merged with nc393 branch (d531d201) · Commits · Elphel / imagej-elphel

src/main/java/Aberration_Correction.java

+2 −2

Original line number	Diff line number	Diff line
		@@ -2514,8 +2514,8 @@ if (PROCESS_PARAMETERS.saveSettings) saveProperties(FILE_PARAMETERS.resultsDirec
		tileY = nTile /tilesX;
		tileX = nTile % tilesX;
		if (tileX==0) {
		if (updateStatus) IJ.showStatus("Reducing sampling aliases, row "+(tileY+1)+" of "+tilesY);
		if (MASTER_DEBUG_LEVEL>2) System.out.println("Reducing sampling aliases, row "+(tileY+1)+" of "+tilesY+" : "+IJ.d2s(0.000000001*(System.nanoTime()-startTime),3));
		if (updateStatus) IJ.showStatus("(3)Reducing sampling aliases, row "+(tileY+1)+" of "+tilesY);
		if (MASTER_DEBUG_LEVEL>2) System.out.println("(3)Reducing sampling aliases, row "+(tileY+1)+" of "+tilesY+" : "+IJ.d2s(0.000000001*(System.nanoTime()-startTime),3));
		}

		if ((tileY==yTileDebug) && (tileX==xTileDebug)) DEBUG_LEVEL=4;

src/main/java/CalibrationHardwareInterface.java

+357 −144

File changed.

Preview size limit exceeded, changes collapsed.

src/main/java/DebayerScissors.java

+151 −86

Original line number	Diff line number	Diff line
		@@ -30,6 +30,8 @@ import ij.ImageStack;

		import java.util.concurrent.atomic.AtomicInteger;

		import javax.swing.SwingUtilities;


		public class DebayerScissors {
		// showDoubleFloatArrays SDFA_INSTANCE= new showDoubleFloatArrays();
		@@ -96,7 +98,29 @@ public class DebayerScissors {
		final Thread[] threads = newThreadArray(threadsMax);
		final AtomicInteger ai = new AtomicInteger(0);
		final int numberOfKernels=tilesY*tilesX;

		int indx,dx,dy,tx,ty,li;
		final int [] nonOverlapSeq = new int[numberOfKernels];
		int [] nextFirstFindex=new int[4];
		indx = 0;
		li=0;

		for (dy=0;dy<2;dy++) for (dx=0;dx<2;dx++) {
		for (ty=dy; ty < tilesY; ty+=2) for (tx=dx; tx < tilesX; tx+=2){
		nonOverlapSeq[indx++] = ty*tilesX + tx;
		}
		nextFirstFindex[li++] = indx;
		}
		final AtomicInteger aStopIndex = new AtomicInteger(0);
		final long startTime = System.nanoTime();
		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++){
		aStopIndex.set(nextFirstFindex[li]);
		if (li>0){
		ai.set(nextFirstFindex[li-1]);
		}
		for (int ithread = 0; ithread < threads.length; ithread++) {
		threads[ithread] = new Thread() {
		public void run() {
		@@ -114,17 +138,19 @@ public class DebayerScissors {
		debayerParameters.debayerRelativeWidthRedblue, // result red/blue mask mpy by scaled default (square)
		debayerParameters.debayerRelativeWidthRedblueMain, // green mask when applied to red/blue, main (center)
		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 < aStopIndex.get(); nTile0 = ai.getAndIncrement()) {

		for (int nTile = ai.getAndIncrement(); nTile < numberOfKernels; nTile = ai.getAndIncrement()) {
		int nTile = nonOverlapSeq[nTile0];
		tileY = nTile /tilesX;
		tileX = nTile % tilesX;
		if (tileX==0) {
		if (updateStatus) IJ.showStatus("Reducing sampling aliases, row "+(tileY+1)+" of "+tilesY);
		if (globalDebugLevel>2) System.out.println("Reducing sampling aliases, row "+(tileY+1)+" of "+tilesY+" : "+IJ.d2s(0.000000001*(System.nanoTime()-startTime),3));
		if (tileX < 2) {
		int trow=(tileY+((2(tileY & 1) + (tileX & 1))tilesY))/4;
		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));
		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++){
		extractSquareTile( pixels[chn], // source pixel array,
		tile[chn], // will be filled, should have correct size before call
		@@ -149,8 +175,8 @@ public class DebayerScissors {
		debayerParameters.debayerThreshold, // no high frequencies - use default uniform filter
		debayerParameters.debayerGamma, // power function applied to the amplitudes before generating spectral masks
		debayerParameters.debayerBonus, // scale far pixels as (1.0+bonus*r/rmax)
		debayerParameters.mainToAlias,// relative main/alias amplitudes to enable lixels (i.e. 0.5 means that if alias is >0.5*main, the pixel will be masked out)
		debayerParameters.debayerMaskBlur, // for both masks sigma for gaussian blur of the binary masks (<0 -do not use "scissors")
		debayerParameters.mainToAlias,// relative main/alias amplitudes to enable pixels (i.e. 0.5 means that if alias is >0.5*main, the pixel will be masked out)
		debayerParameters.debayerMaskBlur, // for both masks sigma for Gaussian blur of the binary masks (<0 -do not use "scissors")
		debayerParameters.debayerUseScissors, // use "scissors", if false - just apply "diamond" ands "square" with DEBAYER_PARAMETERS.debayerRelativeWidthGreen and DEBAYER_PARAMETERS.debayerRelativeWidthRedblue
		((tileY==yTileDebug) && (tileX==xTileDebug))?4:1);
		// 1); // internal debug level ((this.debugLevel>2) && (yTile==yTile0) && (xTile==xTile0))?3:1;
		@@ -166,11 +192,13 @@ public class DebayerScissors {
		fht_instance.inverseTransform(tile[chn]);
		fht_instance.swapQuadrants(tile[chn]);
		/* 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
		* takes just small fraction of severtal FHTs, it should be OK - reasonable number of threads will spread and not "stay in line"
		/*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"
		*/

		accumulateSquareTile(outPixles[chn], // float pixels array to accumulate tile
		//accumulateSquareTile(
		nonSyncAccumulateSquareTile (
		outPixles[chn], // float pixels array to accumulate tile
		tile[chn], // data to accumulate to the pixels array
		imgWidth, // width of pixels array
		tileX*step, // left corner X
		@@ -178,22 +206,34 @@ public class DebayerScissors {
		}
		if ((tileY==yTileDebug) && (tileX==xTileDebug) && (SDFA_instance!=null)) SDFA_instance.showArrays (tile.clone(),debayerParameters.size,debayerParameters.size, "B00");

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

		if (globalDebugLevel>0) System.out.println("Reducing sampling aliases done in "+IJ.d2s(0.000000001*(System.nanoTime()-startTime),3));
		return outStack;
		}

		@@ -273,6 +313,31 @@ public class DebayerScissors {
		}
		}
		}

		void nonSyncAccumulateSquareTile(
		float [] pixels, // float pixels array to accumulate tile
		double [] tile, // data to accumulate to the pixels array
		int width, // width of pixels array
		int x0, // left corner X
		int y0) { // top corner Y
		int length=tile.length;
		int size=(int) Math.sqrt(length);
		int i,j,x,y;
		int height=pixels.length/width;
		int index=0;
		for (i=0;i<size;i++) {
		y=y0+i;
		if ((y>=0) && (y<height)) {
		index=i*size;
		for (j=0;j<size;j++) {
		x=x0+j;
		if ((x>=0) && (x<width)) pixels[y*width+x]+=tile [index];
		index++;
		}
		}
		}
		}

		synchronized void accumulateSquareTile(
		double [] pixels, // float pixels array to accumulate tile
		double [] tile, // data to accumulate to the pixels array

src/main/java/DenseCorrespondence.java

+1 −1

Original line number	Diff line number	Diff line
		@@ -39,7 +39,7 @@ public class DenseCorrespondence {



		private void disparitySweepTile (
		public void disparitySweepTile ( // never used so far
		int tileX,
		int tileY,
		CyclopeanTile [][] allCyclopeanMap,

src/main/java/Distortions.java

+2 −0

Original line number	Diff line number	Diff line
		@@ -5989,6 +5989,8 @@ List calibration
		imp.setProperty("channel", ""+numSensor);
		imp.setProperty("comment_subcamera", "number of the subcamera with individual IP, starting with 0");
		imp.setProperty("subcamera", ""+camerasInterface.getSubCamera(numSensor));
		imp.setProperty("sensor_port",""+camerasInterface.getSensorPort(numSensor));

		imp.setProperty("comment_subchannel", "number of the sensor port on a subcamera (0..2)");
		imp.setProperty("subchannel", ""+camerasInterface.getSubChannel(numSensor));
		imp.setProperty("comment_entrancePupilForward", "entrance pupil distance from the azimuth/radius/height, outwards in mm");

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