From 8c4bf40047e2131119bfdee78bca82c5844e225a Mon Sep 17 00:00:00 2001 From: neuronflow Date: Wed, 13 Dec 2023 17:57:02 +0100 Subject: [PATCH 1/4] move niftyreg Signed-off-by: neuronflow --- brainles_preprocessing/registration/__init__.py | 2 +- brainles_preprocessing/registration/{ => niftyreg}/niftyreg.py | 0 tests/test_niftyreg_registrator.py | 2 +- 3 files changed, 2 insertions(+), 2 deletions(-) rename brainles_preprocessing/registration/{ => niftyreg}/niftyreg.py (100%) diff --git a/brainles_preprocessing/registration/__init__.py b/brainles_preprocessing/registration/__init__.py index ab86e04..6f56b85 100644 --- a/brainles_preprocessing/registration/__init__.py +++ b/brainles_preprocessing/registration/__init__.py @@ -1 +1 @@ -from .niftyreg import NiftyRegRegistrator +from .niftyreg.niftyreg import NiftyRegRegistrator diff --git a/brainles_preprocessing/registration/niftyreg.py b/brainles_preprocessing/registration/niftyreg/niftyreg.py similarity index 100% rename from brainles_preprocessing/registration/niftyreg.py rename to brainles_preprocessing/registration/niftyreg/niftyreg.py diff --git a/tests/test_niftyreg_registrator.py b/tests/test_niftyreg_registrator.py index 2315960..94bcaca 100644 --- a/tests/test_niftyreg_registrator.py +++ b/tests/test_niftyreg_registrator.py @@ -4,7 +4,7 @@ from auxiliary.turbopath import turbopath -from brainles_preprocessing.registration.niftyreg import NiftyRegRegistrator +from brainles_preprocessing.registration.niftyreg.niftyreg import NiftyRegRegistrator class TestNiftyRegRegistrator(unittest.TestCase): From 23dbf15544c2189cc2554cf9b7871f57093d0381 Mon Sep 17 00:00:00 2001 From: neuronflow Date: Wed, 13 Dec 2023 17:57:40 +0100 Subject: [PATCH 2/4] move binaries and scripts Signed-off-by: neuronflow --- .../bin/groupwise_niftyreg_params.sh | 0 .../niftyreg_1.5.68/bin/groupwise_niftyreg_run.sh | 0 .../niftyreg_scripts/niftyreg_1.5.68/bin/reg_aladin | Bin .../niftyreg_1.5.68/bin/reg_average | Bin .../niftyreg_scripts/niftyreg_1.5.68/bin/reg_f3d | Bin .../niftyreg_1.5.68/bin/reg_jacobian | Bin .../niftyreg_1.5.68/bin/reg_measure | Bin .../niftyreg_1.5.68/bin/reg_resample | Bin .../niftyreg_scripts/niftyreg_1.5.68/bin/reg_tools | Bin .../niftyreg_1.5.68/bin/reg_transform | Bin .../include/AffineDeformationFieldKernel.h | 0 .../niftyreg_1.5.68/include/AladinContent.h | 0 .../niftyreg_1.5.68/include/BlockMatchingKernel.h | 0 .../include/CPUAffineDeformationFieldKernel.h | 0 .../include/CPUBlockMatchingKernel.h | 0 .../niftyreg_1.5.68/include/CPUConvolutionKernel.h | 0 .../niftyreg_1.5.68/include/CPUKernelFactory.h | 0 .../niftyreg_1.5.68/include/CPUOptimiseKernel.h | 0 .../include/CPUResampleImageKernel.h | 0 .../niftyreg_1.5.68/include/ConvolutionKernel.h | 0 .../niftyreg_1.5.68/include/Kernel.h | 0 .../niftyreg_1.5.68/include/KernelFactory.h | 0 .../niftyreg_1.5.68/include/OptimiseKernel.h | 0 .../niftyreg_1.5.68/include/Platform.h | 0 .../niftyreg_1.5.68/include/ResampleImageKernel.h | 0 .../niftyreg_1.5.68/include/_reg_ReadWriteImage.h | 0 .../niftyreg_1.5.68/include/_reg_ReadWriteMatrix.h | 0 .../niftyreg_1.5.68/include/_reg_aladin.cpp | 0 .../niftyreg_1.5.68/include/_reg_aladin.h | 0 .../niftyreg_1.5.68/include/_reg_aladin_sym.cpp | 0 .../niftyreg_1.5.68/include/_reg_aladin_sym.h | 0 .../niftyreg_1.5.68/include/_reg_base.h | 0 .../niftyreg_1.5.68/include/_reg_blockMatching.h | 0 .../niftyreg_1.5.68/include/_reg_dti.h | 0 .../niftyreg_1.5.68/include/_reg_f3d.h | 0 .../niftyreg_1.5.68/include/_reg_f3d2.h | 0 .../niftyreg_1.5.68/include/_reg_f3d_sym.h | 0 .../niftyreg_1.5.68/include/_reg_femTrans.h | 0 .../niftyreg_1.5.68/include/_reg_globalTrans.h | 0 .../niftyreg_1.5.68/include/_reg_kld.h | 0 .../niftyreg_1.5.68/include/_reg_lncc.h | 0 .../niftyreg_1.5.68/include/_reg_localTrans.h | 0 .../niftyreg_1.5.68/include/_reg_localTrans_jac.h | 0 .../niftyreg_1.5.68/include/_reg_localTrans_regul.h | 0 .../niftyreg_1.5.68/include/_reg_macros.h | 0 .../niftyreg_1.5.68/include/_reg_maths.h | 0 .../niftyreg_1.5.68/include/_reg_maths_eigen.h | 0 .../niftyreg_1.5.68/include/_reg_measure.h | 0 .../niftyreg_1.5.68/include/_reg_mind.h | 0 .../niftyreg_1.5.68/include/_reg_nmi.h | 0 .../niftyreg_1.5.68/include/_reg_optimiser.cpp | 0 .../niftyreg_1.5.68/include/_reg_optimiser.h | 0 .../niftyreg_1.5.68/include/_reg_resampling.h | 0 .../niftyreg_1.5.68/include/_reg_splineBasis.h | 0 .../niftyreg_1.5.68/include/_reg_ssd.h | 0 .../niftyreg_1.5.68/include/_reg_stringFormat.h | 0 .../niftyreg_1.5.68/include/_reg_tools.h | 0 .../niftyreg_1.5.68/include/nifti1.h | 0 .../niftyreg_1.5.68/include/nifti1_io.h | 0 .../niftyreg_scripts/niftyreg_1.5.68/include/png.h | 0 .../niftyreg_1.5.68/include/pngconf.h | 0 .../niftyreg_1.5.68/include/pngdebug.h | 0 .../niftyreg_1.5.68/include/pnginfo.h | 0 .../niftyreg_1.5.68/include/pnglibconf.h | 0 .../niftyreg_1.5.68/include/pngpriv.h | 0 .../niftyreg_1.5.68/include/pngstruct.h | 0 .../niftyreg_1.5.68/include/readpng.h | 0 .../niftyreg_1.5.68/include/reg_png.h | 0 .../niftyreg_scripts/niftyreg_1.5.68/include/zlib.h | 0 .../niftyreg_1.5.68/include/znzlib.h | 0 .../niftyreg_1.5.68/include/zutil.h | 0 .../{ => niftyreg}/niftyreg_scripts/reg_aladin | Bin .../{ => niftyreg}/niftyreg_scripts/reg_resample | Bin .../{ => niftyreg}/niftyreg_scripts/rigid_reg.sh | 0 .../{ => niftyreg}/niftyreg_scripts/transform.sh | 0 75 files changed, 0 insertions(+), 0 deletions(-) rename brainles_preprocessing/registration/{ => niftyreg}/niftyreg_scripts/niftyreg_1.5.68/bin/groupwise_niftyreg_params.sh (100%) rename brainles_preprocessing/registration/{ => niftyreg}/niftyreg_scripts/niftyreg_1.5.68/bin/groupwise_niftyreg_run.sh (100%) rename brainles_preprocessing/registration/{ => niftyreg}/niftyreg_scripts/niftyreg_1.5.68/bin/reg_aladin (100%) rename brainles_preprocessing/registration/{ => niftyreg}/niftyreg_scripts/niftyreg_1.5.68/bin/reg_average (100%) rename brainles_preprocessing/registration/{ => niftyreg}/niftyreg_scripts/niftyreg_1.5.68/bin/reg_f3d (100%) rename brainles_preprocessing/registration/{ => niftyreg}/niftyreg_scripts/niftyreg_1.5.68/bin/reg_jacobian (100%) rename brainles_preprocessing/registration/{ => niftyreg}/niftyreg_scripts/niftyreg_1.5.68/bin/reg_measure (100%) rename brainles_preprocessing/registration/{ => niftyreg}/niftyreg_scripts/niftyreg_1.5.68/bin/reg_resample (100%) rename brainles_preprocessing/registration/{ => niftyreg}/niftyreg_scripts/niftyreg_1.5.68/bin/reg_tools (100%) rename brainles_preprocessing/registration/{ => niftyreg}/niftyreg_scripts/niftyreg_1.5.68/bin/reg_transform (100%) rename brainles_preprocessing/registration/{ => niftyreg}/niftyreg_scripts/niftyreg_1.5.68/include/AffineDeformationFieldKernel.h (100%) rename brainles_preprocessing/registration/{ => niftyreg}/niftyreg_scripts/niftyreg_1.5.68/include/AladinContent.h (100%) rename brainles_preprocessing/registration/{ => niftyreg}/niftyreg_scripts/niftyreg_1.5.68/include/BlockMatchingKernel.h (100%) rename brainles_preprocessing/registration/{ => niftyreg}/niftyreg_scripts/niftyreg_1.5.68/include/CPUAffineDeformationFieldKernel.h (100%) rename brainles_preprocessing/registration/{ => niftyreg}/niftyreg_scripts/niftyreg_1.5.68/include/CPUBlockMatchingKernel.h (100%) rename brainles_preprocessing/registration/{ => niftyreg}/niftyreg_scripts/niftyreg_1.5.68/include/CPUConvolutionKernel.h (100%) rename brainles_preprocessing/registration/{ => niftyreg}/niftyreg_scripts/niftyreg_1.5.68/include/CPUKernelFactory.h (100%) rename brainles_preprocessing/registration/{ => niftyreg}/niftyreg_scripts/niftyreg_1.5.68/include/CPUOptimiseKernel.h (100%) rename brainles_preprocessing/registration/{ => niftyreg}/niftyreg_scripts/niftyreg_1.5.68/include/CPUResampleImageKernel.h (100%) rename brainles_preprocessing/registration/{ => niftyreg}/niftyreg_scripts/niftyreg_1.5.68/include/ConvolutionKernel.h (100%) rename brainles_preprocessing/registration/{ => niftyreg}/niftyreg_scripts/niftyreg_1.5.68/include/Kernel.h (100%) rename brainles_preprocessing/registration/{ => niftyreg}/niftyreg_scripts/niftyreg_1.5.68/include/KernelFactory.h (100%) rename brainles_preprocessing/registration/{ => niftyreg}/niftyreg_scripts/niftyreg_1.5.68/include/OptimiseKernel.h (100%) rename brainles_preprocessing/registration/{ => niftyreg}/niftyreg_scripts/niftyreg_1.5.68/include/Platform.h (100%) rename brainles_preprocessing/registration/{ => niftyreg}/niftyreg_scripts/niftyreg_1.5.68/include/ResampleImageKernel.h (100%) rename brainles_preprocessing/registration/{ => niftyreg}/niftyreg_scripts/niftyreg_1.5.68/include/_reg_ReadWriteImage.h (100%) rename brainles_preprocessing/registration/{ => niftyreg}/niftyreg_scripts/niftyreg_1.5.68/include/_reg_ReadWriteMatrix.h (100%) rename brainles_preprocessing/registration/{ => niftyreg}/niftyreg_scripts/niftyreg_1.5.68/include/_reg_aladin.cpp (100%) rename brainles_preprocessing/registration/{ => niftyreg}/niftyreg_scripts/niftyreg_1.5.68/include/_reg_aladin.h (100%) rename brainles_preprocessing/registration/{ => niftyreg}/niftyreg_scripts/niftyreg_1.5.68/include/_reg_aladin_sym.cpp (100%) rename brainles_preprocessing/registration/{ => niftyreg}/niftyreg_scripts/niftyreg_1.5.68/include/_reg_aladin_sym.h (100%) rename brainles_preprocessing/registration/{ => niftyreg}/niftyreg_scripts/niftyreg_1.5.68/include/_reg_base.h (100%) rename brainles_preprocessing/registration/{ => niftyreg}/niftyreg_scripts/niftyreg_1.5.68/include/_reg_blockMatching.h (100%) rename brainles_preprocessing/registration/{ => niftyreg}/niftyreg_scripts/niftyreg_1.5.68/include/_reg_dti.h (100%) rename brainles_preprocessing/registration/{ => niftyreg}/niftyreg_scripts/niftyreg_1.5.68/include/_reg_f3d.h (100%) rename brainles_preprocessing/registration/{ => niftyreg}/niftyreg_scripts/niftyreg_1.5.68/include/_reg_f3d2.h (100%) rename brainles_preprocessing/registration/{ => niftyreg}/niftyreg_scripts/niftyreg_1.5.68/include/_reg_f3d_sym.h (100%) rename brainles_preprocessing/registration/{ => niftyreg}/niftyreg_scripts/niftyreg_1.5.68/include/_reg_femTrans.h (100%) rename brainles_preprocessing/registration/{ => niftyreg}/niftyreg_scripts/niftyreg_1.5.68/include/_reg_globalTrans.h (100%) rename brainles_preprocessing/registration/{ => niftyreg}/niftyreg_scripts/niftyreg_1.5.68/include/_reg_kld.h (100%) rename brainles_preprocessing/registration/{ => niftyreg}/niftyreg_scripts/niftyreg_1.5.68/include/_reg_lncc.h (100%) rename brainles_preprocessing/registration/{ => niftyreg}/niftyreg_scripts/niftyreg_1.5.68/include/_reg_localTrans.h (100%) rename brainles_preprocessing/registration/{ => niftyreg}/niftyreg_scripts/niftyreg_1.5.68/include/_reg_localTrans_jac.h (100%) rename brainles_preprocessing/registration/{ => 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niftyreg}/niftyreg_scripts/niftyreg_1.5.68/include/_reg_optimiser.h (100%) rename brainles_preprocessing/registration/{ => niftyreg}/niftyreg_scripts/niftyreg_1.5.68/include/_reg_resampling.h (100%) rename brainles_preprocessing/registration/{ => niftyreg}/niftyreg_scripts/niftyreg_1.5.68/include/_reg_splineBasis.h (100%) rename brainles_preprocessing/registration/{ => niftyreg}/niftyreg_scripts/niftyreg_1.5.68/include/_reg_ssd.h (100%) rename brainles_preprocessing/registration/{ => niftyreg}/niftyreg_scripts/niftyreg_1.5.68/include/_reg_stringFormat.h (100%) rename brainles_preprocessing/registration/{ => niftyreg}/niftyreg_scripts/niftyreg_1.5.68/include/_reg_tools.h (100%) rename brainles_preprocessing/registration/{ => niftyreg}/niftyreg_scripts/niftyreg_1.5.68/include/nifti1.h (100%) rename brainles_preprocessing/registration/{ => niftyreg}/niftyreg_scripts/niftyreg_1.5.68/include/nifti1_io.h (100%) rename brainles_preprocessing/registration/{ => niftyreg}/niftyreg_scripts/niftyreg_1.5.68/include/png.h (100%) rename brainles_preprocessing/registration/{ => niftyreg}/niftyreg_scripts/niftyreg_1.5.68/include/pngconf.h (100%) rename brainles_preprocessing/registration/{ => niftyreg}/niftyreg_scripts/niftyreg_1.5.68/include/pngdebug.h (100%) rename brainles_preprocessing/registration/{ => niftyreg}/niftyreg_scripts/niftyreg_1.5.68/include/pnginfo.h (100%) rename brainles_preprocessing/registration/{ => niftyreg}/niftyreg_scripts/niftyreg_1.5.68/include/pnglibconf.h (100%) rename brainles_preprocessing/registration/{ => niftyreg}/niftyreg_scripts/niftyreg_1.5.68/include/pngpriv.h (100%) rename brainles_preprocessing/registration/{ => niftyreg}/niftyreg_scripts/niftyreg_1.5.68/include/pngstruct.h (100%) rename brainles_preprocessing/registration/{ => niftyreg}/niftyreg_scripts/niftyreg_1.5.68/include/readpng.h (100%) rename brainles_preprocessing/registration/{ => niftyreg}/niftyreg_scripts/niftyreg_1.5.68/include/reg_png.h (100%) rename brainles_preprocessing/registration/{ => niftyreg}/niftyreg_scripts/niftyreg_1.5.68/include/zlib.h (100%) rename brainles_preprocessing/registration/{ => niftyreg}/niftyreg_scripts/niftyreg_1.5.68/include/znzlib.h (100%) rename brainles_preprocessing/registration/{ => niftyreg}/niftyreg_scripts/niftyreg_1.5.68/include/zutil.h (100%) rename brainles_preprocessing/registration/{ => niftyreg}/niftyreg_scripts/reg_aladin (100%) rename brainles_preprocessing/registration/{ => niftyreg}/niftyreg_scripts/reg_resample (100%) rename brainles_preprocessing/registration/{ => niftyreg}/niftyreg_scripts/rigid_reg.sh (100%) rename brainles_preprocessing/registration/{ => niftyreg}/niftyreg_scripts/transform.sh (100%) diff --git a/brainles_preprocessing/registration/niftyreg_scripts/niftyreg_1.5.68/bin/groupwise_niftyreg_params.sh b/brainles_preprocessing/registration/niftyreg/niftyreg_scripts/niftyreg_1.5.68/bin/groupwise_niftyreg_params.sh similarity index 100% rename from brainles_preprocessing/registration/niftyreg_scripts/niftyreg_1.5.68/bin/groupwise_niftyreg_params.sh rename to brainles_preprocessing/registration/niftyreg/niftyreg_scripts/niftyreg_1.5.68/bin/groupwise_niftyreg_params.sh diff --git a/brainles_preprocessing/registration/niftyreg_scripts/niftyreg_1.5.68/bin/groupwise_niftyreg_run.sh b/brainles_preprocessing/registration/niftyreg/niftyreg_scripts/niftyreg_1.5.68/bin/groupwise_niftyreg_run.sh similarity index 100% rename from brainles_preprocessing/registration/niftyreg_scripts/niftyreg_1.5.68/bin/groupwise_niftyreg_run.sh rename to brainles_preprocessing/registration/niftyreg/niftyreg_scripts/niftyreg_1.5.68/bin/groupwise_niftyreg_run.sh diff --git a/brainles_preprocessing/registration/niftyreg_scripts/niftyreg_1.5.68/bin/reg_aladin b/brainles_preprocessing/registration/niftyreg/niftyreg_scripts/niftyreg_1.5.68/bin/reg_aladin similarity index 100% rename from brainles_preprocessing/registration/niftyreg_scripts/niftyreg_1.5.68/bin/reg_aladin rename to brainles_preprocessing/registration/niftyreg/niftyreg_scripts/niftyreg_1.5.68/bin/reg_aladin diff --git a/brainles_preprocessing/registration/niftyreg_scripts/niftyreg_1.5.68/bin/reg_average b/brainles_preprocessing/registration/niftyreg/niftyreg_scripts/niftyreg_1.5.68/bin/reg_average similarity index 100% rename from brainles_preprocessing/registration/niftyreg_scripts/niftyreg_1.5.68/bin/reg_average rename to brainles_preprocessing/registration/niftyreg/niftyreg_scripts/niftyreg_1.5.68/bin/reg_average diff --git a/brainles_preprocessing/registration/niftyreg_scripts/niftyreg_1.5.68/bin/reg_f3d b/brainles_preprocessing/registration/niftyreg/niftyreg_scripts/niftyreg_1.5.68/bin/reg_f3d similarity index 100% rename from brainles_preprocessing/registration/niftyreg_scripts/niftyreg_1.5.68/bin/reg_f3d rename to brainles_preprocessing/registration/niftyreg/niftyreg_scripts/niftyreg_1.5.68/bin/reg_f3d diff --git a/brainles_preprocessing/registration/niftyreg_scripts/niftyreg_1.5.68/bin/reg_jacobian b/brainles_preprocessing/registration/niftyreg/niftyreg_scripts/niftyreg_1.5.68/bin/reg_jacobian similarity index 100% rename from brainles_preprocessing/registration/niftyreg_scripts/niftyreg_1.5.68/bin/reg_jacobian rename to brainles_preprocessing/registration/niftyreg/niftyreg_scripts/niftyreg_1.5.68/bin/reg_jacobian diff --git a/brainles_preprocessing/registration/niftyreg_scripts/niftyreg_1.5.68/bin/reg_measure b/brainles_preprocessing/registration/niftyreg/niftyreg_scripts/niftyreg_1.5.68/bin/reg_measure similarity index 100% rename from brainles_preprocessing/registration/niftyreg_scripts/niftyreg_1.5.68/bin/reg_measure rename to brainles_preprocessing/registration/niftyreg/niftyreg_scripts/niftyreg_1.5.68/bin/reg_measure diff --git a/brainles_preprocessing/registration/niftyreg_scripts/niftyreg_1.5.68/bin/reg_resample b/brainles_preprocessing/registration/niftyreg/niftyreg_scripts/niftyreg_1.5.68/bin/reg_resample similarity index 100% rename from brainles_preprocessing/registration/niftyreg_scripts/niftyreg_1.5.68/bin/reg_resample rename to brainles_preprocessing/registration/niftyreg/niftyreg_scripts/niftyreg_1.5.68/bin/reg_resample diff --git a/brainles_preprocessing/registration/niftyreg_scripts/niftyreg_1.5.68/bin/reg_tools b/brainles_preprocessing/registration/niftyreg/niftyreg_scripts/niftyreg_1.5.68/bin/reg_tools similarity index 100% rename from brainles_preprocessing/registration/niftyreg_scripts/niftyreg_1.5.68/bin/reg_tools rename to brainles_preprocessing/registration/niftyreg/niftyreg_scripts/niftyreg_1.5.68/bin/reg_tools diff --git a/brainles_preprocessing/registration/niftyreg_scripts/niftyreg_1.5.68/bin/reg_transform b/brainles_preprocessing/registration/niftyreg/niftyreg_scripts/niftyreg_1.5.68/bin/reg_transform similarity index 100% rename from brainles_preprocessing/registration/niftyreg_scripts/niftyreg_1.5.68/bin/reg_transform rename to brainles_preprocessing/registration/niftyreg/niftyreg_scripts/niftyreg_1.5.68/bin/reg_transform diff --git a/brainles_preprocessing/registration/niftyreg_scripts/niftyreg_1.5.68/include/AffineDeformationFieldKernel.h b/brainles_preprocessing/registration/niftyreg/niftyreg_scripts/niftyreg_1.5.68/include/AffineDeformationFieldKernel.h similarity index 100% rename from brainles_preprocessing/registration/niftyreg_scripts/niftyreg_1.5.68/include/AffineDeformationFieldKernel.h rename to brainles_preprocessing/registration/niftyreg/niftyreg_scripts/niftyreg_1.5.68/include/AffineDeformationFieldKernel.h diff --git a/brainles_preprocessing/registration/niftyreg_scripts/niftyreg_1.5.68/include/AladinContent.h b/brainles_preprocessing/registration/niftyreg/niftyreg_scripts/niftyreg_1.5.68/include/AladinContent.h similarity index 100% rename from brainles_preprocessing/registration/niftyreg_scripts/niftyreg_1.5.68/include/AladinContent.h rename to brainles_preprocessing/registration/niftyreg/niftyreg_scripts/niftyreg_1.5.68/include/AladinContent.h diff --git a/brainles_preprocessing/registration/niftyreg_scripts/niftyreg_1.5.68/include/BlockMatchingKernel.h b/brainles_preprocessing/registration/niftyreg/niftyreg_scripts/niftyreg_1.5.68/include/BlockMatchingKernel.h similarity index 100% rename from brainles_preprocessing/registration/niftyreg_scripts/niftyreg_1.5.68/include/BlockMatchingKernel.h rename to brainles_preprocessing/registration/niftyreg/niftyreg_scripts/niftyreg_1.5.68/include/BlockMatchingKernel.h diff --git a/brainles_preprocessing/registration/niftyreg_scripts/niftyreg_1.5.68/include/CPUAffineDeformationFieldKernel.h b/brainles_preprocessing/registration/niftyreg/niftyreg_scripts/niftyreg_1.5.68/include/CPUAffineDeformationFieldKernel.h similarity index 100% rename from brainles_preprocessing/registration/niftyreg_scripts/niftyreg_1.5.68/include/CPUAffineDeformationFieldKernel.h rename to brainles_preprocessing/registration/niftyreg/niftyreg_scripts/niftyreg_1.5.68/include/CPUAffineDeformationFieldKernel.h diff --git a/brainles_preprocessing/registration/niftyreg_scripts/niftyreg_1.5.68/include/CPUBlockMatchingKernel.h b/brainles_preprocessing/registration/niftyreg/niftyreg_scripts/niftyreg_1.5.68/include/CPUBlockMatchingKernel.h similarity index 100% rename from brainles_preprocessing/registration/niftyreg_scripts/niftyreg_1.5.68/include/CPUBlockMatchingKernel.h rename to brainles_preprocessing/registration/niftyreg/niftyreg_scripts/niftyreg_1.5.68/include/CPUBlockMatchingKernel.h diff --git a/brainles_preprocessing/registration/niftyreg_scripts/niftyreg_1.5.68/include/CPUConvolutionKernel.h b/brainles_preprocessing/registration/niftyreg/niftyreg_scripts/niftyreg_1.5.68/include/CPUConvolutionKernel.h similarity index 100% rename from brainles_preprocessing/registration/niftyreg_scripts/niftyreg_1.5.68/include/CPUConvolutionKernel.h rename to brainles_preprocessing/registration/niftyreg/niftyreg_scripts/niftyreg_1.5.68/include/CPUConvolutionKernel.h diff --git a/brainles_preprocessing/registration/niftyreg_scripts/niftyreg_1.5.68/include/CPUKernelFactory.h b/brainles_preprocessing/registration/niftyreg/niftyreg_scripts/niftyreg_1.5.68/include/CPUKernelFactory.h similarity index 100% rename from brainles_preprocessing/registration/niftyreg_scripts/niftyreg_1.5.68/include/CPUKernelFactory.h rename to brainles_preprocessing/registration/niftyreg/niftyreg_scripts/niftyreg_1.5.68/include/CPUKernelFactory.h diff --git a/brainles_preprocessing/registration/niftyreg_scripts/niftyreg_1.5.68/include/CPUOptimiseKernel.h b/brainles_preprocessing/registration/niftyreg/niftyreg_scripts/niftyreg_1.5.68/include/CPUOptimiseKernel.h similarity index 100% rename from brainles_preprocessing/registration/niftyreg_scripts/niftyreg_1.5.68/include/CPUOptimiseKernel.h rename to brainles_preprocessing/registration/niftyreg/niftyreg_scripts/niftyreg_1.5.68/include/CPUOptimiseKernel.h diff --git a/brainles_preprocessing/registration/niftyreg_scripts/niftyreg_1.5.68/include/CPUResampleImageKernel.h b/brainles_preprocessing/registration/niftyreg/niftyreg_scripts/niftyreg_1.5.68/include/CPUResampleImageKernel.h similarity index 100% rename from brainles_preprocessing/registration/niftyreg_scripts/niftyreg_1.5.68/include/CPUResampleImageKernel.h rename to brainles_preprocessing/registration/niftyreg/niftyreg_scripts/niftyreg_1.5.68/include/CPUResampleImageKernel.h diff --git a/brainles_preprocessing/registration/niftyreg_scripts/niftyreg_1.5.68/include/ConvolutionKernel.h b/brainles_preprocessing/registration/niftyreg/niftyreg_scripts/niftyreg_1.5.68/include/ConvolutionKernel.h similarity index 100% rename from brainles_preprocessing/registration/niftyreg_scripts/niftyreg_1.5.68/include/ConvolutionKernel.h rename to brainles_preprocessing/registration/niftyreg/niftyreg_scripts/niftyreg_1.5.68/include/ConvolutionKernel.h diff --git a/brainles_preprocessing/registration/niftyreg_scripts/niftyreg_1.5.68/include/Kernel.h b/brainles_preprocessing/registration/niftyreg/niftyreg_scripts/niftyreg_1.5.68/include/Kernel.h similarity index 100% rename from brainles_preprocessing/registration/niftyreg_scripts/niftyreg_1.5.68/include/Kernel.h rename to brainles_preprocessing/registration/niftyreg/niftyreg_scripts/niftyreg_1.5.68/include/Kernel.h diff --git a/brainles_preprocessing/registration/niftyreg_scripts/niftyreg_1.5.68/include/KernelFactory.h b/brainles_preprocessing/registration/niftyreg/niftyreg_scripts/niftyreg_1.5.68/include/KernelFactory.h similarity index 100% rename from brainles_preprocessing/registration/niftyreg_scripts/niftyreg_1.5.68/include/KernelFactory.h rename to brainles_preprocessing/registration/niftyreg/niftyreg_scripts/niftyreg_1.5.68/include/KernelFactory.h diff --git a/brainles_preprocessing/registration/niftyreg_scripts/niftyreg_1.5.68/include/OptimiseKernel.h b/brainles_preprocessing/registration/niftyreg/niftyreg_scripts/niftyreg_1.5.68/include/OptimiseKernel.h similarity index 100% rename from brainles_preprocessing/registration/niftyreg_scripts/niftyreg_1.5.68/include/OptimiseKernel.h rename to brainles_preprocessing/registration/niftyreg/niftyreg_scripts/niftyreg_1.5.68/include/OptimiseKernel.h diff --git a/brainles_preprocessing/registration/niftyreg_scripts/niftyreg_1.5.68/include/Platform.h b/brainles_preprocessing/registration/niftyreg/niftyreg_scripts/niftyreg_1.5.68/include/Platform.h similarity index 100% rename from brainles_preprocessing/registration/niftyreg_scripts/niftyreg_1.5.68/include/Platform.h rename to brainles_preprocessing/registration/niftyreg/niftyreg_scripts/niftyreg_1.5.68/include/Platform.h diff --git a/brainles_preprocessing/registration/niftyreg_scripts/niftyreg_1.5.68/include/ResampleImageKernel.h b/brainles_preprocessing/registration/niftyreg/niftyreg_scripts/niftyreg_1.5.68/include/ResampleImageKernel.h similarity index 100% rename from brainles_preprocessing/registration/niftyreg_scripts/niftyreg_1.5.68/include/ResampleImageKernel.h rename to brainles_preprocessing/registration/niftyreg/niftyreg_scripts/niftyreg_1.5.68/include/ResampleImageKernel.h diff --git a/brainles_preprocessing/registration/niftyreg_scripts/niftyreg_1.5.68/include/_reg_ReadWriteImage.h b/brainles_preprocessing/registration/niftyreg/niftyreg_scripts/niftyreg_1.5.68/include/_reg_ReadWriteImage.h similarity index 100% rename from brainles_preprocessing/registration/niftyreg_scripts/niftyreg_1.5.68/include/_reg_ReadWriteImage.h rename to brainles_preprocessing/registration/niftyreg/niftyreg_scripts/niftyreg_1.5.68/include/_reg_ReadWriteImage.h diff --git a/brainles_preprocessing/registration/niftyreg_scripts/niftyreg_1.5.68/include/_reg_ReadWriteMatrix.h b/brainles_preprocessing/registration/niftyreg/niftyreg_scripts/niftyreg_1.5.68/include/_reg_ReadWriteMatrix.h similarity index 100% rename from brainles_preprocessing/registration/niftyreg_scripts/niftyreg_1.5.68/include/_reg_ReadWriteMatrix.h rename to brainles_preprocessing/registration/niftyreg/niftyreg_scripts/niftyreg_1.5.68/include/_reg_ReadWriteMatrix.h diff --git a/brainles_preprocessing/registration/niftyreg_scripts/niftyreg_1.5.68/include/_reg_aladin.cpp b/brainles_preprocessing/registration/niftyreg/niftyreg_scripts/niftyreg_1.5.68/include/_reg_aladin.cpp similarity index 100% rename from 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rename to brainles_preprocessing/registration/niftyreg/niftyreg_scripts/niftyreg_1.5.68/include/_reg_aladin_sym.cpp diff --git a/brainles_preprocessing/registration/niftyreg_scripts/niftyreg_1.5.68/include/_reg_aladin_sym.h b/brainles_preprocessing/registration/niftyreg/niftyreg_scripts/niftyreg_1.5.68/include/_reg_aladin_sym.h similarity index 100% rename from brainles_preprocessing/registration/niftyreg_scripts/niftyreg_1.5.68/include/_reg_aladin_sym.h rename to brainles_preprocessing/registration/niftyreg/niftyreg_scripts/niftyreg_1.5.68/include/_reg_aladin_sym.h diff --git a/brainles_preprocessing/registration/niftyreg_scripts/niftyreg_1.5.68/include/_reg_base.h b/brainles_preprocessing/registration/niftyreg/niftyreg_scripts/niftyreg_1.5.68/include/_reg_base.h similarity index 100% rename from brainles_preprocessing/registration/niftyreg_scripts/niftyreg_1.5.68/include/_reg_base.h rename to 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--git a/brainles_preprocessing/registration/niftyreg_scripts/niftyreg_1.5.68/include/_reg_f3d.h b/brainles_preprocessing/registration/niftyreg/niftyreg_scripts/niftyreg_1.5.68/include/_reg_f3d.h similarity index 100% rename from brainles_preprocessing/registration/niftyreg_scripts/niftyreg_1.5.68/include/_reg_f3d.h rename to brainles_preprocessing/registration/niftyreg/niftyreg_scripts/niftyreg_1.5.68/include/_reg_f3d.h diff --git a/brainles_preprocessing/registration/niftyreg_scripts/niftyreg_1.5.68/include/_reg_f3d2.h b/brainles_preprocessing/registration/niftyreg/niftyreg_scripts/niftyreg_1.5.68/include/_reg_f3d2.h similarity index 100% rename from brainles_preprocessing/registration/niftyreg_scripts/niftyreg_1.5.68/include/_reg_f3d2.h rename to brainles_preprocessing/registration/niftyreg/niftyreg_scripts/niftyreg_1.5.68/include/_reg_f3d2.h diff --git a/brainles_preprocessing/registration/niftyreg_scripts/niftyreg_1.5.68/include/_reg_f3d_sym.h b/brainles_preprocessing/registration/niftyreg/niftyreg_scripts/niftyreg_1.5.68/include/_reg_f3d_sym.h similarity index 100% rename from brainles_preprocessing/registration/niftyreg_scripts/niftyreg_1.5.68/include/_reg_f3d_sym.h rename to brainles_preprocessing/registration/niftyreg/niftyreg_scripts/niftyreg_1.5.68/include/_reg_f3d_sym.h diff --git a/brainles_preprocessing/registration/niftyreg_scripts/niftyreg_1.5.68/include/_reg_femTrans.h b/brainles_preprocessing/registration/niftyreg/niftyreg_scripts/niftyreg_1.5.68/include/_reg_femTrans.h similarity index 100% rename from brainles_preprocessing/registration/niftyreg_scripts/niftyreg_1.5.68/include/_reg_femTrans.h rename to brainles_preprocessing/registration/niftyreg/niftyreg_scripts/niftyreg_1.5.68/include/_reg_femTrans.h diff --git a/brainles_preprocessing/registration/niftyreg_scripts/niftyreg_1.5.68/include/_reg_globalTrans.h 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a/brainles_preprocessing/registration/niftyreg_scripts/niftyreg_1.5.68/include/_reg_nmi.h b/brainles_preprocessing/registration/niftyreg/niftyreg_scripts/niftyreg_1.5.68/include/_reg_nmi.h similarity index 100% rename from brainles_preprocessing/registration/niftyreg_scripts/niftyreg_1.5.68/include/_reg_nmi.h rename to brainles_preprocessing/registration/niftyreg/niftyreg_scripts/niftyreg_1.5.68/include/_reg_nmi.h diff --git a/brainles_preprocessing/registration/niftyreg_scripts/niftyreg_1.5.68/include/_reg_optimiser.cpp b/brainles_preprocessing/registration/niftyreg/niftyreg_scripts/niftyreg_1.5.68/include/_reg_optimiser.cpp similarity index 100% rename from brainles_preprocessing/registration/niftyreg_scripts/niftyreg_1.5.68/include/_reg_optimiser.cpp rename to brainles_preprocessing/registration/niftyreg/niftyreg_scripts/niftyreg_1.5.68/include/_reg_optimiser.cpp diff --git a/brainles_preprocessing/registration/niftyreg_scripts/niftyreg_1.5.68/include/_reg_optimiser.h 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similarity index 100% rename from brainles_preprocessing/registration/niftyreg_scripts/niftyreg_1.5.68/include/_reg_stringFormat.h rename to brainles_preprocessing/registration/niftyreg/niftyreg_scripts/niftyreg_1.5.68/include/_reg_stringFormat.h diff --git a/brainles_preprocessing/registration/niftyreg_scripts/niftyreg_1.5.68/include/_reg_tools.h b/brainles_preprocessing/registration/niftyreg/niftyreg_scripts/niftyreg_1.5.68/include/_reg_tools.h similarity index 100% rename from brainles_preprocessing/registration/niftyreg_scripts/niftyreg_1.5.68/include/_reg_tools.h rename to brainles_preprocessing/registration/niftyreg/niftyreg_scripts/niftyreg_1.5.68/include/_reg_tools.h diff --git a/brainles_preprocessing/registration/niftyreg_scripts/niftyreg_1.5.68/include/nifti1.h b/brainles_preprocessing/registration/niftyreg/niftyreg_scripts/niftyreg_1.5.68/include/nifti1.h similarity index 100% rename from brainles_preprocessing/registration/niftyreg_scripts/niftyreg_1.5.68/include/nifti1.h rename to brainles_preprocessing/registration/niftyreg/niftyreg_scripts/niftyreg_1.5.68/include/nifti1.h diff --git a/brainles_preprocessing/registration/niftyreg_scripts/niftyreg_1.5.68/include/nifti1_io.h b/brainles_preprocessing/registration/niftyreg/niftyreg_scripts/niftyreg_1.5.68/include/nifti1_io.h similarity index 100% rename from brainles_preprocessing/registration/niftyreg_scripts/niftyreg_1.5.68/include/nifti1_io.h rename to brainles_preprocessing/registration/niftyreg/niftyreg_scripts/niftyreg_1.5.68/include/nifti1_io.h diff --git a/brainles_preprocessing/registration/niftyreg_scripts/niftyreg_1.5.68/include/png.h b/brainles_preprocessing/registration/niftyreg/niftyreg_scripts/niftyreg_1.5.68/include/png.h similarity index 100% rename from brainles_preprocessing/registration/niftyreg_scripts/niftyreg_1.5.68/include/png.h rename to brainles_preprocessing/registration/niftyreg/niftyreg_scripts/niftyreg_1.5.68/include/png.h diff --git a/brainles_preprocessing/registration/niftyreg_scripts/niftyreg_1.5.68/include/pngconf.h b/brainles_preprocessing/registration/niftyreg/niftyreg_scripts/niftyreg_1.5.68/include/pngconf.h similarity index 100% rename from brainles_preprocessing/registration/niftyreg_scripts/niftyreg_1.5.68/include/pngconf.h rename to brainles_preprocessing/registration/niftyreg/niftyreg_scripts/niftyreg_1.5.68/include/pngconf.h diff --git a/brainles_preprocessing/registration/niftyreg_scripts/niftyreg_1.5.68/include/pngdebug.h b/brainles_preprocessing/registration/niftyreg/niftyreg_scripts/niftyreg_1.5.68/include/pngdebug.h similarity index 100% rename from brainles_preprocessing/registration/niftyreg_scripts/niftyreg_1.5.68/include/pngdebug.h rename to brainles_preprocessing/registration/niftyreg/niftyreg_scripts/niftyreg_1.5.68/include/pngdebug.h diff --git a/brainles_preprocessing/registration/niftyreg_scripts/niftyreg_1.5.68/include/pnginfo.h b/brainles_preprocessing/registration/niftyreg/niftyreg_scripts/niftyreg_1.5.68/include/pnginfo.h similarity index 100% rename from brainles_preprocessing/registration/niftyreg_scripts/niftyreg_1.5.68/include/pnginfo.h rename to brainles_preprocessing/registration/niftyreg/niftyreg_scripts/niftyreg_1.5.68/include/pnginfo.h diff --git a/brainles_preprocessing/registration/niftyreg_scripts/niftyreg_1.5.68/include/pnglibconf.h b/brainles_preprocessing/registration/niftyreg/niftyreg_scripts/niftyreg_1.5.68/include/pnglibconf.h similarity index 100% rename from brainles_preprocessing/registration/niftyreg_scripts/niftyreg_1.5.68/include/pnglibconf.h rename to brainles_preprocessing/registration/niftyreg/niftyreg_scripts/niftyreg_1.5.68/include/pnglibconf.h diff --git a/brainles_preprocessing/registration/niftyreg_scripts/niftyreg_1.5.68/include/pngpriv.h b/brainles_preprocessing/registration/niftyreg/niftyreg_scripts/niftyreg_1.5.68/include/pngpriv.h similarity index 100% rename from brainles_preprocessing/registration/niftyreg_scripts/niftyreg_1.5.68/include/pngpriv.h rename to brainles_preprocessing/registration/niftyreg/niftyreg_scripts/niftyreg_1.5.68/include/pngpriv.h diff --git a/brainles_preprocessing/registration/niftyreg_scripts/niftyreg_1.5.68/include/pngstruct.h b/brainles_preprocessing/registration/niftyreg/niftyreg_scripts/niftyreg_1.5.68/include/pngstruct.h similarity index 100% rename from brainles_preprocessing/registration/niftyreg_scripts/niftyreg_1.5.68/include/pngstruct.h rename to brainles_preprocessing/registration/niftyreg/niftyreg_scripts/niftyreg_1.5.68/include/pngstruct.h diff --git a/brainles_preprocessing/registration/niftyreg_scripts/niftyreg_1.5.68/include/readpng.h b/brainles_preprocessing/registration/niftyreg/niftyreg_scripts/niftyreg_1.5.68/include/readpng.h similarity index 100% rename from brainles_preprocessing/registration/niftyreg_scripts/niftyreg_1.5.68/include/readpng.h rename to brainles_preprocessing/registration/niftyreg/niftyreg_scripts/niftyreg_1.5.68/include/readpng.h diff --git a/brainles_preprocessing/registration/niftyreg_scripts/niftyreg_1.5.68/include/reg_png.h b/brainles_preprocessing/registration/niftyreg/niftyreg_scripts/niftyreg_1.5.68/include/reg_png.h similarity index 100% rename from brainles_preprocessing/registration/niftyreg_scripts/niftyreg_1.5.68/include/reg_png.h rename to brainles_preprocessing/registration/niftyreg/niftyreg_scripts/niftyreg_1.5.68/include/reg_png.h diff --git a/brainles_preprocessing/registration/niftyreg_scripts/niftyreg_1.5.68/include/zlib.h b/brainles_preprocessing/registration/niftyreg/niftyreg_scripts/niftyreg_1.5.68/include/zlib.h similarity index 100% rename from brainles_preprocessing/registration/niftyreg_scripts/niftyreg_1.5.68/include/zlib.h rename to brainles_preprocessing/registration/niftyreg/niftyreg_scripts/niftyreg_1.5.68/include/zlib.h diff --git a/brainles_preprocessing/registration/niftyreg_scripts/niftyreg_1.5.68/include/znzlib.h b/brainles_preprocessing/registration/niftyreg/niftyreg_scripts/niftyreg_1.5.68/include/znzlib.h similarity index 100% rename from brainles_preprocessing/registration/niftyreg_scripts/niftyreg_1.5.68/include/znzlib.h rename to brainles_preprocessing/registration/niftyreg/niftyreg_scripts/niftyreg_1.5.68/include/znzlib.h diff --git a/brainles_preprocessing/registration/niftyreg_scripts/niftyreg_1.5.68/include/zutil.h b/brainles_preprocessing/registration/niftyreg/niftyreg_scripts/niftyreg_1.5.68/include/zutil.h similarity index 100% rename from brainles_preprocessing/registration/niftyreg_scripts/niftyreg_1.5.68/include/zutil.h rename to brainles_preprocessing/registration/niftyreg/niftyreg_scripts/niftyreg_1.5.68/include/zutil.h diff --git a/brainles_preprocessing/registration/niftyreg_scripts/reg_aladin b/brainles_preprocessing/registration/niftyreg/niftyreg_scripts/reg_aladin similarity index 100% rename from brainles_preprocessing/registration/niftyreg_scripts/reg_aladin rename to brainles_preprocessing/registration/niftyreg/niftyreg_scripts/reg_aladin diff --git a/brainles_preprocessing/registration/niftyreg_scripts/reg_resample b/brainles_preprocessing/registration/niftyreg/niftyreg_scripts/reg_resample similarity index 100% rename from brainles_preprocessing/registration/niftyreg_scripts/reg_resample rename to brainles_preprocessing/registration/niftyreg/niftyreg_scripts/reg_resample diff --git a/brainles_preprocessing/registration/niftyreg_scripts/rigid_reg.sh b/brainles_preprocessing/registration/niftyreg/niftyreg_scripts/rigid_reg.sh similarity index 100% rename from brainles_preprocessing/registration/niftyreg_scripts/rigid_reg.sh rename to brainles_preprocessing/registration/niftyreg/niftyreg_scripts/rigid_reg.sh diff --git a/brainles_preprocessing/registration/niftyreg_scripts/transform.sh b/brainles_preprocessing/registration/niftyreg/niftyreg_scripts/transform.sh similarity index 100% rename from brainles_preprocessing/registration/niftyreg_scripts/transform.sh rename to brainles_preprocessing/registration/niftyreg/niftyreg_scripts/transform.sh From 085313062b09060ad76212ae1d110ec64151b164 Mon Sep 17 00:00:00 2001 From: neuronflow Date: Wed, 13 Dec 2023 17:58:37 +0100 Subject: [PATCH 3/4] give it init Signed-off-by: neuronflow --- brainles_preprocessing/registration/niftyreg/__init__.py | 0 1 file changed, 0 insertions(+), 0 deletions(-) create mode 100644 brainles_preprocessing/registration/niftyreg/__init__.py diff --git a/brainles_preprocessing/registration/niftyreg/__init__.py b/brainles_preprocessing/registration/niftyreg/__init__.py new file mode 100644 index 0000000..e69de29 From 33f1ab5c82c498072d24494e3c8dda923c27c657 Mon Sep 17 00:00:00 2001 From: neuronflow Date: Wed, 13 Dec 2023 18:04:45 +0100 Subject: [PATCH 4/4] fix: registration call Signed-off-by: neuronflow --- brainles_preprocessing/modality.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/brainles_preprocessing/modality.py b/brainles_preprocessing/modality.py index 94bb669..042b009 100644 --- a/brainles_preprocessing/modality.py +++ b/brainles_preprocessing/modality.py @@ -119,7 +119,7 @@ def register( registrator.register( fixed_image_path=fixed_image_path, moving_image_path=self.current, - transformed_image=registered, + transformed_image_path=registered, matrix_path=registered_matrix, log_file_path=registered_log, )