More on output of geolocated TIFFs with transparency (ff164bbf) · Commits · Elphel / imagej-elphel

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

+3 −0

Original line number	Diff line number	Diff line
		@@ -486,6 +486,9 @@ public class CLTParameters {
		public int gmap_crop_extra = 20;
		public int [] gmap_tex_pals = {0,1,2};

		public boolean gmap_save_alt = true; // save height map (meters ASL)
		public boolean gmap_save_tiff = true; // save transparent TIFF with geo metadata (top left corner)
		public int gmap_tiff_pal = 0; // LWIR palette for TIFF


		public boolean generate_bg = true; // Generate background image for 3dmodels

src/main/java/com/elphel/imagej/ims/Imx5.java

+12 −2

Original line number	Diff line number	Diff line
		@@ -257,5 +257,15 @@ public class Imx5 {
		return ned;
		}


		/*
		* Offset Latitude, Longitude, Altitude by North, East, Up (in meters)
		*/
		public static double [] offsetLla(double [] lla, double [] ned) {
		double [] offset_lla = new double [] {
		lla[0] + (ned[0]/EARTH_RADIUS / Math.PI * 180 / Math.cos(lla[0])), // degrees
		lla[1] + (ned[1]/EARTH_RADIUS / Math.PI * 180), // degrees
		lla[2] - ned[2]
		};
		return offset_lla;
		}
		}

src/main/java/com/elphel/imagej/readers/ElphelTiffWriter.java

+2 −3

Original line number	Diff line number	Diff line
		@@ -78,9 +78,8 @@ public class ElphelTiffWriter {
		int debugLevel
		) {
		File outputFile = new File(path);
		if (debugLevel > 0) {
		System.out.println("saveTiffARGB32(): will write to "+outputFile);
		System.out.println("ElphelTiffWriter.saveTiffARGB32");
		if (debugLevel > -3) {
		System.out.println("ElphelTiffWriter.saveTiffARGB32(): will write to "+outputFile);
		}
		ImageWriter tiffWriter = ImageIO.getImageWritersByFormatName("tiff").next();
		ImageWriteParam tiffWriteParam = tiffWriter.getDefaultWriteParam();

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

+93 −4

Original line number	Diff line number	Diff line
		@@ -38,6 +38,7 @@ import java.nio.file.Files;
		import java.nio.file.Path;
		import java.nio.file.Paths;
		import java.nio.file.attribute.PosixFilePermission;
		import java.time.LocalDateTime;
		import java.util.ArrayList;
		import java.util.Arrays;
		import java.util.Collections;
		@@ -72,6 +73,7 @@ import com.elphel.imagej.ims.Did_ins_2;
		import com.elphel.imagej.ims.Did_pimu;
		import com.elphel.imagej.ims.EventLogger;
		import com.elphel.imagej.ims.Imx5;
		import com.elphel.imagej.readers.ElphelTiffWriter;
		import com.elphel.imagej.readers.ImagejJp4Tiff;
		import com.elphel.imagej.x3d.export.TriMesh;
		import com.elphel.imagej.x3d.export.WavefrontExport;
		@@ -227,6 +229,13 @@ public class QuadCLTCPU {
		return dxyzatyr;
		}

		public double [] getLla() {
		return did_ins_2.lla;
		}

		public LocalDateTime getLocalDateTime() {
		return did_ins_2.getLocalDateTime();
		}
		public static double [][] scaleDtToErs(
		CLTParameters clt_parameters,
		double [][] cam_dxyzatr){
		@@ -413,7 +422,7 @@ public class QuadCLTCPU {
		double discard_rdisp, // discard above/below this fraction of average height
		double pix_size, // in meters
		int max_image_width,// increase pixel size as a power of 2 until image fits
		double [] x0y0, // initialize to double[2] to return width, height
		double [] x0y0, // top level offset in meters
		int [] whs, // initialize to int[3] to return {width, height, scale reduction}
		int debug_level
		) {
		@@ -745,7 +754,7 @@ public class QuadCLTCPU {
		max_disparity, // double max_disparity,
		discard_low, // double discard_low, // fraction of all pixels
		discard_high, // double discard_high, // fraction of all pixels
		xy_range, // double [][] xy_range, // should be double[2][];
		xy_range, // double [][] xy_range, // should be double[2][]; meters
		debug_level); // int debug_level)
		// camera position and orientation relative to the same lat/long on the ground below it
		// double [][] scene_abs_xyzatr_enu = new double [][] {new double[] {0,0,-agl}, scene_abs_atr_enu};
		@@ -3247,6 +3256,25 @@ public class QuadCLTCPU {
		return imp;
		}

		public ImagePlus saveDoubleArrayInTopModelDirectory(
		String suffix,
		String [] labels, // or null
		double [][] data,
		int width,
		int height)
		{
		String x3d_path = getX3dTopDirectory();
		String file_name = image_name + suffix;
		String file_path = x3d_path + Prefs.getFileSeparator() + file_name + ".tiff";
		ImageStack imageStack = ShowDoubleFloatArrays.makeStack(data, width, height, labels);
		ImagePlus imp = new ImagePlus( file_name, imageStack);
		FileSaver fs=new FileSaver(imp);
		fs.saveAsTiff(file_path);
		System.out.println("saveDoubleArrayInModelDirectory(): saved "+file_path);
		return imp;
		}


		public ImagePlus saveDoubleArrayInModelDirectory(
		String suffix,
		double [] data,
		@@ -16299,6 +16327,7 @@ public class QuadCLTCPU {
		suffix,
		debugLevel);
		}

		public boolean writeLwirPreview(
		final CLTParameters clt_parameters,
		double [] data,
		@@ -16315,7 +16344,6 @@ public class QuadCLTCPU {
		for (int i = 0; i < rendered_texture[0].length; i++) {
		rendered_texture[1][i] = Double.isNaN(rendered_texture[0][i])? 0.0: 1.0;
		}
		// double [] minmax = scene.getColdHot(); // used in linearStackToColor (from this current scene)
		if (!suffix.equals("")) {
		if (minmax == null) { // to replace standard preview file name
		minmax = scene.getColdHot(); // used in linearStackToColor (from this current scene)
		@@ -16324,7 +16352,6 @@ public class QuadCLTCPU {
		suffix +="-RANGE"+(minmax[1]-minmax[0]);
		}
		}
		// int width = getTileProcessor().getTilesX() *getTileProcessor().getTileSize();
		int height = data.length/width;
		String set_name = getImageName();
		if (set_name == null ) {
		@@ -16367,6 +16394,68 @@ public class QuadCLTCPU {
		return true;
		}

		public boolean writeLwirGeoTiffARGB(
		final CLTParameters clt_parameters,
		double [] data,
		double [] lla, // latitude, longitude, altitude (or null)
		LocalDateTime dt, // local date/time or null
		double pix_in_meters,
		int width,
		double [] minmax, // null for auto
		QuadCLT scene,
		int tex_palette,
		String suffix, // include "-geo"
		int debugLevel) {
		if (scene == null) {
		scene = (QuadCLT) this;
		}
		double [][] rendered_texture = new double[][] {data, new double[data.length]};
		for (int i = 0; i < rendered_texture[0].length; i++) {
		rendered_texture[1][i] = Double.isNaN(rendered_texture[0][i])? 0.0: 1.0;
		}
		if (!suffix.equals("")) {
		if (minmax == null) { // to replace standard preview file name
		minmax = scene.getColdHot(); // used in linearStackToColor (from this current scene)
		suffix +="-AUTORANGE";
		} else {
		suffix +="-RANGE"+(minmax[1]-minmax[0]);
		}
		}
		int height = data.length/width;
		String set_name = getImageName();
		if (set_name == null ) {
		QuadCLTCPU.SetChannels [] set_channels = setChannels(debugLevel);
		set_name = set_channels[0].set_name;
		}
		String model_dir= correctionsParameters.selectX3dDirectory(
		set_name, // quad timestamp. Will be ignored if correctionsParameters.use_x3d_subdirs is false
		null,
		true, // smart,
		true); //newAllowed, // save\
		String title = getImageName()+suffix;
		ImagePlus imp = QuadCLTCPU.linearStackToColorLWIR(
		clt_parameters, // CLTParameters clt_parameters,
		tex_palette, // int lwir_palette, // <0 - do not convert
		minmax, // double [] minmax,
		title, // String name,
		"", // String suffix, // such as disparity=...
		true, // boolean toRGB,
		rendered_texture, // faded_textures[nslice], // double [][] texture_data,
		width, // int width, // int tilesX,
		height, // int height, // int tilesY,
		debugLevel); // int debugLevel )
		String image_path = model_dir + Prefs.getFileSeparator() + title+".tiff";
		ElphelTiffWriter.saveTiffARGB32(
		imp,
		image_path,
		lla, // double [] lla, // latitude, longitude, altitude (or null)
		dt, // LocalDateTime dt, // local date/time or null
		pix_in_meters, //double pix_in_meters, // resolution or Double.NaN
		false, // imageJTags,
		debugLevel);
		return true;
		}


		/** broke
		public boolean writeRatingFile( // USED in lwir

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

+101 −28

Original line number	Diff line number	Diff line
		@@ -24,6 +24,7 @@ package com.elphel.imagej.tileprocessor;
		//import java.awt.Point;
		import java.awt.Rectangle;
		import java.io.IOException;
		import java.time.LocalDateTime;
		import java.util.ArrayList;
		import java.util.Arrays;
		import java.util.Collections;
		@@ -39,6 +40,7 @@ import com.elphel.imagej.common.DoubleGaussianBlur;
		import com.elphel.imagej.common.ShowDoubleFloatArrays;
		import com.elphel.imagej.correction.EyesisCorrections;
		import com.elphel.imagej.gpu.TpTask;
		import com.elphel.imagej.ims.Imx5;
		import com.elphel.imagej.x3d.export.GlTfExport;
		import com.elphel.imagej.x3d.export.Render3D;
		import com.elphel.imagej.x3d.export.TriMesh;
		@@ -2468,6 +2470,10 @@ public class TexturedModel {
		final boolean crop_empty = clt_parameters.gmap_crop_empty ; //true;
		final int crop_extra = clt_parameters.gmap_crop_extra ; //20;
		final int [] tex_pals = clt_parameters.gmap_tex_pals ; //{0,1,2};
		final boolean gmap_save_alt = clt_parameters.gmap_save_alt; // true; // save height map (meters ASL)
		final boolean gmap_save_tiff = clt_parameters.gmap_save_tiff; // true; // save transparent TIFF with geo metadata (top left corner)
		final int gmap_tiff_pal = clt_parameters.gmap_tiff_pal; // 0; // LWIR palette for TIFF


		final double range_disparity_offset = clt_parameters.imp.range_disparity_offset;// double range_disparity_offset
		final boolean batch_mode = clt_parameters.multiseq_run; // batch_run;
		@@ -3046,15 +3052,15 @@ public class TexturedModel {
		hdr_whs[0], // int out_width, // output rendered image width in pixels
		hdr_whs[1]); // int out_height); // output rendered image height in pixels
		boolean last_is_alpha = true; // last channel in textures slices is alpha
		double [][] full_render;
		double [][] full_render_z;
		if (use_parallel_proj) {
		full_render =render3D.render3dPlaneParallelProj(
		full_render_z =render3D.render3dPlaneParallelProj(
		tri_meshes, // final ArrayList<TriMesh> tri_meshes,
		last_is_alpha, // final boolean last_is_alpha,
		// scenes[ref_index], //final QuadCLT ref_scene, // all coordinates relative to this scene
		debugLevel); //int debugLevel)
		} else {
		full_render =render3D.render3dPlaneCenterProj(
		full_render_z =render3D.render3dPlaneCenterProj(
		tri_meshes, // final ArrayList<TriMesh> tri_meshes,
		last_is_alpha, // final boolean last_is_alpha,
		// scenes[ref_index], //final QuadCLT ref_scene, // all coordinates relative to this scene
		@@ -3069,33 +3075,100 @@ public class TexturedModel {
		scenes[ref_index].saveDoubleArrayInModelDirectory(
		suffix+"-FULL", // String suffix,
		null, // String [] labels, // or null
		full_render, // double [][] data,
		full_render_z, // double [][] data, // including Z as it was
		hdr_whs[0], // int width, // int tilesX,
		hdr_whs[1]); // int height, // int tilesY,
		double [][] img_cropped_z = full_render_z;
		// int [] wh = hdr_whs.clone();
		if (crop_empty \|\| (crop_extra > 0)) {
		int [] wh = new int[2];
		double [][] img_cropped = Render3D.cropRectified(
		int [] ltwh = new int[4];
		img_cropped_z = Render3D.cropRectified(
		crop_empty, // boolean crop_empty,
		last_is_alpha, // boolean last_is_alpha,
		// last_is_alpha, // boolean last_is_alpha,
		full_render_z.length - 2, // last is Z, previous is alpha
		crop_extra, // int crop_extra,
		hdr_whs[0], // int width,
		wh, // int [] wh, // should be initialized to int [2]
		full_render); // double [][] img_src)
		if (img_cropped != null) { // has NaN and alpha 0-1
		scenes[ref_index].saveDoubleArrayInModelDirectory(
		ltwh, // int [] wh, // should be initialized to int [2]
		full_render_z); // double [][] img_src)
		if (img_cropped_z != null) { // has NaN and alpha 0-1
		hdr_whs[0] = ltwh[2]; // cropped width
		hdr_whs[1] = ltwh[3]; // cropped height
		hdr_x0y0[0] +=ltwh[0]* scaled_pixel_size; // meters corrected by pixels
		hdr_x0y0[1] +=ltwh[1]* scaled_pixel_size; // meters corrected by pixels
		scenes[ref_index].saveDoubleArrayInModelDirectory( // save with Z
		suffix+"-CROP", // String suffix,
		null, // String [] labels, // or null
		img_cropped, // double [][] data,
		wh[0], // int width, // int tilesX,
		wh[1]); // int height, // int tilesY,
		// for (int tex_palette = tex_palette_start; tex_palette <= tex_palette_end; tex_palette++) {
		img_cropped_z, // double [][] data,
		hdr_whs[0], // int width, // int tilesX,
		hdr_whs[1]); // int height, // int tilesY,
		} else {
		img_cropped_z = full_render_z; // restore
		}
		}
		// Here use cropped or full (non-cropped) if not calculated and save separately
		// textures and altitude ASL
		if (img_cropped_z != null) { // has NaN and alpha 0-1
		double [][] img_cropped = new double [img_cropped_z.length - 1][];
		for (int i = 0; i < img_cropped.length; i++) {
		img_cropped[i] = img_cropped_z[i];
		}
		double [][] cropped_z = new double [][] {img_cropped_z[img_cropped_z.length-1].clone(), img_cropped_z[img_cropped_z.length-2]};
		// scale units, add altitude, add NaNs
		double [] ref_lla = scenes[ref_index].getLla();
		if (ref_lla == null) {
		ref_lla = new double[3];
		}
		// correct GPS coordinates to top-left corner of the result (full) image
		double [] top_left_lla_offset_ned = new double[] {
		hdr_x0y0[1], // North // hdr_x0y0 - in meters !
		hdr_x0y0[0], // East
		0}; // no altitude offset here
		double [] top_left_lla = Imx5.offsetLla(ref_lla,top_left_lla_offset_ned);
		int num_pix = 0;
		double sum_z = 0.0;
		for (int i = 0; i < cropped_z[0].length; i++) {
		if (cropped_z[1][i] <= 0.0) {
		cropped_z[0][i] = Double.NaN;
		} else {
		cropped_z[0][i] = ref_lla[2] - cropped_z[0][i] * scaled_pixel_size;
		num_pix++;
		sum_z += cropped_z[0][i];
		}
		}
		double avg_z = sum_z/num_pix;
		top_left_lla[2] = avg_z; // average altitude. Maybe keep drone altitude?
		if (gmap_save_alt) {
		scenes[ref_index].saveDoubleArrayInTopModelDirectory( // save with Z
		suffix+"-ALT", // String suffix,
		null, // String [] labels, // or null
		new double[][] {cropped_z[0]}, // double [][] data,
		hdr_whs[0], // int width, // int tilesX,
		hdr_whs[1]); // int height, // int tilesY,
		}
		double [] minmax = tex_um_fixed ? (new double[] {-tex_um_range/2, tex_um_range/2}): null;
		if (gmap_save_tiff && (gmap_tiff_pal >=0)) {
		LocalDateTime dt = scenes[ref_index].getLocalDateTime();
		scenes[ref_index].writeLwirGeoTiffARGB(
		clt_parameters, // final CLTParameters clt_parameters,
		img_cropped[0], // double [] data,
		top_left_lla, // double [] lla, // latitude, longitude, altitude (or null)
		dt, // LocalDateTime dt, // local date/time or null
		scaled_pixel_size, // double pix_in_meters,
		hdr_whs[0], // int width,
		minmax, // double [] minmax, // null for auto
		null, // QuadCLT scene,
		gmap_tiff_pal, // int tex_palette,
		suffix+"-GEO"+"-PAL"+gmap_tiff_pal, // String suffix,
		debugLevel); // int debugLevel)
		}

		for (int tex_palette: tex_pals) {
		// try with fixed range?
		double [] minmax = tex_um_fixed ? (new double[] {-tex_um_range/2, tex_um_range/2}): null;
		// double [] minmax = tex_um_fixed ? (new double[] {-tex_um_range/2, tex_um_range/2}): null;
		scenes[ref_index].writeLwirPreview(
		clt_parameters, // final CLTParameters clt_parameters,
		img_cropped[0], // double [] data,
		wh[0], // int width, // int tilesX,
		hdr_whs[0], // int width,
		minmax, // double [] minmax, // null for auto
		null, // QuadCLT scene,
		tex_palette, // int tex_palette,
		@@ -3103,7 +3176,7 @@ public class TexturedModel {
		debugLevel); // int debugLevel)
		}
		}
		}

		}
		}
		}