diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml index 9735917213..ae20c046fe 100644 --- a/.github/workflows/build.yml +++ b/.github/workflows/build.yml @@ -32,12 +32,15 @@ jobs: steps: - uses: actions/checkout@v4 with: {fetch-depth: 0, submodules: recursive} + - name: Set up uv + uses: astral-sh/setup-uv@v5 + with: + version: "0.6.9" - id: reqs name: set requirements run: | envname="${GITHUB_REPOSITORY##*/}-${GITHUB_RUN_ID}.${GITHUB_RUN_NUMBER}" echo "envname=$envname" >> $GITHUB_OUTPUT - sed -ri -e 's/^(name: ).*/\1$envname/' -e '/ python /d' -e 's/(.* numpy) .*/\1=${{ matrix.numpy-version }}/' scripts/requirements-test.yml - uses: conda-incubator/setup-miniconda@v3 with: python-version: ${{ matrix.python-version }} @@ -48,12 +51,13 @@ jobs: name: build run: | conda activate "${{ steps.reqs.outputs.envname }}" + UV_PROJECT_ENVIRONMENT=$CONDA_PREFIX uv sync --dev --inexact --all-extras cmake -S . -B ./build -DCMAKE_BUILD_TYPE=RelWithDebInfo -DCONDA_BUILD=ON -DCMAKE_INSTALL_PREFIX="$CONDA_PREFIX" cmake --build ./build --target install - name: test run: | conda activate "${{ steps.reqs.outputs.envname }}" - TESTS_FORCE_GPU=1 python -m unittest discover -v -k tigre -k TIGRE -k astra -k ASTRA -k gpu -k GPU ./Wrappers/Python/test + TESTS_FORCE_GPU=1 UV_PROJECT_ENVIRONMENT=$CONDA_PREFIX uv run --no-sync python -m unittest discover -v -k tigre -k TIGRE -k astra -k ASTRA -k gpu -k GPU ./Wrappers/Python/test - if: always() name: Post Run conda-incubator/setup-miniconda@v3 shell: bash @@ -74,6 +78,11 @@ jobs: steps: - uses: actions/checkout@v4 with: {fetch-depth: 0, submodules: recursive} + - name: Set up uv + uses: astral-sh/setup-uv@v5 + with: + version: "0.6.9" + enable-cache: true - name: set requirements run: sed -ri -e '/ python /d' -e 's/(.* numpy) .*/\1=${{ matrix.numpy-version }}/' -e 's/=cuda*//' -e '/tigre/d' scripts/requirements-test.yml - uses: conda-incubator/setup-miniconda@v3 @@ -83,10 +92,11 @@ jobs: activate-environment: cil_dev - name: build run: | + UV_PROJECT_ENVIRONMENT=$CONDA_PREFIX uv sync --dev --inexact cmake -S . -B ./build -DCMAKE_BUILD_TYPE=RelWithDebInfo -DCONDA_BUILD=ON -DCMAKE_INSTALL_PREFIX="$CONDA_PREFIX" cmake --build ./build --target install - name: test - run: python -m unittest discover -v ./Wrappers/Python/test + run: UV_PROJECT_ENVIRONMENT=$CONDA_PREFIX uv run --no-sync python -m unittest discover -v ./Wrappers/Python/test conda-matrix: runs-on: ubuntu-22.04 outputs: @@ -175,8 +185,20 @@ jobs: fetch-depth: 0 submodules: recursive ref: ${{ github.event.pull_request.head.sha || github.ref }} # fix SHA - - uses: conda-incubator/setup-miniconda@v3 - with: {python-version: 3.11} + - name: Set up uv + uses: astral-sh/setup-uv@v5 + with: + version: "0.6.9" + enable-cache: true + - name: set requirements + working-directory: . + run: sed -ri -e '/ python /d' -e 's/(.* numpy) .*/\1=${{ matrix.numpy-version }}/' -e 's/=cuda*//' -e '/tigre/d' scripts/requirements-test.yml + - name: Set conda environment + uses: conda-incubator/setup-miniconda@v3 + with: + python-version: ${{ matrix.python-version }} + environment-file: scripts/requirements-test.yml + activate-environment: cil_dev - uses: ruby/setup-ruby@v1 with: ruby-version: '3.2' @@ -184,13 +206,11 @@ jobs: cache-version: 0 - name: install dependencies run: | - conda install -c conda-forge -yq conda-merge - conda-merge ../scripts/requirements-test.yml docs_environment.yml > environment.yml - conda env update -n test - conda list + conda install -c conda-forge -yq pandoc - name: build cil working-directory: . run: | + UV_PROJECT_ENVIRONMENT=$CONDA_PREFIX uv sync --dev --group docs --inexact cmake -S . -B ./build -DCMAKE_BUILD_TYPE=RelWithDebInfo -DCONDA_BUILD=ON -DCMAKE_INSTALL_PREFIX="$CONDA_PREFIX" cmake --build ./build --target install - name: checkout docs @@ -208,7 +228,7 @@ jobs: docs_dir="${{ github.ref_name }}" docs_dir="${docs_dir//\//_}" if test "$docs_dir" = master; then docs_dir=nightly; fi - make BUILDSUBDIR="$docs_dir" dirhtml + UV_PROJECT_ENVIRONMENT=$CONDA_PREFIX uv run --dev --group docs --no-sync make BUILDSUBDIR="$docs_dir" dirhtml - uses: actions/upload-artifact@v4 with: name: DocumentationHTML @@ -263,7 +283,7 @@ jobs: - name: test run: > docker run --rm -v .:/CIL tomographicimaging/cil:test /bin/bash -c - 'python -m unittest discover -v /CIL/Wrappers/Python/test' + 'uv run --dev --inexact python -m unittest discover -v /CIL/Wrappers/Python/test' - uses: docker/build-push-action@v6 with: cache-from: type=gha diff --git a/.github/workflows/build_uv.yml b/.github/workflows/build_uv.yml new file mode 100644 index 0000000000..b4c7ed059a --- /dev/null +++ b/.github/workflows/build_uv.yml @@ -0,0 +1,95 @@ +name: build_uv +on: + release: + types: [published] + push: + branches: [master] + tags: ['**'] + paths-ignore: + - 'CHANGELOG.md' + - 'CITATION.cff' + - 'LICENSE' + - 'scripts/**' + - 'NOTICE.txt' + - 'README.md' + pull_request: + branches: [master] + paths-ignore: + - 'CHANGELOG.md' + - 'CITATION.cff' + - 'LICENSE' + - 'scripts/**' + - 'NOTICE.txt' + - 'README.md' +jobs: + uv-test-cuda: + defaults: {run: {shell: 'bash -el {0}'}} + runs-on: [self-hosted, python, cuda] + strategy: + matrix: + python-version: [3.11] + numpy-version: [1.25] + steps: + - uses: actions/checkout@v4 + with: {fetch-depth: 0, submodules: recursive} + - name: Install uv + uses: astral-sh/setup-uv@v5 + with: + version: "0.6.5" + - id: reqs + name: set requirements + run: | + envname="${GITHUB_REPOSITORY##*/}-${GITHUB_RUN_ID}.${GITHUB_RUN_NUMBER}" + echo "envname=$envname" >> $GITHUB_OUTPUT + - uses: conda-incubator/setup-miniconda@v3 + with: + python-version: ${{ matrix.python-version }} + environment-file: scripts/requirements-cuda.yml + activate-environment: ${{ steps.reqs.outputs.envname }} + run-post: false + - name: "Set up Python" + uses: actions/setup-python@v5 + with: + python-version: ${{ matrix.python-version }} + - name: "Install Project" + run: | + conda activate "${{ steps.reqs.outputs.envname }}" + conda install conda-forge::cudatoolkit-dev=11.7.0 + uv sync --dev --all-extras + - name: test + run: CIL_DATA_DIR=./Wrappers/Python/data uv run --dev python -m unittest discover -v -k tigre -k TIGRE -k astra -k ASTRA -k gpu -k GPU ./Wrappers/Python/test + - if: always() + name: Post Run conda-incubator/setup-miniconda@v3 + shell: bash + run: | + sed -i '/${{ steps.reqs.outputs.envname }}/d' ~/.profile + source ~/.profile + conda env remove -n "${{ steps.reqs.outputs.envname }}" + uv-test: + defaults: {run: {shell: 'bash -el {0}'}} + runs-on: ubuntu-22.04 + strategy: + matrix: + include: + - python-version: '3.10' + - python-version: 3.12 + steps: + - uses: actions/checkout@v4 + with: {fetch-depth: 0, submodules: recursive} + - name: Install uv + uses: astral-sh/setup-uv@v5 + with: + version: "0.6.5" + enable-cache: true + - name: "Set up Python" + uses: actions/setup-python@v5 + with: + python-version: ${{ matrix.python-version }} + - name: "Install Project" + run: uv sync --dev + - name: test + run: CIL_DATA_DIR=./Wrappers/Python/data uv run --dev python -m unittest discover -v ./Wrappers/Python/test + pass: + needs: [uv-test-cuda, uv-test] + runs-on: ubuntu-22.04 + steps: [{run: echo success}] diff --git a/.gitignore b/.gitignore index db3970f85a..5a0c2df361 100644 --- a/.gitignore +++ b/.gitignore @@ -5,3 +5,4 @@ __pycache__/ /build* *.vscode* *.egg* +.ropeproject/ diff --git a/CMakeLists.txt b/CMakeLists.txt index e4c3f229b6..9a436c2fba 100644 --- a/CMakeLists.txt +++ b/CMakeLists.txt @@ -23,17 +23,21 @@ else() cmake_minimum_required(VERSION 3.4) endif() -project(cil LANGUAGES CXX) +project(${SKBUILD_PROJECT_NAME} LANGUAGES CXX) -if (CMAKE_VERSION VERSION_GREATER_EQUAL 3.27) + +if(CMAKE_VERSION VERSION_GREATER_EQUAL 3.27) cmake_policy(SET CMP0148 OLD) endif() # If APPLE don't use @rpath -if (APPLE) - option(SHARED_LIBS_ABS_PATH "Force shared libraries to be installed with absolute paths (as opposed to rpaths)" ON) - mark_as_advanced( SHARED_LIBS_ABS_PATH ) - if (SHARED_LIBS_ABS_PATH) +if(APPLE) + option( + SHARED_LIBS_ABS_PATH + "Force shared libraries to be installed with absolute paths (as opposed to rpaths)" + ON) + mark_as_advanced(SHARED_LIBS_ABS_PATH) + if(SHARED_LIBS_ABS_PATH) # Set install_name_dir as the absolute path to install_prefix/lib GET_FILENAME_COMPONENT(CMAKE_INSTALL_NAME_DIR ${CMAKE_INSTALL_PREFIX}/lib REALPATH) set(CMAKE_INSTALL_RPATH_USE_LINK_PATH TRUE) @@ -44,5 +48,5 @@ if(NOT DEFINED CMAKE_BUILD_TYPE) set(CMAKE_BUILD_TYPE "RelWithDebInfo") endif() -add_subdirectory(src/Core) -add_subdirectory(Wrappers/Python) + +add_subdirectory(src/cilacc) diff --git a/Dockerfile b/Dockerfile index 5dc5f25bca..cf6356a30d 100644 --- a/Dockerfile +++ b/Dockerfile @@ -16,13 +16,15 @@ ARG CIL_EXTRA_PACKAGES="tigre=2.6 astra-toolbox=2.1.0=cuda*" COPY --chown="${NB_USER}" scripts/requirements-test.yml environment.yml # channel_priority: https://stackoverflow.com/q/58555389 RUN sed -ri '/tigre|astra-toolbox| python /d' environment.yml \ + && curl -LsSf https://astral.sh/uv/0.6.9/install.sh | sh \ && for pkg in 'jupyter-server-proxy>4.1.0' $CIL_EXTRA_PACKAGES; do echo " - $pkg" >> environment.yml; done \ && conda config --env --set channel_priority strict \ && for ch in defaults nvidia ccpi https://software.repos.intel.com/python/conda conda-forge; do conda config --env --add channels $ch; done \ && mamba env update -n base \ && mamba clean -a -y -f \ && rm environment.yml \ - && fix-permissions "${CONDA_DIR}" /home/${NB_USER} + && fix-permissions "${CONDA_DIR}" /home/${NB_USER} \ + && UV_PROJECT_ENVIRONMENT=$CONDA_DIR uv sync --all-extras --dev --inexact # NB: trailing `/` is required ENV TENSORBOARD_PROXY_URL=/user-redirect/proxy/6006/ diff --git a/Wrappers/Python/CMakeLists.txt b/Wrappers/Python/CMakeLists.txt deleted file mode 100644 index 9cb60e0f60..0000000000 --- a/Wrappers/Python/CMakeLists.txt +++ /dev/null @@ -1,30 +0,0 @@ -find_package(Python COMPONENTS Interpreter REQUIRED) - -if(PYTHON_DEST_DIR) - file(TO_CMAKE_PATH "${PYTHON_DEST_DIR}" PYTHON_DEST) -endif() - -message("CMAKE_CXX_FLAGS ${CMAKE_CXX_FLAGS}") -if(NOT DEFINED) - set(CMAKE_BUILD_TYPE "RelWithDebInfo") -endif() - -# TODO: add to add_custom_command DEPENDS the list of python files of the project. -# file(GLOB_RECURSE DEPS ${CMAKE_CURRENT_SOURCE_DIR}/cil/*.py ) -message("SETUPTOOLS_SCM_PRETEND_VERSION_FOR_CIL: $ENV{SETUPTOOLS_SCM_PRETEND_VERSION_FOR_CIL}") -message("CMAKE_SOURCE_DIR: ${CMAKE_SOURCE_DIR}") -if(PYTHON_DEST_DIR) - message(STATUS "CIL install using ${Python_EXECUTABLE} -m pip install -t ${PYTHON_DEST}") - add_custom_target(pythonsetup ALL - COMMAND ${Python_EXECUTABLE} -m pip install ${CMAKE_SOURCE_DIR} -t ${PYTHON_DEST} --upgrade - DEPENDS cilacc) -else() - message(STATUS "CIL install using ${Python_EXECUTABLE} -m pip install") - add_custom_target(pythonsetup ALL - COMMAND ${Python_EXECUTABLE} -m pip install ${CMAKE_SOURCE_DIR} --upgrade - DEPENDS cilacc) -endif() -# install the data if not a conda build. With conda the data is in the dependency package cil-data -if (NOT CONDA_BUILD) - install(DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}/data/ DESTINATION ${CMAKE_INSTALL_PREFIX}/share/cil) -endif() diff --git a/Wrappers/Python/cil/__init__.py b/Wrappers/Python/cil/__init__.py index 91bbd22021..a1d5369393 100644 --- a/Wrappers/Python/cil/__init__.py +++ b/Wrappers/Python/cil/__init__.py @@ -15,5 +15,4 @@ # # Authors: # CIL Developers, listed at: https://github.com/TomographicImaging/CIL/blob/master/NOTICE.txt - from .version import version as __version__ diff --git a/Wrappers/Python/cil/framework/__init__.py b/Wrappers/Python/cil/framework/__init__.py index bda9fdb11e..66aaab679a 100644 --- a/Wrappers/Python/cil/framework/__init__.py +++ b/Wrappers/Python/cil/framework/__init__.py @@ -16,7 +16,7 @@ # Authors: # CIL Developers, listed at: https://github.com/TomographicImaging/CIL/blob/master/NOTICE.txt -from .cilacc import cilacc +from cil import cilacc from .acquisition_data import AcquisitionData from .acquisition_geometry import AcquisitionGeometry, SystemConfiguration from .data_container import DataContainer diff --git a/Wrappers/Python/cil/framework/cilacc.py b/Wrappers/Python/cil/framework/cilacc.py deleted file mode 100644 index fa96ba4c51..0000000000 --- a/Wrappers/Python/cil/framework/cilacc.py +++ /dev/null @@ -1,33 +0,0 @@ -# Copyright 2018 United Kingdom Research and Innovation -# Copyright 2018 The University of Manchester -# -# Licensed under the Apache License, Version 2.0 (the "License"); -# you may not use this file except in compliance with the License. -# You may obtain a copy of the License at -# -# http://www.apache.org/licenses/LICENSE-2.0 -# -# Unless required by applicable law or agreed to in writing, software -# distributed under the License is distributed on an "AS IS" BASIS, -# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -# See the License for the specific language governing permissions and -# limitations under the License. -# -# Authors: -# CIL Developers, listed at: https://github.com/TomographicImaging/CIL/blob/master/NOTICE.txt -import ctypes -import platform -from ctypes import util -# check for the extension - -if platform.system() == 'Linux': - dll = 'libcilacc.so' -elif platform.system() == 'Windows': - dll_file = 'cilacc.dll' - dll = util.find_library(dll_file) -elif platform.system() == 'Darwin': - dll = 'libcilacc.dylib' -else: - raise ValueError('Not supported platform, ', platform.system()) - -cilacc = ctypes.cdll.LoadLibrary(dll) diff --git a/Wrappers/Python/cil/framework/data_container.py b/Wrappers/Python/cil/framework/data_container.py index 4febd7a449..326dd0ffcc 100644 --- a/Wrappers/Python/cil/framework/data_container.py +++ b/Wrappers/Python/cil/framework/data_container.py @@ -16,14 +16,13 @@ # Authors: # CIL Developers, listed at: https://github.com/TomographicImaging/CIL/blob/master/NOTICE.txt import copy -import ctypes import warnings from functools import reduce from numbers import Number import numpy -from .cilacc import cilacc +from cil import cilacc from cil.utilities.multiprocessing import NUM_THREADS @@ -553,8 +552,6 @@ def _axpby(self, a, b, y, out, dtype=numpy.float32, num_threads=NUM_THREADS): :type num_threads: int, optional, default 1/2 CPU of the system ''' - c_float_p = ctypes.POINTER(ctypes.c_float) - c_double_p = ctypes.POINTER(ctypes.c_double) #convert a and b to numpy arrays and get the reference to the data (length = 1 or ndx.size) try: @@ -593,19 +590,19 @@ def _axpby(self, a, b, y, out, dtype=numpy.float32, num_threads=NUM_THREADS): ndb = ndb.astype(dtype, casting='same_kind') if dtype == numpy.float32: - x_p = ndx.ctypes.data_as(c_float_p) - y_p = ndy.ctypes.data_as(c_float_p) - out_p = ndout.ctypes.data_as(c_float_p) - a_p = nda.ctypes.data_as(c_float_p) - b_p = ndb.ctypes.data_as(c_float_p) + x_p = ndx + y_p = ndy + out_p = ndout + a_p = nda + b_p = ndb f = cilacc.saxpby elif dtype == numpy.float64: - x_p = ndx.ctypes.data_as(c_double_p) - y_p = ndy.ctypes.data_as(c_double_p) - out_p = ndout.ctypes.data_as(c_double_p) - a_p = nda.ctypes.data_as(c_double_p) - b_p = ndb.ctypes.data_as(c_double_p) + x_p = ndx + y_p = ndy + out_p = ndout + a_p = nda + b_p = ndb f = cilacc.daxpby else: @@ -615,24 +612,6 @@ def _axpby(self, a, b, y, out, dtype=numpy.float32, num_threads=NUM_THREADS): # int psaxpby(float * x, float * y, float * out, float a, float b, long size) - cilacc.saxpby.argtypes = [ctypes.POINTER(ctypes.c_float), # pointer to the first array - ctypes.POINTER(ctypes.c_float), # pointer to the second array - ctypes.POINTER(ctypes.c_float), # pointer to the third array - ctypes.POINTER(ctypes.c_float), # pointer to A - ctypes.c_int, # type of type of A selector (int) - ctypes.POINTER(ctypes.c_float), # pointer to B - ctypes.c_int, # type of type of B selector (int) - ctypes.c_longlong, # type of size of first array - ctypes.c_int] # number of threads - cilacc.daxpby.argtypes = [ctypes.POINTER(ctypes.c_double), # pointer to the first array - ctypes.POINTER(ctypes.c_double), # pointer to the second array - ctypes.POINTER(ctypes.c_double), # pointer to the third array - ctypes.POINTER(ctypes.c_double), # type of A (c_double) - ctypes.c_int, # type of type of A selector (int) - ctypes.POINTER(ctypes.c_double), # type of B (c_double) - ctypes.c_int, # type of type of B selector (int) - ctypes.c_longlong, # type of size of first array - ctypes.c_int] # number of threads if f(x_p, y_p, out_p, a_p, a_vec, b_p, b_vec, ndx.size, num_threads) != 0: raise RuntimeError('axpby execution failed') diff --git a/Wrappers/Python/cil/optimisation/operators/GradientOperator.py b/Wrappers/Python/cil/optimisation/operators/GradientOperator.py index ae6bbc6922..1d2d627af5 100644 --- a/Wrappers/Python/cil/optimisation/operators/GradientOperator.py +++ b/Wrappers/Python/cil/optimisation/operators/GradientOperator.py @@ -269,60 +269,8 @@ def adjoint(self, x, out=None): import ctypes, platform from ctypes import util -# check for the extension -if platform.system() == 'Linux': - dll = 'libcilacc.so' -elif platform.system() == 'Windows': - dll_file = 'cilacc.dll' - dll = util.find_library(dll_file) -elif platform.system() == 'Darwin': - dll = 'libcilacc.dylib' -else: - raise ValueError('Not supported platform, ', platform.system()) - -cilacc = ctypes.cdll.LoadLibrary(dll) - -c_float_p = ctypes.POINTER(ctypes.c_float) - -cilacc.openMPtest.restypes = ctypes.c_int32 -cilacc.openMPtest.argtypes = [ctypes.c_int32] - -cilacc.fdiff4D.restype = ctypes.c_int32 -cilacc.fdiff4D.argtypes = [ctypes.POINTER(ctypes.c_float), - ctypes.POINTER(ctypes.c_float), - ctypes.POINTER(ctypes.c_float), - ctypes.POINTER(ctypes.c_float), - ctypes.POINTER(ctypes.c_float), - ctypes.c_size_t, - ctypes.c_size_t, - ctypes.c_size_t, - ctypes.c_size_t, - ctypes.c_int32, - ctypes.c_int32, - ctypes.c_int32] - -cilacc.fdiff3D.restype = ctypes.c_int32 -cilacc.fdiff3D.argtypes = [ctypes.POINTER(ctypes.c_float), - ctypes.POINTER(ctypes.c_float), - ctypes.POINTER(ctypes.c_float), - ctypes.POINTER(ctypes.c_float), - ctypes.c_size_t, - ctypes.c_size_t, - ctypes.c_size_t, - ctypes.c_int32, - ctypes.c_int32, - ctypes.c_int32] - -cilacc.fdiff2D.restype = ctypes.c_int32 -cilacc.fdiff2D.argtypes = [ctypes.POINTER(ctypes.c_float), - ctypes.POINTER(ctypes.c_float), - ctypes.POINTER(ctypes.c_float), - ctypes.c_size_t, - ctypes.c_size_t, - ctypes.c_int32, - ctypes.c_int32, - ctypes.c_int32] +import cil.cilacc as cilacc class Gradient_C(LinearOperator): @@ -391,7 +339,7 @@ def ndarray_as_c_pointer(ndx): def direct(self, x, out=None): ndx = np.asarray(x.as_array(), dtype=np.float32, order='C') - x_p = Gradient_C.ndarray_as_c_pointer(ndx) + x_p = ndx if out is None: out = self.range_geometry().allocate(None) @@ -404,7 +352,7 @@ def direct(self, x, out=None): ndout.insert(ind, out.get_item(0).as_array()) #insert channels dc at correct point for channel data #pass list of all arguments - arg1 = [Gradient_C.ndarray_as_c_pointer(ndout[i]) for i in range(len(ndout))] + arg1 = [ndout[i] for i in range(len(ndout))] arg2 = [el for el in self.domain_shape] args = arg1 + arg2 + [self.bnd_cond, 1, self.num_threads] status = self.fd(x_p, *args) @@ -437,7 +385,7 @@ def adjoint(self, x, out=None): out = self.domain_geometry().allocate(None) ndout = np.asarray(out.as_array(), dtype=np.float32, order='C') - out_p = Gradient_C.ndarray_as_c_pointer(ndout) + out_p = ndout if self.split is False: ndx = [el.as_array() for el in x.containers] @@ -450,7 +398,7 @@ def adjoint(self, x, out=None): if el != 1: ndx[i]/=el - arg1 = [Gradient_C.ndarray_as_c_pointer(ndx[i]) for i in range(self.ndim)] + arg1 = [ndx[i] for i in range(self.ndim)] arg2 = [el for el in self.domain_shape] args = arg1 + arg2 + [self.bnd_cond, 0, self.num_threads] diff --git a/Wrappers/Python/cil/processors/cilacc_binner.py b/Wrappers/Python/cil/processors/cilacc_binner.py index 5b9edccbef..5f26a022ef 100644 --- a/Wrappers/Python/cil/processors/cilacc_binner.py +++ b/Wrappers/Python/cil/processors/cilacc_binner.py @@ -19,10 +19,7 @@ from cil.framework import cilacc import numpy as np -import ctypes -c_float_p = ctypes.POINTER(ctypes.c_float) -c_size_t_p = ctypes.POINTER(ctypes.c_size_t) class Binner_IPP(object): @@ -48,30 +45,17 @@ def __init__(self, shape_in, shape_out, start_index, binning): """ - cilacc.Binner_new.argtypes = [c_size_t_p,c_size_t_p,c_size_t_p,c_size_t_p] - cilacc.Binner_new.restype = ctypes.c_void_p - - cilacc.Binner_bin.argtypes = [ ctypes.c_void_p, c_float_p,c_float_p] - cilacc.Binner_bin.restype = ctypes.c_int32 - - cilacc.Binner_delete.argtypes = [ ctypes.c_void_p] - cilacc.Binner_delete.restype = ctypes.c_void_p shape_in_arr = np.array(shape_in, np.uintp) shape_out_arr = np.array(shape_out, np.uintp) start_index_arr = np.array(start_index, np.uintp) binning_arr = np.array(binning, np.uintp) - shape_in_p = shape_in_arr.ctypes.data_as(c_size_t_p) - shape_out_p = shape_out_arr.ctypes.data_as(c_size_t_p) - ind_start_p = start_index_arr.ctypes.data_as(c_size_t_p) - binning_p = binning_arr.ctypes.data_as(c_size_t_p) - for i in range(4): - if shape_out_p[i] * binning_p[i] + ind_start_p[i] > shape_in_p[i]: + if shape_out_arr[i] * binning_arr[i] + start_index_arr[i] > shape_in_arr[i]: raise ValueError("Input dimension mismatch on dimension {0}".format(i)) - self.obj = cilacc.Binner_new(shape_in_p, shape_out_p, ind_start_p, binning_p) + self.obj = cilacc.Binner_new(shape_in_arr, shape_out_arr, start_index_arr, binning_arr) def bin(self, array_in, array_binned): @@ -88,10 +72,8 @@ def bin(self, array_in, array_binned): array_binned : ndarray Must have shape corresponding to shape_out. Data type float32. C ordered, contiguous memory """ - data_p = array_in.ctypes.data_as(c_float_p) - data_out_p = array_binned.ctypes.data_as(c_float_p) - return cilacc.Binner_bin(self.obj, data_p, data_out_p) + return cilacc.Binner_bin(self.obj, array_in, array_binned) def __del__(self): """This deletes the cilacc Binner object diff --git a/Wrappers/Python/cil/recon/FBP.py b/Wrappers/Python/cil/recon/FBP.py index 7218d05352..06baed6fdf 100644 --- a/Wrappers/Python/cil/recon/FBP.py +++ b/Wrappers/Python/cil/recon/FBP.py @@ -22,11 +22,8 @@ from scipy.fft import fftfreq import numpy as np -import ctypes from tqdm import tqdm -c_float_p = ctypes.POINTER(ctypes.c_float) -c_double_p = ctypes.POINTER(ctypes.c_double) try: cilacc.filter_projections_avh @@ -34,23 +31,6 @@ except AttributeError: has_ipp = False -if has_ipp: - cilacc.filter_projections_avh.argtypes = [ctypes.POINTER(ctypes.c_float), # pointer to the data array - ctypes.POINTER(ctypes.c_float), # pointer to the filter array - ctypes.POINTER(ctypes.c_float), # pointer to the weights array - ctypes.c_int16, #order of the fft - ctypes.c_long, #num_proj - ctypes.c_long, #pix_v - ctypes.c_long] #pix_x - - cilacc.filter_projections_vah.argtypes = [ctypes.POINTER(ctypes.c_float), # pointer to the data array - ctypes.POINTER(ctypes.c_float), # pointer to the filter array - ctypes.POINTER(ctypes.c_float), # pointer to the weights array - ctypes.c_int16, #order of the fft - ctypes.c_long, #pix_v - ctypes.c_long, #num_proj - ctypes.c_long] #pix_x - class GenericFilteredBackProjection(Reconstructor): """ Abstract Base Class GenericFilteredBackProjection holding common and virtual methods for FBP and FDK @@ -318,9 +298,9 @@ def _pre_filtering(self,acquistion_data): .format(filter_array.size,self.fft_order)) #call ext function - data_ptr = acquistion_data.array.ctypes.data_as(c_float_p) - filter_ptr = filter_array.ctypes.data_as(c_float_p) - weights_ptr = self._weights.ctypes.data_as(c_float_p) + data_ptr = acquistion_data.array + filter_ptr = filter_array + weights_ptr = self._weights ag = acquistion_data.geometry if ag.dimension_labels == ('angle','vertical','horizontal'): diff --git a/Wrappers/Python/cil/utilities/dataexample.py b/Wrappers/Python/cil/utilities/dataexample.py index 32dc35071d..3424f1c92f 100644 --- a/Wrappers/Python/cil/utilities/dataexample.py +++ b/Wrappers/Python/cil/utilities/dataexample.py @@ -29,13 +29,16 @@ from cil.io import NEXUSDataReader, NikonDataReader, ZEISSDataReader from zenodo_get import zenodo_get +import importlib.resources + class DATA(object): + @classmethod def dfile(cls): return None class CILDATA(DATA): - data_dir = os.path.abspath(os.path.join(sys.prefix, 'share','cil')) + data_dir = os.environ["CIL_DATA_DIR"] @classmethod def get(cls, size=None, scale=(0,1), **kwargs): ddir = kwargs.get('data_dir', CILDATA.data_dir) diff --git a/Wrappers/Python/cil/version.py b/Wrappers/Python/cil/version.py new file mode 100644 index 0000000000..3b04f3d6e7 --- /dev/null +++ b/Wrappers/Python/cil/version.py @@ -0,0 +1,3 @@ +import importlib.metadata + +version = importlib.metadata.version("cil") diff --git a/Wrappers/Python/test/test_io.py b/Wrappers/Python/test/test_io.py index bf82d72d7e..6a8b66e9e8 100644 --- a/Wrappers/Python/test/test_io.py +++ b/Wrappers/Python/test/test_io.py @@ -64,7 +64,7 @@ # change basedir to point to the location of the walnut dataset which can # be downloaded from https://zenodo.org/record/4822516 # basedir = os.path.abspath('/home/edo/scratch/Data/Walnut/valnut_2014-03-21_643_28/tomo-A/') -basedir = data_dir = os.path.abspath(os.path.join(sys.prefix, 'share','cil')) +basedir = data_dir = os.environ["CIL_DATA_DIR"] filename = os.path.join(basedir, "valnut_tomo-A.txrm") has_file = os.path.isfile(filename) diff --git a/Wrappers/Python/test/test_version.py b/Wrappers/Python/test/test_version.py index 1125a5d05a..5ea4035013 100644 --- a/Wrappers/Python/test/test_version.py +++ b/Wrappers/Python/test/test_version.py @@ -27,22 +27,27 @@ def test_version(self): import cil self.assertEqual(cil.__version__, version.version) + @unittest.skip("Statically declaring version in pyproject.toml") def test_version_major(self): from cil import version self.assertTrue(isinstance(version.major, int)) + @unittest.skip("Statically declaring version in pyproject.toml") def test_version_minor(self): from cil import version self.assertTrue(isinstance(version.minor, int)) + @unittest.skip("Statically declaring version in pyproject.toml") def test_version_patch(self): from cil import version self.assertTrue(isinstance(version.patch, int)) + @unittest.skip("Statically declaring version in pyproject.toml") def test_version_num_commit(self): from cil import version self.assertTrue(isinstance(version.num_commit, int)) + @unittest.skip("Statically declaring version in pyproject.toml") def test_version_commit_hash(self): from cil import version self.assertTrue(isinstance(version.commit_hash, str)) diff --git a/Wrappers/Python/test/utils.py b/Wrappers/Python/test/utils.py index ac0dbf338e..89413587b1 100644 --- a/Wrappers/Python/test/utils.py +++ b/Wrappers/Python/test/utils.py @@ -22,7 +22,7 @@ import importlib import logging -import cil.version +import cil import pprint import unittest @@ -37,7 +37,7 @@ def startTestRun(self): print("\n----------------------------------------------------------------------") print("TEST SYSTEM CONFIGURATION") - print("CIL version: ", cil.version.version) + print("CIL version: ", cil.__version__) pprint.pprint(system_state) print("----------------------------------------------------------------------\n") sys.stdout.flush() diff --git a/docs/docs_environment.yml b/docs/docs_environment.yml index c24e24d6e0..b7815a45b7 100644 --- a/docs/docs_environment.yml +++ b/docs/docs_environment.yml @@ -18,23 +18,4 @@ channels: - ccpi - defaults dependencies: - # in addition to CIL deps (see ../scripts/requirements-test.yml) - - jinja2 - # - pydata-sphinx-theme - - recommonmark - - sphinx - - sphinx_rtd_theme - - sphinx-autobuild - - sphinx-click - - sphinx-copybutton - - sphinx-panels - - sphinxcontrib-bibtex - - nbsphinx - - sphinx-gallery - - sphinx-copybutton - - notebook - # TODO: remove after https://github.com/pydata/pydata-sphinx-theme/pull/1795 is released - - pip - - pip: - - git+https://github.com/pydata/pydata-sphinx-theme - - unittest-parametrize # Needs to be here? + - pandoc diff --git a/pyproject.toml b/pyproject.toml index 5daa8ddbd8..9707440656 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,44 +1,91 @@ [build-system] -requires = ["setuptools>=64", "setuptools_scm>=8"] -build-backend = "setuptools.build_meta" - -[tool.setuptools_scm] -version_file = "Wrappers/Python/cil/version.py" -version_file_template = """ -version = '{version}' -major = {version_tuple[0]} -minor = {version_tuple[1]} -patch = {version_tuple[2]} -commit_hash = '{scm_version.node}' -num_commit = {scm_version.distance} -# work-around for https://github.com/pypa/setuptools_scm/issues/1059 -if (commit_hash, num_commit) == ('None', 0): - import re - if (_v := re.search(r'\\.dev(\\d+)\\+(\\w+)', version)): - num_commit, commit_hash = int(_v.group(1)), _v.group(2) -""" - -[tool.setuptools] -package-dir = {"" = "Wrappers/Python"} - -[tool.setuptools.packages.find] -where = ["Wrappers/Python"] -include = ["cil", "cil.*"] -exclude = ["data", "test"] +requires = [ + "ipp-static>=2022.0,<2022.1", + "ipp-devel>=2022.0,<2022.1", + "nanobind", + "scikit-build-core>=0.11.0", + "intel-openmp==2025.0.5", +] +build-backend = "scikit_build_core.build" -[project.urls] -#homepage = "https://ccpi.ac.uk/cil" -homepage = "https://tomographicimaging.github.io/CIL" -documentation = "https://tomographicimaging.github.io/CIL/nightly" -repository = "https://github.com/TomographicImaging/CIL" -changelog = "https://github.com/TomographicImaging/CIL/blob/master/CHANGELOG.md" [project] name = "cil" -dynamic = ["version"] +version = "0.25.0" description = "Core Imaging Library" license = {text = "Apache-2.0"} +authors = [{name="CIL developers", email="tomography+cil@stfc.ac.uk"}] maintainers = [{name="CIL developers", email="tomography+cil@stfc.ac.uk"}] requires-python = ">=3.10" readme = "README.md" keywords = ["tomography", "optimisation"] +dependencies = [ + "dxchange>=0.0.1", + "h5py>=3.13.0", + "numba>=0.61.0", + "olefile>=0.46", + "pillow>=11.1.0", + "pywavelets>=1.8.0", + "scipy>=1.4.0", + "tqdm>=4.67.1", + "zenodo-get>=1.6", + "numpy>=1.26,<2.0", +] + +[project.urls] +#homepage = "https://ccpi.ac.uk/cil" +homepage = "https://tomographicimaging.github.io/CIL" +documentation = "https://tomographicimaging.github.io/CIL/nightly" +repository = "https://github.com/TomographicImaging/CIL" +changelog = "https://github.com/TomographicImaging/CIL/blob/master/CHANGELOG.md" + +[project.optional-dependencies] +astra = [ + "astra-toolbox>=2.3.0", +] +tigre = [ + "pytigre", +] + +[dependency-groups] +dev = [ + "scikit-image>=0.25.2", + "unittest-parametrize>=1.6.0", + "cvxpy>=1.6.4", + "matplotlib>=3.10.1", + "packaging>=24.2", + "pip>=25.0.1", + "setuptools>=64", + "setuptools_scm>=8" + ] + docs = [ + "jinja2>=3.1.6", + "nbsphinx>=0.9.7", + "notebook>=7.3.3", + "pandoc>=2.4", + "pydata-sphinx-theme>=0.16.1", + "recommonmark>=0.7.1", + "sphinx>=8.1.3", + "sphinx-autobuild>=2024.10.3", + "sphinx-click>=6.0.0", + "sphinx-copybutton>=0.5.2", + "sphinx-gallery>=0.19.0", + "sphinx-panels>=0.4.1", + "sphinx-rtd-theme>=3.0.2", + "sphinxcontrib-bibtex>=2.6.3", +] + + + +[tool.scikit-build] +minimum-version = "0.11.0" +search.site-packages = true + + + +[tool.scikit-build.wheel.packages] +cil = "Wrappers/Python/cil" +"cil/cilacc" = "src/cilacc" + +[tool.uv.sources] +pytigre = { git = "https://github.com/purepani/TIGRE", branch = "push-myxtropotyqx" } diff --git a/recipe/meta.yaml b/recipe/meta.yaml index 3305bcc3ca..5baca8c67c 100644 --- a/recipe/meta.yaml +++ b/recipe/meta.yaml @@ -17,20 +17,14 @@ build: test: requires: - python-wget - - cvxpy # [linux] - - scikit-image - tomophantom=2.0.0 # [linux] - tigre=2.6 - - packaging - ccpi-regulariser=24.0.1 # [not osx] - - astra-toolbox=2.1=cuda* # [not osx] - - matplotlib-base >=3.3.0 source_files: - ./Wrappers/Python/test commands: - - pip install unittest-parametrize - python -m unittest discover -v -s Wrappers/Python/test # [win] - python -m unittest discover -s Wrappers/Python/test -v # [not win] @@ -40,8 +34,6 @@ requirements: - python - numpy {{ numpy }} - pip - - setuptools >=64 - - setuptools_scm >=8 - cmake # [not osx] - cmake >=3.16 # [osx] - libgcc-ng # [linux] @@ -55,28 +47,17 @@ requirements: run: - python - - {{ pin_compatible('numpy', min_pin='x.x', max_pin='x.x') }} - - scipy >=1.4.0 - - h5py - - pillow - libgcc-ng # [linux] - libstdcxx-ng # [linux] - _openmp_mutex # [linux] - openmp # [osx] - vc 14 # [win] - - dxchange - - olefile >=0.46 - - pywavelets - cil-data >=22 - {{ pin_compatible('ipp', min_pin='x.x', max_pin='x.x') }} - - tqdm - - numba - - zenodo_get >=1.6 #optional packages with version dependancies run_constrained: - tomophantom=2.0.0 - - astra-toolbox>=1.9.9.dev5,<=2.1 - tigre>=2.4,<=2.6 - ccpi-regulariser=24.0.1 - ipywidgets diff --git a/scripts/requirements-cuda.yml b/scripts/requirements-cuda.yml new file mode 100644 index 0000000000..7f38e5a23e --- /dev/null +++ b/scripts/requirements-cuda.yml @@ -0,0 +1,20 @@ +# Copyright 2023 United Kingdom Research and Innovation +# Copyright 2023 The University of Manchester +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# http://www.apache.org/licenses/LICENSE-2.0 +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. +# Authors: +# CIL Developers, listed at: https://github.com/TomographicImaging/CIL/blob/master/NOTICE.txt +name: cuda_dev +channels: + - conda-forge + #- nvidia +dependencies: + # base (vis. recipe/conda_build_config.yaml) + - python >=3.10 diff --git a/scripts/requirements-test.yml b/scripts/requirements-test.yml index 9abef82307..6f812aa338 100644 --- a/scripts/requirements-test.yml +++ b/scripts/requirements-test.yml @@ -19,35 +19,16 @@ channels: dependencies: # base (vis. recipe/conda_build_config.yaml) - python >=3.10 - - numpy >=1.23 - ccpi::cil-data - ccpi::tigre=2.6 - ccpi::ccpi-regulariser=24.0.1 - ccpi::tomophantom=2.0.0 - - astra-toolbox=2.1=cuda* - - cvxpy - python-wget - - scikit-image - - packaging - cmake >=3.16 - - setuptools <71 - ipp-include=2021.12 - ipp-devel=2021.12 - ipp=2021.12 - ipywidgets - - scipy - - matplotlib-base - - h5py - - pillow - libgcc-ng # [linux] - libstdcxx-ng # [linux] - _openmp_mutex # [linux] - - dxchange - - olefile - - pywavelets - - numba - - tqdm - - zenodo_get >=1.6 - - pip - - pip: - - unittest-parametrize diff --git a/src/Core/CMakeLists.txt b/src/Core/CMakeLists.txt deleted file mode 100644 index da824d83e9..0000000000 --- a/src/Core/CMakeLists.txt +++ /dev/null @@ -1,131 +0,0 @@ -# Copyright 2019 United Kingdom Research and Innovation -# Copyright 2019 The University of Manchester -# -# Licensed under the Apache License, Version 2.0 (the "License"); -# you may not use this file except in compliance with the License. -# You may obtain a copy of the License at -# -# http://www.apache.org/licenses/LICENSE-2.0 -# -# Unless required by applicable law or agreed to in writing, software -# distributed under the License is distributed on an "AS IS" BASIS, -# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -# See the License for the specific language governing permissions and -# limitations under the License. -# -# Authors: -# CIL Developers, listed at: https://github.com/TomographicImaging/CIL/blob/master/NOTICE.txt -# Richard Brown (UCL) - -set (CMAKE_CXX_STANDARD 11) -set (CMAKE_CXX_STANDARD_REQUIRED ON) -if(NOT DEFINED CMAKE_BUILD_TYPE) - set(CMAKE_BUILD_TYPE RelWithDebInfo) -endif() - -message ("OpenMP_CXX_FLAGS ${OpenMP_CXX_FLAGS}") -find_package(OpenMP REQUIRED) -add_definitions(${OpenMP_CXX_FLAGS}) - - -if (WIN32) - set (CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} /Ddll_EXPORTS") -endif() - -if (${CMAKE_CXX_COMPILER_ID} STREQUAL "GNUCC") - # appends some flags - add_compile_options(-ftree-vectorize -fopt-info-vec-optimized -fopt-info-vec) - # add_compile_options(-march=native -mavx ) -endif() - -message("CMAKE_CXX_FLAGS ${CMAKE_CXX_FLAGS}") -message("CMAKE_EXE_LINKER_FLAGS ${CMAKE_EXE_LINKER_FLAGS}") -message("CMAKE_SHARED_LINKER_FLAGS ${CMAKE_SHARED_LINKER_FLAGS}") -message("CMAKE_STATIC_LINKER_FLAGS ${CMAKE_STATIC_LINKER_FLAGS}") - -if(${CMAKE_VERSION} VERSION_GREATER_EQUAL "3.9.0") - set (OpenMP_EXE_LINKER_FLAGS OpenMP::OpenMP_CXX) -else() - message(WARNING "Your CMake version is old. OpenMP linking flags might be incorrect.") - # need to explicitly set this. Definitely for gcc, hopefully also for other systems. - # See https://gitlab.kitware.com/cmake/cmake/issues/15392 - set (OpenMP_EXE_LINKER_FLAGS ${OpenMP_C_FLAGS}) -endif() - -if(NOT DEFINED IPP_LIBRARY) - if (UNIX) - set(IPP_LIBRARY ${CMAKE_INSTALL_PREFIX}/lib) - elseif(WIN32) - set(IPP_LIBRARY ${CMAKE_INSTALL_PREFIX}/Library/lib) - endif() -endif() - -if(NOT DEFINED IPP_INCLUDE) - set(IPP_INCLUDE ${CMAKE_INSTALL_PREFIX}/include) -endif() - -if (UNIX) - find_library(IPP_CORE libippcore.so PATHS ${IPP_LIBRARY}) - find_library(IPP_S libipps.so PATHS ${IPP_LIBRARY}) - find_library(IPP_VM libippvm.so PATHS ${IPP_LIBRARY}) - find_library(IPP_I libippi.so PATHS ${IPP_LIBRARY}) -elseif(WIN32) - find_library(IPP_CORE ippcore PATHS ${IPP_LIBRARY}) - find_library(IPP_S ipps PATHS ${IPP_LIBRARY}) - find_library(IPP_VM ippvm PATHS ${IPP_LIBRARY}) - find_library(IPP_I ippi PATHS ${IPP_LIBRARY}) -endif() - -if(IPP_CORE AND IPP_S AND IPP_VM AND IPP_I) - set(USE_IPP TRUE) - message("IPP libraries found") -else() - set(USE_IPP FALSE) - message("IPP libraries not found, FBP_filtering not in build") -endif() - -if(USE_IPP) - add_library(cilacc SHARED ${CMAKE_CURRENT_SOURCE_DIR}/utilities.cpp - ${CMAKE_CURRENT_SOURCE_DIR}/axpby.cpp - ${CMAKE_CURRENT_SOURCE_DIR}/FiniteDifferenceLibrary.cpp - ${CMAKE_CURRENT_SOURCE_DIR}/FBP_filtering.cpp - ${CMAKE_CURRENT_SOURCE_DIR}/Binning.cpp) - - - target_link_libraries(cilacc ${OpenMP_EXE_LINKER_FLAGS} ${IPP_CORE} ${IPP_S} ${IPP_I} ${IPP_VM}) - include_directories(cilacc PUBLIC ${IPP_INCLUDE} ${CMAKE_CURRENT_SOURCE_DIR}/include) -else() - add_library(cilacc SHARED ${CMAKE_CURRENT_SOURCE_DIR}/utilities.cpp - ${CMAKE_CURRENT_SOURCE_DIR}/axpby.cpp - ${CMAKE_CURRENT_SOURCE_DIR}/FiniteDifferenceLibrary.cpp ) - - target_link_libraries(cilacc ${OpenMP_EXE_LINKER_FLAGS}) - include_directories(cilacc PUBLIC ${CMAKE_CURRENT_SOURCE_DIR}/include) -endif() - -## Install -#include(GNUInstallDirs) -#install(TARGETS cilacc -# RUNTIME DESTINATION bin -# LIBRARY DESTINATION lib -# ARCHIVE DESTINATION lib -# CONFIGURATIONS ${CMAKE_BUILD_TYPE} -# ) - -if (UNIX) -message ("I'd install into ${CMAKE_INSTALL_PREFIX}/lib") -install(TARGETS cilacc - LIBRARY DESTINATION lib - CONFIGURATIONS ${CMAKE_BUILD_TYPE} - ) -elseif(WIN32) -message ("I'd install into ${CMAKE_INSTALL_PREFIX} lib bin") - install(TARGETS cilacc - RUNTIME DESTINATION Library/bin - ARCHIVE DESTINATION lib - CONFIGURATIONS ${CMAKE_BUILD_TYPE} - ) -endif() - -install(DIRECTORY ${PROJECT_SOURCE_DIR}/src/Core/include/ - DESTINATION ${CMAKE_INSTALL_PREFIX}/include/cil) diff --git a/src/Core/include/dll_export.h b/src/Core/include/dll_export.h deleted file mode 100644 index b803702650..0000000000 --- a/src/Core/include/dll_export.h +++ /dev/null @@ -1,50 +0,0 @@ -// Copyright 2019 United Kingdom Research and Innovation -// Copyright 2019 The University of Manchester -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. -// -// Authors: -// CIL Developers, listed at: https://github.com/TomographicImaging/CIL/blob/master/NOTICE.txt - -#pragma once -#ifndef DLLEXPORT_H -#define DLLEXPORT_H - -#if defined(_WIN32) || defined(__WIN32__) -#if defined(dll_EXPORTS) // add by CMake -#define DLL_EXPORT __declspec(dllexport) -#define EXPIMP_TEMPLATE -#else -#define DLL_EXPORT __declspec(dllexport) -#define EXPIMP_TEMPLATE extern -#endif -#elif defined(linux) || defined(__linux) || defined(__APPLE__) -#define DLL_EXPORT -#ifndef __cdecl -#define __cdecl -#endif -#endif - -#endif -//define int64_t -#if defined(dll_EXPORTS) -using int64_t = __int64; -#endif - -#ifdef _MSC_VER -//typedef __int64 int64; // 64-bit unsigned integer - using int64 = __int64; -#else -//typedef long long int64; //64-bit unsigned integer - using int64 = long long; -#endif diff --git a/src/Core/Binning.cpp b/src/cilacc/Binning.cpp similarity index 91% rename from src/Core/Binning.cpp rename to src/cilacc/Binning.cpp index b5631267d0..076e165b39 100644 --- a/src/Core/Binning.cpp +++ b/src/cilacc/Binning.cpp @@ -24,6 +24,8 @@ #include "ipp.h" #include #include "utilities.h" +#include +#include class Binner { @@ -190,9 +192,15 @@ void Binner::bin_4D(const float* data_in, float* data_binned) } -extern "C" -{ - void Binner_delete(void* binner) { delete (Binner*)binner; } - void* Binner_new(const size_t* shape_in, const size_t* shape_out, const size_t* pixel_index_start, const size_t* binning_list) { return new Binner(shape_in, shape_out, pixel_index_start, binning_list); } - int Binner_bin(void* binner, const float* data_in, float* data_binned) { return ((Binner*)binner)->bin(data_in, data_binned); } -} +void Binner_delete(void* binner) { delete (Binner*)binner; } +void* Binner_new( + Shape shape_in, + Shape shape_out, + Shape pixel_index_start, + Shape binning_list) { + return new Binner(shape_in.data(), shape_out.data(), pixel_index_start.data(), binning_list.data()); + } +int Binner_bin(void* binner, DataInput data_in, DataBinned data_binned) { + return ((Binner*)binner)->bin(data_in.data(), data_binned.data()); + } + diff --git a/src/cilacc/CMakeLists.txt b/src/cilacc/CMakeLists.txt new file mode 100644 index 0000000000..0c867aa688 --- /dev/null +++ b/src/cilacc/CMakeLists.txt @@ -0,0 +1,90 @@ +# Copyright 2019 United Kingdom Research and Innovation +# Copyright 2019 The University of Manchester +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. +# +# Authors: +# CIL Developers, listed at: https://github.com/TomographicImaging/CIL/blob/master/NOTICE.txt +# Richard Brown (UCL) + +set (CMAKE_CXX_STANDARD 11) +set (CMAKE_CXX_STANDARD_REQUIRED ON) +if(NOT DEFINED CMAKE_BUILD_TYPE) + set(CMAKE_BUILD_TYPE RelWithDebInfo) +endif() + +message ("OpenMP_CXX_FLAGS ${OpenMP_CXX_FLAGS}") +find_package(OpenMP REQUIRED) +add_definitions(${OpenMP_CXX_FLAGS}) + +cmake_minimum_required(VERSION 3.15) + +find_package(Python REQUIRED COMPONENTS Interpreter Development.Module OPTIONAL_COMPONENTS Development.SABIModule) + +if (NOT CMAKE_BUILD_TYPE AND NOT CMAKE_CONFIGURATION_TYPES) + set(CMAKE_BUILD_TYPE Release CACHE STRING "Choose the type of build." FORCE) + set_property(CACHE CMAKE_BUILD_TYPE PROPERTY STRINGS "Debug" "Release" "MinSizeRel" "RelWithDebInfo") +endif() + +find_package(nanobind CONFIG REQUIRED) + + +####Needed to find IPP libraries +execute_process( + COMMAND "${Python_EXECUTABLE}" -c "import sysconfig; print(sysconfig.get_paths()[\"data\"])" + OUTPUT_STRIP_TRAILING_WHITESPACE OUTPUT_VARIABLE DATA_DIR) +list(APPEND CMAKE_PREFIX_PATH ${DATA_DIR}/cmake) +find_package(IPP REQUIRED CONFIG) + + + +if (${CMAKE_CXX_COMPILER_ID} STREQUAL "GNUCC") + # appends some flags + add_compile_options(-ftree-vectorize -fopt-info-vec-optimized -fopt-info-vec) + # add_compile_options(-march=native -mavx ) +endif() + + +if(${CMAKE_VERSION} VERSION_GREATER_EQUAL "3.9.0") + set (OpenMP_EXE_LINKER_FLAGS OpenMP::OpenMP_CXX) +else() + message(WARNING "Your CMake version is old. OpenMP linking flags might be incorrect.") + # need to explicitly set this. Definitely for gcc, hopefully also for other systems. + # See https://gitlab.kitware.com/cmake/cmake/issues/15392 + set (OpenMP_EXE_LINKER_FLAGS ${OpenMP_C_FLAGS}) +endif() + + + + +nanobind_add_module( + cilacc + NB_STATIC + ${CMAKE_CURRENT_SOURCE_DIR}/nanobind.cpp + ${CMAKE_CURRENT_SOURCE_DIR}/include/axpby.h + ${CMAKE_CURRENT_SOURCE_DIR}/include/Binning.h + ${CMAKE_CURRENT_SOURCE_DIR}/include/FBP_filtering.h + ${CMAKE_CURRENT_SOURCE_DIR}/include/FiniteDifferenceLibrary.h + ${CMAKE_CURRENT_SOURCE_DIR}/include/utilities.h + ${CMAKE_CURRENT_SOURCE_DIR}/axpby.cpp + ${CMAKE_CURRENT_SOURCE_DIR}/Binning.cpp + ${CMAKE_CURRENT_SOURCE_DIR}/FBP_filtering.cpp + ${CMAKE_CURRENT_SOURCE_DIR}/FiniteDifferenceLibrary.cpp + ${CMAKE_CURRENT_SOURCE_DIR}/utilities.cpp +) +target_link_libraries(cilacc PUBLIC ${OpenMP_EXE_LINKER_FLAGS} ${IPP_LIBRARIES}) +include_directories(cilacc PUBLIC + ${CMAKE_CURRENT_SOURCE_DIR}/include/ +) + +install(TARGETS cilacc LIBRARY DESTINATION cil) diff --git a/src/Core/FBP_filtering.cpp b/src/cilacc/FBP_filtering.cpp similarity index 83% rename from src/Core/FBP_filtering.cpp rename to src/cilacc/FBP_filtering.cpp index 82a694ce82..2fe3b28628 100644 --- a/src/Core/FBP_filtering.cpp +++ b/src/cilacc/FBP_filtering.cpp @@ -18,7 +18,7 @@ #include "FBP_filtering.h" -int filter_projections_avh(float * data, const float * filter, const float* weights, int order, long num_proj, long pix_y, long pix_x) +int filter_projections_avh(DataFloat data, DataFloatConst filter, DataFloatConst weights, int order, long num_proj, long pix_y, long pix_x) { //set up int width = 1 << order; @@ -61,12 +61,12 @@ int filter_projections_avh(float * data, const float * filter, const float* weig for (j = 0; j < half_pixy; j++) { row_start = (size_t)2 * j * pix_x; - out_ptr = &data[proj_start + row_start]; - ippsMul_32f_I(weights+row_start, out_ptr, 2* pix_x); + out_ptr = &data.data()[proj_start + row_start]; + ippsMul_32f_I(weights.data()+row_start, out_ptr, 2* pix_x); ippsSet_32fc({ 0.f,0.f }, src, width); ippsRealToCplx_32f(out_ptr, out_ptr + pix_x, src + offset, pix_x); ippsFFTFwd_CToC_32fc(src, dst, pSpec, pMemBuffer); - ippsMul_32f32fc_I(filter, dst, width); ++ ippsMul_32f32fc_I(filter.data(), dst, width); ippsFFTInv_CToC_32fc(dst, src, pSpec, pMemBuffer); ippsCplxToReal_32fc(src + offset, out_ptr, out_ptr+pix_x, pix_x); } @@ -76,13 +76,13 @@ int filter_projections_avh(float * data, const float * filter, const float* weig if (pix_y % 2) { row_start = (size_t)pix_y * pix_x - pix_x; - out_ptr = &data[proj_start + row_start]; + out_ptr = &data.data()[proj_start + row_start]; - ippsMul_32f_I(weights + row_start, out_ptr, pix_x); + ippsMul_32f_I(weights.data() + row_start, out_ptr, pix_x); ippsSet_32fc({ 0.f,0.f }, src, width); ippsRealToCplx_32f(out_ptr, NULL, src + offset, pix_x); ippsFFTFwd_CToC_32fc(src, dst, pSpec, pMemBuffer); - ippsMul_32f32fc_I(filter, dst, width); + ippsMul_32f32fc_I(filter.data(), dst, width); ippsFFTInv_CToC_32fc(dst, src, pSpec, pMemBuffer); ippsReal_32fc(src + offset, out_ptr, pix_x); } @@ -96,7 +96,7 @@ int filter_projections_avh(float * data, const float * filter, const float* weig ippFree(pMemSpec); return 0; } -int filter_projections_vah(float* data, const float* filter, const float* weights, int order, long pix_y, long num_proj, long pix_x) +int filter_projections_vah(DataFloat data, DataFloatConst filter, DataFloatConst weights, int order, long pix_y, long num_proj, long pix_x) { //set up int width = 1 << order; @@ -124,7 +124,7 @@ int filter_projections_vah(float* data, const float* filter, const float* weight while (k < pix_y) { size_t col_start = (size_t)k * num_proj * pix_x; - const float* weights_ptr = &weights[(size_t)k * pix_x]; + const float* weights_ptr = &weights.data()[(size_t)k * pix_x]; k++; #pragma omp parallel @@ -140,14 +140,14 @@ int filter_projections_vah(float* data, const float* filter, const float* weight for (j = 0; j < half_proj; j++) { row_start = (size_t)2 * j * pix_x; - out_ptr = &data[col_start + row_start]; + out_ptr = &data.data()[col_start + row_start]; ippsMul_32f_I(weights_ptr, out_ptr, pix_x); ippsMul_32f_I(weights_ptr, out_ptr + pix_x, pix_x); ippsSet_32fc({ 0.f,0.f }, src, width); ippsRealToCplx_32f(out_ptr, out_ptr + pix_x, src + offset, pix_x); ippsFFTFwd_CToC_32fc(src, dst, pSpec, pMemBuffer); - ippsMul_32f32fc_I(filter, dst, width); + ippsMul_32f32fc_I(filter.data(), dst, width); ippsFFTInv_CToC_32fc(dst, src, pSpec, pMemBuffer); ippsCplxToReal_32fc(src + offset, out_ptr, out_ptr + pix_x, pix_x); } @@ -157,12 +157,12 @@ int filter_projections_vah(float* data, const float* filter, const float* weight if (num_proj % 2) { row_start = (size_t)num_proj * pix_x - pix_x; - out_ptr = &data[col_start + row_start]; + out_ptr = &data.data()[col_start + row_start]; ippsMul_32f_I(weights_ptr, out_ptr, pix_x); ippsSet_32fc({ 0.f,0.f }, src, width); ippsRealToCplx_32f(out_ptr, NULL, src + offset, pix_x); ippsFFTFwd_CToC_32fc(src, dst, pSpec, pMemBuffer); - ippsMul_32f32fc_I(filter, dst, width); + ippsMul_32f32fc_I(filter.data(), dst, width); ippsFFTInv_CToC_32fc(dst, src, pSpec, pMemBuffer); ippsReal_32fc(src + offset, out_ptr, pix_x); } diff --git a/src/Core/FiniteDifferenceLibrary.cpp b/src/cilacc/FiniteDifferenceLibrary.cpp similarity index 85% rename from src/Core/FiniteDifferenceLibrary.cpp rename to src/cilacc/FiniteDifferenceLibrary.cpp index e5776bb848..87c628faff 100644 --- a/src/Core/FiniteDifferenceLibrary.cpp +++ b/src/cilacc/FiniteDifferenceLibrary.cpp @@ -17,10 +17,9 @@ // CIL Developers, listed at: https://github.com/TomographicImaging/CIL/blob/master/NOTICE.txt // Sam Tygier (UKRI-STFC) - #include "FiniteDifferenceLibrary.h" -DLL_EXPORT int openMPtest(int nThreads) +int openMPtest(int nThreads) { omp_set_num_threads(nThreads); @@ -538,7 +537,14 @@ int fdiff_adjoint_periodic(float *outimagefull, const float *inimageXfull, const return 0; } -DLL_EXPORT int fdiff4D(float *imagefull, float *gradCfull, float *gradZfull, float *gradYfull, float *gradXfull, size_t nc, size_t nz, size_t ny, size_t nx, int boundary, int direction, int nThreads) + int fdiff4D(nb::ndarray imagefull, + nb::ndarray gradCfull, + nb::ndarray gradZfull, + nb::ndarray gradYfull, + nb::ndarray gradXfull, + size_t nc, size_t nz, size_t ny, size_t nx, + int boundary, int direction, + int nThreads) { int nThreads_initial; threads_setup(nThreads, &nThreads_initial); @@ -547,22 +553,28 @@ DLL_EXPORT int fdiff4D(float *imagefull, float *gradCfull, float *gradZfull, flo if (boundary) { if (direction) - status = fdiff_direct_periodic(imagefull, gradXfull, gradYfull, gradZfull, gradCfull, nx, ny, nz, nc); + status = fdiff_direct_periodic(imagefull.data(), gradXfull.data(), gradYfull.data(), gradZfull.data(), gradCfull.data(), nx, ny, nz, nc); else - status = fdiff_adjoint_periodic(imagefull, gradXfull, gradYfull, gradZfull, gradCfull, nx, ny, nz, nc); + status = fdiff_adjoint_periodic(imagefull.data(), gradXfull.data(), gradYfull.data(), gradZfull.data(), gradCfull.data(), nx, ny, nz, nc); } else { if (direction) - status = fdiff_direct_neumann(imagefull, gradXfull, gradYfull, gradZfull, gradCfull, nx, ny, nz, nc); + status = fdiff_direct_neumann(imagefull.data(), gradXfull.data(), gradYfull.data(), gradZfull.data(), gradCfull.data(), nx, ny, nz, nc); else - status = fdiff_adjoint_neumann(imagefull, gradXfull, gradYfull, gradZfull, gradCfull, nx, ny, nz, nc); + status = fdiff_adjoint_neumann(imagefull.data(), gradXfull.data(), gradYfull.data(), gradZfull.data(), gradCfull.data(), nx, ny, nz, nc); } omp_set_num_threads(nThreads_initial); return status; } -DLL_EXPORT int fdiff3D(float *imagefull, float *gradZfull, float *gradYfull, float *gradXfull, size_t nz, size_t ny, size_t nx, int boundary, int direction, int nThreads) +int fdiff3D(nb::ndarray imagefull, + nb::ndarray gradZfull, + nb::ndarray gradYfull, + nb::ndarray gradXfull, + size_t nz, size_t ny, size_t nx, + int boundary, int direction, + int nThreads) { int nThreads_initial; threads_setup(nThreads, &nThreads_initial); @@ -571,22 +583,27 @@ DLL_EXPORT int fdiff3D(float *imagefull, float *gradZfull, float *gradYfull, flo if (boundary) { if (direction) - status = fdiff_direct_periodic(imagefull, gradXfull, gradYfull, gradZfull, NULL, nx, ny, nz, 1); + status = fdiff_direct_periodic(imagefull.data(), gradXfull.data(), gradYfull.data(), gradZfull.data(), NULL, nx, ny, nz, 1); else - status = fdiff_adjoint_periodic(imagefull, gradXfull, gradYfull, gradZfull, NULL, nx, ny, nz, 1); + status = fdiff_adjoint_periodic(imagefull.data(), gradXfull.data(), gradYfull.data(), gradZfull.data(), NULL, nx, ny, nz, 1); } else { if (direction) - status = fdiff_direct_neumann(imagefull, gradXfull, gradYfull, gradZfull, NULL, nx, ny, nz, 1); + status = fdiff_direct_neumann(imagefull.data(), gradXfull.data(), gradYfull.data(), gradZfull.data(), NULL, nx, ny, nz, 1); else - status = fdiff_adjoint_neumann(imagefull, gradXfull, gradYfull, gradZfull, NULL, nx, ny, nz, 1); + status = fdiff_adjoint_neumann(imagefull.data(), gradXfull.data(), gradYfull.data(), gradZfull.data(), NULL, nx, ny, nz, 1); } omp_set_num_threads(nThreads_initial); return status; } -DLL_EXPORT int fdiff2D(float *imagefull, float *gradYfull, float *gradXfull, size_t ny, size_t nx, int boundary, int direction, int nThreads) +int fdiff2D(nb::ndarray imagefull, + nb::ndarray gradYfull, + nb::ndarray gradXfull, + size_t ny, size_t nx, + int boundary, int direction, + int nThreads) { int nThreads_initial; threads_setup(nThreads, &nThreads_initial); @@ -595,16 +612,16 @@ DLL_EXPORT int fdiff2D(float *imagefull, float *gradYfull, float *gradXfull, siz if (boundary) { if (direction) - status = fdiff_direct_periodic(imagefull, gradXfull, gradYfull, NULL, NULL, nx, ny, 1, 1); + status = fdiff_direct_periodic(imagefull.data(), gradXfull.data(), gradYfull.data(), NULL, NULL, nx, ny, 1, 1); else - status = fdiff_adjoint_periodic(imagefull, gradXfull, gradYfull, NULL, NULL, nx, ny, 1, 1); + status = fdiff_adjoint_periodic(imagefull.data(), gradXfull.data(), gradYfull.data(), NULL, NULL, nx, ny, 1, 1); } else { if (direction) - status = fdiff_direct_neumann(imagefull, gradXfull, gradYfull, NULL, NULL, nx, ny, 1, 1); + status = fdiff_direct_neumann(imagefull.data(), gradXfull.data(), gradYfull.data(), NULL, NULL, nx, ny, 1, 1); else - status = fdiff_adjoint_neumann(imagefull, gradXfull, gradYfull, NULL, NULL, nx, ny, 1, 1); + status = fdiff_adjoint_neumann(imagefull.data(), gradXfull.data(), gradYfull.data(), NULL, NULL, nx, ny, 1, 1); } omp_set_num_threads(nThreads_initial); diff --git a/src/Core/axpby.cpp b/src/cilacc/axpby.cpp similarity index 68% rename from src/Core/axpby.cpp rename to src/cilacc/axpby.cpp index 3bdcab726a..c147a5d30f 100644 --- a/src/Core/axpby.cpp +++ b/src/cilacc/axpby.cpp @@ -104,7 +104,13 @@ int daxpby_asbv(const double * x, const double * y, double * out, double a, cons } return 0; } -DLL_EXPORT int saxpby(const float * x, const float * y, float * out, const float *a, int a_type, const float* b, int b_type, int64 size, int nThreads) + +int saxpby(DataFloatInput x, DataFloatInput y, + DataFloatOutput out, + DataFloatInput a, int type_a, + DataFloatInput b, int type_b, + int64 size, int nThreads + ) { //type = 0 float //type = 1 array of floats @@ -114,20 +120,25 @@ DLL_EXPORT int saxpby(const float * x, const float * y, float * out, const float int nThreads_initial; threads_setup(nThreads, &nThreads_initial); - if (a_type == 0 && b_type == 0) - saxpby_asbs(x, y, out, *a, *b, size, nThreads); - else if (a_type == 1 && b_type == 1) - saxpby_avbv(x, y, out, a, b, size, nThreads); - else if (a_type == 0 && b_type == 1) - saxpby_asbv(x, y, out, *a, b, size, nThreads); - else if (a_type == 1 && b_type == 0) - saxpby_asbv(y, x, out, *b, a, size, nThreads); + if (type_a == 0 && type_b == 0) + saxpby_asbs(x.data(), y.data(), out.data(), *a.data(), *b.data(), size, nThreads); + else if (type_a == 1 && type_b == 1) + saxpby_avbv(x.data(), y.data(), out.data(), a.data(), b.data(), size, nThreads); + else if (type_a == 0 && type_b == 1) + saxpby_asbv(x.data(), y.data(), out.data(), *a.data(), b.data(), size, nThreads); + else if (type_a == 1 && type_b == 0) + saxpby_asbv(y.data(), x.data(), out.data(), *b.data(), a.data(), size, nThreads); omp_set_num_threads(nThreads_initial); return 0; } -DLL_EXPORT int daxpby(const double * x, const double * y, double * out, const double *a, int a_type, const double* b, int b_type, int64 size, int nThreads) + +int daxpby(DataDoubleInput x, DataDoubleInput y, + DataDoubleOutput out, + DataDoubleInput a, int type_a, + DataDoubleInput b, int type_b, + int64 size, int nThreads) { //type = 0 double //type = 1 array of double @@ -137,14 +148,14 @@ DLL_EXPORT int daxpby(const double * x, const double * y, double * out, const do int nThreads_initial; threads_setup(nThreads, &nThreads_initial); - if (a_type == 0 && b_type == 0) - daxpby_asbs(x, y, out, *a, *b, size, nThreads); - else if (a_type == 1 && b_type == 1) - daxpby_avbv(x, y, out, a, b, size, nThreads); - else if (a_type == 0 && b_type == 1) - daxpby_asbv(x, y, out, *a, b, size, nThreads); - else if (a_type == 1 && b_type == 0) - daxpby_asbv(y, x, out, *b, a, size, nThreads); + if (type_a == 0 && type_b == 0) + daxpby_asbs(x.data(), y.data(), out.data(), *a.data(), *b.data(), size, nThreads); + else if (type_a == 1 && type_b == 1) + daxpby_avbv(x.data(), y.data(), out.data(), a.data(), b.data(), size, nThreads); + else if (type_a == 0 && type_b == 1) + daxpby_asbv(x.data(), y.data(), out.data(), *a.data(), b.data(), size, nThreads); + else if (type_a == 1 && type_b == 0) + daxpby_asbv(y.data(), x.data(), out.data(), *b.data(), a.data(), size, nThreads); omp_set_num_threads(nThreads_initial); diff --git a/src/Core/include/Binning.h b/src/cilacc/include/Binning.h similarity index 65% rename from src/Core/include/Binning.h rename to src/cilacc/include/Binning.h index 669a10c0c7..c2a343790b 100644 --- a/src/Core/include/Binning.h +++ b/src/cilacc/include/Binning.h @@ -15,16 +15,22 @@ // // Authors: // CIL Developers, listed at: https://github.com/TomographicImaging/CIL/blob/master/NOTICE.txt -#ifndef _BINNER_H_ -#define _BINNER_H_ #include -#include "dll_export.h" +#include +#include + +namespace nb = nanobind; + +using Shape = nb::ndarray; +using DataInput = nb::ndarray; +using DataBinned = nb::ndarray; + +void Binner_delete(void* binner); +void* Binner_new(Shape shape_in, + Shape shape_out, + Shape pixel_index_start, + Shape binning_list +); +int Binner_bin(void* binner, DataInput data_in, DataBinned data_binned); -extern "C" -{ - DLL_EXPORT void Binner_delete(void* binner); - DLL_EXPORT void* Binner_new(const size_t* shape_in, const size_t* shape_out, const size_t* pixel_index_start, const size_t* binning_list); - DLL_EXPORT int Binner_bin(void* binner, const float* data_in, float* data_binned); -} -#endif diff --git a/src/Core/include/FBP_filtering.h b/src/cilacc/include/FBP_filtering.h similarity index 68% rename from src/Core/include/FBP_filtering.h rename to src/cilacc/include/FBP_filtering.h index 8a8db3b499..d0af6867c7 100644 --- a/src/Core/include/FBP_filtering.h +++ b/src/cilacc/include/FBP_filtering.h @@ -22,15 +22,13 @@ #include #include #include -#include "dll_export.h" #include "utilities.h" +#include +namespace nb = nanobind; -#ifdef __cplusplus -extern "C" { -#endif - DLL_EXPORT int filter_projections_avh(float* data, const float* filter, const float* weights, int order, long num_proj, long pix_y, long pix_x); - DLL_EXPORT int filter_projections_vah(float* data, const float* filter, const float* weights, int order, long pix_y, long num_proj, long pix_x); -#ifdef __cplusplus -} -#endif +using DataFloatConst = nb::ndarray; +using DataFloat = nb::ndarray; + +int filter_projections_avh(DataFloat data, DataFloatConst filter, DataFloatConst weights, int order, long num_proj, long pix_y, long pix_x); +int filter_projections_vah(DataFloat data, DataFloatConst filter, DataFloatConst weights, int order, long pix_y, long num_proj, long pix_x); diff --git a/src/Core/include/FiniteDifferenceLibrary.h b/src/cilacc/include/FiniteDifferenceLibrary.h similarity index 67% rename from src/Core/include/FiniteDifferenceLibrary.h rename to src/cilacc/include/FiniteDifferenceLibrary.h index 80d11c9740..1a50d0684d 100644 --- a/src/Core/include/FiniteDifferenceLibrary.h +++ b/src/cilacc/include/FiniteDifferenceLibrary.h @@ -19,24 +19,39 @@ #include #include #include -#include "omp.h" -#include "dll_export.h" +#include #include "utilities.h" +#include +namespace nb = nanobind; + + int fdiff_direct_neumann(const float *inimagefull, float *outimageXfull, float *outimageYfull, float *outimageZfull, float *outimageCfull, size_t nx, size_t ny, size_t nz, size_t nc); int fdiff_direct_periodic(const float *inimagefull, float *outimageXfull, float *outimageYfull, float *outimageZfull, float *outimageCfull, size_t nx, size_t ny, size_t nz, size_t nc); int fdiff_adjoint_neumann(float *outimagefull, const float *inimageXfull, const float *inimageYfull, const float *inimageZfull, const float *inimageCfull, size_t nx, size_t ny, size_t nz, size_t nc); int fdiff_adjoint_periodic(float *outimagefull, const float *inimageXfull, const float *inimageYfull, const float *inimageZfull, const float *inimageCfull, size_t nx, size_t ny, size_t nz, size_t nc); -#ifdef __cplusplus -extern "C" { -#endif -DLL_EXPORT int openMPtest(int nThreads); -DLL_EXPORT int fdiff4D(float *imagefull, float *gradCfull, float *gradZfull, float *gradYfull, float *gradXfull, size_t nc, size_t nz, size_t ny, size_t nx, int boundary, int direction, int nThreads); -DLL_EXPORT int fdiff3D(float *imagefull, float *gradZfull, float *gradYfull, float *gradXfull, size_t nz, size_t ny, size_t nx, int boundary, int direction, int nThreads); -DLL_EXPORT int fdiff2D(float *imagefull, float *gradYfull, float *gradXfull, size_t ny, size_t nx, int boundary, int direction, int nThreads); +int openMPtest(int nThreads); +int fdiff4D(nb::ndarray imagefull, + nb::ndarray gradCfull, + nb::ndarray gradZfull, + nb::ndarray gradYfull, + nb::ndarray gradXfull, + size_t nc, size_t nz, size_t ny, + size_t nx, int boundary, int direction, + int nThreads); +int fdiff3D(nb::ndarray imagefull, + nb::ndarray gradZfull, + nb::ndarray gradYfull, + nb::ndarray gradXfull, + size_t nz, size_t ny, size_t nx, + int boundary, int direction, + int nThreads); +int fdiff2D(nb::ndarray imagefull, + nb::ndarray gradYfull, + nb::ndarray gradXfull, + size_t ny, size_t nx, + int boundary, int direction, + int nThreads); -#ifdef __cplusplus -} -#endif diff --git a/src/Core/include/axpby.h b/src/cilacc/include/axpby.h similarity index 71% rename from src/Core/include/axpby.h rename to src/cilacc/include/axpby.h index 048a9b7e98..cefc4c44cc 100644 --- a/src/Core/include/axpby.h +++ b/src/cilacc/include/axpby.h @@ -15,12 +15,24 @@ // // Authors: // CIL Developers, listed at: https://github.com/TomographicImaging/CIL/blob/master/NOTICE.txt + #include #include #include -#include "omp.h" -#include "dll_export.h" +#include #include "utilities.h" +#include + +namespace nb = nanobind; + +using int64 = long long; + +using DataFloatInput = nb::ndarray; +using DataDoubleInput = nb::ndarray; + +using DataFloatOutput = nb::ndarray; +using DataDoubleOutput = nb::ndarray; + int saxpby_asbs(const float * x, const float * y, float * out, float a, float b, int64 size, int nThreads); int saxpby_avbv(const float * x, const float * y, float * out, const float * a, const float * b, int64 size, int nThreads); @@ -29,13 +41,14 @@ int daxpby_asbs(const double * x, const double * y, double * out, double a, doub int daxpby_avbv(const double * x, const double * y, double * out, const double * a, const double * b, int64 size, int nThreads); int daxpby_asbv(const double * x, const double * y, double * out, double a, const double * b, int64 size, int nThreads); -#ifdef __cplusplus -extern "C" { -#endif - -DLL_EXPORT int saxpby(const float * x, const float * y, float * out, const float * a, int type_a, const float * b, int type_b, int64 size, int nThreads); -DLL_EXPORT int daxpby(const double * x, const double * y, double * out, const double * a, int type_a, const double * b, int type_b, int64 size, int nThreads); +int saxpby(DataFloatInput x, DataFloatInput y, + DataFloatOutput out, + DataFloatInput a, int type_a, + DataFloatInput b, int type_b, + int64 size, int nThreads); +int daxpby(DataDoubleInput x, DataDoubleInput y, + DataDoubleOutput out, + DataDoubleInput a, int type_a, + DataDoubleInput b, int type_b, + int64 size, int nThreads); -#ifdef __cplusplus -} -#endif diff --git a/src/Core/include/utilities.h b/src/cilacc/include/utilities.h similarity index 97% rename from src/Core/include/utilities.h rename to src/cilacc/include/utilities.h index 54a75ccc16..f3d0a47838 100644 --- a/src/Core/include/utilities.h +++ b/src/cilacc/include/utilities.h @@ -15,6 +15,7 @@ // // Authors: // CIL Developers, listed at: https://github.com/TomographicImaging/CIL/blob/master/NOTICE.txt -#include "omp.h" + +#include void threads_setup(int nThreads_requested, int *nThreads_current); diff --git a/src/cilacc/nanobind.cpp b/src/cilacc/nanobind.cpp new file mode 100644 index 0000000000..14adfc4194 --- /dev/null +++ b/src/cilacc/nanobind.cpp @@ -0,0 +1,25 @@ + +#include +#include "axpby.h" +#include "Binning.h" +#include "FBP_filtering.h" +#include "FiniteDifferenceLibrary.h" + +NB_MODULE(cilacc, m) { + m.def("saxpby", &saxpby); + m.def("daxpby", &daxpby); + + m.def("Binner_delete", &Binner_delete); + m.def("Binner_new", &Binner_new); + m.def("Binner_bin", &Binner_bin); + + m.def("filter_projections_avh", &filter_projections_avh); + m.def("filter_projections_vah", &filter_projections_vah); + + m.def("openMPtest", &openMPtest); + m.def("fdiff4D", &fdiff4D); + m.def("fdiff3D", &fdiff3D); + m.def("fdiff2D", &fdiff2D); 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