merging planes (f60cc3af) · Commits · Elphel / imagej-elphel

src/main/java/EyesisCorrectionParameters.java

+34 −14

Original line number	Original line	Diff line number	Diff line
	@@ -2150,9 +2150,13 @@ public class EyesisCorrectionParameters {
	public double plMinStrength = 0.1; // Minimal total strength of a plane		public double plMinStrength = 0.1; // Minimal total strength of a plane
	public double plMaxEigen = 0.3; // Maximal eigenvalue of a plane		public double plMaxEigen = 0.3; // Maximal eigenvalue of a plane
	public boolean plDbgMerge = true; // Combine 'other' plane with current		public boolean plDbgMerge = true; // Combine 'other' plane with current
	public double plWorstWorsening = 2.0; // Worst case worsening after merge		public double plWorstWorsening = 1.0; // Worst case worsening after merge
	public boolean plMutualOnly = true; // keep only mutual links, remove weakest if conflict		public boolean plMutualOnly = true; // keep only mutual links, remove weakest if conflict

			public double plPull = .1; // Relative weight of original (measured) plane when combing with neighbors
			public int plIterations = 10; // Maximal number of smoothing iterations for each step
			public int plPrecision = 6; // Maximal step difference (1/power of 10)


	// other debug images		// other debug images
	public boolean show_ortho_combine = false; // Show 'ortho_combine'		public boolean show_ortho_combine = false; // Show 'ortho_combine'
	@@ -2397,6 +2401,10 @@ public class EyesisCorrectionParameters {
	properties.setProperty(prefix+"plWorstWorsening", this.plWorstWorsening +"");		properties.setProperty(prefix+"plWorstWorsening", this.plWorstWorsening +"");
	properties.setProperty(prefix+"plMutualOnly", this.plMutualOnly+"");		properties.setProperty(prefix+"plMutualOnly", this.plMutualOnly+"");

			properties.setProperty(prefix+"plPull", this.plPull +"");
			properties.setProperty(prefix+"plIterations", this.plIterations+"");
			properties.setProperty(prefix+"plPrecision", this.plPrecision+"");

	properties.setProperty(prefix+"show_ortho_combine", this.show_ortho_combine+"");		properties.setProperty(prefix+"show_ortho_combine", this.show_ortho_combine+"");
	properties.setProperty(prefix+"show_refine_supertiles", this.show_refine_supertiles+"");		properties.setProperty(prefix+"show_refine_supertiles", this.show_refine_supertiles+"");
	properties.setProperty(prefix+"show_bgnd_nonbgnd", this.show_bgnd_nonbgnd+"");		properties.setProperty(prefix+"show_bgnd_nonbgnd", this.show_bgnd_nonbgnd+"");
	@@ -2631,6 +2639,10 @@ public class EyesisCorrectionParameters {
	if (properties.getProperty(prefix+"plWorstWorsening")!=null) this.plWorstWorsening=Double.parseDouble(properties.getProperty(prefix+"plWorstWorsening"));		if (properties.getProperty(prefix+"plWorstWorsening")!=null) this.plWorstWorsening=Double.parseDouble(properties.getProperty(prefix+"plWorstWorsening"));
	if (properties.getProperty(prefix+"plMutualOnly")!=null) this.plMutualOnly=Boolean.parseBoolean(properties.getProperty(prefix+"plMutualOnly"));		if (properties.getProperty(prefix+"plMutualOnly")!=null) this.plMutualOnly=Boolean.parseBoolean(properties.getProperty(prefix+"plMutualOnly"));

			if (properties.getProperty(prefix+"plPull")!=null) this.plPull=Double.parseDouble(properties.getProperty(prefix+"plPull"));
			if (properties.getProperty(prefix+"plIterations")!=null) this.plIterations=Integer.parseInt(properties.getProperty(prefix+"plIterations"));
			if (properties.getProperty(prefix+"plPrecision")!=null) this.plPrecision=Integer.parseInt(properties.getProperty(prefix+"plPrecision"));

	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"));
	if (properties.getProperty(prefix+"show_refine_supertiles")!=null) this.show_refine_supertiles=Boolean.parseBoolean(properties.getProperty(prefix+"show_refine_supertiles"));		if (properties.getProperty(prefix+"show_refine_supertiles")!=null) this.show_refine_supertiles=Boolean.parseBoolean(properties.getProperty(prefix+"show_refine_supertiles"));
	if (properties.getProperty(prefix+"show_bgnd_nonbgnd")!=null) this.show_bgnd_nonbgnd=Boolean.parseBoolean(properties.getProperty(prefix+"show_bgnd_nonbgnd"));		if (properties.getProperty(prefix+"show_bgnd_nonbgnd")!=null) this.show_bgnd_nonbgnd=Boolean.parseBoolean(properties.getProperty(prefix+"show_bgnd_nonbgnd"));
	@@ -2887,6 +2899,10 @@ public class EyesisCorrectionParameters {
	gd.addNumericField("Worst case worsening after merge", this.plWorstWorsening, 6);		gd.addNumericField("Worst case worsening after merge", this.plWorstWorsening, 6);
	gd.addCheckbox ("Keep only mutual links, remove weakest if conflict", this.plMutualOnly);		gd.addCheckbox ("Keep only mutual links, remove weakest if conflict", this.plMutualOnly);

			gd.addNumericField("Relative weight of original (measured) plane when combing with neighbors", this.plPull, 6);
			gd.addNumericField("Maximal number of smoothing iterations for each step", this.plIterations, 0);
			gd.addNumericField("Maximal step difference (1/power of 10) ", this.plPrecision, 0);

	gd.addMessage ("--- Other debug images ---");		gd.addMessage ("--- Other debug images ---");
	gd.addCheckbox ("Show 'ortho_combine'", this.show_ortho_combine);		gd.addCheckbox ("Show 'ortho_combine'", this.show_ortho_combine);
	gd.addCheckbox ("Show 'refine_disparity_supertiles'", this.show_refine_supertiles);		gd.addCheckbox ("Show 'refine_disparity_supertiles'", this.show_refine_supertiles);
	@@ -3130,6 +3146,10 @@ public class EyesisCorrectionParameters {
	this.plWorstWorsening= gd.getNextNumber();		this.plWorstWorsening= gd.getNextNumber();
	this.plMutualOnly= gd.getNextBoolean();		this.plMutualOnly= gd.getNextBoolean();

			this.plPull= gd.getNextNumber();
			this.plIterations= (int) gd.getNextNumber();
			this.plPrecision= (int) gd.getNextNumber();

	this.show_ortho_combine= gd.getNextBoolean();		this.show_ortho_combine= gd.getNextBoolean();
	this.show_refine_supertiles=gd.getNextBoolean();		this.show_refine_supertiles=gd.getNextBoolean();
	this.show_bgnd_nonbgnd= gd.getNextBoolean(); // first on second pass		this.show_bgnd_nonbgnd= gd.getNextBoolean(); // first on second pass

src/main/java/QuadCLT.java

+1 −1

Original line number	Original line	Diff line number	Diff line
	@@ -5126,7 +5126,7 @@ public class QuadCLT {
	System.out.println("Generating cluster images (limit is set to "+clt_parameters.max_clusters+") largest, scan #"+scanIndex);		System.out.println("Generating cluster images (limit is set to "+clt_parameters.max_clusters+") largest, scan #"+scanIndex);
	}		}
	// ImagePlus cluster_image = getPassImage( // get image form a single pass		// ImagePlus cluster_image = getPassImage( // get image form a single pass
	String texturePath = getPassImage( // get image form a single pass		String texturePath = getPassImage( // get image from a single pass
	clt_parameters,		clt_parameters,
	colorProcParameters,		colorProcParameters,
	rgbParameters,		rgbParameters,

src/main/java/SuperTiles.java

+298 −47

File changed.

Preview size limit exceeded, changes collapsed.

src/main/java/TilePlanes.java

+53 −24

Original line number	Original line	Diff line number	Diff line
	@@ -57,8 +57,8 @@ public class TilePlanes {
	double [] world_v1 = null; // world in-plane vector, corresponding to vectors[1]		double [] world_v1 = null; // world in-plane vector, corresponding to vectors[1]
	double [] world_v2 = null; // world in-plane vector, corresponding to vectors[1]		double [] world_v2 = null; // world in-plane vector, corresponding to vectors[1]
	// double [] daxy = null; // disparity and 2 relative angles (ax and ay) corresponding to fisheye view, near (0,0) scale is pixel size		// double [] daxy = null; // disparity and 2 relative angles (ax and ay) corresponding to fisheye view, near (0,0) scale is pixel size
	double [][] neib_match = null; // for each of the directions (N, NE, .. NW) quality match for each layer		double [][] merged_eig_val = null; // for each of the directions (N, NE, .. NW) quality match for each layer
	int [] neib_best = new int [8]; // for each of the directions (N, NE, .. NW) index of best match, -1 if none		int [] neib_best = null; // new int [8]; // for each of the directions (N, NE, .. NW) index of best match, -1 if none
	// stores "worsening" of merging 2 planes. if L1,L2,L = values[0] of plane1, plane2 plane composite: w1, w2 - weights for plane1, plane2		// stores "worsening" of merging 2 planes. if L1,L2,L = values[0] of plane1, plane2 plane composite: w1, w2 - weights for plane1, plane2
	// Lav = Math.sqrt((L1 * L1 * w1 + L2 * L2 * w2)/(w1 + w2))		// Lav = Math.sqrt((L1 * L1 * w1 + L2 * L2 * w2)/(w1 + w2))
	// worsening_12 = (L - Lav) * (w1 + w2) * (w1 + w2) / (Lav * x1 * w2)		// worsening_12 = (L - Lav) * (w1 + w2) * (w1 + w2) / (Lav * x1 * w2)
	@@ -92,18 +92,44 @@ public class TilePlanes {
	pd.vectors[1] = this.vectors[1].clone();		pd.vectors[1] = this.vectors[1].clone();
	pd.vectors[2] = this.vectors[2].clone();		pd.vectors[2] = this.vectors[2].clone();
	}		}
	if (this.neib_match != null){		copyNeib(this,pd);
	pd.neib_match = this.neib_match.clone();		/*
	for (int i = 0; i<this.neib_match.length; i++){		if (this.merged_eig_val != null){
	if (this.neib_match[i] != null){		pd.merged_eig_val = this.merged_eig_val.clone();
	pd.neib_match[i] = this.neib_match[i].clone();		for (int i = 0; i<this.merged_eig_val.length; i++){
			if (this.merged_eig_val[i] != null){
			pd.merged_eig_val[i] = this.merged_eig_val[i].clone();
	}		}
	}		}
	}		}
	if (this.neib_best != null) pd.neib_best = this.neib_best.clone();		if (this.neib_best != null) pd.neib_best = this.neib_best.clone();
			*/
	return pd;		return pd;
	}		}

			public void copyNeib(
			PlaneData src,
			PlaneData dst)
			{
			if (src.merged_eig_val != null){
			dst.merged_eig_val = src.merged_eig_val.clone();
			for (int i = 0; i < src.merged_eig_val.length; i++){
			if (src.merged_eig_val[i] != null){
			dst.merged_eig_val[i] = src.merged_eig_val[i].clone();
			}
			}
			}
			if (src.neib_best != null) dst.neib_best = src.neib_best.clone();
			}

			public void invalidateCalculated()
			{
			this.center_xyz = null; // center of this supertile this plane center in world coordinates
			this.world_xyz = null; // world coordinates of the nearest point of the plane, in meters
			this.world_v1 = null; // world in-plane vector, corresponding to vectors[1]
			this.world_v2 = null; // world in-plane vector, corresponding to vectors[1]
			}


	public PlaneData (		public PlaneData (
	int [] sTileXY,		int [] sTileXY,
	@@ -117,40 +143,40 @@ public class TilePlanes {
	this.sTileXY = sTileXY.clone();		this.sTileXY = sTileXY.clone();
	}		}

	public double [][] initNeibMatch()		public double [][] initMergedValue()
	{		{
	this.neib_match = new double[8][];		this.merged_eig_val = new double[8][];
	return this.neib_match;		return this.merged_eig_val;
	}		}
	public double [][] getNeibMatch()		public double [][] getMergedValue()
	{		{
	return this.neib_match;		return this.merged_eig_val;
	}		}
	public double [] initNeibMatch(int dir, int leng)		public double [] initMergedValue(int dir, int leng)
	{		{
	this.neib_match[dir] = new double[leng];		this.merged_eig_val[dir] = new double[leng];
	for (int i = 0; i < leng; i++) this.neib_match[dir][i] = Double.NaN;		for (int i = 0; i < leng; i++) this.merged_eig_val[dir][i] = Double.NaN;
	return getNeibMatch(dir);		return getMergedValue(dir);
	}		}

	public double [] getNeibMatch(int dir)		public double [] getMergedValue(int dir)
	{		{
	if (this.neib_match == null) {		if (this.merged_eig_val == null) {
	return null;		return null;
	}		}
	return this.neib_match[dir];		return this.merged_eig_val[dir];
	}		}

	public double getNeibMatch(int dir, int plane)		public double getMergedValue(int dir, int plane)
	{		{
	if ((this.neib_match == null) \|\|(this.neib_match[dir] == null)){		if ((this.merged_eig_val == null) \|\|(this.merged_eig_val[dir] == null)){
	return Double.NaN;		return Double.NaN;
	}		}
	return this.neib_match[dir][plane];		return this.merged_eig_val[dir][plane];
	}		}
	public void setNeibMatch(int dir, int plane, double value)		public void setNeibMatch(int dir, int plane, double value)
	{		{
	this.neib_match[dir][plane] = value;		this.merged_eig_val[dir][plane] = value;
	}		}

	public int [] initNeibBest()		public int [] initNeibBest()
	@@ -452,6 +478,7 @@ public class TilePlanes {


	PlaneData pd = this.clone(); // will copy selections too		PlaneData pd = this.clone(); // will copy selections too
			pd.invalidateCalculated(); // real world vectors
	pd.setValues(eig_val[oindx][oindx],eig_val[vindx][vindx],eig_val[hindx][hindx]); // eigenvalues [0] - thickness, 2 other to detect skinny (poles)		pd.setValues(eig_val[oindx][oindx],eig_val[vindx][vindx],eig_val[hindx][hindx]); // eigenvalues [0] - thickness, 2 other to detect skinny (poles)
	pd.setVectors(plane);		pd.setVectors(plane);

	@@ -477,7 +504,8 @@ public class TilePlanes {
	PlaneData otherPd,		PlaneData otherPd,
	int debugLevel)		int debugLevel)
	{		{
	PlaneData pd = otherPd.clone();		PlaneData pd = otherPd.clone(); // TODO: use clone of this, copy only needed info from otherPD
			// keep world vectors from otherPd
	if (debugLevel > 0) {		if (debugLevel > 0) {
	System.out.println("getPlaneToThis()");		System.out.println("getPlaneToThis()");
	}		}
	@@ -596,6 +624,7 @@ public class TilePlanes {
	// System.out.println("getPlaneToThis(): "+pd.sTileXY[0]+":"+pd.sTileXY[1]+" -> "+pd.vectors[0][0]+", disp = "+disp+		// System.out.println("getPlaneToThis(): "+pd.sTileXY[0]+":"+pd.sTileXY[1]+" -> "+pd.vectors[0][0]+", disp = "+disp+
	// ", other_det = "+((new Matrix(otherPd.vectors).det()) +", pdr_det = "+((new Matrix(pd.vectors).det()))));		// ", other_det = "+((new Matrix(otherPd.vectors).det()) +", pdr_det = "+((new Matrix(pd.vectors).det()))));
	}		}
			copyNeib(this, pd);
	return pd; // make sure pd are updated // "this" is not used. Should it be used instead of pd?		return pd; // make sure pd are updated // "this" is not used. Should it be used instead of pd?
	}		}

src/main/java/TileProcessor.java

+29 −13

Original line number	Original line	Diff line number	Diff line
	@@ -2823,7 +2823,6 @@ public class TileProcessor {
	clt_parameters.tileX,		clt_parameters.tileX,
	clt_parameters.tileY);		clt_parameters.tileY);

	if (clt_parameters.plMutualOnly) {
	st.selectNeighborPlanesMutual(		st.selectNeighborPlanesMutual(
	clt_parameters.plWorstWorsening, // final double worst_worsening,		clt_parameters.plWorstWorsening, // final double worst_worsening,
	clt_parameters.plMaxEigen,		clt_parameters.plMaxEigen,
	@@ -2831,19 +2830,30 @@ public class TileProcessor {
	0, // final int debugLevel)		0, // final int debugLevel)
	clt_parameters.tileX,		clt_parameters.tileX,
	clt_parameters.tileY);		clt_parameters.tileY);
			TilePlanes.PlaneData [][] planes_mod = null;
			if (clt_parameters.plMutualOnly) { // temporarily re-use obsolete parameter to test smoothing

			planes_mod = st.planesSmooth(
			clt_parameters.plPull, // final double meas_pull,// relative pull of the original (measured) plane with respect to the average of the neighbors
			clt_parameters.plIterations, // final int num_passes,
			Math.pow(10.0, -clt_parameters.plPrecision), // final double maxDiff, // maximal change in any of the disparity values
			0, // final int debugLevel)
			clt_parameters.tileX,
			clt_parameters.tileY);

	} else {		// } else {
	st.selectNeighborPlanes(		// st.selectNeighborPlanes(
	clt_parameters.plWorstWorsening, // final double worst_worsening,		// clt_parameters.plWorstWorsening, // final double worst_worsening,
	clt_parameters.plMutualOnly, // final boolean mutual_only,		// clt_parameters.plMutualOnly, // final boolean mutual_only,
	0); // final int debugLevel)		// 0); // final int debugLevel)
	}		}

	if (clt_parameters.show_planes){		if (clt_parameters.show_planes){


	int [] wh = st.getShowPlanesWidthHeight();		int [] wh = st.getShowPlanesWidthHeight();
	double [][] plane_data_nonan = st.getShowPlanes(		double [][] plane_data_nonan = st.getShowPlanes(
	st.getPlanes(),		(planes_mod != null) ? st.getPlanesMod():st.getPlanes(),
	clt_parameters.plMinStrength, // minWeight,		clt_parameters.plMinStrength, // minWeight,
	clt_parameters.plMaxEigen, // maxEigen,		clt_parameters.plMaxEigen, // maxEigen,
	clt_parameters.plDispNorm,		clt_parameters.plDispNorm,
	@@ -2851,7 +2861,7 @@ public class TileProcessor {
	0.0,		0.0,
	10.0);		10.0);
	double [][] plane_data_nan = st.getShowPlanes(		double [][] plane_data_nan = st.getShowPlanes(
	st.getPlanes(),		(planes_mod != null) ? st.getPlanesMod():st.getPlanes(),
	clt_parameters.plMinStrength, // minWeight,		clt_parameters.plMinStrength, // minWeight,
	clt_parameters.plMaxEigen, // maxEigen,		clt_parameters.plMaxEigen, // maxEigen,
	clt_parameters.plDispNorm,		clt_parameters.plDispNorm,
	@@ -2870,6 +2880,12 @@ public class TileProcessor {
	// sdfa_instance.showArrays(plane_data_nonan, wh[0], wh[1], true, "plane_data_noNaN");		// sdfa_instance.showArrays(plane_data_nonan, wh[0], wh[1], true, "plane_data_noNaN");
	// sdfa_instance.showArrays(plane_data_nan, wh[0], wh[1], true, "plane_data_NaN");		// sdfa_instance.showArrays(plane_data_nan, wh[0], wh[1], true, "plane_data_NaN");
	sdfa_instance.showArrays(plane_data, wh[0], wh[1], true, "plane_data");		sdfa_instance.showArrays(plane_data, wh[0], wh[1], true, "plane_data");






	// show plane data		// show plane data

	/*		/*