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Python tools for interacting with XML files associated with RECONSTRUCT

Project description

===========
PyRECONSTRUCT
===========
Date Created: 3/7/2013
Authors: Michael Musslewhite, Larry Lindsey

PyRECONSTRUCT provides easy access to XML files associated with the program RECONSTRUCT.
This package should also be used to develop scripts/programs for various tasks that use
these XML files. Included examples are mergeTool for merging multiple RECONSTRUCT series
and excelTool for pushing object data into an excel workbook (.xlsx).

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INSTALLATION (Linux and Windows)
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# Linux :D
-------------
PyRECONSTRUCT can be installed in multiple ways:

[Preferred]: From parent folder:
python setup.py install
*this command must be run every time changes are made locally to any file in PyRECONSTRUCT

[Optional]: Through PIP*:
pip install PyRECONSTRUCT
*this method commonly has problems. Prerequisite packages may not install correctly on their own and will interrupt the PyRECONSTRUCT installation

These dependencies are required to run on most linux systems:
python-dev
python-setuptools
libgeos-dev
libblas-dev
liblapack-dev
libfreetype6-dev
libpng-dev
gfortran
libxml2-dev
libxslt-dev
cmake
libshiboken-dev

# Windows :(
-------------
PyRECONSTRUCT for Windows has only been tested using the following method:
1. Download and install Python2.7:
http://www.python.org/download/releases/2.7.5/
2. Download and install python-setuptools (setup.py install):
http://python-distribute.org/distribute_setup.py
3. Download PyRECONSTRUCT code from pypi:
https://pypi.python.org/pypi/PyRECONSTRUCT
4. Run 'setup.py install' after cding into parent folder
*This will be unsuccessful due to missing dependencies, but it will tell you why.
This will most likely be resolved in the following steps, but rerun this command after every step to determine if problems are being resolved successfully

5. Download and install lxml (includes libxml2/libxslt):
https://pypi.python.org/packages/2.7/l/lxml/lxml-3.2.3.win-amd64-py2.7.exe#md5=3720e7d124275b728f553eb93831869c
6. Download and install Cython:
http://www.lfd.uci.edu/~gohlke/pythonlibs/#cython
7. Download and install Scipy-stack:
http://www.lfd.uci.edu/~gohlke/pythonlibs/#scipy-stack
8. Download and install scikit-image:
http://www.lfd.uci.edu/~gohlke/pythonlibs/#scikit-image
9. Download and install scipy (fixes missing scipy.special package):
http://www.lfd.uci.edu/~gohlke/pythonlibs/#scipy
10. ...Should work now?*
*email me (address located in setup.py) if there are problems!



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IMPORTING INTO PYTHON
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PyRECONSTRUCT should be imported with the name 'pyrecon' (i.e. import pyrecon)

To import only the XML-parse portion of PyRECONSTRUCT:

from pyrecon.tools import classes
or
from pyrecon.tool.classes import *



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More Information
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More info on RECONSTRUCT can be found here:
http://synapses.clm.utexas.edu/tools/index.stm

Project details


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PyRECONSTRUCT-1.4.2.tar.gz (53.2 kB) Copy SHA256 hash SHA256 Source None Nov 27, 2013

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