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PERF: Make AdvancedNormalizedCorrelationImageToImageMetric faster #556

Merged
merged 1 commit into from
Nov 26, 2021
Merged

PERF: Make AdvancedNormalizedCorrelationImageToImageMetric faster #556

merged 1 commit into from
Nov 26, 2021

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Added a new member function to AdvancedImageToImageMetric, FastEvaluateMovingImageValueAndDerivative, which calls the multi-threaded overload of ITK's itk::BSplineInterpolateImageFunction::EvaluateValueAndDerivativeAtContinuousIndex, indirectly. (It does so via EvaluateMovingImageValueAndDerivativeWithOptionalThreadId, another new member function.)

Made AdvancedNormalizedCorrelationImageToImageMetric::ThreadedGetValueAndDerivative faster, by calling this new FastEvaluateMovingImageValueAndDerivative.

A large performance improvement was observed for GoogleTest unit test itkElastixRegistrationMethod.EulerDiscRotation2D (which uses the "AdvancedNormalizedCorrelation" metric), from ~1.5 second before this commit down to ~0.9 second after this commit, using Visual Studio 2019, Release configuration. (For a Debug configuration even from ~15 seconds before, down to ~4 seconds after this commit.)

@N-Dekker
PERF: Make AdvancedNormalizedCorrelationImageToImageMetric faster
3675cd1 
Added a new member function to `AdvancedImageToImageMetric`, `FastEvaluateMovingImageValueAndDerivative`, which calls the multi-threaded overload of ITK's `itk::BSplineInterpolateImageFunction::EvaluateValueAndDerivativeAtContinuousIndex`, indirectly. (It does so via `EvaluateMovingImageValueAndDerivativeWithOptionalThreadId`, another new member function.)

Made `AdvancedNormalizedCorrelationImageToImageMetric::ThreadedGetValueAndDerivative` faster, by calling this new `FastEvaluateMovingImageValueAndDerivative`.

A large performance improvement was observed for GoogleTest unit test `itkElastixRegistrationMethod.EulerDiscRotation2D` (which uses the "AdvancedNormalizedCorrelation" metric), from ~1.5 second before this commit down to ~0.9 second after this commit, using Visual Studio 2019, Release configuration. (For a Debug configuration even from ~15 seconds before, down to ~4 seconds after this commit.)
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N-Dekker commented Nov 26, 2021 •
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@mstaring @stefanklein Here is the EvaluateValueAndDerivativeAtContinuousIndex overload that was called before, by the metric:

"Slower, but safer"
https://github.com/InsightSoftwareConsortium/ITK/blob/v5.3rc02/Modules/Core/ImageFunction/include/itkBSplineInterpolateImageFunction.h#L239-L257

Here is the faster overload (which has a threadId parameter):

"FIXME -- Review this "fix" and ensure it works."
https://github.com/InsightSoftwareConsortium/ITK/blob/v5.3rc02/Modules/Core/ImageFunction/include/itkBSplineInterpolateImageFunction.hxx#L276-L284

The performance improvement comes from skipping the memory allocation of local vnl_matrix variables, not just from using multiple threads!

For the record, the "FIXME" was there already with commit InsightSoftwareConsortium/ITK@6abbc79 (6 August 2010): https://github.com/InsightSoftwareConsortium/ITK/blob/6abbc7969a90786c4c73f5d191f634db536c2d1d/Code/BasicFilters/itkBSplineInterpolateImageFunction.txx#L297

@N-Dekker N-Dekker merged commit c8c4a6a into develop Nov 26, 2021
@N-Dekker N-Dekker deleted the FastEvaluateMovingImageValueAndDerivative branch November 26, 2021 16:18
N-Dekker added a commit that referenced this pull request Nov 27, 2021
@N-Dekker
PERF: Call FastEvaluateMovingImageValueAndDerivative in 4 more metrics
a57e282 
Replace `this->EvaluateMovingImageValueAndDerivative(...)` calls by `this->FastEvaluateMovingImageValueAndDerivative(..., threadId)` in four more metrics:

   itkAdvancedKappaStatisticImageToImageMetric
   itkParzenWindowMutualInformationImageToImageMetric
   itkAdvancedMeanSquaresImageToImageMetric
   itkPCAMetric_F_multithreaded

Follow-up to pull request #556 commit c8c4a6a "PERF: Make AdvancedNormalizedCorrelationImageToImageMetric faster"
N-Dekker added a commit that referenced this pull request Nov 27, 2021
@N-Dekker
PERF: Call FastEvaluateMovingImageValueAndDerivative in 6 more metrics
00e810e 
Replace `this->EvaluateMovingImageValueAndDerivative(...)` calls by `this->FastEvaluateMovingImageValueAndDerivative(..., threadId)` in the "Threaded" member functions of six more metrics:

    itkAdvancedKappaStatisticImageToImageMetric
    itkAdvancedMeanSquaresImageToImageMetric
    itkParzenWindowHistogramImageToImageMetric
    itkParzenWindowMutualInformationImageToImageMetric
    itkPCAMetric_F_multithreaded
    itkSumSquaredTissueVolumeDifferenceImageToImageMetric

Expected a significant performance gain on the run-time duration.

Follow-up to pull request #556 commit c8c4a6a "PERF: Make AdvancedNormalizedCorrelationImageToImageMetric faster"
N-Dekker added a commit that referenced this pull request Nov 27, 2021
@N-Dekker
PERF: Call FastEvaluateMovingImageValueAndDerivative in 6 more metrics
fb4cfdb 
Replace `this->EvaluateMovingImageValueAndDerivative(...)` calls by `this->FastEvaluateMovingImageValueAndDerivative(..., threadId)` in the "Threaded" member functions of six more metrics:

    itkAdvancedKappaStatisticImageToImageMetric
    itkAdvancedMeanSquaresImageToImageMetric
    itkParzenWindowHistogramImageToImageMetric
    itkParzenWindowMutualInformationImageToImageMetric
    itkPCAMetric_F_multithreaded
    itkSumSquaredTissueVolumeDifferenceImageToImageMetric

Expected a significant performance gain on the run-time duration.

Follow-up to pull request #556 commit c8c4a6a "PERF: Make AdvancedNormalizedCorrelationImageToImageMetric faster"
N-Dekker added a commit that referenced this pull request Nov 27, 2021
@N-Dekker
PERF: Call FastEvaluateMovingImageValueAndDerivative in 6 more metrics
dd05544 
Replaced `this->EvaluateMovingImageValueAndDerivative(...)` calls by `this->FastEvaluateMovingImageValueAndDerivative(..., threadId)` in the "Threaded" member functions of six more metrics:

    itkAdvancedKappaStatisticImageToImageMetric
    itkAdvancedMeanSquaresImageToImageMetric
    itkParzenWindowHistogramImageToImageMetric
    itkParzenWindowMutualInformationImageToImageMetric
    itkPCAMetric_F_multithreaded
    itkSumSquaredTissueVolumeDifferenceImageToImageMetric

Expected a significant performance gain on the run-time duration.

`AdvancedKappaStatisticImageToImageMetric::ThreadedGetValueAndDerivative` is being tested by 55/161 - elastix_run_3DCT_lung.Kappa.bspline.ASGD.001_OUTPUT

`AdvancedMeanSquaresImageToImageMetric::ThreadedGetValueAndDerivative` is being tested by:

 - 43/161 - elastix_run_3DCT_lung.SSD.bspline.ASGD.001_OUTPUT
 - 98/161 - elastix_run_3DCT_lung.SSD.bspline.ASGD.002_OUTPUT
 - 102/161 - elastix_run_3DCT_lung.SSD.bspline.ASGD.003_OUTPUT
 - 106/161 - elastix_run_3DCT_lung.SSD.bspline.ASGD.001-Threads1_OUTPUT
 - 110/161 - elastix_run_3DCT_lung.SSD.bspline.ASGD.001-Threads2_OUTPUT
 - 114/161 - elastix_run_3DCT_lung.SSD.bspline.ASGD.001-Threads4_OUTPUT

`ParzenWindowHistogramImageToImageMetric::ThreadedComputePDFs` is being tested by:

 - 20/161 - elastix_run_example_OUTPUT
 - 47/161 - elastix_run_3DCT_lung.MI.bspline.ASGD.001_OUTPUT
 - 82/161 - elastix_run_3DCT_lung.MI.bspline.SGD.001_OUTPUT
 - 86/161 - elastix_run_3DCT_lung.MI.bspline.SGD.002_OUTPUT
 - 90/161 - elastix_run_3DCT_lung.MI.bspline.SGD.003_OUTPUT
 - 94/161 - elastix_run_3DCT_lung.MI.bspline.SGD.004_OUTPUT
 - 130/161 - elastix_run_3DCT_lung.MI.bspline.SGD.001-Threads1_OUTPUT
 - 134/161 - elastix_run_3DCT_lung.MI.bspline.SGD.001-Threads2_OUTPUT
 - 138/161 - elastix_run_3DCT_lung.MI.bspline.SGD.001-Threads4_OUTPUT

Follow-up to pull request #556 commit c8c4a6a "PERF: Make AdvancedNormalizedCorrelationImageToImageMetric faster"
@N-Dekker N-Dekker mentioned this pull request Nov 27, 2021
Merged
N-Dekker added a commit that referenced this pull request Nov 28, 2021
@N-Dekker
PERF: Call FastEvaluateMovingImageValueAndDerivative in 6 more metrics
5e720da 
Replaced `this->EvaluateMovingImageValueAndDerivative(...)` calls by `this->FastEvaluateMovingImageValueAndDerivative(..., threadId)` in the "Threaded" member functions of six more metrics:

    itkAdvancedKappaStatisticImageToImageMetric
    itkAdvancedMeanSquaresImageToImageMetric
    itkParzenWindowHistogramImageToImageMetric
    itkParzenWindowMutualInformationImageToImageMetric
    itkPCAMetric_F_multithreaded
    itkSumSquaredTissueVolumeDifferenceImageToImageMetric

Expected a significant performance gain on the run-time duration.

`AdvancedKappaStatisticImageToImageMetric::ThreadedGetValueAndDerivative` is being tested by 55/161 - elastix_run_3DCT_lung.Kappa.bspline.ASGD.001_OUTPUT

`AdvancedMeanSquaresImageToImageMetric::ThreadedGetValueAndDerivative` is being tested by:

 - 43/161 - elastix_run_3DCT_lung.SSD.bspline.ASGD.001_OUTPUT
 - 98/161 - elastix_run_3DCT_lung.SSD.bspline.ASGD.002_OUTPUT
 - 102/161 - elastix_run_3DCT_lung.SSD.bspline.ASGD.003_OUTPUT
 - 106/161 - elastix_run_3DCT_lung.SSD.bspline.ASGD.001-Threads1_OUTPUT
 - 110/161 - elastix_run_3DCT_lung.SSD.bspline.ASGD.001-Threads2_OUTPUT
 - 114/161 - elastix_run_3DCT_lung.SSD.bspline.ASGD.001-Threads4_OUTPUT

`ParzenWindowHistogramImageToImageMetric::ThreadedComputePDFs` is being tested by:

 - 20/161 - elastix_run_example_OUTPUT
 - 47/161 - elastix_run_3DCT_lung.MI.bspline.ASGD.001_OUTPUT
 - 82/161 - elastix_run_3DCT_lung.MI.bspline.SGD.001_OUTPUT
 - 86/161 - elastix_run_3DCT_lung.MI.bspline.SGD.002_OUTPUT
 - 90/161 - elastix_run_3DCT_lung.MI.bspline.SGD.003_OUTPUT
 - 94/161 - elastix_run_3DCT_lung.MI.bspline.SGD.004_OUTPUT
 - 130/161 - elastix_run_3DCT_lung.MI.bspline.SGD.001-Threads1_OUTPUT
 - 134/161 - elastix_run_3DCT_lung.MI.bspline.SGD.001-Threads2_OUTPUT
 - 138/161 - elastix_run_3DCT_lung.MI.bspline.SGD.001-Threads4_OUTPUT

Follow-up to pull request #556 commit c8c4a6a "PERF: Make AdvancedNormalizedCorrelationImageToImageMetric faster"
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