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centering CC
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@ekatrukha
ekatrukha committed Apr 18, 2024
1 parent 5901828 commit eb8dd5e
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Showing 5 changed files with 206 additions and 98 deletions.
2 changes: 1 addition & 1 deletion src/main/java/averagingND/AverageWithoutZero.java
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Original file line number Diff line number Diff line change
Expand Up @@ -140,7 +140,7 @@ public static IntervalView<FloatType> averageArray(final ArrayList<RandomAccessi

}

/** function calculates stendard deviation image from the provided ArrayList of RAI intervals
/** function calculates standard deviation image from the provided ArrayList of RAI intervals
* and an average image RAI.
* The output image is extended to cover all intervals. Intervals are extended with zeros
* to the same extent.
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136 changes: 89 additions & 47 deletions src/main/java/averagingND/GenNormCC.java
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Original file line number Diff line number Diff line change
Expand Up @@ -40,15 +40,25 @@ public class GenNormCC {
/** whether to exclude/ignore voxels that are zeros **/
public boolean bExcludeZeros = false;

/** window limit of CC max localization as a fraction of max displacement **/
public double [] lim_fractions = null;

/** absolute window limit (in voxels) of CC max localization **/
public FinalInterval limInterval = null;

/** if false, the limits window of displacement applied to the origin of coordinates,
* if true, it is applied around position where both images are centered **/
public boolean bCenteredLimit = false;

/** the fraction of max displacement where norm CC looks ok,
* the boundaries are always strange **/
final double max_fraction_shift = 0.9;

/**
* @param image
* @param template
*/
public boolean caclulateGenNormCC(final RandomAccessibleInterval< FloatType > image, final RandomAccessibleInterval< FloatType > template, final boolean bShowCC)//, boolean bRegisterTemplate) //throws ImgIOException, IncompatibleTypeException
public boolean caclulateGenNormCC(final RandomAccessibleInterval< FloatType > image, final RandomAccessibleInterval< FloatType > template, final boolean bShowCC)
{
int i;

Expand All @@ -57,8 +67,6 @@ public boolean caclulateGenNormCC(final RandomAccessibleInterval< FloatType > im
IJ.log("Error! Different dimensions of input and template!");
return false;
}



nDim = image.numDimensions();
if(lim_fractions!= null)
Expand Down Expand Up @@ -269,85 +277,111 @@ public boolean caclulateGenNormCC(final RandomAccessibleInterval< FloatType > im


long [][] cropCorr = new long[2][nDim];
long [][] cropFraction = new long[2][nDim];

//determine the maximum shift of template with respect to original image,
//assuming that zero shift is when both images' are centered
//determine the maximum area (intervalCrop) of shifts for template with respect to original image
double nHalfSpan, nCenter;

for(i=0;i<nDim;i++)
{
nHalfSpan = 0.5*((temDim[i]-1)+(imgDim[i]-1));
nCenter = nHalfSpan-(temDim[i]-1);
if(lim_fractions!=null)
{
cropCorr[0][i]=Math.round(nCenter-nHalfSpan*lim_fractions[i]);
cropCorr[1][i]=Math.round(nCenter+nHalfSpan*lim_fractions[i]);
}
else
cropCorr[0][i] = Math.round(nCenter-nHalfSpan*max_fraction_shift);
cropCorr[1][i] = Math.round(nCenter+nHalfSpan*max_fraction_shift);

if(lim_fractions != null)
{
cropCorr[0][i]=Math.round(nCenter-nHalfSpan*max_fraction_shift);
cropCorr[1][i]=Math.round(nCenter+nHalfSpan*max_fraction_shift);
cropFraction[0][i]=Math.round(-nHalfSpan*lim_fractions[i]);
cropFraction[1][i]=Math.round(nHalfSpan*lim_fractions[i]);
}
//cropCorr[0][i]=Math.round((-1)*((temDim[i]-1)*max_fraction_shift));
//cropCorr[1][i]=Math.round((imgDim[i]-1)*max_fraction_shift);

}
FinalInterval intervalCrop = new FinalInterval( cropCorr[0] , cropCorr[1] );
if(limInterval!=null)

FinalInterval intervalFull = new FinalInterval(cropCorr[0] , cropCorr[1]);
FinalInterval constrainFr = null;
if(lim_fractions != null)
{
intervalCrop = Intervals.intersect(intervalCrop, limInterval);
}
constrainFr = new FinalInterval(cropFraction[0] , cropFraction[1]);
}
// if(limInterval != null)
// {
// intervalCrop = Intervals.intersect(intervalCrop, limInterval);
// }

//Now we need to account for the padding. Since it is changing the origin
//of coordinates of template with respect to the original image
long [] nCCOrigin = new long [nDim];
for(i=0;i<nDim;i++)
{
nCCOrigin[i]=(long) (Math.ceil(0.5*(imgDim[i]))- Math.ceil(0.5*(temDim[i])));
nCCOrigin[i] = (long) ( Math.ceil(0.5*(imgDim[i]))- Math.ceil(0.5*(temDim[i])));
}


//In addition, here we do so called FFT "swap quadrants" procedure (or FFT shift)
//to show frequencies centered/radial. So we can have negative shifts, etc
//Instead of truly swapping the quadrants we just periodically mirror them (extend periodic)
IntervalView< FloatType > ivCCswapped;
//full available shift space
ivCCswapped = Views.interval(Views.translate(Views.extendPeriodic( invF1F2 ), nCCOrigin),intervalFull);


IntervalView< FloatType > ivCCswapped = Views.interval(Views.translate(Views.extendPeriodic( invF1F2 ), nCCOrigin),intervalCrop);
//IntervalView< FloatType > ivCCswapped = Views.interval(Views.extendPeriodic( invF1F2 ),interval);

//let's apply constrains

//voxel constrains
if(limInterval != null)
{
FinalInterval intConstrainPx;
//centered, let's move to the center
if(bCenteredLimit)
{
intConstrainPx = Intervals.intersect(ivCCswapped, Intervals.translate(limInterval, nCCOrigin));

}
//from the origin, no need to move
else
{
intConstrainPx = Intervals.intersect(ivCCswapped, limInterval);
}
ivCCswapped = Views.interval(ivCCswapped, intConstrainPx);
}
//fractional constrains
if(lim_fractions != null)
{
//centered, let's move to the center
if(bCenteredLimit)
{
constrainFr = Intervals.translate(constrainFr, nCCOrigin);

}

ivCCswapped = Views.interval(ivCCswapped, constrainFr);
}


// if(bCenteredLimit)
// {
// ivCCswapped = Views.interval(Views.extendPeriodic( invF1F2 ),intervalCrop);
// }
// else
// {
// //ivCCswapped = Views.interval(Views.extendPeriodic( invF1F2 ),intervalCrop);
// ivCCswapped = Views.interval(Views.translate(Views.extendPeriodic( invF1F2 ), nCCOrigin),intervalCrop);
// //ivCCswapped = Views.interval(Views.translate(Views.extendPeriodic( invF1F2 ), nCCOrigin),intervalCrop);
// }

if(bShowCC)
{
//ImagePlus outIP = ImageJFunctions.wrap(ivCCswapped,"General cross-correlation");
//Calibration cal = outIP.getCalibration();
//cal.xOrigin =
//outIP.show();
ImageJFunctions.show(ivCCswapped).setTitle( "General cross-correlation" );
}
//ImageJFunctions.show(Views.interval( Views.extendPeriodic( invF1F1I2 ),interval)).setTitle( "Denominator" );

}

//now find max value
Point shift = new Point(nDim);

FloatType fCCvalue;

fCCvalue = MiscUtils.computeMaxLocation(ivCCswapped,shift);

/*
else
{
//Point shiftZeroX =new Point(nDim-1);
long [] minX = ivCCswapped.minAsLongArray();
long [] maxX = ivCCswapped.maxAsLongArray();
minX[0]=0;
maxX[0]=0;
//minX[1]=-179;
//maxX[1]=180;
FinalInterval valX = new FinalInterval(minX,maxX);
//ImageJFunctions.show(Views.interval(ivCCswapped, valX)).setTitle( "XZero" );
fCCvalue = MiscUtils.computeMaxLocation(Views.interval(ivCCswapped, valX),shift);
}
*/

if (bVerbose)
{
String sOutput = "Translation for template to overlap with image (px):\n("+Integer.toString(shift.getIntPosition(0)) ;
Expand All @@ -363,6 +397,14 @@ public boolean caclulateGenNormCC(final RandomAccessibleInterval< FloatType > im

// final shift of images
shift.localize(dShift);
// if(bCenteredLimit)
// {
// //add center position
// for(i=0;i<nDim;i++)
// {
// dShift[i] += nCCOrigin[i];
// }
// }
// max of cross-correlation
dMaxCC = fCCvalue.get();

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2 changes: 1 addition & 1 deletion src/main/java/averagingND/ImageSet.java
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Original file line number Diff line number Diff line change
Expand Up @@ -162,7 +162,7 @@ boolean loadAllImages()
{
if(!bMultiCh)
{
imgs.add(ImagePlusAdapter.convertFloat(imageIn));
imgs.add(ImagePlusAdapter.convertFloat(imageIn));
}
else
{
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