Merge branch 'development'

.appveyor.yml

@@ -0,0 +1,42 @@
+version: '{branch}-{build}'
+
+image:
+- Visual Studio 2017
+
+platform:
+- x64
+
+configuration:
+- Release
+
+build:
+  parallel: true
+  verbosity: minimal
+
+matrix:
+  fast_finish: true
+
+environment:
+  matrix:
+  - PYTHON: "C:\\Python36-x64"
+
+install:
+- git submodule update --init --recursive
+- set PATH=%PYTHON%;%PYTHON%\Scripts;%PATH%
+- pip install -r requirements.txt
+
+before_build:
+- mkdir build
+- cd build
+- cmake .. -DCMAKE_BUILD_TYPE=%CONFIGURATION% -DCMAKE_GENERATOR_PLATFORM=%PLATFORM% -DDF_BUILD_TESTS=1 -DDF_WARNINGS_ARE_ERRORS=1
+
+build_script:
+- cmake --build . --config %CONFIGURATION%
+- cd ..
+- python setup.py install -DCMAKE_GENERATOR_PLATFORM=%PLATFORM%
+
+test_script:
+- cd build
+- ctest --output-on-failure
+- cd ..
+- python -m unittest discover test

.travis.yml

@@ -1,39 +1,43 @@
-language:
-- cpp
-- python
+language: python
 python:
 - 3.6
-compiler:
-- gcc
-dist: trusty
+
 matrix:
   include:
-  - env: CONFIG=Release
-  - env: CONFIG=Debug
-git:
-  submodules: false
-before_install:
-- sed -i 's,git@github.com:,https://github.com/,g' .gitmodules
-- git submodule update --init --recursive
-- sudo add-apt-repository -y ppa:ubuntu-toolchain-r/test
-- sudo apt-get update -qq
-- pyenv global 3.6
+  - name: trusty
+    os: linux
+    dist: trusty
+  - name: xenial
+    os: linux
+    dist: xenial
+  - name: g++8
+    os: linux
+    addons:
+      apt:
+        sources:
+        - ubuntu-toolchain-r-test
+        packages:
+        - 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
+
 install:
-- sudo apt-get install -qq g++-8
-- sudo update-alternatives --install /usr/bin/g++ g++ /usr/bin/g++-8 90
-- pip3 install sphinx m2r numpy SimpleITK sphinx_rtd_theme PyYAML
+- pip install -r requirements.txt
+
 script:
 - mkdir build
 - cd build
-- cmake .. -DDF_BUILD_TESTS=1 -DDF_WARNINGS_ARE_ERRORS=1 -DCMAKE_BUILD_TYPE=${CONFIG} -DDF_BUILD_PYTHON_WRAPPER=ON -DDF_BUILD_DOCS=ON
-- cmake --build . --config ${CONFIG}
+- cmake .. -DCMAKE_BUILD_TYPE=Release -DDF_BUILD_TESTS=1 -DDF_WARNINGS_ARE_ERRORS=1
+  -DDF_BUILD_PYTHON_WRAPPER=ON -DPYTHON_EXECUTABLE=~/virtualenv/python3.6/bin/python
+- cmake --build . --config Release
 - ctest --output-on-failure
 - cd ..
-- python3 setup.py install --user
-- python3 -m unittest discover test
+- python setup.py install
+- python -m unittest discover test
+
 notifications:
   slack:
     secure: 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
     on_success: change
     on_failure: always
-

CMakeLists.txt

@@ -70,7 +70,7 @@ if(DF_STACK_TRACE)
 endif()
 
 set(CMAKE_POSITION_INDEPENDENT_CODE ON)
-set(CMAKE_CXX_STANDARD 17)
+set(CMAKE_CXX_STANDARD 11)
 set(CMAKE_CXX_STANDARD_REQUIRED ON)
 set(CMAKE_CXX_EXTENSIONS OFF)
 
@@ -124,6 +124,7 @@ if (DF_USE_CUDA)
     add_definitions(-DDF_USE_CUDA)
     add_definitions(-DSTK_USE_CUDA)
     enable_language(CUDA)
+    set(CMAKE_CUDA_STANDARD 14)
 
     if (DF_ENABLE_FAST_MATH)
         set(CMAKE_CUDA_FLAGS "${CMAKE_CUDA_FLAGS} --use_fast_math")

MANIFEST.in

@@ -1,2 +1,4 @@
 recursive-include src *
 recursive-include third_party *
+include cmake/*
+include CMakeLists.txt

README.md

@@ -2,13 +2,27 @@
 
 deform is an implementation of an efficient graph-cut based method for dense deformable image registration. If you find this useful, please cite https://arxiv.org/abs/1810.08427.
 
-## Prerequisites
+The method can be used either as a module through Python (recommended) or a standalone executable. Currently no pre-built binaries for the standalone executable are provided, but the Python module (excluding GPU support) can be installed through pip.
+
+## Install
+
+To download and install the pre-compiled Python module from pip:
+
+```
+pip install pydeform
+```
+
+Note: to enable GPU-supported registration you're currently required to compile the software yourself. See the section below. 
+
+## Building
+
+### Prerequisites
 * CMake : https://cmake.org/
 
 Optional
 * ISPC : https://ispc.github.io/
 
-## Download
+### Download
 
 Retrieve the repository and associated dependencies by running
 
@@ -18,15 +32,15 @@ $ cd deform
 $ git submodule update --init --recursive
 ```
 
-## Build
+### Build
 
 Use CMake (>=3.8) to generate build options of your own choosing.
 
 If CMake cannot find the ISPC executable on your installation, it is possible
 to hint the installation directory with `-DISPC_DIR_HINTS`, or to specify the
 full path to the executable with `-DISPC_EXECUTABLE`.
 
-### Build options
+#### Build options
 
 The build can be configured with the following CMake boolean options:
 
@@ -45,7 +59,7 @@ The build can be configured with the following CMake boolean options:
 + `DF_ENABLE_MICROPROFILE`: Enable `microprofile` profiler (default: `OFF`)
 + `DF_ENABLE_NVTOOLSEXT`: Enable `nvtoolsext` profiler (default: `OFF`)
 
-## Build and install Python wrapper
+### Build and install Python wrapper
 ```
 # python setup.py install
 ```
@@ -58,8 +72,9 @@ Flags accepted by `setup.py`:
 
 Additional flags starting with `-D` are also recognised and forwarded to CMake.
 
-## Run
-To perform a registration
+# Run
+To perform a registration using the standalone executable
+
 `deform registration -p <param file> -f0 <fixed_0> ... -f<i> <fixed_i> -m0 <moving_0> ... -m<i> <moving_i>`
 
 | Argument                    |                                             |
@@ -90,6 +105,7 @@ To perform a registration
 ```yaml
 pyramid_levels: 6
 pyramid_stop_level: 0
+regularize_initial_displacement: false
 constraints_weight: 1000.0
 landmarks_weight: 1.0
 landmarks_decay: 2.0
@@ -143,6 +159,10 @@ halves the resolution of the input volumes. Setting `pyramid_stop_level` to > 0
 specifies that the registration should not be run on the original resolution
 (level 0).
 
+`regularize_initial_displacement` controls whether to include the initial
+displacement in the regularization. This is disabled by default, meaning the
+initial displacement have no effect on the regularization.
+
 `constraints_weight` sets the weight that is applied for constrained voxels. A
 really high value means hard constraints while a lower value may allow
 constraints to move a certain amount. Cost for constrained voxels are applied

requirements.txt

@@ -0,0 +1,3 @@
+numpy
+SimpleITK
+PyYAML

setup.py

@@ -8,6 +8,9 @@
 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-ispc', '--use-itk']}
 for flag in flags.keys():
@@ -20,7 +23,9 @@
 for f in sys.argv:
     if f.startswith('-D'):
         cmake_cmd_args.append(f)
-        sys.argv.remove(f)
+
+for f in cmake_cmd_args:
+    sys.argv.remove(f)
 
 
 class CMakeExtension(Extension):
@@ -74,11 +79,11 @@ def build_extension(self, ext):
 
 setup(
     name='pydeform',
-    version='0.0.1',
+    version='0.4',
     author='Simon Ekström',
     author_email='',
     description='',
-    long_description=open('README.md').read(),
+    long_description=readme,
     long_description_content_type='text/markdown',
     install_requires=['numpy', 'PyYAML'],
     packages=['pydeform'],

src/deform/main.cpp

@@ -3,6 +3,7 @@
 #include <deform_lib/defer.h>
 #include <deform_lib/filters/resample.h>
 #include <deform_lib/jacobian.h>
+#include <deform_lib/make_unique.h>
 #include <deform_lib/profiler/profiler.h>
 #include <deform_lib/registration/landmarks.h>
 #include <deform_lib/registration/registration.h>
@@ -26,7 +27,6 @@
 #include <iostream>
 #include <map>
 #include <omp.h>
-#include <optional>
 #include <sstream>
 #include <string>
 #include <vector>
@@ -82,19 +82,19 @@ int main(int argc, char* argv[])
 
     std::unique_ptr<DeformCommand> command;
     if (argc >= 2 && std::strcmp(argv[1], "registration") == 0) {
-        command = std::make_unique<RegistrationCommand>(argc, argv, true);
+        command = make_unique<RegistrationCommand>(argc, argv, true);
     }
     else if (argc >= 2 && std::strcmp(argv[1], "transform") == 0) {
-        command = std::make_unique<TransformCommand>(argc, argv);
+        command = make_unique<TransformCommand>(argc, argv);
     }
     else if (argc >= 2 && std::strcmp(argv[1], "regularize") == 0) {
-        command = std::make_unique<RegularisationCommand>(argc, argv);
+        command = make_unique<RegularisationCommand>(argc, argv);
     }
     else if (argc >= 2 && std::strcmp(argv[1], "jacobian") == 0) {
-        command = std::make_unique<JacobianCommand>(argc, argv);
+        command = make_unique<JacobianCommand>(argc, argv);
     }
     else if (argc >= 2 && std::strcmp(argv[1], "divergence") == 0) {
-        command = std::make_unique<DivergenceCommand>(argc, argv);
+        command = make_unique<DivergenceCommand>(argc, argv);
     }
     else {
         print_command_help(argv[0]);

src/deform/registration.cpp

@@ -69,7 +69,11 @@ int RegistrationCommand::_execute(void)
         LOG(Info) << "Parameters:" << std::endl << param_str.str();
 
         // Print all settings to Verbose
-        LOG(Verbose) << print_registration_settings(settings).rdbuf();
+
+        std::stringstream settings_str;
+        print_registration_settings(settings, settings_str);
+
+        LOG(Verbose) << settings_str.rdbuf();
     }
     else {
         LOG(Info) << "Running with default settings.";
@@ -115,13 +119,19 @@ int RegistrationCommand::_execute(void)
     const std::string fixed_mask_file = _args.get<std::string>("fixed_mask", "");
     const std::string moving_mask_file = _args.get<std::string>("moving_mask", "");
 
-    std::optional<stk::Volume> fixed_mask;
-    std::optional<stk::Volume> moving_mask;
+    stk::Volume fixed_mask;
+    stk::Volume moving_mask;
+
     if (!fixed_mask_file.empty()) {
         fixed_mask = stk::read_volume(fixed_mask_file);
+        if (!fixed_mask.valid()) 
+            return EXIT_FAILURE;
     }
+
     if (!moving_mask_file.empty()) {
         moving_mask = stk::read_volume(moving_mask_file);
+        if (!moving_mask.valid()) 
+            return EXIT_FAILURE;
     }
 
     LOG(Info) << "Fixed mask: '" << fixed_mask_file << "'";
@@ -131,9 +141,11 @@ int RegistrationCommand::_execute(void)
     std::string init_deform_file = _args.get<std::string>("init_deform", "");
     LOG(Info) << "Initial displacement: '" << init_deform_file << "'";
 
-    std::optional<stk::Volume> initial_displacement;
+    stk::Volume initial_displacement;
     if (!init_deform_file.empty()) {
         initial_displacement = stk::read_volume(init_deform_file.c_str());
+        if (!initial_displacement.valid()) 
+            return EXIT_FAILURE;
     }
 
     // Constraints
@@ -143,11 +155,16 @@ int RegistrationCommand::_execute(void)
     LOG(Info) << "Constraint mask: '" << constraint_mask_file << "'";
     LOG(Info) << "Constraint values: '" << constraint_values_file << "'";
 
-    std::optional<stk::Volume> constraint_mask;
-    std::optional<stk::Volume> constraint_values;
+    stk::Volume constraint_mask;
+    stk::Volume constraint_values;
     if (!constraint_mask_file.empty() && !constraint_values_file.empty()) {
         constraint_mask = stk::read_volume(constraint_mask_file.c_str());
+        if (!constraint_mask.valid()) 
+            return EXIT_FAILURE;
+
         constraint_values = stk::read_volume(constraint_values_file.c_str());
+        if (!constraint_values.valid()) 
+            return EXIT_FAILURE;
     }
     else if (!constraint_mask_file.empty() || !constraint_values_file.empty()) {
         // Just a check to make sure the user didn't forget something
@@ -162,8 +179,8 @@ int RegistrationCommand::_execute(void)
     LOG(Info) << "Fixed landmarks: '" << fixed_landmarks_file << "'";
     LOG(Info) << "Moving landmarks: '" << moving_landmarks_file << "'";
 
-    std::optional<std::vector<float3>> fixed_landmarks;
-    std::optional<std::vector<float3>> moving_landmarks;
+    std::vector<float3> fixed_landmarks;
+    std::vector<float3> moving_landmarks;
     try{
         if (!fixed_landmarks_file.empty()) {
             fixed_landmarks = parse_landmarks_file(fixed_landmarks_file.c_str());