Metadata-Version: 2.1
Name: disptools
Version: 0.4.0
Summary: Generate displacement fields with known volume changes
Home-page: https://github.com/m-pilia/disptools
Author: Martino Pilia
Author-email: martino.pilia@gmail.com
License: UNKNOWN
Download-URL: https://github.com/m-pilia/disptools/archive/v0.4.0.tar.gz
Description: disptools
        =========
        Generate displacement fields with known volume changes
        ------------------------------------------------------
        [![GitHub release](https://img.shields.io/github/release/m-pilia/disptools.svg)](https://github.com/m-pilia/disptools/releases/latest)
        [![PyPI](https://img.shields.io/pypi/v/disptools.svg)](https://pypi.python.org/pypi/disptools)
        [![Wheels](https://img.shields.io/pypi/wheel/disptools.svg)](https://pypi.org/project/disptools)
        [![License](https://img.shields.io/badge/License-MIT-blue.svg)](https://github.com/m-pilia/disptools/blob/master/LICENSE)
        [![Appveyor](https://ci.appveyor.com/api/projects/status/github/m-pilia/disptools?svg=true)](https://www.appveyor.com/)
        
        This library provides utilities to generate and manipulate displacement fields with known volume changes. It implements three search-based algorithms for the generation of deformation fields, along with a small collection of utility functions, and provides optional GPU acceleration through a CUDA implementation.
        
        The three algorithms implemented are referred as:
        + <tt>gradient</tt>: a gradient descent method (default).
        + <tt>greedy</tt>: a greedy search method proposed in [[1]](#1).
        + <tt>matching</tt>: a volume matching method proposed in [[2]](#2) and [[3]](#3). The implementation comes from the [PREDICT atrophysim tool](https://www.nitrc.org/projects/atrophysim).
        
        The library is built on top of SimpleITK, in order to provide a simple yet powerful set of functionalities for image analysis. Images stored as numpy arrays can be easily converted from and to [SimpleITK](http://simpleitk.github.io/SimpleITK-Notebooks/01_Image_Basics.html) and [ITK](https://blog.kitware.com/convert-itk-data-structures-to-numpy-arrays/) image objects.
        
        ### Documentation
        
        The complete documentation for this package is available on https://martinopilia.com/disptools.
        
        ### Quick example
        ```python
        import SimpleITK as sitk
        import disptools.displacements as dsp
        import disptools.drawing as drw
        
        # Create an example Jacobian map
        # A spherical ROI with a Jacobian of 1.1 (expansion)
        jacobian = drw.create_sphere(10, 40, fg_val=1.1, bg_val=1.0)
        
        # Create a binary mask for the ROI
        mask = drw.create_sphere(10, 40) > 0
        
        # Generate the displacement
        displacement = dsp.displacement(jacobian, mask=mask)
        
        # Check the correctness of the result within the ROI
        error = jacobian - dsp.jacobian(displacement)
        error = sitk.Mask(error, mask)
        ```
        
        A 3D rendering of the resulting displacement field with [ParaView](https://www.paraview.org/), and a visualisation of the the error on the Jacobian within the ROI:
        
        <img src="https://github.com/m-pilia/disptools/blob/master/sphinx/img/example_2.png?raw=true" alt="displacement" width=45% /> <img src="https://github.com/m-pilia/disptools/blob/master/sphinx/img/example_1.png?raw=true" alt="error" width=45% />
        
        ### Architecture
        
        The project is structured in three layers:
        + a pure standard [C99](https://en.wikipedia.org/wiki/C99) library (whose headers are in <tt>src/headers</tt>), with no external dependencies, implementing the core algorithms for the generation of deformation fields. It is a standalone library that can be directly included in a C or C++ project. It is paired with an optional [CUDA](https://en.wikipedia.org/wiki/CUDA) library, whose headers are in <tt>cuda/headers</tt>, that depends on <tt>src/headers</tt> and provides a GPGPU implementation of the key routines.
        + a [Python C extension](https://docs.python.org/3.6/extending/extending.html) package <tt>_disptools</tt> (whose source is in the file <tt>python_c_extension/_disptools.c</tt>), providing a bare Python wrapper to the aforementioned library, using the [NumPy C API](https://docs.scipy.org/doc/numpy-1.14.0/reference/c-api.html) to pass arrays. This can be directly included in a Python project with no dependencies other than NumPy.
        + a Python package (<tt>disptools</tt>), that wraps the <tt>_disptools</tt> package providing file IO (through SimpleITK) and implementing high-level features (such as the multi-resolution framework) and auxiliary utilities and functions.
            - <tt>disptools.displacements</tt>: module providing the main functions for the generation and manipulation of displacement fields.
            - <tt>disptools.drawing</tt>: collection of utilities to create test images.
            - <tt>disptools.io</tt>: collection of utilities to read and write to file.
            - <tt>disptools.measure</tt>: collection of utilities to measure some image features.
            - <tt>disptools.simulatrophy</tt>: routines to interface with the [Simul@atrophy](https://github.com/Inria-Asclepios/simul-atrophy) tool.
            - <tt>disptools.predict</tt>: routines to interface with the [PREDICT](https://www.nitrc.org/projects/atrophysim) tool.
        
        ### Install
        
        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>:
        ```bash
         python3 -m pip install disptools
        ```
        
        ### Build from source
        
        #### Requirements
        
        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 <tt>disptools.drawing.extract_slice</tt>, and to run the unit tests
        
        #### Build options
        
        The following build flags are recognised by <tt>setup.py</tt>:
        + <tt>--opt</tt>: enable non-portable optimisations.
        + <tt>--debug</tt>: disable optimisations, compile with debug symbols.
        + <tt>--cuda</tt>: enable CUDA support.
        
        Additional flags starting with <tt>-D</tt> are also accepted and passed directly to <tt>CMake</tt>.
        
        #### Windows (Visual Studio) and Linux
        
        Install the dependencies with your favourite package manager. For example, with <tt>pip</tt>:
        ```bash
        python3 -m pip install scikit-build numpy scipy SimpleITK
        ```
        
        The package provides a <tt>setuptools</tt> based install script. To install the library, run from the project root folder
        ```bash
        python3 setup.py install
        ```
        which should build the C extension and install the Python package.
        
        #### Windows (MinGW)
        
        1. 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).
        
        2. Ensure that <tt>gcc</tt> is working correctly:
        ```none
        > gcc --version
        gcc (x86_64-posix-seh-rev1, Built by MinGW-W64 project) 7.2.0
        Copyright (C) 2017 Free Software Foundation, Inc.
        This is free software; see the source for copying conditions.  There is NO
        warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
        ```
        
        3. 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:
        ```python
        def get_msvcr():
            """Include the appropriate MSVC runtime library if Python was built
            with MSVC 7.0 or later.
            """
            msc_pos = sys.version.find('MSC v.')
            if msc_pos != -1:
                msc_ver = sys.version[msc_pos+6:msc_pos+10]
                if msc_ver == '1300':
                    # MSVC 7.0
                    return ['msvcr70']
                elif msc_ver == '1310':
                    # MSVC 7.1
                    return ['msvcr71']
                elif msc_ver == '1400':
                    # VS2005 / MSVC 8.0
                    return ['msvcr80']
                elif msc_ver == '1500':
                    # VS2008 / MSVC 9.0
                    return ['msvcr90']
                elif msc_ver == '1600':
                    # VS2010 / MSVC 10.0
                    return ['msvcr100']
                elif msc_ver == '1700':
                    # Visual Studio 2012 / Visual C++ 11.0
                    return ['msvcr110']
                elif msc_ver == '1800':
                    # Visual Studio 2013 / Visual C++ 12.0
                    return ['msvcr120']
                elif msc_ver == '1900':
                    # Visual Studio 2015 / Visual C++ 14.0
                    # "msvcr140.dll no longer exists" http://blogs.msdn.com/b/vcblog/archive/2014/06/03/visual-studio-14-ctp.aspx
                    return ['vcruntime140']
                else:
                    raise ValueError("Unknown MS Compiler version %s " % msc_ver)
        ```
        
        4. 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).
        
        5. Install the dependencies:
        ```cmd
        > python -m pip install scikit-build numpy scipy SimpleITK
        ```
        
        6. 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.
        ```cmd
        > cd C:\Users\yourname\disptools
        > python setup.py setopt --command=build --option=compiler --set-value=mingw32
        > python setup.py install
        ```
        
        ### References
        + <a id="1"></a>[1] van Eede, M. C., Scholz, J., Chakravarty, M. M., Henkelman, R. M., and Lerch, J. P. *Mapping registration sensitivity in MR mouse brain images.* Neuroimage 82 (2013), 226–236.
        + <a id="2"></a>[2] Karaçali, B., and Davatzikos, C. *Estimating topology preserving and smooth displacement fields.* IEEE Transactions on Medical Imaging 23, 7 (2004), 868–880.
        + <a id="3"></a>[3] Karaçali, B., and Davatzikos, C. *Simulation of tissue atrophy using a topology preserving transformation model.* IEEE transactions on medical imaging 25, 5 (2006), 649–652.
        
        ### License
        
        The software is distributed under the MIT license.
        
Keywords: jacobian,displacement,image processing
Platform: UNKNOWN
Description-Content-Type: text/markdown
Provides-Extra: ITK
Provides-Extra: elastix
Provides-Extra: testing
Provides-Extra: VTK
