ENH: move c++ wrapping from pybind11 to nanobind

.github/workflows/ci-pytest.yml

@@ -11,93 +11,51 @@ on:
 
 env:
   # Updates or changes to this, or the runner OS or arch will invalidate the cache
-  python_version: '3.10' # Python version to use for testing - update when needed
+  python_version: "3.10" # Python version to use for testing - update when needed
 
 jobs:
   test:
     runs-on: ubuntu-20.04
     # Default shell needs to be bash for conda
     # https://github.com/conda-incubator/setup-miniconda?tab=readme-ov-file#important
     defaults:
-        run:
-          shell: bash -el {0}
+      run:
+        shell: bash -el {0}
     steps:
-    - name: Setup Miniconda
-      uses: conda-incubator/setup-miniconda@030178870c779d9e5e1b4e563269f3aa69b04081 # v3.0.3, devs recommend using hash
-      with:
-        miniconda-version: "latest"
-        python-version: ${{ env.python_version }}
-        auto-update-conda: true
-        activate-environment: "test-env"
-
-    - name: Configure Conda to use only .tar.bz2
-      run: |
-        conda config --set use_only_tar_bz2 true
-
-    - name: Checkout code
-      uses: actions/checkout@v4 # Checkout PR code to 'antspy-pr'
-      with:
-        path: antspy-pr
-
-    - name: Load conda environment from cache if available
-      id: cache-env
-      uses: actions/cache@v4
-      with:
-        path: ~/conda-env.tar.bz2
-        key: >-
-            ${{ runner.os }}-conda-${{ env.python_version }}-${{ hashFiles('antspy-pr/ants/environment.yml',
-            'antspy-pr/ants/requirements.txt', 'antspy-pr/ants/setup.py', 'antspy-pr/scripts/configure_ITK.sh',
-            'antspy-pr/scripts/configure_ANTsPy.sh', 'antspy-pr/ants/lib/*') }}
-
-    - name: Unpack cached environment
-      if: steps.cache-env.outputs.cache-hit == 'true'
-      run: |
-        mkdir -p ${CONDA}/envs/antspy-env
-        tar -xjf ~/conda-env.tar.bz2 -C ${CONDA}/envs/antspy-env
-        conda activate antspy-env
-        conda-unpack
-
-    - name: Install dependencies and ANTsPy from PR
-      if: steps.cache-env.outputs.cache-hit != 'true'
-      run: |
-        conda create -n antspy-env python=${{ env.python_version }} -y
-        conda activate antspy-env
-        conda install -c conda-forge conda-pack coverage
-        conda info
-        pip install ./antspy-pr
-        conda list
-        antspy-pr/tests/run_tests.sh -c
-        conda pack -n antspy-env -o ~/conda-env.tar.bz2
-
-    - name: Cache Conda environment
-      if: steps.cache-env.outputs.cache-hit != 'true'
-      uses: actions/cache@v4
-      with:
-        path: ~/conda-env.tar.bz2
-        key: >-
-            ${{ runner.os }}-conda-${{ env.python_version }}-${{ hashFiles('antspy-pr/ants/environment.yml',
-            'antspy-pr/ants/requirements.txt', 'antspy-pr/ants/setup.py', 'antspy-pr/scripts/configure_ITK.sh',
-            'antspy-pr/scripts/configure_ANTsPy.sh', 'antspy-pr/ants/lib/*') }}) }}
-
-    - name: Replace installed ANTsPy with PR code
-      if: steps.cache-env.outputs.cache-hit == 'true'
-      run: |
-        conda activate antspy-env
-        ANTS_SITE_PACKAGES="${CONDA}/envs/antspy-env/lib/python${{ env.python_version }}/site-packages/ants"
-        for d in contrib core learn registration segmentation utils viz; do
-          rm -rf $ANTS_SITE_PACKAGES/$d;
-          cp -r antspy-pr/ants/$d $ANTS_SITE_PACKAGES/$d;
-          done
-        find $ANTS_SITE_PACKAGES -name '__pycache__' -exec rm -rf {} +
-
-    - name: Run tests
-      if: steps.cache-env.outputs.cache-hit == 'true'
-      run: |
-        conda activate antspy-env
-        bash antspy-pr/tests/run_tests.sh -c
-
-    - name: Coveralls
-      uses: coverallsapp/github-action@v2
-      with:
-        files: antspy-pr/tests/coverage.xml
-
+      - name: Setup Miniconda
+        uses: conda-incubator/setup-miniconda@030178870c779d9e5e1b4e563269f3aa69b04081 # v3.0.3, devs recommend using hash
+        with:
+          miniconda-version: "latest"
+          python-version: ${{ env.python_version }}
+          auto-update-conda: true
+          activate-environment: "test-env"
+
+      - name: Configure Conda to use only .tar.bz2
+        run: |
+          conda config --set use_only_tar_bz2 true
+
+      - name: Checkout code
+        uses: actions/checkout@v4 # Checkout PR code to 'antspy-pr'
+        with:
+          path: antspy-pr
+
+      - name: Install dependencies and ANTsPy from PR
+        run: |
+          conda create -n antspy-env python=${{ env.python_version }} -y
+          conda activate antspy-env
+          conda install -c conda-forge conda-pack coverage
+          conda info
+          pip install ./antspy-pr
+          conda list
+          antspy-pr/tests/run_tests.sh -c
+          conda pack -n antspy-env -o ~/conda-env.tar.bz2
+
+      - name: Run tests
+        run: |
+          conda activate antspy-env
+          bash antspy-pr/tests/run_tests.sh -c
+
+      - name: Coveralls
+        uses: coverallsapp/github-action@v2
+        with:
+          files: antspy-pr/tests/coverage.xml

.vscode/settings.json

@@ -0,0 +1,90 @@
+{
+  "files.associations": {
+    "iosfwd": "cpp",
+    "__bit_reference": "cpp",
+    "__bits": "cpp",
+    "__config": "cpp",
+    "__debug": "cpp",
+    "__errc": "cpp",
+    "__functional_base": "cpp",
+    "__hash_table": "cpp",
+    "__locale": "cpp",
+    "__mutex_base": "cpp",
+    "__node_handle": "cpp",
+    "__nullptr": "cpp",
+    "__split_buffer": "cpp",
+    "__string": "cpp",
+    "__threading_support": "cpp",
+    "__tuple": "cpp",
+    "algorithm": "cpp",
+    "array": "cpp",
+    "atomic": "cpp",
+    "bit": "cpp",
+    "bitset": "cpp",
+    "cctype": "cpp",
+    "chrono": "cpp",
+    "clocale": "cpp",
+    "cmath": "cpp",
+    "complex": "cpp",
+    "cstdarg": "cpp",
+    "cstddef": "cpp",
+    "cstdint": "cpp",
+    "cstdio": "cpp",
+    "cstdlib": "cpp",
+    "cstring": "cpp",
+    "ctime": "cpp",
+    "cwchar": "cpp",
+    "cwctype": "cpp",
+    "deque": "cpp",
+    "exception": "cpp",
+    "fstream": "cpp",
+    "functional": "cpp",
+    "initializer_list": "cpp",
+    "iomanip": "cpp",
+    "ios": "cpp",
+    "iostream": "cpp",
+    "istream": "cpp",
+    "iterator": "cpp",
+    "limits": "cpp",
+    "locale": "cpp",
+    "memory": "cpp",
+    "mutex": "cpp",
+    "new": "cpp",
+    "optional": "cpp",
+    "ostream": "cpp",
+    "ratio": "cpp",
+    "sstream": "cpp",
+    "stack": "cpp",
+    "stdexcept": "cpp",
+    "streambuf": "cpp",
+    "string": "cpp",
+    "string_view": "cpp",
+    "system_error": "cpp",
+    "tuple": "cpp",
+    "type_traits": "cpp",
+    "typeinfo": "cpp",
+    "unordered_map": "cpp",
+    "utility": "cpp",
+    "vector": "cpp",
+    "random": "cpp",
+    "__tree": "cpp",
+    "any": "cpp",
+    "cfenv": "cpp",
+    "condition_variable": "cpp",
+    "csetjmp": "cpp",
+    "csignal": "cpp",
+    "future": "cpp",
+    "list": "cpp",
+    "map": "cpp",
+    "numeric": "cpp",
+    "queue": "cpp",
+    "regex": "cpp",
+    "set": "cpp",
+    "unordered_set": "cpp",
+    "valarray": "cpp",
+    "variant": "cpp",
+    "*.in": "cpp",
+    "*.inc": "cpp",
+    "*.tmpl": "cpp"
+  }
+}

CMakeLists.txt

@@ -0,0 +1,69 @@
+cmake_minimum_required(VERSION 3.16.3...3.26)
+
+project(ants LANGUAGES CXX)
+
+set(CMAKE_POSITION_INDEPENDENT_CODE ON)
+
+# Try to import all Python components potentially needed by nanobind
+find_package(Python 3.8
+  REQUIRED COMPONENTS Interpreter Development.Module
+  OPTIONAL_COMPONENTS Development.SABIModule)
+
+# Import nanobind through CMake's find_package mechanism
+find_package(nanobind CONFIG REQUIRED)
+
+# TODO: make this run only if ITK + ANTs are not already built (for now: comment these 2 lines out to quickly rebuild antspy)
+# TODO: handle different OS either here or within the configure script
+# TODO: move this outside of CMakeLists.txt like in the old antspy (issue: how to run scripts from pyproject.toml?)
+execute_process(COMMAND bash ${PROJECT_SOURCE_DIR}/scripts/configure_ITK.sh)
+execute_process(COMMAND bash ${PROJECT_SOURCE_DIR}/scripts/configure_ANTs.sh)
+
+# ITK
+set(ITK_DIR "./itkbuild")
+find_package(ITK REQUIRED)
+include(${ITK_USE_FILE})
+
+# ANTS
+add_library(antsUtilities STATIC src/antscore/antsUtilities.cxx src/antscore/antsCommandLineOption.cxx src/antscore/antsCommandLineParser.cxx src/antscore/ReadWriteData.cxx src/antscore/ANTsVersion.cxx)
+add_library(registrationUtilities STATIC  src/antscore/antsRegistrationTemplateHeader.cxx
+                                          src/antscore/antsRegistration2DDouble.cxx src/antscore/antsRegistration2DFloat.cxx
+                                          src/antscore/antsRegistration3DDouble.cxx src/antscore/antsRegistration3DFloat.cxx
+                                          src/antscore/antsRegistration4DDouble.cxx src/antscore/antsRegistration4DFloat.cxx)
+
+
+add_library(imageMathUtilities STATIC  src/antscore/ImageMathHelper2D.cxx src/antscore/ImageMathHelper3D.cxx src/antscore/ImageMathHelper4D.cxx)
+
+# this may not be needed
+target_link_libraries(antsUtilities ${ITK_LIBRARIES})
+target_link_libraries(registrationUtilities ${ITK_LIBRARIES})
+target_link_libraries(imageMathUtilities ${ITK_LIBRARIES})
+
+nanobind_add_module(
+  lib
+  STABLE_ABI
+  NB_STATIC
+  src/main.cpp
+  src/antscore/antsAffineInitializer.cxx
+  src/antscore/antsApplyTransforms.cxx
+  src/antscore/antsApplyTransformsToPoints.cxx
+  src/antscore/antsJointFusion.cxx
+  src/antscore/antsRegistration.cxx
+  src/antscore/Atropos.cxx
+  src/antscore/AverageAffineTransform.cxx
+  src/antscore/AverageAffineTransformNoRigid.cxx
+  src/antscore/CreateJacobianDeterminantImage.cxx
+  src/antscore/DenoiseImage.cxx
+  src/antscore/iMath.cxx
+  src/antscore/KellyKapowski.cxx
+  src/antscore/LabelClustersUniquely.cxx
+  src/antscore/LabelGeometryMeasures.cxx
+  src/antscore/N3BiasFieldCorrection.cxx
+  src/antscore/N4BiasFieldCorrection.cxx
+  src/antscore/ResampleImage.cxx
+  src/antscore/ThresholdImage.cxx
+  src/antscore/TileImages.cxx
+)
+target_link_libraries(lib PRIVATE ${ITK_LIBRARIES} antsUtilities registrationUtilities imageMathUtilities)
+
+# Install directive for scikit-build-core
+install(TARGETS lib LIBRARY DESTINATION ants)

ants/__init__.py

@@ -1,5 +1,5 @@
 
-__version__ = '0.5.2'
+__version__ = '0.6.0'
 
 from .core import *
 from .utils import *

ants/core/ants_image.py

@@ -80,7 +80,7 @@ def __init__(self, pixeltype='float', dimension=3, components=1, pointer=None, i
 
         self._libsuffix = '%s%s%i' % (self._shortpclass, utils.short_ptype(self.pixeltype), self.dimension)
 
-        self.shape = utils.get_lib_fn('getShape%s'%self._libsuffix)(self.pointer)
+        self.shape = tuple(utils.get_lib_fn('getShape')(self.pointer))
         self.physical_shape = tuple([round(sh*sp,3) for sh,sp in zip(self.shape, self.spacing)])
 
         self._array = None
@@ -94,8 +94,8 @@ def spacing(self):
         -------
         tuple
         """
-        libfn = utils.get_lib_fn('getSpacing%s'%self._libsuffix)
-        return libfn(self.pointer)
+        libfn = utils.get_lib_fn('getSpacing')
+        return tuple(libfn(self.pointer))
 
     def set_spacing(self, new_spacing):
         """
@@ -116,7 +116,7 @@ def set_spacing(self, new_spacing):
         if len(new_spacing) != self.dimension:
             raise ValueError('must give a spacing value for each dimension (%i)' % self.dimension)
 
-        libfn = utils.get_lib_fn('setSpacing%s'%self._libsuffix)
+        libfn = utils.get_lib_fn('setSpacing')
         libfn(self.pointer, new_spacing)
 
     @property
@@ -128,8 +128,8 @@ def origin(self):
         -------
         tuple
         """
-        libfn = utils.get_lib_fn('getOrigin%s'%self._libsuffix)
-        return libfn(self.pointer)
+        libfn = utils.get_lib_fn('getOrigin')
+        return tuple(libfn(self.pointer))
 
     def set_origin(self, new_origin):
         """
@@ -150,7 +150,7 @@ def set_origin(self, new_origin):
         if len(new_origin) != self.dimension:
             raise ValueError('must give a origin value for each dimension (%i)' % self.dimension)
 
-        libfn = utils.get_lib_fn('setOrigin%s'%self._libsuffix)
+        libfn = utils.get_lib_fn('setOrigin')
         libfn(self.pointer, new_origin)
 
     @property
@@ -162,8 +162,8 @@ def direction(self):
         -------
         tuple
         """
-        libfn = utils.get_lib_fn('getDirection%s'%self._libsuffix)
-        return libfn(self.pointer)
+        libfn = utils.get_lib_fn('getDirection')
+        return np.array(libfn(self.pointer)).reshape(self.dimension,self.dimension)
 
     def set_direction(self, new_direction):
         """
@@ -187,7 +187,7 @@ def set_direction(self, new_direction):
         if len(new_direction) != self.dimension:
             raise ValueError('must give a origin value for each dimension (%i)' % self.dimension)
 
-        libfn = utils.get_lib_fn('setDirection%s'%self._libsuffix)
+        libfn = utils.get_lib_fn('setDirection')
         libfn(self.pointer, new_direction)
 
     @property
@@ -221,7 +221,7 @@ def view(self, single_components=False):
         shape = img.shape[::-1]
         if img.has_components or (single_components == True):
             shape = list(shape) + [img.components]
-        libfn = utils.get_lib_fn('toNumpy%s'%img._libsuffix)
+        libfn = utils.get_lib_fn('toNumpy')
         memview = libfn(img.pointer)
         return np.asarray(memview).view(dtype = dtype).reshape(shape).view(np.ndarray).T
 
@@ -281,7 +281,7 @@ def clone(self, pixeltype=None):
             p1_short = utils.short_ptype(self.pixeltype)
             p2_short = utils.short_ptype(pixeltype)
             ndim = self.dimension
-            fn_suffix = '%s%i%s%i' % (p1_short,ndim,p2_short,ndim)
+            fn_suffix = '%s%i' % (p2_short,ndim)
             libfn = utils.get_lib_fn('antsImageClone%s'%fn_suffix)
             pointer_cloned = libfn(self.pointer)
             return ANTsImage(pixeltype=pixeltype,
@@ -348,7 +348,7 @@ def to_file(self, filename):
             filepath to which the image will be written
         """
         filename = os.path.expanduser(filename)
-        libfn = utils.get_lib_fn('toFile%s'%self._libsuffix)
+        libfn = utils.get_lib_fn('toFile')
         libfn(self.pointer, filename)
     to_filename = to_file