient
 		oos.writeObject(agl);
+		oos.writeObject(num_scenes);
+		oos.writeObject(sfm_gain);
 	}
 
 	private void readObject(ObjectInputStream ois) throws ClassNotFoundException, IOException {
+//		sfm_gain = Double.NaN;
+//		num_scenes = -1;
 		ois.defaultReadObject();
 		path = (String) ois.readObject();
 		name = getNameFromPath(path);
@@ -149,8 +155,8 @@ public class OrthoMap implements Comparable <OrthoMap>, Serializable{
 		// alt_image was not saved
 		temp_data = (SensorTemperatureData[]) ois.readObject();
 		agl = (double)  ois.readObject();
-		
-		
+		num_scenes = (int) ois.readObject();
+		sfm_gain = (double) ois.readObject();
 		images = new HashMap <Integer, FloatImageData>(); // field images was not saved
 		averageImagePixel = Double.NaN; // average image pixel value (to combine with raw)
 		
@@ -211,6 +217,78 @@ public class OrthoMap implements Comparable <OrthoMap>, Serializable{
 		return getModelPathFromPath(this.path)+"/jp4";
 	}
 
+	/**
+	 * Get number of scenes used to generate this ortho image. Looks in subdirectories of the directory
+	 * where the image file is stored (currently they are v01, vo2, ...) and in subdirectories finds the
+	 * latest *-MERGED.tiff file. Each scene has a slice in this file 
+	 * @return number of scenes that made this ortho image, also sets the num_scenes (saved in database)
+	 * so next time reading files will not be needed
+	 */
+	public int getNumberScenes() {
+		if (num_scenes < 0) {
+			String merged_path = getLatestFilePath(MERGED_SUFFIX);
+			if (merged_path != null) {
+				ImagePlus imp_merged = new ImagePlus(merged_path);
+				if (imp_merged.getWidth() > 0) {
+					num_scenes = imp_merged.getImageStack().getSize();
+				}
+			}
+		}
+		return num_scenes;
+	}
+	
+	/**
+	 * Get maximal "SfM gain" - ratio between used interscene offset and the camera baseline.
+	 * Looks in subdirectories of the directory  where the image file is stored (currently they are
+	 * v01, vo2, ...) and in subdirectories finds the latest *-INTER-INTRA-LMA.tiff file. 
+	 * Those files have a slice (OpticalFlow.COMBO_DSN_INDX_SFM_GAIN + 1 as slices a numbered from 1)
+	 * that contains per-tile SfM gain.
+	 * @return Maximal SfM gain 
+	 */
+	
+	public double getSfmGain() {
+		if (Double.isNaN(sfm_gain)) {
+			String dsi_path = getLatestFilePath(DSI_SUFFIX);
+			if (dsi_path != null) {
+				ImagePlus imp_dsi = new ImagePlus(dsi_path);
+				if (imp_dsi.getWidth() > 0) {
+					float [] pixels = (float[]) imp_dsi.getImageStack().getPixels(OpticalFlow.COMBO_DSN_INDX_SFM_GAIN + 1);
+					sfm_gain = 0;
+					for (int i = 0; i < pixels.length; i++) {
+						if (pixels[i] > sfm_gain) {
+							sfm_gain = pixels[i];
+						}
+					}
+				}
+			}
+		}
+		return sfm_gain;
+	}
+	
+	
+	
+	public String getLatestFilePath(String suffix) {
+		String model_dir = getModelPathFromPath(this.path);
+		File [] subdirs = (new File(model_dir)).listFiles();
+		long latest_ms = 0;
+		File latest_file = null;
+		for (File subdir:subdirs) if (subdir.isDirectory()) {
+			File [] file_vers = subdir.listFiles();
+			for (File file:file_vers) if (file.isFile() && file.toString().endsWith(suffix)){
+				long modified = file.lastModified();
+				if (modified > latest_ms) {
+					latest_ms = modified;
+					latest_file = file;
+				}
+			}
+		}
+		if (latest_file != null) {
+			return latest_file.getPath();
+		}
+		return null;
+	}
+	
+	
 	public void updateLLA() {
 		Properties imp_prop = null;
 		try {
@@ -520,6 +598,41 @@ public class OrthoMap implements Comparable <OrthoMap>, Serializable{
 		return agl;
 	}
 	
+	/**
+	 * Get coordinates and altitude
+	 * @return {latitude(deg), longitude(deg), altitude(m)}
+	 */
+	public double [] getLLA() {
+		return lla;
+	}
+	
+	/**
+	 * Get original image resolution as pixel size in meters
+	 * @return image pixel size in meters
+	 */
+	public double getOrigPixMeters() {
+		return orig_pix_meters;
+	}
+	
+	/**
+	 * Get vertical point offset from the top-left corner of the original orthoimage in meters
+	 * @return vertical point X,Y offset in meters from the top-left image corner
+	 */
+	public double [] getVertMeters() {
+		return vert_meters;
+	}
+
+	/**
+	 * Get vertical point offset from the top-left corner of the original orthoimage in pixels
+	 * of the original resolution
+	 * @return vertical point X,Y offset in pixels from the top-left image corner in original resolution
+	 */
+	public int [] getVertPixels() {
+		return new int [] {
+				(int) Math.round(vert_meters[0]/orig_pix_meters),
+				(int) Math.round(vert_meters[0]/orig_pix_meters)};
+	}
+	
 	
 	public ImagePlus getOriginalImage(boolean show_markers) {
 		FloatImageData orig_image = getImageData();