disptools | Generate displacement fields with known volume changes

This package is available on [PyPI](https://pypi.org/project/disptools) both as source distribution and as a Windows pre-compiled binary wheel. You can install it with <tt>pip</tt>:. As always, it is recommended to use the package inside a [virtual environment](https://docs.python.org/3/tutorial/venv.html).
Requirements are specified by the <tt>requirements.txt</tt> file and can be installed with <tt>pip</tt>. The library is a cross-platform Python 3.5+ package, with a compiled C extension. The Python dependencies are: + [numpy](https://github.com/numpy/numpy) ([pypi package](https://pypi.python.org/pypi/numpy)) + [scipy](https://github.com/scipy/scipy) ([pypi package](https://pypi.org/pypi/scipy)) + [SimpleITK](https://github.com/SimpleITK/SimpleITK) ([pypi package](https://pypi.org/pypi/SimpleITK)). Build dependencies are a standard C compiler (tested with gcc 8.2 on Linux, mingw-w64 7.2 and MSVC 19 on Windows 10), [CMake](https://cmake.org/), the [numpy](https://pypi.python.org/pypi/numpy) and the [setuptools](https://pypi.python.org/pypi/setuptools) packages. [scikit-build](https://pypi.python.org/pypi/scikit-build) may be required to build the other Python dependencies. Some optional dependencies are required only for a limited set of features, and the package should build and run without them: + [itk](https://github.com/InsightSoftwareConsortium/ITK) ([pypi package](https://pypi.org/project/itk)): for <tt>disptools.drawing.sitk_to_itk</tt> + [vtk](https://github.com/Kitware/VTK) ([pypi package](https://pypi.org/project/vtk)): for <tt>disptools.io.write_vtk_points</tt> + [ply](https://github.com/dabeaz/ply) ([pypi package](https://pypi.org/project/ply)): for <tt>disptools.io.read_elastix_parameters</tt> + [scikit-image](https://github.com/scikit-image/scikit-image) ([pypi package](https://pypi.org/project/scikit-image)): for some features of <tt>disptools.drawing.extract_slice</tt>, and to run the unit tests. The following environment variables affect the <tt>setup.py</tt>: + <tt>DISPTOOLS_OPT=ON</tt>: enable non-portable optimisations. + <tt>DISPTOOLS_DEBUG=ON</tt>: disable optimisations, compile with debug symbols. + <tt>DISPTOOLS_CUDA_SUPPORT=ON</tt>: enable CUDA support.
First, be sure that [mingw](https://mingw-w64.org), CMake and Python are installed and their executables [are in your PATH](https://docs.python.org/3/using/windows.html#excursus-setting-environment-variables).
Ensure that <tt>gcc</tt> is working correctly:
Ensure that <tt>distutils</tt> correctly recognises your version of Visual Studio (even when using <tt>mingw</tt>). Open the file <tt>C:\Users\yourname\AppData\Local\Programs\Python\Python3x\Lib\distutils\cygwinccompiler.py</tt> (the exact location may vary according to your setup) and check that your version of Visual Studio is present in the function <tt>get_msvcr()</tt>; if not, adjust it according to the following:
Ensure that the library <tt>vcruntime140.dll</tt> is present in your library path. Otherwise, download it and place it in <tt>C:\Users\yourname\AppData\Local\Programs\Python\Python3x\libs</tt> (the exact path may vary according to your setup).
Clone the sources of this package with <tt>git</tt>, or download and extract them as a <tt>zip</tt> archive. Move to the root folder of the sources (<tt>C:\Users\yourname\disptools</tt> in this example), specify the right compiler, and launch the setup script to build and install the package.