circular deconvolution kernels (2ebcdb9c) · Commits · Elphel / imagej-elphel

src/main/java/com/elphel/imagej/common/DoubleFHT.java

+57 −0

Original line number	Original line	Diff line number	Diff line
	@@ -25,6 +25,7 @@ package com.elphel.imagej.common;
	**		**
	*/		*/
	import java.util.ArrayList;		import java.util.ArrayList;
			import java.util.Arrays;
	import java.util.List;		import java.util.List;

	import ij.IJ;		import ij.IJ;
	@@ -292,6 +293,60 @@ public class DoubleFHT {
	return result;		return result;
	}		}

			/**
			* Invert kernel for deconvolutions. Kernel is assumed to fade near edges
			* @param data source kernel, square, power of 2 sides. Data is destroyed
			* @param fat_zero add to denominator to prevent noise amplification
			* @param highPassSigma high-pass sigma to create frequency filter or 0
			* @param lowPassSigma low-pass sigma to create frequency filter or 0
			* @return inverted kernel
			*/
			public double [] invert (
			double [] data,
			double fat_zero,
			double highPassSigma,
			double lowPassSigma
			) {
			double [] filter= null;
			if ((highPassSigma> 0.0) \|\| (lowPassSigma> 0.0)) {
			updateMaxN(data);
			createFrequencyFilter(highPassSigma, lowPassSigma); // for repetitive calls will reuse mask
			filter =this.freqMask;
			}
			return invert (data, fat_zero, filter);

			}

			/**
			* Invert kernel for deconvolutions. Kernel is assumed to fade near edges
			* @param data source kernel, square, power of 2 sides. Data is destroyed
			* @param fat_zero add to denominator to prevent noise amplification
			* @param filter low-pass/high-pass filter or null
			* @return inverted kernel
			*/
			public double [] invert (
			double [] data, // destroyed
			double fat_zero,
			double [] filter
			) {
			updateMaxN(data);
			int size = (int) Math.sqrt(data.length);
			double nominator_FD_value = size*size; // fill FD of the nominator. what is the best value?
			double [] nominator_FD = new double[data.length];
			Arrays.fill(nominator_FD, nominator_FD_value);
			swapQuadrants(data);
			if (!transform(data,false)) return null; // direct FHT
			double [] inverted = divide(nominator_FD,data, fat_zero);
			if (filter != null) {
			multiplyByReal(inverted, filter);
			}
			transform(inverted, true); // inverse transform
			swapQuadrants(inverted);
			return inverted;
			}



	/* calculates correlation, destroys original arrays */		/* calculates correlation, destroys original arrays */

	public double[] correlate(double[] first, double[] second, double highPassSigma, double lowPassSigma,		public double[] correlate(double[] first, double[] second, double highPassSigma, double lowPassSigma,
	@@ -2320,6 +2375,8 @@ public class DoubleFHT {
	return result;		return result;
	}		}



	public double[] setReal(double[] amp) { // only first half used		public double[] setReal(double[] amp) { // only first half used
	double[] result = new double[maxN * maxN];		double[] result = new double[maxN * maxN];
	int rowMod, colMod;		int rowMod, colMod;

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

+103 −3

Original line number	Original line	Diff line number	Diff line
	@@ -282,9 +282,20 @@ public class ComboMatch {
	double reversal_rad = 0; // 26;// 22; // cut at first direction reversal after		double reversal_rad = 0; // 26;// 22; // cut at first direction reversal after
	double frac_outliers = 0.4;		double frac_outliers = 0.4;
	int default_kernel = 1; // 0; // 1; // default kernel choice 25-> 50// 1 for simulated, 0 - for extracted		int default_kernel = 1; // 0; // 1; // default kernel choice 25-> 50// 1 for simulated, 0 - for extracted
	boolean only_correlate = true;		boolean only_correlate = true; // false; // true;
	int sub_pattern_index = 0;		int sub_pattern_index = 0;

			double inv_fat_zero = 300;
			double inv_lpf_sigma = .05;
			int inv_scale_radial = 8; // scale up radial resolution
			double inv_lim_rad = 50.0; // outside all 0
			double inv_trans_width = 20.0; // lim_rad-trans_width - start reducing
			double inv_blur_center = 1.0; // cosine blur (in original pixels) in the center (<blur_radius) area
			double inv_blur_radius =100.0; // constant blur radius
			double inv_blur_rate = 0.2; // blur increase outside of blur_radius



	// String pattern_dir= "/media/elphel/SSD3-4GB/lwir16-proc/ortho_videos/debug/mines/pattern_25m_zoom1/synthetic/";		// String pattern_dir= "/media/elphel/SSD3-4GB/lwir16-proc/ortho_videos/debug/mines/pattern_25m_zoom1/synthetic/";
	String pattern_dir= "/media/elphel/NVME/lwir16-proc/ortho_videos/mines_extract/evening_50m_sept12/debug_cross/new_synth/";		String pattern_dir= "/media/elphel/NVME/lwir16-proc/ortho_videos/mines_extract/evening_50m_sept12/debug_cross/new_synth/";
	String [] pattern_files={		String [] pattern_files={
	@@ -301,7 +312,17 @@ public class ComboMatch {
	"patterns_r30.0_e5.0_ir12.0_ie5.0_is-1.0_or45.0_oe20.0_os-1.0_h8_w0.6_s-60.0_200x200.tif",		"patterns_r30.0_e5.0_ir12.0_ie5.0_is-1.0_or45.0_oe20.0_os-1.0_h8_w0.6_s-60.0_200x200.tif",
	"patterns_r30.0_e5.0_ir12.0_ie5.0_is-1.0_or50.0_oe40.0_os-1.0_h8_w0.6_s-60.0_200x200.tif", // best		"patterns_r30.0_e5.0_ir12.0_ie5.0_is-1.0_or50.0_oe40.0_os-1.0_h8_w0.6_s-60.0_200x200.tif", // best
	"patterns_r30.0_e5.0_ir12.0_ie5.0_is-1.0_or55.0_oe50.0_os-1.0_h8_w0.6_s-60.0_200x200.tif",		"patterns_r30.0_e5.0_ir12.0_ie5.0_is-1.0_or55.0_oe50.0_os-1.0_h8_w0.6_s-60.0_200x200.tif",
	"patterns_r30.0_e5.0_ir12.0_ie5.0_is0.0_or50.0_oe40.0_os-1.0_h8_w0.6_s-60.0_200x200.tif"		"patterns_r30.0_e5.0_ir12.0_ie5.0_is0.0_or50.0_oe40.0_os-1.0_h8_w0.6_s-60.0_200x200.tif",
			"mine2_multi_zoom-1-INV_PATTERN_fo0.4_lr80.0_tw60.0_rr0.0_128x128.tif",
			"mine2_multi_zoom-1-INV_RADIAL_PATTERN_fo0.4_lr80.0_tw60.0_rr0.0_128x128.tif",
			"patterns_r17.0_e15.0_ir10.0_ie8.0_is0.0_or50.0_oe30.0_os-1.0_h8_w0.6_s-60.0_200x200.tif", // mine2
			"patterns_r17.0_e22.0_ir10.0_ie8.0_is0.0_or50.0_oe30.0_os-1.0_h8_w0.6_s-60.0_200x200.tif",
			"patterns_r20.0_e25.0_ir10.0_ie8.0_is0.0_or50.0_oe25.0_os-1.0_h8_w0.6_s-60.0_200x200.tif",
			"patterns_r20.0_e25.0_ir10.0_ie8.0_is0.0_or55.0_oe25.0_os-1.0_h8_w0.6_s-60.0_200x200.tif",
			"patterns_r20.0_e25.0_ir10.0_ie8.0_is0.0_or45.0_oe20.0_os-1.0_h8_w0.6_s-60.0_200x200.tif",
			"patterns_r20.0_e25.0_ir10.0_ie8.0_is0.0_or40.0_oe20.0_os-1.0_h8_w0.6_s-60.0_200x200.tif",
			"patterns_r20.0_e25.0_ir10.0_ie8.0_is0.0_or35.0_oe15.0_os-1.0_h8_w0.6_s-60.0_200x200.tif",
			"patterns_r20.0_e20.0_ir10.0_ie8.0_is0.0_or35.0_oe15.0_os-1.0_h8_w0.6_s-60.0_200x200.tif"
	};		};


	@@ -328,6 +349,17 @@ public class ComboMatch {
	gdo.addCheckbox ("Only correlate", only_correlate, "do not generate circular kernel.");		gdo.addCheckbox ("Only correlate", only_correlate, "do not generate circular kernel.");
	gdo.addNumericField("subpattern index", sub_pattern_index,0,4,"", "0 - full pattern, 1-8 - half-pattern.");		gdo.addNumericField("subpattern index", sub_pattern_index,0,4,"", "0 - full pattern, 1-8 - half-pattern.");

			gdo.addMessage("Radial kernel inversion");
			gdo.addNumericField("Inversion fat zero", inv_fat_zero, 3,7,"", "Add to amplitude to reduce noise.");
			gdo.addNumericField("LPF sigma", inv_lpf_sigma, 3,7,"", "Filter inversion result.");
			gdo.addNumericField("Scale up radial resolution", inv_scale_radial,0,4,"", "Increase radial resolution for artifacts reduction.");
			gdo.addNumericField("Inverted kernel max radius", inv_lim_rad, 3,7,"pix", "Crop result kernel to this radius.");
			gdo.addNumericField("Fade out width", inv_trans_width, 3,7,"pix", "Fade-out width for radial crop.");
			gdo.addNumericField("Center area blur", inv_blur_center, 3,7,"pix", "Blur while integrating radial profile (center high-res area).");
			gdo.addNumericField("Start radial blur", inv_blur_radius, 3,7,"pix", "Center area radius, blur more outside of it.");
			gdo.addNumericField("Radial blur increase rate", inv_blur_rate, 3,7,"pix/pix", "Rate of the radial blur increase outside of the central area "+
			"- pixel of (biderectional) blur for each radial pixel outside of center area.");

	//only_correlate		//only_correlate
	gdo.showDialog();		gdo.showDialog();
	if (gdo.wasCanceled()) return false;		if (gdo.wasCanceled()) return false;
	@@ -349,6 +381,15 @@ public class ComboMatch {
	only_correlate = gdo.getNextBoolean();		only_correlate = gdo.getNextBoolean();
	sub_pattern_index= (int) gdo.getNextNumber();		sub_pattern_index= (int) gdo.getNextNumber();

			inv_fat_zero = gdo.getNextNumber();
			inv_lpf_sigma = gdo.getNextNumber();
			inv_scale_radial = (int) gdo.getNextNumber();
			inv_lim_rad = gdo.getNextNumber();
			inv_trans_width = gdo.getNextNumber();
			inv_blur_center = gdo.getNextNumber();
			inv_blur_radius = gdo.getNextNumber();
			inv_blur_rate = gdo.getNextNumber();

	System.out.println("Will extract objects here, image zoom_level="+zool_lev_objects);		System.out.println("Will extract objects here, image zoom_level="+zool_lev_objects);
	for (ObjectLocation ol: object_list) {		for (ObjectLocation ol: object_list) {
	System.out.println(ol.name+": "+ol.xy_meters[0]+"/"+ol.xy_meters[1]);		System.out.println(ol.name+": "+ol.xy_meters[0]+"/"+ol.xy_meters[1]);
	@@ -459,6 +500,65 @@ public class ComboMatch {
	for (int j = 0; j < output_patterns[0].length; j++) {		for (int j = 0; j < output_patterns[0].length; j++) {
	output_patterns[object_stack.length][j] /= object_stack.length;		output_patterns[object_stack.length][j] /= object_stack.length;
	}		}

			double [][] inverted_patterns = new double [output_patterns.length][];
			for (int i = 0; i < output_patterns.length; i++) {
			//pattern_file
			String dbg_prefix = OrthoMap.removeKnownExtension(pattern_file)+"-"+i;
			inverted_patterns[i] = ObjectLocation.invertRadialKernel(
			output_patterns[i], // double [] kernel,
			inv_fat_zero, // double fat_zero,
			inv_lpf_sigma, // double lpf_sigma,
			inv_scale_radial, // int scale_radial, // scale up radial resolution
			inv_lim_rad, // double lim_rad, // outside all 0
			inv_trans_width, // double trans_width, // lim_rad-trans_width - start reducing
			inv_blur_center, // double blur_center, // cosine blur (in original pixels) in the center (<blur_radius) area
			inv_blur_radius, // double blur_radius, // constant blur radius
			inv_blur_rate, // double blur_rate, // blur increase outside of blur_radius
			centers, // // double [][] centers,
			object_stack, // double [][] src_cuts,
			dbg_prefix, // String dbg_prefix,
			1); // int debugLevel)
			}
			ImagePlus imp_inv_patt = ShowDoubleFloatArrays.makeArrays(
			inverted_patterns,
			corr_size,
			corr_size,
			OrthoMap.removeKnownExtension(imp_sel.getTitle())+"-INV_RADIAL_PATTERN"+settings_str+"_"+corr_size+"x"+corr_size+".tiff",
			output_patt_titles); // test_titles,
			imp_inv_patt.show();

			// select kernel and correlatde with every cut image?


			// Test invert patterns
			/*

			boolean test_invert = debugLevel > -1000;
			if (test_invert) {
			double invert_fz = 0;
			double [][] inverted_patterns = new double [output_patterns.length][];
			for (int i = 0; i < output_patterns.length; i++) {
			inverted_patterns[i] = output_patterns[i].clone();
			double [] dfr = new double [corr_size*corr_size];
			dfr[corr_size/2(corr_size+1)] = corr_sizecorr_size;
			double [][] data_pair = new double[][] {inverted_patterns[i],dfr};
			inverted_patterns[i]=OrthoMap.deconvolvePair(
			data_pair,
			invert_fz,
			1);


			}
			ImagePlus imp_inv_patt = ShowDoubleFloatArrays.makeArrays(
			inverted_patterns,
			corr_size,
			corr_size,
			OrthoMap.removeKnownExtension(imp_sel.getTitle())+"-INV_PATTERN"+settings_str+"_"+corr_size+"x"+corr_size+".tiff",
			output_patt_titles); // test_titles,
			imp_inv_patt.show();
			}
			*/
	ImagePlus imp_out_patt = ShowDoubleFloatArrays.makeArrays(		ImagePlus imp_out_patt = ShowDoubleFloatArrays.makeArrays(
	output_patterns,		output_patterns,
	corr_size,		corr_size,
	@@ -684,7 +784,7 @@ public class ComboMatch {
	}		}
	}		}
	if (pattern_match) {		if (pattern_match) {
	ImagePlus imp_pat_match = maps_collection.patterMatchDualWrap (		ImagePlus imp_pat_match = maps_collection.patternMatchDualWrap (
	gpu_pair, // int [] indices, // null or which indices to use (normally just 2 for pairwise comparison)		gpu_pair, // int [] indices, // null or which indices to use (normally just 2 for pairwise comparison)
	affines, // double [][][] affines, // null or [indices.length][2][3]		affines, // double [][][] affines, // null or [indices.length][2][3]
	warp); // FineXYCorr warp)		warp); // FineXYCorr warp)

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

+224 −0

Original line number	Original line	Diff line number	Diff line
	@@ -5,6 +5,7 @@ import java.util.Arrays;
	import java.util.Collections;		import java.util.Collections;
	import java.util.Comparator;		import java.util.Comparator;

			import com.elphel.imagej.common.DoubleFHT;
	import com.elphel.imagej.common.ShowDoubleFloatArrays;		import com.elphel.imagej.common.ShowDoubleFloatArrays;
	import com.elphel.imagej.tileprocessor.Correlation2d;		import com.elphel.imagej.tileprocessor.Correlation2d;
	import com.elphel.imagej.tileprocessor.TileNeibs;		import com.elphel.imagej.tileprocessor.TileNeibs;
	@@ -197,6 +198,229 @@ public class ObjectLocation {
	return xys;		return xys;
	}		}

			/**
			* Invert kernel in frequency domain, then condition it knowing it is radial. Conditioning
			* involves converting to 1d radial (linear interpolation with optionally increased radial
			* resolution and simultaneous cosine blurring. Blurring may increase for the outer areas
			* of the result kernel
			* @param kernel direct radial kernel from extracted objects, centered at size/2,size/2
			* @param fat_zero fat zero for frequency-domain inversion
			* @param lpf_sigma low-pass sigma after frequency-domain inversion
			* @param scale_radial resolution
			* @param lim_rad limit inverted kernel by radius
			* @param trans_width transition width for radial limiting (cosine)
			* @param blur_center spread data in +/- blur_radius (cosine) among radial bins
			* @param blur_radius radius of the constant radial blurring, outside increase blur
			* @param blur_rate rate of blur increase (pix/pix) in the peripheral areas
			* @param debugLevel debug level
			* @return inverted kernel, same dimension. Normalize to have convolution of derect and inverted be 1.0
			* in the center?
			*/
			public static double [] invertRadialKernel(
			double [] kernel,
			double fat_zero,
			double lpf_sigma,
			int scale_radial, // scale up radial resolution
			double lim_rad, // outside all 0
			double trans_width, // lim_rad-trans_width - start reducing
			double blur_center, // cosine blur (in original pixels) in the center (<blur_radius) area
			double blur_radius, // constant blur radius
			double blur_rate, // blur increase outside of blur_radius
			// just for testing - source images and corresponding centers to convolve
			double [][] centers,
			double [][] src_cuts,
			String dbg_prefix,
			int debugLevel
			) {
			int size = (int) Math.sqrt(kernel.length);
			double [] kernel0 = kernel.clone();
			double [] inverted0 = (new DoubleFHT()).invert (
			kernel0, // double [] data,
			fat_zero, // double fat_zero,
			0, // double highPassSigma,
			lpf_sigma); // double lowPassSigma);
			int irad = (int) Math.ceil(scale_radial*lim_rad) +2;
			double [] sw = new double [irad], swd = new double[irad];
			// double maxrad2 = irad*irad;
			double xc = size/2, yc=size/2;
			for (int y = 0; y < size; y++) {
			double y2 = (y - yc)*(y-yc);
			for (int x = 0; x < size; x++) {
			double r = Math.sqrt(y2+ (x-xc)*(x-xc));
			double blur = (r < blur_radius) ? blur_center : ((r - blur_center) * blur_rate);
			double low_r = (r - blur) * scale_radial;
			if (((int) low_r) < sw.length) {
			double d = inverted0[y*size + x];
			double high_r = (r + blur) * scale_radial;
			double s = Math.PI/(high_r-low_r);
			int ilr = Math.max(0, (int) Math.ceil(low_r));
			int ihr = Math.min(irad-1, (int) Math.floor(high_r));
			for (int i = ilr; i <= ihr; i++) {
			double w = Math.sin(s * (i - low_r));
			sw[i] += w;
			swd[i] += w * d;
			}
			}
			}
			}
			for (int i = 0; i < sw.length; i++) {
			if (sw[i] > 0) {
			swd[i] /= sw[i];
			}
			}

			// limit by lim_rad, trans_width
			if (trans_width > 0) {
			double lim_rad_scaled = lim_rad * scale_radial;
			double trans_width_scaled = trans_width * scale_radial;
			for (int i = (int) (lim_rad_scaled-trans_width_scaled); i < sw.length; i++) {
			if (i < lim_rad_scaled) {
			swd[i] = 0.5(1.0 + Math.cos(Math.PI*(i - (lim_rad_scaled-trans_width_scaled))/trans_width_scaled));
			} else {
			swd[i] = 0;
			}
			}
			}
			double [] inverted = new double [size*size];
			double lr2 = lim_rad * lim_rad;
			// generate output pattern
			int oc = size/2;
			for (int y = 0; y < size; y++) {
			double dy = y - oc;
			double y2 = dy*dy;
			if (y2 <= lr2) {
			for (int x = 0; x < size; x++) {
			double dx = x - oc;
			double r2 = y2 + dx*dx;
			if (r2 <= lr2) {
			double sr = Math.sqrt(r2)* scale_radial;
			int isr = (int) Math.floor(sr);
			double w1 = sr-isr;
			double w0 = 1.0 - w1;
			inverted[x + size * y] = w0 * swd[isr] + w1 * swd[isr + 1];
			}
			}
			}
			}
			double [] convolved = (new DoubleFHT()).convolve(
			kernel.clone(), // double[] first,
			inverted.clone()); // double[] second)
			double center_data = convolved[size*(size+1)/2];

			double [] normalized = inverted.clone();
			double k = 1.0/center_data;
			for (int i = 0; i < normalized.length; i++) {
			normalized[i]*=k;
			}
			if (debugLevel > -4) {
			System.out.println("invertRadialKernel(): direct*inverted = "+center_data);
			if (debugLevel >0) {
			String dbg_title = dbg_prefix + "_invertRK_fz"+fat_zero+
			"_lpf"+lpf_sigma+"_sr"+scale_radial+"_lr"+lim_rad+
			"_tw"+trans_width+"_bc"+blur_center+"_br"+blur_radius+
			"_brt"+blur_rate;
			String [] dbg_titles= {"direct","inverted","radial","convolved","normalized"};
			double [][] dbg_img = {kernel,inverted0,inverted,convolved,normalized};
			ImagePlus imp_dbg = ShowDoubleFloatArrays.makeArrays(
			dbg_img,
			size,
			size,
			dbg_title,
			dbg_titles); // test_titles,
			// PointRoi roi = new PointRoi();
			// roi.setOptions("label");
			imp_dbg.show();
			}
			}

			/*
			public double[] convolve(double[] first, double[] second) {
			return convolve(first, second, null);
			}
			*/
			// testing by convolving with the source images
			if (debugLevel>0) {
			double [] wnd1d = new double[size];
			boolean sq= false;
			for (int i= 0; i < size; i++) {
			wnd1d[i] = Math.sin(Math.PI*i/size);
			if (sq) {
			wnd1d[i]*=wnd1d[i];
			}
			}
			double [] wnd = new double[size*size];
			for (int i = 0; i < size; i++) {
			for (int j = 0; j < size; j++) {
			wnd[isize+j] = wnd1d[i]wnd1d[j];
			}
			}

			int extr_size = (int) Math.sqrt(src_cuts[0].length);
			double [][] test_src = new double [src_cuts.length][size*size];
			for (int i = 0; i < src_cuts.length; i++) {
			double xcent = extr_size/2+centers[i][0];
			double ycent = extr_size/2+centers[i][1];
			int x0 = (int) Math.round(xcent - size/2);
			int y0 = (int) Math.round(ycent - size/2);
			for (int y = 0; y < size; y++) {
			int ys = y0+y;
			if ((ys >= 0) && (ys < extr_size)) {
			for (int x = 0; x < size; x++) {
			int xs = x0+x;
			if ((xs >= 0) && (xs < extr_size)) {
			int indx = y*size + x;
			test_src[i][indx] = src_cuts[i][ys * extr_size + xs];
			}
			}
			}
			}
			OrthoMap.removeDC(test_src[i]);
			for (int j = 0; j < test_src[i].length; j++) {
			test_src[i][j] *= wnd[j];
			}
			}
			double [][] test_conv = new double [src_cuts.length][];
			for (int i = 0; i < src_cuts.length; i++) {
			test_conv[i] = (new DoubleFHT()).convolve(
			test_src[i].clone(), // double[] first,
			normalized.clone()); // double[] second)
			}

			String dbg_title = dbg_prefix + "_conv_src_+fz"+fat_zero+
			"_lpf"+lpf_sigma+"_sr"+scale_radial+"_lr"+lim_rad+
			"_tw"+trans_width+"_bc"+blur_center+"_br"+blur_radius+
			"_brt"+blur_rate;
			String [] dbg_titles= new String[src_cuts.length] ; // {"direct","inverted","radial","convolved","normalized"};
			for (int i = 0; i < src_cuts.length; i++) {
			dbg_titles[i] = "img-"+i;
			}
			// double [][] dbg_img = {kernel,inverted0,inverted,convolved,normalized};
			ImagePlus imp_dbg = ShowDoubleFloatArrays.makeArrays(
			test_conv,
			size,
			size,
			dbg_title,
			dbg_titles); // test_titles,
			// PointRoi roi = new PointRoi();
			// roi.setOptions("label");
			imp_dbg.show();
			ImagePlus imp_dbg_src = ShowDoubleFloatArrays.makeArrays(
			test_src,
			size,
			size,
			dbg_prefix+"-src_cut",
			dbg_titles); // test_titles,
			// PointRoi roi = new PointRoi();
			// roi.setOptions("label");
			imp_dbg_src.show();

			}

			return normalized;
			}


			// Needs improvement. Probably look at neighbors when deleting outliers. Multipass and pull to neighbors?
	public static double [] getRadialPattern(		public static double [] getRadialPattern(
	final double [] data,		final double [] data,
	double [] xy_offs,		double [] xy_offs,

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

+14 −2

Original line number	Original line	Diff line number	Diff line
	@@ -1820,6 +1820,8 @@ public class OrthoMap implements Comparable <OrthoMap>, Serializable{
	}		}
	return kernel;		return kernel;
	}		}


	public static double [] deconvolvePair(		public static double [] deconvolvePair(
	double [][] data,		double [][] data,
	double fat_zero, // 1000		double fat_zero, // 1000
	@@ -1842,6 +1844,14 @@ public class OrthoMap implements Comparable <OrthoMap>, Serializable{
	doubleFHT.swapQuadrants(data[1]);		doubleFHT.swapQuadrants(data[1]);
	if (!doubleFHT.transform(data[1],false)) return null; // direct FHT		if (!doubleFHT.transform(data[1],false)) return null; // direct FHT
	if (!doubleFHT.transform(data[0],false)) return null; // direct FHT {		if (!doubleFHT.transform(data[0],false)) return null; // direct FHT {
			if (debugLevel > 0) {
			ShowDoubleFloatArrays.showArrays( // here every element
			data[1],
			fft_size,
			fft_size,
			"data[1]");
			}

	if (debugLevel > 0) {		if (debugLevel > 0) {
	double [] amp = doubleFHT.calculateAmplitude(data[0]);		double [] amp = doubleFHT.calculateAmplitude(data[0]);
	ShowDoubleFloatArrays.showArrays(		ShowDoubleFloatArrays.showArrays(
	@@ -1850,7 +1860,7 @@ public class OrthoMap implements Comparable <OrthoMap>, Serializable{
	fft_size,		fft_size,
	"amp");		"amp");
	}		}
	double [] deconv = doubleFHT.divide(data[1],data[0], fft_size);		double [] deconv = doubleFHT.divide(data[1],data[0], fat_zero);
	if (debugLevel > 0) {		if (debugLevel > 0) {
	ShowDoubleFloatArrays.showArrays(		ShowDoubleFloatArrays.showArrays(
	deconv,		deconv,
	@@ -1860,7 +1870,7 @@ public class OrthoMap implements Comparable <OrthoMap>, Serializable{
	}		}
	// if (zero_phase) {		// if (zero_phase) {
	double [] div_amp = doubleFHT.calculateAmplitudeNoSwap(deconv);		double [] div_amp = doubleFHT.calculateAmplitudeNoSwap(deconv);
	double [] div_phase = doubleFHT.calculatePhaseNoSwap(deconv);		double [] div_phase = DoubleFHT.calculatePhaseNoSwap(deconv);
	double [][] amp_phase = {div_amp, div_phase};		double [][] amp_phase = {div_amp, div_phase};
	ShowDoubleFloatArrays.showArrays(		ShowDoubleFloatArrays.showArrays(
	amp_phase,		amp_phase,
	@@ -1903,6 +1913,8 @@ public class OrthoMap implements Comparable <OrthoMap>, Serializable{
	}		}




	public static void removeDC(		public static void removeDC(
	final double [] data) {		final double [] data) {
	final Thread[] threads = ImageDtt.newThreadArray(QuadCLT.THREADS_MAX);		final Thread[] threads = ImageDtt.newThreadArray(QuadCLT.THREADS_MAX);

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

+1 −1

Original line number	Original line	Diff line number	Diff line
	@@ -1650,7 +1650,7 @@ public class OrthoMapsCollection implements Serializable{
	return vf_out;		return vf_out;
	}		}

	public ImagePlus patterMatchDualWrap (		public ImagePlus patternMatchDualWrap (
	int [] indices, // null or which indices to use (normally just 2 for pairwise comparison)		int [] indices, // null or which indices to use (normally just 2 for pairwise comparison)
	double [][][] affines, // null or [indices.length][2][3]		double [][][] affines, // null or [indices.length][2][3]
	FineXYCorr warp) { // use for a single pair only		FineXYCorr warp) { // use for a single pair only

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