pylmeasure 0.1.2

A Python wrapper for L-Measure

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# PyLMeasure: A Python Wrapper for L-Measure.

[PyLMeasure](https://pypi.org/project/pylmeasure/) is a Python wrapper library for the command-line interface of the neuronal morphology analysis tool [L-Measure](http://cng.gmu.edu:8080/Lm/help/index.htm).

# Installation

To install the library, simply type in `pip install pylmeasure` in your terminal.

There is no need to separately download L-Measure or install Java. The above command includes the necessary binaries.

# Usage

# Issues

# Contributing


Mainly, three functions are implemented getMeasure(), getMeasureDistribution() and
getMeasureDependence().

Operating systems Supported:
1. Linux 32 and 64 bit

Installation:
Linux:
Caution: Do not place these files in a system path.
1. Copy the folder 'python-Lmeasure' to a location(for example <home directory>/installations/)
2. Add the path '<path to python-Lmeasure>/LMIO/' to the system PYTHONPATH by adding the following line to .profile or .bashrc

export PYTHONPATH="$PYTHONPATH:<path to python-Lmeasure>/LMIO/"

Source the .profile or .bashrc file.


Output Format:

The object returned by any of the three functions is a list of a dictionaries, each dictionary with the following
structure. Each dictionary corresponds to one measure specified as input to the function being used(in measureNames or
measure1Names).

LMOutputTemplate = dict(rawData=None,
measure1BinCentres=None,
measure1BinCounts=None,
measure2BinAverages=None,
measure2BinStdDevs=None,
WholeCellMeasures=None,
)


WholeCellMeasures is a (# of swc files given)x7 numpy array. The seven entries along the second dimension correspond
respectively to

TotalSum, CompartmentsConsidered, Compartments Discarded, Minimum, Average, Maximum, StdDev

All meaure**** fields are (# of swc files given) x (nBins +1) numpy arrays.

getMeasure() has its results in WholeCellMeasures.

getMeasureDistribution has its results in measure1BinCentres and measure1BinCounts

getMeasureDependence has its results in measure1BinCentres, measure2BinAverages and measure2BinStdDevs


Misc:

See the file ExampleUsage.py for example usage.

Look at the documentation strings for more information