tellurium.analysis package¶
Submodules¶
tellurium.analysis.annotations module¶
tellurium.analysis.bifurcation module¶
Utility classes for computing bifurcations.
tellurium.analysis.parameterestimation module¶
Parameter estimation in tellurium.
- class tellurium.analysis.parameterestimation.ParameterEstimation(stochastic_simulation_model, bounds, data=None)[source]¶
Bases:
object
Parameter Estimation
- run(func=None)[source]¶
Allows the user to set the data from a File This data is to be compared with the simulated data in the process of parameter estimation
- Args:
- func: An Optional Variable with default value (None) which by default run differential evolution
which is from scipy function. Users can provide reference to their defined function as argument.
- Returns:
The Value of the parameter(s) which are estimated by the function provided.
- setDataFromFile(FILENAME, delimiter=',', headers=True)[source]¶
Allows the user to set the data from a File This data is to be compared with the simulated data in the process of parameter estimation
- Args:
FILENAME: A Complete/relative readable Filename with proper permissions delimiter: An Optional variable with comma (“,”) as default value.
A delimiter with which the File is delimited by. It can be Comma (“,”) , Tab (” “) or anyother thing
- headers: Another optional variable, with Boolean True as default value
If headers are not available in the File, it can be set to False
- Returns:
None but sets class Variable data with the data provided
tellurium.analysis.parameterscan module¶
Utility classes for parameter scans.
- class tellurium.analysis.parameterscan.ParameterScan(rr, startTime=0, endTime=20, numberOfPoints=50, polyNumber=10, startValue=None, endValue=None, value=None, independent=None, selection=None, dependent=None, integrator='cvode', color=None, width=2.5, alpha=0.7, title=None, xlabel='toSet', ylabel='toSet', zlabel='toSet', colormap='seismic', colorbar=True, antialias=True, sameColor=False, legend=True)[source]¶
Bases:
object
- createColorPoints()[source]¶
Sets self.color to a set of values that allow plotPolyArray, plotArray, or plotGraduatedArray to take on colors from a colormap. The colormap can either be user-defined using createColormap or one of the standard colormaps.
- classmethod createColormap(color1, color2)[source]¶
Creates a color map for plotSurface using two colors as RGB tuplets, standard color names, e.g. ‘aqua’; or hex strings.
p.colormap = p.createColorMap([0,0,0], [1,1,1])
- plotArray()[source]¶
Plots result of simulation with options for linewdith and line color.
p.plotArray()
- plotGraduatedArray()[source]¶
Plots array with either default multiple colors or user sepcified colors using results from graduatedSim().
p.plotGraduatedArray()
- plotPolyArray()[source]¶
Plots results as individual graphs parallel to each other in 3D space using results from graduatedSim().
p.plotPolyArray()
- plotSurface()[source]¶
Plots results of simulation as a colored surface. Takes three variables, two independent and one dependent. Legal colormap names can be found at http://matplotlib.org/examples/color/colormaps_reference.html.
p.plotSurface()
- class tellurium.analysis.parameterscan.ParameterScan2D(rr, p1=None, p1Range=None, p2=None, p2Range=None, start=0, end=100, points=101, independent=None, selection=None, dependent=None, integrator='cvode', color=None, width=2.5, alpha=0.7, title=None, xlabel='toSet', ylabel='toSet', zlabel='toSet', colormap='seismic', colorbar=True, antialias=True, sameColor=False, legend=True)[source]¶
Bases:
object
- class tellurium.analysis.parameterscan.SteadyStateScan(rr, startTime=0, endTime=20, numberOfPoints=50, polyNumber=10, startValue=None, endValue=None, value=None, independent=None, selection=None, color=None, width=2.5, alpha=0.7, title=None, xlabel=None, ylabel=None, zlabel=None, colormap='seismic', colorbar=True, antialias=True, sameColor=False, legend=None)[source]¶
Bases:
object
tellurium.analysis.sensitivityanalysis module¶
tellurium.analysis.simulator module¶
tellurium.analysis.stochasticmodel module¶
- class tellurium.analysis.stochasticmodel.StochasticSimulationModel(model=None, integrator='gillespie', seed=1234, variable_step_size=False, from_time=0, to_time=40, step_points=50)[source]¶
Bases:
object
- property from_time¶
- property integrator¶
- property model¶
- property seed¶
- property step_points¶
- property to_time¶
- property variable_step_size¶
tellurium.analysis.test module¶
Working