netpyne.sim package

Package for handling simulations

Contains all the model shared variables and modules. It is imported as “sim” from all other files, so any variable or module can be referenced from any module using sim.varName.

Submodules

• netpyne.sim.gather module
  • gatherData()
  • gatherDataFromFiles()
• netpyne.sim.load module
  • loadSimCfg()
  • loadNetParams()
  • loadNet()
  • loadSimData()
  • loadAll()
  • loadFromIndexFile()
  • loadModel()
  • processModFiles()
  • compactToLongConnFormat()
  • loadHDF5()
  • ijsonLoad()
• netpyne.sim.run module
  • preRun()
  • runSim()
  • postRun()
  • runSimWithIntervalFunc()
  • prepareSimWithIntervalFunc()
  • runForInterval()
  • calculateLFP()
  • calculateDipole()
  • loadBalance()
• netpyne.sim.save module
  • saveJSON()
  • saveData()
  • distributedSaveHDF5()
  • compactConnFormat()
  • intervalSave()
  • saveDataInNodes()
  • saveModel()
• netpyne.sim.setup module
  • initialize()
  • setNet()
  • setNetParams()
  • setSimCfg()
  • createParallelContext()
  • readCmdLineArgs()
  • setupRecordLFP()
  • setupRecordDipole()
  • setupRecording()
  • setGlobals()
• netpyne.sim.utils module
  • loadPythonModule()
  • cellByGid()
  • getCellsList()
  • timing()
  • version()
  • gitChangeset()
  • gitInfo()
  • hashStr()
  • hashList()
  • fileDigest()
  • unique()
  • checkMemory()
  • copyReplaceItemObj()
  • copyRemoveItemObj()
  • replaceItemObj()
  • replaceKeys()
  • replaceFuncObj()
  • replaceDictODict()
  • rename()
  • tupleToList()
  • decimalToFloat()
  • clearObj()
  • clearAll()
  • checkConditions()
  • NpSerializer
    • NpSerializer.default()
• netpyne.sim.validator module
  • ValidationContext
  • general_specs()
  • pop_specs()
  • cell_specs()
  • synmech_specs()
  • conn_specs()
  • subconn_specs()
  • stimsource_specs()
  • stimtarget_specs()
  • rxd_specs()
  • validateNetParams()
  • ValidationError
    • ValidationError.formattedMessage()
  • checkValidation()
• netpyne.sim.wrappers module
  • create()
  • simulate()
  • intervalSimulate()
  • distributedSimulate()
  • analyze()
  • createSimulate()
  • createSimulateAnalyze()
  • createSimulateAnalyzeInterval()
  • createSimulateAnalyzeDistributed()
  • runFromIndexFile()
  • load()
  • loadSimulate()
  • loadSimulateAnalyze()
  • createExportNeuroML2()
  • importNeuroML2SimulateAnalyze()
  • runSimIntervalSaving()