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Fix crazy Interactive DoG #55

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merged 3 commits into from
Sep 26, 2024
Merged

Fix crazy Interactive DoG #55

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4682cc1
modified: src/main/java/net/preibisch/mvrecon/fiji/plugin/interest…
mhdominguez Aug 27, 2024
af126be
modified: HelperFunctions.java
mhdominguez Aug 27, 2024
3b10a21
modified: src/main/java/net/preibisch/mvrecon/fiji/plugin/interest…
mhdominguez Aug 27, 2024
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21 changes: 11 additions & 10 deletions ...net/preibisch/mvrecon/fiji/plugin/interestpointdetection/interactive/HelperFunctions.java
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Original file line number Diff line number Diff line change
Expand Up @@ -110,18 +110,19 @@ public static <L extends RealLocalizable> void drawRealLocalizable(final Collect

for (final L peak : peaks) {

// we only draw a 3d peak when it is +- 1.0 pixel away
if ( peak.numDimensions() > 2 && imp.getNSlices() > 1 )
if ( Math.abs( peak.getDoublePosition( 2 ) - currentSlice ) > 1.0 )
continue;

// determine Z distance from peak center and adjust scale radius
final float x = peak.getFloatPosition(0);
final float y = peak.getFloatPosition(1);

// +0.5 is to center in on the middle of the detection pixel
final OvalRoi or = new OvalRoi(x - radius + 0.5, y - radius + 0.5, radius * 2, radius * 2);
or.setStrokeColor(col);
overlay.add(or);
final float zDistance = Math.abs(peak.getFloatPosition(2) - currentSlice) + 1;
double drawRadius = 1.5 * radius / Math.sqrt( zDistance );

// only draw nearby peaks
if ( drawRadius > 0.67 )
{
final OvalRoi or = new OvalRoi(x - radius + 0.5, y - radius + 0.5, drawRadius * 2, drawRadius * 2);
or.setStrokeColor(col);
overlay.add(or);
}
}

// this part might be useful for debugging
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8 changes: 4 additions & 4 deletions .../net/preibisch/mvrecon/fiji/plugin/interestpointdetection/interactive/InteractiveDoG.java
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Hi, thanks so much for going through this. I am not sure that the extension of the z-range works as you intended, but I'll try it out!

Original file line number Diff line number Diff line change
Expand Up @@ -265,11 +265,11 @@ protected void updatePreview(final ValueChange change) {
min = new long []{
rectangle.x,
rectangle.y,
Math.max( imgTmp.min( 2 ), currentSlice - 1 ) };
Math.max( imgTmp.min( 2 ), currentSlice - (long) (2.5 * Math.ceil(params.sigma) ) ) };
max = new long []{
rectangle.width + rectangle.x - 1,
rectangle.height + rectangle.y - 1,
Math.min( imgTmp.max( 2 ), currentSlice + 1 ) };
Math.min( imgTmp.max( 2 ), currentSlice + (long) (2.5 * Math.ceil(params.sigma) ) ) };
}
else { // 2d or 2d+t case

Expand All @@ -296,8 +296,8 @@ protected void updatePreview(final ValueChange change) {
}

final double radius = ( ( params.sigma + HelperFunctions.computeSigma2( params.sigma, sensitivity ) ) / 2.0 );
final ArrayList< RefinedPeak< Point > > filteredPeaksMax = HelperFunctions.filterPeaks( peaksMax, rectangle, params.threshold );
final ArrayList< RefinedPeak< Point > > filteredPeaksMin = HelperFunctions.filterPeaks( peaksMin, rectangle, params.threshold );
final ArrayList< RefinedPeak< Point > > filteredPeaksMax = HelperFunctions.filterPeaks( peaksMax, rectangle, params.threshold / 2.5 ); // correction factor of 2.5 applied to match thresholding in final DoG IP detection
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I am wondering why this makes sense (I assume you tested it and it does make sense) ... will test this as well and merge for now, thanks so much!

final ArrayList< RefinedPeak< Point > > filteredPeaksMin = HelperFunctions.filterPeaks( peaksMin, rectangle, params.threshold / 2.5 ); // correction factor of 2.5 applied to match thresholding in

HelperFunctions.drawRealLocalizable( filteredPeaksMax, imagePlus, radius, Color.RED, true );
HelperFunctions.drawRealLocalizable( filteredPeaksMin, imagePlus, radius, Color.GREEN, false );
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