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Python ProjectManager.doRunNeuron方法代码示例

本文整理汇总了Python中ucl.physiol.neuroconstruct.project.ProjectManager.doRunNeuron方法的典型用法代码示例。如果您正苦于以下问题：Python ProjectManager.doRunNeuron方法的具体用法？Python ProjectManager.doRunNeuron怎么用？Python ProjectManager.doRunNeuron使用的例子？那么恭喜您, 这里精选的方法代码示例或许可以为您提供帮助。您也可以进一步了解该方法所在类ucl.physiol.neuroconstruct.project.ProjectManager的用法示例。


在下文中一共展示了ProjectManager.doRunNeuron方法的5个代码示例，这些例子默认根据受欢迎程度排序。您可以为喜欢或者感觉有用的代码点赞，您的评价将有助于系统推荐出更棒的Python代码示例。

示例1: ArrayList

# 需要导入模块: from ucl.physiol.neuroconstruct.project import ProjectManager [as 别名]
# 或者: from ucl.physiol.neuroconstruct.project.ProjectManager import doRunNeuron [as 别名]
							  0, 0, 0, 0.5, 0,
							  stim_seg_detailed,
							  0.5, 0, None)
# delete all existing probes
project.generatedPlotSaves.reset()

# set up voltage recording at the specified points along the dendrite being stimulated
project.generatedPlotSaves.addPlotSaveDetails('Golgi_reduced_v', project.simPlotInfo.getSimPlot('Golgi_reduced_v'), ArrayList([0]), ArrayList(rec_segs_reduced), False, False)
project.generatedPlotSaves.addPlotSaveDetails('Golgi_detailed_v', project.simPlotInfo.getSimPlot('Golgi_detailed_v'), ArrayList([0]), ArrayList(rec_segs_detailed), False, False)

# generate and compile neuron files
print "Generating NEURON scripts..."
simulator_seed = random.getrandbits(32)
project.neuronFileManager.generateTheNeuronFiles(sim_config, None, NeuronFileManager.RUN_HOC,simulator_seed)
compile_process = ProcessManager(project.neuronFileManager.getMainHocFile())
compile_success = compile_process.compileFileWithNeuron(0,0)
# simulate
if compile_success:
    print "Simulating: simulation reference " + sim_ref
    pm.doRunNeuron(sim_config)
    timefile_path = sim_path + '/time.dat'
    while not os.path.exists(timefile_path):
	time.sleep(0.1)

data_string = "Data reference " + sim_ref
for k,i in enumerate(rec_segs_detailed):
    data_string = data_string + " " + str(i) + " " + str(rec_dists_detailed[k])
print data_string

System.exit(0)
开发者ID:RokasSt，项目名称:GJGolgi_ReducedMorph，代码行数:32，代码来源:dendritic_attenuation.py

示例2: ProcessManager

# 需要导入模块: from ucl.physiol.neuroconstruct.project import ProjectManager [as 别名]
# 或者: from ucl.physiol.neuroconstruct.project.ProjectManager import doRunNeuron [as 别名]
	  pm.doGenerate(simConfig.getName(), randomseed)
	
	  while pm.isGenerating():
	    print "Waiting for the project to be generated..."
	    time.sleep(2)	
	 
	  myProject.neuronFileManager.setSuggestedRemoteRunTime(10)
	  myProject.neuronFileManager.generateTheNeuronFiles(simConfig, None, NeuronFileManager.RUN_HOC, randomseed)
      
	  print "Generated NEURON files for: "+simRef	
	  compileProcess = ProcessManager(myProject.neuronFileManager.getMainHocFile())	
	  compileSuccess = compileProcess.compileFileWithNeuron(0,0)	
	  print "Compiled NEURON files for: "+simRef

	  if compileSuccess:
	     pm.doRunNeuron(simConfig)
	     print "Set running simulation: "+simRef

	  time.sleep(5) # wait for the process to be sent out   

	  #####################'''
	  	  
	  '''##### Rerunning the same configuration + background exc #####
	  
	  simRef = prefix+"syn"+str(synapses)+"E1500_"+str(t)
	  print "Simref: "+simRef
	  myProject.simulationParameters.setReference(simRef)
	  refStored.append(simRef)
	  
	  ##### RUN BLOCK background exc #####
开发者ID:pgleeson，项目名称:TestArea，代码行数:32，代码来源:PNMDAs_distributedinput.py

示例3: generateF_ICurve

# 需要导入模块: from ucl.physiol.neuroconstruct.project import ProjectManager [as 别名]
# 或者: from ucl.physiol.neuroconstruct.project.ProjectManager import doRunNeuron [as 别名]

#.........这里部分代码省略.........
							preStim.setDel(NumberGenerator(preStimDel))
							preStim.setDur(NumberGenerator(preStimDur))
							self.myProject.elecInputInfo.updateStim(preStim)


							# stim = self.myProject.elecInputInfo.getStim(simConfig.getInputs().get(1))
							stim = self.myProject.elecInputInfo.getStim("Input_4")
							

							stim.setAmp(NumberGenerator(stimAmp))
							stim.setDel(NumberGenerator(stimDel))
							stim.setDur(NumberGenerator(stimDur))
							self.myProject.elecInputInfo.updateStim(stim)

							print "Next stim: "+ str(stim)

							self.myProject.simulationParameters.setReference(simRef)

							if simulator == "NEURON":
									self.myProject.neuronFileManager.generateTheNeuronFiles(simConfig,
																							None,
																							NeuronFileManager.RUN_HOC,
																							self.simulatorSeed)

									print "Generated NEURON files for: "+simRef

									compileProcess = ProcessManager(self.myProject.neuronFileManager.getMainHocFile())

									compileSuccess = compileProcess.compileFileWithNeuron(0,0)

									print "Compiled NEURON files for: "+simRef

									if compileSuccess:
													pm.doRunNeuron(simConfig)
													print "Set running simulation: "+simRef
													self.simsRunning.append(simRef)

							if simulator == "GENESIS":
									compartmentalisation = GenesisCompartmentalisation()

									self.myProject.genesisFileManager.generateTheGenesisFiles(simConfig,
																							None,
																							compartmentalisation,
																							self.simulatorSeed)
									print "Generated GENESIS files for: "+simRef

									pm.doRunGenesis(simConfig)
									print "Set running simulation: "+simRef
									self.simsRunning.append(simRef)

							time.sleep(1) # Wait for sim to be kicked off
							simReferences[simRef] = stimAmp
							stimAmp = stimAmp +stimAmpInc

					print
					print "Finished running "+str(len(simReferences))+" simulations for project "+ projFile.getAbsolutePath()
					print "These can be loaded and replayed in the previous simulation browser in the GUI"
					print

			while (len(self.simsRunning)>0):
					print "Sims currently running: "+str(self.simsRunning)
					print "Waiting..."
					time.sleep(4) # wait a while...
					self.updateSimsRunning()

			#simReferences = {'PySim_0.3':0.3,'PySim_0.4':0.4,'PySim_0.5':0.5}
开发者ID:pgleeson，项目名称:TestArea，代码行数:70，代码来源:GenerateF_ICurve.py

示例4: make_fF_Curve

# 需要导入模块: from ucl.physiol.neuroconstruct.project import ProjectManager [as 别名]
# 或者: from ucl.physiol.neuroconstruct.project.ProjectManager import doRunNeuron [as 别名]

#.........这里部分代码省略.........

                                                        TEXT_START_FINITIALIZE = "\n" + "gTrainFile = new File() \n" + "vector = new Vector(100000) \n" + "access GranuleCell_mod_tonic[0].Soma \n" + "clamp = new SEClamp(0.5) \n" + "clamp.amp1 = 0 \n" + "clamp.dur1 = 1e9 \n" + """gTrainFile.ropen("E:/neuroConstruct/models/Dan_GranCell/gTrains_nS/gAMPA_""" + str(currentTrain) + """.txt") \n""" + "vector.scanf(gTrainFile) \n" + "gTrainFile.close \n" + "for i = 0, vector.size() -1 { \n" + "     if (vector.x[i] <= 0) { \n" + "          vector.x[i] = 1e-20 \n" + "              } \n" + "        } \n" + "for i = 0, vector.size() -1 { \n" + "    vector.x[i] = ( 1 / vector.x[i] ) * 1000 \n" + "    } \n" + "vector.play(&clamp.rs, 0.03) \n" # This

                                                        TEXT_START_FINITIALIZE = TEXT_START_FINITIALIZE + ADD_TO_START_FINITIALIZE

                                                        TEXT_TO_RECORD_I = """// currently not used \n"""

                                                        TEXT_TO_RECORD_I = TEXT_TO_RECORD_I + ADD_TO_RECORD_I

                                                        self.myProject.neuronSettings.setNativeBlock(NativeCodeLocation.BEFORE_CELL_CREATION, TEXT_BEFORE_CREATION)
                                                        self.myProject.neuronSettings.setNativeBlock(NativeCodeLocation.START_FINITIALIZE, TEXT_START_FINITIALIZE)
                                                        self.myProject.neuronSettings.setNativeBlock(NativeCodeLocation.AFTER_SIMULATION, TEXT_TO_RECORD_I)

					
							print "Next Train: "+ str(currentTrain)

							self.myProject.simulationParameters.setReference(simRef)

							if simulator == "NEURON":
									self.myProject.neuronFileManager.generateTheNeuronFiles(simConfig,
																							None,
																							NeuronFileManager.RUN_HOC,
																							self.simulatorSeed)

									print "Generated NEURON files for: "+simRef

									compileProcess = ProcessManager(self.myProject.neuronFileManager.getMainHocFile())

									compileSuccess = compileProcess.compileFileWithNeuron(0,0)

									print "Compiled NEURON files for: "+simRef

									if compileSuccess:
													pm.doRunNeuron(simConfig)
													print "Set running simulation: "+simRef
													self.simsRunning.append(simRef)

							if simulator == "GENESIS":
									compartmentalisation = GenesisCompartmentalisation()

									self.myProject.genesisFileManager.generateTheGenesisFiles(simConfig,
																							None,
																							compartmentalisation,
																							self.simulatorSeed)
									print "Generated GENESIS files for: "+simRef

									pm.doRunGenesis(simConfig)
									print "Set running simulation: "+simRef
									self.simsRunning.append(simRef)

							time.sleep(1) # Wait for sim to be kicked off
							simReferences[simRef] = currentTrain
							currentTrain = currentTrain + 1

					print
					print "Finished running "+str(len(simReferences))+" simulations for project "+ projFile.getAbsolutePath()
					print "These can be loaded and replayed in the previous simulation browser in the GUI"
					print

			while (len(self.simsRunning)>0):
					print "Sims currently running: "+str(self.simsRunning)
					print "Waiting..."
					time.sleep(4) # wait a while...
					self.updateSimsRunning()

			#simReferences = {'PySim_0.3':0.3,'PySim_0.4':0.4,'PySim_0.5':0.5}
开发者ID:pgleeson，项目名称:TestArea，代码行数:70，代码来源:Generate_fF_Curve.py

示例5: generateV_ICurve

# 需要导入模块: from ucl.physiol.neuroconstruct.project import ProjectManager [as 别名]
# 或者: from ucl.physiol.neuroconstruct.project.ProjectManager import doRunNeuron [as 别名]

#.........这里部分代码省略.........
                                                        TEXT_START_FINITIALIZE = "GranuleCell_mod_tonic[0].Soma {\n" + "clampobj = new SEClamp(0.5)\n" + "clampobj.dur1 = 150.0" + "\n" + "clampobj.amp1 = -100.0" + "\n" + "clampobj.dur2 = " + str(stimDur) + "\n" + "clampobj.amp2 = " + str(stimAmp) + "\n" + "clampobj.dur3 = 150.0" + "\n" + "clampobj.amp3 = -40.0" + "\n" + "clampobj.rs = 0.00001\n" + "record_current = new Vector()" + "\n" + "record_current.record(&clampobj.i)" + "\n" + "}\n" #This should do the trick

                                                        TEXT_START_FINITIALIZE = TEXT_START_FINITIALIZE + ADD_TO_START_FINITIALIZE

                                                        TEXT_TO_RECORD_I = """data_save = new File() \n""" + """strdef filename \n""" + """sprint(filename, """" + self.myProject.getProjectMainDirectory().getAbsolutePath() + """/simulations/current%.3f.txt", clampobj.amp2) \n""" + """data_save.wopen(filename) \n""" + """record_current.printf(data_save) \n""" + """data_save.close() \n"""

                                                        TEXT_TO_RECORD_I = TEXT_TO_RECORD_I + ADD_TO_RECORD_I

                                                        self.myProject.neuronSettings.setNativeBlock(NativeCodeLocation.BEFORE_CELL_CREATION, TEXT_BEFORE_CREATION)
                                                        # self.myProject.neuronSettings.setNativeBlock(NativeCodeLocation.BEFORE_INITIAL, TEXT_BEFORE_INIT)
                                                        self.myProject.neuronSettings.setNativeBlock(NativeCodeLocation.START_FINITIALIZE, TEXT_START_FINITIALIZE)
                                                        self.myProject.neuronSettings.setNativeBlock(NativeCodeLocation.AFTER_SIMULATION, TEXT_TO_RECORD_I)

					
							print "Next stim: "+ str(stimAmp)

							self.myProject.simulationParameters.setReference(simRef)

							if simulator == "NEURON":
									self.myProject.neuronFileManager.generateTheNeuronFiles(simConfig,
																							None,
																							NeuronFileManager.RUN_HOC,
																							self.simulatorSeed)

									print "Generated NEURON files for: "+simRef

									compileProcess = ProcessManager(self.myProject.neuronFileManager.getMainHocFile())

									compileSuccess = compileProcess.compileFileWithNeuron(0,0)

									print "Compiled NEURON files for: "+simRef

									if compileSuccess:
													pm.doRunNeuron(simConfig)
													print "Set running simulation: "+simRef
													self.simsRunning.append(simRef)

							if simulator == "GENESIS":
									compartmentalisation = GenesisCompartmentalisation()

									self.myProject.genesisFileManager.generateTheGenesisFiles(simConfig,
																							None,
																							compartmentalisation,
																							self.simulatorSeed)
									print "Generated GENESIS files for: "+simRef

									pm.doRunGenesis(simConfig)
									print "Set running simulation: "+simRef
									self.simsRunning.append(simRef)

							time.sleep(1) # Wait for sim to be kicked off
							simReferences[simRef] = stimAmp
							stimAmp = stimAmp +stimAmpInc

					print
					print "Finished running "+str(len(simReferences))+" simulations for project "+ projFile.getAbsolutePath()
					print "These can be loaded and replayed in the previous simulation browser in the GUI"
					print

			while (len(self.simsRunning)>0):
					print "Sims currently running: "+str(self.simsRunning)
					print "Waiting..."
					time.sleep(4) # wait a while...
					self.updateSimsRunning()

			#simReferences = {'PySim_0.3':0.3,'PySim_0.4':0.4,'PySim_0.5':0.5}
开发者ID:pgleeson，项目名称:TestArea，代码行数:70，代码来源:GenerateV_ICurve.py


注：本文中的ucl.physiol.neuroconstruct.project.ProjectManager.doRunNeuron方法示例由纯净天空整理自Github/MSDocs等开源代码及文档管理平台，相关代码片段筛选自各路编程大神贡献的开源项目，源码版权归原作者所有，传播和使用请参考对应项目的License；未经允许，请勿转载。