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
pygcopip install pygco
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 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: