Orthographic videos generation

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

@@ -109,6 +109,7 @@ import com.elphel.imagej.ims.EventLogger;
 import com.elphel.imagej.ims.Imx5;
 import com.elphel.imagej.jp4.JP46_Reader_camera;
 import com.elphel.imagej.lwir.LwirReader;
+import com.elphel.imagej.orthomosaic.ComboMap;
 import com.elphel.imagej.orthomosaic.ComboMatch;
 import com.elphel.imagej.readers.ChangeImageResolution;
 import com.elphel.imagej.readers.DumpImageMetadata;
@@ -847,6 +848,7 @@ public class Eyesis_Correction implements PlugIn, ActionListener {
 			addButton("Warp pair",  panelLWIRWorld, color_process);
 			addButton("Read Tiff",  panelLWIRWorld, color_process);
 			addButton("Set pair GPS",  panelLWIRWorld, color_process);
+			addButton("Test video",  panelLWIRWorld, color_process);
 			plugInFrame.add(panelLWIRWorld);
 			
 		}
@@ -5705,21 +5707,6 @@ public class Eyesis_Correction implements PlugIn, ActionListener {
 		} else if (label.equals("Set pair GPS")) {
 			DEBUG_LEVEL = MASTER_DEBUG_LEVEL;
 			EYESIS_CORRECTIONS.setDebug(DEBUG_LEVEL);
-			/*
-			boolean run_pre = true; // false;
-			if (run_pre) {
-				String path = loadProperties(null, CORRECTION_PARAMETERS.resultsDirectory, true, PROPERTIES);
-				if (path != null) {
-					getAllProperties(PROPERTIES);
-					if (DEBUG_LEVEL > -3)
-						System.out.println("Configuration parameters are restored from " + path);
-				} else {
-					if (DEBUG_LEVEL > -10)
-						System.out.println("Failed to restore configuration parameters");
-					return;
-				}
-			}
-			*/
 			if (GPU_TILE_PROCESSOR == null) {
 				try {
 					GPU_TILE_PROCESSOR = new GPUTileProcessor(CORRECTION_PARAMETERS.tile_processor_gpu);
@@ -5730,23 +5717,6 @@ public class Eyesis_Correction implements PlugIn, ActionListener {
 					return;
 				} // final int debugLevel);
 			}
-			/*
-			if (!run_pre) {
-				String path = loadProperties(null, CORRECTION_PARAMETERS.resultsDirectory, true, PROPERTIES);
-				if (path != null) {
-					getAllProperties(PROPERTIES);
-					if (DEBUG_LEVEL > -3)
-						System.out.println("Configuration parameters are restored from " + path);
-				} else {
-					if (DEBUG_LEVEL > -10)
-						System.out.println("Failed to restore configuration parameters");
-					return;
-				}
-			}
-			*/
-			
-//////////////////////
-// Temporarily initialize on scene GPU
 			
 			boolean init_scene = false; // true;
 			if (init_scene) {
@@ -5756,6 +5726,13 @@ public class Eyesis_Correction implements PlugIn, ActionListener {
 					CLT_PARAMETERS,     // CLTParameters    clt_parameters,
 					GPU_TILE_PROCESSOR,
 					DEBUG_LEVEL);
+		} else if (label.equals("Test video")) {
+			ImagePlus imp_sel = WindowManager.getCurrentImage();
+			if (imp_sel == null) {
+				IJ.showMessage("Error", "No images selected");
+				return;
+			}
+			ComboMap.testVideo(imp_sel);
 		}
 		
 	}

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

 package com.elphel.imagej.orthomosaic;
 
+import java.awt.Color;
+import java.awt.Font;
 import java.io.File;
 import java.io.IOException;
 import java.nio.charset.StandardCharsets;
 import java.nio.file.Files;
 import java.nio.file.Path;
 import java.nio.file.Paths;
+import java.text.SimpleDateFormat;
 import java.time.LocalDateTime;
 import java.util.ArrayList;
 import java.util.Arrays;
+import java.util.Calendar;
 import java.util.HashMap;
 import java.util.List;
 import java.util.Properties;
 import java.util.concurrent.atomic.AtomicInteger;
 
 import com.elphel.imagej.cameras.CLTParameters;
+import com.elphel.imagej.common.GenericJTabbedDialog;
 import com.elphel.imagej.common.ShowDoubleFloatArrays;
 import com.elphel.imagej.gpu.TpTask;
 import com.elphel.imagej.ims.Imx5;
 import com.elphel.imagej.readers.ElphelTiffReader;
 import com.elphel.imagej.tileprocessor.ImageDtt;
+import com.elphel.imagej.tileprocessor.IntersceneMatchParameters;
+import com.elphel.imagej.tileprocessor.QuadCLT;
 
 import Jama.Matrix;
 import ij.ImagePlus;
 import ij.ImageStack;
 import ij.Prefs;
 import ij.gui.PointRoi;
+import ij.plugin.filter.AVI_Writer;
+import ij.plugin.filter.GaussianBlur;
+import ij.process.FloatProcessor;
+import ij.process.ImageConverter;
+import ij.process.ImageProcessor;
 
 public class ComboMap {
 	public static boolean FIX_VERT_Y = false; // true; // temporarily fix vertical Y coordinate bug (use -GCORR in the filename?)
@@ -97,6 +109,10 @@ public class ComboMap {
 		images = new HashMap <Integer, FloatImageData>();
 	}
 	
+	
+	public LocalDateTime getLocalDateTime() {
+		return dt;
+	}
 	public static ComboMap[] initializeComboMaps(
 			String [] image_paths) { // full paths, including ext
 		double [][] affine = {{1,0,0},{0,1,0}}; // maybe later calculate from mage_enuatr
@@ -595,7 +611,7 @@ public class ComboMap {
 				centers); // double [][] centers)
 		String [] map_names = new String[maps.length];
 		for (int n = 0; n < maps.length; n++) { 
-			map_names[n] = maps[n].getName();
+			map_names[n] = maps[n].getName()+"_"+maps[n].getLocalDateTime().toString().replace("T","_")+"_UTC";
 		}
 		
         ImageStack stack = ShowDoubleFloatArrays.makeStack( 
@@ -750,5 +766,313 @@ public class ComboMap {
 		
 		return null;
 	}
+	public static void testVideo(ImagePlus imp) {
+		String path_prefix = "/media/elphel/SSD3-4GB/lwir16-proc/ortho_videos/videos/video_";
+		boolean   keep_original =        true;
+		boolean   um_apply =             true;
+		double    um_sigma =             10.0;
+		double    um_weight =            0.9;
+		boolean   auto_range =           false;
+		double    mono_range =           300.0; 
+		boolean   annotate   =           true;
+		Color     annotate_color =       new Color( 255, 180,  50);
+		boolean   annotate_transparent = false;
+		int       annotate_font_size =   36;
+		boolean   annotate_font_bold =   true;
+		double    video_fps =            10;
+		boolean   avi_compress_jpeg =    false;
+		int       aviJpegQuality =       95;
+		boolean   run_ffmpeg =           true;
+		String    video_ext =            ".webm";
+		String    video_codec =          "vp8";
+		int       video_crf =            10; // lower - better, larger file size
+		boolean   remove_avi =           true;
+		int       debugLevel =           0;
+		GenericJTabbedDialog gd = new GenericJTabbedDialog("Parameters for video from orthographic imges",1200,800);
+		gd.addStringField ("Output video path prefix",  path_prefix, 180,
+				"Absolute path prefix for the video (image title will be added).");
+		gd.addCheckbox    ("Keep original image", keep_original, "If true, will generate new RGB image, if false - replace existent.");
+		gd.addCheckbox    ("Apply unsharp mask filter", um_apply, "Apply unsharp mask filter.");
+		gd.addNumericField("Unsharp mask sigma", um_sigma,  3,7,"",	"Unsharp mask sigma.");
+		gd.addNumericField("Unsharp mask weight", um_weight,  3,7,"",	"Unsharp mask weight.");
+		gd.addCheckbox    ("Auto range while congerting to RGB", auto_range, "Autorange 32-bit floating point image when converting to RGB.");
+		gd.addNumericField("Fixed range during conversion to RGB", mono_range,  3,7,"",	"Fixed range.");
+		gd.addCheckbox    ("Annotate each frame with timestamp+date/time", annotate,
+				"Embed annotation in the bottom-right corner of each frame of the converted image file and video.");
+		{
+			String scolor = (annotate_color==null)?"none":String.format("%08x", IntersceneMatchParameters.getLongColor(annotate_color));
+			gd.addStringField ("Annotation color (hex number)",scolor, 8, "Any invalid hex number disables annotation");
+		}
+		gd.addCheckbox    ("Annotation transparent background", annotate_transparent, "Put annotation text directly over images.");
+		gd.addNumericField("Annotation font size", annotate_font_size, 0, 4, "", "Annotation font size.");
+		gd.addCheckbox    ("Bold annotation", annotate_font_bold, "Use bold font for annotations.");
+		gd.addNumericField("Video output frame rate", video_fps,  3,7,"fps", "Frame rate of the video.");
+		gd.addCheckbox    ("Compress AVI with JPEG", avi_compress_jpeg, "Use JPEG for AVI compression (false - use raw).");
+		gd.addNumericField("AVI JPEG quality", aviJpegQuality, 0, 4, "", "AVI JPEG quality if JPEG compression is used.");
+		gd.addCheckbox    ("Convert AVI to WEBM", run_ffmpeg, "Use ffmped to convert intermediate AVI video to WEBM.");
+		gd.addStringField ("WEBM output extension",  video_ext, 5,"WEBM output file extension including dot, normally \".webm\".");
+		gd.addStringField ("WEBM codec",  video_codec, 5,"WEBM codec \"vp8\" or \"vp9\"(vp9 had problems).");
+		gd.addNumericField("WEBM CRF", video_crf, 0, 4, "", "WEBM compression quality (lower - better, 10 - good).");
+		gd.addCheckbox    ("Remove AVI", remove_avi, "Remove AVI (large file) after WEBM generation.");
+		gd.addNumericField("Debug level", debugLevel, 0, 4, "", "Debug level (not yet used).");
+		gd.showDialog();
+		if (gd.wasCanceled()) return;
+		path_prefix =          gd.getNextString();
+		keep_original =        gd.getNextBoolean();
+		um_apply =             gd.getNextBoolean();
+		um_sigma=              gd.getNextNumber();
+		um_weight=             gd.getNextNumber();
+		auto_range =           gd.getNextBoolean();
+		mono_range =           gd.getNextNumber();
+		annotate =             gd.getNextBoolean();
+        {
+			String scolor =             gd.getNextString();
+			long lcolor = -1;
+			try {
+				lcolor = Long.parseLong(scolor,16);
+				annotate_color = IntersceneMatchParameters.setLongColor(lcolor);
+			} catch(NumberFormatException e){
+				annotate_color = null;
+			}
+        }
+		annotate_transparent =     gd.getNextBoolean();
+		annotate_font_size = (int) gd.getNextNumber();		
+		annotate_font_bold =       gd.getNextBoolean();
+		video_fps =                gd.getNextNumber();
+		avi_compress_jpeg =        gd.getNextBoolean();
+		aviJpegQuality =     (int) gd.getNextNumber();
+		run_ffmpeg =               gd.getNextBoolean();
+		video_ext =                gd.getNextString();
+		video_codec =              gd.getNextString();
+		video_crf =          (int) gd.getNextNumber();
+		remove_avi =               gd.getNextBoolean();
+		debugLevel =         (int) gd.getNextNumber();
+		
+		ImagePlus imp_um;
+		if (um_apply) {
+			imp_um = applyUnsharpMask(
+					imp,           // final ImagePlus imp,
+					keep_original, // final boolean   keep_original,
+					um_sigma,      // 10,            // final double    um_sigma,
+					um_weight);    // 0.9);          // final double    um_weight
+		} else {
+			imp_um = keep_original? imp.duplicate():imp;
+		}
+        System.out.println("applyUnsharpMask() DONE!");	
+    	ImagePlus imp_rgb = convertToColorAnnotate(
+    			imp_um,               // ImagePlus imp_src,
+    			false,                // boolean   keep_original,
+    			auto_range? 0:mono_range, // 300,  // double    mono_range,  // >0 - apply 
+    			annotate,             // boolean   annotate,
+    			annotate_color,       // Color.RED,  //Color    annotate_color,
+    			annotate_transparent, // boolean   annotate_transparent,
+    			annotate_font_size,   // int       annotate_font_size, // 12
+    			annotate_font_bold,   // boolean   annotate_font_bold,
+    			debugLevel);          // int       debugLevel)
+    	imp_rgb.show();
+        System.out.println("convertToColorAnnotate() DONE!");
+        String path = path_prefix+imp_rgb.getTitle();
+        int mode_avi = avi_compress_jpeg? 1 : 0;
+        saveRGBSlicesAsVideo(
+        		imp_rgb,        // ImagePlus  imp,
+//    			0,              // int        col_mode, // 0 - mono, 1 - color
+    			path,           // String     path,
+    			video_fps,      // double     video_fps,
+    			mode_avi,       // int        mode_avi, // 0 - raw, 1 - JPEG, 2 - PNG
+    			aviJpegQuality, // int        aviJpegQuality,
+    			run_ffmpeg,     // boolean    run_ffmpeg,
+    			video_ext,      // ".webm",   // String     video_ext,
+    			video_codec,    // "vp8",     // String     video_codec,
+    			video_crf,      // 10,        // int        video_crf, // lower - better, larger file size
+    			remove_avi,     // boolean    remove_avi,
+    			debugLevel);    // final int  debugLevel
+    			        
+        System.out.println("saveRGBSlicesAsVideo() DONE!");
+	}
+	
+	
+	public static ImagePlus applyUnsharpMask(
+			final ImagePlus imp_src,
+			final boolean   keep_original, 
+			final double    um_sigma,
+			final double    um_weight
+			) {
+		final float fum_weight=(float) um_weight;
+		final ImagePlus imp = keep_original? imp_src.duplicate() : imp_src;
+		final ImageStack fstack_scenes = imp.getStack();
+		final int nSlices = fstack_scenes.getSize();
+		final Thread[] threads = ImageDtt.newThreadArray(QuadCLT.THREADS_MAX);
+		final AtomicInteger ai = new AtomicInteger(0);
+		for (int ithread = 0; ithread < threads.length; ithread++) {
+			threads[ithread] = new Thread() {
+				public void run() {
+					for (int nSlice = ai.getAndIncrement(); nSlice < nSlices; nSlice = ai.getAndIncrement()) {
+						FloatProcessor fp = (FloatProcessor) fstack_scenes.getProcessor(nSlice+1);
+						float [] fpixels = (float[]) fstack_scenes.getPixels(nSlice+1);
+						float [] fpixels_orig = fpixels.clone();
+						(new GaussianBlur()).blurFloat(
+								fp,       // FloatProcessor ip,
+								um_sigma, // double sigmaX,
+								um_sigma, // double sigmaY,
+								0.01);    // double accuracy)
+						for (int i = 0; i < fpixels.length; i++) {
+							fpixels[i] = fpixels_orig[i] - fum_weight * fpixels[i];
+						}
+					}
+				}
+			};
+		}		      
+		ImageDtt.startAndJoin(threads);
+		imp.setTitle(removeKnownExtension(imp.getTitle())+String.format("-UM%.1f_%.2f",um_sigma,um_weight));
+		return imp;
+	}
+	
+	public static ImagePlus convertToColorAnnotate(
+			ImagePlus imp_src,
+			boolean   keep_original,
+			double    mono_range,  // >0 - apply 
+			boolean   annotate,
+			Color     annotate_color,
+			boolean   annotate_transparent,
+			int       annotate_font_size, // 12
+			boolean   annotate_font_bold,
+			int       debugLevel) {
+		final ImagePlus imp = keep_original? imp_src.duplicate() : imp_src;
+		if (imp.getType() != ImagePlus.COLOR_RGB) {
+			if (mono_range > 0) {
+				imp.getProcessor().setMinAndMax(-mono_range/2, mono_range/2);
+			}
+			ImageConverter imageConverter = new ImageConverter(imp);
+			imageConverter.convertToRGB();
+		}
+		final Color fcolor = annotate_color;
+		final ImageStack fstack_scenes = imp.getImageStack();
+		int title_len = 0;
+		final int nSlices = fstack_scenes.getSize();
+		for (int i = 0; i < nSlices; i++) {
+			if (fstack_scenes.getSliceLabel(i+1).length() > title_len) {
+				title_len=fstack_scenes.getSliceLabel(i+1).length();
+			}
+		}
+		final int annotate_size = title_len; //
+		final int width =  imp_src.getWidth();
+		final int height = imp_src.getHeight();
+		final double char_wtoh = 0.6;
+		final int posX= width - ((int) (char_wtoh* annotate_size * annotate_font_size)); //  119; // 521;
+		final int posY= height + 1;  // 513;
+		final Font font = new Font("Monospaced", Font.PLAIN | (annotate_font_bold ? Font.BOLD: 0), annotate_font_size);
+		final Thread[] threads = ImageDtt.newThreadArray(QuadCLT.THREADS_MAX);
+		final AtomicInteger ai = new AtomicInteger(0);
+		for (int ithread = 0; ithread < threads.length; ithread++) {
+			threads[ithread] = new Thread() {
+				public void run() {
+					for (int nSlice = ai.getAndIncrement(); nSlice < nSlices; nSlice = ai.getAndIncrement()) {
+						String scene_title = fstack_scenes.getSliceLabel(nSlice+1);
+						ImageProcessor ip = fstack_scenes.getProcessor(nSlice+1);
+						ip.setColor(fcolor); // Color.BLUE);
+						ip.setFont(font);
+						if (!annotate_transparent) { // toRGB || !annotate_transparent_mono) {
+							ip.drawString(scene_title, posX, posY,Color.BLACK);
+						} else {
+							ip.drawString(scene_title, posX, posY); // transparent
+						}
+					}
+				}
+			};
+		}		      
+		ImageDtt.startAndJoin(threads);
+		imp.setTitle(removeKnownExtension(imp.getTitle())+((mono_range > 0) ? String.format("_%.0f",mono_range):"_A"));
+		return imp;
+	}
 	
+	public static String removeKnownExtension(String path) {
+		String [] remove_ext = {".tiff", ".tif", ".avi"};
+		for (String ext:remove_ext) {
+			if (path.endsWith(ext)) {
+				path = path.substring(0,path.length()-ext.length());
+			}
+		}
+		return path;
+
+	}
+	public static boolean saveRGBSlicesAsVideo(
+			ImagePlus  imp,
+//			int        col_mode, // 0 - mono, 1 - color
+			String     path,
+			double     video_fps,
+			int        mode_avi, // compression
+			int        aviJpegQuality,
+			boolean    run_ffmpeg,
+			String     video_ext,
+			String     video_codec,
+			int        video_crf,
+			boolean    remove_avi,
+			final int  debugLevel
+			) {
+		boolean generate_mapped = true; // false - here just simulate
+		// no_combine, stereo_2_images, stereo_anaglyth
+		String avi_path = removeKnownExtension(path)+String.format("-FPS%04.1f",video_fps)+".avi";
+		imp.getCalibration().fps = video_fps;
+		video:
+		{
+			try {
+				(new AVI_Writer()).writeImage (
+						imp, // ImagePlus imp,
+						avi_path, // String path,
+						mode_avi, // int compression,
+						aviJpegQuality); //int jpegQuality)
+			} catch (IOException e) {
+				// TODO Auto-generated catch block
+				e.printStackTrace();
+				break video;
+			}
+			System.out.println("saveAVIInModelDirectory(): saved "+avi_path);
+			if (!run_ffmpeg) {
+				break video; // webm not requested
+			}
+
+			String webm_path = avi_path.substring(0, avi_path.length()-4)+video_ext;
+			// added -y not to as "overwrite y/n?"
+			//ffmpeg -i input_file.mkv -c copy -metadata:s:v:0 stereo_mode=1 output_file.mkv 
+			//https://ffmpeg.org/ffmpeg-formats.html
+			//ffmpeg -i sample_left_right_clip.mpg -an -c:v libvpx -metadata stereo_mode=left_right -y stereo_clip.webm
+			//anaglyph_cyan_red 
+			String stereo_meta = ""; // used in OpticalFlow
+			String shellCommand = String.format("ffmpeg -y -i %s -c %s -b:v 0 -crf %d %s %s",
+					avi_path, video_codec, video_crf, stereo_meta, webm_path);
+			Process p = null;
+			if (generate_mapped) {
+				int exit_code = -1;
+				try {
+					p = Runtime.getRuntime().exec(shellCommand);
+				} catch (IOException e) {
+					System.out.println("Failed shell command: \""+shellCommand+"\"");
+				}
+				if (p != null) {
+					try {
+						p.waitFor();
+					} catch (InterruptedException e) {
+						System.out.println("saveRGBSlicesAsVideo(): failed waiting for process to finish.");
+						// TODO Auto-generated catch block
+						e.printStackTrace();
+						return false;
+					}
+					exit_code = p.exitValue();
+				}
+				System.out.println("Ran shell command: \""+shellCommand+"\" -> "+exit_code);
+				// Check if webm file exists
+				if ((exit_code != 0) || !(new File(webm_path)).exists()) {
+					System.out.println("Failed to create : \""+webm_path+"\"");
+					break video;
+				}
+			} else {
+				System.out.println("Simulated shell command: \""+shellCommand);
+			}
+			if (remove_avi && generate_mapped) {
+				(new File(avi_path)).delete();
+				System.out.println("Deleted AVI video file: \""+avi_path+"\"");
+			}
+		}
+		return true;
+	}
 }

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

@@ -43,29 +43,9 @@ public class ComboMatch {
 			 GPUTileProcessor gpu_tile_processor, // initialized by the caller
 			 final int        debugLevel) {
 		GPU_TILE_PROCESSOR = gpu_tile_processor;
-		String [] image_paths_pre_0 = {
-//				"/media/elphel/SSD3-4GB/lwir16-proc/berdich3/linked/linked_1697875868-1697879449-b/1697877410_420287/1697877410_420287-RECT-PIX0.01-FLAT_CLN-VERT-GEO",
-//				"/media/elphel/SSD3-4GB/lwir16-proc/berdich3/linked/linked_1697875868-1697879449-b/1697877412_004148/1697877412_004148-RECT-PIX0.01-FLAT_CLN-VERT-GEO",
-				
-				"/media/elphel/SSD3-4GB/lwir16-proc/berdich3/linked/linked_1697875868-1697879449-c/1697877409_353265/1697877409_353265-RECT-PIX0.01-FLAT_CLN-VERT-GEO",
-				"/media/elphel/SSD3-4GB/lwir16-proc/berdich3/linked/linked_1697875868-1697879449-c/1697877410_403615/1697877410_403615-RECT-PIX0.01-FLAT_CLN-VERT-GEO",
-				"/media/elphel/SSD3-4GB/lwir16-proc/berdich3/linked/linked_1697875868-1697879449-c/1697877411_987476/1697877411_987476-RECT-PIX0.01-FLAT_CLN-VERT-GEO",
-				"/media/elphel/SSD3-4GB/lwir16-proc/berdich3/linked/linked_1697875868-1697879449-c/1697877413_137859/1697877413_137859-RECT-PIX0.01-FLAT_CLN-VERT-GEO",
-				"/media/elphel/SSD3-4GB/lwir16-proc/berdich3/linked/linked_1697875868-1697879449-c/1697877414_404948/1697877414_404948-RECT-PIX0.01-FLAT_CLN-VERT-GEO",
-				"/media/elphel/SSD3-4GB/lwir16-proc/berdich3/linked/linked_1697875868-1697879449-c/1697877415_521986/1697877415_521986-RECT-PIX0.01-FLAT_CLN-VERT-GEO"
-		};
-
-		String [] image_paths_pre = {
-				"/media/elphel/SSD3-4GB/lwir16-proc/berdich3/linked/linked_1697875868-1697879449-c/1697877409_353265/1697877409_353265-RECT-PIX0.01-FLAT_CLN-VERT-GCORR-GEO",
-				"/media/elphel/SSD3-4GB/lwir16-proc/berdich3/linked/linked_1697875868-1697879449-c/1697877410_403615/1697877410_403615-RECT-PIX0.01-FLAT_CLN-VERT-GCORR-GEO",
-				"/media/elphel/SSD3-4GB/lwir16-proc/berdich3/linked/linked_1697875868-1697879449-c/1697877411_987476/1697877411_987476-RECT-PIX0.01-FLAT_CLN-VERT-GCORR-GEO",
-				"/media/elphel/SSD3-4GB/lwir16-proc/berdich3/linked/linked_1697875868-1697879449-c/1697877413_137859/1697877413_137859-RECT-PIX0.01-FLAT_CLN-VERT-GCORR-GEO",
-				"/media/elphel/SSD3-4GB/lwir16-proc/berdich3/linked/linked_1697875868-1697879449-c/1697877414_404948/1697877414_404948-RECT-PIX0.01-FLAT_CLN-VERT-GCORR-GEO",
-				"/media/elphel/SSD3-4GB/lwir16-proc/berdich3/linked/linked_1697875868-1697879449-c/1697877415_521986/1697877415_521986-RECT-PIX0.01-FLAT_CLN-VERT-GCORR-GEO"
-		};
 		// find -L /media/elphel/SSD3-4GB/lwir16-proc/berdich3/linked/linked_1697875868-1697879449-b/ -type f -name "*-GCORR-GEO.tiff" | sort  > GCORR-GEO.list
 
-		String files_list_path = "/media/elphel/SSD3-4GB/lwir16-proc/berdich3/linked/linked_1697875868-1697879449-b/maps_01.list";
+		String files_list_path = "/media/elphel/SSD3-4GB/lwir16-proc/ortho_videos/maps_berdich2.list";
 		
 		double [][][] image_enuatr = {{{0,0,0},{0,0,0}},{{0,0,0},{0,0,0}}};
 		int gpu_width=  clt_parameters.imp.rln_gpu_width; // 3008;
@@ -122,10 +102,6 @@ public class ComboMatch {
 		
 		show_centers =              gd.getNextBoolean();
 		use_alt =                   gd.getNextBoolean();
-		String [] full_paths = new String[image_paths_pre.length];
-		for (int n = 0; n < full_paths.length; n++) { 
-			full_paths[n] = image_paths_pre[n]+".tiff";
-		}		
 //		ComboMap[] combo_maps = ComboMap.initializeComboMaps(
 //				full_paths); // String [] image_paths);
 		ComboMap[] combo_maps = ComboMap.initializeComboMaps(
@@ -170,14 +146,14 @@ public class ComboMatch {
         		true,
         		"gpu_pair-zoom"+zoom_lev+"-"+combo_maps[gpu_pair[0]].getName()+"-"+combo_maps[gpu_pair[1]].getName(),
         		map_names);
-		if (image_paths_pre.length > 2) {
+		if (debugLevel <1000) {
 			return true;
 		}
 		/* */
 		int [] widths = new int[imp_src.length];
 		int [] heights = new int[imp_src.length];
 		for (int n = 0; n < imp_src.length; n++) { 
-			imp_src[n] = new ImagePlus(image_paths_pre[n]+".tiff"); // may use +"-ALT.tiff"
+//			imp_src[n] = new ImagePlus(image_paths_pre[n]+".tiff"); // may use +"-ALT.tiff"
 			widths[n] = imp_src[n].getWidth();
 			heights[n] = imp_src[n].getHeight();
 		}
@@ -186,13 +162,15 @@ public class ComboMatch {
 		LocalDateTime [] dts = new LocalDateTime[2];
 		double [][] xy_pix_centers = new double [2][];
 		double [] pix_sizes = new double[2]; // ElphelTiffReader.getPixelSize(imp_prop[0])[0];
-		for (int n = 0; n < imp_src.length; n++) { 
+		for (int n = 0; n < imp_src.length; n++) {
+			/*
 			try {
-				imp_prop[n] = ElphelTiffReader.getTiffMeta(image_paths_pre[n]+".tiff");				
+//				imp_prop[n] = ElphelTiffReader.getTiffMeta(image_paths_pre[n]+".tiff");				
 			} catch (IOException e) {
 				// TODO Auto-generated catch block
 				e.printStackTrace();
 			}
+			*/
 			llas[n] = ElphelTiffReader.getLLA(imp_prop[n]);
 			dts[n] = ElphelTiffReader.getLocalDateTime(imp_prop[n]);
 			xy_pix_centers[n] = ElphelTiffReader.getXYOffsetPixels(imp_prop[n]);

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

@@ -5907,7 +5907,7 @@ public class OpticalFlow {
 	        								imp_scenes_pair[nstereo].getProcessor().setMinAndMax(-mono_range/2, mono_range/2);
 	        							}
 	        							ImageConverter imageConverter = new ImageConverter(imp_scenes_pair[nstereo]);
-	        							imageConverter.convertToRGB(); // Did it convert imp_scenes ?
+	        							imageConverter.convertToRGB(); // Did it convert imp_scenes ? YES
 	        						}
 
 	        						final Color fcolor = toRGB ? annotate_color_color: annotate_color_mono;
@@ -6079,13 +6079,13 @@ public class OpticalFlow {
 	        				    		//https://ffmpeg.org/ffmpeg-formats.html
 	        				    		//ffmpeg -i sample_left_right_clip.mpg -an -c:v libvpx -metadata stereo_mode=left_right -y stereo_clip.webm
 	        				    		//anaglyph_cyan_red 
-	        							String streo_meta = "";
+	        							String stereo_meta = "";
 	        							if ((webm_path.contains("-STEREO-")) || (webm_path.contains("-SBS-"))) {
 	        								if (stereo_gap == 0) {
 	        									if (debugLevel > -3) {
 	        										System.out.println("Adding 3D meta: stereo_mode=left_right");
 	        									}
-	        									streo_meta = " -metadata:s:v:0 stereo_mode=left_right ";
+	        									stereo_meta = " -metadata:s:v:0 stereo_mode=left_right ";
 	        								} else {
 	        									if (debugLevel > -3) {
 	        										System.out.println("stereo_gap !=0, skipping 3D meta as firefox/vlc halves display width");
@@ -6095,11 +6095,11 @@ public class OpticalFlow {
         									if (debugLevel > -3) {
         										System.out.println("Adding 3D meta: stereo_mode=anaglyph_cyan_red");
         									}
-		        							streo_meta = " -metadata:s:v:0 stereo_mode=anaglyph_cyan_red ";
+		        							stereo_meta = " -metadata:s:v:0 stereo_mode=anaglyph_cyan_red ";
 	        							}
 
 	        							String shellCommand = String.format("ffmpeg -y -i %s -c %s -b:v 0 -crf %d %s %s",
-	        									avi_path, video_codec, video_crf, streo_meta, webm_path);
+	        									avi_path, video_codec, video_crf, stereo_meta, webm_path);
 	        							Process p = null;
 	        							if (generate_mapped) {
 	        								int exit_code = -1;