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| Deletions are marked like this. | Additions are marked like this. |
| Line 4: | Line 4: |
| Each face had a normal vector and area stored in the nx,ny,nz,orig_area members of the FACE struct. | mris_fix_topology has a hot loop, which does unnecessary calculations of the face normals |
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| mris_fix_topology has a hot loop | mrisComputeOptimalRetessellation and mrisComputeRandomRetessellation have a similar structure |
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| ___: mrisComputeOptimalRetessellation and mrisComputeRandomRetessellation have a similar structure | _:_: it loops over a set of patches, or iterates on one patch. For each patch it calls |
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| ___: ___: a computeDefectContext is constructed here | _:_:_: mrisDefectPatchFitness, which calls |
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| ___:___: then it loops over a set of patches, or iterates on one patch. For each patch it calls | _:_:_:_: mrisComputeDefectLogLikelihood, which calls |
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| ___:___:___: mrisDefectPatchFitness, which calls | _:_:_:_:_: mrisComputeDefectMRILogUnlikelihood, which |
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| ___:___:___: ___: mrisComputeDefectLogLikelihood, which calls | _:_:_:_:_:_: does an expensive computation all the face normals for ALL the faces |
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| ___:___:___: ___: ___: mrisComputeDefectMRILogUnlikelihood, which | _:_:_:_:_:_: does two other expensive steps, which only use a few of the face normals |
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| ___:___:___: ___: ___:___: does an expensive computation all the face normals for ALL the faces | To simplify, the original code does this |
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| ___:___:___: ___: ___:___: does two other expensive steps, which only use a few of the face normals | _: loop _:_: for all fno normal[fno] = f (inputs) _:_: for a few fno use normal[fno] _: end loop _: change some inputs _: use some normal[fno] Since only a few of the face normals are used, it is a waste of time to calculate all of them every time around the loop! This is replaced by code that does _: loop _:_: for all fno: normal[fno].deferred = true _:_: for a few fno: use normal[fno], computing it from f (inputs) if is deferred, and changing it to being no-longer deferred _: end loop _: compute any remaining deferred normal[fno] before their inputs can change _: change some inputs _: use some normal[fno] |
A variety of techniques have been used.
Deferring calculations until needed
mris_fix_topology has a hot loop, which does unnecessary calculations of the face normals
mrisComputeOptimalRetessellation and mrisComputeRandomRetessellation have a similar structure
_:_: it loops over a set of patches, or iterates on one patch. For each patch it calls
_:_:_: mrisDefectPatchFitness, which calls
_:_:_:_: mrisComputeDefectLogLikelihood, which calls
_:_:_:_:_: mrisComputeDefectMRILogUnlikelihood, which
_:_:_:_:_:_: does an expensive computation all the face normals for ALL the faces
_:_:_:_:_:_: does two other expensive steps, which only use a few of the face normals
To simplify, the original code does this
_: loop
_:_: for all fno normal[fno] = f (inputs)
_:_: for a few fno use normal[fno]
_: end loop
_: change some inputs
_: use some normal[fno]
Since only a few of the face normals are used, it is a waste of time to calculate all of them every time around the loop!
This is replaced by code that does
_: loop
_:_: for all fno: normal[fno].deferred = true
_:_: for a few fno: use normal[fno], computing it from f (inputs) if is deferred, and changing it to being no-longer deferred
_: end loop
_: compute any remaining deferred normal[fno] before their inputs can change
_: change some inputs
_: use some normal[fno]