Linear output for GRAY32 GEO output, UM for ARGB (slow fillNaNs) (a47aabbe) · Commits · Elphel / imagej-elphel

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

+47 −3

Original line number	Original line	Diff line number	Diff line
	@@ -489,7 +489,14 @@ public class CLTParameters {
	public boolean gmap_save_alt = true; // save height map (meters ASL)		public boolean gmap_save_alt = true; // save height map (meters ASL)
	public boolean gmap_save_tiff32 = true; // save float TIFF (NaN for transparency) with geo metadata (top left corner)		public boolean gmap_save_tiff32 = true; // save float TIFF (NaN for transparency) with geo metadata (top left corner)
	public boolean gmap_save_tiff = true; // save transparent TIFF with geo metadata (top left corner)		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 int gmap_tiff_pal = 0; // LWIR palette for ARGB TIFF

			public boolean gmap_um = true; // Use unsharp mask filter for ARGB TIFF maps
			public double gmap_um_sigma = 0.4; // Unsharp mask sigma for ARGB TIFF maps (in meters)
			public double gmap_um_weight = 0.8; // Unsharp mask weight for ARGB TIFF maps
			public boolean gmap_lwir_autorange = true; // Autorange LWIR textures for ARGB TIFF maps
			public boolean gmap_um_fixed = false; // Use fixed range after unsharp mask instead of autorange for ARGB TIFF maps
			public double gmap_um_range = 500; // Full range after unsharp mask for ARGB TIFF maps

	public boolean generate_bg = true; // Generate background image for 3dmodels		public boolean generate_bg = true; // Generate background image for 3dmodels
	public boolean show_textures = true; // show generated textures		public boolean show_textures = true; // show generated textures
	@@ -1640,6 +1647,13 @@ public class CLTParameters {
	properties.setProperty(prefix+"gmap_save_tiff", this.gmap_save_tiff+""); // boolean		properties.setProperty(prefix+"gmap_save_tiff", this.gmap_save_tiff+""); // boolean
	properties.setProperty(prefix+"gmap_tiff_pal", this.gmap_tiff_pal+""); // int		properties.setProperty(prefix+"gmap_tiff_pal", this.gmap_tiff_pal+""); // int

			properties.setProperty(prefix+"gmap_um", this.gmap_um+""); // boolean
			properties.setProperty(prefix+"gmap_um_sigma", this.gmap_um_sigma+""); // double
			properties.setProperty(prefix+"gmap_um_weight", this.gmap_um_weight+""); // double
			properties.setProperty(prefix+"gmap_lwir_autorange", this.gmap_lwir_autorange+""); // boolean
			properties.setProperty(prefix+"gmap_um_fixed", this.gmap_um_fixed+""); // boolean
			properties.setProperty(prefix+"gmap_um_range", this.gmap_um_range+""); // double

	properties.setProperty(prefix+"generate_bg", this.generate_bg+"");		properties.setProperty(prefix+"generate_bg", this.generate_bg+"");
	properties.setProperty(prefix+"show_textures", this.show_textures+"");		properties.setProperty(prefix+"show_textures", this.show_textures+"");
	properties.setProperty(prefix+"debug_filters", this.debug_filters+"");		properties.setProperty(prefix+"debug_filters", this.debug_filters+"");
	@@ -2664,6 +2678,13 @@ public class CLTParameters {
	if (properties.getProperty(prefix+"gmap_save_tiff")!=null) this.gmap_save_tiff=Boolean.parseBoolean(properties.getProperty(prefix+ "gmap_save_tiff"));		if (properties.getProperty(prefix+"gmap_save_tiff")!=null) this.gmap_save_tiff=Boolean.parseBoolean(properties.getProperty(prefix+ "gmap_save_tiff"));
	if (properties.getProperty(prefix+"gmap_tiff_pal")!=null) this.gmap_tiff_pal=Integer.parseInt(properties.getProperty(prefix+ "gmap_tiff_pal"));// int		if (properties.getProperty(prefix+"gmap_tiff_pal")!=null) this.gmap_tiff_pal=Integer.parseInt(properties.getProperty(prefix+ "gmap_tiff_pal"));// int

			if (properties.getProperty(prefix+"gmap_um")!=null) this.gmap_um=Boolean.parseBoolean(properties.getProperty(prefix+"gmap_um"));
			if (properties.getProperty(prefix+"gmap_um_sigma")!=null) this.gmap_um_sigma=Double.parseDouble(properties.getProperty(prefix+"gmap_um_sigma"));
			if (properties.getProperty(prefix+"gmap_um_weight")!=null) this.gmap_um_weight=Double.parseDouble(properties.getProperty(prefix+"gmap_um_weight"));
			if (properties.getProperty(prefix+"gmap_lwir_autorange")!=null) this.gmap_lwir_autorange=Boolean.parseBoolean(properties.getProperty(prefix+"gmap_lwir_autorange"));
			if (properties.getProperty(prefix+"gmap_um_fixed")!=null) this.gmap_um_fixed=Boolean.parseBoolean(properties.getProperty(prefix+"gmap_um_fixed"));
			if (properties.getProperty(prefix+"gmap_um_range")!=null) this.gmap_um_range=Double.parseDouble(properties.getProperty(prefix+"gmap_um_range"));

	if (properties.getProperty(prefix+"generate_bg")!=null) this.generate_bg=Boolean.parseBoolean(properties.getProperty(prefix+"generate_bg"));		if (properties.getProperty(prefix+"generate_bg")!=null) this.generate_bg=Boolean.parseBoolean(properties.getProperty(prefix+"generate_bg"));
	if (properties.getProperty(prefix+"show_textures")!=null) this.show_textures=Boolean.parseBoolean(properties.getProperty(prefix+"show_textures"));		if (properties.getProperty(prefix+"show_textures")!=null) this.show_textures=Boolean.parseBoolean(properties.getProperty(prefix+"show_textures"));
	if (properties.getProperty(prefix+"debug_filters")!=null) this.debug_filters=Boolean.parseBoolean(properties.getProperty(prefix+"debug_filters"));		if (properties.getProperty(prefix+"debug_filters")!=null) this.debug_filters=Boolean.parseBoolean(properties.getProperty(prefix+"debug_filters"));
	@@ -3939,9 +3960,25 @@ public class CLTParameters {
	"Save float (32-bit) TIFF with geo and resolution metadata (coordinates correspond to the top left image corner), NAN for transparency.");		"Save float (32-bit) TIFF with geo and resolution metadata (coordinates correspond to the top left image corner), NAN for transparency.");
	gd.addCheckbox ("Save ARGB Tiff with transparency and Geo",this.gmap_save_tiff, // true; // enable change FG pixel to opaque from transparent		gd.addCheckbox ("Save ARGB Tiff with transparency and Geo",this.gmap_save_tiff, // true; // enable change FG pixel to opaque from transparent
	"Save transparent TIFF with geo and resolution metadata (coordinates correspond to the top left image corner).");		"Save transparent TIFF with geo and resolution metadata (coordinates correspond to the top left image corner).");
	gd.addNumericField("Crop maps extra", this.gmap_tiff_pal, 0,3,"", // minimal neighbors to keep alpha		gd.addNumericField("LWIR palette for Geo", this.gmap_tiff_pal, 0,3,"", // minimal neighbors to keep alpha
	"LWIR palette for Geo/transparency TIFF output.");		"LWIR palette for Geo/transparency TIFF output.");

			gd.addMessage ("Unsharp mask parameters for ARGB render of the ground maps");
			gd.addCheckbox ("Apply unsharp mask to ARGB render", this.gmap_um,
			"Use unsharp mask filter for texture.");
			gd.addNumericField("Unsharp mask sigma", this.gmap_um_sigma, 5,7,"m",
			"Unsharp mask sigma for ARGB ground map render in meters.");
			gd.addNumericField("Unsharp mask weight", this.gmap_um_weight, 5,7,"",
			"Unsharp mask weight for ARGB ground map render.");
			gd.addCheckbox ("Autorange LWIR textures", this.gmap_lwir_autorange,
			"Autorange LWIR ARGB ground map render (after unsharp mask).");
			gd.addCheckbox ("Fixed range (after unsharp only)", this.gmap_um_fixed,
			"Use fixed range after unsharp mask for ARGB ground map instead of autorange.");
			gd.addNumericField("Full range for ARGB ground map render",this.gmap_um_range, 5,7,"counts",
			"Full range after unsharp mask when fixed range is selected.");



	gd.addMessage ("Earlier 3D generation parameters");		gd.addMessage ("Earlier 3D generation parameters");
	gd.addCheckbox ("Generate background (infinity) image for 3D (not needed for view down)", this.generate_bg);		gd.addCheckbox ("Generate background (infinity) image for 3D (not needed for view down)", this.generate_bg);
	gd.addCheckbox ("Show generated textures", this.show_textures);		gd.addCheckbox ("Show generated textures", this.show_textures);
	@@ -5163,6 +5200,13 @@ public class CLTParameters {
	this.gmap_save_tiff= gd.getNextBoolean();		this.gmap_save_tiff= gd.getNextBoolean();
	this.gmap_tiff_pal= (int) gd.getNextNumber();		this.gmap_tiff_pal= (int) gd.getNextNumber();

			this.gmap_um = gd.getNextBoolean();
			this.gmap_um_sigma = gd.getNextNumber();
			this.gmap_um_weight = gd.getNextNumber();
			this.gmap_lwir_autorange = gd.getNextBoolean();
			this.gmap_um_fixed = gd.getNextBoolean();
			this.gmap_um_range = gd.getNextNumber();

	this.generate_bg= gd.getNextBoolean();		this.generate_bg= gd.getNextBoolean();
	this.show_textures= gd.getNextBoolean();		this.show_textures= gd.getNextBoolean();
	this.debug_filters= gd.getNextBoolean();		this.debug_filters= gd.getNextBoolean();

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

+7 −7

Original line number	Original line	Diff line number	Diff line
	@@ -194,13 +194,13 @@ public class ElphelTiffWriter {
	int bands = 1; // 4 bands for ARGB, 3 for RGB etc		int bands = 1; // 4 bands for ARGB, 3 for RGB etc
	int[] bandOffsets = {0}; // length == bands, 0 == R, 1 == G, 2 == B and 3 == A		int[] bandOffsets = {0}; // length == bands, 0 == R, 1 == G, 2 == B and 3 == A
	// Create a TYPE_FLOAT sample model (specifying how the pixels are stored)		// Create a TYPE_FLOAT sample model (specifying how the pixels are stored)
	SampleModel sampleModel0 = new PixelInterleavedSampleModel(		// SampleModel sampleModel0 = new PixelInterleavedSampleModel(
	DataBuffer.TYPE_FLOAT,		// DataBuffer.TYPE_FLOAT,
	width,		// width,
	height,		// height,
	bands,		// bands,
	width * bands,		// width * bands,
	bandOffsets);		// bandOffsets);

	// Create a color model compatible with this sample model/raster (TYPE_FLOAT)		// Create a color model compatible with this sample model/raster (TYPE_FLOAT)
	// Note that the number of bands must equal the number of color components in the		// Note that the number of bands must equal the number of color components in the

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

+47 −1

Original line number	Original line	Diff line number	Diff line
	@@ -8668,7 +8668,7 @@ public class QuadCLTCPU {
	double [][][] textures // [nslices][nchn][i]		double [][][] textures // [nslices][nchn][i]
	) {		) {
	if ((textures == null) \|\| (textures.length==0)) {		if ((textures == null) \|\| (textures.length==0)) {
	throw new IllegalArgumentException ("umTextures(): Empty textures");		throw new IllegalArgumentException ("getMinMaxTextures(): Empty textures");
	}		}
	final boolean is_mono = textures[0].length <= 2;		final boolean is_mono = textures[0].length <= 2;
	final int alpha_chn = is_mono? 1 : 3;		final int alpha_chn = is_mono? 1 : 3;
	@@ -16456,6 +16456,52 @@ public class QuadCLTCPU {
	return true;		return true;
	}		}

			// Currently only a single-slice 32-bit file (with NaN for tranparency)
			public boolean writeLwirGeoTiff32(
			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,
			QuadCLT scene,
			String suffix, // include "-geo"
			int debugLevel) {
			if (scene == null) {
			scene = (QuadCLT) this;
			}
			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 = ShowDoubleFloatArrays.makeArrays(
			data, // double[] pixels,
			width, // int width,
			height, // int height,
			title); // String title);
			String image_path = model_dir + Prefs.getFileSeparator() + title+".tiff";
			ElphelTiffWriter.saveTiffARGBOrGray32(
			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		/** broke
	public boolean writeRatingFile( // USED in lwir		public boolean writeRatingFile( // USED in lwir

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

+137 −76

Original line number	Original line	Diff line number	Diff line
	@@ -2471,9 +2471,15 @@ public class TexturedModel {
	final int crop_extra = clt_parameters.gmap_crop_extra ; //20;		final int crop_extra = clt_parameters.gmap_crop_extra ; //20;
	final int [] tex_pals = clt_parameters.gmap_tex_pals ; //{0,1,2};		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_alt = clt_parameters.gmap_save_alt; // true; // save height map (meters ASL)
			final boolean gmap_save_tiff32= clt_parameters.gmap_save_tiff32; // save float TIFF (NaN for transparency) with geo metadata (top left corner)
	final boolean gmap_save_tiff = clt_parameters.gmap_save_tiff; // true; // save transparent TIFF with geo metadata (top left corner)		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 int gmap_tiff_pal = clt_parameters.gmap_tiff_pal; // 0; // LWIR palette for TIFF
			final boolean gmap_um = clt_parameters.gmap_um; // true; // Use unsharp mask filter for ARGB TIFF maps
			final double gmap_um_sigma = clt_parameters.gmap_um_sigma; // 0.4; // Unsharp mask sigma for ARGB TIFF maps (in meters)
			final double gmap_um_weight = clt_parameters.gmap_um_weight; // 0.8; // Unsharp mask weight for ARGB TIFF maps
			final boolean gmap_lwir_autorange = clt_parameters.gmap_lwir_autorange;// true; // Autorange LWIR textures for ARGB TIFF maps
			final boolean gmap_um_fixed = clt_parameters.gmap_um_fixed; // false; // Use fixed range after unsharp mask instead of autorange for ARGB TIFF maps
			final double gmap_um_range = clt_parameters.gmap_um_range; // 500; // Full range after unsharp mask for ARGB TIFF maps

	final double range_disparity_offset = clt_parameters.imp.range_disparity_offset;// double range_disparity_offset		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;		final boolean batch_mode = clt_parameters.multiseq_run; // batch_run;
	@@ -3068,9 +3074,6 @@ public class TexturedModel {
	}		}
	// String model_name = ref_scene.correctionsParameters.getModelName(ref_scene.getImageName());		// String model_name = ref_scene.correctionsParameters.getModelName(ref_scene.getImageName());
	String suffix ="-RECT";		String suffix ="-RECT";
	if (clt_parameters.tex_um) {
	suffix+="-UM"+(clt_parameters.tex_um_sigma)+"_"+(clt_parameters.tex_um_weight);
	}
	suffix +="-PIX"+pix_size * hdr_whs[2];		suffix +="-PIX"+pix_size * hdr_whs[2];
	scenes[ref_index].saveDoubleArrayInModelDirectory(		scenes[ref_index].saveDoubleArrayInModelDirectory(
	suffix+"-FULL", // String suffix,		suffix+"-FULL", // String suffix,
	@@ -3136,18 +3139,75 @@ public class TexturedModel {
	}		}
	}		}
	double avg_z = sum_z/num_pix;		double avg_z = sum_z/num_pix;
			LocalDateTime dt = scenes[ref_index].getLocalDateTime();
	top_left_lla[2] = avg_z; // average altitude. Maybe keep drone altitude?		top_left_lla[2] = avg_z; // average altitude. Maybe keep drone altitude?
	if (gmap_save_alt) {		if (gmap_save_alt) {
			/*
	scenes[ref_index].saveDoubleArrayInTopModelDirectory( // save with Z		scenes[ref_index].saveDoubleArrayInTopModelDirectory( // save with Z
	suffix+"-ALT", // String suffix,		suffix+"-ALT", // String suffix,
	null, // String [] labels, // or null		null, // String [] labels, // or null
	new double[][] {cropped_z[0]}, // double [][] data,		new double[][] {cropped_z[0]}, // double [][] data,
	hdr_whs[0], // int width, // int tilesX,		hdr_whs[0], // int width, // int tilesX,
	hdr_whs[1]); // int height, // int tilesY,		hdr_whs[1]); // int height, // int tilesY,
			*/
			scenes[ref_index].writeLwirGeoTiff32(
			clt_parameters, // final CLTParameters clt_parameters,
			cropped_z[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,
			null, // QuadCLT scene,
			suffix+"-GEO-ALT", // String suffix,
			debugLevel); // int debugLevel)
	}		}
	double [] minmax = tex_um_fixed ? (new double[] {-tex_um_range/2, tex_um_range/2}): null;		if (gmap_save_tiff32) {
			scenes[ref_index].writeLwirGeoTiff32(
			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,
			null, // QuadCLT scene,
			suffix+"-GEO", // String suffix,
			debugLevel); // int debugLevel)
			}
			if ((gmap_save_tiff && (gmap_tiff_pal >=0)) \|\| (tex_pals.length > 0)) {
			// TODO: Move UM here, save 32-bit GEO w/o UM
			if (gmap_um) {
			double um_sigma = gmap_um_sigma / scaled_pixel_size;
			int grow_pix = (int) (4 * um_sigma); // experimentally - UM grows by 4*sigma;
			// it is needed before Gaussian blur which extends NaN
			double [] um_data = TileProcessor.fillNaNs(
			img_cropped[0], // final double [] data,
			null, // final boolean [] prohibit,
			hdr_whs[0], // int width,
			// CAREFUL ! Remaining NaN is grown by unsharp mask filter ************* !
			2grow_pix, // 2width, // 16, // final int grow,
			0.7, // double diagonal_weight, // relative to ortho
			100, // int num_passes,
			0.03, // final double max_rchange, // = 0.01 - does not need to be accurate
			THREADS_MAX); // final int threadsMax) // maximal number of threads to launch
			double [][][] um_data3 = {{um_data}};
			QuadCLTCPU.umTextures(
			um_data3, // final double [][][] textures, // [nslices][nchn][i]
			hdr_whs[0], // tilesX * transform_size, // final int width,
			false, // um_ignore_alpha, // final boolean ignore_alpha,
			um_sigma, // final double um_sigma,
			gmap_um_weight); // final double um_weight)
			for (int i = 0; i < um_data.length; i++) {
			if (Double.isNaN(img_cropped[0][i])) {
			um_data[i] = Double.NaN;
			}
			}
			img_cropped[0] = um_data; // replaced with UM
			suffix+="-UM"+(clt_parameters.tex_um_sigma)+"_"+(clt_parameters.tex_um_weight);

			}

			double [] minmax = gmap_um_fixed ? (new double[] {-gmap_um_range/2, gmap_um_range/2}): null;
	if (gmap_save_tiff && (gmap_tiff_pal >=0)) {		if (gmap_save_tiff && (gmap_tiff_pal >=0)) {
	LocalDateTime dt = scenes[ref_index].getLocalDateTime();
	scenes[ref_index].writeLwirGeoTiffARGB(		scenes[ref_index].writeLwirGeoTiffARGB(
	clt_parameters, // final CLTParameters clt_parameters,		clt_parameters, // final CLTParameters clt_parameters,
	img_cropped[0], // double [] data,		img_cropped[0], // double [] data,
	@@ -3176,6 +3236,7 @@ public class TexturedModel {
	debugLevel); // int debugLevel)		debugLevel); // int debugLevel)
	}		}
	}		}
			}

	}		}
	}		}
	@@ -7593,18 +7654,7 @@ public class TexturedModel {
	tilesX * transform_size, // int width, // int tilesX,		tilesX * transform_size, // int width, // int tilesX,
	tilesY * transform_size); // int height, // int tilesY,		tilesY * transform_size); // int height, // int tilesY,
	}		}
			// save linear textures before applying UM
	// Optionally apply UM (before auto/manual range)
	final boolean um_ignore_alpha = true;
	final boolean hist_ignore_alpha = true;
	if (tex_um) {
	QuadCLTCPU.umTextures(
	faded_textures, // final double [][][] textures, // [nslices][nchn][i]
	tilesX * transform_size, // final int width,
	um_ignore_alpha, // final boolean ignore_alpha,
	tex_um_sigma, // final double um_sigma,
	tex_um_weight); // final double um_weight)
	}
	if (lin_textures != null) {		if (lin_textures != null) {
	// duplicate texture before normalization		// duplicate texture before normalization
	lin_textures[0] = new double [faded_textures.length][][];		lin_textures[0] = new double [faded_textures.length][][];
	@@ -7619,6 +7669,17 @@ public class TexturedModel {
	}		}
	}		}
	}		}
			// Optionally apply UM (before auto/manual range)
			final boolean um_ignore_alpha = true;
			final boolean hist_ignore_alpha = true;
			if (tex_um) {
			QuadCLTCPU.umTextures(
			faded_textures, // final double [][][] textures, // [nslices][nchn][i]
			tilesX * transform_size, // final int width,
			um_ignore_alpha, // final boolean ignore_alpha,
			tex_um_sigma, // final double um_sigma,
			tex_um_weight); // final double um_weight)
			}
	if (save_interm_textures \|\| save_um_texture0) {		if (save_interm_textures \|\| save_um_texture0) {
	double [][] dbg_textures = new double [faded_textures.length * faded_textures[0].length][faded_textures[0][0].length];		double [][] dbg_textures = new double [faded_textures.length * faded_textures[0].length][faded_textures[0][0].length];
	String [] dbg_titles = new String[dbg_textures.length];		String [] dbg_titles = new String[dbg_textures.length];

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