assigning tiles to surfaces (d129b782) · Commits · Elphel / imagej-elphel

src/main/java/EyesisCorrectionParameters.java

+92 −2

Original line number	Original line	Diff line number	Diff line
	@@ -2215,6 +2215,18 @@ public class EyesisCorrectionParameters {
	public double msScaleProj = 1.5; // Scale projection of the plane ellipsoid		public double msScaleProj = 1.5; // Scale projection of the plane ellipsoid
	public double msFractUni = 0.3; // Spread this fraction of the ellipsoid weight among extended (double) supertile		public double msFractUni = 0.3; // Spread this fraction of the ellipsoid weight among extended (double) supertile

			public double tsMaxDiff = 0.3; // Maximal disparity difference when assigning tiles
			public double tsMinDiffOther = 0.35; // Minimal disparity difference to be considered as a competitor surface
			public double tsMinStrength = 0.05; // Minimal tile correlation strength to be assigned
			public double tsMaxStrength = 10.0; // Maximal tile correlation strength to be assigned
			public int tsMoveDirs = 3; // Allowed tile disparity correction: 1 increase, 2 - decrease, 3 - both directions
			public boolean tsEnMulti = false; // Allow assignment when several surfaces fit
			public double tsSurfStrPow = 0.0; // Raise surface strengths ratio to this power when comparing candidates
			public double tsSigma = 2.0; // Radius of influence (in tiles) of the previously assigned tiles
			public double tsNSigma = 2.0; // Maximal relative to radius distance to calculate influence
			public double tsMinAdvantage = 3.0; // Minimal ratio of the best surface candidate to the next one to make selection
			public boolean tsReset = false; // Reset tiles to surfaces assignment

	public boolean replaceWeakOutlayers = true; // false;		public boolean replaceWeakOutlayers = true; // false;

	public boolean dbg_migrate = true;		public boolean dbg_migrate = true;
	@@ -2519,6 +2531,17 @@ public class EyesisCorrectionParameters {
	properties.setProperty(prefix+"msScaleProj", this.msScaleProj +"");		properties.setProperty(prefix+"msScaleProj", this.msScaleProj +"");
	properties.setProperty(prefix+"msFractUni", this.msFractUni +"");		properties.setProperty(prefix+"msFractUni", this.msFractUni +"");

			properties.setProperty(prefix+"tsMaxDiff", this.tsMaxDiff +"");
			properties.setProperty(prefix+"tsMinDiffOther", this.tsMinDiffOther +"");
			properties.setProperty(prefix+"tsMinStrength", this.tsMinStrength +"");
			properties.setProperty(prefix+"tsMaxStrength", this.tsMaxStrength +"");
			properties.setProperty(prefix+"tsMoveDirs", this.tsMoveDirs+"");
			properties.setProperty(prefix+"tsEnMulti", this.tsEnMulti+"");
			properties.setProperty(prefix+"tsSurfStrPow", this.tsSurfStrPow +"");
			properties.setProperty(prefix+"tsSigma", this.tsSigma +"");
			properties.setProperty(prefix+"tsNSigma", this.tsNSigma +"");
			properties.setProperty(prefix+"tsMinAdvantage", this.tsMinAdvantage +"");

	properties.setProperty(prefix+"dbg_migrate", this.dbg_migrate+"");		properties.setProperty(prefix+"dbg_migrate", this.dbg_migrate+"");

	properties.setProperty(prefix+"show_ortho_combine", this.show_ortho_combine+"");		properties.setProperty(prefix+"show_ortho_combine", this.show_ortho_combine+"");
	@@ -2817,6 +2840,18 @@ public class EyesisCorrectionParameters {
	if (properties.getProperty(prefix+"msFractUni")!=null) this.msFractUni=Double.parseDouble(properties.getProperty(prefix+"msFractUni"));		if (properties.getProperty(prefix+"msFractUni")!=null) this.msFractUni=Double.parseDouble(properties.getProperty(prefix+"msFractUni"));


			if (properties.getProperty(prefix+"tsMaxDiff")!=null) this.tsMaxDiff=Double.parseDouble(properties.getProperty(prefix+"tsMaxDiff"));
			if (properties.getProperty(prefix+"tsMinDiffOther")!=null) this.tsMinDiffOther=Double.parseDouble(properties.getProperty(prefix+"tsMinDiffOther"));
			if (properties.getProperty(prefix+"tsMinStrength")!=null) this.tsMinStrength=Double.parseDouble(properties.getProperty(prefix+"tsMinStrength"));
			if (properties.getProperty(prefix+"tsMaxStrength")!=null) this.tsMaxStrength=Double.parseDouble(properties.getProperty(prefix+"tsMaxStrength"));
			if (properties.getProperty(prefix+"tsMoveDirs")!=null) this.tsMoveDirs=Integer.parseInt(properties.getProperty(prefix+"tsMoveDirs"));
			if (properties.getProperty(prefix+"tsEnMulti")!=null) this.tsEnMulti=Boolean.parseBoolean(properties.getProperty(prefix+"tsEnMulti"));
			if (properties.getProperty(prefix+"tsSurfStrPow")!=null) this.tsSurfStrPow=Double.parseDouble(properties.getProperty(prefix+"tsSurfStrPow"));
			if (properties.getProperty(prefix+"tsSigma")!=null) this.tsSigma=Double.parseDouble(properties.getProperty(prefix+"tsSigma"));
			if (properties.getProperty(prefix+"tsNSigma")!=null) this.tsNSigma=Double.parseDouble(properties.getProperty(prefix+"tsNSigma"));
			if (properties.getProperty(prefix+"tsMinAdvantage")!=null) this.tsMinAdvantage=Double.parseDouble(properties.getProperty(prefix+"tsMinAdvantage"));


	if (properties.getProperty(prefix+"dbg_migrate")!=null) this.dbg_migrate=Boolean.parseBoolean(properties.getProperty(prefix+"dbg_migrate"));		if (properties.getProperty(prefix+"dbg_migrate")!=null) this.dbg_migrate=Boolean.parseBoolean(properties.getProperty(prefix+"dbg_migrate"));

	if (properties.getProperty(prefix+"show_ortho_combine")!=null) this.show_ortho_combine=Boolean.parseBoolean(properties.getProperty(prefix+"show_ortho_combine"));		if (properties.getProperty(prefix+"show_ortho_combine")!=null) this.show_ortho_combine=Boolean.parseBoolean(properties.getProperty(prefix+"show_ortho_combine"));
	@@ -3139,6 +3174,17 @@ public class EyesisCorrectionParameters {
	gd.addNumericField("Scale projection of the plane ellipsoid", this.msScaleProj, 6);		gd.addNumericField("Scale projection of the plane ellipsoid", this.msScaleProj, 6);
	gd.addNumericField("Spread this fraction of the ellipsoid weight among extended (double) supertile",this.msFractUni, 6);		gd.addNumericField("Spread this fraction of the ellipsoid weight among extended (double) supertile",this.msFractUni, 6);

			gd.addNumericField("Maximal disparity difference when assigning tiles", this.tsMaxDiff, 6);
			gd.addNumericField("Minimal disparity difference to be considered as a competitor surface", this.tsMinDiffOther, 6);
			gd.addNumericField("Minimal tile correlation strength to be assigned", this.tsMinStrength, 6);
			gd.addNumericField("Maximal tile correlation strength to be assigned", this.tsMaxStrength, 6);
			gd.addNumericField("Allowed tile disparity correction: 1 increase, 2 - decrease, 3 - both directions",this.tsMoveDirs, 0);
			gd.addCheckbox ("Allow assignment when several surfaces fit", this.tsEnMulti);
			gd.addNumericField("Raise surface strengths ratio to this power when comparing candidates", this.tsSurfStrPow, 6);
			gd.addNumericField("Radius of influence (in tiles) of the previously assigned tiles", this.tsSigma, 6);
			gd.addNumericField("Maximal relative to radius distance to calculate influence", this.tsNSigma, 6);
			gd.addNumericField("Minimal ratio of the best surface candidate to the next one to make selection", this.tsMinAdvantage, 6);

	gd.addCheckbox ("Test new mode after migration", this.dbg_migrate);		gd.addCheckbox ("Test new mode after migration", this.dbg_migrate);

	gd.addMessage ("--- Other debug images ---");		gd.addMessage ("--- Other debug images ---");
	@@ -3443,6 +3489,18 @@ public class EyesisCorrectionParameters {
	this.msScaleProj= gd.getNextNumber();		this.msScaleProj= gd.getNextNumber();
	this.msFractUni= gd.getNextNumber();		this.msFractUni= gd.getNextNumber();

			this.tsMaxDiff= gd.getNextNumber();
			this.tsMinDiffOther= gd.getNextNumber();
			this.tsMinStrength= gd.getNextNumber();
			this.tsMaxStrength= gd.getNextNumber();
			this.tsMoveDirs= (int) gd.getNextNumber();
			this.tsEnMulti= gd.getNextBoolean();
			this.tsSurfStrPow= gd.getNextNumber();
			this.tsSigma= gd.getNextNumber();
			this.tsNSigma= gd.getNextNumber();
			this.tsMinAdvantage= gd.getNextNumber();
			this.tsReset = false; // Reset tiles to surfaces assignment

	this.dbg_migrate= gd.getNextBoolean();		this.dbg_migrate= gd.getNextBoolean();

	this.show_ortho_combine= gd.getNextBoolean();		this.show_ortho_combine= gd.getNextBoolean();
	@@ -3458,8 +3516,40 @@ public class EyesisCorrectionParameters {
	this.show_flaps_dirs= gd.getNextBoolean();		this.show_flaps_dirs= gd.getNextBoolean();
	this.show_first_clusters= gd.getNextBoolean();		this.show_first_clusters= gd.getNextBoolean();
	this.show_planes= gd.getNextBoolean();		this.show_planes= gd.getNextBoolean();

	return true;		return true;
	}		}

			public boolean showTsDialog() {
			GenericDialog gd = new GenericDialog("Set CLT parameters");
			gd.addNumericField("Maximal disparity difference when assigning tiles", this.tsMaxDiff, 6);
			gd.addNumericField("Minimal disparity difference to be considered as a competitor surface", this.tsMinDiffOther, 6);
			gd.addNumericField("Minimal tile correlation strength to be assigned", this.tsMinStrength, 6);
			gd.addNumericField("Maximal tile correlation strength to be assigned", this.tsMaxStrength, 6);
			gd.addNumericField("Allowed tile disparity correction: 1 increase, 2 - decrease, 3 - both directions",this.tsMoveDirs, 0);
			gd.addCheckbox ("Allow assignment when several surfaces fit", this.tsEnMulti);
			gd.addNumericField("Raise surface strengths ratio to this power when comparing candidates", this.tsSurfStrPow, 6);
			gd.addNumericField("Radius of influence (in tiles) of the previously assigned tiles", this.tsSigma, 6);
			gd.addNumericField("Maximal relative to radius distance to calculate influence", this.tsNSigma, 6);
			gd.addNumericField("Minimal ratio of the best surface candidate to the next one to make selection", this.tsMinAdvantage, 6);
			gd.addCheckbox ("Reset tiles to surfaces assignment", false);
			WindowTools.addScrollBars(gd);
			gd.showDialog();
			if (gd.wasCanceled()) return false;
			this.tsMaxDiff= gd.getNextNumber();
			this.tsMinDiffOther= gd.getNextNumber();
			this.tsMinStrength= gd.getNextNumber();
			this.tsMaxStrength= gd.getNextNumber();
			this.tsMoveDirs= (int) gd.getNextNumber();
			this.tsEnMulti= gd.getNextBoolean();
			this.tsSurfStrPow= gd.getNextNumber();
			this.tsSigma= gd.getNextNumber();
			this.tsNSigma= gd.getNextNumber();
			this.tsMinAdvantage= gd.getNextNumber();
			this.tsReset= gd.getNextBoolean();
			return true;
			}

	}		}

	public static class DCTParameters {		public static class DCTParameters {

src/main/java/Eyesis_Correction.java

+21 −1

Original line number	Original line	Diff line number	Diff line
	@@ -507,6 +507,7 @@ private Panel panel1,
	addButton("CLT reset 3D", panelClt1, color_stop);		addButton("CLT reset 3D", panelClt1, color_stop);
	addButton("CLT 3D", panelClt1, color_conf_process);		addButton("CLT 3D", panelClt1, color_conf_process);
	addButton("CLT planes", panelClt1, color_conf_process);		addButton("CLT planes", panelClt1, color_conf_process);
			addButton("CLT ASSIGN", panelClt1, color_process);
	addButton("CLT OUT 3D", panelClt1, color_process);		addButton("CLT OUT 3D", panelClt1, color_process);

	add(panelClt1);		add(panelClt1);
	@@ -4782,6 +4783,26 @@ private Panel panel1,
	UPDATE_STATUS, //final boolean updateStatus,		UPDATE_STATUS, //final boolean updateStatus,
	DEBUG_LEVEL); //final int debugLevel);		DEBUG_LEVEL); //final int debugLevel);
	return;		return;
			} else if (label.equals("CLT ASSIGN")) {
			DEBUG_LEVEL=MASTER_DEBUG_LEVEL;
			EYESIS_CORRECTIONS.setDebug(DEBUG_LEVEL);
			if (QUAD_CLT == null){
			System.out.println("QUAD_CLT is null, nothing to show");
			return;
			}

			if (!CLT_PARAMETERS.showTsDialog()) return;

			boolean OK = QUAD_CLT.assignCLTPlanes(
			CLT_PARAMETERS, // EyesisCorrectionParameters.DCTParameters dct_parameters,
			THREADS_MAX, //final int threadsMax, // maximal number of threads to launch
			UPDATE_STATUS, //final boolean updateStatus,
			DEBUG_LEVEL); //final int debugLevel);
			if (!OK){
			System.out.println("Could not assign tiles to surfaces, probably \"CLT planes\" command did not run");
			return;
			}
			return;

	} else if (label.equals("CLT OUT 3D")) {		} else if (label.equals("CLT OUT 3D")) {
	DEBUG_LEVEL=MASTER_DEBUG_LEVEL;		DEBUG_LEVEL=MASTER_DEBUG_LEVEL;
	@@ -4791,7 +4812,6 @@ private Panel panel1,
	return;		return;
	}		}


	String configPath=null;		String configPath=null;
	if (EYESIS_CORRECTIONS.correctionsParameters.saveSettings) {		if (EYESIS_CORRECTIONS.correctionsParameters.saveSettings) {
	configPath=EYESIS_CORRECTIONS.correctionsParameters.selectResultsDirectory(		configPath=EYESIS_CORRECTIONS.correctionsParameters.selectResultsDirectory(

src/main/java/QuadCLT.java

+25 −2

Original line number	Original line	Diff line number	Diff line
	@@ -4460,7 +4460,6 @@ public class QuadCLT {
	}		}
	return rslt;		return rslt;
	}		}
	// public ImagePlus [] cltDisparityScan(
	public void showCLTPlanes(		public void showCLTPlanes(
	EyesisCorrectionParameters.CLTParameters clt_parameters,		EyesisCorrectionParameters.CLTParameters clt_parameters,
	final int threadsMax, // maximal number of threads to launch		final int threadsMax, // maximal number of threads to launch
	@@ -4481,9 +4480,33 @@ public class QuadCLT {
	threadsMax,		threadsMax,
	updateStatus,		updateStatus,
	debugLevel);		debugLevel);
	// CLTPass3d last_scan = tp.clt_3d_passes.get(tp.clt_3d_passes.size() -1); // get last one

	}		}

			public boolean assignCLTPlanes(
			EyesisCorrectionParameters.CLTParameters clt_parameters,
			final int threadsMax, // maximal number of threads to launch
			final boolean updateStatus,
			final int debugLevel)
			{
			if (tp == null){
			System.out.println("showCLTPlanes(): tp is null");
			return false;
			}
			if (tp.clt_3d_passes == null){
			System.out.println("showCLTPlanes(): tp.clt_3d_passes is null");
			return false;
			}
			return tp.assignTilesToSurfaces(
			clt_parameters,
			geometryCorrection,
			threadsMax,
			updateStatus,
			debugLevel);

			}


	public void out3d(		public void out3d(
	EyesisCorrectionParameters.CLTParameters clt_parameters,		EyesisCorrectionParameters.CLTParameters clt_parameters,
	final int threadsMax, // maximal number of threads to launch		final int threadsMax, // maximal number of threads to launch

src/main/java/SuperTiles.java

+12 −0

Original line number	Original line	Diff line number	Diff line
	@@ -73,6 +73,9 @@ public class SuperTiles{
	int [][] shell_map = null; // per supertile, per disparity plane - shell index + 1 (0 - none)		int [][] shell_map = null; // per supertile, per disparity plane - shell index + 1 (0 - none)
	double [][] surfaces; // per shell, per tile (linescan order) disparity value or NaN in missing supertiles		double [][] surfaces; // per shell, per tile (linescan order) disparity value or NaN in missing supertiles

			TileSurface tileSurface = null;


	/**		/**
	* currently lowest plane for each includes all tiles, so do not use it. May change in the future		* currently lowest plane for each includes all tiles, so do not use it. May change in the future
	* @param np total number of planes in a supertile		* @param np total number of planes in a supertile
	@@ -185,6 +188,15 @@ public class SuperTiles{
	}		}
	}		}

			public void setTileSurface( TileSurface tileSurface)
			{
			this.tileSurface = tileSurface;
			}
			public TileSurface getTileSurface()
			{
			return tileSurface;
			}

	public void initFuseCoeff(		public void initFuseCoeff(
	double scale_diag,		double scale_diag,
	boolean debug)		boolean debug)

src/main/java/TileProcessor.java

+63 −12

Original line number	Original line	Diff line number	Diff line
	@@ -2942,6 +2942,53 @@ public class TileProcessor {
	}		}


			public boolean assignTilesToSurfaces(
			EyesisCorrectionParameters.CLTParameters clt_parameters,
			GeometryCorrection geometryCorrection,
			final int threadsMax, // maximal number of threads to launch
			final boolean updateStatus,
			final int debugLevel)
			{
			CLTPass3d scan_prev = clt_3d_passes.get(clt_3d_passes.size() -1); // get last one
			// boolean show_st = clt_parameters.stShow \|\| (debugLevel > 1);
			SuperTiles st = scan_prev.getSuperTiles();
			TileSurface tileSurface = st.getTileSurface();
			if (tileSurface == null){
			return false;
			}

			double [][][] dispStrength = st.getDisparityStrengths(
			clt_parameters.stMeasSel); // int stMeasSel) // = 1; // Select measurements for supertiles : +1 - combo, +2 - quad +4 - hor +8 - vert)

			boolean [][] tileSel = st.getMeasurementSelections(
			clt_parameters.stMeasSel); // int stMeasSel) // = 1; // Select measurements for supertiles : +1 - combo, +2 - quad +4 - hor +8 - vert)

			tileSurface.InitTilesAssignment(
			clt_parameters.tsReset,
			dispStrength, // final double [][][] dispStrength,
			tileSel, // final boolean [][] tileSel,
			debugLevel); // final int debugLevel,

			int [] stats= tileSurface.assignTilesToSurfaces(
			clt_parameters.tsMaxDiff, //final double maxDiff,
			clt_parameters.tsMinDiffOther, //final double minDiffOther, // should be >= maxDiff
			clt_parameters.tsMinStrength, //final double minStrength,
			clt_parameters.tsMaxStrength, //final double maxStrength,
			clt_parameters.tsMoveDirs, //final int moveDirs, // 1 increase disparity, 2 - decrease disparity, 3 - both directions
			clt_parameters.tsEnMulti, //final boolean enMulti,
			clt_parameters.tsSurfStrPow, //final double surfStrPow, // surface strength power
			clt_parameters.tsSigma, //final double sigma,
			clt_parameters.tsNSigma, //final double nSigma,
			clt_parameters.tsMinAdvantage, //final double minAdvantage,
			clt_parameters.plDispNorm, // final double dispNorm, // disparity normalize (proportionally scale down disparity difference if above
			dispStrength, // final double [][][] dispStrength,
			0, // -1, // debugLevel, // final int debugLevel)
			clt_parameters.tileX,
			clt_parameters.tileY);
			tileSurface.printStats(stats);
			return true;
			}

	//======================		//======================
	public void showPlanes(		public void showPlanes(
	EyesisCorrectionParameters.CLTParameters clt_parameters,		EyesisCorrectionParameters.CLTParameters clt_parameters,
	@@ -3174,9 +3221,11 @@ public class TileProcessor {
	st.tileProcessor.getTilesY(), // int tilesY,		st.tileProcessor.getTilesY(), // int tilesY,
	geometryCorrection, // GeometryCorrection geometryCorrection,		geometryCorrection, // GeometryCorrection geometryCorrection,
	st.tileProcessor.threadsMax); // int threadsMax);		st.tileProcessor.threadsMax); // int threadsMax);
			st.setTileSurface(tileSurface);


	TileSurface.TileData [][] tileData = tileSurface.createTileShells (		// TileSurface.TileData [][] tileData =
			tileSurface.createTileShells (
	clt_parameters.msUseSel, // final boolean use_sel,		clt_parameters.msUseSel, // final boolean use_sel,
	clt_parameters.msDivideByArea, // final boolean divide_by_area,		clt_parameters.msDivideByArea, // final boolean divide_by_area,
	clt_parameters.msScaleProj, // final double scale_projection,		clt_parameters.msScaleProj, // final double scale_projection,
	@@ -3186,16 +3235,14 @@ public class TileProcessor {
	clt_parameters.tileX,		clt_parameters.tileX,
	clt_parameters.tileY);		clt_parameters.tileY);

	int [][] tiles_layers = tileSurface.sortTilesToSurfaces(		tileSurface.InitTilesAssignment(
			true,
	dispStrength, // final double [][][] dispStrength,		dispStrength, // final double [][][] dispStrength,
	tileSel, // final boolean [][] tileSel,		tileSel, // final boolean [][] tileSel,
	tileData, // final TileData [][] tileData_src,		debugLevel); // final int debugLevel,
	// parameters		if (debugLevel > -10){
	clt_parameters, // final EyesisCorrectionParameters.CLTParameters clt_parameters,		return; // just cut off the rest
	debugLevel, // final int debugLevel,		}
	clt_parameters.tileX,
	clt_parameters.tileY);




	@@ -3572,6 +3619,10 @@ public class TileProcessor {
	}		}
	}		}





	public void secondPassSetup( // prepare tile tasks for the second pass based on the previous one(s)		public void secondPassSetup( // prepare tile tasks for the second pass based on the previous one(s)
	// final double [][][] image_data, // first index - number of image in a quad		// final double [][][] image_data, // first index - number of image in a quad
	EyesisCorrectionParameters.CLTParameters clt_parameters,		EyesisCorrectionParameters.CLTParameters clt_parameters,