Compiler notes

For installation with pip on windows you will need compiler.

• Download and install miniconda
• Download and install C++ Compiler for Windows
  • Python 2.7: MS Visual C++ compiler for Python 2.7

  • Python 3.6: Microsoft Build Tools for Visual Studio 2017

    Check “Python development” and “Desktop Application C++ development” during install. You may remove all submodules. Keep just VC++ 2017 tools.

• Install depenencies

    conda install -c simpleitk -c mjirik -c conda-forge --file requirements_conda.txt
  

• Install pygco

    pip install pygco
  

• Compilers for Windows

Installation Instructions

Installing requires you to have installed:

• numpy (http://www.numpy.org)
• scipy (http://scipy.org)
• scikit-learn (http://scikit-learn.org)
• Cython - C-extension for Python (http://cython.org)
• pyqt - Python bindings for Qt application framework (http://www.riverbankcomputing.com/software/pyqt)
• git - distributed version control system (http://git-scm.com)
• pygco - Graphcuts for Python (https://github.com/amueller/gco_python)
• pydicom - package for working with DICOM files (http://code.google.com/p/pydicom)

On Linux, ask the package manager of your distribution.

On Windows, packages numpy, scipy, scikit-learn, Cython, pydicom are part of Python(x,y) distribution (http://code.google.com/p/pythonxy).

Pygco install

Pygco has to be installed manually, in gitbash write:

Linux:

git clone https://github.com/amueller/gco_python.git cd gco_python make python setup.py install

Windows:

git clone https://github.com/amueller/gco_python.git cd gco_python mkdir gco_src && cd gco_src curl -O http://vision.csd.uwo.ca/code/gco-v3.0.zip unzip gco-v3.0.zip cd .. curl -O https://raw2.github.com/mjirik/pyseg_base/master/distr/gco_python.pyx.patch patch gco_python.pyx < gco_python.pyx.patch python setup.py build_ext -i –compiler=mingw32 python.exe setup.py build –compiler=mingw32 python.exe setup.py install –skip-build

Mac:

git clone https://github.com/amueller/gco_python.git cd gco_python mkdir gco_src cd gco_src curl -O http://vision.csd.uwo.ca/code/gco-v3.0.zip unzip gco-v3.0.zip curl -O https://raw.github.com/mjirik/pyseg_base/master/distr/energy.patch patch energy.h < energy.patch cd .. sudo python setup.py install

Install PYSEG_BASE:

pip install imcut

or:

git clone https://github.com/mjirik/pyseg_base.git

Sample DICOM data can be found at:

• http://www.mathworks.com/matlabcentral/fileexchange/2762-dicom-example-files?download=true
• http://www.osirix-viewer.com/datasets/