pylmeasure 0.1.3

A Python wrapper for L-Measure

PyLMeasure: A Python Wrapper for L-Measure.

PyLMeasure is a Python wrapper library for the command-line interface of the neuronal morphology analysis tool L-Measure.

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 /installations/)

2. Add the path '/LMIO/' to the system PYTHONPATH by adding the following line to .profile or .bashrc

   export PYTHONPATH="$PYTHONPATH:/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