Orthographic videos generation (624f1144) · Commits · Elphel / imagej-elphel

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

+9 −32

Original line number	Diff line number	Diff line
		@@ -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

+325 −1

Original line number	Diff line number	Diff line
		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

+7 −29

Original line number	Diff line number	Diff line
		@@ -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();
		}
		@@ -187,12 +163,14 @@ public class ComboMatch {
		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++) {
		/*
		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

+5 −5

Original line number	Diff line number	Diff line
		@@ -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;

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