fixed old bug, used macro correlation (92f321f5) · Commits · Elphel / imagej-elphel

src/main/java/AlignmentCorrection.java

+41 −44

Original line number	Diff line number	Diff line
		@@ -141,6 +141,7 @@ public class AlignmentCorrection {
		}

		ArrayList<Sample> samples_list = selectInfinityTiles(
		clt_parameters.fcorr_radius, // final double fcorr_radius,
		clt_parameters.fcorr_inf_vert,// final boolean use_vertical,
		min_strength,
		max_diff,
		@@ -195,33 +196,44 @@ public class AlignmentCorrection {
		mismatch_corr_coefficiants, // double [][][] corr,
		"");// String prefix)
		}
		/*
		if (disparity_corr_coefficiants == null) {
		disparity_corr_coefficiants = mismatch_corr_coefficiants;
		if (debugLevel > -1){
		System.out.println("infinityCorrection(): using only coefficient increments from infinityMismatchCorrection");
		return mismatch_corr_coefficiants;
		}

		} else {
		for (int i = 0; i < disparity_corr_coefficiants.length; i++){
		for (int j = 0; j < disparity_corr_coefficiants[i].length; j++){
		for (int k = 0; k < disparity_corr_coefficiants[i][j].length; k++){
		disparity_corr_coefficiants[i][j][k] += mismatch_corr_coefficiants[i][j][k];
		}
		}
		}
		if (debugLevel > -1){
		System.out.println("infinityCorrection(): combining coefficient increments from infinityCorrection and infinityMismatchCorrection");
		/**
		* Discard correction data outside of the center image area
		* @param fcorr_radius fraction of the image to use (1.0 - 100%)
		* @param tilesX width in tiles
		* @param tilesY height in tiles
		* @return boolean array in linescan order
		*/
		public boolean[] getCenterMask(
		double fcorr_radius,
		int tilesX,
		int tilesY)
		{
		boolean [] mask = new boolean [tilesX * tilesY];

		int y0 = (int) (0.5 * tilesY*(1.0 - fcorr_radius));
		int y1 = (int) (0.5 * tilesY*(1.0 + fcorr_radius));
		int x0 = (int) (0.5 * tilesX*(1.0 - fcorr_radius));
		int x1 = (int) (0.5 * tilesX*(1.0 + fcorr_radius));
		if (y0 < 0) y0 = 0;
		if (y1 > tilesY) y1 = tilesY;
		if (x0 < 0) x0 = 0;
		if (x1 > tilesX) x1 = tilesX;
		for (int ty = y0; ty < y1; ty++){
		for (int tx = x0; tx < x1; tx++){
		mask[tx + tilesX * ty] = true;
		}
		}
		*/
		// }
		return mismatch_corr_coefficiants;
		return mask;
		}


		/**
		* Select infinity tiles from a single or multiple image sets
		* Next parameters are made separate to be able to modify them between different runs keeping clt_parameters
		* @param fcorr_radius do not use peripheral tiles
		* @param min_strength minimal correlation strength to use tile
		* @param max_diff maximal disparity difference between tiles and previous approximation to use tiles
		* @param max_iterations maximal number of iterations to find disparity surface
		@@ -236,6 +248,7 @@ public class AlignmentCorrection {
		* @return per sub-camera, per direction (x,y) 6 quadratic polynomial coefficients, same format as fine_geometry_correction()
		*/
		public ArrayList<Sample> selectInfinityTiles(
		final double fcorr_radius,
		final boolean use_vertical,
		final double min_strength,
		final double max_diff,
		@@ -250,6 +263,7 @@ public class AlignmentCorrection {
		{
		final int numTiles = disp_strength[0].length;
		final int tilesY = numTiles/tilesX;
		final boolean [] center_mask = getCenterMask(fcorr_radius, tilesX, tilesY);
		double [] disparity_poly = new double[6];
		PolynomialApproximation pa = new PolynomialApproximation();
		double thresholdLin = 1.0E-20; // threshold ratio of matrix determinant to norm for linear approximation (det too low - fail)
		@@ -275,7 +289,7 @@ public class AlignmentCorrection {
		for (int num_set = 0; num_set < disp_strength.length/NUM_SLICES; num_set++){
		int disp_index = NUM_SLICES * num_set;
		int str_index = NUM_SLICES * num_set + 1;
		for (int nTile = 0; nTile < numTiles; nTile++){
		for (int nTile = 0; nTile < numTiles; nTile++) if (center_mask[nTile]){
		if ((disp_strength[str_index][nTile] > min_strength) &&
		// (Math.abs(disp_strength[disp_index][nTile] - disp_surface[nTile]) < max_diff)){
		((disp_strength[disp_index][nTile] - disp_surface[nTile]) < max_diff)){
		@@ -1505,6 +1519,7 @@ public class AlignmentCorrection {


		public double [][][] lazyEyeCorrection(
		final double fcorr_radius,
		final double min_strength_in,
		final double max_diff,
		// final double comp_strength_var,
		@@ -1538,6 +1553,7 @@ public class AlignmentCorrection {
		final int num_scans = scans_14.length/NUM_ALL_SLICES;
		final int num_tiles = scans_14[0].length;
		final int tilesY = num_tiles/tilesX;
		final boolean [] center_mask = getCenterMask(fcorr_radius, tilesX, tilesY);
		final double [][] scans = new double [num_scans * NUM_SLICES][];
		final int [] indices_14_10 = {0,1,2,3,5,6,8,9,11,12};
		final double [][] comp_strength_rms = new double [num_scans][num_tiles];
		@@ -1546,9 +1562,6 @@ public class AlignmentCorrection {
		scans[ns * NUM_SLICES + i] = scans_14[ns * NUM_ALL_SLICES + indices_14_10[i]];
		}
		}
		// (new showDoubleFloatArrays()).showArrays(scans_14, tilesX, tilesY, true, "scans14");
		// (new showDoubleFloatArrays()).showArrays(scans, tilesX, tilesY, true, "scans10");


		for (int ns = 0; ns < num_scans; ns++){
		for (int nTile = 0; nTile < num_tiles; nTile++){
		@@ -1563,24 +1576,6 @@ public class AlignmentCorrection {
		comp_strength_rms[ns][nTile] = Math.sqrt(s2 - s1*s1);
		}
		}
		/*
		for (int ns = 0; ns < num_scans; ns++){
		for (int nTile = 0; nTile < num_tiles; nTile++){
		double s1=0.0, s2=0.0;
		for (int pair = 0; pair <4; pair++){
		double s = scans_14[ns * NUM_ALL_SLICES + 4 + 3 * pair][nTile];
		if (pair == 0){
		s1 = s;
		s2 = s;
		} else {
		s1= Math.min(s, s1);
		s2= Math.max(s, s2);
		}
		}
		comp_strength_rms[ns][nTile] = s2 - s1;
		}
		}
		*/
		/*
		* None of comp_strength_rms methods works to detect potential outliers for horizontal/vertical features
		*/
		@@ -1809,6 +1804,7 @@ public class AlignmentCorrection {

		// create list for infinity data
		ArrayList<Sample> inf_samples_list = selectInfinityTiles(
		clt_parameters.fcorr_radius, // final double fcorr_radius,
		clt_parameters.fcorr_inf_vert,// final boolean use_vertical,
		0.0, // any > 0.0
		max_diff, // max_diff, //clt_parameters.fcorr_inf_diff
		@@ -1836,7 +1832,7 @@ public class AlignmentCorrection {
		total_weights[0] += s.weight;
		}

		for (int nTile = 0; nTile < num_tiles; nTile++) {
		for (int nTile = 0; nTile < num_tiles; nTile++) if (center_mask[nTile]){
		total_weights[1]+= inf_and_ly[1 * NUM_SLICES + 1][nTile];
		}

		@@ -1855,7 +1851,7 @@ public class AlignmentCorrection {
		}

		// Supplement list with the lazy eye scans data - use all tiles
		for (int nTile = 0; nTile < num_tiles; nTile++) {
		for (int nTile = 0; nTile < num_tiles; nTile++) if (center_mask[nTile]) {
		double w = inf_and_ly[1 * NUM_SLICES + 1][nTile];
		if (w > 0.0) {
		inf_samples_list.add(new Sample(1,nTile,w));
		@@ -2124,6 +2120,7 @@ public class AlignmentCorrection {


		ArrayList<Sample> inf_samples_list = selectInfinityTiles(
		clt_parameters.fcorr_radius, // final double fcorr_radius,
		clt_parameters.fcorr_inf_vert,// final boolean use_vertical,
		0.0, // any > 0.0
		clt_parameters.fcorr_inf_diff, // max_diff, //clt_parameters.fcorr_inf_diff

src/main/java/CLTPass3d.java

+15 −2

Original line number	Diff line number	Diff line
		@@ -67,6 +67,19 @@ public class CLTPass3d{
		{
		this.tileProcessor = tileProcessor;
		}

		public CLTPass3d (TileProcessor tileProcessor, int mode)
		{
		this.tileProcessor = tileProcessor;
		switch (mode){
		case 0:
		tile_op = new int [tileProcessor.getTilesY()][tileProcessor.getTilesX()];
		disparity = new double [tileProcessor.getTilesY()][tileProcessor.getTilesX()];
		break;

		}
		}

		public TileProcessor getTileProcessor()
		{
		return this.tileProcessor;

src/main/java/EyesisCorrectionParameters.java

+57 −12

File changed.

Preview size limit exceeded, changes collapsed.

src/main/java/GeometryCorrection.java

+3 −2

Original line number	Diff line number	Diff line
		@@ -633,7 +633,8 @@ public class GeometryCorrection {
		double rri = 1.0;
		for (int j = 0; j < a.length; j++){
		rri *= ri;
		rD2rND += a[j]*(rri - a[j]); // BUG here !!!! - fix later, will need to re-adjust all fine corr
		// rD2rND += a[j]*(rri - a[j]); // BUG here !!!! - fix later, will need to re-adjust all fine corr
		rD2rND += a[j]*(rri - 1.0); // Fixed
		}
		double pXid = pXci * rD2rND;
		double pYid = pYci * rD2rND;
		@@ -672,7 +673,7 @@ public class GeometryCorrection {
		double rri = 1.0;
		for (int j = 0; j < a.length; j++){
		rri *= ri;
		rD2rND += a[j]*(rri - a[j]);
		rD2rND += a[j]*(rri - 1.0);
		}
		double pXid = pXci * rD2rND;
		double pYid = pYci * rD2rND;

src/main/java/ImageDtt.java

+4 −4

Original line number	Diff line number	Diff line
		@@ -3606,12 +3606,12 @@ public class ImageDtt {
		} else { // copy by 1
		for (int i = 0; i < transform_size2; i++){
		int pi = ctile_top + i;
		if (pi < 0) pi = 0;
		else if (pi >= height) pi = height - 1;
		if (pi < 0) pi &= 1;
		else if (pi >= height) pi = height - 2 + (pi & 1);
		for (int j = 0; j < transform_size2; j++){
		int pj = ctile_left + j;
		if (pj < 0) pj = 0;
		else if (pj >= width) pj = width - 1;
		if (pj < 0) pj &= 1;
		else if (pj >= width) pj = width - 2 + (pj & 1);
		tile_in[transform_size2 * i + j] = image_data[chn][pi * width + pj];
		}
		}

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