Requirements

Installing requires you to have installed:

GIT - distributed version control system (http://git-scm.com)
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)
pygco - Graphcuts for Python (https://github.com/amueller/gco_python)
pydicom - package for working with DICOM files (http://code.google.com/p/pydicom)
pyqt - QT4 for python (https://wiki.python.org/moin/PyQt)
ITK (optional) - Package for medical image analysis (http://www.itk.org/)
VTK (optional) - The Visualization Toolkit (http://www.vtk.org/)

Install (L)Ubuntu 14.04

Tested with Ubuntu 14.04 32-bit and Linux Mint 16 Petra

Use package manager to satisfy requirements

sudo apt-get install python git python-dev g++ python-numpy python-scipy python-matplotlib python-sklearn python-dicom cython python-yaml sox make python-qt4 python-vtk python-setuptools curl

SimpleITK is not in ubuntu packages. You can use easy_install

sudo easy_install -U SimpleITK

For pygco use following (more info https://github.com/mjirik/pyseg_base/blob/master/INSTALL)

mkdir ~/projects
cd ~/projects
git clone https://github.com/mjirik/gco_python.git
cd gco_python
make
sudo python setup.py install
cd ..

Get stable branche

git clone --recursive -b stable https://github.com/mjirik/lisa.git

or for current developement (if you want to participate)

git clone --recursive git@github.com:mjirik/lisa.git

Install (L)Ubuntu 12.04 (13.10)

Use package manager

sudo apt-get install python git python-numpy python-scipy python-matplotlib python-sklearn python-dicom cython python-yaml sox python-insighttoolkit3 make python-qt4 python-vtk python-setuptools

SimpleITK is not in ubuntu packages. You can use easy_install

sudo easy_install -U SimpleITK

For pygco use following (more info https://github.com/mjirik/pyseg_base/blob/master/INSTALL)

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

Get stable branche

mkdir ~/projects
cd ~/projects
git clone --recursive -b stable https://github.com/mjirik/lisa.git

Problems on Linux:

Permission denied. You can try following command if there is a problem "Permission denied"

sudo chmod a+r /usr/local/lib/python2.7/dist-packages/SimpleITK-0.7.0-py2.7-linux-x86_64.egg/EGG-INFO/top_level.txt

Install Mac OS

Xcode, gcc and make

Install Xcode from appstore. You will need an AppleID. Then add terminal tools (http://stackoverflow.com/questions/10265742/how-to-install-make-and-gcc-on-a-mac)
- Start XCode
- Go to XCode/Preferences.
- Click the "Downloads" tab.
- Click "Components".
- Click "Install" on the command line tools line.
MacPorts

Use standard pkg package. (http://www.macports.org/install.php)

Tested on OS X 10.8 Mountain Lion installer and OSX 10.9 Mavericks installer
GIT

Use mac ports
```
 sudo port install git-core +svn +doc +bash_completion +gitweb
```
Use mac installer (http://git-scm.com/download/mac) There is a need to allow install applications from unknown developers (Settings - Security & Privacy - General - Allow applications downloaded from)

Numpy, Scipy, ...

 sudo port selfupdate
 sudo port upgrade outdated
 sudo port install py27-pyqt4 py27-numpy py27-scipy py27-matplotlib py27-ipython +notebook py27-pandas py27-sympy py27-nose  py-scikit-learn py-pydicom py27-yaml py27-cython vtk5 +qt4_mac +python27 py27-distutils-extra

Select default python

 sudo port select --set python python27

Cython (may work from port)

 sudo easy_install cython

 sudo -E easy_install cython

gco_python

Try this
```
 git clone https://github.com/amueller/gco_python.git
 cd gco_python
 make
 sudo -E python setup.py install
```
or this

See install notes to pyseg_base (https://github.com/mjirik/pyseg_base/blob/master/INSTALL). If there is a problem with clang compiler, you are should edit gco source files and add "this->" string. Also you can use patch from pyseg_base

source files

 git clone git@github.com:mjirik/pyseg_base.git
 git submodule update --init --recursive

Known problems on Mac OS

Cython installation fail

 command 'cc' failed with exit status 1

 import Cython.Distutils

Install cython with easy_install

 sudo -E easy_install cython

Use VirtualBox

Install VirtualBox (https://www.virtualbox.org/)
Download Lisa Image (http://uloz.to/xU4oHfKw/lisa-ubuntu14-04-vdi)

Download Lisa Image (http://147.228.240.61/queetech/install/lisa_ubuntu14.04.vdi)

In VirtualBox

Create new computer
- Name: Lisa
- Type: Linux
- Version: Ubuntu (32bit)
Set memory size to 1024MB and more
Use existing hard disk and locate downloaded Lisa Image (lisa_ubuntu14.04.vdi)
Password to Lisa account is: L1v3r.

Install Windows

Python XY (http://code.google.com/p/pythonxy/)

Add all packages.
Git (http://www.git-scm.com/download/win)

Select "Run Git from the Windows Command Prompt" or "Run Git and included Unix tools from the Windows Command Prompt"

gco_python

Fallowing lines downloads gco and gco_python. Then it makes build with mingw compiler and install.

  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

Problems on Windows:

Cython not found. Install cython from https://code.google.com/p/pythonxy/wiki/Downloads#Plugin_updates
UnicodeDecodeError: 'ascii' codec can't decode byte 0x82 in position 0: ordinal not in range(128)

You can either find and remove the offending font (the best idea) or try to patch your installation using the following procedure:
- Open the following in a text editor:
```
  \Users\dafonseca\AppData\Local\Enthought\Canopy\User\lib\site- packages\matplotlib\font_manager.py
```
- Search for
```
  sfnt4 = sfnt4.decode('ascii').lower()
```
- And replace with
```
  sfnt4 = sfnt4.decode('ascii', 'ignore').lower()
```
Note that this bug won't exist in the next release of matplotlib.

For more information see: http://stackoverflow.com/questions/18689854/enthought-matplotlib-problems-with-plot-function

Windows Install - old version in czech

http://www.lfd.uci.edu/~gohlke/pythonlibs/

Python (*)
Numpy (musi byt nainstalovan drive nez Scipy) (*)
Scipy (musi byt nainstalovan po Numpy) (*)

*) Poznamky: Je potreba pozorne volit 64/32 bit knihovny a nezamenovat je. Python, i knihovny museji byt jen 64 bit nebo jen 32 bit. Doporucujeme uzivat Numpy MKL. Jsou to vypocetni optimalizace, ktere pozdeji pozadujici navazujici baliky.

Errory:

V pripade zavaznejsich problemu (tzn. nefunkcnost) vymazat dane verze Pythonu, Numpy a Scipy a preinstalovat je.
Resit na strankach vyrobce softwaru.

Dodatecne instalace:

matplotlib Navod je zde: (http://matplotlib.org/users/installing.html) Melo by stacit ze stranky (http://sourceforge.net/projects/matplotlib/files/) ve slozce "matplotlib" stahnout prislusnou verzi matplotlib a nainstalovat po nainstalovani Numpy a Scipy.

gco_python v sedmi snadných krocích

ověřeno pro python 2.7 32

Python 2.7 pro 32-bit architekturu
Zdrojové kódy

V zásadě je potřeba mít zdrojové kódy gco a gco_python.

gco_python (https://github.com/amueller/gco_python/archive/master.zip)
gco (http://vision.csd.uwo.ca/code/gco-v3.0.zip)

Gco se normálně překládá pomocí matlabu. My to uděláme jinak. Zdrojové kódy uspořádejme tak, že bude adresář gco_python se zdrojovými kódy gco_python a v něm bude adresář gco_src s kódy gco.

Překladač

Patrně lze použít jakýkoliv, ale mě to (po mnoha problémech) fungovalo s 32-bitovým mingw

Moduly Pythonu

Musí se jednat o příslušné verze - 32bit

numpy scipy scikit-learn matplotlib cython pydicom pyyaml

lze nainstalovat pomocí pip:

pip install numpy scipy scikit-learn matplotlib cython pydicom pyyaml

Oprava konfiguračního souboru v Pythonu V konfiguračním souboru je volání gcc se zastaralým parametrem -mno-cygwin. Je potřeba odstranit všechny výskyty tohoto slova z konfiguračního souboru:

"C:\Python27\Lib\distutils\cygwinccompiler.py"
Kompilace

Všechny následující příkazy spouštíme v adresáři gco_python s pythonem 27

Překlad gco_src s překladačem mingw

python.exe setup.py build_ext -i --compiler=mingw32

Vytvoření knihoven z gco_python

python.exe setup.py build --compiler=mingw32
python.exe setup.py install --skip-build

nakopírování knihoven na příslušná místa. Od teď půjde knihovna gco_python volat z jakéhokoliv python skriptu.

Ověření

python example.py

Výsledek by se měl podobat obrázkům na adrese: http://peekaboo-vision.blogspot.cz/2012/05/graphcuts-for-python-pygco.html

nainstalovat mingw

Testování funkčnosti windows pomocí wine

sudo apt-get install wine

mkdir ~/tmp/winpython

wget -P ~/tmp/winpython/ http://msysgit.googlecode.com/files/Git-1.8.0-preview20121022.exe

Install with linux tools

wine ~/tmp/winpython/Git-1.8.0-preview20121022.exe

Next, Next, Next, Finish wget -P ~/tmp/winpython/ http://www.python.org/ftp/python/2.7.3/python-2.7.3.msi wine msiexec /i /home/mjirik/tmp/winpython/python-2.7.3.msi

wget -P ~/tmp/winpython/  http://www.cmake.org/files/v2.8/cmake-2.8.10.2-win32-x86.exe
wine ~/tmp/winpython/cmake-2.8.10.2-win32-x86.exe

Add CMake to system PATH for all users

Balíky (numpy a scipy) lze získad z následujících stránek,

http://www.lfd.uci.edu/~gohlke/pythonlibs/

Teoreticky by mohlo jít stáhnout soubory přes wget, ale občas se změní název souboru (za něj se přidá znak '$'), nebo se soubor nestáhne celý

wget -P ~/tmp/winpython/ http://www.lfd.uci.edu/~gohlke/pythonlibs/z86mtkth/numpy-MKL-1.6.2.win32-py2.7.exe
wget -P ~/tmp/winpython/ http://www.lfd.uci.edu/~gohlke/pythonlibs/z86mtkth/scipy-0.11.0.win32-py2.7.exe

instalace pomocí pip

Nejprve potřebujeme distribute a pip

wget -P ~/tmp/winpython/ http://python-distribute.org/distribute_setup.pyp
wine c:\\python27\\python /home/mjirik/tmp/winpython/distribute_setup.py



wget -P ~/tmp/winpython/ https://raw.github.com/pypa/pip/master/contrib/get-pip.py
wine c:\\python27\\python /home/mjirik/tmp/winpython/get-pip.py

cython nainstalujeme pomocí pip, možná by tak šlo instalovat i numpy a scipy wine cmd c:\python27\scripts\pip install cython c:\python27\scripts\pip install matplotlib exit

instalace gco

wget -P ~/tmp/winpython/ http://vision.csd.uwo.ca/code/gco-v3.0.zip
unzip /home/mjirik/tmp/winpython/gco-v3.0.zip -d/home/mjirik/tmp/winpython/gco/

cd ~/tmp/winpython/
wine cmd

git clone pycat

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Requirements

Install (L)Ubuntu 14.04

Install (L)Ubuntu 12.04 (13.10)

Install Mac OS

Known problems on Mac OS

Use VirtualBox

Install Windows

Windows Install - old version in czech

gco_python v sedmi snadných krocích

Testování funkčnosti windows pomocí wine

Install with linux tools

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INSTALL.md

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Requirements

Install (L)Ubuntu 14.04

Install (L)Ubuntu 12.04 (13.10)

Install Mac OS

Known problems on Mac OS

Use VirtualBox

Install Windows

Windows Install - old version in czech

gco_python v sedmi snadných krocích

Testování funkčnosti windows pomocí wine

Install with linux tools