PyRECONSTRUCT 2.0.0

Python tools for interacting with XML files associated with RECONSTRUCT

[PyRECONSTRUCT](https://pypi.python.org/pypi/PyRECONSTRUCT)
=============
Authors: Michael Musslewhite, Larry Lindsey<br>
Date Created: 3/7/2013<br>


# Overview
[PyRECONSTRUCT](https://pypi.python.org/pypi/PyRECONSTRUCT) provides easy access to data in XML files associated with the program [RECONSTRUCT](http://synapses.clm.utexas.edu/tools/reconstruct/reconstruct.stm).
This package also contains several tools for managing this data:
* mergeTool - merge series together with built-in conflict resolution (graphical or non-graphical)
* excelTool - output data into excel workbooks (.xlsx)
* calibrationTool - rescale contours representing images in a section
* curationTool - check for various properties of objects in a series

The functions/tools already in place can be used to develop solutions to a wide range of problems associated with RECONSTRUCT data.

To start graphical tool loader, use commands in python shell:
* `import pyrecon`
* `pyrecon.start()`

# Install Instructions
*The build found on GitHub is the development build and may be unstable.*<br>
*The stable version can be found here: [PyPI](https://pypi.python.org/pypi/PyRECONSTRUCT) (Python Package Index)*

### Linux
* Install the following dependencies:
* `python-dev`
* `python-setuptools`
* `libgeos-dev`
* `libblas-dev`
* `liblapack-dev`
* `libfreetype6-dev`
* `libpng-dev`
* `gfortran`
* `libxml2-dev`
* `libxslt-dev`
* `cmake`
* `libshiboken-dev`
* Install [PySide](http://qt-project.org/wiki/PySide)
* Install [PyRECONSTRUCT](https://pypi.python.org/pypi/PyRECONSTRUCT) by running `python setup.py install` from its parent folder

### Windows *(discouraged: currently testing, run successfully pre 2.0.0)*
* Download and install [Python2.7](http://www.python.org/download/releases/2.7.5/)
* Download and install [python-setuptools](http://python-distribute.org/distribute_setup.py)
* Download [PyRECONSTRUCT](https://pypi.python.org/pypi/PyRECONSTRUCT)
* Run `python setup.py install` from parent folder
* Dependencies will likely be missing, but the errors will tell you what you need
* Download and install [lxml](https://pypi.python.org/packages/2.7/l/lxml/lxml-3.2.3.win-amd64-py2.7.exe#md5=3720e7d124275b728f553eb93831869c)
* Download and install [Cython](http://www.lfd.uci.edu/~gohlke/pythonlibs/#cython)
* Download and install [Scipy-stack](http://www.lfd.uci.edu/~gohlke/pythonlibs/#scipy-stack)
* Download and install [scikit-image](http://www.lfd.uci.edu/~gohlke/pythonlibs/#scikit-image)
* Download and install [scipy](http://www.lfd.uci.edu/~gohlke/pythonlibs/#scipy)
* fixes missing scipy.special package
* ...Should work now?
*email me if there are problems (address located in setup.py)!*

### PyRECONSTRUCT + Git Installation
* 1) Add the following lines to your Series' repository's `.git/config` file, replacing PATH_TO_gitmerge.py appropriately:
<pre>
[merge "pymerge"]
name = pyrecon mergetool driver
driver = PATH_TO_gitmerge.py %A %B
</pre>

* 2) Add the following line to your Series' repository's `.git/info/attributes` file:
<pre>
`* merge=pymerge`