Installation

clone or download the repository

pip install pylattice
pip install -r requirements.txt
cd src/jupyter
jupyter notebook

You can find the package on `pypi`_.

in browser open

src/jupyter/latticeFrame_showFrame.ipynb

Test data

A small test data set can be found here: https://www.dropbox.com/sh/znznvp1lmvwfykp/AADzJB456aFHll1bYCPzdQhNa?dl=0

Matlab on Macs

If matlab throws errors like this:

Invalid MEX-file
'/Users/johannesschoeneberg/git/JohSchoeneberg/pyLattice/src/matlab/trackingModule/dependencies/u-track/software/mex/createDistanceMatrix.mexmaci64':
dlopen(/Users/johannesschoeneberg/git/JohSchoeneberg/pyLattice/src/matlab/trackingModule/dependencies/u-track/software/mex/createDistanceMatrix.mexmaci64,
6): Library not loaded: @loader_path/libmex.dylib
Referenced from:
/Users/johannesschoeneberg/git/JohSchoeneberg/pyLattice/src/matlab/trackingModule/dependencies/u-track/software/mex/createDistanceMatrix.mexmaci64
Reason: image not found.

The solution can be found here:

https://stackoverflow.com/questions/48458660/library-not-loaded-loader-path-libmex-dylib-in-matlab

First, find out your matlab version:

find /Applications/ -maxdepth 1 -type d -name 'MAT*'

In my case this is:

MATLAB_R2017b.app

In the subsequent steps, the 2017b matlab version is used. If you have a different version, replace MATLAB_R2017b.app with your version below.

You have to add the libraries to your matlab startup script:

/Applications/MATLAB_R2017b.app/bin/.matlab7rc.sh.

Add:

DYLD_LIBRARY_PATH="/Applications/MATLAB_R2017b.app/bin/maci64:/Applications/MATLAB_R2017b.app/sys/os/maci64"

Then startup matlab from the command line:

/Applications/MATLAB_R2017b.app/bin/matlab