install_linux.md

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

Script way

wget https://raw.githubusercontent.com/mjirik/lisa/master/installer.sh -O installer.sh
source installer.sh

Manual way

Tested with Ubuntu 14.04 and Linux Mint 16 Petra

# 1. deb package requirements
sudo apt-get install python git python-dev g++ python-numpy python-scipy python-matplotlib python-sklearn python-skimage python-dicom cython python-yaml sox make python-qt4 python-vtk python-setuptools curl

# 2. install miniconda
wget http://repo.continuum.io/miniconda/Miniconda-latest-Linux-x86_64.sh
bash Miniconda-latest-Linux-x86_64.sh -b
cd ~
export PATH=`pwd`/miniconda/bin:$PATH

# 2. easy_install requirements simpleITK  
sudo easy_install -U SimpleITK mahotas

# 3. pip install our packages pyseg_base and dicom2fem
sudo pip install imcut dicom2fem sed3 sed3 io3d skelet3d ipdb

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

# 5. skelet3d - optional for Histology Analyser
sudo apt-get install cmake python-numpy libinsighttoolkit3-dev libpng12-dev
cd ~/projects
git clone https://github.com/mjirik/skelet3d.git
cd skelet3d
mkdir build
cd build
cmake ..
make
sudo make install

1. First use package manager to satisfy requirements.
2. SimpleITK is not in ubuntu packages. You can use easy_install
3. Our support packages can be installed with pip
4. For pygco use following (more info https://github.com/mjirik/pyseg_base/blob/master/INSTALL)
5. Last step is optional for Histology Analyser and some functions Lisa

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 [email protected]:mjirik/lisa.git

Make an icon

cd lisa
python mysetup.py -icn

Download sample data

cd ~/projects/lisa
python mysetup.py -d
mkdir ~/lisa_data
cp -r sample_data/ ~/lisa_data/

Test

cd ~/projects/lisa
nosetests

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

Testování funkčnosti windows pomocí wine (czech)

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