emodel_generalisation.tasks.workflow

Main workflow to generalise electrical models using MCMC.

See example/workflow for an example on how to run it.

TODO: improve docstrings.

Classes

AdaptAisSoma(*args, **kwargs)	Adapt AIS and Soma.
CompareNoAdaptation(*args, **kwargs)	Compare non adapted cells.
CreateComboDF(*args, **kwargs)	Create dataframe with combos mixing mtype, etype and emodels.
CreateExemplar(*args, **kwargs)	Create the exemplar morphology for an emodel and a population of morphologies.
CreateMLGeneralisationModels(*args, **kwargs)	Create an xgboost model for generalisable emodels.
CreateMLResistanceModels(*args, **kwargs)	Create xgboost models of resistance parameter fits.
CreateMLRhoModels(*args, **kwargs)	Create xgboost model of rhos factos as function of emodel parameter.
CreateSynthesisComboDF(*args, **kwargs)	Create dataframe with combos mixing mtype, etype and emodels for synthesized cells.
Evaluate(*args, **kwargs)	Test the various parameters using AIS/soma adaptation.
EvaluateMoreModels(*args, **kwargs)	Generate more models from MCMC with rho factor and resistances.
GenerateMoreModels(*args, **kwargs)	Generate more models from MCMC with rho factor and resistances.
GetEmodelConfig(*args, **kwargs)	Get config folder with emodel setting via emodeldb (not OS) or locally.
PlotMCMCResults(*args, **kwargs)	Make various plots of MCMC results.
PlotTraces(*args, **kwargs)	Plot traces, higlhlighting exemplar.
ReDiametrize(*args, **kwargs)	Rediametrize morphologies with diameter model from exemplar.
ResistanceModels(*args, **kwargs)	Constructs the AIS/soma input resistance models.
RhoFactors(*args, **kwargs)	Estimate the target rho value per me-types.
Run(*args, **kwargs)	Main task to run the entire workflow.
RunMCMC(*args, **kwargs)	Run MCMC exploration for an emodel using best emodels from burn-in phase for speed up.
RunMCMCBurnIn(*args, **kwargs)	Run burn-in phase MCMC exploration for an emodel.
SelectMoreValidParameters(*args, **kwargs)	Select valid set of pameters.
SelectRobustParams(*args, **kwargs)	Select a small set of robust parameters.
SelectValidParameters(*args, **kwargs)	Select valid set of pameters.
SelectValidParametersNoAdapt(*args, **kwargs)	Select valid set of pameters.
ValidateMoreModels(*args, **kwargs)	Validation plot for generated models.
ValidateMoreMorphologies(*args, **kwargs)	Asses which morphologies are outliers.
ValidateMorphologies(*args, **kwargs)	Asses which morphologies are outliers.
ValidateMorphologiesNoAdapt(*args, **kwargs)	Asses which morphologies are outliers.

class emodel_generalisation.tasks.workflow.AdaptAisSoma(*args, **kwargs)

Bases: EmodelAwareTask, ParallelTask, WorkflowTask

Adapt AIS and Soma.

class emodel_generalisation.tasks.workflow.CompareNoAdaptation(*args, **kwargs)

Bases: WorkflowTask

Compare non adapted cells.

class emodel_generalisation.tasks.workflow.CreateComboDF(*args, **kwargs)

Bases: EmodelAwareTask, WorkflowTask

Create dataframe with combos mixing mtype, etype and emodels.

class emodel_generalisation.tasks.workflow.CreateExemplar(*args, **kwargs)

Bases: WorkflowTask

Create the exemplar morphology for an emodel and a population of morphologies.

class emodel_generalisation.tasks.workflow.CreateMLGeneralisationModels(*args, **kwargs)

Bases: WorkflowTask

Create an xgboost model for generalisable emodels.

class emodel_generalisation.tasks.workflow.CreateMLResistanceModels(*args, **kwargs)

Bases: WorkflowTask

Create xgboost models of resistance parameter fits.

class emodel_generalisation.tasks.workflow.CreateMLRhoModels(*args, **kwargs)

Bases: WorkflowTask

Create xgboost model of rhos factos as function of emodel parameter.

class emodel_generalisation.tasks.workflow.CreateSynthesisComboDF(*args, **kwargs)

Bases: WorkflowTask

Create dataframe with combos mixing mtype, etype and emodels for synthesized cells.

class emodel_generalisation.tasks.workflow.Evaluate(*args, **kwargs)

Bases: EmodelAwareTask, ParallelTask, WorkflowTask

Test the various parameters using AIS/soma adaptation.

class emodel_generalisation.tasks.workflow.EvaluateMoreModels(*args, **kwargs)

Bases: EmodelAwareTask, ParallelTask, WorkflowTask

Generate more models from MCMC with rho factor and resistances.

class emodel_generalisation.tasks.workflow.GenerateMoreModels(*args, **kwargs)

Bases: WorkflowTask

Generate more models from MCMC with rho factor and resistances.

class emodel_generalisation.tasks.workflow.GetEmodelConfig(*args, **kwargs)

Bases: WorkflowTask

Get config folder with emodel setting via emodeldb (not OS) or locally.

If mode ==’local’, use ‘config_path’ for the config folder, and ‘mechanisms_path’ for the mechanisms folder to compile, and ‘generalisation_rule’ with filters for morphologies generalisation.

class emodel_generalisation.tasks.workflow.PlotMCMCResults(*args, **kwargs)

Bases: EmodelAwareTask, WorkflowTask

Make various plots of MCMC results.

class emodel_generalisation.tasks.workflow.PlotTraces(*args, **kwargs)

Bases: WorkflowTask

Plot traces, higlhlighting exemplar.

class emodel_generalisation.tasks.workflow.ReDiametrize(*args, **kwargs)

Bases: WorkflowTask

Rediametrize morphologies with diameter model from exemplar.

class emodel_generalisation.tasks.workflow.ResistanceModels(*args, **kwargs)

Bases: EmodelAwareTask, WorkflowTask

Constructs the AIS/soma input resistance models.

class emodel_generalisation.tasks.workflow.RhoFactors(*args, **kwargs)

Bases: EmodelAwareTask, ParallelTask, WorkflowTask

Estimate the target rho value per me-types.

class emodel_generalisation.tasks.workflow.Run(*args, **kwargs)

Bases: WorkflowWrapperTask

Main task to run the entire workflow.

class emodel_generalisation.tasks.workflow.RunMCMC(*args, **kwargs)

Bases: EmodelAwareTask, ParallelTask, WorkflowTask

Run MCMC exploration for an emodel using best emodels from burn-in phase for speed up.

class emodel_generalisation.tasks.workflow.RunMCMCBurnIn(*args, **kwargs)

Bases: EmodelAwareTask, ParallelTask, WorkflowTask

Run burn-in phase MCMC exploration for an emodel.

class emodel_generalisation.tasks.workflow.SelectMoreValidParameters(*args, **kwargs)

Bases: EmodelAwareTask, WorkflowTask

Select valid set of pameters.

class emodel_generalisation.tasks.workflow.SelectRobustParams(*args, **kwargs)

Bases: EmodelAwareTask, ParallelTask, WorkflowTask

Select a small set of robust parameters.

class emodel_generalisation.tasks.workflow.SelectValidParameters(*args, **kwargs)

Bases: EmodelAwareTask, WorkflowTask

Select valid set of pameters.

class emodel_generalisation.tasks.workflow.SelectValidParametersNoAdapt(*args, **kwargs)

Bases: EmodelAwareTask, WorkflowTask

Select valid set of pameters.

class emodel_generalisation.tasks.workflow.ValidateMoreModels(*args, **kwargs)

Bases: WorkflowTask

Validation plot for generated models.

class emodel_generalisation.tasks.workflow.ValidateMoreMorphologies(*args, **kwargs)

Bases: WorkflowTask

Asses which morphologies are outliers.

class emodel_generalisation.tasks.workflow.ValidateMorphologies(*args, **kwargs)

Bases: WorkflowTask

Asses which morphologies are outliers.

class emodel_generalisation.tasks.workflow.ValidateMorphologiesNoAdapt(*args, **kwargs)

Bases: WorkflowTask

Asses which morphologies are outliers.