building models from bi-quad data (b3cf8b8a) · Commits · Elphel / imagej-elphel

src/main/java/BiCamDSI.java

+18 −0

Original line number	Diff line number	Diff line
		@@ -197,6 +197,24 @@ public class BiCamDSI {
		return selection;
		}

		public double [][] filterDisparityStrength(
		double min_disparity,
		double [] disparity,
		double [] strength,
		boolean [] selected){
		int num_tiles = disparity.length;
		double [][] fds = new double [2][num_tiles];
		for (int nTile = 0; nTile < num_tiles; nTile++) {
		fds[0][nTile] = Double.NaN;
		if ((strength[nTile] > 0.0) && (disparity[nTile] >= min_disparity) && ((selected == null) \|\| selected[nTile])) {
		fds[0][nTile] = disparity[nTile];
		fds[1][nTile] = strength[nTile];
		}
		}
		return fds;
		}


		/**
		* Filter selection by expending, then shrinking (fills small gaps) shrinking (combined with
		* previous step) and expanding again (removes small clusters)

src/main/java/BiQuadParameters.java

+20 −0

Original line number	Diff line number	Diff line
		@@ -128,6 +128,9 @@ public class BiQuadParameters {
		public int rf_shrink_near = 8; // Shrink selection after expanding
		public int rf_post_expand_near = 4; // Expand selection after shrinking

		public double rf_min_disp = 0.02; // Minimal tile disparity to keep in scan
		public boolean rf_remove_unselected = true; // Remove tiles that are not selected

		public int ml_hwidth = 2; // Half-width of the ML tiles to export (0-> 1x1, 1->3x3, 2 -> 5x5)
		public double ml_disparity_sweep = 2.0; // Disparity sweep around ground truth, each side
		public int ml_sweep_steps = 5; // Number of disparity sweep steps
		@@ -325,6 +328,11 @@ public class BiQuadParameters {
		gd.addNumericField("Expand selection after shrinking (non-infinity regions only)", this.rf_post_expand_near, 0,3,"",
		"Last step of expand-shrink-expand filtering (1 - only vert/hor, 2 -vert/hor/diagonal)");

		gd.addNumericField("Minimal usable disparity for tile to be preserved", this.rf_min_disp, 4,6,"pix",
		"Minimal disparity (in master camera pixels) for the tile to be saved for plane extraction");
		gd.addCheckbox ("Remove tiles that are not selected", this.rf_remove_unselected,
		"Remove (set strength to 0.0, disparity to Double.NaN for all tiles that are not selected");

		gd.addTab("ML","Parameters related to the ML files generation for the dual-quad camera rig");

		gd.addNumericField("Half-width of the ML tiles to export (0-> 1x1, 1->3x3, 2 -> 5x5)", this.ml_hwidth, 0,3,"",
		@@ -443,6 +451,9 @@ public class BiQuadParameters {
		this.rf_shrink_near= (int) gd.getNextNumber();
		this.rf_post_expand_near= (int) gd.getNextNumber();

		this.rf_min_disp= gd.getNextNumber();
		this.rf_remove_unselected= gd.getNextBoolean();

		this.ml_hwidth= (int) gd.getNextNumber();
		this.ml_disparity_sweep= gd.getNextNumber();
		this.ml_sweep_steps= (int) gd.getNextNumber();
		@@ -549,6 +560,9 @@ public class BiQuadParameters {
		properties.setProperty(prefix+"rf_shrink_near", this.rf_shrink_near+"");
		properties.setProperty(prefix+"rf_post_expand_near", this.rf_post_expand_near+"");

		properties.setProperty(prefix+"rf_min_disp", this.rf_min_disp+"");
		properties.setProperty(prefix+"rf_remove_unselected", this.rf_remove_unselected+"");

		properties.setProperty(prefix+"ml_hwidth", this.ml_hwidth+"");
		properties.setProperty(prefix+"ml_disparity_sweep", this.ml_disparity_sweep+"");
		properties.setProperty(prefix+"ml_sweep_steps", this.ml_sweep_steps+"");
		@@ -654,6 +668,9 @@ public class BiQuadParameters {
		if (properties.getProperty(prefix+"rf_shrink_near")!=null) this.rf_shrink_near=Integer.parseInt(properties.getProperty(prefix+"rf_shrink_near"));
		if (properties.getProperty(prefix+"rf_post_expand_near")!=null) this.rf_post_expand_near=Integer.parseInt(properties.getProperty(prefix+"rf_post_expand_near"));

		if (properties.getProperty(prefix+"rf_min_disp")!=null) this.rf_min_disp=Double.parseDouble(properties.getProperty(prefix+"rf_min_disp"));
		if (properties.getProperty(prefix+"rf_remove_unselected")!=null) this.rf_remove_unselected=Boolean.parseBoolean(properties.getProperty(prefix+"rf_remove_unselected"));

		if (properties.getProperty(prefix+"ml_disparity_sweep")!=null) this.ml_disparity_sweep=Double.parseDouble(properties.getProperty(prefix+"ml_disparity_sweep"));
		if (properties.getProperty(prefix+"ml_sweep_steps")!=null) this.ml_sweep_steps=Integer.parseInt(properties.getProperty(prefix+"ml_sweep_steps"));
		if (properties.getProperty(prefix+"ml_keep_aux")!=null) this.ml_keep_aux=Boolean.parseBoolean(properties.getProperty(prefix+"ml_keep_aux"));
		@@ -757,6 +774,9 @@ public class BiQuadParameters {
		bqp.rf_shrink_near= this.rf_shrink_near;
		bqp.rf_post_expand_near= this.rf_post_expand_near;

		bqp.rf_min_disp= this.rf_min_disp;
		bqp.rf_remove_unselected= this.rf_remove_unselected;

		bqp.ml_hwidth= this.ml_hwidth;
		bqp.ml_disparity_sweep= this.ml_disparity_sweep;
		bqp.ml_sweep_steps= this.ml_sweep_steps;

src/main/java/CLTPass3d.java

+2 −1

Original line number	Diff line number	Diff line
		@@ -392,7 +392,8 @@ public class CLTPass3d{
		* @return line-scan array of per-tile horizontal pairs correlation strength by reference (not a copy)
		*/
		public double [] getOriginalStrength(){
		return disparity_map[ImageDtt.DISPARITY_STRENGTH_INDEX];
		if (disparity_map != null) return disparity_map[ImageDtt.DISPARITY_STRENGTH_INDEX];
		else return getStrength(); // after replacing with rig data
		}
		/**
		* Get horizontal pairs correlation strength for vertical features. Not a copy

src/main/java/Eyesis_Correction.java

+43 −1

Original line number	Diff line number	Diff line
		@@ -590,6 +590,8 @@ private Panel panel1,
		// addButton("Rig enhance", panelClt4, color_conf_process);
		addButton("Ground truth", panelClt4, color_conf_process);
		addButton("ML export", panelClt4, color_conf_process);
		addButton("Rig planes", panelClt4, color_conf_process);


		add(panelClt4);
		}
		@@ -4598,6 +4600,14 @@ private Panel panel1,
		enhanceByRig();

		return;
		/* ======================================================================== */
		} else if (label.equals("CLT planes")) {
		DEBUG_LEVEL=MASTER_DEBUG_LEVEL;
		EYESIS_CORRECTIONS.setDebug(DEBUG_LEVEL);
		rigPlanes();
		return;


		/* ======================================================================== */
		} else if (label.equals("ML export")) {
		DEBUG_LEVEL=MASTER_DEBUG_LEVEL;
		@@ -5020,8 +5030,32 @@ private Panel panel1,
		return true;
		}

		public boolean rigPlanes() {
		if ((QUAD_CLT == null) \|\| (QUAD_CLT.tp == null) \|\| (QUAD_CLT.tp.clt_3d_passes == null)) {
		String msg = "DSI data is not available. Please run \"CLT 3D\" first";
		IJ.showMessage("Error",msg);
		System.out.println(msg);
		return false;
		}
		if (!prepareRigImages()) return false;
		String configPath=getSaveCongigPath();
		if (configPath.equals("ABORT")) return false;

		if (DEBUG_LEVEL > -2){
		System.out.println("++++++++++++++ Extracting planes using a dual-quad camera rig DSI data ++++++++++++++");
		}
		QUAD_CLT.showCLTPlanes(
		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);
		return true;

		}

		public boolean enhanceByRig() {
		long startTime=System.nanoTime();

		if ((QUAD_CLT == null) \|\| (QUAD_CLT.tp == null) \|\| (QUAD_CLT.tp.clt_3d_passes == null)) {
		String msg = "DSI data is not available. Please run \"CLT 3D\" first";
		IJ.showMessage("Error",msg);
		@@ -5055,10 +5089,15 @@ private Panel panel1,
		true,
		PROPERTIES);
		}
		System.out.println("enhanceByRig(): Processing finished at "+
		IJ.d2s(0.000000001*(System.nanoTime()-startTime),3)+" sec, --- Free memory="+
		Runtime.getRuntime().freeMemory()+" (of "+Runtime.getRuntime().totalMemory()+")");

		return true;
		}

		public boolean exportMLData() {
		long startTime=System.nanoTime();
		if ((QUAD_CLT == null) \|\| (QUAD_CLT.tp == null) \|\| (QUAD_CLT.tp.clt_3d_passes == null)) {
		String msg = "DSI data is not available. Please run \"CLT 3D\" first";
		IJ.showMessage("Error",msg);
		@@ -5092,10 +5131,13 @@ private Panel panel1,
		true,
		PROPERTIES);
		}
		System.out.println("exportMLData(): Processing finished at "+
		IJ.d2s(0.000000001*(System.nanoTime()-startTime),3)+" sec, --- Free memory="+
		Runtime.getRuntime().freeMemory()+" (of "+Runtime.getRuntime().totalMemory()+")");

		return true;
		}


		public boolean infinityRig() {
		if (!prepareRigImages()) return false;
		String configPath=getSaveCongigPath();

src/main/java/MeasuredLayers.java

+27 −3

Original line number	Diff line number	Diff line
		@@ -1101,7 +1101,10 @@ public class MeasuredLayers {
		if (weight[indxe_center] >= mlfp.strength_sure) { // tile does not need filtering
		ds[0][indx] = disp[indxe_center];
		ds[1][indx] = weight[indxe_center];

		if (Double.isNaN(ds[0][indx])){
		System.out.println("** this is a BUG6 in getDisparityStrengthML() **"); // all smpl_d are NaNs
		// break;
		}
		} else {
		int num_in_sample = 0;
		double sum_wnd = 0.0;
		@@ -1124,6 +1127,10 @@ public class MeasuredLayers {
		int indxs = sy * mlfp.smplSide + sx;
		smpl_sel[indxs] = true;
		smpl_d[indxs] = disp[indxe];
		if (Double.isNaN(smpl_d[indxs])){
		System.out.println("** this is a BUG5 in getDisparityStrengthML() **"); // all smpl_d are NaNs
		// break;
		}
		smpl_w[indxs] = weight[indxe] * smpl_weights[indxs];
		sum_wnd += smpl_weights[indxs];
		num_in_sample ++;
		@@ -1292,15 +1299,27 @@ public class MeasuredLayers {
		tiltXY = atiltXY[0]; // common for all tiles (such as constant disparity)
		} else if (atiltXY[indx] != null){
		tiltXY = atiltXY[indx];
		if (Double.isNaN(tiltXY[0]) \|\| Double.isNaN(tiltXY[1])){
		System.out.println("** this is a BUG4A in getDisparityStrengthML() **");
		System.out.println("atilt["+indx+"]= {"+tiltXY[0]+","+tiltXY[1]+"}");
		tiltXY[0] = 0.0;
		tiltXY[1] = 0.0;
		}

		}
		}

		if ((tiltXY != null) && (tiltXY[0] != 0.0) && (tiltXY[1] != 0.0)){
		if ((tiltXY != null) && (tiltXY[0] != 0.0) && (tiltXY[1] != 0.0)){ // {NaN,NaN}
		for (int sy = 0; sy < mlfp.smplSide; sy++){
		for (int sx = 0; sx < mlfp.smplSide; sx++){
		int indxs = sy * mlfp.smplSide + sx;
		if (smpl_w[indxs] > 0.0) {
		smpl_d[indxs] -= tiltXY[0]* (sx - smpl_dcenter) + tiltXY[1]* (sy - smpl_dcenter);
		if (Double.isNaN(smpl_d[indxs])){
		System.out.println("** this is a BUG4 in getDisparityStrengthML() **"); // all smpl_d are NaNs
		// break;
		}

		}
		}
		}
		@@ -1310,6 +1329,11 @@ public class MeasuredLayers {
		// calculate
		double sd=0.0, sd2 = 0.0, sw = 0.0;
		for (int i = 0; i < smplLen; i++) if (smpl_sel[i]) {
		if (Double.isNaN(smpl_d[i])){
		System.out.println("** this is a BUG3 in getDisparityStrengthML() **"); // all smpl_d are NaNs
		// break;
		}

		double dw = smpl_d[i] * smpl_w[i];
		sd += dw;
		sd2 += dw * smpl_d[i];
		@@ -1330,7 +1354,7 @@ public class MeasuredLayers {
		//remove_far_only
		}
		if (iworst < 0){
		System.out.println("** this is a BUG2 in getDisparityStrengthML() **");
		System.out.println("** this is a BUG2 in getDisparityStrengthML() **"); // all smpl_d are NaNs
		break;
		}
		// remove worst sample

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