More untested mapping code, bug fix in variable DSI average disparity (590d3aba) · Commits · Elphel / imagej-elphel

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

+7 −0

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

+160 −0

Original line number	Original line	Diff line number	Diff line
	@@ -112,6 +112,7 @@ import com.elphel.imagej.lwir.LwirReader;
	import com.elphel.imagej.orthomosaic.ComboMatch;		import com.elphel.imagej.orthomosaic.ComboMatch;
	import com.elphel.imagej.readers.ChangeImageResolution;		import com.elphel.imagej.readers.ChangeImageResolution;
	import com.elphel.imagej.readers.DumpImageMetadata;		import com.elphel.imagej.readers.DumpImageMetadata;
			import com.elphel.imagej.readers.ElphelTiffReader;
	import com.elphel.imagej.readers.EyesisTiff;		import com.elphel.imagej.readers.EyesisTiff;
	import com.elphel.imagej.tensorflow.TensorflowInferModel;		import com.elphel.imagej.tensorflow.TensorflowInferModel;
	import com.elphel.imagej.tileprocessor.Clt1d;		import com.elphel.imagej.tileprocessor.Clt1d;
	@@ -844,6 +845,8 @@ public class Eyesis_Correction implements PlugIn, ActionListener {
	addButton("Show mice", panelLWIRWorld, color_process);		addButton("Show mice", panelLWIRWorld, color_process);
	addButton("Set pair", panelLWIRWorld, color_process);		addButton("Set pair", panelLWIRWorld, color_process);
	addButton("Warp pair", panelLWIRWorld, color_process);		addButton("Warp pair", panelLWIRWorld, color_process);
			addButton("Read Tiff", panelLWIRWorld, color_process);
			addButton("Set pair GPS", panelLWIRWorld, color_process);
	plugInFrame.add(panelLWIRWorld);		plugInFrame.add(panelLWIRWorld);

	}		}
	@@ -5683,8 +5686,165 @@ public class Eyesis_Correction implements PlugIn, ActionListener {
	DEBUG_LEVEL = MASTER_DEBUG_LEVEL;		DEBUG_LEVEL = MASTER_DEBUG_LEVEL;
	EYESIS_CORRECTIONS.setDebug(DEBUG_LEVEL);		EYESIS_CORRECTIONS.setDebug(DEBUG_LEVEL);
	ComboMatch.testPair();		ComboMatch.testPair();
			} else if (label.equals("Read Tiff")) {
			DEBUG_LEVEL = MASTER_DEBUG_LEVEL;
			EYESIS_CORRECTIONS.setDebug(DEBUG_LEVEL);
			ImagePlus imp_sel = WindowManager.getCurrentImage();
			if (imp_sel == null) {
			IJ.showMessage("Error", "No images selected");
			return;
			}
			String orig_path = imp_sel.getOriginalFileInfo().getFilePath();
			try {
			ElphelTiffReader.getTiffMeta(orig_path);
			} catch (IOException e) {
			// TODO Auto-generated catch block
			e.printStackTrace();
			}
			// ComboMatch.testReadTiff();
			} 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);
			} catch (Exception e) {
			System.out.println("Failed to initialize GPU class");
			// TODO Auto-generated catch block
			e.printStackTrace();
			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) {
			debugInitOneScene();
			}
			ComboMatch.openTestPairGps(
			CLT_PARAMETERS, // CLTParameters clt_parameters,
			GPU_TILE_PROCESSOR,
			DEBUG_LEVEL);
			}

			}

			public boolean debugInitOneScene() {
			DEBUG_LEVEL = MASTER_DEBUG_LEVEL;
			if (EYESIS_CORRECTIONS_AUX == null) {
			EYESIS_CORRECTIONS_AUX = new EyesisCorrections(SYNC_COMMAND.stopRequested,
			CORRECTION_PARAMETERS.getAux());
			}
			EYESIS_CORRECTIONS_AUX.setDebug(DEBUG_LEVEL);
			if (QUAD_CLT_AUX == null) {
			QUAD_CLT_AUX = new QuadCLT(QuadCLT.PREFIX_AUX, PROPERTIES, EYESIS_CORRECTIONS_AUX,
			CORRECTION_PARAMETERS.getAux());
			if (DEBUG_LEVEL > 0) {
			System.out.println("Created new QuadCLT AUX instance, will need to read CLT kernels");
	}		}
	}		}
			String configPath = getSaveCongigPath();
			if (configPath.equals("ABORT"))
			return false;

			EYESIS_CORRECTIONS_AUX.initSensorFiles(DEBUG_LEVEL, false, // boolean missing_ok,
			true, // boolean all_sensors, Otherwise - Eyesis
			COLOR_PROC_PARAMETERS_AUX.correct_vignetting); // boolean correct_vignetting

			int numChannels = EYESIS_CORRECTIONS_AUX.getNumChannels();
			// NONLIN_PARAMETERS.modifyNumChannels(numChannels);
			CHANNEL_GAINS_PARAMETERS_AUX.modifyNumChannels(numChannels);

			if (!QUAD_CLT_AUX.CLTKernelsAvailable()) {
			if (DEBUG_LEVEL > 0) {
			System.out.println("Reading AUX CLT kernels");
			}
			QUAD_CLT_AUX.readCLTKernels(CLT_PARAMETERS, THREADS_MAX, UPDATE_STATUS, // update status info
			DEBUG_LEVEL);

			if (DEBUG_LEVEL > 1) {
			QUAD_CLT_AUX.showCLTKernels(THREADS_MAX, UPDATE_STATUS, // update status info
			DEBUG_LEVEL);
			}
			}

			if (!QUAD_CLT_AUX.geometryCorrectionAvailable()) {
			if (DEBUG_LEVEL > 0) {
			System.out.println("Calculating geometryCorrection");
			}
			if (!QUAD_CLT_AUX.initGeometryCorrection(DEBUG_LEVEL + 2)) {
			return false;
			}
			}
			// After kernels and GeometryCorrection
			if (CLT_PARAMETERS.useGPU()) { // only init GPU instances if it is used
			if (GPU_TILE_PROCESSOR == null) {
			try {
			GPU_TILE_PROCESSOR = new GPUTileProcessor(CORRECTION_PARAMETERS.tile_processor_gpu);
			} catch (Exception e) {
			System.out.println("Failed to initialize GPU class");
			// TODO Auto-generated catch block
			e.printStackTrace();
			return false;
			} // final int debugLevel);
			}
			/*
			* if (CLT_PARAMETERS.useGPU(false) && (QUAD_CLT != null) && (GPU_QUAD == null))
			* { // if GPU main is needed try { GPU_QUAD = new GpuQuad( GPU_TILE_PROCESSOR,
			* QUAD_CLT); } catch (Exception e) {
			* System.out.println("Failed to initialize GpuQuad class"); // TODO
			* Auto-generated catch block e.printStackTrace(); return; // false; } //final
			* int debugLevel); QUAD_CLT.setGPU(GPU_QUAD); }
			*/
			if (CLT_PARAMETERS.useGPU(true) && (QUAD_CLT_AUX != null) && (GPU_QUAD_AUX == null)) { // if GPU AUX is
			try {
			GPU_QUAD_AUX = new GpuQuad(//
			GPU_TILE_PROCESSOR, QUAD_CLT_AUX, CLT_PARAMETERS.gpu_debug_level);
			} catch (Exception e) {
			System.out.println("Failed to initialize GpuQuad class");
			// TODO Auto-generated catch block
			e.printStackTrace();
			return false; // false;
			} // final int debugLevel);
			QUAD_CLT_AUX.setGPU(GPU_QUAD_AUX);
			}
			}


			return true;
			}


	/* ======================================================================== */		/* ======================================================================== */
	public boolean editIMU(boolean aux) {		public boolean editIMU(boolean aux) {

src/main/java/com/elphel/imagej/gpu/GpuQuad.java

+591 −14

File changed.

Preview size limit exceeded, changes collapsed.

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

0 → 100644

+382 −0

Original line number	Original line	Diff line number	Diff line
			package com.elphel.imagej.orthomosaic;

			import java.io.IOException;
			import java.time.LocalDateTime;
			import java.util.Arrays;
			import java.util.HashMap;
			import java.util.Properties;
			import java.util.concurrent.atomic.AtomicInteger;

			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 Jama.Matrix;
			import ij.ImagePlus;
			import ij.Prefs;
			import ij.gui.PointRoi;

			public class ComboMap {
			public final String name; // timestamp
			public String path; // full path to the model directory (including /vXX?)
			public double [] lla; // lat/long/alt
			public LocalDateTime dt;
			private double [][] affine = new double[][] {{1,0,0},{0,1,0}}; // relative to vert_meters[]
			public double orig_pix_meters;
			public double [] vert_meters; // offset of the image vertical in meters (scale-invariant)
			public FloatImageData orig_image;
			public int orig_zoom_level;
			public boolean orig_zoom_valid;
			public double need_extra_zoom;
			HashMap <Integer, FloatImageData> images;

			// Generate ALT image path from the GEO
			public static String getNameFromPath(String path) {
			int p1 = path.lastIndexOf(Prefs.getFileSeparator());
			if (p1 < 0) return null;
			int p2 = path.indexOf("-", p1+1);
			if (p2 < 0) return null;
			return path.substring(p1+1, p2);
			}

			public ComboMap (String path) {
			this.path = path;
			name = getNameFromPath(path);
			Properties imp_prop = null;
			try {
			imp_prop = ElphelTiffReader.getTiffMeta(path);
			} catch (IOException e) {
			// TODO Auto-generated catch block
			e.printStackTrace();
			}
			lla = ElphelTiffReader.getLLA(imp_prop);
			dt = ElphelTiffReader.getLocalDateTime(imp_prop);
			vert_meters = ElphelTiffReader.getXYOffsetMeters(imp_prop);
			orig_pix_meters = ElphelTiffReader.getPixelSize(imp_prop)[0];
			orig_zoom_level = FloatImageData.getZoomLevel(orig_pix_meters);
			orig_zoom_valid = FloatImageData.isZoomValid(orig_pix_meters);
			need_extra_zoom = FloatImageData.needZoomIn(orig_pix_meters);
			images = new HashMap <Integer, FloatImageData>();
			}

			public void setAffine(double [][] affine) {
			this.affine = affine;
			}
			public double [][] getAffine(){
			return affine;
			}
			public boolean readImageData() {
			ImagePlus imp = new ImagePlus(path);
			int width = imp.getWidth();
			int height = imp.getHeight();
			orig_image = new FloatImageData (
			width, // int width,
			height, // int height,
			orig_zoom_level, // int zoom_lev,
			vert_meters, // double [] vert, // x,y pixel offset of the point under the camera
			(float[]) (imp.getProcessor().getPixels())); // data);
			if (orig_zoom_valid) {
			images.put(orig_zoom_level, orig_image);
			}
			return true;
			}
			public ImagePlus getOriginalImage(boolean show_markers) {
			if (orig_image != null) {
			String full_name = path.substring(path.lastIndexOf(Prefs.getFileSeparator()) + 1);
			ImagePlus imp = ShowDoubleFloatArrays.makeArrays(
			orig_image.data, // float[] pixels,
			orig_image.width,
			orig_image.height,
			full_name);
			if (show_markers) {
			PointRoi roi = new PointRoi();
			roi.addPoint(orig_image.vert[0],orig_image.vert[1]);
			roi.setOptions("label");
			imp.setRoi(roi);
			}
			return imp;
			}
			return null;
			}

			public double [] enuOffsetTo(ComboMap other) {
			return Imx5.enuFromLla(other.lla, lla);
			}

			public static double getPixelSizeMeters (int zoom_level ) {
			double ps = 0.01; // 1 cm;
			if (zoom_level >0) {
			for (int i = 0; i < zoom_level; i++) {
			ps /= 2;
			}
			} else {
			for (int i = 0; i > zoom_level; i++) {
			ps *= 2;
			}
			}
			return ps;
			}
			// private double [][] affine = new double[2][3];
			// vert_meters = ElphelTiffReader.getXYOffsetMeters(imp_prop);
			public double [][] getBoundsMeters (boolean inverse){ // inverse - from source to rectified
			// orig_pix_meters
			double width_meters = orig_image.width * orig_pix_meters;
			double height_meters = orig_image.height * orig_pix_meters;
			double [][] corners = new double[][] { // CW from TL
			{ vert_meters[0], vert_meters[1]},
			{width_meters - vert_meters[0], vert_meters[1]},
			{width_meters - vert_meters[0], height_meters - vert_meters[1]},
			{ vert_meters[0], height_meters - vert_meters[1]}};
			double [][] aff_corners = new double [4][2];
			for (int n = 0; n < aff_corners.length; n++) {
			aff_corners[n][0] = affine[0][0]corners[n][0] + affine[0][1]corners[n][1] + affine[0][2];
			aff_corners[n][1] = affine[1][0]corners[n][0] + affine[1][1]corners[n][1] + affine[1][2];
			}
			double [][] bounds = new double [2][2]; // rows: x,y. Columns: min,max.
			for (int n = 0; n < 2; n++) {
			bounds[n][0] = aff_corners[0][0];
			bounds[n][1] = bounds[n][0];
			for (int i = 1; i < aff_corners.length; i++) {
			bounds[n][0]=Math.min(bounds[n][0], aff_corners[i][n]);
			bounds[n][1]=Math.max(bounds[n][1], aff_corners[i][n]);
			}
			}
			return bounds;
			}
			public static double [][] getBoundsMeters(ComboMap [] maps){ // maps[0] as a reference
			double [][] bounds = maps[0].getBoundsMeters(false);
			for (int nmap = 1; nmap < maps.length; nmap++) {
			double [][] bounds_other = maps[nmap].getBoundsMeters(false);
			double [] enuOffset = maps[0].enuOffsetTo(maps[nmap]);
			double [] rd = {enuOffset[0], -enuOffset[1]}; // {right,down} of the image
			for (int n = 0; n < bounds.length; n++) {
			bounds[n][0] = Math.min(bounds[n][0],bounds_other[n][0]+ rd[n]);
			bounds[n][1] = Math.max(bounds[n][1],bounds_other[n][1]+ rd[n]);
			}
			}
			return bounds;
			}
			public static int [][] getBoundsPixels(
			ComboMap [] maps,
			int zoom_level){ // maps[0] as a reference
			double [][] bounds_meters = getBoundsMeters(maps);
			double pix_size = getPixelSizeMeters (zoom_level);
			int [][] bounds_pix = new int[2][2];
			for (int n = 0; n < bounds_pix.length; n++) {
			bounds_pix[n][0] = (int) Math.floor(bounds_meters[n][0]/pix_size);
			bounds_pix[n][1] = (int) Math.ceil (bounds_meters[n][1]/pix_size);
			}
			return bounds_pix;
			}

			public static double [][] invertAffine(double [][] affine){
			Matrix A = new Matrix (
			new double [][] {{affine[0][0],affine[0][1]},{affine[1][0],affine[1][1]}});
			Matrix Ai = A.inverse();
			Matrix B = new Matrix(new double [][] {{affine[0][2]},{affine[1][2]}});
			Matrix AiB = Ai.times(B);
			double [][] iaffine = {
			{Ai.get(0,0),Ai.get(0,1), -AiB.get(0,0)},
			{Ai.get(1,0),Ai.get(1,1), -AiB.get(1,0)}};
			return iaffine;
			}

			public void removeZoomLevel(int zoom_level) { // either to save memory or remove to later replace
			images.remove(zoom_level);
			}
			public boolean downScaleForGPU (int zoom_level){
			if (orig_image == null) {
			System.out.println("Original image is null");
			return false;
			}
			if (!orig_zoom_valid) {
			System.out.println("Original zoom level is invalid, need_extra_zoom = "+need_extra_zoom);
			return false;
			}
			if (zoom_level > orig_zoom_level) {
			System.out.println("Requested zoom level is too high ("+zoom_level+" > "+orig_zoom_level+")");
			return false;
			}
			if (images.get(zoom_level) != null) {
			return true; // already exists
			}
			int rscale = 1;
			for (int i = orig_zoom_level; i > zoom_level; i--) {
			rscale *= 2;
			}
			final int frscale = rscale;
			int swidth = orig_image.width;
			int sheight = orig_image.height;
			final float [] spix = orig_image.data;
			final int width = (swidth+frscale-1)/frscale;
			final int height = (sheight+frscale-1)/frscale;
			final int tiles = width * height;
			final float [] opix = new float [tiles];
			Arrays.fill(opix, Float.NaN);
			final double [][] wnd = new double [frscale] [frscale];
			for (int i = 0; i <frscale; i++) {
			for (int j = 0; j <frscale; j++) {
			wnd[i][j] = Math.sin((i+0.5)/frscale*Math.PI);
			}
			}
			final Thread[] threads = ImageDtt.newThreadArray();
			final AtomicInteger ai = new AtomicInteger(0);
			for (int ithread = 0; ithread < threads.length; ithread++) {
			threads[ithread] = new Thread() {
			public void run() {
			for (int tile = ai.getAndIncrement(); tile < tiles; tile = ai.getAndIncrement()) {
			int tileX = tile%width;
			int tileY = tile/width;
			int tileW= (frscale(tileX+1) <= swidth) ? frscale:(swidth - frscaletileX);
			int tileH= (frscale(tileY+1) <= sheight) ? frscale:(sheight - frscaletileY);
			double sw = 0.0, swd = 0.0;
			for (int py = 0; py < tileH; py++) {
			int ls = (tileYfrscale + py)swidth;
			for (int px = 0; px < tileW; px++) {
			double d = spix[ls + tileX*frscale+px];
			if (!Double.isNaN(d)) {
			double w = wnd[py][px];
			sw += w;
			swd += w*d;
			}
			if (sw > 0) {
			opix[tileY * width + tileX] = (float) (swd/sw);
			}
			}
			}
			}
			}
			};
			}
			ImageDtt.startAndJoin(threads);
			images.put(zoom_level, new FloatImageData (
			width, // int width,
			height, // int height,
			zoom_level, // int zoom_lev,
			vert_meters, // double [] vert, // x,y pixel offset of the point under the camera
			opix)); // data);
			return true;
			}

			/**
			* Copy prepared scaled image to the top-left corner of the fixed-size
			* float[] array for the GPU input
			* @param zoom_level
			* @param gpu_width
			* @param gpu_height
			* @return
			*/
			public float [] getPaddedGPU (
			int zoom_level,
			int gpu_width,
			int gpu_height){
			boolean got_image = downScaleForGPU (zoom_level); // will create if does not exist
			if (!got_image) {
			System.out.println("getPaddedGPU(): failed to prepare a scaled image");
			return null;
			}
			final float [] padded_gpu = new float[gpu_width*gpu_height];
			final int swidth = orig_image.width;
			final int sheight = orig_image.height;
			final float [] spix = orig_image.data;
			Arrays.fill(padded_gpu, Float.NaN);
			final int cheight = Math.min(sheight,gpu_height);
			final int cwidth = Math.min(swidth, gpu_width);

			final Thread[] threads = ImageDtt.newThreadArray();
			final AtomicInteger ai = new AtomicInteger(0);
			for (int ithread = 0; ithread < threads.length; ithread++) {
			threads[ithread] = new Thread() {
			public void run() {
			for (int row = ai.getAndIncrement(); row < cheight; row = ai.getAndIncrement()) {
			System.arraycopy(
			spix,
			row*swidth,
			padded_gpu,
			row*gpu_width,
			cwidth);
			}
			}
			};
			}
			ImageDtt.startAndJoin(threads);
			return padded_gpu;
			}


			public static float [][] renderMulti (
			ComboMap [] maps,
			int zoom_level){ // maps[0] as a reference

			int [][] bounds = getBoundsPixels(
			maps,
			zoom_level);
			int width = bounds[0][1] - bounds[0][0]; // bounds[x][0] - negative
			int height = bounds[1][1] - bounds[1][0];
			final float [][] fpixels = new float [maps.length][width * height];
			for (int nmap = 0; nmap< maps.length; nmap++) {
			final int fnmap = nmap;
			Arrays.fill(fpixels[nmap], Float.NaN);
			final double scale = getPixelSizeMeters(maps[nmap].orig_zoom_level)/getPixelSizeMeters(zoom_level);
			double [][] inv_bounds = maps[nmap].getBoundsMeters(true);
			double [] enu_offset = maps[0].enuOffsetTo(maps[nmap]);
			final double [] scaled_out_center = { // xy center to apply affine to
			-bounds[0][0]+scale * enu_offset[0],
			-bounds[1][0]+scale * enu_offset[1]};
			final int [][] ibounds = new int [2][2];
			for (int n = 0; n< 2; n++) {
			ibounds[n][0] = (int) Math.floor(-bounds[n][0] + scale*(inv_bounds[n][0] + enu_offset[n]));
			ibounds[n][1] = (int) Math.ceil (-bounds[n][0] + scale*(inv_bounds[n][0] + enu_offset[n]));
			}
			final int local_width = ibounds[0][1] - ibounds[0][0];
			final int local_height = ibounds[1][1] - ibounds[1][0];
			final int local_len = local_width * local_height;
			double [][] src_bounds=maps[nmap].getBoundsMeters (false);
			final double [] src_center = {-src_bounds[0][0],-src_bounds[1][0]}; // x,y center offset in the source image
			final double [][] affine = maps[nmap].affine;
			final int src_width = maps[nmap].orig_image.width;
			final int src_height = maps[nmap].orig_image.height;
			final float [] src_img = maps[nmap].orig_image.data;
			final Thread[] threads = ImageDtt.newThreadArray();
			final AtomicInteger ai = new AtomicInteger(0);
			for (int ithread = 0; ithread < threads.length; ithread++) {
			threads[ithread] = new Thread() {
			public void run() {
			for (int nPix = ai.getAndIncrement(); nPix < local_len; nPix = ai.getAndIncrement()) {
			int opX = nPix % local_width + ibounds[0][0]; // absolute output pX, pY
			int opY = nPix / local_width + ibounds[1][0];
			double dX = (opX - scaled_out_center[0]) /scale; // in original image scale
			double dY = (opY - scaled_out_center[1]) /scale;
			double [] xy_src = {
			affine[0][0]dX+affine[0][1]dY+affine[0][2]+src_center[0],
			affine[1][0]dX+affine[1][1]dY+affine[1][2]+src_center[1]};
			// limit to the source image
			if (xy_src[0] < 0) xy_src[0] = 0;
			else if (xy_src[0] >= (src_width-1)) xy_src[0] = src_width-2; // to be on the safe side
			if (xy_src[1] < 0) xy_src[1] = 0;
			else if (xy_src[1] >= (src_height-1)) xy_src[1] = src_height-2;
			int [] ixy_src = {(int) Math.floor(xy_src[0]), (int)Math.floor(xy_src[1]) };
			double [] kxy = {xy_src[0]-ixy_src[0], xy_src[1]-ixy_src[1]};
			double d00 = src_img[ixy_src[0] + ixy_src[1]*src_width];
			if (!Double.isNaN(d00)) {
			double d01 = src_img[ixy_src[0] + 1 + ixy_src[1]*src_width];
			double d10 = src_img[ixy_src[0] + (ixy_src[1] + 1) *src_width];
			double d11 = src_img[ixy_src[0] + 1 + (ixy_src[1] + 1) *src_width];
			double d = d00(1.0 - kxy[0])(1.0 - kxy[1])+
			d01* kxy[0] *(1.0 - kxy[1])+
			d10(1.0 - kxy[0]) kxy[1]+
			d11* kxy[0] * kxy[1];
			fpixels[fnmap][opX + opY*width] = (float) d;
			}
			}
			}
			};
			}
			ImageDtt.startAndJoin(threads);
			}
			return fpixels;
			}

			}

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

+579 −0

File changed.

Preview size limit exceeded, changes collapsed.

Original line number	Original line	Diff line number	Diff line
	@@ -509,6 +509,8 @@ public class CLTParameters {
	public int gmap_crop_extra = 20;		public int gmap_crop_extra = 20;
	public int [] gmap_tex_pals = {0,1,2};		public int [] gmap_tex_pals = {0,1,2};

			public boolean gmap_gnss_vert = true; // reference ll to the point below (false - top left corner)
			// use Tiff XPosition, YPosition to specify offset to the vertical in the image
	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)
	@@ -1687,6 +1689,7 @@ public class CLTParameters {
	properties.setProperty(prefix+"gmap_crop_extra", this.gmap_crop_extra+""); // int		properties.setProperty(prefix+"gmap_crop_extra", this.gmap_crop_extra+""); // int
	properties.setProperty(prefix+"gmap_tex_pals", CLTParameters.arr_to_str(this.gmap_tex_pals)); // int[]		properties.setProperty(prefix+"gmap_tex_pals", CLTParameters.arr_to_str(this.gmap_tex_pals)); // int[]

			properties.setProperty(prefix+"gmap_gnss_vert", this.gmap_gnss_vert+""); // boolean
	properties.setProperty(prefix+"gmap_save_alt", this.gmap_save_alt+""); // boolean		properties.setProperty(prefix+"gmap_save_alt", this.gmap_save_alt+""); // boolean
	properties.setProperty(prefix+"gmap_save_tiff32", this.gmap_save_tiff32+""); // boolean		properties.setProperty(prefix+"gmap_save_tiff32", this.gmap_save_tiff32+""); // boolean
	properties.setProperty(prefix+"gmap_save_tiff", this.gmap_save_tiff+""); // boolean		properties.setProperty(prefix+"gmap_save_tiff", this.gmap_save_tiff+""); // boolean
	@@ -2737,6 +2740,7 @@ public class CLTParameters {
	if (properties.getProperty(prefix+"gmap_crop_extra")!=null) this.gmap_crop_extra=Integer.parseInt(properties.getProperty(prefix+ "gmap_crop_extra"));// int		if (properties.getProperty(prefix+"gmap_crop_extra")!=null) this.gmap_crop_extra=Integer.parseInt(properties.getProperty(prefix+ "gmap_crop_extra"));// int
	if (properties.getProperty(prefix+"gmap_tex_pals")!=null) this.gmap_tex_pals=CLTParameters.str_to_iarr(properties.getProperty(prefix+"gmap_tex_pals"));		if (properties.getProperty(prefix+"gmap_tex_pals")!=null) this.gmap_tex_pals=CLTParameters.str_to_iarr(properties.getProperty(prefix+"gmap_tex_pals"));

			if (properties.getProperty(prefix+"gmap_gnss_vert")!=null) this.gmap_gnss_vert=Boolean.parseBoolean(properties.getProperty(prefix+ "gmap_gnss_vert"));
	if (properties.getProperty(prefix+"gmap_save_alt")!=null) this.gmap_save_alt=Boolean.parseBoolean(properties.getProperty(prefix+ "gmap_save_alt"));		if (properties.getProperty(prefix+"gmap_save_alt")!=null) this.gmap_save_alt=Boolean.parseBoolean(properties.getProperty(prefix+ "gmap_save_alt"));
	if (properties.getProperty(prefix+"gmap_save_tiff32")!=null) this.gmap_save_tiff32=Boolean.parseBoolean(properties.getProperty(prefix+ "gmap_save_tiff32"));		if (properties.getProperty(prefix+"gmap_save_tiff32")!=null) this.gmap_save_tiff32=Boolean.parseBoolean(properties.getProperty(prefix+ "gmap_save_tiff32"));
	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"));
	@@ -4055,6 +4059,8 @@ public class CLTParameters {
	gd.addStringField ("LWIR palettes to render the maps", CLTParameters.arr_to_str(this.gmap_tex_pals), 40,		gd.addStringField ("LWIR palettes to render the maps", CLTParameters.arr_to_str(this.gmap_tex_pals), 40,
	"Enter space-separated list of the palette numbers, such as, such as '0 1 2'");		"Enter space-separated list of the palette numbers, such as, such as '0 1 2'");

			gd.addCheckbox ("Reference GNSS LLA to below the camera", this.gmap_gnss_vert, // true; // enable change FG pixel to opaque from transparent
			"If false - to the top left image corner(NW). Use Tiff XPosition, YPosition for the offset to the vertical.");
	gd.addCheckbox ("Save height map (meters ASL)", this.gmap_save_alt, // true; // enable change FG pixel to opaque from transparent		gd.addCheckbox ("Save height map (meters ASL)", this.gmap_save_alt, // true; // enable change FG pixel to opaque from transparent
	"Save height map (meters Above Seal Level) as a floating-point single-slice TIFF (NAN for transparency).");		"Save height map (meters Above Seal Level) as a floating-point single-slice TIFF (NAN for transparency).");
	gd.addCheckbox ("Save float Tiff with transparency and Geo",this.gmap_save_tiff32, // true; // enable change FG pixel to opaque from transparent		gd.addCheckbox ("Save float Tiff with transparency and Geo",this.gmap_save_tiff32, // true; // enable change FG pixel to opaque from transparent
	@@ -5315,6 +5321,7 @@ public class CLTParameters {
	this.gmap_crop_extra= (int) gd.getNextNumber();		this.gmap_crop_extra= (int) gd.getNextNumber();
	this.gmap_tex_pals = CLTParameters.str_to_iarr(gd.getNextString());		this.gmap_tex_pals = CLTParameters.str_to_iarr(gd.getNextString());

			this.gmap_gnss_vert= gd.getNextBoolean();
	this.gmap_save_alt= gd.getNextBoolean();		this.gmap_save_alt= gd.getNextBoolean();

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