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Rearchitect and Reinstate GPU #114

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Rearchitect and Reinstate GPU #114

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onurulgen
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  • Reinstated GPU into the project by fixing or implementing missing functions.
  • Rearchitected the project to combine GPU and CPU implementations by using virtual functions.
  • Increased the performance up to 11 times by using GPU.
  • Implemented unit and regression tests for GPU and CPU by using Catch2 framework.
  • Developed GitHub Actions for tests, coverage, static code analysis, and producing CPU and GPU executables for Windows, Linux and macOS.

@onurulgen
Bump NiftyReg version
9423847
@onurulgen
Generate coverage and upload it to Coveralls
323182c
@onurulgen
Add badge for the coverage
07e0558
@onurulgen
Add RNifti library
8538e7f
@onurulgen
Add NiftiImageData::Iterator::reset() to reset the iterator
414622b
@onurulgen
Add move constructor and assignment operator for NiftiImage
c631dc0
@onurulgen
Refactorise NiftiImage
4015cbf
@onurulgen
Add utility functions to NiftiImage
5bf6ca8
@onurulgen
Fix dimensions after initialisation of NiftiImage
a3b0cc9
@onurulgen
Fix a bug causing accessing freed memory in reg_io_WriteImageFile()
c863946
@onurulgen
Refactorisations
43686ab
@onurulgen
Refactor reg_createControlPointGrid() using automatic memory management
61de023
@onurulgen
Refactor reg_createSymmetricControlPointGrids() using automatic memor…
001d498 
…y management
@onurulgen
Refactor reg_createImagePyramid() using automatic memory management
058d4e9
@onurulgen
Refactor reg_createMaskPyramid() using automatic memory management
0c1e715
@onurulgen
Refactor reg_aladin class using automatic memory management
3a6d10c
@onurulgen
Refactor reg_aladin_sym class using automatic memory management
1130e1f
@onurulgen
Refactor reg_aladin app using automatic memory management
591fa91
@onurulgen
Refactor reg_base class using automatic memory management
4e5db2c
@onurulgen
Refactor reg_f3d class using automatic memory management
099572c
@onurulgen
Refactor reg_f3d2 class using automatic memory management
76c6652
@onurulgen
Refactor reg_f3d app using automatic memory management
ea8fac0
@onurulgen
Refactor reg_test_imageGradient using NiftiImage
d9bc22b
@onurulgen
Small fixes
4f22230
@onurulgen
Add NiftiImage::disown() to release the wrapped pointer
876a88d
@onurulgen
Use NiftiImage::disown() in reg_test_imageGradient
495ce95
@onurulgen
Refactor reg_test_interpolation using NiftiImage
8f96921
@onurulgen
Add NiftiImage::realloc() to reallocate the image data
751f447
@onurulgen
Add NiftiImage::setDim() to set a dimension of the image
19883fb
@onurulgen
Add ability to NiftiImage for copying only image info
d13cf2d
@onurulgen
Fix linting issues
f5e227f
@onurulgen
Eliminate dead code
1c99a7a
@onurulgen
Use git to download Eigen library
a560060 
Also, upgrade Eigen library to 3.3.*
@onurulgen
Refactorisations
e6d09fc
@onurulgen
Rename Measure as MeasureCreator
cee3df5
@onurulgen
Refactor _reg_maths* and _reg_common_cuda_kernels
e568f95
@onurulgen
Embed Eigen library
e9f51fe
@onurulgen
Replace Divide() with IndexToDims()
ebf0387
@onurulgen
Add include directories for OpenMP
f680bce
@onurulgen
Refactorisations
43c39fa
@onurulgen
Update macOS images in GitHub Actions
7cfe146
@onurulgen
Update the OS image for Coverage
41cd5a1
@onurulgen
Fix linting issues
65934f2
@onurulgen
Use NiftiImage instead of nifti_image in _reg_ReadWriteImage
dd78e8e 
Delete duplicate reg_io_ReadImageHeader() and add this ability to reg_io_ReadImageFile()
@onurulgen
Change the image acquisition behaviour of NiftiImage
cbbdd00 
Don't own the image pointer if it's constructed by using a nifti_image pointer
@onurulgen
Revert "Enable CRT secure warnings"
1cea3df 
This reverts commit 6cbbccd.
@onurulgen
Fix *Content::CastImageData() and eliminate its duplicates
2915900
@onurulgen
Use NiftiImage in Content classes
d515493
@onurulgen
Revert "Use float gam instead of double in CudaOptimiser"
7e1e926 
This reverts commit b9c9bec.
@onurulgen
Fix Floor(), Ceil(), and Round() functions
a148f14
@onurulgen onurulgen self-assigned this Aug 29, 2024
@onurulgen onurulgen linked an issue Aug 29, 2024 that may be closed by this pull request
Rearchitect F3D to reinstate GPU #92
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✅Code Analysis Results - no issues found! ✅

@msseibel
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I had to add set(CMAKE_CUDA_ARCHITECTURES "native") to the CMakeLists.txt file. Otherwise, I got the following error, "CMAKE_CUDA_ARCHITECTURES must be non-empty if set".

Besides that, the build worked, and I was able to run the program.

@onurulgen
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I had to add set(CMAKE_CUDA_ARCHITECTURES "native") to the CMakeLists.txt file. Otherwise, I got the following error, "CMAKE_CUDA_ARCHITECTURES must be non-empty if set".

Besides that, the build worked, and I was able to run the program.

CMAKE_CUDA_ARCHITECTURES are set in here. If you need to set that, your cmake configure command must've failed while detecting CUDA, right?

@msseibel
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Yes, that is correct. It failed as soon as it reached line 156 enable_language(CUDA).

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@mmodat mmodat Awaiting requested review from mmodat

@ericspod ericspod Awaiting requested review from ericspod

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Rearchitect F3D to reinstate GPU
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@onurulgen @msseibel @mmodat