pylmeasure 0.1.5

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.

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

Usage

The basic usage is:

from pylmeasure import *

# Specify the L-Measure to compute, full list: http://cng.gmu.edu:8080/Lm/help/index.htm
LMOutput = getMeasure(['Surface', 'Diameter'], ["path/to/file.swc"])

#                                              V-- measure index           V-- file index
print("Surface area of first file:",  LMOutput[0]["WholeCellMeasuresDict"][0]["TotalSum"])
print("Mean diameter in first file:", LMOutput[1]["WholeCellMeasuresDict"][0]["Average"])

For more examples, see this Jupyter notebook.

Issues

If you encounter an issues, first make sure it's not due to L-Measure itself -- this library simply wraps the L-Measure executables. If it is, please contact the L-Measure team. If the issue is with this library, please create an issue on Github.

Contributing

To contribute, please open an issue first and discuss your plan for contributing. Then fork this repository and commit a pull-request with your changes.

Acknowledgements

This wrapper library project was initialy started by Ajayrama Kumaraswamy. View the original source.