Commit 6fa32fa8 authored by Andrey Filippov's avatar Andrey Filippov
Browse files

correcting kernel combine, interpolate and invert to work with mono 

(LWIR) data
parent 001d0838

src/main/java/com/elphel/imagej/calibration/EyesisAberrations.java

+17 −8
Original line number Diff line number Diff line
@@ -117,10 +117,11 @@ public class EyesisAberrations { 
   				System.out.println("Failed to open interpolated PSF kernel stack "+srcPaths[nChn]);

   				continue;

   			}

   			if (impSpsf.getStackSize()<3) {

   				System.out.println("Need a 3-layer stack with interpolated PSF kernels");

   			if ((impSpsf.getStackSize() < 3) && (impSpsf.getStackSize() != 1)) {

   				System.out.println("Need a 3-layer stack (for color) or single (for mono) with interpolated PSF kernels");

   				continue;

   			}



   			ImageStack stack= reversePSFKernelStack(

   					impSpsf.getStack(), // stack of 3 32-bit (float) images, made of square kernels

   					inverseParameters, // size (side of square) of direct PSF kernel
@@ -142,7 +143,9 @@ public class EyesisAberrations { 
   			if (saveResult){

   				if (globalDebugLevel>0) System.out.println((numProcessed+1)+" of "+numToProcess+": saving invered (of the file"+srcPaths[nChn]+") kernel to "+resultPaths[nChn]+ " at "+ IJ.d2s(0.000000001*(System.nanoTime()-startTime),3));

   				FileSaver fs=new FileSaver(impInvertedPSF);

   				fs.saveAsTiffStack(resultPaths[nChn]);

//   				fs.saveAsTiffStack(resultPaths[nChn]);

   				fs.saveAsTiff(resultPaths[nChn]);



   			}

   			numProcessed++;

    		if 	(stopRequested.get()>0) {
@@ -714,8 +717,8 @@ public class EyesisAberrations { 
   				System.out.println("Failed to open raw PSF kernel stack "+srcPaths[nChn]);

   				continue;

   			}

   			if (impSpsf.getStackSize()<3) {

   				System.out.println("Need a 3-layer stack with raw PSF kernels");

   			if ((impSpsf.getStackSize() < 3) && (impSpsf.getStackSize() != 1)) {

   				System.out.println("Need a 3-layer stack (for color) or single (for mono) with raw PSF kernels");

   				continue;

   			}

   			ImageStack stack= interpolateKernelStack(
@@ -739,7 +742,8 @@ public class EyesisAberrations { 
   				if (globalDebugLevel>0) System.out.println((numProcessed+1)+" of "+numToProcess+": saving interpolation result (of the file"+srcPaths[nChn]+") to "+

   						resultPaths[nChn]+ " at "+ IJ.d2s(0.000000001*(System.nanoTime()-startTime),3));

   				FileSaver fs=new FileSaver(impInterpolatedPSF);

   				fs.saveAsTiffStack(resultPaths[nChn]);

//   				fs.saveAsTiffStack(resultPaths[nChn]);

   				fs.saveAsTiff(resultPaths[nChn]);

   			}

   			numProcessed++;

    		if 	(stopRequested.get()>0) {
@@ -1610,6 +1614,10 @@ public class EyesisAberrations { 
			for (int color=0;color<nChn;color++) sdfa_instance.showArrays(pxfCenterY[color], kWidth, kHeight,  true, "pxfCenterY-"+color);

		}

		double [][][] radiusRatio=new double[nChn][nFiles+1][kLength];

		int ref_color = 2; // green

		if (ref_color >= nChn) {

			ref_color = 0;

		}

		for (int tileY=0;tileY<kHeight;tileY++) for (int tileX=0;tileX<kWidth;tileX++) {

			int index=tileY*kWidth+tileX;

			int totalNumSamples=0;
@@ -1635,7 +1643,7 @@ public class EyesisAberrations { 
							int indexNeib=xn+ kWidth*yn;

							double weight=weightsMasked[nFile+1][indexNeib];

							if (multiFilePSF.sharpBonusPower>0) {

								weight/=Math.pow(psfRadius[2][nFile+1][indexNeib],multiFilePSF.sharpBonusPower); // use green color

								weight/=Math.pow(psfRadius[ref_color][nFile+1][indexNeib],multiFilePSF.sharpBonusPower); // use green color ava.lang.ArrayIndexOutOfBoundsException: 2

							}

							sumWeights+=weight;

							for (int color=0;color<nChn;color++) {
@@ -1868,7 +1876,8 @@ public class EyesisAberrations { 
			if (numMissing==0) {

			  if (thisDebugLevel>1) System.out.println("Saving result to "+resultPath);

			  FileSaver fs=new FileSaver(imp_psf);

			  fs.saveAsTiffStack(resultPath);

//			  fs.saveAsTiffStack(resultPath);

			  fs.saveAsTiff(resultPath);

			  if (multiFilePSF.fillMissing && (filledMissing>0)) {

					System.out.println("*** Warning "+filledMissing+" kernel tiles are missing from the results (insufficient overlap) \n"+

					"You may disable filling missing kernels from neighbors in Conf. Multifile");