Bug fixing to make run for many scenes. Started LPF for the ground w/o (ab8d3318) · Commits · Elphel / imagej-elphel

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

+1 −1

Original line number	Diff line number	Diff line
		@@ -5090,7 +5090,7 @@ public class Eyesis_Correction implements PlugIn, ActionListener {
		System.out.println("=== IMS ===");
		QUAD_CLT_AUX.showQuatCorr();
		System.out.println("=== IMU ===");
		QUAD_CLT_AUX.showPimuOffsets();
		QUAD_CLT_AUX.showPimuOffsets(CLT_PARAMETERS); //
		@SuppressWarnings("unused")
		QuadCLT dbg_QUAD_CLT = QUAD_CLT;
		@SuppressWarnings("unused")

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

+1 −1

Original line number	Diff line number	Diff line
		@@ -295,7 +295,7 @@ public class ElphelTiffWriter {
		private static IIOMetadataNode createTimeStamp(LocalDateTime dt, int digits_after) { // 3
		int denom = 1;
		for (int i = 0; i < digits_after; i++) denom *= 10;
		int fsec = dt.getSecond()denom+((int) Math.round(denom dt.getNano()*1E-9));
		int fsec = dt.getSecond()denom+((int) Math.round(denom (dt.getNano()*1E-9)));

		IIOMetadataNode node_rationals = new IIOMetadataNode(TIFF_RATIONALS_TAG);
		IIOMetadataNode node_hrs = new IIOMetadataNode(TIFF_RATIONAL_TAG);

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

+180 −9

Original line number	Diff line number	Diff line
		@@ -23,8 +23,10 @@
		*/
		package com.elphel.imagej.tileprocessor;

		import java.text.SimpleDateFormat;
		import java.util.ArrayList;
		import java.util.Arrays;
		import java.util.Calendar;
		import java.util.concurrent.atomic.AtomicInteger;

		import org.apache.commons.math3.geometry.euclidean.threed.Rotation;
		@@ -508,6 +510,11 @@ public class Interscene {
		double sfm_fracall = clt_parameters.imp.sfm_fracall; // 0.3; // minimal relative area of the SfM-e
		boolean fmg_initial_en = clt_parameters.imp.fmg_initial_en; // enable IMS-based FPN mitigation for initial orientation
		double fmg_distance = clt_parameters.imp.fmg_distance; // try to find other reference scene not closer than this pixels
		// todo: improve to use "preferred" distance
		if (fmg_distance < (min_offset + 2)) {
		fmg_distance = min_offset + 2;
		}

		double fmg_max_quad = clt_parameters.imp.fmg_max_quad; // estimate offset by 4 points (rooll-aware, 25% from center) if center
		// offset is too small
		boolean fmg_rectilinear = clt_parameters.imp.fmg_rectilinear;// use rectilinear model for scene offset estimation
		@@ -680,6 +687,10 @@ public class Interscene {
		if (fmg_initial_en && !fpn_list.isEmpty()) {
		// here max_offset is not critical, min_offset can be 0 too
		//double [] min_max = {min_offset, max_offset, 0.0} ; // {min, max, actual rms)
		if (fmg_distance < (min_max[0] + 2)) {
		fmg_distance = min_max[0] + 2;
		}

		int [][] fpn_pairs = getFPNPairs(
		fpn_list, // ArrayList<Integer> fpn_list,
		fmg_distance, // double fpn_mitigate_dist,
		@@ -689,6 +700,15 @@ public class Interscene {
		avg_z, // double avg_z,
		last_index, // ref_index, // int ref_index, // >= earliest_scene
		earliest_index); // int earliest_scene)
		// mitigating problem, that in the process of adjusting offset can fall below
		// the minimum and coordinates will be NaN:
		/*
		Mitigating FPN for scene 361 being too close to reference 344, using scene 367 as a reference
		interCorrPair(): avg_offs = 10.755562139763402 <= 256.0, sw = 4217.0 iter=3, RMS=0.5364197453455559 (Pure RMS=0.5364197453455559)
		interCorrPair(): avg_offs = 7.795390182218127 < 8.0, sw = 4219.0
		adjustPairsLMAInterscene() returned null
		*/
		double [] min_max_fpn = {0,min_max[1]};
		for (int ipair = 0; ipair < fpn_pairs.length; ipair++) if (fpn_pairs[ipair][1] >= 0) {
		if (debugLevel > -4) {
		System.out.println("Mitigating FPN for scene "+fpn_pairs[ipair][0]+
		@@ -701,7 +721,7 @@ public class Interscene {
		use_lma_dsi, // clt_parameters.imp.use_lma_dsi,
		false, // boolean fpn_disable, // disable fpn filter if images are known to be too close
		true, // boolean disable_ers,
		min_max, // double [] min_max, // null or pair of minimal and maximal offsets
		min_max_fpn,// min_max,// double [] min_max, // null or pair of minimal and maximal offsets
		fail_reason, // int [] fail_reason, // null or int[1]: 0 - OK, 1 - LMA, 2 - min, 3 - max
		quadCLTs, // QuadCLT [] quadCLTs,
		ref_index, // int ref_index,
		@@ -755,6 +775,23 @@ public class Interscene {
		}
		}
		}
		// Add to log
		StringBuffer sb = new StringBuffer();
		sb.append(new SimpleDateFormat("yyyy/MM/dd HH:mm:ss").format(Calendar.getInstance().getTime())+"\n");
		sb.append("Finished invertInitialOrientation():\n");
		sb.append("getNumOrient()= "+quadCLTs[ref_index].getNumOrient()+" of "+clt_parameters.imp.min_num_orient+"\n");
		sb.append("getNumAccum()= "+quadCLTs[ref_index].getNumAccum()+ " of "+clt_parameters.imp.min_num_interscene+"\n");
		sb.append("earliest_scene= "+earliest_index+"\n");
		sb.append("ref_index= "+ref_index+"\n");
		sb.append("last_index= "+last_index+"\n");
		sb.append("old_ref_index= "+ref_old+"\n");
		sb.append("Maximal RMSE= "+maximal_series_rms+"\n");
		sb.append("------------------------\n\n");
		quadCLTs[ref_index].saveStringInModelDirectory(sb.toString(), QuadCLT.ORIENTATION_LOGS_SUFFIX); // String suffix)




		}
		return 0;
		}
		@@ -1161,6 +1198,9 @@ public class Interscene {
		if (fmg_initial_en && !fpn_list.isEmpty()) {
		// here max_offset is not critical, min_offset can be 0 too
		double [] min_max = {min_offset, max_offset, 0.0} ; // {min, max, actual rms)
		if (fmg_distance < (min_max[0] + 2)) {
		fmg_distance = min_max[0] + 2;
		}
		int [][] fpn_pairs = getFPNPairs(
		fpn_list, // ArrayList<Integer> fpn_list,
		fmg_distance, // double fpn_mitigate_dist,
		@@ -1170,6 +1210,15 @@ public class Interscene {
		avg_z, // double avg_z,
		ref_index, // int ref_index, // >= earliest_scene
		earliest_scene); // int earliest_scene)
		// mitigating problem, that in the process of adjusting offset can fall below
		// the minimum and coordinates will be NaN:
		/*
		Mitigating FPN for scene 361 being too close to reference 344, using scene 367 as a reference
		interCorrPair(): avg_offs = 10.755562139763402 <= 256.0, sw = 4217.0 iter=3, RMS=0.5364197453455559 (Pure RMS=0.5364197453455559)
		interCorrPair(): avg_offs = 7.795390182218127 < 8.0, sw = 4219.0
		adjustPairsLMAInterscene() returned null
		*/
		double [] min_max_fpn = {0,min_max[1]};
		for (int ipair = 0; ipair < fpn_pairs.length; ipair++) if (fpn_pairs[ipair][1] >= 0) {
		if (debugLevel > -4) {
		System.out.println("Mitigating FPN for scene "+fpn_pairs[ipair][0]+
		@@ -1182,7 +1231,7 @@ public class Interscene {
		use_lma_dsi, // clt_parameters.imp.use_lma_dsi,
		false, // boolean fpn_disable, // disable fpn filter if images are known to be too close
		true, // boolean disable_ers,
		min_max, // double [] min_max, // null or pair of minimal and maximal offsets
		min_max_fpn, // min_max,// double [] min_max, // null or pair of minimal and maximal offsets
		fail_reason, // int [] fail_reason, // null or int[1]: 0 - OK, 1 - LMA, 2 - min, 3 - max
		quadCLTs, // QuadCLT [] quadCLTs,
		ref_index, // int ref_index,
		@@ -1249,6 +1298,17 @@ public class Interscene {
		quadCLTs[ref_index].saveInterProperties( // save properties for interscene processing (extrinsics, ers, ...) // null pointer
		null, // String path, // full name with extension or w/o path to use x3d directory
		debugLevel+1);
		// Add to log
		StringBuffer sb = new StringBuffer();
		sb.append(new SimpleDateFormat("yyyy/MM/dd HH:mm:ss").format(Calendar.getInstance().getTime())+"\n");
		sb.append("Finished setInitialOrientationsIms():\n");
		sb.append("getNumOrient()= "+quadCLTs[ref_index].getNumOrient()+" of "+clt_parameters.imp.min_num_orient+"\n");
		sb.append("getNumAccum()= "+quadCLTs[ref_index].getNumAccum()+ " of "+clt_parameters.imp.min_num_interscene+"\n");
		sb.append("earliest_scene= "+earliest_scene+"\n");
		sb.append("ref_index= "+ref_index+"\n");
		sb.append("Maximal RMSE= "+maximal_series_rms+"\n");
		sb.append("------------------------\n\n");
		quadCLTs[ref_index].saveStringInModelDirectory(sb.toString(), QuadCLT.ORIENTATION_LOGS_SUFFIX); // String suffix)
		return earliest_scene;
		}

		@@ -1919,6 +1979,7 @@ public class Interscene {
		double fmg_distance = clt_parameters.imp.fmg_distance; // try to find other reference scene not closer than this pixels
		double fmg_max_quad = clt_parameters.imp.fmg_max_quad; // estimate offset by 4 points (rooll-aware, 25% from center) if center
		boolean fmg_rectilinear = clt_parameters.imp.fmg_rectilinear;// use rectilinear model for scene offset estimation
		boolean use_precomp = clt_parameters.imp.use_precomp;// try to predict initial error from previous scenes

		// int avg_len = clt_parameters.imp.avg_len;
		// Set up velocities from known coordinates, use averaging
		@@ -2091,6 +2152,28 @@ public class Interscene {
		last_scene); // int last_index)
		// } else if (readjust_xy_ims && (reg_weight_xy > 0.0)) {
		} else if (readjust_xy_ims) {
		// optionally run adjustment here (QuadCLT.rotateImsToCameraXYZ()? Or only
		scenes_xyzatr_pull = QuadCLT.refineXYZFromIMU(
		clt_parameters, // CLTParameters clt_parameters,
		false, // true, // false, // boolean common_scale_only // false - individual by direction
		use_Z, // boolean keepZ, // if adjusting Z, qill use its old value
		quadCLTs, // QuadCLT[] quadCLTs,
		scenes_xyzatr, // double [][][] xyzatr,
		null, // double [][][] pimu_xyzatr, // if null - will be recalculated
		ref_index, // int ref_index,
		earliest_scene, // int early_index,
		last_scene, // int last_index,
		debugLevel); //int debugLevel)
		for (int nscene = earliest_scene; nscene <= last_scene; nscene++) if (scenes_xyzatr[nscene] != null) {
		scenes_xyzatr_pull[nscene] = modifyATRtoXYZ(
		scenes_xyzatr[nscene], // double [][] cur_xyzatr, // careful with Z - using the new one
		scenes_xyzatr_pull[nscene][0], // double [] new_xyz,
		avg_z); // double avg_z
		}


		/*

		double [][][] pimu_xyzatr = QuadCLT.integratePIMU(
		clt_parameters, // final CLTParameters clt_parameters,
		quadCLTs, // final QuadCLT[] quadCLTs,
		@@ -2146,6 +2229,7 @@ public class Interscene {
		avg_z); // double avg_z
		}
		}
		*/
		// old version
		/*
		scenes_xyzatr_pull = QuadCLT.refineFromImsVelocities(
		@@ -2287,6 +2371,18 @@ public class Interscene {
		System.out.println("test_adjust = "+test_adjust);
		}

		// Main cycle - first goes down from the center, then up, and finally processes "fpn" scenes (close to reference)
		double [][] precomp_xyzatr = new double [2][3];
		int last_processed_scene = -2; // none
		/*
		* There is still a problem with a large mismatch at start position for far off-reference scenes,
		* especiall those that were not refined after inversion - reversing order of earlier processed "later"
		* half (after the reference in the center) earlier processed as the bottom half of the other sub-sequence.
		*
		* For mitigation we'll use that both half-sequences start from the center with small mismatches. The
		* precomp_xyzatr will be used to store how much LMA corrected from the original estimation and add it
		* to the next scene (only when it is the next), similar to the initial orientation.
		*/

		for (int nscene:scene_seq) {
		if (nscene == debug_scene) {
		@@ -2351,6 +2447,26 @@ public class Interscene {
		if (est_shift < min_max[0]) {
		fail_reason[0]=FAIL_REASON_MIN;
		} else {
		double [][] corr_xyzatr_pull = new double [][] {scenes_xyzatr_pull[nscene][0].clone(), scenes_xyzatr_pull[nscene][1].clone()};
		/*
		* scenes_xyzatr[ref_index],// double [][] scene0_xyzatr, - scene to compare to
		* scenes_xyzatr[nscene], // double [][] scene1_xyzatr - previous known pose?
		* scenes_xyzatr_pull[nscene], // double [][] scene1_xyzatr_pull, - now not a pull,
		* but a rigid target set as initial approximation
		*/
		boolean applied_precomp = false;
		if (use_precomp && (last_processed_scene >= nscene-1) && (last_processed_scene <= nscene+1)) {
		corr_xyzatr_pull=ErsCorrection.combineXYZATR(
		scenes_xyzatr_pull[nscene],
		precomp_xyzatr);
		applied_precomp = true;
		if (debugLevel > -2) {
		System.out.println(String.format(
		"Applied precompensation: [%9.6f, %9.6f, %9.6f] [%9.6f, %9.6f, %9.6f]",
		precomp_xyzatr[0][0], precomp_xyzatr[0][1], precomp_xyzatr[0][2],
		precomp_xyzatr[1][0], precomp_xyzatr[1][1], precomp_xyzatr[1][2]));
		}
		}
		scenes_xyzatr[nscene] = adjustDiffPairsLMAInterscene( // compare two scenes, first may be reference, use motion blur
		clt_parameters, //CLTParameters clt_parameters,
		use_lma_dsi, //,boolean use_lma_dsi,
		@@ -2371,7 +2487,7 @@ public class Interscene {
		scenes_xyzatr[ref_index],// double [][] scene0_xyzatr,
		scenes_xyzatr[nscene], // double [][] scene1_xyzatr,
		avg_z, // double average_z,
		scenes_xyzatr_pull[nscene], // double [][] scene1_xyzatr_pull,
		corr_xyzatr_pull, // scenes_xyzatr_pull[nscene], // double [][] scene1_xyzatr_pull,
		param_select, // boolean[] param_select,
		param_regweights, // double [] param_regweights,
		lma_rms, // double [] rms_out, // null or double [2]
		@@ -2381,6 +2497,22 @@ public class Interscene {
		mb_max_gain, // double mb_max_gain, // 5.0; // motion blur maximal gain (if more - move second point more than a pixel
		clt_parameters.imp.debug_level); // int debugLevel)
		adjust_OK = scenes_xyzatr[nscene] != null;
		if (!adjust_OK) {
		last_processed_scene = -2;
		} else if (use_precomp) {
		double [][] last_corr_xyzatr = ErsCorrection.combineXYZATR(
		scenes_xyzatr[nscene],
		ErsCorrection.invertXYZATR(corr_xyzatr_pull));
		// add precomp_xyzatr if it was applied:
		if (applied_precomp) {
		precomp_xyzatr = ErsCorrection.combineXYZATR(
		precomp_xyzatr,
		last_corr_xyzatr);
		} else { // just use difference
		precomp_xyzatr = last_corr_xyzatr;
		}
		last_processed_scene = nscene;
		}
		}
		if (adjust_OK && fail_on_zoom_roll) { // check only for initial orientation, do not check on readjustments
		if (Math.abs(scenes_xyzatr[nscene][1][2]) > max_roll) {
		@@ -2460,6 +2592,9 @@ public class Interscene {
		System.out.println("num_fpn_mitigate= "+fpn_list.size());
		}
		if (fmg_reorient_en && !fpn_list.isEmpty()) {
		if (fmg_distance < (min_max[0] + 2)) {
		fmg_distance = min_max[0] + 2;
		}
		int [][] fpn_pairs = getFPNPairs(
		fpn_list, // ArrayList<Integer> fpn_list,
		fmg_distance, // double fpn_mitigate_dist,
		@@ -2469,6 +2604,15 @@ public class Interscene {
		avg_z, // double avg_z,
		last_scene, // latest_scene, // int ref_index, // >= earliest_scene
		earliest_scene); // int earliest_scene)
		// mitigating problem, that in the process of adjusting offset can fall below
		// the minimum and coordinates will be NaN:
		/*
		Mitigating FPN for scene 361 being too close to reference 344, using scene 367 as a reference
		interCorrPair(): avg_offs = 10.755562139763402 <= 256.0, sw = 4217.0 iter=3, RMS=0.5364197453455559 (Pure RMS=0.5364197453455559)
		interCorrPair(): avg_offs = 7.795390182218127 < 8.0, sw = 4219.0
		adjustPairsLMAInterscene() returned null
		*/
		double [] min_max_fpn = {0,min_max[1]};
		boolean test_adjust1 = debugLevel > 1000;
		if (test_adjust1) {
		int [][] fpn_pairs_dbg = new int [fpn_pairs.length+3][2];
		@@ -2503,7 +2647,7 @@ public class Interscene {
		use_lma_dsi, //,boolean use_lma_dsi,
		fpn_disable, // boolean fpn_disable, // disable fpn filter if images are known to be too close
		disable_ers, // boolean disable_ers,
		min_max, // double [] min_max, // null or pair of minimal and maximal offsets
		min_max_fpn, // min_max, // double [] min_max, // null or pair of minimal and maximal offsets
		fail_reason, // int [] fail_reason, // null or int[1]: 0 - OK, 1 - LMA, 2 - min, 3 - max
		quadCLTs, // QuadCLT [] quadCLTs,
		ref_index, // int ref_index,
		@@ -2624,6 +2768,31 @@ public class Interscene {
		quadCLTs[ref_index].saveInterProperties( // save properties for interscene processing (extrinsics, ers, ...)
		null, // String path, // full name with extension or w/o path to use x3d directory
		debugLevel+1);

		// Add to log
		StringBuffer sb = new StringBuffer();
		sb.append(new SimpleDateFormat("yyyy/MM/dd HH:mm:ss").format(Calendar.getInstance().getTime())+"\n");
		sb.append("Finished reAdjustPairsLMAInterscene():\n");
		sb.append("getNumOrient()= "+quadCLTs[ref_index].getNumOrient()+" of "+clt_parameters.imp.min_num_orient+"\n");
		sb.append("getNumAccum()= "+quadCLTs[ref_index].getNumAccum()+ " of "+clt_parameters.imp.min_num_interscene+"\n");
		sb.append("earliest_scene= "+range[0]+"\n");
		sb.append("ref_index= "+ref_index+"\n");
		sb.append("last_index= "+range[1]+"\n");
		sb.append("Maximal RMSE= "+maximal_series_rms+"\n");
		sb.append("lpf_xy= "+lpf_xy+"\n");
		sb.append("readjust_xy_ims="+readjust_xy_ims+"\n");
		sb.append("lma_xyzatr= "+lma_xyzatr+"\n");
		sb.append("use_R= "+use_R+"\n");
		sb.append("use_R= "+use_R+"\n");
		sb.append("mb_max_gain= "+mb_max_gain+"\n");
		sb.append("avg_z= "+avg_z+"m\n");
		sb.append("reg_weight_xy= "+reg_weight_xy+"\n");
		sb.append("disable_ers= "+disable_ers+"\n");
		sb.append("disable_ers_y= "+disable_ers_y+"\n");
		sb.append("disable_ers_r= "+disable_ers_r+"\n");
		sb.append("use_precomp= "+use_precomp+"\n");
		sb.append("------------------------\n\n");
		quadCLTs[ref_index].saveStringInModelDirectory(sb.toString(), QuadCLT.ORIENTATION_LOGS_SUFFIX); // String suffix)
		return earliest_scene;
		}

		@@ -2644,13 +2813,15 @@ public class Interscene {
		){
		double dx = new_xyz[0] - cur_xyzatr[0][0];
		double dy = new_xyz[1] - cur_xyzatr[0][1];
		// System.out.println(String.format("modifyATRtoXYZ(): dx=%7.3f, dy=%7.3f", dx, dy));
		double [][] diff_xyzatr = new double[][] {{dx, dy, 0},{dx/avg_z, -dy/avg_z,0}};
		double [][] new_xyzatr = ErsCorrection.combineXYZATR(cur_xyzatr,diff_xyzatr);
		return new_xyzatr;
		}





		// Make it the only entry point
		// uses *_dt from
		// quadCLTs[nscene*].getErsCorrection().getErsXYZATR_dt()
		@@ -5186,9 +5357,9 @@ public class Interscene {
		double [] corr_angles = rot.getAngles(RotationOrder.YXZ, ErsCorrection.ROT_CONV);
		double [] corr_degrees = new double[3];
		for (int i = 0; i < 3; i++) corr_degrees[i]=corr_angles[i]*180/Math.PI;
		System.out.println("quatCorr=["+quatCorr[0]+", "+quatCorr[1]+", "+quatCorr[2]+", "+quatCorr[3]+"]");
		System.out.println("ATR(rad)=["+corr_angles[0]+", "+corr_angles[1]+", "+corr_angles[2]+"]");
		System.out.println("ATR(deg)=["+corr_degrees[0]+", "+corr_degrees[1]+", "+corr_degrees[2]+"]");
		System.out.println("generateEgomotionTable(): quatCorr=["+quatCorr[0]+", "+quatCorr[1]+", "+quatCorr[2]+", "+quatCorr[3]+"]");
		System.out.println("generateEgomotionTable(): ATR(rad)=["+corr_angles[0]+", "+corr_angles[1]+", "+corr_angles[2]+"]");
		System.out.println("generateEgomotionTable(): ATR(deg)=["+corr_degrees[0]+", "+corr_degrees[1]+", "+corr_degrees[2]+"]");
		}

		for (int nscene = earliest_scene; nscene < quadCLTs.length; nscene++) {
		@@ -5544,7 +5715,7 @@ public class Interscene {
		}
		}


		// relative to the GPS/compass
		public static double [] getQuaternionCorrection(
		CLTParameters clt_parameters,
		QuadCLT [] quadCLTs,

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