added more diagnostic output (cc2b631c) · Commits · Elphel / imagej-elphel

src/main/java/DebayerScissors.java

+22 −18

Original line number	Original line	Diff line number	Diff line
	@@ -28,6 +28,7 @@
	import ij.IJ;		import ij.IJ;
	import ij.ImageStack;		import ij.ImageStack;

			import java.lang.reflect.InvocationTargetException;
	import java.util.concurrent.atomic.AtomicInteger;		import java.util.concurrent.atomic.AtomicInteger;

	import javax.swing.SwingUtilities;		import javax.swing.SwingUtilities;
	@@ -114,13 +115,13 @@ public class DebayerScissors {
	final AtomicInteger aStopIndex = new AtomicInteger(0);		final AtomicInteger aStopIndex = new AtomicInteger(0);
	final long startTime = System.nanoTime();		final long startTime = System.nanoTime();
	final AtomicInteger tilesFinishedAtomic = new AtomicInteger(1); // first finished will be 1		final AtomicInteger tilesFinishedAtomic = new AtomicInteger(1); // first finished will be 1
			if (updateStatus) IJ.showStatus("Reducing sampling aliases, "+tilesY+" rows, threadsMax="+threadsMax);
			if (updateStatus) System.out.println("Reducing sampling aliases, "+tilesY+" rows, threadsMax="+threadsMax);
	for (li = 0; li < nextFirstFindex.length; li++){		for (li = 0; li < nextFirstFindex.length; li++){
	aStopIndex.set(nextFirstFindex[li]);		aStopIndex.set(nextFirstFindex[li]);
	if (li>0){		if (li>0){
	ai.set(nextFirstFindex[li-1]);		ai.set(nextFirstFindex[li-1]);
	}		}
	// System.out.println("\n=== nextFirstFindex["+li+"] =" + nextFirstFindex[li]+" === ");

	for (int ithread = 0; ithread < threads.length; ithread++) {		for (int ithread = 0; ithread < threads.length; ithread++) {
	threads[ithread] = new Thread() {		threads[ithread] = new Thread() {
	public void run() {		public void run() {
	@@ -140,18 +141,17 @@ public class DebayerScissors {
	debayerParameters.debayerRelativeWidthRedblueClones);// green mask when applied to red/blue, clones		debayerParameters.debayerRelativeWidthRedblueClones);// green mask when applied to red/blue, clones
	// for (int nTile0 = ai.getAndIncrement(); nTile0 < numberOfKernels; nTile0 = ai.getAndIncrement()) {		// for (int nTile0 = ai.getAndIncrement(); nTile0 < numberOfKernels; nTile0 = ai.getAndIncrement()) {
	for (int nTile0 = ai.getAndIncrement(); nTile0 < aStopIndex.get(); nTile0 = ai.getAndIncrement()) {		for (int nTile0 = ai.getAndIncrement(); nTile0 < aStopIndex.get(); nTile0 = ai.getAndIncrement()) {

	int nTile = nonOverlapSeq[nTile0];		int nTile = nonOverlapSeq[nTile0];
	tileY = nTile /tilesX;		tileY = nTile /tilesX;
	tileX = nTile % tilesX;		tileX = nTile % tilesX;
	if (tileX < 2) {		if (tileX < 2) {
	int trow=(tileY+((tileY & 1)*tilesY))/2;		int trow=(tileY+((2(tileY & 1) + (tileX & 1))tilesY))/4;
	if (updateStatus) IJ.showStatus("Reducing sampling aliases, row "+(trow+1)+" of "+tilesY);		if (updateStatus) IJ.showStatus("Reducing sampling aliases, row "+(trow+1)+" of "+tilesY);
	// System.out.println("(1)Reducing sampling aliases, row "+(tileY+1)+" of "+tilesY+" ("+nTile+"/"+nTile0+") col="+(tileX+1));		// System.out.println("(1)Reducing sampling aliases, row "+(tileY+1)+" of "+tilesY+" ("+nTile+"/"+nTile0+") col="+(tileX+1));
	if (globalDebugLevel>2) System.out.println("(1)Reducing sampling aliases, row "+(tileY+1)+" of "+tilesY+" : "+IJ.d2s(0.000000001*(System.nanoTime()-startTime),3));		if (globalDebugLevel>2) System.out.println("Reducing sampling aliases, row "+(trow+1)+" of "+tilesY+" : "+IJ.d2s(0.000000001*(System.nanoTime()-startTime),3));
	}		}

	// if ((tileY==yTileDebug) && (tileX==xTileDebug)) this.debugLevel=4;
	// else this.debugLevel=wasDebugLevel;
	for (chn=0;chn<nChn;chn++){		for (chn=0;chn<nChn;chn++){
	extractSquareTile( pixels[chn], // source pixel array,		extractSquareTile( pixels[chn], // source pixel array,
	tile[chn], // will be filled, should have correct size before call		tile[chn], // will be filled, should have correct size before call
	@@ -193,7 +193,7 @@ public class DebayerScissors {
	fht_instance.inverseTransform(tile[chn]);		fht_instance.inverseTransform(tile[chn]);
	fht_instance.swapQuadrants(tile[chn]);		fht_instance.swapQuadrants(tile[chn]);
	/* accumulate result */		/* accumulate result */
	/*This is synchronized method. It is possible to make threads to write to non-overlapping regions of the outPixles, but as the accumulation		/*This is (now was) a synchronized method. It is possible to make threads to write to non-overlapping regions of the outPixles, but as the accumulation
	* takes just small fraction of several FHTs, it should be OK - reasonable number of threads will spread and not "stay in line"		* takes just small fraction of several FHTs, it should be OK - reasonable number of threads will spread and not "stay in line"
	*/		*/

	@@ -206,31 +206,35 @@ public class DebayerScissors {
	tileY*step); // top corner Y		tileY*step); // top corner Y
	}		}
	if ((tileY==yTileDebug) && (tileX==xTileDebug) && (SDFA_instance!=null)) SDFA_instance.showArrays (tile.clone(),debayerParameters.size,debayerParameters.size, "B00");		if ((tileY==yTileDebug) && (tileX==xTileDebug) && (SDFA_instance!=null)) SDFA_instance.showArrays (tile.clone(),debayerParameters.size,debayerParameters.size, "B00");

	final int numFinished=tilesFinishedAtomic.getAndIncrement();		final int numFinished=tilesFinishedAtomic.getAndIncrement();
			// final double dprogr= (1.0+numFinished)/numberOfKernels;
			if (numFinished % (numberOfKernels/50+1) == 0) {
			// System.out.print(numFinished);
	SwingUtilities.invokeLater(new Runnable() {		SwingUtilities.invokeLater(new Runnable() {
	public void run() {		public void run() {
			// System.out.println(" --- "+numFinished+"("+numberOfKernels+"): "+dprogr);
	IJ.showProgress(numFinished, numberOfKernels);		IJ.showProgress(numFinished, numberOfKernels);
	}		}
	});		});
	}		}
	}		}
			}
	};		};
	}		}
	startAndJoin(threads);		startAndJoin(threads);
			IJ.showProgress(tilesFinishedAtomic.get(), numberOfKernels);
	}		}
			// System.out.println("tilesFinishedAtomic.get()="+tilesFinishedAtomic.get()+", numberOfKernels="+numberOfKernels);
	if (updateStatus) IJ.showStatus("Reducing sampling aliases DONE");		if (updateStatus) IJ.showStatus("Reducing sampling aliases DONE");
	IJ.showProgress(1.0);		IJ.showProgress(1.0);
	// this.debugLevel=wasDebugLevel;
	/* prepare result stack to return */		/* prepare result stack to return */
	ImageStack outStack=new ImageStack(imgWidth,imgHeight);		ImageStack outStack=new ImageStack(imgWidth,imgHeight);
	for (chn=0;chn<nChn;chn++) {		for (chn=0;chn<nChn;chn++) {
	outStack.addSlice(imageStack.getSliceLabel(chn+1), outPixles[chn]);		outStack.addSlice(imageStack.getSliceLabel(chn+1), outPixles[chn]);
	}		}
	debayerEnergyWidth= (debayerEnergy!=null)?tilesX:0; // for the image to be displayed externally		debayerEnergyWidth= (debayerEnergy!=null)?tilesX:0; // for the image to be displayed externally
	// if (debayerParameters.showEnergy) {		if (globalDebugLevel>0) System.out.println("Reducing sampling aliases done in "+IJ.d2s(0.000000001*(System.nanoTime()-startTime),3));
	// SDFA_INSTANCE.showArrays (debayerEnergy,tilesX,tilesY, "Debayer-Energy");
	// }
	if (globalDebugLevel>0) System.out.println("(1)Reducing sampling aliases done in "+IJ.d2s(0.000000001*(System.nanoTime()-startTime),3));
	return outStack;		return outStack;
	}		}

src/main/java/EyesisCorrections.java

+9 −7

Original line number	Original line	Diff line number	Diff line
	@@ -1744,7 +1744,7 @@ public class EyesisCorrections {
	"kernelNumHor="+kernelNumHor+"\n"+		"kernelNumHor="+kernelNumHor+"\n"+
	"numberOfKernelsInChn="+numberOfKernelsInChn+"\n");		"numberOfKernelsInChn="+numberOfKernelsInChn+"\n");

			if (updateStatus) IJ.showStatus("Convolving image with kernels, "+nChn+" channels, "+tilesY+" rows");
	final long startTime = System.nanoTime();		final long startTime = System.nanoTime();
	for (li = 0; li < nextFirstFindex.length; li++){		for (li = 0; li < nextFirstFindex.length; li++){
	aStopIndex.set(nextFirstFindex[li]);		aStopIndex.set(nextFirstFindex[li]);
	@@ -1776,7 +1776,7 @@ public class EyesisCorrections {
	if (tileX < 4) {		if (tileX < 4) {
	int trow=(tileY+ ((tileY & 3) * tilesY))/4;		int trow=(tileY+ ((tileY & 3) * tilesY))/4;
	if (updateStatus) IJ.showStatus("Convolving image with kernels, channel "+(chn+1)+" of "+nChn+", row "+(trow+1)+" of "+tilesY);		if (updateStatus) IJ.showStatus("Convolving image with kernels, channel "+(chn+1)+" of "+nChn+", row "+(trow+1)+" of "+tilesY);
	if (globalDebugLevel>2) System.out.println("Processing kernels, channel "+(chn+1)+" of "+nChn+", row "+(tileY+1)+" of "+tilesY+" : "+IJ.d2s(0.000000001*(System.nanoTime()-startTime),3));		if (globalDebugLevel>2) System.out.println("Processing kernels, channel "+(chn+1)+" of "+nChn+", row "+(trow+1)+" of "+tilesY+" : "+IJ.d2s(0.000000001*(System.nanoTime()-startTime),3));
	}		}

	if (chn!=chn0) {		if (chn!=chn0) {
	@@ -1837,11 +1837,13 @@ public class EyesisCorrections {
	(tileX-1)*step, // left corner X		(tileX-1)*step, // left corner X
	(tileY-1)*step); // top corner Y		(tileY-1)*step); // top corner Y
	final int numFinished=tilesFinishedAtomic.getAndIncrement();		final int numFinished=tilesFinishedAtomic.getAndIncrement();
			if (numFinished % (numberOfKernels/100+1) == 0) {
	SwingUtilities.invokeLater(new Runnable() {		SwingUtilities.invokeLater(new Runnable() {
	public void run() {		public void run() {
	IJ.showProgress(numFinished,numberOfKernels);		IJ.showProgress(numFinished,numberOfKernels);
	}		}
	});		});
			}

	//numberOfKernels		//numberOfKernels
	}		}

src/main/java/deBayerScissors.java

+114 −35

Original line number	Original line	Diff line number	Diff line
	@@ -35,6 +35,12 @@ public class deBayerScissors {
	private double lastMidEnergy; // last midrange spectral energy		private double lastMidEnergy; // last midrange spectral energy
	private showDoubleFloatArrays SDFA_instance; // just for debugging?		private showDoubleFloatArrays SDFA_instance; // just for debugging?
	private DoubleFHT fht_instance;		private DoubleFHT fht_instance;
			private int [][] aliasMapRedBlue={
			{-2,-2},{-2,-1},{-2,0},{-2,1},
			{-1,-2},{-1,-1},{-1,0},{-1,1},
			{ 0,-2},{ 0,-1}, { 0,1},
			{ 1,-2},{ 1,-1},{ 1,0},{ 1,1}};
			private int [][][][] speedTable = null;

	public double getMidEnergy() {return lastMidEnergy; } // instead of the DOUBLE_DEBUG_RESULT		public double getMidEnergy() {return lastMidEnergy; } // instead of the DOUBLE_DEBUG_RESULT
	public deBayerScissors(		public deBayerScissors(
	@@ -59,6 +65,29 @@ public class deBayerScissors {
	debayer_width_redblue_clones, // green mask when applied to red/blue, clones		debayer_width_redblue_clones, // green mask when applied to red/blue, clones
	size, // side of the square		size, // side of the square
	4); // should be 4 now		4); // should be 4 now

			int hsize=size/2;
			int subpixel=4; // hardwired - when changing it will need to change alias maps
			int aliasX=size/subpixel;
			speedTable = new int [hsize+1][size][aliasMapRedBlue.length][3];
			int i,j,nAlias,x,y;
			for (i = 0;i <= hsize;i++) for (j = 0;j < size;j++) {
			speedTable[i][j][0][0] = i*size+j;
			speedTable[i][j][0][1] = ((size-i) % size) * size + ((size-j) % size);
			for(nAlias=0;nAlias<aliasMapRedBlue.length; nAlias++) {
			y = (i-aliasX*aliasMapRedBlue[nAlias][0]+size) % size;
			x = (j-aliasX*aliasMapRedBlue[nAlias][1]+size) % size;
			if (y > hsize) {
			y = size - y;
			x = (size - x) % size;
			}
			if (y>hsize) {
			y=size-y;
			x=(size-x)%size;
			}
			speedTable[i][j][nAlias][2]=y*size+x;
			}
			}
	}		}

	/* returns 2 masks (0:0 in the top left corner, match fht) [0] - for greens, [1] - for red/blue */		/* returns 2 masks (0:0 in the top left corner, match fht) [0] - for greens, [1] - for red/blue */
	@@ -171,9 +200,9 @@ public class deBayerScissors {
	int length=green_amp.length;		int length=green_amp.length;
	int size = (int) Math.sqrt(length);		int size = (int) Math.sqrt(length);
	int hsize=size/2;		int hsize=size/2;
	int subpixel=4; // hardwired - when changing it will need to change alias maps		// int subpixel=4; // hardwired - when changing it will need to change alias maps
	int aliasX=size/subpixel;		// int aliasX=size/subpixel;
	int i,j,index,index_back,x,y;		int i,j,index,index_back; //,x,y;
	double [] amp= green_amp.clone();		double [] amp= green_amp.clone();
	double [] amp_clones=green_amp.clone();		double [] amp_clones=green_amp.clone();
	if (green_mask!=null) for (i=0;i<amp.length;i++) amp[i]*=green_mask[i];		if (green_mask!=null) for (i=0;i<amp.length;i++) amp[i]*=green_mask[i];
	@@ -183,13 +212,14 @@ public class deBayerScissors {
	/* Combine into mask by comparing pixels[] from the zero and 7 aliases */		/* Combine into mask by comparing pixels[] from the zero and 7 aliases */
	double d;		double d;
	int nAlias;		int nAlias;
			/*
	int [][] aliasMapRedBlue={		int [][] aliasMapRedBlue={
	{-2,-2},{-2,-1},{-2,0},{-2,1},		{-2,-2},{-2,-1},{-2,0},{-2,1},
	{-1,-2},{-1,-1},{-1,0},{-1,1},		{-1,-2},{-1,-1},{-1,0},{-1,1},
	{ 0,-2},{ 0,-1}, { 0,1},		{ 0,-2},{ 0,-1}, { 0,1},
	{ 1,-2},{ 1,-1},{ 1,0},{ 1,1}};		{ 1,-2},{ 1,-1},{ 1,0},{ 1,1}};

	/* First step - mask out all the pixels where at least one of the alias amplitude is above the main one */		// First step - mask out all the pixels where at least one of the alias amplitude is above the main one
	if (this_debug>2) SDFA_instance.showArrays(amp.clone(), "amp");		if (this_debug>2) SDFA_instance.showArrays(amp.clone(), "amp");
	if (this_debug>2) SDFA_instance.showArrays(amp_clones, "amp_clones");		if (this_debug>2) SDFA_instance.showArrays(amp_clones, "amp_clones");

	@@ -204,26 +234,65 @@ public class deBayerScissors {
	for(nAlias=0;nAlias<aliasMapRedBlue.length; nAlias++) {		for(nAlias=0;nAlias<aliasMapRedBlue.length; nAlias++) {
	y=(i-aliasX*aliasMapRedBlue[nAlias][0]+size) % size;		y=(i-aliasX*aliasMapRedBlue[nAlias][0]+size) % size;
	x=(j-aliasX*aliasMapRedBlue[nAlias][1]+size) % size;		x=(j-aliasX*aliasMapRedBlue[nAlias][1]+size) % size;
	/*		if (y>hsize) {
	if (amp_clones[(y>hsize)? ((size-y)size+((size-x)%size)):ysize+x]>d) {		y=size-y;
			x=(size-x)%size;
			}
			if (amp_clones[y*size+x]>d) {
	mask[index]=-1.0;		mask[index]=-1.0;
	mask[index_back]=-1.0;		mask[index_back]=-1.0;
	break;		break;
	}		}

			}
			}
			}
	*/		*/
			/*
			speedTable = new int [hsize][size][aliasMapRedBlue.length][3];
			int i,j,nAlias,x,y;
			for (i=0;i<=hsize;i++) for (j=0;j<size;j++) {
			speedTable[i][j][0][0] = i*size+j;
			speedTable[i][j][0][1] = ((size-i) % size) * size + ((size-j) % size);
			for(nAlias=0;nAlias<aliasMapRedBlue.length; nAlias++) {
			y = (i-aliasX*aliasMapRedBlue[nAlias][0]+size) % size;
			x = (j-aliasX*aliasMapRedBlue[nAlias][1]+size) % size;
	if (y > hsize) {		if (y > hsize) {
	y = size - y;		y = size - y;
	x = (size - x) % size;		x = (size - x) % size;
	}		}
	if (amp_clones[y*size+x]>d) {		if (y>hsize) {
			y=size-y;
			x=(size-x)%size;
			}
			speedTable[i][j][nAlias][2]=y*size+x;
			}
			}
			*/

			// First step - mask out all the pixels where at least one of the alias amplitude is above the main one
			if (this_debug>2) SDFA_instance.showArrays(amp.clone(), "amp");
			if (this_debug>2) SDFA_instance.showArrays(amp_clones, "amp_clones");

			for (i=0;i<=hsize;i++) for (j=0;j<size;j++) {
			index = speedTable[i][j][0][0]; // i*size+j;
			index_back = speedTable[i][j][0][1]; //((size-i) % size) * size + ((size-j) % size);
			d=amp[index]*mainToAlias;
			if (d>0.0) {
			mask[index]=1.0;
			mask[index_back]=1.0;
			for(nAlias=0;nAlias<aliasMapRedBlue.length; nAlias++) {
			if (amp_clones[speedTable[i][j][nAlias][2]]>d) {
	mask[index]=-1.0;		mask[index]=-1.0;
	mask[index_back]=-1.0;		mask[index_back]=-1.0;
	break;		break;
	}		}

	}		}
	}		}
	}		}

			// End of replacement code

	if (this_debug>2) SDFA_instance.showArrays(mask, "mask");		if (this_debug>2) SDFA_instance.showArrays(mask, "mask");

	if (pol_instace==null) return mask;		if (pol_instace==null) return mask;
	@@ -231,20 +300,22 @@ public class deBayerScissors {
	for (i=0;i<amp.length;i++) amp[i]*=mask[i];		for (i=0;i<amp.length;i++) amp[i]*=mask[i];
	if (this_debug>2) SDFA_instance.showArrays(amp, "amp-mask");		if (this_debug>2) SDFA_instance.showArrays(amp, "amp-mask");
	double [] polar_amp=pol_instace.cartesianToPolar(amp);		double [] polar_amp=pol_instace.cartesianToPolar(amp);
	if (this_debug>2) SDFA_instance.showArrays(polar_amp.clone(),pol_instace.getWidth(),pol_instace.getHeight(), "RB-polar-amp");		int width = pol_instace.getWidth();
	double k= bonus/pol_instace.getWidth();		int height = pol_instace.getHeight();
	for (i=0;i<pol_instace.getHeight();i++) for (j=0;j<pol_instace.getWidth();j++) polar_amp[ipol_instace.getWidth()+j]=1.0+k*j;		if (this_debug>2) SDFA_instance.showArrays(polar_amp.clone(),width, height, "RB-polar-amp");
			double k= bonus/width;
			for (i=0;i<pol_instace.getHeight();i++) for (j = 0; j < width; j++) polar_amp[i * width + j]=1.0+kj;
	double [] polar_mask_pixels=pol_instace.genPolarRedBlueMask(polar_amp,0); // 0 - just 1.0/0.0, 1 - "analog"		double [] polar_mask_pixels=pol_instace.genPolarRedBlueMask(polar_amp,0); // 0 - just 1.0/0.0, 1 - "analog"
	double [] cart_mask_pixels= pol_instace.polarToCartesian (polar_mask_pixels,size,0.0);		double [] cart_mask_pixels= pol_instace.polarToCartesian (polar_mask_pixels,size,0.0);
	if (this_debug>2) {		if (this_debug>2) {
	SDFA_instance.showArrays(polar_amp, pol_instace.getWidth(),pol_instace.getHeight(), "RB-amp-bonus");		SDFA_instance.showArrays(polar_amp, width, height, "RB-amp-bonus");
	SDFA_instance.showArrays(polar_mask_pixels,pol_instace.getWidth(),pol_instace.getHeight(), "pRBm");		SDFA_instance.showArrays(polar_mask_pixels, width, height, "pRBm");
	SDFA_instance.showArrays(cart_mask_pixels, size, size, "cRBm");		SDFA_instance.showArrays(cart_mask_pixels, size, size, "cRBm");
	}		}
	if (this_debug>2) {		if (this_debug>2) {
	double [] polar_mask_pixels1=pol_instace.genPolarRedBlueMask(polar_amp,1);		double [] polar_mask_pixels1=pol_instace.genPolarRedBlueMask(polar_amp,1);
	double [] cart_mask_pixels1= pol_instace.polarToCartesian (polar_mask_pixels1,size,0.0);		double [] cart_mask_pixels1= pol_instace.polarToCartesian (polar_mask_pixels1,size,0.0);
	SDFA_instance.showArrays(polar_mask_pixels1,pol_instace.getWidth(),pol_instace.getHeight(), "pRBm1");		SDFA_instance.showArrays(polar_mask_pixels1, width, height, "pRBm1");
	SDFA_instance.showArrays(cart_mask_pixels1, size, size, "cRBm1");		SDFA_instance.showArrays(cart_mask_pixels1, size, size, "cRBm1");
	}		}
	return cart_mask_pixels;		return cart_mask_pixels;
	@@ -418,8 +489,10 @@ public class deBayerScissors {
	double [] polPixels=new double[iRadiusPlus1*(iAngle+1)];		double [] polPixels=new double[iRadiusPlus1*(iAngle+1)];
	int i;		int i;
	for (i=0;i<polPixels.length;i++) {		for (i=0;i<polPixels.length;i++) {
	polPixels[i]=(1-polar2CartesianFractions[i][1])( (1-polar2CartesianFractions[i][0])cartPixels[polar2CartesianIndices[i][0]] + polar2CartesianFractions[i][0]*cartPixels[polar2CartesianIndices[i][1]])+		polPixels[i]=(1-polar2CartesianFractions[i][1])( (1-polar2CartesianFractions[i][0])cartPixels[polar2CartesianIndices[i][0]] +
	polar2CartesianFractions[i][1] ( (1-polar2CartesianFractions[i][0])cartPixels[polar2CartesianIndices[i][2]] + polar2CartesianFractions[i][0]*cartPixels[polar2CartesianIndices[i][3]]) ;		polar2CartesianFractions[i][0]*cartPixels[polar2CartesianIndices[i][1]])+
			polar2CartesianFractions[i][1] ( (1-polar2CartesianFractions[i][0])cartPixels[polar2CartesianIndices[i][2]] +
			polar2CartesianFractions[i][0]*cartPixels[polar2CartesianIndices[i][3]]) ;
	}		}
	return polPixels;		return polPixels;
	}		}
	@@ -503,12 +576,14 @@ public class deBayerScissors {
	return genPolarMask(polarAmps,0,mode);		return genPolarMask(polarAmps,0,mode);
	}		}

	public double [] genPolarRedBlueMask(double [] polarAmps, // polar array of amplitude values, <0 - stop		public double [] genPolarRedBlueMask(
	int mode){ // result mode - 0: output mask as 0/1, 1 -output proportional, positive - pass, negative - rejected		double [] polarAmps, // polar array of amplitude values, <0 - stop
			int mode)
			{ // result mode - 0: output mask as 0/1, 1 -output proportional, positive - pass, negative - rejected
	return genPolarMask(polarAmps, 1, mode);		return genPolarMask(polarAmps, 1, mode);
	}		}

			// ** Seems to be most time-critical **
	public double [] genPolarMask(double [] polarAmps, // polar array of amplitude values, <0 - stop		public double [] genPolarMask(double [] polarAmps, // polar array of amplitude values, <0 - stop
	int type, // 0 - green, 1 red/blue		int type, // 0 - green, 1 red/blue
	int mode){ // result mode - 0: output mask as 0/1, 1 -output proportional, positive - pass, negative - rejected		int mode){ // result mode - 0: output mask as 0/1, 1 -output proportional, positive - pass, negative - rejected
	@@ -536,11 +611,14 @@ public class deBayerScissors {
	step++;		step++;
	/* add polar point index */		/* add polar point index */
	newVal=good?step:-step;		newVal=good?step:-step;
	// index=iMax*iRadiusPlus1+rayLength[iMax]; // rayLength[iMax] should point to a new cell (with intMap[]==0) may ommit - set in the end of the loop and before the loop?
	intMap[index]=newVal;		intMap[index]=newVal;
	if (sameCartesian[index]!=null) for (i=0;i<sameCartesian[index].length;i++) intMap[sameCartesian[index][i]]=newVal;		if (sameCartesian[index]!=null)
			for (i=0;i<sameCartesian[index].length;i++)
			intMap[sameCartesian[index][i]]=newVal;
	/* add aliases of point index (as negative values) */		/* add aliases of point index (as negative values) */
	if ((good) &&(polarMap[index]!=null)) for (i=0;i<polarMap[index].length;i++) intMap[polarMap[index][i]]=-step;		if ((good) &&(polarMap[index]!=null))
			for (i=0;i<polarMap[index].length;i++)
			intMap[polarMap[index][i]]=-step;
	/* update ray lengths and status */		/* update ray lengths and status */
	max=-1.0;		max=-1.0;
	iMax=-1;		iMax=-1;
	@@ -550,13 +628,13 @@ public class deBayerScissors {
	lastIndex=base+iRadiusPlus1; // first in the next row		lastIndex=base+iRadiusPlus1; // first in the next row
	while ((l<lastIndex) && (intMap[l]>0)) l++;		while ((l<lastIndex) && (intMap[l]>0)) l++;
	rayLength[ia]=l-base; // last "good" ( >0 and in the same row)		rayLength[ia]=l-base; // last "good" ( >0 and in the same row)
	if ((l==lastIndex) \|\| (intMap[l]<0) \|\| (polarAmps[l]<0.0) ) rayOpen[ia]=false;		if ((l==lastIndex) \|\| (intMap[l]<0) \|\| (polarAmps[l]<0.0) )
	else {		rayOpen[ia]=false;
	if (polarAmps[l]>max) {		else if (polarAmps[l]>max) {
	max=polarAmps[l];		max=polarAmps[l];
	iMax=ia;		iMax=ia;
	}		}
	}
	}		}
	if (iMax>=0) {		if (iMax>=0) {
	rayLength[iMax]++;		rayLength[iMax]++;
	@@ -580,8 +658,9 @@ public class deBayerScissors {
	}		}
	return result;		return result;
	}		}

	public PolarSpectrums(		public PolarSpectrums(
	int isize, // size of the square array, centar is at size/2, size/2, only top half+line will be used		int isize, // size of the square array, center is at size/2, size/2, only top half+line will be used
	double fullAngle, // i.e. Math.PI, 2*Math.PI		double fullAngle, // i.e. Math.PI, 2*Math.PI
	int maxRadius, // width of the polar array - should be <= size/2-2		int maxRadius, // width of the polar array - should be <= size/2-2
	double outerStep, // maximal step in pixels on the maxRadius for 1 angular step (i.e. 0.5)		double outerStep, // maximal step in pixels on the maxRadius for 1 angular step (i.e. 0.5)

src/main/java/EyesisAberrations.java

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