Python Wrapper for L-measure.
It is advised that one be familiar with L-measure and it's functionalities before using this wrapper.
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