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Reduce pixel and array lookups to get a c. 35% reduction in execution…
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… time (#281)

* Reduce pixel lookups to get a c. 20-25% reduction in execution time

* Javadoc: use getOctant() only during x-y-z raster scans

getOctant() will return wrong results if called on a random pixel (x, y
z) or in a scan order other than x-y-z.

* Store octant values as bytes not byte[] to reduce array lookups.

Achieves another c .20% speedup.
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@mdoube
mdoube authored Feb 4, 2021
1 parent 9de045f commit c944b75
Showing 1 changed file with 56 additions and 94 deletions.
150 changes: 56 additions & 94 deletions Legacy/bonej/src/main/java/org/bonej/plugins/Connectivity.java
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Original file line number Diff line number Diff line change
Expand Up @@ -227,13 +227,25 @@ public double getSumEuler(final ImagePlus imp) {
threads[thread] = new Thread(new Runnable() {
@Override
public void run() {
byte o1 = 0, o2 = 0, o3 = 0, o4 = 0, o5 = 0, o6 = 0, o7 = 0, o8 = 0;
for (int z = ai.getAndIncrement(); z <= depth; z = ai.getAndIncrement()) {
for (int y = 0; y <= height; y++) {
for (int x = 0; x <= width; x++) {
final byte[] octant = getOctant(stack, x, y, z);
if (octant[0] == 0)
continue;
sumEulerInt[z] += getDeltaEuler(octant);

final int y1 = y - 1;
final int z1 = z - 1;

o1 = o3;
o2 = o4;
o3 = getPixel(stack, x, y1, z1);
o4 = getPixel(stack, x, y, z1);
o5 = o7;
o6 = o8;
o7 = getPixel(stack, x, y1, z);
o8 = getPixel(stack, x, y, z);

if ( o1 != 0 || o2 != 0 || o3 != 0 || o4 != 0 || o5 != 0 || o6 != 0 || o7 != 0 || o8 != 0 )
sumEulerInt[z] += getDeltaEuler(o1, o2, o3, o4, o5, o6, o7, o8);
}
}
}
Expand All @@ -254,51 +266,6 @@ private void setDimensions(final ImagePlus imp) {
return;
}

/*
* -----------------------------------------------------------------------
*/
/**
* Get octant of a vertex at (0,0,0) of a voxel (upper top left) in a 3D
* image (0 border conditions)
*
* @param stack
* 3D image (ImageStack)
* @param x
* x- coordinate
* @param y
* y- coordinate
* @param z
* z- coordinate (in image stacks the indexes start at 1)
* @return corresponding 8-pixel octant (0 if out of image)
*/
private byte[] getOctant(final ImageStack stack, final int x, final int y, final int z) {
final byte[] octant = new byte[9];

final int x1 = x - 1;
final int y1 = y - 1;
final int z1 = z - 1;

octant[1] = getPixel(stack, x1, y1, z1);
octant[2] = getPixel(stack, x1, y, z1);
octant[3] = getPixel(stack, x, y1, z1);
octant[4] = getPixel(stack, x, y, z1);
octant[5] = getPixel(stack, x1, y1, z);
octant[6] = getPixel(stack, x1, y, z);
octant[7] = getPixel(stack, x, y1, z);
octant[8] = getPixel(stack, x, y, z);

for (int i = 1; i < 9; i++)
if (octant[i] != 0) {
octant[0] = 1;
break;
}

return octant;
} /* end getNeighborhood */

/*
* -----------------------------------------------------------------------
*/
/**
* Get pixel in 3D image stack (0 border conditions)
*
Expand All @@ -322,62 +289,57 @@ private byte getPixel(final ImageStack stack, final int x, final int y, final in
/**
* Get delta euler value for an octant (~= vertex) from look up table
*
* Only use this method when there is at least one foreground voxel in
* Use this method only when there is at least one foreground voxel in
* octant.
*
* In binary images, foreground is -1, background = 0
*
* @param octant
* 9 element array containing nVoxels in zeroth element and 8
* voxel values
* @return or false if the point is Euler invariant or not
* In binary images, foreground is -1, background = 0. o1 = 08 are the octant values.
* @return delta Euler for the octant or false if the point is Euler invariant or not
*/
private int getDeltaEuler(final byte[] octant) {
if (octant[0] == 0)
return 0;
private int getDeltaEuler(final byte o1, final byte o2, final byte o3, final byte o4,
final byte o5, final byte o6, final byte o7, final byte o8) {

char n = 1;
if (octant[8] == -1) {
if (octant[1] == -1) n |= 128;
if (octant[2] == -1) n |= 64;
if (octant[3] == -1) n |= 32;
if (octant[4] == -1) n |= 16;
if (octant[5] == -1) n |= 8;
if (octant[6] == -1) n |= 4;
if (octant[7] == -1) n |= 2;
if (o8 == -1) {
if (o1 == -1) n |= 128;
if (o2 == -1) n |= 64;
if (o3 == -1) n |= 32;
if (o4 == -1) n |= 16;
if (o5 == -1) n |= 8;
if (o6 == -1) n |= 4;
if (o7 == -1) n |= 2;
}
else if (octant[7] == -1) {
if (octant[2] == -1) n |= 128;
if (octant[4] == -1) n |= 64;
if (octant[1] == -1) n |= 32;
if (octant[3] == -1) n |= 16;
if (octant[6] == -1) n |= 8;
if (octant[5] == -1) n |= 2;
else if (o7 == -1) {
if (o2 == -1) n |= 128;
if (o4 == -1) n |= 64;
if (o1 == -1) n |= 32;
if (o3 == -1) n |= 16;
if (o6 == -1) n |= 8;
if (o5 == -1) n |= 2;
}
else if (octant[6] == -1) {
if (octant[3] == -1) n |= 128;
if (octant[1] == -1) n |= 64;
if (octant[4] == -1) n |= 32;
if (octant[2] == -1) n |= 16;
if (octant[5] == -1) n |= 4;
else if (o6 == -1) {
if (o3 == -1) n |= 128;
if (o1 == -1) n |= 64;
if (o4 == -1) n |= 32;
if (o2 == -1) n |= 16;
if (o5 == -1) n |= 4;
}
else if (octant[5] == -1) {
if (octant[4] == -1) n |= 128;
if (octant[3] == -1) n |= 64;
if (octant[2] == -1) n |= 32;
if (octant[1] == -1) n |= 16;
else if (o5 == -1) {
if (o4 == -1) n |= 128;
if (o3 == -1) n |= 64;
if (o2 == -1) n |= 32;
if (o1 == -1) n |= 16;
}
else if (octant[4] == -1) {
if (octant[1] == -1) n |= 8;
if (octant[3] == -1) n |= 4;
if (octant[2] == -1) n |= 2;
else if (o4 == -1) {
if (o1 == -1) n |= 8;
if (o3 == -1) n |= 4;
if (o2 == -1) n |= 2;
}
else if (octant[3] == -1) {
if (octant[2] == -1) n |= 8;
if (octant[1] == -1) n |= 4;
else if (o3 == -1) {
if (o2 == -1) n |= 8;
if (o1 == -1) n |= 4;
}
else if (octant[2] == -1) {
if (octant[1] == -1) n |= 2;
else if (o2 == -1) {
if (o1 == -1) n |= 2;
}
else return 1;

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