Master Thesis about finding local shape variations in sheep bones.
This has been tested on a new Ubuntu 14.04 box. The requirements outside of PyPi are python2.7, Qt4, PyQt4 and VTK
Install Dependencies:
sudo apt-get install git gfortran libqt4-dev libblas-dev liblapack-dev libfreetype6-dev libpng-dev python-dev python-vtk6 python-qt4 python-virtualenv
Clone Repo:
git clone https://github.com/selaux/master-of-bones.git
Create and Activate Virtualenv:
cd master-of-bones && virtualenv ./venv && source ./venv/bin/activate
Link global libraries into venv:
cp -r /usr/lib/python2.7/dist-packages/PyQt4 ./venv/lib/python2.7/site-packages/
cp -r /usr/lib/python2.7/dist-packages/sip.so ./venv/lib/python2.7/site-packages/
cp -r /usr/lib/python2.7/dist-packages/vtk ./venv/lib/python2.7/site-packages/
Fix VTK installation as su (https://bugs.launchpad.net/ubuntu/+source/vtk6/+bug/1354127):
for link in `ls /usr/lib/python2.7/dist-packages/vtk/vtk*.so`; do target=$(readlink $link).6.0; echo $link; sudo rm $link; sudo ln -s $target $link ; done
Install Dependencies (this might take a while):
pip install numpy && pip install scipy && pip install -r requirements.txt
Note: The Virtualenv has to be activated before starting anything:
source ./venv/bin/activate
Comparison Helper: Actually does the Comparison
python comparison_helper.py
Registration Helper: Register Bones
python registration_helper.py
Triangulation Helper: Extract bone outlines from images
python registration_helper.py
Synthetic Generation Helper: Generate Synthetic Bone Data
python synthetic_generation_helper.py
thesis: The masters thesis in source form and pdf from (dbsma.tex, dbsma.pdf)
algorithms: The algorithms presented in this thesis
helpers: Helper Functions and UI