pySTDLM.PostProcessing Namespace Reference

Functions
	openLMFile (filename)
	closeLMFile (f)
	showTraceFromFile (filename, species, replicate, **kwargs)
	plotTraceFromFile (filename, species, replicate, outfile, **kwargs)
	showTrace (f, species, replicate, **kwargs)
	plotTrace (f, species=None, replicate=1, filename=None, **kwargs)
	showAvgVarFromFile (filename, species, **kwargs)
	plotAvgVarFromFile (filename, species, outfile, **kwargs)
	showAvgVar (f, species, **kwargs)
	plotAvgVar (f, species=None, filename=None, **kwargs)
	getOccupancyKymograph (f, species=None, replicate=1)
	plotOccupancyKymograph (f, species=None, replicate=1, filename=None)
	showOccupancyKymograph (f, species=None, replicate=1)
	plotPhaseSpace (f, species=None, replicate=1, withHistogram=False)
	getSpecies (f)
	getTimesteps (f)
	getSpecieTrace (f, specie, replicate=1, doublingTime=None)
	getAvgVarTrace (f, specie, doublingTime=None)
	getHistogram (f, species)
	getPhaseSpace (f, species, replicate)

Function Documentation

closeLMFile()

pySTDLM.PostProcessing.closeLMFile

(

f

)

Close a Lattice Microbes File

Args:
    f:
        A previously opened lattice microbes file

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getAvgVarTrace()

pySTDLM.PostProcessing.getAvgVarTrace	(		f,
			specie,
			doublingTime = None )

Get the average and variance of the specie trace over time

Args:
    f:
        The HDF5 file handle to extract from or the name of a file to open
    specie:
        The specie to extract
    doublingTime:
        An optional doubling time parameter that will normalize average each trace by time 
        in the cell cycle assuming exponentially growing cell (2log2 * x/2^(t/DT)), 
        effectively normalizing against cell size. Default: no averaging is performed

Returns:
    avg, var, time

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getHistogram()

pySTDLM.PostProcessing.getHistogram	(		f,
			species )

Get the histogram for a specie

Args:
    f:
        The HDF5 file handle to extract from or the name of a file to open
    specie:
        An array of specie/s to extract. returns a nD histogram of the data.

Returns:
    bins, edges (len(bins)+1)

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getOccupancyKymograph()

pySTDLM.PostProcessing.getOccupancyKymograph	(		f,
			species = None,
			replicate = 1 )

Compute the specie density(occupancy) among a slice of the simulation domain as a function over time for the given direciton

Args:
    filename:
        Name of file to extract data from
    specie:
        A particular specie to plot density for
    replicate:
        The replicate to show trace for

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getPhaseSpace()

pySTDLM.PostProcessing.getPhaseSpace	(		f,
			species,
			replicate )

Get the nD phase space associated with the traces of species. 

If a single replicate is specified, a single trace will be returned, otherwise a 2/3D density matrix will be returned.

Args:
    f:
        The HDF5 file handle to extract from or the name of a file to open
    specie:
        An iterable of 2 more specie names
    replicate:
        The replicate for which to extract the phase space

Returns:
    A numpy array of a trace from a single replicate (specie1, specie2, ...) 

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getSpecies()

pySTDLM.PostProcessing.getSpecies

(

f

)

Exract the species names

Args:
    f:
        The HDF5 file handle to extract from or the name of a file to open

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getSpecieTrace()

pySTDLM.PostProcessing.getSpecieTrace	(		f,
			specie,
			replicate = 1,
			doublingTime = None )

Extract data for a particular specie for the specified replicate

Args:
    f:
        The HDF5 file handle to extract from or the name of a file to open
    specie:
        The specie to extract data 
    replicate:
        The number of the replicate to extract from (default: 1)
    doublingTime:
        An optional doubling time parameter that will normalize average each trace by 
        time in the cell cycle assuming exponentially growing cell 
        (2log2 * x/2^(t/DT)), effectively normalizing against cell size. 
        Default: no averaging is performed

Returns:
    The species time trace in a numpy array

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getTimesteps()

pySTDLM.PostProcessing.getTimesteps

(

f

)

Extract the timestep times

Args:
    f:
        The HDF5 file handle to extract from or the name of a file to open

Returns:
    The timestep times in a numpy array

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openLMFile()

pySTDLM.PostProcessing.openLMFile

(

filename

)

Open a Lattice Microbes File for reading

Args:
    filename:
        Name of the file
Returns:
    a handle to the file

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plotAvgVar()

pySTDLM.PostProcessing.plotAvgVar	(		f,
			species = None,
			filename = None,
		**	kwargs )

Plot a specific species average over time and variance

Args:
    f:
        An h5py object handle
    species:
        A list of species to show
    filename:
        A filename to print to (default None, gives the same behavior as showAvgVar(...))
    kwargs:
        Additional arguments to be passed on to matplotlib.plot.  These are any arguments that are valid with matplotlib.plot

Returns:
    A handle to the figure object created which allows customization of plot attributes

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plotAvgVarFromFile()

pySTDLM.PostProcessing.plotAvgVarFromFile	(		filename,
			species,
			outfile,
		**	kwargs )

Plot species from an output file

Args:
    filename:
        The name of an HDF5 output file generated by LatticeMicrobes
    species:
        A list of species to plot
    kwargs:
        Additional arguments to be passed on to matplotlib.plot.  These are any arguments that are valid with matplotlib.plot
    outfile:
        A filename to plot to

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plotOccupancyKymograph()

pySTDLM.PostProcessing.plotOccupancyKymograph	(		f,
			species = None,
			replicate = 1,
			filename = None )

Plot a specific specie density(occupancy) among a slice of the simulation domain as a function of a direction over time

Args:
    f:
        The name of the LM file
    specie:
        A particular specie to plot density for
    filename:
        A filename to print to (default None, gives the same behavior as showAvgVar(...))
    replicate:
        The replicate to show trace for the kymograph from the file

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plotPhaseSpace()

pySTDLM.PostProcessing.plotPhaseSpace	(		f,
			species = None,
			replicate = 1,
			withHistogram = False )

Plot the 2D or 3D phase space associated with the given species over the replicates indicated

Args:
    f:
        An h5py object handle
    specie:
        An iterable of 2 or 3 specie names indicating whether to plot in 2D or 3D space
    replicate:
        The replicate to show trace for
    withHistogram:
        If set to true, a heatmap of the phase space over all replicates will be plotted in the background.  (NOTE: this only works in 2D.)

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plotTrace()

pySTDLM.PostProcessing.plotTrace	(		f,
			species = None,
			replicate = 1,
			filename = None,
		**	kwargs )

Plot a specific species trace

Args:
    f:
        An h5py object handle
    species:
        A specie name or a list of species to show; can be a single string or a iterable list of species
    filename:
        A filename to print to (default None, gives the same behavior as showAvgVar(...))
    replicate:
        The replicate to show trace for. Can be an integer or an iterable list of replicte numbers
    kwargs:
        Additional arguments to be passed on to matplotlib.plot.  These are any arguments that are valid with matplotlib.plot

Returns:
    A handle to the figure object created which allows customization of plot attributes

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plotTraceFromFile()

pySTDLM.PostProcessing.plotTraceFromFile	(		filename,
			species,
			replicate,
			outfile,
		**	kwargs )

Plot species from an output file

Args:
    filename:
        The patch to an HDF5 output file generated by LatticeMicrobes
    species:
        A list of species to plot
    replicate:
        The replicate to show trace for
    kwargs:
        Additional arguments to be passed on to matplotlib.plot.  These are any arguments that are valid with matplotlib.plot
    outfile:
        A filename to plot to

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showAvgVar()

pySTDLM.PostProcessing.showAvgVar	(		f,
			species,
		**	kwargs )

Show a specific species average over time and variance

Args:
    f:
        An h5py object handle
    species:
        A list of species to show
    kwargs:
        Additional arguments to be passed on to matplotlib.plot.  These are any arguments that are valid with matplotlib.plot

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showAvgVarFromFile()

pySTDLM.PostProcessing.showAvgVarFromFile	(		filename,
			species,
		**	kwargs )

Show species from an output file
Args:
    filename:
        The name of an HDF5 output file generated by LatticeMicrobes
    species:
        A list of species to plot
    kwargs:
        Additional arguments to be passed on to matplotlib.plot.  These are any arguments that are valid with matplotlib.plot

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showOccupancyKymograph()

pySTDLM.PostProcessing.showOccupancyKymograph	(		f,
			species = None,
			replicate = 1 )

Show a specific specie density(occupancy) among a slice of the simulation domain as a function of a direction over time

Args:
    f:
        An h5py object handle
    specie:
        A particular specie to plot density for
    replicate:
        The replicate to show trace for

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showTrace()

pySTDLM.PostProcessing.showTrace	(		f,
			species,
			replicate,
		**	kwargs )

Show a specific species trace

Args:
    f:
        An h5py object handle
    species:
        A list of species to show
    replicate:
        The replicate to show trace for
    kwargs:
        Additional arguments to be passed on to matplotlib.plot.  These are any arguments that are valid with matplotlib.plot

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showTraceFromFile()

pySTDLM.PostProcessing.showTraceFromFile	(		filename,
			species,
			replicate,
		**	kwargs )

Show species trace from a particular replicate

Args:
    filename:
        The patch to an HDF5 output file generated by LatticeMicrobes
    species:
        A list of species to plot
    replicate:
        The replicate to show trace for
    kwargs:
        Additional arguments to be passed on to matplotlib.plot.  These are any arguments that are valid with matplotlib.plot

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