rrplugins 2.11.0__cp315-cp315-win_amd64.whl

rrplugins/README.txt

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+Tellurium PluginAPI Python Wrapper
+
+The telplugins_c_api.py file is a python wrapper around the telplugins_c_api library.
+
+On top of the raw API defined by telplugins_c_api.py, is another more user friendly API defined, in the file telplugins.py.
+
+Necessary files in this folder should be installed to your systems python installations site-packages folder. 
+
+=================================================================================
+Totte Karlsson and Herbert Sauro.

rrplugins/__init__.py

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+from .telplugins import *
+from .telplugins_c_api import *
+
+__version__ = '2.11.0'

rrplugins/add_noise_example.py

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+import roadrunner
+
+import rrplugins as tel
+
+rr = roadrunner.RoadRunner() 
+
+rr.load("path to any model. Eg. some models are provided in source code, like, sbml_test_0001") 
+
+data = rr.simulate(0, 10, 511)
+
+noisePlugin = tel.Plugin ("tel_add_noise") 
+
+d = tel.getDataSeries (data) 
+
+noisePlugin.InputData = d 
+
+noisePlugin.Sigma = 3.e-6 
+
+noisePlugin.execute()
+
+noisePlugin.InputData.plot()
+

rrplugins/auto2000_example1.py

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+from rrplugins import *
+auto = Plugin("tel_auto2000")
+
+
+# path to any model. Eg. some models are provided in source code, like BIOMD0000000203.xml
+sbmlModel = "BIOMD0000000203.xml"
+
+auto.setProperty("SBML", readAllText(sbmlModel))
+
+auto.setProperty("NMX", 5000)
+
+auto.setProperty("ScanDirection", "Positive")
+
+auto.setProperty("PrincipalContinuationParameter", "A")
+auto.setProperty("PCPLowerBound", 10)
+auto.setProperty("PCPUpperBound", 200)
+
+#Max numberof points 
+auto.setProperty("NMX", 5000) 
+ 
+#Execute the plugin 
+auto.execute() 
+ 
+# Bifurcation summary 
+print("Summary: " + auto.BifurcationSummary) 
+ 
+#Plot Bifurcation diagram 
+pts     = auto.BifurcationPoints 
+lbls    = auto.BifurcationLabels 
+biData  = auto.BifurcationData 
+ 
+biData.plotBifurcationDiagram(pts, lbls) 

rrplugins/auto2000_example2.py

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+import tellurium as te
+from rrplugins import *
+auto = Plugin("tel_auto2000")
+
+
+r = te.loada (
+	'''   
+    	$Xo -> x; 0.1 + k1*x^4/(k2+x^4);    
+     	x -> $w; k3*x;
+    	// Initialization here    
+    	k1 = 0.9;
+    	k2 = 0.3;    
+    	k3 = 0.7;
+	'''
+)
+ 
+auto.setProperty("SBML", r.getCurrentSBML())
+auto.setProperty("NMX", 5000)
+auto.setProperty("ScanDirection", "Positive")
+auto.setProperty("PrincipalContinuationParameter", "k3")
+
+auto.setProperty("PCPLowerBound", 0.2)
+auto.setProperty("PCPUpperBound", 1.8)
+ 
+#Execute the plugin 
+auto.execute() 
+ 
+# Bifurcation summary 
+print("Summary: " + auto.BifurcationSummary) 
+ 
+#Plot Bifurcation diagram 
+pts     = auto.BifurcationPoints 
+lbls    = auto.BifurcationLabels 
+biData  = auto.BifurcationData 
+ 
+biData.plotBifurcationDiagram(pts, lbls) 

rrplugins/chi_squared_example.py

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+from rrplugins import * 
+
+modelPlugin     = Plugin("tel_test_model") 
+noisePlugin     = Plugin("tel_add_noise") 
+chiSquarePlugin = Plugin("tel_chisquare") 
+ 
+#Generate internal test data 
+modelPlugin.execute() 
+modelData = modelPlugin.TestData 
+expData = modelPlugin.TestDataWithNoise 
+ 
+chiSquarePlugin.ExperimentalData = expData 
+chiSquarePlugin.ModelData = modelData 
+chiSquarePlugin.NrOfModelParameters = 1 
+ 
+chiSquarePlugin.execute() 
+ 
+chi = chiSquarePlugin.ChiSquare 
+reduced_chi = chiSquarePlugin.ReducedChiSquare 
+ 
+print("ChiSquare is: +", chi)
+print("Reduced ChiSquare is: ",reduced_chi)

rrplugins/hello_roadrunner_example.py

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+import rrplugins as tel
+hello = tel.Plugin("tel_hello")
+hello.execute()

rrplugins/telAuto2000.py

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+import rrplugins
+
+sbmlModel ="BIOMD0000000203.xml"                              
+auto = rrplugins.Plugin("tel_auto2000")              
+
+#print auto.listOfPropertyNames()
+
+#Setup Auto Propertys
+auto.setProperty("SBML", rrplugins.readAllText(sbmlModel))
+
+#Auto specific properties
+auto.setProperty("ScanDirection", "Positive")    
+auto.setProperty("PrincipalContinuationParameter", "A")
+auto.setProperty("PCPLowerBound", 10)
+auto.setProperty("PCPUpperBound", 200)
+
+#Max numberof points
+auto.setProperty("NMX", 5000)  
+       
+#Execute the plugin
+auto.execute()
+     
+# Bifurcation summary
+print("Summary: ", auto.BifurcationSummary)
+
+#Plot Bifurcation diagram
+pts     = auto.BifurcationPoints
+lbls    = auto.BifurcationLabels
+biData  = auto.BifurcationData    
+
+biData.plotBifurcationDiagram(pts, lbls) 
+    
+print("Done")

rrplugins/telLevenbergMarquardt.py

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+import rrplugins
+from rrplugins import tpc
+
+# Load Plugins
+chiPlugin       = rrplugins.Plugin("tel_chisquare")
+lm              = rrplugins.Plugin("tel_levenberg_marquardt")
+modelPlugin     = rrplugins.Plugin("tel_test_model")
+addNoisePlugin  = rrplugins.Plugin("tel_add_noise")
+
+#========== EVENT FUNCTION SETUP ===========================
+def myEvent(dummy, dummy2): #We are not capturing any data from the plugin, so just pass a dummy
+    print('Iteration, Norm = ', lm.getProperty("NrOfIter") , ', ', lm.getProperty("Norm"))
+
+#Setup progress event function
+progressEvent =  rrplugins.NotifyEventEx(myEvent)     
+rrplugins.assignOnProgressEvent(lm.plugin, progressEvent)
+#============================================================
+
+#Create model data, with and without noise using the test_model plugin
+modelPlugin.execute()     
+
+#Setup lmfit properties.
+lm.SBML             = modelPlugin.Model 
+lm.ExperimentalData = modelPlugin.TestDataWithNoise
+
+# Add the parameters that we're going to fit and an initial 'start' value
+lm.setProperty("InputParameterList", ["k1", .3])
+lm.setProperty("FittedDataSelectionList", "[S1] [S2]")
+lm.setProperty("ExperimentalDataSelectionList", "[S1] [S2]")
+
+# Start minimization
+lm.execute()
+
+print('Minimization finished. \n==== Result ====')
+print('Fit engine status: ', lm.getProperty('StatusMessage'))
+
+print('Hessian Matrix')
+print(lm.getProperty("Hessian"))
+
+print('Covariance  Matrix')
+print(lm.getProperty("CovarianceMatrix"))
+         
+print('ChiSquare = '           , lm.getProperty("ChiSquare"))
+print('Reduced ChiSquare = '   , lm.getProperty("ReducedChiSquare"))
+    
+#This is a list of parameters
+parameters = tpc.getPluginProperty (lm.plugin, "OutputParameterList")
+confLimits = tpc.getPluginProperty (lm.plugin, "ConfidenceLimits")    
+
+#Iterate trough list of parameters and confidence limits
+para  = rrplugins.getFirstProperty(parameters)
+limit = rrplugins.getFirstProperty(confLimits)     
+while para and limit:           
+    print(rrplugins.getPropertyName(para), ' = ', rrplugins.getPropertyValue(para), ' +/- ', rrplugins.getPropertyValue(limit))
+    para  = rrplugins.getNextProperty(parameters)
+    limit = rrplugins.getNextProperty(confLimits)                        
+                             
+
+# Get the fitted and residual data
+fittedData = lm.getProperty ("FittedData").toNumPy()
+residuals  = lm.getProperty ("Residuals").toNumPy()
+
+# Get the experimental data as a numpy array
+experimentalData = modelPlugin.TestDataWithNoise.toNumPy()
+
+rrplugins.plot(fittedData         [:,[0,1]], "blue", "-",    "",    "S1 Fitted")
+rrplugins.plot(fittedData         [:,[0,2]], "blue", "-",    "",    "S2 Fitted")
+rrplugins.plot(residuals          [:,[0,1]], "blue", "None", "x",   "S1 Residual")
+rrplugins.plot(residuals          [:,[0,2]], "red",  "None", "x",   "S2 Residual")
+rrplugins.plot(experimentalData   [:,[0,1]], "red",  "",     "*",   "S1 Data")
+rrplugins.plot(experimentalData   [:,[0,2]], "blue", "",     "*",   "S2 Data")
+rrplugins.plt.show()

rrplugins/telMonteCarlo.py

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+import rrplugins
+import matplotlib.pyplot as plt
+import numpy as np
+
+#Load plugins        
+modelP      = rrplugins.Plugin("tel_test_model")
+nP          = rrplugins.Plugin("tel_add_noise")    
+chiP        = rrplugins.Plugin("tel_chisquare")
+lmP         = rrplugins.Plugin("tel_levenberg_marquardt")
+nmP         = rrplugins.Plugin("tel_nelder_mead")
+mcP         = rrplugins.Plugin("tel_monte_carlo_bs") 
+
+#========== EVENT FUNCTION SETUP ===========================
+def myEventFunction(ignore, ignore2):           
+    # Get the fitted and residual data
+    experimentalData    = lmP.getProperty ("ExperimentalData").toNumPy()
+    fittedData          = lmP.getProperty ("FittedData").toNumPy()
+    residuals           = lmP.getProperty ("Residuals").toNumPy()
+    
+    rrplugins.plot(fittedData         [:,[0,1]], "blue", "-",    "",    "S1 Fitted")
+    rrplugins.plot(fittedData         [:,[0,2]], "blue", "-",    "",    "S2 Fitted")
+    rrplugins.plot(residuals          [:,[0,1]], "blue", "None", "x",   "S1 Residual")
+    rrplugins.plot(residuals          [:,[0,2]], "red",  "None", "x",   "S2 Residual")
+    rrplugins.plot(experimentalData   [:,[0,1]], "red",  "",     "*",   "S1 Data")
+    rrplugins.plot(experimentalData   [:,[0,2]], "blue", "",     "*",   "S2 Data")
+    
+    print('Minimization finished. \n==== Result ====')
+    print(rrplugins.getPluginResult(lmP.plugin))
+    rrplugins.plt.show()       
+                 
+#Communicating event
+myEvent =  rrplugins.NotifyEventEx(myEventFunction)
+
+#Uncomment the event assignment below to plot each monte carlo data set
+#assignOnFinishedEvent(lmP.plugin, myEvent, None)                    
+
+#This will create test data with noise. We will use that as 'experimental' data
+modelP.execute() 
+       
+#Setup Monte Carlo properties.
+mcP.SBML                             = modelP.Model
+mcP.ExperimentalData                 = modelP.TestDataWithNoise
+
+#Select what minimization plugin to use                     
+#mcP.MinimizerPlugin                  = "Nelder-Mead"
+mcP.MinimizerPlugin                  = "Levenberg-Marquardt"
+mcP.NrOfMCRuns                       = 100
+mcP.InputParameterList               = ["k1", 1.5]
+mcP.FittedDataSelectionList          = "[S1] [S2]"
+mcP.ExperimentalDataSelectionList    = "[S1] [S2]"
+
+# Start Monte Carlo
+mcP.execute()
+
+print('Monte Carlo Finished. \n==== Result ====')
+print(mcP.MonteCarloParameters.getColumnHeaders())
+paras = mcP.MonteCarloParameters.toNumPy()
+print(paras)
+   
+#Get mean (assuming normal distribution).
+print("The mean: k1= ", np.mean(paras))
+
+ 
+PropertyOfTypeListHandle = rrplugins.getPluginProperty(mcP.plugin, "ConfidenceIntervals")
+print(rrplugins.getNamesFromPropertyList(PropertyOfTypeListHandle))
+aProperty = rrplugins.getFirstProperty(PropertyOfTypeListHandle)
+if aProperty:
+    print(rrplugins.getPropertyValueAsString(aProperty))
+
+PercentileHandle = rrplugins.getPluginProperty(mcP.plugin, "Percentiles")
+print(rrplugins.getNamesFromPropertyList(PercentileHandle))
+aProperty = rrplugins.getFirstProperty(PercentileHandle)
+while aProperty:
+    print(rrplugins.getPropertyName(aProperty), ":", rrplugins.getPropertyValueAsString(aProperty))
+    aProperty = rrplugins.getNextProperty(PercentileHandle)
+
+#Show MOnte Carlo parameters as a histogram
+plt.hist(paras, 50)
+plt.show()
+
+#Plot Monte Carlo data sets        
+#dataSeries =  DataSeries.readDataSeries("MCDataSets.dat")    
+#dataSeries.plot()           
+
+#Finally, view the manual and version
+# mcP.viewManual()    
+print('Plugin version: ', mcP.getVersion())
+         

rrplugins/telNelderMead.py

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+import rrplugins
+from rrplugins import tpc
+
+# Load Plugins
+chiPlugin       = rrplugins.Plugin("tel_chisquare")
+nm              = rrplugins.Plugin("tel_nelder_mead")
+modelPlugin     = rrplugins.Plugin("tel_test_model")
+addNoisePlugin  = rrplugins.Plugin("tel_add_noise")
+
+#========== EVENT FUNCTION SETUP ===========================
+def myEvent(dummy, dummy2): #We are not capturing any data from the plugin, so just pass a dummy
+    print('Iteration, Norm = ', nm.getProperty("NrOfIter") , ', ', nm.getProperty("Norm"))
+
+#Setup progress event function
+progressEvent =  rrplugins.NotifyEventEx(myEvent)     
+rrplugins.assignOnProgressEvent(nm.plugin, progressEvent)
+#============================================================
+
+#Create model data, with and without noise using the test_model plugin
+modelPlugin.execute()     
+
+#Setup plugin properties.
+nm.SBML             = modelPlugin.Model 
+nm.ExperimentalData = modelPlugin.TestDataWithNoise
+
+# Add the parameters that we're going to fit and an initial 'start' value
+nm.setProperty("InputParameterList", ["k1", .3])
+nm.setProperty("FittedDataSelectionList", "[S1] [S2]")
+nm.setProperty("ExperimentalDataSelectionList", "[S1] [S2]")
+
+# Start minimization
+nm.execute()
+
+print('Minimization finished. \n==== Result ====')
+
+print('ChiSquare = '           , nm.getProperty("ChiSquare"))
+print('Reduced ChiSquare = '   , nm.getProperty("ReducedChiSquare"))
+    
+#This is a list of parameters
+parameters = tpc.getPluginProperty (nm.plugin, "OutputParameterList")
+
+#Iterate trough list of parameters and confidence limits
+para  = rrplugins.getFirstProperty(parameters)
+while para:           
+    print(rrplugins.getPropertyName(para), ' = ', rrplugins.getPropertyValue(para))
+    para  = rrplugins.getNextProperty(parameters)
+
+
+# Get the fitted and residual data
+fittedData = nm.getProperty ("FittedData").toNumPy()
+residuals  = nm.getProperty ("Residuals").toNumPy()
+
+# Get the experimental data as a numpy array
+experimentalData = modelPlugin.TestDataWithNoise.toNumPy()
+
+rrplugins.plot(fittedData         [:,[0,1]], "blue", "-",    "",    "S1 Fitted")
+rrplugins.plot(fittedData         [:,[0,2]], "blue", "-",    "",    "S2 Fitted")
+rrplugins.plot(residuals          [:,[0,1]], "blue", "None", "x",   "S1 Residual")
+rrplugins.plot(residuals          [:,[0,2]], "red",  "None", "x",   "S2 Residual")
+rrplugins.plot(experimentalData   [:,[0,1]], "red",  "",     "*",   "S1 Data")
+rrplugins.plot(experimentalData   [:,[0,2]], "blue", "",     "*",   "S2 Data")
+rrplugins.plt.show()
+
+#Finally, view the manual and version
+# nm.viewManual()    
+print('Plugin version: ', nm.getVersion())