A Python wrapper for L-Measure
Project description
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:
- Linux 32 and 64 bit
Installation: Linux: Caution: Do not place these files in a system path.
-
Copy the folder 'python-Lmeasure' to a location(for example /installations/)
-
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
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