bug fixing for chained segments (748d396b) · Commits · Elphel / imagej-elphel

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

+9 −5

Original line number	Diff line number	Diff line
		@@ -220,15 +220,15 @@ public class Interscene {
		adjusted_scene_index++;
		if ((ref_index - adjusted_scene_index) >= min_num_scenes_half) {
		if (adjusted_scene_index > cent_index) {
		cent_index = adjusted_scene_index;
		if (debugLevel > -3) {
		System.out.println("Overlap mode, reusing previous scenes adjustment scenes, number of scenes = "+
		(ref_index - adjusted_scene_index));
		System.out.println("Overlap mode 1, reusing previous scenes adjustment scenes, number of scenes = "+
		(ref_index - adjusted_scene_index)+", cent_index = "+cent_index+", ref_index="+ref_index);
		}
		cent_index = adjusted_scene_index;
		} else {
		if (debugLevel > -3) {
		System.out.println("Overlap mode, partially reusing previous scenes adjustment scenes, number of scenes = "+
		(ref_index - cent_index)+ " of "+(ref_index - adjusted_scene_index));
		System.out.println("Overlap mode 2, partially reusing previous scenes adjustment scenes, number of scenes = "+
		(ref_index - cent_index)+ " of "+(ref_index - adjusted_scene_index)+", cent_index = "+cent_index+", ref_index="+ref_index);
		}
		}
		reused_overlap = true;
		@@ -283,6 +283,10 @@ public class Interscene {
		}
		}

		if (debugLevel > -3) {
		System.out.println("setInitialOrientationsCenterIms(): Running OpticalFlow.buildRefDSI() for center scene # "+cent_index+", : "+quadCLTs[cent_index].getImageName());
		}

		// create new dsi for quadCLTs[earliest_scene1]
		OpticalFlow.buildRefDSI( // returned is a different instance than input -FIXED
		clt_parameters, // CLTParameters clt_parameters,

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

+41 −17

Original line number	Diff line number	Diff line
		@@ -4077,8 +4077,8 @@ public class OpticalFlow {
		final boolean updateStatus,
		final int debugLevel) {
		final int debugLevelInner= clt_parameters.batch_run? -2: debugLevel; // copied from TQ
		if (debugLevelInner > -2) {
		System.out.println("buildRefDSI(): clt_parameters.batch_run="+clt_parameters.batch_run+", debugLevel="+debugLevel+", debugLevelInner="+debugLevelInner);
		if (debugLevelInner > -3) {
		System.out.println("buildRefDSI(): clt_parameters.batch_run="+clt_parameters.batch_run+", debugLevel="+debugLevel+", debugLevelInner="+debugLevelInner+", fast="+fast);
		}
		boolean photo_each = clt_parameters.photo_each; // true; // perform photogrammetric calibration to equalize pixel values
		boolean sky_extract = clt_parameters.imp.sky_extract;
		@@ -4158,6 +4158,25 @@ public class OpticalFlow {
		photo_each = false;
		sky_extract = false;
		}
		if (debugLevel > -3) {
		System.out.println("buildRefDSI(): Running preExpandCLTQuad3d() for scene "+quadCLT_ref.getImageName());
		System.out.println("buildRefDSI(): quadCLT_ref.hasNewImageData() -> "+quadCLT_ref.hasNewImageData());
		}
		quadCLT_ref.saveQuadClt(); // to re-load new set of Bayer images to the GPU (do nothing for CPU). Spend several days to find this bug!


		if (debugLevel > -3) {
		//quadCLT_main
		System.out.println("buildRefDSI():quadCLT_ref.tp.clt_3d_passes.size()="+quadCLT_ref.tp.clt_3d_passes.size());
		System.out.println("buildRefDSI(): suspecting processing *-DSI_MAIN.tiff without loading new images to the GPU, running quadCLT_ref.saveQuadClt(). 12/07/2025");
		boolean show_sources = debugLevel > 1000;
		if (show_sources) {
		quadCLT_ref.showImageData();
		}


		}


		quadCLT_ref.preExpandCLTQuad3d( // returns ImagePlus, but it already should be saved/shown
		clt_parameters,
		@@ -5179,7 +5198,10 @@ public class OpticalFlow {
		if (center_reference) { // invalidate pointer to recalculate
		quadCLTs[last_index].setRefPointer((String) null);
		}
		// quadCLTs[ref_index] =
		if (debugLevel > -3) {
		System.out.println("buildSeries(): Running OpticalFlow.buildRefDSI() for last_index scene # "+last_index+", : "+quadCLTs[last_index].getImageName());
		}

		buildRefDSI( // returned is a different instance than input -FIXED
		clt_parameters, // CLTParameters clt_parameters,
		fast, // boolean fast,
		@@ -5241,25 +5263,27 @@ public class OpticalFlow {
		}
		} // while (blue_sky == null)
		boolean early_try_back = false; // true;

		// if (!force_initial_orientations) { // moved here as setDSRBG fails with .dsi={null, null,...,null};
		// by now if it was center_reference the last ref_dsi is restored with optional blue sky.
		boolean bypass_last_index = (debugLevel > 1000); // && (quadCLTs[last_index] != null); // always. DEbugging 12/06/2025
		if (center_CLT == null) { // does not work in CUAS mode
		ref_blue_sky = quadCLTs[last_index].getDoubleBlueSky();
		ref_blue_sky = quadCLTs[last_index].getDoubleBlueSky(); // new
		if (!bypass_last_index) {
		quadCLTs[last_index] = (QuadCLT) quadCLT_main.spawnQuadCLT( // restores dsi from "DSI-MAIN"
		set_channels[last_index].set_name,
		clt_parameters,
		colorProcParameters, //
		threadsMax,
		debugLevel);
		}
		quadCLTs[last_index].setQuadClt(); // just in case ?
		quadCLTs[last_index].setBlueSky(ref_blue_sky); //quadCLTs[ref_index].dsi has it
		quadCLTs[last_index].setDSRBG( // null
		quadCLTs[last_index].setDSRBG( // DSI is needed in I244: cent_index = setInitialOrientationsIms(

		clt_parameters, // CLTParameters clt_parameters,
		threadsMax, // int threadsMax, // maximal number of threads to launch
		updateStatus, // boolean updateStatus,
		debugLevel); // int debugLevel)

		}
		if (!force_initial_orientations) {
		// use master_clt? - where to look for stage. in CUAS mode build directory name and look there
		@@ -6439,7 +6463,7 @@ public class OpticalFlow {
		}
		}
		final boolean toRGB = col_mode > 0;
		String scenes_suffix = quadCLTs[quadCLTs.length-1].getImageName()+
		String scenes_suffix = master_CLT.getImageName()+ // uadCLTs[quadCLTs.length-1].getImageName()+
		"-SEQ-" + IntersceneMatchParameters.MODES3D[mode3d+1] + "-"+(toRGB?"COLOR":"MONO");
		String um_suffix = "";
		if (!toRGB && um_mono) {
		@@ -7027,14 +7051,14 @@ public class OpticalFlow {
		}
		}

		boolean export_terrain_sequence = true;
		boolean export_terrain_sequence = true; // check master_CLT
		if (export_terrain_sequence && !clt_parameters.imp.lock_position) {
		combo_dsn_final =master_CLT.restoreComboDSI(true);
		if ((combo_dsn_final.length <= COMBO_DSN_INDX_TERRAIN) \|\| (combo_dsn_final[COMBO_DSN_INDX_TERRAIN] == null)) {
		System.out.println ("No terrain data available");
		} else {
		double [] terrain_disparity = combo_dsn_final[COMBO_DSN_INDX_TERRAIN];
		String scenes_suffix = quadCLTs[quadCLTs.length-1].getImageName()+"-TERRAIN";
		String scenes_suffix = master_CLT.getImageName()+"-TERRAIN"; // quadCLTs[quadCLTs.length-1][quadCLTs.length-1].getImageName()+"-TERRAIN";
		ImagePlus imp_terrain = renderSceneSequence(
		clt_parameters, // CLTParameters clt_parameters,
		master_CLT.hasCenterClt(), // boolean mode_cuas,
		@@ -7063,7 +7087,7 @@ public class OpticalFlow {
		System.out.println ("No terrain data available");
		} else {
		double [] elevation_disparity = combo_dsn_final[COMBO_DSN_INDX_DISP];
		String scenes_suffix = quadCLTs[quadCLTs.length-1].getImageName()+"-ELEVATION";
		String scenes_suffix = master_CLT.getImageName()+"-ELEVATION"; // quadCLTs[quadCLTs.length-1].getImageName()+"-ELEVATION";
		ImagePlus imp_elevation = renderSceneSequence(
		clt_parameters, // CLTParameters clt_parameters,
		master_CLT.hasCenterClt(), // boolean mode_cuas,

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

+34 −4

Original line number	Diff line number	Diff line
		@@ -96,7 +96,7 @@ public class QuadCLT extends QuadCLTCPU {
		}


		public QuadCLT saveQuadClt() {
		public QuadCLT saveQuadClt() { // used a lot!
		if (gpuQuad == null) {
		return null;
		}
		@@ -108,7 +108,7 @@ public class QuadCLT extends QuadCLTCPU {
		}
		return savedQuadClt;
		}
		void restoreQuadClt(QuadCLT savedQuadClt) {
		void restoreQuadClt(QuadCLT savedQuadClt) { // only used in QCC5185: getTileRBG()
		if (savedQuadClt != null) {
		gpuQuad.updateQuadCLT(savedQuadClt);
		}
		@@ -5028,7 +5028,7 @@ public class QuadCLT extends QuadCLTCPU {
		}

		/**
		* Get GPU-calculated tiles centers coordinates for each sesnor
		* Get GPU-calculated tiles centers coordinates for each sensor
		* @return per-tile null 2*num_sesnors array of alternating X and Y
		*/
		public double [][] getPortsXY() // run after GPU
		@@ -5154,6 +5154,36 @@ public class QuadCLT extends QuadCLTCPU {
		titles);
		}

		public void showImageData() {
		showImageData(null, null);
		}

		public void showImageData(
		double [][][] data,
		String title) {
		if (data == null) {
		data = this.image_data;
		}
		if (title == null) {
		title = this.getImageName()+"-IMAGE_DATA";
		}
		String [] sports = new String [data.length];
		String [] scolors = new String [data[0].length];
		for (int i = 0; i < sports.length; i++) sports[i]="port-"+i;
		for (int i = 0; i < scolors.length; i++) scolors[i]="col-"+i;
		int width = tp.getTilesX()*tp.getTileSize();
		// int height = tp.getTilesY()*tp.getTileSize();
		ShowDoubleFloatArrays.showArraysHyperstack(
		data, // double[][][] pixels,
		width, // int width,
		title, // String title,
		scolors, // String [] titles, // all slices*frames titles or just slice titles or null
		sports, // String [] frame_titles, // frame titles or null
		true); // boolean show)
		return;
		}

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

+17 −1

Original line number	Diff line number	Diff line
		@@ -14249,7 +14249,7 @@ public class QuadCLTCPU {
		tp.clt_3d_passes.get(tp.clt_3d_passes.size()-1).setAvgVal(tp.clt_3d_passes.get(bg_pass).getAvgVal());
		///// Refining after all added - end
		Runtime.getRuntime().gc();
		System.out.println("preExpandCLTQuad3d(): processing finished at "+
		System.out.println("preExpandCLTQuad3d(): processing scene "+getImageName()+" finished at "+
		IJ.d2s(0.000000001*(System.nanoTime()-this.startStepTime),3)+" sec, --- Free memory23="+Runtime.getRuntime().freeMemory()+" (of "+Runtime.getRuntime().totalMemory()+")");
		return true;
		}
		@@ -17918,6 +17918,7 @@ public class QuadCLTCPU {
		final boolean updateStatus,
		final int debugLevel)
		{
		saveQuadClt(); // to re-load new set of Bayer images to the GPU (do nothing for CPU). Spend several days to find this bug!
		boolean float_center = true; // false - center around provided value TODO: Move to clt_parameters?
		boolean show_2d_correlations = (debugLevel>100); // true; // debug feature
		final int tilesX = tp.getTilesX();
		@@ -18053,6 +18054,21 @@ public class QuadCLTCPU {
		mcorr_sel, // final int mcorr_sel, // Which pairs to correlate // +1 - all, +2 - dia, +4 - sq, +8 - neibs, +16 - hor + 32 - vert
		threadsMax, // maximal number of threads to launch
		debugLevel);
		boolean show_dbg_img = debugLevel > 1000;
		if (show_dbg_img) {
		int tile_size = getTileSize();
		int [] wh_dbg = {tilesXtile_size,tilesYtile_size};
		double [][] dbg = ((QuadCLT) this).renderDoubleFromTDMono (
		-1, // final int sensor_mask,
		wh_dbg, // null, // int [] wh,
		false); // boolean use_reference
		ShowDoubleFloatArrays.showArrays(
		dbg,
		wh_dbg[0],
		wh_dbg[1],
		true,
		getImageName()+"-test_CLTMeas");
		}

		} else {
		clt_data = image_dtt.quadCorrTD( // clt_data [task][sensor][color][][];

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