bluepyemodel.efeatures_extraction.targets_configuration

TargetsConfiguration

Classes

TargetsConfiguration([files, targets, ...])

The goal of this class is to configure the targets and files metadata that will be used during efeature extraction

class TargetsConfiguration(files=None, targets=None, protocols_rheobase=None, available_traces=None, available_efeatures=None, auto_targets=None, additional_fitness_efeatures=None, additional_fitness_protocols=None, protocols_mapping=None)

Bases: object

The goal of this class is to configure the targets and files metadata that will be used during efeature extraction

Init

Parameters:

• files (list of dict) –

  File names with their metadata in the format:

  [file1_metadata, file2_metadata, ...]
  file1_metadata = {
      cell_name=XXX,
      filename=XXX,
      resource_id=XXX,
      etype=XXX,
      species=XXX,
      brain_region=XXX,
      ecodes={},
      other_metadata={},
  }
  

• targets (list) –

  define the efeatures to extract as well as which protocols and current amplitude they should be extracted for. Of the form:

  [{
      "efeature_name": "AP_amplitude_1",
      "efeature": "AP_amplitude",
      "protocol": "IDRest",
      "amplitude": 150.,
      "tolerance": 10.,
      "weight": 1.0,  # optional
      "efel_settings": {
          'stim_start': 200.,
          'stim_end': 500.,
          'Threshold': -10.
      }
  }]
  

• protocols_rheobase (list) – names of the protocols that will be used to compute the rheobase of the cells. E.g: [‘IDthresh’].

• available_traces (list of TraceFile)

• available_efeatures (llist of strings)

• auto_targets (list) –

  if targets is not given, auto_targets define the efeatures to extract as well as which protocols and current amplitude they should be extracted for, given a list of possible protocols and amplitudes. min_recordings_per_amplitude, preferred_number_protocols and tolerance are optional. Of the form:

  [{
      "protocols": ["IDRest", "IV"],
      "amplitudes": [150, 250],
      "efeatures": ["AP_amplitude", "mean_frequency"],
      "min_recordings_per_amplitude": 10,
      "preferred_number_protocols": 1,
      "tolerance": 10.,
  }]
  

• additional_fitness_efeatures (list of dicts) –

  efeatures to add to the output of the extraction, i.e. to the FitnessCalculatorConfiguration (FCC). These efeatures will not be extracted from the targets, but will be used during optimisation and / or validation. They should have the same format as the efeatures of the FCC, e.g.

  [
      {
          "efel_feature_name": "Spikecount",
          "protocol_name": "IDrest_130",
          "recording_name": "soma.v",
          "mean": 6.026,
          "original_std": 4.016,
          "efeature_name": "Spikecount",
          "efel_settings": {
              "strict_stiminterval": true,
              "Threshold": -30.0,
              "interp_step": 0.025,
              "stim_start": 700.0,
              "stim_end": 2700.0
          }
      }
  ]
  

• additional_fitness_protocols (list of dicts) –

  protocols to add to

  the output of the extraction, i.e. to the FitnessCalculatorConfiguration (FCC). These protocols will not be used during extraction, but will be used during optimisation and / or validation. They should have the same format as the protocols of the FCC, e.g.

  [
      {
          "name": "IDrest_130",
          "stimuli": [
              {
              "delay": 663.3473451327434,
              "amp": 0.3491827776582547,
              "thresh_perc": 130.56103157894464,
              "duration": 2053.050884955752,
              "totduration": 3000.0,
              "holding_current": -0.13307330411636328
              }
          ],
          "recordings_from_config": [
              {
              "type": "CompRecording",
              "name": "IDrest_130.soma.v",
              "location": "soma",
              "variable": "v"
              }
          ],
          "validation": false,
          "protocol_type": "ThresholdBasedProtocol",
          "stochasticity": false
      }
  ]
  

  protocols_mapping (dict, optional): maps original protocol

  identifiers to renamed versions for standardization. Defaults to None if not provided.

  Example:

  {
      "IDRest_150": 'Step_150_hyp',
      "IDRest_200": 'Step_200_hyp',
      "IDRest_250": 'Step_250_hyp',
      "IV_-120": 'IV_-120_hyp',
  }
  

property auto_targets_BPE

In BPE2 input format

check_presence_RMP_Rin_efeatures(name_rmp_protocol, name_Rin_protocol)

Check that the protocols supposed to be used for RMP and Rin are present in the target and that they have the correct efeatures. If some features are missing, add them.

property files_metadata_BPE

In BPE2 input format

property is_configuration_valid

Checks that the configuration has targets, traces and that the targets can be found in the traces. This check can only be performed if the ecodes present in each files are known.

property protocols_rheobase_BPE

Returns None if empty

property targets_BPE

In BPE2 input format