BioMembrane

CMPUT 401 Project 5 "Simulation and analysis of images for studies of biological membranes" for Dr Nils O. Petersen.

Copryight (c) 2013 Nick Klose, Richard Leung, Cameron Mann, Glen Nelson, Omar Qadri, and James Wang under the 401 IP License.

Required Packages

A few packages are required for the program:

1. scipy. scipy is Copyright (c) 2005-2013, SciPy Developers and is licensed under the BSD License.
2. numpy. numpy is Copyright (c) 2005-2013, NumPy Developers and is licensed under the BSD License.
3. django. django is Copyright (c) 2005-2013, Django Software Foundation and is licensed under the BSD License.
4. fftw3. FFTW is Copyright (c) 2003, 2007-11 Matteo Frigo, Copyright (c) 2003, 2007-11 Massachusetts Institute of Technology and is licensed under the GPL (version 2 or later) License.
5. pythonmagick (Ubuntu package: python-pythonmagick). pythonmagick Copyright 1999-2011 ImageMagick Studio LLC, a non-profit organization dedicated to making software imaging solutions freely available.
6. wand (sudo apt-get install libmagickwand-dev, sudo pip install Wand) Copyright 2013 Hong Minhee, http://dahlia.kr/ minhee@dahlia.kr under the MIT License.
7. PyQT. PyQT is Copyright (c) 2013, Riverbank Computing Limited. Riverbank Computing Limited is a company registered in England and Wales with company number 4314904.

It is also necessary to install ImageMagick. Please install at least version 6.7.7-10. Some issues have been seen with loading single-channel images with that version, but they appear to be fixed in ImageMagick-6.7.9-1.

In addition, if you wish to run testcases, the following modules are required:

1. mock (sudo pip install -U mock). mock is Copyright (c) 2003-2010, Michael Foord and is licensed under the BSD License.

Compiling Windows Executables

Windows 64 bit executables turned out to be too difficult to support. A few items are required:

1. Install python 2.7.3 (32-bit) to C:\Python27 (To use different paths, edit the Makefile).

2. Install mingw (32-bit).

3. Install required libraries: a. scipy, numpy, pythonmagick, matplotlib, and pil (use pillow) for 32-bit. Use premade packages available at: http://www.lfd.uci.edu/~gohlke/pythonlibs/ b. py2exe: http://sourceforge.net/projects/py2exe/files/py2exe/0.6.9/ c. pyqt: http://www.riverbankcomputing.com/software/pyqt/download Version 4.10 has been successfully used. d. wand: Follow http://docs.wand-py.org/en/0.2-maintenance/guide/install.html#install-imagemagick-on-windows then use the pip premade package in the pythonlibs link above. Then open a command prompt, navigate to pip (C:\Python27\Scripts) and call

        pip.exe install Wand
   
    Wand should be successfully installed.
   

4. Install the Visual Studio C++ Redistributable version here: http://www.microsoft.com/en-us/download/details.aspx?id=29 (included in repo)

5. Open mingw 32-bit shell, navigate to C:\Python27\Lib\site-packages\matplotlib

6. Call

   ls -r .py | xargs sed -i.bak "s/.doc.*//g" chmod -R 644 *

This will remove a lot of docstring manipulating code preventing optimization. Additional changes will have to be done to many files. vendor contains a zip of my matplotlib changes confirmed to work. 5. Launch the mingw 32-bit shell, navigate to this repo: a. To create the 32 bit version, call "make" b. (DOESN'T WORK) To create the 64 bit version, call "make DLL_64=1" 6. To make the icon work, install pywin32: http://sourceforge.net/projects/pywin32/files/pywin32/Build%20218/

Compliing Linux Executables

1. Install cx-freeze:

   sudo apt-get install cx-freeze

2. edit /usr/lib/pymodules/python2.7/cx_Freeze/finder.py, on line 232 change

   path = parentModule.path

to

path = parentModule.path or parentModule.file

3. Find the mpl-data directory (for me was in /usr/share/matplotlib/mpl-data)

4. Make a link to it in /usr/lib/pymodules/python2.7/matplotlib/mpl-data

   sudo ln -s /usr/share/matplotlib/mpl-data /usr/lib/pymodules/python2.7/matplotlib/mpl-data

5. Fix the broken font links, if any, in mpl-data/fonts/ttf (in my case, cmex10.ttf, cmmi10.ttf, cmr10.ttf, and cmsy10.ttf were broken, had to point them to my LyX installation)

6. Run the makefile

7. Distribute bin