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imagej-elphel
Commit 43fae5db authored by Andrey Filippov's avatar Andrey Filippov
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Fixed old bug in "Calculate grids", introdudced temporary debugs

parent db4561f4
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Showing with 68 additions and 24 deletions
src/main/java/MatchSimulatedPattern.java
View file @ 43fae5db
......@@ -965,7 +965,23 @@ public class MatchSimulatedPattern {
double ringWidth, // ring (around r=0.5 dist to opposite corr) width
double x0, // center coordinates
double y0,
String title) { // title base for optional plots names
String title){
return correlationContrast (
pixels, // square pixel array
wVectors, // wave vectors (same units as the pixels array)
ringWidth, // ring (around r=0.5 dist to opposite corr) width
x0, // center coordinates
y0,
title, // title base for optional plots names
this.debugLevel);
}
public double correlationContrast ( double [] pixels, // square pixel array
double [][] wVectors, // wave vectors (same units as the pixels array)
double ringWidth, // ring (around r=0.5 dist to opposite corr) width
double x0, // center coordinates
double y0,
String title, // title base for optional plots names
int debugLevel){
int size=(int) Math.sqrt(pixels.length);
double [] xy= new double [2];
double [] uv;
......@@ -977,7 +993,7 @@ public class MatchSimulatedPattern {
double r2WingsOuter= 0.0625*(1.0+ringWidth)*(1.0+ringWidth);
double r2WingsInner= 0.0625*(1.0-ringWidth)*(1.0-ringWidth);
double r2Center=0.0625*(ringWidth)*(ringWidth);
if (this.debugLevel>2) System.out.println("rWingsOuter="+Math.sqrt(r2WingsOuter)+" rWingsInner="+Math.sqrt(r2WingsInner)+" rCenter="+Math.sqrt(r2Center));
if (debugLevel>2) System.out.println("rWingsOuter="+Math.sqrt(r2WingsOuter)+" rWingsInner="+Math.sqrt(r2WingsInner)+" rCenter="+Math.sqrt(r2Center));
double valCenter=0.0;
double valWings=0.0;
......@@ -1002,14 +1018,16 @@ public class MatchSimulatedPattern {
}
}
if ((numWings==0.0) || (numCenter==0.0)) {
if (this.debugLevel>1) System.out.println("Not enough data for correlation contrast: numCenter="+numCenter+" numWings="+numWings+
if (debugLevel>1) System.out.println("Not enough data for correlation contrast: numCenter="+numCenter+" numWings="+numWings+
" valCenter="+IJ.d2s(valCenter,2)+" valWings="+IJ.d2s(valWings,2));
return -1.0;
}
double contrast=Math.sqrt((valCenter/numCenter)/(valWings/numWings));
if (this.debugLevel>2) {
if (debugLevel>2) {
System.out.println("Correlation contrast is "+contrast);
float [] floatPixels=new float[size*size];
double [] maskedPixels=new double[size*size];
double [] u_value=new double[size*size];
double [] v_value=new double[size*size];
int index;
for (i=0;i<size;i++) {
xy[1]=i-size/2-y0;
......@@ -1018,22 +1036,27 @@ public class MatchSimulatedPattern {
uv=matrix2x2_mul(wVectors,xy);
r2=uv[0]*uv[0]+uv[1]*uv[1];
index=i*size+j;
u_value[index]=uv[0];
v_value[index]=uv[1];
/* r=Math.sqrt(r2);
r-=Math.floor(r);
floatPixels[index]=(float) r;*/
if (((r2<=r2WingsOuter) && (r2>r2WingsInner)) || (r2<=r2Center)){
floatPixels[index]=(float) pixels[index];
maskedPixels[index]= pixels[index];
} else {
floatPixels[index]=0.0F;
maskedPixels[index]=0.0;
}
}
}
ImageProcessor ip = new FloatProcessor(size,size);
ip.setPixels(floatPixels);
ip.resetMinAndMax();
ImagePlus imp= new ImagePlus(title+"_CORR_MASK", ip);
imp.show();
double [][] dbgPixels={pixels,maskedPixels,u_value,v_value};
String [] titles={"all","masked","u","v"};
(new showDoubleFloatArrays()).showArrays(
dbgPixels,
size,
size,
true,
title+"_CORR_MASK",
titles);
}
return contrast;
}
......@@ -2977,6 +3000,7 @@ public class MatchSimulatedPattern {
point[0]=(selection.x+nh*selection.width/(1<<tryHor)) & ~1;
point[1]=(selection.y+nv*selection.height/(1<<tryVert)) & ~1;
if (debugLevel>2) System.out.println("trying xc="+point[0]+", yc="+point[1]+"(nv="+nv+", nh="+nh+")");
// System.out.println("### trying xc="+point[0]+", yc="+point[1]+"(nv="+nv+", nh="+nh+")");
if ((debugLevel>2) && (startScanIndex==3)) debugLevel=3; // show debug images for the first point only
node=tryPattern (
point, // xy to try
......@@ -7332,7 +7356,15 @@ y=xy0[1] + dU*deltaUV[0]*(xy1[1]-xy0[1])+dV*deltaUV[1]*(xy2[1]-xy0[1])
double [][] locsNeib, // locations and weights of neighbors to average
int debug_level
){
double dbg_x=1005.0;
double dbg_y=1284.0;
double dbg_tolerance=5.0;
boolean dbgThis=(Math.abs(beforeXY[0]-dbg_x)<dbg_tolerance) && (Math.abs(beforeXY[1]-dbg_y)<dbg_tolerance);
if (dbgThis) {
System.out.println("correctedPatternCrossLocationAverage4(), beforeXY[0]="+beforeXY[0]+", beforeXY[1]="+beforeXY[1]);
debug_level+=3;
}
// System.out.println("correctedPatternCrossLocationAverage4(): beforeXY[0]="+beforeXY[0]+". beforeXY[1]="+beforeXY[1]);
// Just for testing
beforeXY[0]+=distortionParameters.correlationDx; // offset, X (in pixels)
beforeXY[1]+=distortionParameters.correlationDy; // offset y (in pixels)
......@@ -7551,7 +7583,8 @@ y=xy0[1] + dU*deltaUV[0]*(xy1[1]-xy0[1])+dV*deltaUV[1]*(xy2[1]-xy0[1])
//TODO: verify that displacement is correct here (sign, direction)
centerXY[0], // x0, // center coordinates
centerXY[1], //y0,
"test-contrast"); // title base for optional plots names
"test-contrast", // title base for optional plots names
debug_level);
result[2]=contrast;
......@@ -8029,7 +8062,7 @@ d()/dy=C*x+2*B*y+E=0
for (i=1;i<size1/4;i++) hammingMod[size1-i]=preHammingMod[i];
for (i=size1/4;i<=(size1-size1/4);i++) hammingMod[i]=1.0;
if (showDebug) System.out.println("scale="+scale+ "borderAverage="+borderAverage);
if (showDebug) System.out.println("scale="+scale+ " borderAverage="+borderAverage);
for (i=0;i<size1;i++) for (j=0;j<size1;j++) {
corr1[(i*size+j)*decimateFFT] = scale*(corr[index+i*size+j]-borderAverage)*hammingMod[i]*hammingMod[j]+borderAverage;
}
......@@ -8042,20 +8075,31 @@ d()/dy=C*x+2*B*y+E=0
for (i=size1/2+1;i<size -(size1/2);i++) for (j=0;j<size;j++) corr1[i*size+j]=0.0;
for (i=size -(size1/2); i<size;i++) for (j=size1/2+1;j<size -(size1/2);j++) corr1[i*size+j]=0.0;
// apply window for now - just
double [] hamming=fht_instance.getHamming1d(size1);
/*
if (showDebug) {
System.out.println("Getting hamming1d ("+size1+")");
}
*/
double [] hamming=fht_instance.getHamming1d(size1).clone();
/*
if (showDebug) {
for (i=0;i<hamming.length;i++) System.out.println("hamming["+i+"]="+hamming[i]);
}
if (showDebug) SDFA_INSTANCE.showArrays(corr1.clone(), "NO_ALIAS");
// Combine with low-pass Gaussian (if it is >0)
if (lowpass>0){
double [] gaussian1d=fht_instance.getGaussian1d(lowpass,size1); // no need to divide by /decimateFFT as we use size1, not size
for (i=0;i<hammingMod.length;i++) hamming[i]*=gaussian1d[i];
// if (showDebug) {
// System.out.println("lowpass="+lowpass);
// for (i=0;i<gaussian1d.length;i++) System.out.println("gaussian1d["+i+"]="+gaussian1d[i]);
// }
if (showDebug) {
System.out.println("lowpass="+lowpass);
for (i=0;i<gaussian1d.length;i++) System.out.println("gaussian1d["+i+"]="+gaussian1d[i]);
}
}
// if (showDebug) {
// for (i=0;i<hamming.length;i++) System.out.println("hamming["+i+"]="+hamming[i]);
// }
if (showDebug) {
for (i=0;i<hamming.length;i++) System.out.println("hamming["+i+"]="+hamming[i]);
}
*/
int halfSize1=size1/2, shiftZero=size-halfSize1;
for (i=0;i<=size1;i++) for (j=0;j<=size1;j++){
int im=i%size1,jm=j%size1;
......
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