Improved fillNaNs, tested terrain-only tiles (af55d764) · Commits · Elphel / imagej-elphel

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

+13 −4

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

+2 −1

Original line number	Original line	Diff line number	Diff line
	@@ -5531,7 +5531,8 @@ public class TexturedModel {
	0.7, // double diagonal_weight, // relative to ortho		0.7, // double diagonal_weight, // relative to ortho
	100, // int num_passes,		100, // int num_passes,
	0.01, // final double max_rchange, // = 0.01		0.01, // final double max_rchange, // = 0.01
	THREADS_MAX); // final int threadsMax) // maximal number of threads to launch		THREADS_MAX, // final int threadsMax) // maximal number of threads to launch
			0); // final int debugLevel) // 0 - none, 1 - when done, 2 - all iterations
	if (dbg_img != null) dbg_img[4] = sky_pixels_filled.clone();		if (dbg_img != null) dbg_img[4] = sky_pixels_filled.clone();
	if (blur_sigma > 0.0) {		if (blur_sigma > 0.0) {
	(new DoubleGaussianBlur()).blurDouble(		(new DoubleGaussianBlur()).blurDouble(

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

+203 −7

Original line number	Original line	Diff line number	Diff line
	@@ -24,8 +24,10 @@ package com.elphel.imagej.tileprocessor;
	*/		*/

	import java.awt.Rectangle;		import java.awt.Rectangle;
			import java.text.SimpleDateFormat;
	import java.util.ArrayList;		import java.util.ArrayList;
	import java.util.Arrays;		import java.util.Arrays;
			import java.util.Calendar;
	import java.util.Collections;		import java.util.Collections;
	import java.util.Comparator;		import java.util.Comparator;
	//import java.util.concurrent.atomic.AtomicInteger;		//import java.util.concurrent.atomic.AtomicInteger;
	@@ -8805,7 +8807,8 @@ ImageDtt.startAndJoin(threads);
	diagonal_weight, //double diagonal_weight, // relative to ortho		diagonal_weight, //double diagonal_weight, // relative to ortho
	num_passes, // int num_passes,		num_passes, // int num_passes,
	max_rchange, // final double max_rchange, // = 0.01		max_rchange, // final double max_rchange, // = 0.01
	ImageDtt.THREADS_MAX); // final int threadsMax)		ImageDtt.THREADS_MAX, // final int threadsMax)
			0); // final int debugLevel) // 0 - none, 1 - when done, 2 - all iterations
	}		}
	public static double [] fillNaNs(		public static double [] fillNaNs(
	final double [] data,		final double [] data,
	@@ -8826,15 +8829,201 @@ ImageDtt.startAndJoin(threads);
	diagonal_weight, //double diagonal_weight, // relative to ortho		diagonal_weight, //double diagonal_weight, // relative to ortho
	num_passes, // int num_passes,		num_passes, // int num_passes,
	max_rchange, // final double max_rchange, // = 0.01		max_rchange, // final double max_rchange, // = 0.01
	threadsMax); // final int threadsMax)		threadsMax, // final int threadsMax)
			0); // final int debugLevel) // 0 - none, 1 - when done, 2 - all iterations

	}		}

			/**
			* Us this one when filling full frame and prohibit is not used. Faster as it first tries lower resolution, then full
			* @param data_in input data array
			* @param width_full width of the input dtata
			* @param decimate_step decimation step (such as 16)
			* @param num_decimate number of decimation steps (should be >=1). If 1 just two passes
			* @param num_passes number of passes for each decimation step (100)
			* @param max_rchange maximal relative change to exit
			* @param debugTitle Generate images if non-null
			* @param debugLevel debug inner method: 0 - none, 1 - when done, 2 - all iterations
			* @return
			*/
			public static double [] fillNaNs(
			final double [] data_in,
			int width_full,
			final int decimate_step, // 16
			final int num_decimate,
			int num_passes,
			final double max_rchange, // = 0.01
			String debugTitle,
			final int debugLevel) { // 0 - none, 1 - when done, 2 - all iterations
			final int dbg_pix = (debugTitle == null) ? -1 : -1205;
			final double diagonal_weight = 0.7; // relative to ortho
			int height_full = data_in.length/width_full;
			if (debugTitle != null) {
			ShowDoubleFloatArrays.showArrays(
			data_in,
			width_full,
			height_full,
			debugTitle+"-data_in");
			}

			double [] data_prev_filled = null;
			int width_prev = -1;
			double [] dbg_bkp = null;
			for (int ndecimate = num_decimate; ndecimate >= 0; ndecimate--) {
			int dcm = 1;
			for (int i = 0; i < ndecimate; i++) {
			dcm *= decimate_step;
			}
			final int decimate = dcm;
			final int width = (width_full+(decimate-1))/decimate;
			final int height = (height_full+(decimate-1))/decimate;
			final int num_pixels = width*height;
			final double [] data = new double[num_pixels];
			final double [] data_nan = new double[num_pixels]; // only nan/non-nan
			final int grow = 2 * Math.max(width, height);
			if (ndecimate == num_decimate) { // prepare initial lo-res 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 nDecPix = ai.getAndIncrement(); nDecPix < num_pixels; nDecPix = ai.getAndIncrement()) {
			if (nDecPix == dbg_pix) {
			System.out.println("fillNaNs(multi) nDecPix="+nDecPix);
			}
			int x_dcm = nDecPix % width;
			int y_dcm = nDecPix / width;
			int num_defined = 0;
			double sum_val = 0;
			int x0_full = x_dcm*decimate;
			int x1_full = Math.min((x_dcm + 1) * decimate, width_full);
			int y0_full = y_dcm*decimate;
			int y1_full = Math.min((y_dcm + 1) * decimate, height_full);
			for (int y_full = y0_full; y_full < y1_full; y_full++) {
			for (int x_full = x0_full; x_full < x1_full; x_full++) {
			int pix_full = y_full * width_full + x_full;
			double d = data_in[pix_full];
			if (!Double.isNaN(d)) {
			sum_val += d;
			num_defined++;
			}
			}
			}
			if (num_defined > 0) {
			data[nDecPix] = sum_val/num_defined;
			} else {
			data[nDecPix] = Double.NaN;
			}
			}
			}
			};
			}
			ImageDtt.startAndJoin(threads);
			if (debugTitle != null) {
			dbg_bkp = data.clone();
			}
			data_prev_filled = fillNaNs(
			data, // final double [] data,
			null, // final double [] data_nan, // only modify tiles that are not fixed
			null, // final boolean [] prohibit,
			width, // int width,
			grow, // final int grow,
			diagonal_weight, // double diagonal_weight, // relative to ortho
			num_passes, // int num_passes,
			max_rchange, //final double max_rchange, // = 0.01
			ImageDtt.THREADS_MAX, // final int threadsMax) // maximal number of threads to launch
			debugLevel); // final int debugLevel) // 0 - none, 1 - when done, 2 - all iterations

			} else {
			// assuming no NaN in data_prev_filled
			final double [] fdata_prev_filled = data_prev_filled;
			final int fwidth_prev = width_prev;
			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 nDecPix = ai.getAndIncrement(); nDecPix < num_pixels; nDecPix = ai.getAndIncrement()) {
			int x_dcm = nDecPix % width;
			int y_dcm = nDecPix / width;

			double sum_val = 0;
			int x0_full = x_dcm*decimate;
			int x1_full = Math.min((x_dcm + 1) * decimate, width_full);
			int y0_full = y_dcm*decimate;
			int y1_full = Math.min((y_dcm + 1) * decimate, height_full);
			int y_pdcm = y_dcm / decimate_step;
			int x_pdcm = x_dcm / decimate_step;
			int pix_prev = y_pdcm * fwidth_prev + x_pdcm;
			double d_prev = fdata_prev_filled[pix_prev];
			int num_defined = (y1_full-y0_full) * (x1_full-x0_full);
			int num_defined1 = 0;
			int num_fixed = 0; // number of actually defined pixels (not filled in the previous steps
			for (int y_full = y0_full; y_full < y1_full; y_full++) {
			for (int x_full = x0_full; x_full < x1_full; x_full++) {
			int pix_full = y_full * width_full + x_full;
			double d = data_in[pix_full];
			if (!Double.isNaN(d)) {
			sum_val += d;
			num_fixed ++;
			} else {
			sum_val += d_prev;
			}
			num_defined1++;
			}
			}
			if ((num_defined1 != num_defined) \|\| (num_defined == 0)) {
			System.out.println("fillNaNs(multi) BUG: num_defined="+num_defined+", num_defined1="+num_defined1);
			}
			data[nDecPix] = sum_val/num_defined;
			data_nan[nDecPix] = (num_fixed > 0) ? data[nDecPix] : Double.NaN; // non-NaN may be any value, like 0.0;
			}
			}
			};
			}
			ImageDtt.startAndJoin(threads);
			if (debugTitle != null) {
			dbg_bkp = data.clone();
			}
			data_prev_filled = fillNaNs(
			data, // final double [] data,
			data_nan, // final double [] data_nan, // only modify tiles that are not fixed
			null, // final boolean [] prohibit,
			width, // int width,
			grow, // final int grow,
			diagonal_weight, // double diagonal_weight, // relative to ortho
			num_passes, // int num_passes,
			max_rchange, //final double max_rchange, // = 0.01
			ImageDtt.THREADS_MAX, // final int threadsMax) // maximal number of threads to launch
			debugLevel); // final int debugLevel) // 0 - none, 1 - when done, 2 - all iterations
			}
			if (debugTitle != null) {
			String [] dbg_titles = {"data","nan","filled"};
			double [][] dbg_data = {dbg_bkp,data_nan, data_prev_filled};
			ShowDoubleFloatArrays.showArrays(
			dbg_data,
			width,
			height,
			true,
			debugTitle+"-dcm"+decimate,
			dbg_titles);

			}
			width_prev = width;
			}
			return data_prev_filled;
			}




	/**		/**
	* Fill NaN values in 2D array from neighbors using Laplacian==0		* Fill NaN values in 2D array from neighbors using Laplacian==0
	* @param data data array (in line-scan order) with NaN values to be filled,		* @param data data array (in line-scan order) with NaN values to be filled,
	* non-NaN values will not be modified.		* non-NaN values will not be modified.
	* @param data_nan optional "original" data with NaN values to be replaced. If null,		* @param data_nan optional "original" data with NaN values to be replaced. If null,
	* (single-pass) the data[] array will be used		* (single-pass) the data[] array will be used
			* If non-null, will be used as a mask NaN/nonNaN and data - as initial values
	* @param prohibit_in optional (may be null) boolean array of the same size specifying		* @param prohibit_in optional (may be null) boolean array of the same size specifying
	* prohibited pixels.		* prohibited pixels.
	* @param width data width (height = data.length/width)		* @param width data width (height = data.length/width)
	@@ -8843,6 +9032,7 @@ ImageDtt.startAndJoin(threads);
	* @param num_passes maximal number of iterations.		* @param num_passes maximal number of iterations.
	* @param max_rchange max relative (to data RMS) step change to exit iterations.		* @param max_rchange max relative (to data RMS) step change to exit iterations.
	* @param threadsMax maximal number of concurrent threads to launch.		* @param threadsMax maximal number of concurrent threads to launch.
			* @param debugLevel 0 - none, 1 - when done, 2 - all iterations
	* @return data array made of input data with replaced NaN limited by		* @return data array made of input data with replaced NaN limited by
	* optional prohibit array and amount of growth.		* optional prohibit array and amount of growth.
	*/		*/
	@@ -8855,7 +9045,8 @@ ImageDtt.startAndJoin(threads);
	double diagonal_weight, // relative to ortho		double diagonal_weight, // relative to ortho
	int num_passes,		int num_passes,
	final double max_rchange, // = 0.01		final double max_rchange, // = 0.01
	final int threadsMax) // maximal number of threads to launch		final int threadsMax, // maximal number of threads to launch
			final int debugLevel) // 0 - none, 1 - when done, 2 - all iterations
	{		{
	int height = data.length/width;		int height = data.length/width;
	double wdiag = 0.25 *diagonal_weight / (diagonal_weight + 1.0);		double wdiag = 0.25 *diagonal_weight / (diagonal_weight + 1.0);
	@@ -8984,6 +9175,9 @@ ImageDtt.startAndJoin(threads);
	s /= sw;		s /= sw;
	data_io[1][nt] = s;		data_io[1][nt] = s;
	last_change[ti] = Math.max(last_change[ti], Math.abs(data_io[1][nt]-data_io[0][nt]));		last_change[ti] = Math.max(last_change[ti], Math.abs(data_io[1][nt]-data_io[0][nt]));
			if (Double.isNaN(last_change[ti] )) {
			System.out.println("fillNaNs():ti="+ti+",data_io[0]["+nt+"]="+data_io[0][nt]+",data_io[1]["+nt+"]="+data_io[1][nt]);
			}
	}		}
	}		}
	};		};
	@@ -8994,8 +9188,10 @@ ImageDtt.startAndJoin(threads);
	multi_change = Math.max(multi_change, last_change[i]);		multi_change = Math.max(multi_change, last_change[i]);
	}		}
	boolean done = (pass >= (num_passes - 1)) \|\| (multi_change < max_change);		boolean done = (pass >= (num_passes - 1)) \|\| (multi_change < max_change);
	if (data_nan != null) {		if ((debugLevel > 1) \|\| ((debugLevel >0) && done)) {
	System.out.println("fillNaNs(): pass="+pass+" change="+multi_change+" done="+done);		// if (data_nan != null) {
			System.out.println("fillNaNs(): "+(new SimpleDateFormat("yyyy/MM/dd HH:mm:ss").format(Calendar.getInstance().getTime()))+
			" pass="+pass+" change="+multi_change+" done="+done);
	}		}
	if (done) {		if (done) {
	break;		break;

Original line number	Original line	Diff line number	Diff line
	@@ -892,6 +892,8 @@ min_str_neib_fpn 0.35
	public int terr_num_exaggerate = 3; // generate exaggerated rendering		public int terr_num_exaggerate = 3; // generate exaggerated rendering

	// Experimental reconstruction		// Experimental reconstruction
			public boolean terr_rebuild_elev = false; // rebuild elevations and scales
			public int terr_elev_grow = 1024; // was 200
	public double terr_threshold_terrain = 0.05;		public double terr_threshold_terrain = 0.05;
	public double terr_min_max_terrain= 0.1;		public double terr_min_max_terrain= 0.1;
	public double terr_min_terrain = 0.001;		public double terr_min_terrain = 0.001;
	@@ -2249,6 +2251,9 @@ min_str_neib_fpn 0.35
	gd.addNumericField("Exagerrate steps", terr_num_exaggerate, 0,3,"", ".");		gd.addNumericField("Exagerrate steps", terr_num_exaggerate, 0,3,"", ".");

	gd.addMessage ("Experimental");		gd.addMessage ("Experimental");
			gd.addCheckbox ("Rebuild elevations", terr_rebuild_elev, "Regenerate elevations/scales in *.terrveg-tiff file");
			gd.addNumericField("Grow elevations", terr_elev_grow, 0,3,"","Grow elevations over NaNs.");

	gd.addNumericField("Terrain threshold alpha",terr_threshold_terrain, 5,7,"", ".");		gd.addNumericField("Terrain threshold alpha",terr_threshold_terrain, 5,7,"", ".");
	gd.addNumericField("Min max terrain", terr_min_max_terrain, 5,7,"", ".");		gd.addNumericField("Min max terrain", terr_min_max_terrain, 5,7,"", ".");
	gd.addNumericField("Minimal terrain", terr_min_terrain, 5,7,"", ".");		gd.addNumericField("Minimal terrain", terr_min_terrain, 5,7,"", ".");
	@@ -3021,7 +3026,8 @@ min_str_neib_fpn 0.35
	terr_boost_render = gd.getNextNumber(); // double		terr_boost_render = gd.getNextNumber(); // double
	terr_max_render = gd.getNextNumber(); // double		terr_max_render = gd.getNextNumber(); // double
	terr_num_exaggerate = (int)gd.getNextNumber(); // int		terr_num_exaggerate = (int)gd.getNextNumber(); // int
			terr_rebuild_elev = gd.getNextBoolean();// boolean
			terr_elev_grow = (int)gd.getNextNumber(); // int
	terr_threshold_terrain = gd.getNextNumber();// double		terr_threshold_terrain = gd.getNextNumber();// double
	terr_min_max_terrain = gd.getNextNumber();// double		terr_min_max_terrain = gd.getNextNumber();// double
	terr_min_terrain = gd.getNextNumber();// double		terr_min_terrain = gd.getNextNumber();// double
	@@ -3772,7 +3778,8 @@ min_str_neib_fpn 0.35
	properties.setProperty(prefix+"terr_boost_render", terr_boost_render+""); // double		properties.setProperty(prefix+"terr_boost_render", terr_boost_render+""); // double
	properties.setProperty(prefix+"terr_max_render", terr_max_render+""); // double		properties.setProperty(prefix+"terr_max_render", terr_max_render+""); // double
	properties.setProperty(prefix+"terr_num_exaggerate", terr_num_exaggerate+""); // int		properties.setProperty(prefix+"terr_num_exaggerate", terr_num_exaggerate+""); // int
			properties.setProperty(prefix+"terr_rebuild_elev", terr_rebuild_elev+""); // boolean
			properties.setProperty(prefix+"terr_elev_grow", terr_elev_grow+""); // int
	properties.setProperty(prefix+"terr_threshold_terrain", terr_threshold_terrain+""); // double		properties.setProperty(prefix+"terr_threshold_terrain", terr_threshold_terrain+""); // double
	properties.setProperty(prefix+"terr_min_max_terrain", terr_min_max_terrain+""); // double		properties.setProperty(prefix+"terr_min_max_terrain", terr_min_max_terrain+""); // double
	properties.setProperty(prefix+"terr_min_terrain", terr_min_terrain+""); // double		properties.setProperty(prefix+"terr_min_terrain", terr_min_terrain+""); // double
	@@ -4543,7 +4550,8 @@ min_str_neib_fpn 0.35
	if (properties.getProperty(prefix+"terr_boost_render")!= null) terr_boost_render=Double.parseDouble(properties.getProperty(prefix+"terr_boost_render"));		if (properties.getProperty(prefix+"terr_boost_render")!= null) terr_boost_render=Double.parseDouble(properties.getProperty(prefix+"terr_boost_render"));
	if (properties.getProperty(prefix+"terr_max_render")!= null) terr_max_render=Double.parseDouble(properties.getProperty(prefix+"terr_max_render"));		if (properties.getProperty(prefix+"terr_max_render")!= null) terr_max_render=Double.parseDouble(properties.getProperty(prefix+"terr_max_render"));

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