Merge branch 'development'

.appveyor.yml

@@ -17,18 +17,27 @@ build:
 matrix:
     fast_finish: true
 
-before_build:
-  - cmd: if "%PLATFORM%"=="x86" call "C:\Program Files (x86)\Microsoft Visual Studio\2017\Community\VC\Auxiliary\Build\vcvars32.bat"
-  - cmd: if "%PLATFORM%"=="x64" call "C:\Program Files (x86)\Microsoft Visual Studio\2017\Community\VC\Auxiliary\Build\vcvars64.bat"
-  - mkdir build
-  - cd build
+environment:
+  matrix:
+  - PYTHON: "C:\\Python36-x64"
+
+install:
+- git submodule update --init --recursive
+- set PATH=%PYTHON%;%PYTHON%\Scripts;%PATH%
+- pip install -r requirements.txt
 
-  - cmd: if "%PLATFORM%"=="x86" set GENERATOR="Visual Studio 15 2017"
-  - cmd: if "%PLATFORM%"=="x64" set GENERATOR="Visual Studio 15 2017 Win64"
-  - cmd: cmake .. -DSTK_BUILD_TESTS=1 -DSTK_WARNINGS_ARE_ERRORS=1 -DCMAKE_BUILD_TYPE=%CONFIGURATION% -G%GENERATOR%
+before_build:
+- mkdir build
+- cd build
+- cmake .. -DCMAKE_BUILD_TYPE=%CONFIGURATION% -DCMAKE_GENERATOR_PLATFORM=%PLATFORM% -DSTK_BUILD_TESTS=1 -DSTK_WARNINGS_ARE_ERRORS=1
 
 build_script:
-  - cmd: cmake --build . --config %CONFIGURATION%
+- cmake --build . --config %CONFIGURATION%
+- cd ..
+- python setup.py install -DCMAKE_GENERATOR_PLATFORM=%PLATFORM%
 
 test_script:
-  - ctest --output-on-failure
+- cd build
+- ctest --output-on-failure
+- cd ..
+- python -m unittest discover test

.gitignore

@@ -1,5 +1,9 @@
 build_debug/
 build_vs/
 build/
+dist/
+*.egg-info
+__pycache__
+.env/
 .vscode/
-.ycm_extra_conf.py
+.ycm_extra_conf.py

.gitmodules

@@ -0,0 +1,3 @@
+[submodule "third_party/pybind11"]
+	path = third_party/pybind11
+	url = https://github.com/pybind/pybind11.git

.travis.yml

@@ -1,37 +1,56 @@
-language: cpp
+language: python
+python:
+- 3.6
 
 matrix:
-  fast_finish: true
   include:
-  - os: linux
+  - name: trusty
+    os: linux
     dist: trusty
-  - os: linux
+    env: 
+      - PYTHON_EXECUTABLE=~/virtualenv/python3.6/bin/python
+  - name: xenial
+    os: linux
     dist: xenial
-  - os: linux
+    env: 
+      - PYTHON_EXECUTABLE=~/virtualenv/python3.6/bin/python
+  - name: g++8
+    os: linux
     addons:
       apt:
         sources:
-          - ubuntu-toolchain-r-test
+        - ubuntu-toolchain-r-test
         packages:
-          - g++-6
-    env:
-      - MATRIX_EVAL="CC=gcc-6 && CXX=g++-6"
-  - os: linux
-    addons:
-      apt:
-        sources:
-          - ubuntu-toolchain-r-test
-        packages:
-          - g++-7
-    env:
-      - MATRIX_EVAL="CC=gcc-7 && CXX=g++-7"
+        - g++-8
+    before_install:
+    - sudo update-alternatives --install /usr/bin/g++ g++ /usr/bin/g++-8 90
+    - sudo update-alternatives --install /usr/bin/gcc gcc /usr/bin/gcc-8 90
+    env: 
+      - PYTHON_EXECUTABLE=~/virtualenv/python3.6/bin/python
   - name: osx
     os: osx
     language: generic
+    before_install:
+    - brew install llvm libomp
+    - python3 -m pip install virtualenv
+    - virtualenv venv -p python3
+    - source venv/bin/activate
+    env:
+      - PYTHON_EXECUTABLE=../venv/bin/python
+      - HOMEBREW_NO_AUTO_UPDATE=1
+      - CC=/usr/local/opt/llvm/bin/clang
+      - CXX=/usr/local/opt/llvm/bin/clang++
+
+install:
+- pip install -r requirements.txt
 
 script:
 - mkdir build
 - cd build
-- cmake .. -DCMAKE_BUILD_TYPE=Release -DSTK_BUILD_TESTS=1 -DSTK_WARNINGS_ARE_ERRORS=1
+- cmake .. -DCMAKE_BUILD_TYPE=Release -DSTK_BUILD_TESTS=1
+  -DSTK_BUILD_PYTHON_WRAPPER=ON -DPYTHON_EXECUTABLE=$PYTHON_EXECUTABLE
 - cmake --build . --config Release
-- ctest --output-on-failure
+- ctest --output-on-failure
+- cd ..
+- python setup.py install
+- python -m unittest discover test

CMakeLists.txt

@@ -2,6 +2,7 @@ cmake_minimum_required(VERSION 3.8)
 
 option(STK_BUILD_EXAMPLES "Build examples" ON)
 option(STK_BUILD_TESTS "Build unit tests" ON)
+option(STK_BUILD_PYTHON_WRAPPER "Build Python wrapper" OFF)
 option(STK_USE_CUDA "Enables CUDA support" OFF)
 option(STK_WARNINGS_ARE_ERRORS "Warnings are treated as errors" OFF)
 option(STK_BUILD_WITH_DEBUG_INFO "Includes debug info in release builds" OFF)
@@ -56,7 +57,9 @@ if (MSVC)
         set(EXTRA_FLAGS "${extra_flags} /fp:fast")
     endif()
 elseif(CMAKE_CXX_COMPILER_ID MATCHES "GNU")
-    set(EXTRA_FLAGS "-Wall -Wextra -pedantic -Wno-missing-field-initializers")
+    set(EXTRA_FLAGS "-Wall -Wextra -pedantic -Wno-missing-field-initializers -Wno-attributes")
+
+    # -Wno-attributes thanks to pybind11
 
     if (STK_WARNINGS_ARE_ERRORS)
         set(EXTRA_FLAGS "${extra_flags} -Werror")
@@ -88,6 +91,7 @@ endif()
 if (STK_USE_CUDA)
     add_definitions(-DSTK_USE_CUDA)
     enable_language(CUDA)
+    set(CMAKE_CUDA_STANDARD 11)
 
     if (STK_ENABLE_FAST_MATH)
         set(CMAKE_CUDA_FLAGS "${CMAKE_CUDA_FLAGS} --use_fast_math")
@@ -109,10 +113,11 @@ set(CMAKE_C_FLAGS_RELEASE "${CMAKE_C_FLAGS_RELEASE} ${EXTRA_FLAGS_RELEASE}")
 set(CMAKE_EXE_LINKER_FLAGS "${CMAKE_EXE_LINKER_FLAGS} ${EXTRA_LINK_FLAGS}")
 set(CMAKE_EXE_LINKER_FLAGS_RELEASE "${CMAKE_EXE_LINKER_FLAGS_RELEASE} ${EXTRA_LINK_FLAGS_RELEASE}")
 
+include_directories(src)
+
 # TODO: Determine QNANHIBIT for NrrdIO
 set(QNANHIBIT 1)
 
-
 if(NOT WIN32)
     find_package(ZLIB QUIET)
     find_package(NIFTI QUIET)

MANIFEST.in

@@ -0,0 +1,4 @@
+recursive-include src *
+recursive-include third_party *
+include cmake/*
+include CMakeLists.txt

README.md

@@ -23,3 +23,37 @@ CMake was not compatible with the one required by CUDA, it is possible to
 specify a different executable with `-DCMAKE_CUDA_FLAGS="-ccbin gcc-XX"`, where
 `gcc-XX` is a version of `gcc` compatible with your CUDA version.
 
+# Python API
+
+A minimalistic Python API is also provided.
+
+## Install
+
+```bash
+python setup.py install
+```
+
+## Example usage
+
+```python
+import stk
+import numpy as np
+
+# Create volume directly from numpy
+vol = stk.Volume(np.zeros((5,5,5)).astype(np.float32), spacing=(2,2,2))
+# or read volume from file
+vol = stk.read_volume('test.nrrd')
+
+# Modify data (numpy array points to the volume data)
+data = np.array(vol, copy=False)
+data[0:10] = 0.0
+
+# Access meta data
+vol.origin = (2, 2, 2)
+vol.spacing = (3, 3, 3)
+
+# Write volume
+stk.write_volume('test-out.nrrd', vol)
+```
+
+

requirements.txt

@@ -0,0 +1 @@
+numpy

setup.py

@@ -0,0 +1,91 @@
+import os
+import sys
+import platform
+import subprocess
+
+from pprint import pprint
+
+from setuptools import setup, Extension
+from setuptools.command.build_ext import build_ext
+
+with open("README.md", encoding="utf-8") as f:
+    readme = f.read()
+
+# Parse command line flags
+flags = {k: 'OFF' for k in ['--debug', '--use-cuda', '--use-itk']}
+for flag in flags.keys():
+    if flag in sys.argv:
+        flags[flag] = 'ON'
+        sys.argv.remove(flag)
+
+# Command line flags forwarded to CMake
+cmake_cmd_args = []
+for f in sys.argv:
+    if f.startswith('-D'):
+        cmake_cmd_args.append(f)
+
+for f in cmake_cmd_args:
+    sys.argv.remove(f)
+
+
+class CMakeExtension(Extension):
+    def __init__(self, name, cmake_lists_dir=''):
+        Extension.__init__(self, name, sources=[])
+        self.cmake_lists_dir = os.path.abspath(cmake_lists_dir)
+
+
+class CMakeBuild(build_ext):
+    def run(self):
+        try:
+            subprocess.check_output(['cmake', '--version'])
+        except OSError:
+            raise RuntimeError('Cannot find CMake executable')
+
+        for ext in self.extensions:
+            self.build_extension(ext)
+
+    def build_extension(self, ext):
+
+        extdir = os.path.abspath(os.path.dirname(self.get_ext_fullpath(ext.name)))
+        cfg = 'Debug' if flags['--debug'] == 'ON' else 'Release'
+        build_args = ['--config', cfg]
+
+        cmake_args = [
+            '-DSTK_BUILD_PYTHON_WRAPPER=ON',
+            '-DSTK_BUILD_TESTS=OFF',
+            '-DSTK_BUILD_WITH_DEBUG_INFO=%s' % ('ON' if cfg == 'Debug' else 'OFF'),
+            '-DCMAKE_BUILD_TYPE=%s' % cfg,
+            '-DSTK_USE_CUDA=%s' % flags['--use-cuda'],
+            '-DSTK_ITK_BRIDGE=%s' % flags['--use-itk'],
+            '-DPYTHON_EXECUTABLE=' + sys.executable,
+            '-DCMAKE_LIBRARY_OUTPUT_DIRECTORY=' + extdir,
+        ]
+
+        if platform.system() == "Windows":
+            cmake_args += ['-DCMAKE_LIBRARY_OUTPUT_DIRECTORY_{}={}'.format(cfg.upper(), extdir)]
+
+        cmake_args += cmake_cmd_args
+        pprint(cmake_args)
+
+        if not os.path.exists(self.build_temp):
+            os.makedirs(self.build_temp)
+
+        subprocess.check_call(['cmake', ext.cmake_lists_dir] + cmake_args, cwd=self.build_temp)
+        subprocess.check_call(['cmake', '--build', '.'] + build_args, cwd=self.build_temp)
+
+
+setup(
+    name='python-stk',
+    version='0.4',
+    author='Simon Ekström',
+    author_email='',
+    description='',
+    long_description=readme,
+    long_description_content_type='text/markdown',
+    install_requires=['numpy'],
+    packages=['stk'],
+    ext_modules=[CMakeExtension('_stk', '.')],
+    cmdclass={'build_ext': CMakeBuild},
+    zip_safe=False,
+)
+