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Commit cc2b631c authored by Andrey Filippov's avatar Andrey Filippov
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added more diagnostic output

parent 575e240c
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Showing with 146 additions and 61 deletions
src/main/java/DebayerScissors.java
View file @ cc2b631c
......@@ -28,6 +28,7 @@
import ij.IJ;
import ij.ImageStack;
import java.lang.reflect.InvocationTargetException;
import java.util.concurrent.atomic.AtomicInteger;
import javax.swing.SwingUtilities;
......@@ -114,13 +115,13 @@ public class DebayerScissors {
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]);
}
// System.out.println("\n=== nextFirstFindex["+li+"] =" + nextFirstFindex[li]+" === ");
for (int ithread = 0; ithread < threads.length; ithread++) {
threads[ithread] = new Thread() {
public void run() {
......@@ -140,18 +141,17 @@ public class DebayerScissors {
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()) {
int nTile = nonOverlapSeq[nTile0];
tileY = nTile /tilesX;
tileX = nTile % tilesX;
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);
// 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++){
extractSquareTile( pixels[chn], // source pixel array,
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.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
/*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"
*/
......@@ -206,31 +206,35 @@ public class DebayerScissors {
tileY*step); // top corner Y
}
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() {
IJ.showProgress(numFinished,numberOfKernels);
// System.out.println(" --- "+numFinished+"("+numberOfKernels+"): "+dprogr);
IJ.showProgress(numFinished, numberOfKernels);
}
});
}
}
}
};
}
startAndJoin(threads);
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);
// this.debugLevel=wasDebugLevel;
/* 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("(1)Reducing sampling aliases done in "+IJ.d2s(0.000000001*(System.nanoTime()-startTime),3));
if (globalDebugLevel>0) System.out.println("Reducing sampling aliases done in "+IJ.d2s(0.000000001*(System.nanoTime()-startTime),3));
return outStack;
}
......
src/main/java/EyesisCorrections.java
View file @ cc2b631c
......@@ -1744,7 +1744,7 @@ public class EyesisCorrections {
"kernelNumHor="+kernelNumHor+"\n"+
"numberOfKernelsInChn="+numberOfKernelsInChn+"\n");
if (updateStatus) IJ.showStatus("Convolving image with kernels, "+nChn+" channels, "+tilesY+" rows");
final long startTime = System.nanoTime();
for (li = 0; li < nextFirstFindex.length; li++){
aStopIndex.set(nextFirstFindex[li]);
......@@ -1776,7 +1776,7 @@ public class EyesisCorrections {
if (tileX < 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 (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) {
......@@ -1837,11 +1837,13 @@ public class EyesisCorrections {
(tileX-1)*step, // left corner X
(tileY-1)*step); // top corner Y
final int numFinished=tilesFinishedAtomic.getAndIncrement();
if (numFinished % (numberOfKernels/100+1) == 0) {
SwingUtilities.invokeLater(new Runnable() {
public void run() {
IJ.showProgress(numFinished,numberOfKernels);
}
});
}
//numberOfKernels
}
......
src/main/java/deBayerScissors.java
View file @ cc2b631c
......@@ -35,6 +35,12 @@ public class deBayerScissors {
private double lastMidEnergy; // last midrange spectral energy
private showDoubleFloatArrays SDFA_instance; // just for debugging?
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 deBayerScissors(
......@@ -59,6 +65,29 @@ public class deBayerScissors {
debayer_width_redblue_clones, // green mask when applied to red/blue, clones
size, // side of the square
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 */
......@@ -171,9 +200,9 @@ public class deBayerScissors {
int length=green_amp.length;
int size = (int) Math.sqrt(length);
int hsize=size/2;
int subpixel=4; // hardwired - when changing it will need to change alias maps
int aliasX=size/subpixel;
int i,j,index,index_back,x,y;
// int subpixel=4; // hardwired - when changing it will need to change alias maps
// int aliasX=size/subpixel;
int i,j,index,index_back; //,x,y;
double [] amp= 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];
......@@ -183,13 +212,14 @@ public class deBayerScissors {
/* Combine into mask by comparing pixels[] from the zero and 7 aliases */
double d;
int nAlias;
/*
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}};
/* 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_clones, "amp_clones");
......@@ -204,26 +234,65 @@ public class deBayerScissors {
for(nAlias=0;nAlias<aliasMapRedBlue.length; nAlias++) {
y=(i-aliasX*aliasMapRedBlue[nAlias][0]+size) % size;
x=(j-aliasX*aliasMapRedBlue[nAlias][1]+size) % size;
/*
if (amp_clones[(y>hsize)? ((size-y)*size+((size-x)%size)):y*size+x]>d) {
if (y>hsize) {
y=size-y;
x=(size-x)%size;
}
if (amp_clones[y*size+x]>d) {
mask[index]=-1.0;
mask[index_back]=-1.0;
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) {
y = size - y;
x = (size - x) % size;
}
if (y>hsize) {
y=size-y;
x=(size-x)%size;
}
if (amp_clones[y*size+x]>d) {
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_back]=-1.0;
break;
}
}
}
}
// End of replacement code
if (this_debug>2) SDFA_instance.showArrays(mask, "mask");
if (pol_instace==null) return mask;
......@@ -231,21 +300,23 @@ public class deBayerScissors {
for (i=0;i<amp.length;i++) amp[i]*=mask[i];
if (this_debug>2) SDFA_instance.showArrays(amp, "amp-mask");
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");
double k= bonus/pol_instace.getWidth();
for (i=0;i<pol_instace.getHeight();i++) for (j=0;j<pol_instace.getWidth();j++) polar_amp[i*pol_instace.getWidth()+j]*=1.0+k*j;
int width = pol_instace.getWidth();
int height = pol_instace.getHeight();
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+k*j;
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);
if (this_debug>2) {
SDFA_instance.showArrays(polar_amp, pol_instace.getWidth(),pol_instace.getHeight(), "RB-amp-bonus");
SDFA_instance.showArrays(polar_mask_pixels,pol_instace.getWidth(),pol_instace.getHeight(), "pRBm");
SDFA_instance.showArrays(cart_mask_pixels,size,size, "cRBm");
SDFA_instance.showArrays(polar_amp, width, height, "RB-amp-bonus");
SDFA_instance.showArrays(polar_mask_pixels, width, height, "pRBm");
SDFA_instance.showArrays(cart_mask_pixels, size, size, "cRBm");
}
if (this_debug>2) {
double [] polar_mask_pixels1=pol_instace.genPolarRedBlueMask(polar_amp,1);
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(cart_mask_pixels1,size,size, "cRBm1");
SDFA_instance.showArrays(polar_mask_pixels1, width, height, "pRBm1");
SDFA_instance.showArrays(cart_mask_pixels1, size, size, "cRBm1");
}
return cart_mask_pixels;
......@@ -418,8 +489,10 @@ public class deBayerScissors {
double [] polPixels=new double[iRadiusPlus1*(iAngle+1)];
int 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]])+
polar2CartesianFractions[i][1] *( (1-polar2CartesianFractions[i][0])*cartPixels[polar2CartesianIndices[i][2]] + polar2CartesianFractions[i][0]*cartPixels[polar2CartesianIndices[i][3]]) ;
polPixels[i]=(1-polar2CartesianFractions[i][1])*( (1-polar2CartesianFractions[i][0])*cartPixels[polar2CartesianIndices[i][0]] +
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;
}
......@@ -503,12 +576,14 @@ public class deBayerScissors {
return genPolarMask(polarAmps,0,mode);
}
public double [] genPolarRedBlueMask(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);
public double [] genPolarRedBlueMask(
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);
}
// **** Seems to be most time-critical ****
public double [] genPolarMask(double [] polarAmps, // polar array of amplitude values, <0 - stop
int type, // 0 - green, 1 red/blue
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++;
/* add polar point index */
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;
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) */
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 */
max=-1.0;
iMax=-1;
......@@ -550,13 +628,13 @@ public class deBayerScissors {
lastIndex=base+iRadiusPlus1; // first in the next row
while ((l<lastIndex) && (intMap[l]>0)) l++;
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;
else {
if (polarAmps[l]>max) {
if ((l==lastIndex) || (intMap[l]<0) || (polarAmps[l]<0.0) )
rayOpen[ia]=false;
else if (polarAmps[l]>max) {
max=polarAmps[l];
iMax=ia;
}
}
}
if (iMax>=0) {
rayLength[iMax]++;
......@@ -580,8 +658,9 @@ public class deBayerScissors {
}
return result;
}
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
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)
......
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