Merge pull request #48 from BrainLesion/move_niftyreg

Move_niftyreg
BrainLesion · Dec 13, 2023 · d648008 · d648008
2 parents 23838ce + 33f1ab5
commit d648008
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Showing 80 changed files with 3 additions and 3 deletions.
diff --git 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,
         )

diff --git 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/__init__.py b/brainles_preprocessing/registration/niftyreg/__init__.py
diff --git a/...es_preprocessing/registration/niftyreg.py → ...cessing/registration/niftyreg/niftyreg.py b/...es_preprocessing/registration/niftyreg.py → ...cessing/registration/niftyreg/niftyreg.py
diff --git a/...g_1.5.68/bin/groupwise_niftyreg_params.sh → ...g_1.5.68/bin/groupwise_niftyreg_params.sh b/...g_1.5.68/bin/groupwise_niftyreg_params.sh → ...g_1.5.68/bin/groupwise_niftyreg_params.sh
diff --git a/...yreg_1.5.68/bin/groupwise_niftyreg_run.sh → ...yreg_1.5.68/bin/groupwise_niftyreg_run.sh b/...yreg_1.5.68/bin/groupwise_niftyreg_run.sh → ...yreg_1.5.68/bin/groupwise_niftyreg_run.sh
diff --git a/...eg_scripts/niftyreg_1.5.68/bin/reg_aladin → ...eg_scripts/niftyreg_1.5.68/bin/reg_aladin b/...eg_scripts/niftyreg_1.5.68/bin/reg_aladin → ...eg_scripts/niftyreg_1.5.68/bin/reg_aladin
diff --git a/...g_scripts/niftyreg_1.5.68/bin/reg_average → ...g_scripts/niftyreg_1.5.68/bin/reg_average b/...g_scripts/niftyreg_1.5.68/bin/reg_average → ...g_scripts/niftyreg_1.5.68/bin/reg_average
diff --git a/...tyreg_scripts/niftyreg_1.5.68/bin/reg_f3d → ...tyreg_scripts/niftyreg_1.5.68/bin/reg_f3d b/...tyreg_scripts/niftyreg_1.5.68/bin/reg_f3d → ...tyreg_scripts/niftyreg_1.5.68/bin/reg_f3d
diff --git a/..._scripts/niftyreg_1.5.68/bin/reg_jacobian → ..._scripts/niftyreg_1.5.68/bin/reg_jacobian b/..._scripts/niftyreg_1.5.68/bin/reg_jacobian → ..._scripts/niftyreg_1.5.68/bin/reg_jacobian
diff --git a/...g_scripts/niftyreg_1.5.68/bin/reg_measure → ...g_scripts/niftyreg_1.5.68/bin/reg_measure b/...g_scripts/niftyreg_1.5.68/bin/reg_measure → ...g_scripts/niftyreg_1.5.68/bin/reg_measure
diff --git a/..._scripts/niftyreg_1.5.68/bin/reg_resample → ..._scripts/niftyreg_1.5.68/bin/reg_resample b/..._scripts/niftyreg_1.5.68/bin/reg_resample → ..._scripts/niftyreg_1.5.68/bin/reg_resample
diff --git a/...reg_scripts/niftyreg_1.5.68/bin/reg_tools → ...reg_scripts/niftyreg_1.5.68/bin/reg_tools b/...reg_scripts/niftyreg_1.5.68/bin/reg_tools → ...reg_scripts/niftyreg_1.5.68/bin/reg_tools
diff --git a/...scripts/niftyreg_1.5.68/bin/reg_transform → ...scripts/niftyreg_1.5.68/bin/reg_transform b/...scripts/niftyreg_1.5.68/bin/reg_transform → ...scripts/niftyreg_1.5.68/bin/reg_transform
diff --git a/...68/include/AffineDeformationFieldKernel.h → ...68/include/AffineDeformationFieldKernel.h b/...68/include/AffineDeformationFieldKernel.h → ...68/include/AffineDeformationFieldKernel.h
diff --git a/...s/niftyreg_1.5.68/include/AladinContent.h → ...s/niftyreg_1.5.68/include/AladinContent.h b/...s/niftyreg_1.5.68/include/AladinContent.h → ...s/niftyreg_1.5.68/include/AladinContent.h
diff --git a/...yreg_1.5.68/include/BlockMatchingKernel.h → ...yreg_1.5.68/include/BlockMatchingKernel.h b/...yreg_1.5.68/include/BlockMatchingKernel.h → ...yreg_1.5.68/include/BlockMatchingKernel.h
diff --git a/...include/CPUAffineDeformationFieldKernel.h → ...include/CPUAffineDeformationFieldKernel.h b/...include/CPUAffineDeformationFieldKernel.h → ...include/CPUAffineDeformationFieldKernel.h
diff --git a/...g_1.5.68/include/CPUBlockMatchingKernel.h → ...g_1.5.68/include/CPUBlockMatchingKernel.h b/...g_1.5.68/include/CPUBlockMatchingKernel.h → ...g_1.5.68/include/CPUBlockMatchingKernel.h
diff --git a/...reg_1.5.68/include/CPUConvolutionKernel.h → ...reg_1.5.68/include/CPUConvolutionKernel.h b/...reg_1.5.68/include/CPUConvolutionKernel.h → ...reg_1.5.68/include/CPUConvolutionKernel.h
diff --git a/...iftyreg_1.5.68/include/CPUKernelFactory.h → ...iftyreg_1.5.68/include/CPUKernelFactory.h b/...iftyreg_1.5.68/include/CPUKernelFactory.h → ...iftyreg_1.5.68/include/CPUKernelFactory.h
diff --git a/...ftyreg_1.5.68/include/CPUOptimiseKernel.h → ...ftyreg_1.5.68/include/CPUOptimiseKernel.h b/...ftyreg_1.5.68/include/CPUOptimiseKernel.h → ...ftyreg_1.5.68/include/CPUOptimiseKernel.h
diff --git a/...g_1.5.68/include/CPUResampleImageKernel.h → ...g_1.5.68/include/CPUResampleImageKernel.h b/...g_1.5.68/include/CPUResampleImageKernel.h → ...g_1.5.68/include/CPUResampleImageKernel.h
diff --git a/...ftyreg_1.5.68/include/ConvolutionKernel.h → ...ftyreg_1.5.68/include/ConvolutionKernel.h b/...ftyreg_1.5.68/include/ConvolutionKernel.h → ...ftyreg_1.5.68/include/ConvolutionKernel.h
diff --git a/..._scripts/niftyreg_1.5.68/include/Kernel.h → ..._scripts/niftyreg_1.5.68/include/Kernel.h b/..._scripts/niftyreg_1.5.68/include/Kernel.h → ..._scripts/niftyreg_1.5.68/include/Kernel.h
diff --git a/...s/niftyreg_1.5.68/include/KernelFactory.h → ...s/niftyreg_1.5.68/include/KernelFactory.h b/...s/niftyreg_1.5.68/include/KernelFactory.h → ...s/niftyreg_1.5.68/include/KernelFactory.h
diff --git a/.../niftyreg_1.5.68/include/OptimiseKernel.h → .../niftyreg_1.5.68/include/OptimiseKernel.h b/.../niftyreg_1.5.68/include/OptimiseKernel.h → .../niftyreg_1.5.68/include/OptimiseKernel.h
diff --git a/...cripts/niftyreg_1.5.68/include/Platform.h → ...cripts/niftyreg_1.5.68/include/Platform.h b/...cripts/niftyreg_1.5.68/include/Platform.h → ...cripts/niftyreg_1.5.68/include/Platform.h
diff --git a/...yreg_1.5.68/include/ResampleImageKernel.h → ...yreg_1.5.68/include/ResampleImageKernel.h b/...yreg_1.5.68/include/ResampleImageKernel.h → ...yreg_1.5.68/include/ResampleImageKernel.h
diff --git a/...yreg_1.5.68/include/_reg_ReadWriteImage.h → ...yreg_1.5.68/include/_reg_ReadWriteImage.h b/...yreg_1.5.68/include/_reg_ReadWriteImage.h → ...yreg_1.5.68/include/_reg_ReadWriteImage.h
diff --git a/...reg_1.5.68/include/_reg_ReadWriteMatrix.h → ...reg_1.5.68/include/_reg_ReadWriteMatrix.h b/...reg_1.5.68/include/_reg_ReadWriteMatrix.h → ...reg_1.5.68/include/_reg_ReadWriteMatrix.h
diff --git a/...s/niftyreg_1.5.68/include/_reg_aladin.cpp → ...s/niftyreg_1.5.68/include/_reg_aladin.cpp b/...s/niftyreg_1.5.68/include/_reg_aladin.cpp → ...s/niftyreg_1.5.68/include/_reg_aladin.cpp
diff --git a/...pts/niftyreg_1.5.68/include/_reg_aladin.h → ...pts/niftyreg_1.5.68/include/_reg_aladin.h b/...pts/niftyreg_1.5.68/include/_reg_aladin.h → ...pts/niftyreg_1.5.68/include/_reg_aladin.h
diff --git a/...ftyreg_1.5.68/include/_reg_aladin_sym.cpp → ...ftyreg_1.5.68/include/_reg_aladin_sym.cpp b/...ftyreg_1.5.68/include/_reg_aladin_sym.cpp → ...ftyreg_1.5.68/include/_reg_aladin_sym.cpp
diff --git a/...niftyreg_1.5.68/include/_reg_aladin_sym.h → ...niftyreg_1.5.68/include/_reg_aladin_sym.h b/...niftyreg_1.5.68/include/_reg_aladin_sym.h → ...niftyreg_1.5.68/include/_reg_aladin_sym.h
diff --git a/...ripts/niftyreg_1.5.68/include/_reg_base.h → ...ripts/niftyreg_1.5.68/include/_reg_base.h b/...ripts/niftyreg_1.5.68/include/_reg_base.h → ...ripts/niftyreg_1.5.68/include/_reg_base.h
diff --git a/...tyreg_1.5.68/include/_reg_blockMatching.h → ...tyreg_1.5.68/include/_reg_blockMatching.h b/...tyreg_1.5.68/include/_reg_blockMatching.h → ...tyreg_1.5.68/include/_reg_blockMatching.h
diff --git a/...cripts/niftyreg_1.5.68/include/_reg_dti.h → ...cripts/niftyreg_1.5.68/include/_reg_dti.h b/...cripts/niftyreg_1.5.68/include/_reg_dti.h → ...cripts/niftyreg_1.5.68/include/_reg_dti.h
diff --git a/...cripts/niftyreg_1.5.68/include/_reg_f3d.h → ...cripts/niftyreg_1.5.68/include/_reg_f3d.h b/...cripts/niftyreg_1.5.68/include/_reg_f3d.h → ...cripts/niftyreg_1.5.68/include/_reg_f3d.h
diff --git a/...ripts/niftyreg_1.5.68/include/_reg_f3d2.h → ...ripts/niftyreg_1.5.68/include/_reg_f3d2.h b/...ripts/niftyreg_1.5.68/include/_reg_f3d2.h → ...ripts/niftyreg_1.5.68/include/_reg_f3d2.h
diff --git a/...ts/niftyreg_1.5.68/include/_reg_f3d_sym.h → ...ts/niftyreg_1.5.68/include/_reg_f3d_sym.h b/...ts/niftyreg_1.5.68/include/_reg_f3d_sym.h → ...ts/niftyreg_1.5.68/include/_reg_f3d_sym.h
diff --git a/...s/niftyreg_1.5.68/include/_reg_femTrans.h → ...s/niftyreg_1.5.68/include/_reg_femTrans.h b/...s/niftyreg_1.5.68/include/_reg_femTrans.h → ...s/niftyreg_1.5.68/include/_reg_femTrans.h
diff --git a/...iftyreg_1.5.68/include/_reg_globalTrans.h → ...iftyreg_1.5.68/include/_reg_globalTrans.h b/...iftyreg_1.5.68/include/_reg_globalTrans.h → ...iftyreg_1.5.68/include/_reg_globalTrans.h
diff --git a/...cripts/niftyreg_1.5.68/include/_reg_kld.h → ...cripts/niftyreg_1.5.68/include/_reg_kld.h b/...cripts/niftyreg_1.5.68/include/_reg_kld.h → ...cripts/niftyreg_1.5.68/include/_reg_kld.h
diff --git a/...ripts/niftyreg_1.5.68/include/_reg_lncc.h → ...ripts/niftyreg_1.5.68/include/_reg_lncc.h b/...ripts/niftyreg_1.5.68/include/_reg_lncc.h → ...ripts/niftyreg_1.5.68/include/_reg_lncc.h
diff --git a/...niftyreg_1.5.68/include/_reg_localTrans.h → ...niftyreg_1.5.68/include/_reg_localTrans.h b/...niftyreg_1.5.68/include/_reg_localTrans.h → ...niftyreg_1.5.68/include/_reg_localTrans.h
diff --git a/...yreg_1.5.68/include/_reg_localTrans_jac.h → ...yreg_1.5.68/include/_reg_localTrans_jac.h b/...yreg_1.5.68/include/_reg_localTrans_jac.h → ...yreg_1.5.68/include/_reg_localTrans_jac.h
diff --git a/...eg_1.5.68/include/_reg_localTrans_regul.h → ...eg_1.5.68/include/_reg_localTrans_regul.h b/...eg_1.5.68/include/_reg_localTrans_regul.h → ...eg_1.5.68/include/_reg_localTrans_regul.h
diff --git a/...pts/niftyreg_1.5.68/include/_reg_macros.h → ...pts/niftyreg_1.5.68/include/_reg_macros.h b/...pts/niftyreg_1.5.68/include/_reg_macros.h → ...pts/niftyreg_1.5.68/include/_reg_macros.h
diff --git a/...ipts/niftyreg_1.5.68/include/_reg_maths.h → ...ipts/niftyreg_1.5.68/include/_reg_maths.h b/...ipts/niftyreg_1.5.68/include/_reg_maths.h → ...ipts/niftyreg_1.5.68/include/_reg_maths.h
diff --git a/...iftyreg_1.5.68/include/_reg_maths_eigen.h → ...iftyreg_1.5.68/include/_reg_maths_eigen.h b/...iftyreg_1.5.68/include/_reg_maths_eigen.h → ...iftyreg_1.5.68/include/_reg_maths_eigen.h
diff --git a/...ts/niftyreg_1.5.68/include/_reg_measure.h → ...ts/niftyreg_1.5.68/include/_reg_measure.h b/...ts/niftyreg_1.5.68/include/_reg_measure.h → ...ts/niftyreg_1.5.68/include/_reg_measure.h
diff --git a/...ripts/niftyreg_1.5.68/include/_reg_mind.h → ...ripts/niftyreg_1.5.68/include/_reg_mind.h b/...ripts/niftyreg_1.5.68/include/_reg_mind.h → ...ripts/niftyreg_1.5.68/include/_reg_mind.h
diff --git a/...cripts/niftyreg_1.5.68/include/_reg_nmi.h → ...cripts/niftyreg_1.5.68/include/_reg_nmi.h b/...cripts/niftyreg_1.5.68/include/_reg_nmi.h → ...cripts/niftyreg_1.5.68/include/_reg_nmi.h
diff --git a/...iftyreg_1.5.68/include/_reg_optimiser.cpp → ...iftyreg_1.5.68/include/_reg_optimiser.cpp b/...iftyreg_1.5.68/include/_reg_optimiser.cpp → ...iftyreg_1.5.68/include/_reg_optimiser.cpp
diff --git a/.../niftyreg_1.5.68/include/_reg_optimiser.h → .../niftyreg_1.5.68/include/_reg_optimiser.h b/.../niftyreg_1.5.68/include/_reg_optimiser.h → .../niftyreg_1.5.68/include/_reg_optimiser.h
diff --git a/...niftyreg_1.5.68/include/_reg_resampling.h → ...niftyreg_1.5.68/include/_reg_resampling.h b/...niftyreg_1.5.68/include/_reg_resampling.h → ...niftyreg_1.5.68/include/_reg_resampling.h
diff --git a/...iftyreg_1.5.68/include/_reg_splineBasis.h → ...iftyreg_1.5.68/include/_reg_splineBasis.h b/...iftyreg_1.5.68/include/_reg_splineBasis.h → ...iftyreg_1.5.68/include/_reg_splineBasis.h
diff --git a/...cripts/niftyreg_1.5.68/include/_reg_ssd.h → ...cripts/niftyreg_1.5.68/include/_reg_ssd.h b/...cripts/niftyreg_1.5.68/include/_reg_ssd.h → ...cripts/niftyreg_1.5.68/include/_reg_ssd.h
diff --git a/...ftyreg_1.5.68/include/_reg_stringFormat.h → ...ftyreg_1.5.68/include/_reg_stringFormat.h b/...ftyreg_1.5.68/include/_reg_stringFormat.h → ...ftyreg_1.5.68/include/_reg_stringFormat.h
diff --git a/...ipts/niftyreg_1.5.68/include/_reg_tools.h → ...ipts/niftyreg_1.5.68/include/_reg_tools.h b/...ipts/niftyreg_1.5.68/include/_reg_tools.h → ...ipts/niftyreg_1.5.68/include/_reg_tools.h
diff --git a/..._scripts/niftyreg_1.5.68/include/nifti1.h → ..._scripts/niftyreg_1.5.68/include/nifti1.h b/..._scripts/niftyreg_1.5.68/include/nifti1.h → ..._scripts/niftyreg_1.5.68/include/nifti1.h
diff --git a/...ripts/niftyreg_1.5.68/include/nifti1_io.h → ...ripts/niftyreg_1.5.68/include/nifti1_io.h b/...ripts/niftyreg_1.5.68/include/nifti1_io.h → ...ripts/niftyreg_1.5.68/include/nifti1_io.h
diff --git a/...reg_scripts/niftyreg_1.5.68/include/png.h → ...reg_scripts/niftyreg_1.5.68/include/png.h b/...reg_scripts/niftyreg_1.5.68/include/png.h → ...reg_scripts/niftyreg_1.5.68/include/png.h
diff --git a/...scripts/niftyreg_1.5.68/include/pngconf.h → ...scripts/niftyreg_1.5.68/include/pngconf.h b/...scripts/niftyreg_1.5.68/include/pngconf.h → ...scripts/niftyreg_1.5.68/include/pngconf.h
diff --git a/...cripts/niftyreg_1.5.68/include/pngdebug.h → ...cripts/niftyreg_1.5.68/include/pngdebug.h b/...cripts/niftyreg_1.5.68/include/pngdebug.h → ...cripts/niftyreg_1.5.68/include/pngdebug.h
diff --git a/...scripts/niftyreg_1.5.68/include/pnginfo.h → ...scripts/niftyreg_1.5.68/include/pnginfo.h b/...scripts/niftyreg_1.5.68/include/pnginfo.h → ...scripts/niftyreg_1.5.68/include/pnginfo.h
diff --git a/...ipts/niftyreg_1.5.68/include/pnglibconf.h → ...ipts/niftyreg_1.5.68/include/pnglibconf.h b/...ipts/niftyreg_1.5.68/include/pnglibconf.h → ...ipts/niftyreg_1.5.68/include/pnglibconf.h
diff --git a/...scripts/niftyreg_1.5.68/include/pngpriv.h → ...scripts/niftyreg_1.5.68/include/pngpriv.h b/...scripts/niftyreg_1.5.68/include/pngpriv.h → ...scripts/niftyreg_1.5.68/include/pngpriv.h
diff --git a/...ripts/niftyreg_1.5.68/include/pngstruct.h → ...ripts/niftyreg_1.5.68/include/pngstruct.h b/...ripts/niftyreg_1.5.68/include/pngstruct.h → ...ripts/niftyreg_1.5.68/include/pngstruct.h
diff --git a/...scripts/niftyreg_1.5.68/include/readpng.h → ...scripts/niftyreg_1.5.68/include/readpng.h b/...scripts/niftyreg_1.5.68/include/readpng.h → ...scripts/niftyreg_1.5.68/include/readpng.h
diff --git a/...scripts/niftyreg_1.5.68/include/reg_png.h → ...scripts/niftyreg_1.5.68/include/reg_png.h b/...scripts/niftyreg_1.5.68/include/reg_png.h → ...scripts/niftyreg_1.5.68/include/reg_png.h
diff --git a/...eg_scripts/niftyreg_1.5.68/include/zlib.h → ...eg_scripts/niftyreg_1.5.68/include/zlib.h b/...eg_scripts/niftyreg_1.5.68/include/zlib.h → ...eg_scripts/niftyreg_1.5.68/include/zlib.h
diff --git a/..._scripts/niftyreg_1.5.68/include/znzlib.h → ..._scripts/niftyreg_1.5.68/include/znzlib.h b/..._scripts/niftyreg_1.5.68/include/znzlib.h → ..._scripts/niftyreg_1.5.68/include/znzlib.h
diff --git a/...g_scripts/niftyreg_1.5.68/include/zutil.h → ...g_scripts/niftyreg_1.5.68/include/zutil.h b/...g_scripts/niftyreg_1.5.68/include/zutil.h → ...g_scripts/niftyreg_1.5.68/include/zutil.h
diff --git a/.../registration/niftyreg_scripts/reg_aladin → ...tion/niftyreg/niftyreg_scripts/reg_aladin b/.../registration/niftyreg_scripts/reg_aladin → ...tion/niftyreg/niftyreg_scripts/reg_aladin
diff --git a/...egistration/niftyreg_scripts/reg_resample → ...on/niftyreg/niftyreg_scripts/reg_resample b/...egistration/niftyreg_scripts/reg_resample → ...on/niftyreg/niftyreg_scripts/reg_resample
diff --git a/...egistration/niftyreg_scripts/rigid_reg.sh → ...on/niftyreg/niftyreg_scripts/rigid_reg.sh b/...egistration/niftyreg_scripts/rigid_reg.sh → ...on/niftyreg/niftyreg_scripts/rigid_reg.sh
diff --git a/...egistration/niftyreg_scripts/transform.sh → ...on/niftyreg/niftyreg_scripts/transform.sh b/...egistration/niftyreg_scripts/transform.sh → ...on/niftyreg/niftyreg_scripts/transform.sh
diff --git 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):
Original file line number	Diff line number	Diff line change
		@@ -1 +1 @@
		from .niftyreg import NiftyRegRegistrator
		from .niftyreg.niftyreg import NiftyRegRegistrator