Improving code related to the synthetic images, adding comments.

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

@@ -5827,15 +5827,6 @@ public class Eyesis_Correction implements PlugIn, ActionListener {
 					SYNC_COMMAND, // // SyncCommand  SYNC_COMMAND,
 					CLT_PARAMETERS, // CLTParameters    clt_parameters,
 					DEBUG_LEVEL);   // final int debugLevel
-		/*	
-		} else if (label.equals("Test LDLT Cholesky")) {
-			ImagePlus imp_sel = WindowManager.getCurrentImage();
-			if (imp_sel == null) {
-				IJ.showMessage("Error", "No images selected");
-				return;
-			}
-			CholeskyLDLTMulti.testCholesky(imp_sel); // ImagePlus imp.);
-		*/	 
 		} else if (label.equals("Test LLT Cholesky")) {
 			ImagePlus imp_sel = WindowManager.getCurrentImage();
 			if (imp_sel == null) {

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

@@ -989,9 +989,11 @@ min_str_neib_fpn	0.35
 	public String    synth_directory =       "/media/elphel/SSD3-4GB/lwir16-proc/berdich3/restore_foliage/01/";
 	public String    synth_scene =           "1697877490_630338";
 	public String    synth_model =           "-preview_segments-0-0-640-512-ACCUM.tiff";
-//	public String    synth_source =          "_warps.tiff";
+	public String    synth_segments =        ".vegetation-segments"; // serialized: number of models, array of models
 	public String    synth_render =          "_synth-render.tiff";
 	public boolean   synth_crop_real =       true; // crop synthetic by real 
+	public String    synth_scene_offs =      "-0-0-640-512-SCENE_OFFSETS.tiff";
+	public boolean   synth_add_offs =        true; // crop synthetic by real 
 	
 	
 //	public String ter_rendered_path = "/media/elphel/SSD3-4GB/lwir16-proc/berdich3/debug/vegetation/essential/1697877491_613999-terrain_vegetation_render.tiff";
@@ -2491,9 +2493,11 @@ min_str_neib_fpn	0.35
 		gd.addStringField ("Synthesis directory",  synth_directory, 120, "Directory with the terrain/foliage model generation files.");
 		gd.addStringField ("Scene name",           synth_scene,     40,  "Name (timestamp) of the model.");
 		gd.addStringField ("Model suffix",         synth_model,     120, "File name suffix for the model.");
-//		gd.addStringField ("Source suffix",        synth_source,    120, "File name suffix for the camera images, warps and scales.");
+		gd.addStringField ("Vegetation segments",  synth_segments,    120, "File name suffix for partial terrain/vegetation segments.");
 		gd.addStringField ("Rendered suffix",      synth_render,    120, "Result file name suffix for the rendered synthetic images.");
 		gd.addCheckbox    ("Crop by real",         synth_crop_real, "Crop synthetic by real.");
+		gd.addStringField ("Scene offsets",        synth_scene_offs,120, "Filenam suffix with scene offsets.");
+		gd.addCheckbox    ("Add scene offsets",    synth_add_offs,  "Add scene offsets (vignetting corrcetion).");
 	}
 
 	public void dialogAnswers(GenericJTabbedDialog gd) {
@@ -3349,9 +3353,11 @@ min_str_neib_fpn	0.35
 		synth_directory =          gd.getNextString(); // String
 		synth_scene =              gd.getNextString(); // String
 		synth_model =              gd.getNextString(); // String
-//		synth_source =             gd.getNextString(); // String
+		synth_segments =           gd.getNextString(); // String
 		synth_render =             gd.getNextString(); // String
 		synth_crop_real =          gd.getNextBoolean();// boolean
+		synth_scene_offs =         gd.getNextString(); // String
+		synth_add_offs =           gd.getNextBoolean();// boolean
 		
 		if (this.weight_zero_neibs > 1.0) this.weight_zero_neibs = 1.0;
 	}
@@ -4191,9 +4197,11 @@ min_str_neib_fpn	0.35
 		properties.setProperty(prefix+"synth_directory",             synth_directory+"");         // String
 		properties.setProperty(prefix+"synth_scene",                 synth_scene+"");             // String
 		properties.setProperty(prefix+"synth_model",                 synth_model+"");             // String
-//		properties.setProperty(prefix+"synth_source",                synth_source+"");            // String
+		properties.setProperty(prefix+"synth_segments",              synth_segments+"");          // String
 		properties.setProperty(prefix+"synth_render",                synth_render+"");            // String
 		properties.setProperty(prefix+"synth_crop_real",             synth_crop_real+"");         // boolean
+		properties.setProperty(prefix+"synth_scene_offs",            synth_scene_offs+"");        // String
+		properties.setProperty(prefix+"synth_add_offs",              synth_add_offs+"");          // boolean
 	}
 	
 	public void getProperties(String prefix,Properties properties){
@@ -5048,9 +5056,11 @@ min_str_neib_fpn	0.35
 		if (properties.getProperty(prefix+"synth_directory")!=         null) synth_directory=(String) properties.getProperty(prefix+"synth_directory");
 		if (properties.getProperty(prefix+"synth_scene")!=             null) synth_scene=(String) properties.getProperty(prefix+"synth_scene");
 		if (properties.getProperty(prefix+"synth_model")!=             null) synth_model=(String) properties.getProperty(prefix+"synth_model");
-//		if (properties.getProperty(prefix+"synth_source")!=            null) synth_source=(String) properties.getProperty(prefix+"synth_source");
+		if (properties.getProperty(prefix+"synth_segments")!=          null) synth_segments=(String) properties.getProperty(prefix+"synth_segments");
 		if (properties.getProperty(prefix+"synth_render")!=            null) synth_render=(String) properties.getProperty(prefix+"synth_render");
 		if (properties.getProperty(prefix+"synth_crop_real")!=         null) synth_crop_real=Boolean.parseBoolean(properties.getProperty(prefix+"synth_crop_real"));
+		if (properties.getProperty(prefix+"synth_scene_offs")!=        null) synth_scene_offs=(String) properties.getProperty(prefix+"synth_scene_offs");
+		if (properties.getProperty(prefix+"synth_add_offs")!=          null) synth_add_offs=Boolean.parseBoolean(properties.getProperty(prefix+"synth_add_offs"));
 	}
 	
 	@Override
@@ -5861,9 +5871,11 @@ min_str_neib_fpn	0.35
 		imp.synth_directory =                    this.synth_directory;
 		imp.synth_scene =                        this.synth_scene;
 		imp.synth_model =                        this.synth_model;
-//		imp.synth_source =                       this.synth_source;
+		imp.synth_segments =                     this.synth_segments;
 		imp.synth_render =                       this.synth_render;
 		imp.synth_crop_real =                    this.synth_crop_real;
+		imp.synth_scene_offs =                   this.synth_scene_offs;
+		imp.synth_add_offs =                     this.synth_add_offs;
 		return imp;
 	}
 	public static long getLongColor(Color color) {

src/main/java/com/elphel/imagej/vegetation/VegetationLMA.java

@@ -6456,8 +6456,15 @@ public class VegetationLMA {
 			
 			for (int t = 0; t < SAVE_TYPES.length; t++) {
 				int n = SAVE_TYPES[t];
+				if (n ==TVAO_SCENE_OFFSET) {
+					tvao_data[n] = new double [num_scenes];
+					if ( data[t] != null) {
+						System.arraycopy(data[t], 0, tvao_data[n],0, num_scenes);
+					}
+				} else {
 					tvao_data[n] = data[t];
 				}
+			}
 			for (int n = 0; n < tvao_data.length; n++) {
 				if (tvao_data[n] == null) {
 					tvao_data[n] = new double [width*height];
@@ -6735,7 +6742,7 @@ public class VegetationLMA {
 						terrain_offset,          // terrain_offset,
 						tvao[TVAO_SCENE_OFFSET], // double []   scene_offsets,
 						// terrain, vegetation, alpha, elevation, terrain_elevation
-						new double [][] {tvao[0],tvao[1],tvao[2],tvao[3],tvao[5]}, // double [][]  tva) {} {}
+						new double [][] {tvao[0],tvao[1],tvao[2],tvao[3],tvao[5]}, // double [][]  tva) {} {} // skipping common terrain elevation
 						confidence,              // double []   confidence
 						has_vegetation);               //boolean []  overlaid)
 				if (debugLevel>-2) {

src/main/java/com/elphel/imagej/vegetation/VegetationModel.java

@@ -2,6 +2,7 @@ package com.elphel.imagej.vegetation;
 
 import java.awt.Rectangle;
 import java.io.File;
+import java.io.IOException;
 import java.text.SimpleDateFormat;
 import java.util.Arrays;
 import java.util.Calendar;
@@ -2068,7 +2069,46 @@ public class VegetationModel {
 		
 		
 		if (run_combine) {
-			VegetationSegment [] segments = vegetationLMA.readAllSegments(
+			String    synth_directory =  clt_parameters.imp.synth_directory; //      "/media/elphel/SSD3-4GB/lwir16-proc/berdich3/restore_foliage/01/";
+			if (!synth_directory.endsWith(Prefs.getFileSeparator())) {
+				synth_directory+=Prefs.getFileSeparator();
+			}
+			String    synth_segments =   clt_parameters.imp.synth_segments;  //      ".vegetation-segments"; // serialized: number of models, array of models
+			String    synth_scene =       clt_parameters.imp.synth_scene;
+			String    segments_path = synth_directory + synth_scene + synth_segments;
+			// try to read segments from the serialized file (to force recalculation - just remove it)
+			VegetationSegment [] segments = null;
+			try {
+				segments = VegetationSegment.readVegetationSegments (
+						segments_path);
+				System.out.println("processVegetationLMA(): read serialized segment data from "+(segments.length)+" segments to "+segments_path);
+				System.out.println("To rebuild the segments - just remove "+segments_path+" and re-run the program");
+			} catch (ClassNotFoundException | IOException e1) {
+				System.out.println("processVegetationLMA(): failed to read segments data from "+segments_path+", will rebuild it.");
+			} // String path)
+			//fixing wrong scene_offsets
+			boolean fixed_scene_offsets= false;
+			int num_scenes = getSceneNames().length;
+			for (VegetationSegment segment:segments) {
+				if (segment.scene_offsets.length > num_scenes) {
+					double [] s_o = new double [num_scenes];
+					System.arraycopy(segment.scene_offsets, 0, s_o, 0, num_scenes);
+					segment.scene_offsets = s_o;
+					fixed_scene_offsets = true;
+				}
+			}
+			if (fixed_scene_offsets) {
+				try {
+					VegetationSegment.writeVegetationSegments(
+							segments_path, // String path,
+							segments);
+					System.out.println("processVegetationLMA(): Saved fixed scene_offsets serialized data for "+(segments.length)+" segments to "+segments_path);
+				} catch (IOException e) {
+					System.out.println("processVegetationLMA(): failed to save fixed scene_offsets segments data to "+segments_path);
+				}    // VegetationSegment [] segments) throws IOException {
+			}
+			if (segments == null) {
+				segments = vegetationLMA.readAllSegments(
 						segments_dir,          // String dir_path)
 						segments_suffix,       // String suffix);
 						transparency_opaque,   // double        transparency_opaque,
@@ -2081,11 +2121,25 @@ public class VegetationModel {
 						debug_path,            // String        debug_path,
 						debug_save_improved,   // boolean       debug_save_improved, // Save debug image after successful LMA step."); 
 						debug_save_worsened);  // boolean       debug_save_worsened) { // Save debug image after unsuccessful LMA step.");
+
+				//			String segments_path = model_directory+reference_scene+"-foliage_model.foliage-model";
+
+				try {
+					VegetationSegment.writeVegetationSegments(
+							segments_path, // String path,
+							segments);
+					System.out.println("processVegetationLMA(): Saved serialized data for "+(segments.length)+" segments to "+segments_path);
+				} catch (IOException e) {
+					System.out.println("processVegetationLMA(): failed to save segments data to "+segments_path);
+				}    // VegetationSegment [] segments) throws IOException {
+			}
+			
+			if (keep_partial) { // may require too much memory
 				VegetationSegment.combineSegments(
 						vegetationLMA, // VegetationLMA        vegetationLMA,
 						segments,
 						crop_combo,             // boolean              crop_combo,
-					keep_partial,           // boolean   keep_partial,
+						true,                   // boolean   keep_partial,
 						border_width,           // int                  width);
 						um_sigma,               // final double         um_sigma,
 						um_weight,              //final double         um_weight,
@@ -2097,6 +2151,35 @@ public class VegetationModel {
 						boost_parallax_render,  // double boost_parallax) {    // increase weights of scenes with high parallax relative to the reference one
 						max_parallax_render,    // final double        max_parallax,			
 						num_exaggerate);        // final int            num_exaggerate) { // show amplified difference from filtering
+			} else {
+				VegetationSegment.combineSegments(
+						vegetationLMA, // VegetationLMA        vegetationLMA,
+						segments,
+						crop_combo,             // boolean              crop_combo,
+//						keep_partial,           // boolean   keep_partial,
+						border_width,           // int                  width);
+						um_sigma,               // final double         um_sigma,
+						um_weight,              //final double         um_weight,
+						render_open,            // boolean   render_open,      // render open areas (no vegetation offset)
+						render_no_alpha,        // boolean   render_no_alpha,  // render where no opacity is available
+						alpha_min,              // double    alpha_min,        // below - completely transparent vegetation
+						alpha_max,              // double    alpha_max,        // above - completely opaque
+						weight_opaque,          // double    weight_opaque,    // render through completely opaque vegetation
+						boost_parallax_render,  // double boost_parallax) {    // increase weights of scenes with high parallax relative to the reference one
+						max_parallax_render,    // final double        max_parallax,			
+						num_exaggerate);        // final int            num_exaggerate) { // show amplified difference from filtering
+			}
+			
+			ImagePlus imp_scene_offsets = 	VegetationSegment.combineSegmentsSceneOffsets(
+					vegetationLMA,          // VegetationLMA        vegetationLMA,
+					segments,               // VegetationSegment [] segments,
+					crop_combo,             // boolean              crop_combo,
+					border_width,           // int                  width);
+					num_scenes);            // final int            num_scenes
+			if (imp_scene_offsets != null) {
+				imp_scene_offsets.show();
+			}
+
 			return;
 		}
 		Rectangle woi = woi_last_done;