SYMBOL INDEX (1034 symbols across 118 files) FILE: bluepyopt/deapext/CMA_MO.py function get_hyped (line 40) | def get_hyped(pop, ubound_score=250., threshold_improvement=240.): class CMA_MO (line 79) | class CMA_MO(cma.StrategyMultiObjective): method __init__ (line 82) | def __init__( method _select (line 177) | def _select(self, candidates): method get_population (line 211) | def get_population(self, to_space): method get_parents (line 219) | def get_parents(self, to_space): method generate_new_pop (line 227) | def generate_new_pop(self, lbounds, ubounds): method update_strategy (line 232) | def update_strategy(self): method set_fitness (line 235) | def set_fitness(self, fitnesses): method set_fitness_parents (line 239) | def set_fitness_parents(self, fitnesses): method check_termination (line 243) | def check_termination(self, gen): FILE: bluepyopt/deapext/CMA_SO.py class CMA_SO (line 49) | class CMA_SO(cma.Strategy): method __init__ (line 52) | def __init__( method update (line 127) | def update(self, population): method get_population (line 191) | def get_population(self, to_space): method generate_new_pop (line 199) | def generate_new_pop(self, lbounds, ubounds): method update_strategy (line 204) | def update_strategy(self): method set_fitness (line 207) | def set_fitness(self, fitnesses): method check_termination (line 211) | def check_termination(self, gen): FILE: bluepyopt/deapext/algorithms.py function _define_fitness (line 41) | def _define_fitness(pop, obj_size): function _evaluate_invalid_fitness (line 55) | def _evaluate_invalid_fitness(toolbox, population): function _get_offspring (line 68) | def _get_offspring(parents, toolbox, cxpb, mutpb): function _check_stopping_criteria (line 75) | def _check_stopping_criteria(criteria, params): function eaAlphaMuPlusLambdaCheckpoint (line 86) | def eaAlphaMuPlusLambdaCheckpoint( FILE: bluepyopt/deapext/hype.py function hypesub (line 22) | def hypesub(la, A, actDim, bounds, pvec, alpha, k): function hypeIndicatorExact (line 50) | def hypeIndicatorExact(points, bounds, k): function hypeIndicatorSampled (line 77) | def hypeIndicatorSampled(points, bounds, k, nrOfSamples): FILE: bluepyopt/deapext/optimisations.py class WeightedSumFitness (line 47) | class WeightedSumFitness(deap.base.Fitness): method __init__ (line 51) | def __init__(self, values=(), obj_size=None): method weighted_sum (line 57) | def weighted_sum(self): method sum (line 62) | def sum(self): method __le__ (line 66) | def __le__(self, other): method __lt__ (line 69) | def __lt__(self, other): method __deepcopy__ (line 72) | def __deepcopy__(self, _): class WSListIndividual (line 81) | class WSListIndividual(list): method __init__ (line 85) | def __init__(self, *args, **kwargs): class DEAPOptimisation (line 92) | class DEAPOptimisation(bluepyopt.optimisations.Optimisation): method __init__ (line 96) | def __init__(self, evaluator=None, method setup_deap (line 148) | def setup_deap(self): method run (line 253) | def run(self, class IBEADEAPOptimisation (line 331) | class IBEADEAPOptimisation(DEAPOptimisation): method __init__ (line 335) | def __init__(self, *args, **kwargs): FILE: bluepyopt/deapext/optimisationsCMA.py function _ind_convert_space (line 42) | def _ind_convert_space(ind, convert_fcn): class DEAPOptimisationCMA (line 48) | class DEAPOptimisationCMA(bluepyopt.optimisations.Optimisation): method __init__ (line 52) | def __init__( method setup_deap (line 178) | def setup_deap(self): method run (line 243) | def run( method get_stats (line 386) | def get_stats(self): FILE: bluepyopt/deapext/stoppingCriteria.py function isclose (line 34) | def isclose(a, b, rel_tol=1e-09, abs_tol=0.0): class MaxNGen (line 38) | class MaxNGen(bluepyopt.stoppingCriteria.StoppingCriteria): method __init__ (line 43) | def __init__(self, max_ngen): method check (line 48) | def check(self, kwargs): class Stagnation (line 55) | class Stagnation(bluepyopt.stoppingCriteria.StoppingCriteria): method __init__ (line 60) | def __init__(self, lambda_, problem_size): method check (line 71) | def check(self, kwargs): class Stagnationv2 (line 100) | class Stagnationv2(bluepyopt.stoppingCriteria.StoppingCriteria): method __init__ (line 105) | def __init__( method check (line 130) | def check(self, kwargs): class TolHistFun (line 160) | class TolHistFun(bluepyopt.stoppingCriteria.StoppingCriteria): method __init__ (line 165) | def __init__(self, lambda_, problem_size): method check (line 172) | def check(self, kwargs): class EqualFunVals (line 185) | class EqualFunVals(bluepyopt.stoppingCriteria.StoppingCriteria): method __init__ (line 190) | def __init__(self, lambda_, problem_size): method check (line 198) | def check(self, kwargs): class TolX (line 219) | class TolX(bluepyopt.stoppingCriteria.StoppingCriteria): method __init__ (line 224) | def __init__(self): method check (line 229) | def check(self, kwargs): class TolUpSigma (line 239) | class TolUpSigma(bluepyopt.stoppingCriteria.StoppingCriteria): method __init__ (line 244) | def __init__(self, sigma0): method check (line 250) | def check(self, kwargs): class ConditionCov (line 259) | class ConditionCov(bluepyopt.stoppingCriteria.StoppingCriteria): method __init__ (line 264) | def __init__(self): method check (line 269) | def check(self, kwargs): class NoEffectAxis (line 278) | class NoEffectAxis(bluepyopt.stoppingCriteria.StoppingCriteria): method __init__ (line 283) | def __init__(self, problem_size): method check (line 289) | def check(self, kwargs): class NoEffectCoor (line 307) | class NoEffectCoor(bluepyopt.stoppingCriteria.StoppingCriteria): method __init__ (line 312) | def __init__(self): method check (line 316) | def check(self, kwargs): FILE: bluepyopt/deapext/tools/selIBEA.py function selIBEA (line 34) | def selIBEA(population, mu, alpha=None, kappa=.05, tournament_n=4): function _calc_fitness_components (line 55) | def _calc_fitness_components(population, kappa): function _calc_fitnesses (line 93) | def _calc_fitnesses(population, components): function _choice (line 104) | def _choice(seq): function _mating_selection (line 110) | def _mating_selection(population, mu, tournament_n): function _environmental_selection (line 126) | def _environmental_selection(population, selection_size): FILE: bluepyopt/deapext/utils.py class WeightedReducedFitness (line 30) | class WeightedReducedFitness(deap.base.Fitness): method __init__ (line 34) | def __init__(self, values=(), obj_size=None, reduce_fcn=numpy.sum): method reduce (line 41) | def reduce(self): method weighted_reduce (line 46) | def weighted_reduce(self): method __le__ (line 50) | def __le__(self, other): method __lt__ (line 53) | def __lt__(self, other): method __deepcopy__ (line 56) | def __deepcopy__(self, _): class WSListIndividual (line 65) | class WSListIndividual(list): method __init__ (line 69) | def __init__(self, *args, **kwargs): function update_history_and_hof (line 86) | def update_history_and_hof(halloffame, history, population): function record_stats (line 96) | def record_stats(stats, logbook, gen, population, invalid_count): function closest_feasible (line 102) | def closest_feasible(individual, lbounds, ubounds): function bound (line 113) | def bound(population, lbounds, ubounds): function uniform (line 125) | def uniform(lower_list, upper_list, dimensions): function reduce_method (line 137) | def reduce_method(meth): function run_next_gen (line 142) | def run_next_gen(criteria, terminator): FILE: bluepyopt/ephys/acc.py class arbor (line 6) | class arbor: method __getattribute__ (line 7) | def __getattribute__(self, _): class ArbLabel (line 15) | class ArbLabel: method __init__ (line 18) | def __init__(self, type, name, s_expr): method defn (line 26) | def defn(self): method ref (line 31) | def ref(self): method name (line 36) | def name(self): method loc (line 41) | def loc(self): method __eq__ (line 45) | def __eq__(self, other): method __hash__ (line 53) | def __hash__(self): method __repr__ (line 56) | def __repr__(self): FILE: bluepyopt/ephys/base.py class BaseEPhys (line 4) | class BaseEPhys(object): method __init__ (line 7) | def __init__(self, name='', comment=''): method __str__ (line 11) | def __str__(self): FILE: bluepyopt/ephys/create_acc.py class ArbVar (line 31) | class ArbVar: method __init__ (line 34) | def __init__(self, name, conv=None): method __repr__ (line 45) | def __repr__(self): class Nrn2ArbParamAdapter (line 49) | class Nrn2ArbParamAdapter: method _param_name (line 75) | def _param_name(cls, name): method _param_value (line 84) | def _param_value(cls, param): method _conv_param (line 106) | def _conv_param(cls, param, name): method format (line 137) | def format(cls, param, mechs): class Nrn2ArbMechGrouper (line 179) | class Nrn2ArbMechGrouper: method _is_global_property (line 183) | def _is_global_property(loc, param): method _separate_global_properties (line 208) | def _separate_global_properties(cls, loc, mechs): method _format_params_and_group_by_mech (line 240) | def _format_params_and_group_by_mech(params, channels): method process_global (line 263) | def process_global(cls, params): method process_local (line 283) | def process_local(cls, params, channels): function _arb_filter_point_proc_locs (line 319) | def _arb_filter_point_proc_locs(pprocess_mechs): function _arb_append_scaled_mechs (line 342) | def _arb_append_scaled_mechs(mechs, scaled_mechs): class ArbNmodlMechFormatter (line 364) | class ArbNmodlMechFormatter: method __init__ (line 367) | def __init__(self, ext_catalogues): method _load_catalogue_meta (line 377) | def _load_catalogue_meta(cat_dir): method _load_mech_catalogue_meta (line 430) | def _load_mech_catalogue_meta(cls, ext_catalogues): method _mech_name (line 469) | def _mech_name(name): method _translate_mech (line 481) | def _translate_mech(cls, mech_name, mech_params, arb_cats): method translate_density (line 551) | def translate_density(self, mechs): method translate_points (line 560) | def translate_points(self, mechs): function _arb_project_scaled_mechs (line 573) | def _arb_project_scaled_mechs(mechs): function _arb_populate_label_dict (line 583) | def _arb_populate_label_dict(local_mechs, local_scaled_mechs, pprocess_m... function _read_templates (line 616) | def _read_templates(template_dir, template_filename): function _arb_loc_desc (line 647) | def _arb_loc_desc(location, param_or_mech): function create_acc (line 652) | def create_acc( function write_acc (line 855) | def write_acc( function read_acc (line 915) | def read_acc(cell_json_filename): class CreateAccException (line 946) | class CreateAccException(Exception): method __init__ (line 949) | def __init__(self, message): FILE: bluepyopt/ephys/create_hoc.py function generate_channels_by_location (line 52) | def generate_channels_by_location(mechs, location_order): function _generate_channels_by_location (line 65) | def _generate_channels_by_location(mechs, location_order, loc_desc): function generate_reinitrng (line 79) | def generate_reinitrng(mechs) -> str: function range_exprs_to_hoc (line 101) | def range_exprs_to_hoc(range_params): function _loc_desc (line 124) | def _loc_desc(location, param_or_mech): function generate_parameters (line 151) | def generate_parameters(parameters): function _generate_parameters (line 164) | def _generate_parameters(parameters, location_order, loc_desc): function _read_template (line 234) | def _read_template(template_dir, template_filename): function _get_template_params (line 249) | def _get_template_params( function create_hoc (line 302) | def create_hoc(mechs, class CreateHocException (line 359) | class CreateHocException(Exception): method __init__ (line 363) | def __init__(self, message): FILE: bluepyopt/ephys/efeatures.py function masked_cosine_distance (line 34) | def masked_cosine_distance(exp, model): class EFeature (line 50) | class EFeature(BaseEPhys): class eFELFeature (line 56) | class eFELFeature(EFeature, DictMixin): method __init__ (line 64) | def __init__( method _construct_efel_trace (line 123) | def _construct_efel_trace(self, responses): method _setup_efel (line 154) | def _setup_efel(self): method calculate_feature (line 181) | def calculate_feature(self, responses, raise_warnings=False): method calculate_score (line 207) | def calculate_score(self, responses, trace_check=False): method __str__ (line 235) | def __str__(self): class extraFELFeature (line 249) | class extraFELFeature(EFeature, DictMixin): method __init__ (line 257) | def __init__( method _construct_somatic_efel_trace (line 355) | def _construct_somatic_efel_trace(self, responses): method _setup_efel (line 379) | def _setup_efel(self): method _get_peak_times (line 400) | def _get_peak_times(self, responses, raise_warnings=False): method calculate_feature (line 420) | def calculate_feature( method calculate_score (line 494) | def calculate_score(self, responses, trace_check=False): method __str__ (line 535) | def __str__(self): function _interpolate_response (line 550) | def _interpolate_response(response, fs=20.0): function _filter_response (line 566) | def _filter_response(response, fcut=[0.5, 6000], order=2, filt_type="lfi... function _get_waveforms (line 602) | def _get_waveforms(response, peak_times, snippet_len_ms): FILE: bluepyopt/ephys/evaluators.py class CellEvaluator (line 32) | class CellEvaluator(bpopt.evaluators.Evaluator): method __init__ (line 36) | def __init__( method param_dict (line 90) | def param_dict(self, param_array): method objective_dict (line 99) | def objective_dict(self, objective_array): method objective_list (line 116) | def objective_list(self, objective_dict): method seed_from_param_dict (line 127) | def seed_from_param_dict(param_dict): method run_protocol (line 138) | def run_protocol( method run_protocols (line 171) | def run_protocols(self, protocols, param_values): method evaluate_with_dicts (line 185) | def evaluate_with_dicts(self, param_dict=None, target='scores'): method evaluate_with_lists (line 208) | def evaluate_with_lists(self, param_list=None, target='scores'): method init_simulator_and_evaluate_with_lists (line 219) | def init_simulator_and_evaluate_with_lists( method evaluate (line 230) | def evaluate(self, param_list=None, target='scores'): method __str__ (line 235) | def __str__(self): FILE: bluepyopt/ephys/examples/simplecell/simplecell.py class SimpleCell (line 8) | class SimpleCell: method __init__ (line 9) | def __init__(self): FILE: bluepyopt/ephys/extra_features_utils.py function calculate_features (line 39) | def calculate_features( function peak_to_valley (line 133) | def peak_to_valley(waveforms, sampling_frequency): function peak_trough_ratio (line 157) | def peak_trough_ratio(waveforms): function halfwidth (line 187) | def halfwidth(waveforms, sampling_frequency, return_idx=False): function repolarization_slope (line 270) | def repolarization_slope(waveforms, sampling_frequency, return_idx=False): function recovery_slope (line 332) | def recovery_slope(waveforms, sampling_frequency, window): function peak_image (line 380) | def peak_image(waveforms, sign="negative"): function relative_amplitude (line 414) | def relative_amplitude(waveforms, sign="negative"): function peak_time_diff (line 446) | def peak_time_diff(waveforms, fs, sign="negative"): function _get_slope (line 479) | def _get_slope(x, y): function _get_trough_and_peak_idx (line 489) | def _get_trough_and_peak_idx(waveform, after_max_trough=False): function _upsample_wf (line 515) | def _upsample_wf(waveforms, upsample): FILE: bluepyopt/ephys/locations.py class Location (line 37) | class Location(BaseEPhys): function _nth_isectionlist (line 48) | def _nth_isectionlist(isectionlist, index): class NrnSeclistCompLocation (line 61) | class NrnSeclistCompLocation(Location, DictMixin): method __init__ (line 73) | def __init__( method instantiate (line 94) | def instantiate(self, sim=None, icell=None): # pylint: disable=W0613 method acc_label (line 113) | def acc_label(self): method __str__ (line 123) | def __str__(self): class NrnSectionCompLocation (line 129) | class NrnSectionCompLocation(Location, DictMixin): method __init__ (line 141) | def __init__( method instantiate (line 159) | def instantiate(self, sim=None, icell=None): # pylint: disable=W0613 method acc_label (line 169) | def acc_label(self): method __str__ (line 179) | def __str__(self): class NrnPointProcessLocation (line 183) | class NrnPointProcessLocation(Location): method __init__ (line 187) | def __init__( method instantiate (line 202) | def instantiate(self, sim=None, icell=None): # pylint: disable=W0613 method acc_label (line 207) | def acc_label(self): method __str__ (line 211) | def __str__(self): class NrnSeclistLocation (line 217) | class NrnSeclistLocation(Location, DictMixin): method __init__ (line 223) | def __init__( method instantiate (line 238) | def instantiate(self, sim=None, icell=None): # pylint: disable=W0613 method acc_label (line 245) | def acc_label(self): method __str__ (line 249) | def __str__(self): class NrnSeclistSecLocation (line 255) | class NrnSeclistSecLocation(Location, DictMixin): method __init__ (line 261) | def __init__( method instantiate (line 279) | def instantiate(self, sim=None, icell=None): # pylint: disable=W0613 method acc_label (line 286) | def acc_label(self): method __str__ (line 295) | def __str__(self): class NrnSomaDistanceCompLocation (line 301) | class NrnSomaDistanceCompLocation(Location, DictMixin): method __init__ (line 307) | def __init__( method find_icomp (line 327) | def find_icomp(self, sim, iseclist): method instantiate (line 355) | def instantiate(self, sim=None, icell=None): method acc_label (line 366) | def acc_label(self): method __str__ (line 390) | def __str__(self): class NrnSecSomaDistanceCompLocation (line 397) | class NrnSecSomaDistanceCompLocation(NrnSomaDistanceCompLocation): method __init__ (line 405) | def __init__( method instantiate (line 429) | def instantiate(self, sim=None, icell=None): method acc_label (line 462) | def acc_label(self): class NrnTrunkSomaDistanceCompLocation (line 468) | class NrnTrunkSomaDistanceCompLocation(NrnSecSomaDistanceCompLocation): method __init__ (line 481) | def __init__( method set_sec_index (line 512) | def set_sec_index(self, icell=None): method instantiate (line 534) | def instantiate(self, sim=None, icell=None): method acc_label (line 540) | def acc_label(self): class ArbLocation (line 546) | class ArbLocation(Location): method instantiate (line 549) | def instantiate(self, sim=None, icell=None): # pylint: disable=W0613 method __str__ (line 554) | def __str__(self): class ArbSegmentLocation (line 559) | class ArbSegmentLocation(ArbLocation): method __init__ (line 563) | def __init__(self, name, segment, comment=''): method acc_label (line 567) | def acc_label(self): class ArbBranchLocation (line 572) | class ArbBranchLocation(ArbLocation): method __init__ (line 578) | def __init__(self, name, branch, comment=''): method acc_label (line 582) | def acc_label(self): class ArbSegmentRelLocation (line 587) | class ArbSegmentRelLocation(ArbLocation): method __init__ (line 591) | def __init__(self, name, segment, pos, comment=''): method acc_label (line 596) | def acc_label(self): class ArbBranchRelLocation (line 603) | class ArbBranchRelLocation(ArbLocation): method __init__ (line 609) | def __init__(self, name, branch, pos, comment=''): method acc_label (line 614) | def acc_label(self): class ArbLocsetLocation (line 621) | class ArbLocsetLocation(ArbLocation): method __init__ (line 625) | def __init__(self, name, locset, comment=''): method acc_label (line 629) | def acc_label(self): class ArbRegionLocation (line 634) | class ArbRegionLocation(ArbLocation): method __init__ (line 638) | def __init__(self, name, region, comment=''): method acc_label (line 642) | def acc_label(self): class EPhysLocInstantiateException (line 647) | class EPhysLocInstantiateException(Exception): method __init__ (line 651) | def __init__(self, message): class EPhysLocAccException (line 657) | class EPhysLocAccException(Exception): method __init__ (line 661) | def __init__(self, message): FILE: bluepyopt/ephys/mechanisms.py class Mechanism (line 38) | class Mechanism(base.BaseEPhys): class NrnMODMechanism (line 44) | class NrnMODMechanism(Mechanism, serializer.DictMixin): method __init__ (line 57) | def __init__( method instantiate (line 96) | def instantiate(self, sim=None, icell=None): method instantiate_determinism (line 116) | def instantiate_determinism(self, deterministic, icell, isec, sim): method destroy (line 147) | def destroy(self, sim=None): method __str__ (line 152) | def __str__(self): method hash_hoc (line 160) | def hash_hoc(string, sim): method hash_py (line 170) | def hash_py(string): method generate_reinitrng_hoc_block (line 180) | def generate_reinitrng_hoc_block(self): method prefix (line 206) | def prefix(self): method prefix (line 212) | def prefix(self, value): class NrnMODPointProcessMechanism (line 270) | class NrnMODPointProcessMechanism(Mechanism): method __init__ (line 274) | def __init__( method instantiate (line 303) | def instantiate(self, sim=None, icell=None): method destroy (line 319) | def destroy(self, sim=None): method __str__ (line 324) | def __str__(self): FILE: bluepyopt/ephys/models.py class Model (line 41) | class Model(object): method __init__ (line 45) | def __init__(self, name): method instantiate (line 52) | def instantiate(self, sim=None): method destroy (line 56) | def destroy(self, sim=None): class CellModel (line 61) | class CellModel(Model): method __init__ (line 65) | def __init__( method check_name (line 124) | def check_name(self): method params_by_names (line 144) | def params_by_names(self, param_names): method freeze (line 149) | def freeze(self, param_dict): method unfreeze (line 155) | def unfreeze(self, param_names): method create_empty_template (line 162) | def create_empty_template( method create_empty_cell (line 207) | def create_empty_cell( method instantiate_morphology (line 226) | def instantiate_morphology(self, sim=None): method instantiate_morphology_3d (line 247) | def instantiate_morphology_3d(self, sim=None): method instantiate (line 253) | def instantiate(self, sim=None): method destroy (line 267) | def destroy(self, sim=None): # pylint: disable=W0613 method check_nonfrozen_params (line 290) | def check_nonfrozen_params(self, param_names): # pylint: disable=W0613 method _create_sim_desc (line 300) | def _create_sim_desc(self, param_values, method create_hoc (line 371) | def create_hoc(self, param_values, method create_acc (line 382) | def create_acc(self, param_values, method write_acc (line 418) | def write_acc(self, output_dir, param_values, method __str__ (line 430) | def __str__(self): class HocMorphology (line 453) | class HocMorphology(morphologies.Morphology): method __init__ (line 457) | def __init__(self, morphology_path): class HocCellModel (line 465) | class HocCellModel(CellModel): method __init__ (line 469) | def __init__(self, name, morphology_path, hoc_path=None, hoc_string=No... method params_by_names (line 502) | def params_by_names(self, param_names): method freeze (line 505) | def freeze(self, param_dict): method unfreeze (line 508) | def unfreeze(self, param_names): method instantiate (line 511) | def instantiate(self, sim=None): method destroy (line 529) | def destroy(self, sim=None): method check_nonfrozen_params (line 533) | def check_nonfrozen_params(self, param_names): method __str__ (line 536) | def __str__(self): method get_template_name (line 546) | def get_template_name(hoc_string): method load_hoc_template (line 564) | def load_hoc_template(sim, hoc_string): class LFPyCellModel (line 582) | class LFPyCellModel(Model): method __init__ (line 586) | def __init__( method check_name (line 654) | def check_name(self): method params_by_names (line 677) | def params_by_names(self, param_names): method freeze (line 682) | def freeze(self, param_dict): method unfreeze (line 688) | def unfreeze(self, param_names): method create_empty_template (line 695) | def create_empty_template( method create_empty_cell (line 744) | def create_empty_cell(name, sim, seclist_names=None, secarray_names=No... method instantiate (line 758) | def instantiate(self, sim=None): method destroy (line 800) | def destroy(self, sim=None): # pylint: disable=W0613 method check_nonfrozen_params (line 822) | def check_nonfrozen_params(self, param_names): # pylint: disable=W0613 method create_hoc (line 832) | def create_hoc( method __str__ (line 871) | def __str__(self): FILE: bluepyopt/ephys/morphologies.py class Morphology (line 39) | class Morphology(BaseEPhys): class NrnFileMorphology (line 45) | class NrnFileMorphology(Morphology, DictMixin): method __init__ (line 53) | def __init__( method __str__ (line 112) | def __str__(self): method instantiate (line 117) | def instantiate(self, sim=None, icell=None): method destroy (line 173) | def destroy(self, sim=None): method set_nseg (line 177) | def set_nseg(self, icell): method replace_axon (line 183) | def replace_axon(sim=None, icell=None, class ArbFileMorphology (line 275) | class ArbFileMorphology(Morphology, DictMixin): method load (line 306) | def load(morpho_filename, replace_axon): method extract_nrn_seclists (line 337) | def extract_nrn_seclists(icell, seclists): method replace_axon (line 408) | def replace_axon(morphology, replacement=None): FILE: bluepyopt/ephys/objectives.py class EFeatureObjective (line 25) | class EFeatureObjective(bluepyopt.objectives.Objective): method __init__ (line 29) | def __init__(self, name, features=None): method calculate_feature_scores (line 41) | def calculate_feature_scores(self, responses): method calculate_feature_values (line 50) | def calculate_feature_values(self, responses): class SingletonObjective (line 60) | class SingletonObjective(EFeatureObjective): method __init__ (line 64) | def __init__(self, name, feature): method calculate_score (line 74) | def calculate_score(self, responses): method calculate_value (line 79) | def calculate_value(self, responses): method __str__ (line 84) | def __str__(self): class SingletonWeightObjective (line 90) | class SingletonWeightObjective(SingletonObjective): method __init__ (line 94) | def __init__(self, name, feature, weight): method calculate_score (line 105) | def calculate_score(self, responses): method __str__ (line 110) | def __str__(self): class MaxObjective (line 116) | class MaxObjective(EFeatureObjective): method calculate_score (line 120) | def calculate_score(self, responses): class WeightedSumObjective (line 126) | class WeightedSumObjective(EFeatureObjective): method __init__ (line 130) | def __init__(self, name, features, weights): method calculate_score (line 146) | def calculate_score(self, responses): FILE: bluepyopt/ephys/objectivescalculators.py class ObjectivesCalculator (line 23) | class ObjectivesCalculator(object): method __init__ (line 27) | def __init__( method calculate_scores (line 38) | def calculate_scores(self, responses): method calculate_values (line 44) | def calculate_values(self, responses): method __str__ (line 50) | def __str__(self): FILE: bluepyopt/ephys/parameters.py class NrnParameter (line 35) | class NrnParameter(bluepyopt.parameters.Parameter): method __init__ (line 39) | def __init__( method instantiate (line 55) | def instantiate(self, sim=None, icell=None, params=None): method destroy (line 59) | def destroy(self, sim=None): class MetaParameter (line 64) | class MetaParameter(NrnParameter): method __init__ (line 68) | def __init__( method value (line 91) | def value(self, _value): method __str__ (line 97) | def __str__(self): class NrnMetaListEqualParameter (line 105) | class NrnMetaListEqualParameter(bluepyopt.parameters.MetaListEqualParame... method instantiate (line 108) | def instantiate(self, sim=None, icell=None, params=None): method destroy (line 116) | def destroy(self, sim=None): class NrnGlobalParameter (line 122) | class NrnGlobalParameter(NrnParameter, DictMixin): method __init__ (line 127) | def __init__( method instantiate (line 156) | def instantiate(self, sim=None, icell=None, params=None): method __str__ (line 163) | def __str__(self): class NrnSectionParameter (line 170) | class NrnSectionParameter(NrnParameter, DictMixin): method __init__ (line 176) | def __init__( method instantiate (line 219) | def instantiate(self, sim=None, icell=None, params=None): method __str__ (line 242) | def __str__(self): class NrnPointProcessParameter (line 251) | class NrnPointProcessParameter(NrnParameter, DictMixin): method __init__ (line 258) | def __init__( method instantiate (line 293) | def instantiate(self, sim=None, icell=None, params=None): method __str__ (line 309) | def __str__(self): class NrnRangeParameter (line 319) | class NrnRangeParameter(NrnParameter, DictMixin): method __init__ (line 325) | def __init__( method instantiate (line 367) | def instantiate(self, sim=None, icell=None, params=None): method __str__ (line 390) | def __str__(self): FILE: bluepyopt/ephys/parameterscalers/acc_iexpr.py class ArbIExprValueEliminator (line 27) | class ArbIExprValueEliminator(ast.NodeTransformer): method __init__ (line 30) | def __init__(self, variable_name, value): method generic_visit (line 37) | def generic_visit(self, node): method _is_linear (line 66) | def _is_linear(self, node): method visit_Name (line 78) | def visit_Name(self, node): class ArbIExprEmitter (line 91) | class ArbIExprEmitter(ast.NodeVisitor): method __init__ (line 107) | def __init__(self, var_name_to_sexpr, constant_formatter): method emit (line 113) | def emit(self): method _emit (line 116) | def _emit(self, expr): method generic_visit (line 119) | def generic_visit(self, node): method visit_Constant (line 131) | def visit_Constant(self, node): method visit_Num (line 137) | def visit_Num(self, node): method visit_Attribute (line 143) | def visit_Attribute(self, node): method visit_UnaryOp (line 152) | def visit_UnaryOp(self, node): method visit_BinOp (line 166) | def visit_BinOp(self, node): method visit_Call (line 180) | def visit_Call(self, node): method visit_Name (line 211) | def visit_Name(self, node): function generate_acc_scale_iexpr (line 221) | def generate_acc_scale_iexpr(iexpr, variables, constant_formatter): FILE: bluepyopt/ephys/parameterscalers/parameterscalers.py function format_float (line 34) | def format_float(value): class MissingFormatDict (line 39) | class MissingFormatDict(dict): method __missing__ (line 43) | def __missing__(self, key): # pylint: disable=R0201 class ParameterScaler (line 48) | class ParameterScaler(BaseEPhys): class NrnSegmentLinearScaler (line 56) | class NrnSegmentLinearScaler(ParameterScaler, DictMixin): method __init__ (line 61) | def __init__( method scale (line 79) | def scale(self, values, segment=None, sim=None): # pylint: disable=W0613 method __str__ (line 87) | def __str__(self): class NrnSegmentSectionDistanceScaler (line 93) | class NrnSegmentSectionDistanceScaler(ParameterScaler, DictMixin): method __init__ (line 100) | def __init__( method inst_distribution (line 148) | def inst_distribution(self): method scale_dict (line 164) | def scale_dict(self, values, distance): method eval_dist (line 176) | def eval_dist(self, values, distance): method scale (line 182) | def scale(self, values, segment, sim=None): method acc_scale_iexpr (line 212) | def acc_scale_iexpr(self, value, constant_formatter=format_float): method __str__ (line 218) | def __str__(self): class NrnSegmentSomaDistanceScaler (line 224) | class NrnSegmentSomaDistanceScaler(NrnSegmentSectionDistanceScaler, method __init__ (line 230) | def __init__( method acc_scale_iexpr (line 258) | def acc_scale_iexpr(self, value, constant_formatter=format_float): class NrnSegmentSomaDistanceStepScaler (line 271) | class NrnSegmentSomaDistanceStepScaler(NrnSegmentSomaDistanceScaler, method __init__ (line 277) | def __init__( method scale_dict (line 311) | def scale_dict(self, values, distance): FILE: bluepyopt/ephys/protocols.py class Protocol (line 45) | class Protocol(object): method __init__ (line 49) | def __init__(self, name=None): class SequenceProtocol (line 59) | class SequenceProtocol(Protocol): method __init__ (line 63) | def __init__(self, name=None, protocols=None): method run (line 74) | def run( method subprotocols (line 117) | def subprotocols(self): method __str__ (line 127) | def __str__(self): class SweepProtocol (line 139) | class SweepProtocol(Protocol): method __init__ (line 143) | def __init__( method total_duration (line 169) | def total_duration(self): method subprotocols (line 174) | def subprotocols(self): method adjust_stochasticity (line 179) | def adjust_stochasticity(func): method _run_func (line 199) | def _run_func(self, cell_model, param_values, sim=None): method run (line 243) | def run( method instantiate (line 307) | def instantiate(self, sim=None, cell_model=None): method destroy (line 330) | def destroy(self, sim=None): method __str__ (line 339) | def __str__(self): class StepProtocol (line 355) | class StepProtocol(SweepProtocol): method __init__ (line 359) | def __init__( method step_delay (line 392) | def step_delay(self): method step_duration (line 397) | def step_duration(self): class ArbSweepProtocol (line 402) | class ArbSweepProtocol(Protocol): method __init__ (line 406) | def __init__( method total_duration (line 428) | def total_duration(self): method subprotocols (line 433) | def subprotocols(self): method _run_func (line 438) | def _run_func(self, cell_json, param_values, sim=None): method run (line 494) | def run( method instantiate_locations (line 551) | def instantiate_locations(self, label_dict): method instantiate_iclamp_stimuli (line 599) | def instantiate_iclamp_stimuli(self, decor, use_labels=False): method instantiate_synaptic_stimuli (line 625) | def instantiate_synaptic_stimuli(self, cell_model, use_labels=False): method instantiate_recordings (line 635) | def instantiate_recordings(self, cell_model, use_labels=False): method __str__ (line 662) | def __str__(self): class SweepProtocolException (line 678) | class SweepProtocolException(Exception): method __init__ (line 682) | def __init__(self, message): class ArbSweepProtocolException (line 688) | class ArbSweepProtocolException(Exception): method __init__ (line 692) | def __init__(self, message): FILE: bluepyopt/ephys/recordings.py class Recording (line 30) | class Recording(object): method __init__ (line 34) | def __init__(self, name=None): class CompRecording (line 44) | class CompRecording(Recording): method __init__ (line 48) | def __init__( method response (line 75) | def response(self): method instantiate (line 85) | def instantiate(self, sim=None, icell=None): method destroy (line 100) | def destroy(self, sim=None): method __str__ (line 107) | def __str__(self): class LFPRecording (line 113) | class LFPRecording(Recording): method __init__ (line 120) | def __init__(self, name=None): method response (line 137) | def response(self): method instantiate (line 147) | def instantiate(self, sim=None, lfpy_cell=None, electrode=None): method destroy (line 166) | def destroy(self, sim=None): method __str__ (line 176) | def __str__(self): FILE: bluepyopt/ephys/responses.py class Response (line 26) | class Response(object): method __init__ (line 30) | def __init__(self, name): method __str__ (line 40) | def __str__(self): class TimeVoltageResponse (line 44) | class TimeVoltageResponse(Response): method __init__ (line 48) | def __init__(self, name, time=None, voltage=None): method read_csv (line 63) | def read_csv(self, filename): method to_csv (line 68) | def to_csv(self, filename): method __getitem__ (line 73) | def __getitem__(self, index): method plot (line 79) | def plot(self, axes): class TimeLFPResponse (line 89) | class TimeLFPResponse(TimeVoltageResponse): method __init__ (line 93) | def __init__(self, name, time=None, lfp=None): method plot (line 106) | def plot(self, axes): FILE: bluepyopt/ephys/serializer.py class DictMixin (line 11) | class DictMixin(object): method _serializer (line 17) | def _serializer(value): method _deserializer (line 31) | def _deserializer(value): method to_dict (line 44) | def to_dict(self): method from_dict (line 53) | def from_dict(cls, fields): function instantiator (line 64) | def instantiator(fields): FILE: bluepyopt/ephys/simulators.py class NrnSimulator (line 18) | class NrnSimulator(object): method __init__ (line 21) | def __init__( method cvode (line 63) | def cvode(self): method cvode_minstep (line 69) | def cvode_minstep(self): method cvode_minstep (line 75) | def cvode_minstep(self, value): method _nrn_disable_banner (line 81) | def _nrn_disable_banner(): method neuron (line 102) | def neuron(self): method initialize (line 118) | def initialize(self): method run (line 124) | def run( class NrnSimulatorException (line 187) | class NrnSimulatorException(Exception): method __init__ (line 190) | def __init__(self, message, original): class LFPySimulator (line 197) | class LFPySimulator(NrnSimulator): method __init__ (line 200) | def __init__( method run (line 232) | def run( class LFPySimulatorException (line 293) | class LFPySimulatorException(Exception): method __init__ (line 296) | def __init__(self, message, original): class ArbSimulator (line 303) | class ArbSimulator(object): method __init__ (line 306) | def __init__(self, dt=None, ext_catalogues=None): method initialize (line 330) | def initialize(self): method instantiate (line 334) | def instantiate(self, morph, decor, labels): method run (line 371) | def run(self, arb_cell_model, tstop=None, dt=None): class ArbSimulatorException (line 382) | class ArbSimulatorException(Exception): method __init__ (line 385) | def __init__(self, message): FILE: bluepyopt/ephys/stimuli.py class Stimulus (line 32) | class Stimulus(object): class SynapticStimulus (line 38) | class SynapticStimulus(Stimulus): class LFPStimulus (line 44) | class LFPStimulus(Stimulus): method instantiate (line 48) | def instantiate(self, sim=None, lfpy_cell=None): class NrnCurrentPlayStimulus (line 53) | class NrnCurrentPlayStimulus(Stimulus): method __init__ (line 57) | def __init__(self, method envelope (line 78) | def envelope(self): method instantiate (line 85) | def instantiate(self, sim=None, icell=None): method destroy (line 105) | def destroy(self, sim=None): method __str__ (line 112) | def __str__(self): class NrnNetStimStimulus (line 118) | class NrnNetStimStimulus(SynapticStimulus): method __init__ (line 122) | def __init__(self, method instantiate (line 156) | def instantiate(self, sim=None, icell=None): method destroy (line 172) | def destroy(self, sim=None): method acc_events (line 177) | def acc_events(self): method __str__ (line 203) | def __str__(self): class NrnSquarePulse (line 214) | class NrnSquarePulse(Stimulus): method __init__ (line 218) | def __init__(self, method envelope (line 242) | def envelope(self): method instantiate (line 255) | def instantiate(self, sim=None, icell=None): method destroy (line 274) | def destroy(self, sim=None): method __str__ (line 279) | def __str__(self): class NrnRampPulse (line 290) | class NrnRampPulse(Stimulus): method __init__ (line 294) | def __init__(self, method envelope (line 322) | def envelope(self): method instantiate (line 347) | def instantiate(self, sim=None, icell=None): method destroy (line 381) | def destroy(self, sim=None): method __str__ (line 388) | def __str__(self): class LFPySquarePulse (line 401) | class LFPySquarePulse(LFPStimulus): method __init__ (line 405) | def __init__(self, method instantiate (line 428) | def instantiate(self, sim=None, lfpy_cell=None): method destroy (line 469) | def destroy(self, sim=None): method __str__ (line 474) | def __str__(self): FILE: bluepyopt/evaluators.py class Evaluator (line 25) | class Evaluator(object): method __init__ (line 43) | def __init__(self, objectives=None, params=None): method evaluate_with_dicts (line 49) | def evaluate_with_dicts(self, param_dict): method evaluate_with_lists (line 63) | def evaluate_with_lists(self, params): FILE: bluepyopt/ipyp/bpopt_tasksdb.py function get_engine_data (line 35) | def get_engine_data(tasksdb_filename): function plot_usage (line 67) | def plot_usage(tasks, engine_number_map): function plot_duration_histogram (line 92) | def plot_duration_histogram(tasks): function calculate_unused_compute (line 108) | def calculate_unused_compute(tasks): function run (line 126) | def run(arg_list): function main (line 143) | def main(): FILE: bluepyopt/neuroml/biophys.py function get_nml_mech_dir (line 69) | def get_nml_mech_dir(): function adapt_CaDynamics_nml (line 76) | def adapt_CaDynamics_nml( function get_channel_from_param_name (line 122) | def get_channel_from_param_name(param_name): function format_dist_fun (line 143) | def format_dist_fun(raw_expr, value, dist_param_names): function add_nml_channel_to_nml_cell_file (line 166) | def add_nml_channel_to_nml_cell_file( function get_channel_ion (line 210) | def get_channel_ion(channel, custom_channel_ion=None): function get_erev (line 228) | def get_erev(ion, custom_ion_erevs=None): function get_arguments (line 246) | def get_arguments( function extract_parameter_value (line 309) | def extract_parameter_value( function get_density (line 365) | def get_density( function get_specific_capacitance (line 431) | def get_specific_capacitance(capacitance_overwrites): function get_biophys (line 456) | def get_biophys( FILE: bluepyopt/neuroml/cell.py function create_neuroml_cell (line 30) | def create_neuroml_cell( FILE: bluepyopt/neuroml/morphology.py function create_loadcell_hoc (line 28) | def create_loadcell_hoc( function create_morph_nml (line 66) | def create_morph_nml(bpo_cell, network_filename, release_params): function add_segment_groups (line 116) | def add_segment_groups(cell): FILE: bluepyopt/neuroml/simulation.py function create_neuroml_simulation (line 29) | def create_neuroml_simulation( FILE: bluepyopt/objectives.py class Objective (line 23) | class Objective(object): method __init__ (line 27) | def __init__(self, name, value=None): FILE: bluepyopt/optimisations.py class Optimisation (line 23) | class Optimisation(object): method __init__ (line 29) | def __init__(self, evaluator=None): FILE: bluepyopt/parameters.py class Parameter (line 23) | class Parameter(object): method __init__ (line 27) | def __init__(self, name, value=None, frozen=False, bounds=None, method lower_bound (line 42) | def lower_bound(self): method upper_bound (line 50) | def upper_bound(self): method value (line 58) | def value(self): method freeze (line 62) | def freeze(self, value): method unfreeze (line 67) | def unfreeze(self): method value (line 73) | def value(self, value): method check_bounds (line 83) | def check_bounds(self): method __str__ (line 92) | def __str__(self): class MetaListEqualParameter (line 98) | class MetaListEqualParameter(Parameter): method __init__ (line 102) | def __init__(self, name, value=None, frozen=False, method value (line 126) | def value(self, value): method freeze (line 134) | def freeze(self, value): method unfreeze (line 142) | def unfreeze(self): method check_bounds (line 149) | def check_bounds(self): method __str__ (line 157) | def __str__(self): FILE: bluepyopt/stoppingCriteria.py class StoppingCriteria (line 19) | class StoppingCriteria(object): method __init__ (line 22) | def __init__(self): method check (line 27) | def check(self, kwargs): method reset (line 31) | def reset(self): FILE: bluepyopt/tests/disable_simplecell_scoop.py function disabled_scoop (line 27) | def disabled_scoop(): FILE: bluepyopt/tests/test_bluepyopt.py function test_import (line 29) | def test_import(): FILE: bluepyopt/tests/test_deapext/deapext_test_utils.py function make_mock_population (line 8) | def make_mock_population(features_count=5, population_count=5): function make_population (line 31) | def make_population(features_count=5, population_count=5): FILE: bluepyopt/tests/test_deapext/test_algorithms.py function test_eaAlphaMuPlusLambdaCheckpoint (line 16) | def test_eaAlphaMuPlusLambdaCheckpoint(): function test_eaAlphaMuPlusLambdaCheckpoint_with_checkpoint (line 57) | def test_eaAlphaMuPlusLambdaCheckpoint_with_checkpoint(): FILE: bluepyopt/tests/test_deapext/test_hype.py function test_hypeIndicatorExact (line 11) | def test_hypeIndicatorExact(): function test_hypeIndicatorSampled (line 25) | def test_hypeIndicatorSampled(): FILE: bluepyopt/tests/test_deapext/test_optimisations.py function test_DEAPOptimisation_constructor (line 14) | def test_DEAPOptimisation_constructor(): function test_IBEADEAPOptimisation_constructor (line 34) | def test_IBEADEAPOptimisation_constructor(): function test_DEAPOptimisation_run (line 46) | def test_DEAPOptimisation_run(): function test_DEAPOptimisation_run_from_parents (line 64) | def test_DEAPOptimisation_run_from_parents(): function test_selectorname (line 80) | def test_selectorname(): FILE: bluepyopt/tests/test_deapext/test_optimisationsCMA.py function test_optimisationsCMA_normspace (line 9) | def test_optimisationsCMA_normspace(): function test_optimisationsCMA_SO_run (line 26) | def test_optimisationsCMA_SO_run(): function test_optimisationsCMA_MO_run (line 44) | def test_optimisationsCMA_MO_run(): FILE: bluepyopt/tests/test_deapext/test_selIBEA.py function test_calc_fitness_components (line 16) | def test_calc_fitness_components(): function test_mating_selection (line 41) | def test_mating_selection(): function test_selibea_init (line 53) | def test_selibea_init(): FILE: bluepyopt/tests/test_deapext/test_stoppingCriteria.py function test_MaxNGen (line 10) | def test_MaxNGen(): FILE: bluepyopt/tests/test_deapext/test_utils.py function flag (line 10) | def flag(event): function catch_event (line 16) | def catch_event(event): function test_run_next_gen_condition (line 30) | def test_run_next_gen_condition(): FILE: bluepyopt/tests/test_ephys/test_acc.py function test_arbor_labels (line 10) | def test_arbor_labels(): FILE: bluepyopt/tests/test_ephys/test_create_acc.py function test_read_templates (line 40) | def test_read_templates(): function test_Nrn2ArbParamAdapter_param_name (line 52) | def test_Nrn2ArbParamAdapter_param_name(): function test_Nrn2ArbParamAdapter_param_value (line 67) | def test_Nrn2ArbParamAdapter_param_value(): function test_Nrn2ArbParamAdapter_format (line 85) | def test_Nrn2ArbParamAdapter_format(): function test_Nrn2ArbMechGrouper_format_params_and_group_by_mech (line 164) | def test_Nrn2ArbMechGrouper_format_params_and_group_by_mech(): function test_Nrn2ArbMechGrouper_process_global (line 185) | def test_Nrn2ArbMechGrouper_process_global(): function test_Nrn2ArbMechGrouper_is_global_property (line 200) | def test_Nrn2ArbMechGrouper_is_global_property(): function test_separate_global_properties (line 211) | def test_separate_global_properties(): function test_Nrn2ArbMechGrouper_process_local (line 226) | def test_Nrn2ArbMechGrouper_process_local(): function test_ArbNmodlMechFormatter_load_mech_catalogue_meta (line 256) | def test_ArbNmodlMechFormatter_load_mech_catalogue_meta(): function test_ArbNmodlMechFormatter_mech_name (line 266) | def test_ArbNmodlMechFormatter_mech_name(): function test_ArbNmodlMechFormatter_translate_density (line 273) | def test_ArbNmodlMechFormatter_translate_density(): function test_arb_populate_label_dict (line 309) | def test_arb_populate_label_dict(): function test_create_acc (line 330) | def test_create_acc(): function test_create_acc_filename (line 395) | def test_create_acc_filename(): function test_create_acc_replace_axon (line 445) | def test_create_acc_replace_axon(): function make_cell (line 495) | def make_cell(replace_axon): function run_short_sim (line 530) | def run_short_sim(cable_cell): function test_cell_model_write_and_read_acc (line 544) | def test_cell_model_write_and_read_acc(): function test_cell_model_write_and_read_acc_replace_axon (line 575) | def test_cell_model_write_and_read_acc_replace_axon(): function test_cell_model_create_acc_replace_axon_without_instantiate (line 627) | def test_cell_model_create_acc_replace_axon_without_instantiate(): function check_acc_dir (line 642) | def check_acc_dir(test_dir, ref_dir): function test_write_acc_simple (line 675) | def test_write_acc_simple(): function test_write_acc_l5pc (line 719) | def test_write_acc_l5pc(): function test_write_acc_expsyn (line 779) | def test_write_acc_expsyn(): FILE: bluepyopt/tests/test_ephys/test_create_hoc.py function test_generate_channels_by_location (line 28) | def test_generate_channels_by_location(): function test__generate_channels_by_location (line 41) | def test__generate_channels_by_location(): function test_generate_parameters (line 58) | def test_generate_parameters(): function test__generate_parameters (line 69) | def test__generate_parameters(): function test_create_hoc (line 92) | def test_create_hoc(): function test_create_hoc_filename (line 105) | def test_create_hoc_filename(): function test_generate_reinitrng (line 128) | def test_generate_reinitrng(): function test_range_exprs_to_hoc (line 137) | def test_range_exprs_to_hoc(): function test_range_exprs_to_hoc_step_scaler (line 159) | def test_range_exprs_to_hoc_step_scaler(): FILE: bluepyopt/tests/test_ephys/test_evaluators.py function test_CellEvaluator_init (line 22) | def test_CellEvaluator_init(): function test_CellEvaluator_evaluate (line 45) | def test_CellEvaluator_evaluate(): FILE: bluepyopt/tests/test_ephys/test_extra_features_utils.py function test_peak_to_valley (line 21) | def test_peak_to_valley(): function test_peak_trough_ratio (line 29) | def test_peak_trough_ratio(): function test_halfwidth (line 38) | def test_halfwidth(): function test_repolarization_slope (line 49) | def test_repolarization_slope(): function test_recovery_slope (line 64) | def test_recovery_slope(): function test_peak_image (line 75) | def test_peak_image(): function test_relative_amplitude (line 91) | def test_relative_amplitude(): function test_peak_time_diff (line 107) | def test_peak_time_diff(): function test__get_trough_and_peak_idx (line 123) | def test__get_trough_and_peak_idx(): function test_calculate_features (line 133) | def test_calculate_features(): FILE: bluepyopt/tests/test_ephys/test_features.py function test_EFeature (line 15) | def test_EFeature(): function test_eFELFeature (line 22) | def test_eFELFeature(): function test_eFELFeature_max_score (line 52) | def test_eFELFeature_max_score(): function test_eFELFeature_force_max_score (line 89) | def test_eFELFeature_force_max_score(): function test_eFELFeature_double_settings (line 126) | def test_eFELFeature_double_settings(): function test_eFELFeature_int_settings (line 164) | def test_eFELFeature_int_settings(): function test_eFELFeature_string_settings (line 200) | def test_eFELFeature_string_settings(): function test_eFELFeature_serialize (line 234) | def test_eFELFeature_serialize(): function test_extraFELFeature (line 252) | def test_extraFELFeature(): function test_masked_cosine_distance (line 332) | def test_masked_cosine_distance(): FILE: bluepyopt/tests/test_ephys/test_init.py function test_import (line 30) | def test_import(): function test_ephys_base (line 36) | def test_ephys_base(): FILE: bluepyopt/tests/test_ephys/test_locations.py function test_location_init (line 33) | def test_location_init(): class TestNrnSectionCompLocation (line 42) | class TestNrnSectionCompLocation(object): method setup_method (line 45) | def setup_method(self): method test_instantiate (line 56) | def test_instantiate(self): class TestNrnSeclistCompLocation (line 81) | class TestNrnSeclistCompLocation(object): method setup_method (line 84) | def setup_method(self): method test_instantiate (line 95) | def test_instantiate(self): class TestNrnSeclistSecLocation (line 126) | class TestNrnSeclistSecLocation(object): method setup_method (line 129) | def setup_method(self): method test_instantiate (line 140) | def test_instantiate(self): class TestNrnSomaDistanceCompLocation (line 168) | class TestNrnSomaDistanceCompLocation(object): method setup_method (line 171) | def setup_method(self): method test_instantiate (line 179) | def test_instantiate(self): class TestNrnSecSomaDistanceCompLocation (line 213) | class TestNrnSecSomaDistanceCompLocation(object): method setup_method (line 216) | def setup_method(self): method test_instantiate (line 227) | def test_instantiate(self): class TestNrnTrunkSomaDistanceCompLocation (line 265) | class TestNrnTrunkSomaDistanceCompLocation(object): method setup_method (line 268) | def setup_method(self): method test_instantiate (line 280) | def test_instantiate(self): function test_serialize (line 332) | def test_serialize(): FILE: bluepyopt/tests/test_ephys/test_mechanisms.py function test_mechanism_serialize (line 24) | def test_mechanism_serialize(): function test_nrnmod_instantiate (line 34) | def test_nrnmod_instantiate(): function compare_strings (line 84) | def compare_strings(s1, s2): function test_nrnmod_reinitrng_block (line 97) | def test_nrnmod_reinitrng_block(): function test_nrnmod_determinism (line 137) | def test_nrnmod_determinism(): function test_pprocess_instantiate (line 159) | def test_pprocess_instantiate(): function test_string_hash_functions (line 204) | def test_string_hash_functions(): FILE: bluepyopt/tests/test_ephys/test_models.py function yield_blank_hoc (line 23) | def yield_blank_hoc(template_name): function test_create_empty_template (line 37) | def test_create_empty_template(): function test_model (line 46) | def test_model(): function test_cellmodel (line 55) | def test_cellmodel(): function test_cellmodel_namecheck (line 70) | def test_cellmodel_namecheck(): function test_load_hoc_template (line 88) | def test_load_hoc_template(): function test_HocCellModel (line 98) | def test_HocCellModel(): function test_CellModel_create_empty_cell (line 120) | def test_CellModel_create_empty_cell(): function test_CellModel_create_hoc (line 129) | def test_CellModel_create_hoc(): function test_CellModel_destroy (line 153) | def test_CellModel_destroy(): function test_lfpy_create_empty_template (line 184) | def test_lfpy_create_empty_template(): function test_lfpycellmodel (line 195) | def test_lfpycellmodel(): function test_lfpycellmodel_namecheck (line 212) | def test_lfpycellmodel_namecheck(): function test_load_lfpy_hoc_template (line 226) | def test_load_lfpy_hoc_template(): function test_LFPyCellModel_create_empty_cell (line 238) | def test_LFPyCellModel_create_empty_cell(): function test_LFPyCellModel_create_hoc (line 247) | def test_LFPyCellModel_create_hoc(): function test_LFPyCellModel_destroy (line 274) | def test_LFPyCellModel_destroy(): function test_metaparameter (line 303) | def test_metaparameter(): FILE: bluepyopt/tests/test_ephys/test_morphologies.py function test_morphology_init (line 24) | def test_morphology_init(): function test_nrnfilemorphology_init (line 32) | def test_nrnfilemorphology_init(): function test_nrnfilemorphology_replace_axon (line 54) | def test_nrnfilemorphology_replace_axon(): function test_nrnfilemorphology_replace_axon_ax1 (line 78) | def test_nrnfilemorphology_replace_axon_ax1(): function test_nrnfilemorphology_replace_axon_ax2 (line 102) | def test_nrnfilemorphology_replace_axon_ax2(): function test_serialize (line 126) | def test_serialize(): FILE: bluepyopt/tests/test_ephys/test_objectives.py function test_EFeatureObjective (line 13) | def test_EFeatureObjective(): function test_SingletonObjective (line 51) | def test_SingletonObjective(): function test_SingletonWeightObjective (line 92) | def test_SingletonWeightObjective(): function test_MaxObjective (line 133) | def test_MaxObjective(): function test_WeightedSumObjective (line 180) | def test_WeightedSumObjective(): FILE: bluepyopt/tests/test_ephys/test_parameters.py function test_pprocessparam_instantiate (line 17) | def test_pprocessparam_instantiate(): function test_serialize (line 50) | def test_serialize(): function test_metaparameter (line 63) | def test_metaparameter(): FILE: bluepyopt/tests/test_ephys/test_parameterscalers.py function test_NrnSegmentSomaDistanceScaler_dist_params (line 19) | def test_NrnSegmentSomaDistanceScaler_dist_params(): function test_NrnSegmentSectionDistanceScaler_eval_dist_with_dict (line 42) | def test_NrnSegmentSectionDistanceScaler_eval_dist_with_dict(): function test_NrnSegmentSomaDistanceStepScaler_eval_dist_with_dict (line 57) | def test_NrnSegmentSomaDistanceStepScaler_eval_dist_with_dict(): function test_serialize (line 73) | def test_serialize(): function test_parameterscalers_iexpr_generator (line 96) | def test_parameterscalers_iexpr_generator(): function test_parameterscalers_iexpr_generator_non_existent_op (line 115) | def test_parameterscalers_iexpr_generator_non_existent_op(): function test_parameterscalers_iexpr_generator_unsupported_attr (line 133) | def test_parameterscalers_iexpr_generator_unsupported_attr(): function test_parameterscalers_iexpr (line 151) | def test_parameterscalers_iexpr(): FILE: bluepyopt/tests/test_ephys/test_protocols.py function test_distloc_exception (line 32) | def test_distloc_exception(): function run_RuntimeError (line 83) | def run_RuntimeError( function run_NrnSimulatorException (line 93) | def run_NrnSimulatorException( function test_sweepprotocol_init (line 104) | def test_sweepprotocol_init(): function test_sequenceprotocol_init (line 145) | def test_sequenceprotocol_init(): function test_sequenceprotocol_run (line 188) | def test_sequenceprotocol_run(): function test_sequenceprotocol_overwrite (line 233) | def test_sequenceprotocol_overwrite(): function test_stepprotocol_init (line 279) | def test_stepprotocol_init(): function test_sweepprotocol_run_unisolated (line 317) | def test_sweepprotocol_run_unisolated(): function test_sweepprotocol_run_isolated (line 369) | def test_sweepprotocol_run_isolated(): function test_nrnsimulator_exception (line 420) | def test_nrnsimulator_exception(): function test_sweepprotocol_instantiate_with_LFPyCellModel (line 473) | def test_sweepprotocol_instantiate_with_LFPyCellModel(): FILE: bluepyopt/tests/test_ephys/test_recordings.py function test_comprecording_init (line 33) | def test_comprecording_init(): function test_lfprecording_init (line 82) | def test_lfprecording_init(): function test_lfprecording_instantiate (line 94) | def test_lfprecording_instantiate(): FILE: bluepyopt/tests/test_ephys/test_serializer.py class ClassforTesting (line 11) | class ClassforTesting(ephys.serializer.DictMixin): method __init__ (line 16) | def __init__(self, string, boolean, float_, list_, dict_): class NestedClassforTesting (line 24) | class NestedClassforTesting(ephys.serializer.DictMixin): method __init__ (line 30) | def __init__(self, test, tuples, lists, dicts): function test_serializer (line 38) | def test_serializer(): function test_roundtrip_serializer (line 47) | def test_roundtrip_serializer(): function test_nested_serializer (line 57) | def test_nested_serializer(): function test_non_instantiable (line 74) | def test_non_instantiable(): FILE: bluepyopt/tests/test_ephys/test_simulators.py function test_nrnsimulator_init (line 37) | def test_nrnsimulator_init(): function test_nrnsimulator_init_windows (line 45) | def test_nrnsimulator_init_windows(): function test_nrnsimulator_cvode_minstep (line 61) | def test_nrnsimulator_cvode_minstep(): function test_neuron_import (line 110) | def test_neuron_import(): function test_nrnsim_run_dt_exception (line 119) | def test_nrnsim_run_dt_exception(): function test_nrnsim_run_cvodeactive_dt_exception (line 130) | def test_nrnsim_run_cvodeactive_dt_exception(): function test_disable_banner_exception (line 142) | def test_disable_banner_exception(mock_glob): function test_lfpysimulator_init (line 154) | def test_lfpysimulator_init(): function test_lfpyimulator_init_windows (line 163) | def test_lfpyimulator_init_windows(): function test__lfpysimulator_neuron_import (line 180) | def test__lfpysimulator_neuron_import(): function test_lfpysim_run_cvodeactive_dt_exception (line 190) | def test_lfpysim_run_cvodeactive_dt_exception(): function test_lfpysimulator_disable_banner_exception (line 228) | def test_lfpysimulator_disable_banner_exception(mock_glob): FILE: bluepyopt/tests/test_ephys/test_stimuli.py function test_stimulus_init (line 35) | def test_stimulus_init(): function test_NrnNetStimStimulus_init (line 43) | def test_NrnNetStimStimulus_init(): function test_NrnNetStimStimulus_instantiate (line 55) | def test_NrnNetStimStimulus_instantiate(): function test_NrnCurrentPlayStimulus_instantiate (line 97) | def test_NrnCurrentPlayStimulus_instantiate(): function test_NrnRampPulse_init (line 129) | def test_NrnRampPulse_init(): function test_NrnRampPulse_instantiate (line 136) | def test_NrnRampPulse_instantiate(): function test_LFPySquarePulse_init (line 220) | def test_LFPySquarePulse_init(): function test_LFPySquarePulse_instantiate (line 248) | def test_LFPySquarePulse_instantiate(): FILE: bluepyopt/tests/test_ephys/testmodels/dummycells.py class DummyCellModel1 (line 6) | class DummyCellModel1(ephys.models.Model): method __init__ (line 10) | def __init__(self, name=None): method freeze (line 17) | def freeze(self, param_values): method unfreeze (line 21) | def unfreeze(self, param_names): method instantiate (line 25) | def instantiate(self, sim=None): method destroy (line 57) | def destroy(self, sim=None): class DummyLFPyCellModel1 (line 63) | class DummyLFPyCellModel1(ephys.models.Model): method __init__ (line 67) | def __init__(self, name=None): method freeze (line 77) | def freeze(self, param_values): method unfreeze (line 81) | def unfreeze(self, param_names): method instantiate (line 85) | def instantiate(self, sim=None): method destroy (line 127) | def destroy(self, sim=None): FILE: bluepyopt/tests/test_ephys/utils.py function make_mech (line 9) | def make_mech(): function make_parameters (line 23) | def make_parameters(): FILE: bluepyopt/tests/test_evaluators.py function test_evaluator_init (line 31) | def test_evaluator_init(): FILE: bluepyopt/tests/test_l5pc.py function load_from_json (line 59) | def load_from_json(filename): function dump_to_json (line 66) | def dump_to_json(content, filename): function test_import (line 73) | def test_import(): class TestL5PCModel (line 81) | class TestL5PCModel(object): method setup_method (line 84) | def setup_method(self): method test_instantiate (line 94) | def test_instantiate(self): method teardown_method (line 99) | def teardown_method(self): class TestL5PCEvaluator (line 104) | class TestL5PCEvaluator(object): method setup_method (line 107) | def setup_method(self): method test_eval (line 119) | def test_eval(self): method teardown_method (line 137) | def teardown_method(self): function stdout_redirector (line 144) | def stdout_redirector(stream): function test_exec (line 155) | def test_exec(): function test_l5pc_validate_neuron_arbor (line 184) | def test_l5pc_validate_neuron_arbor(): FILE: bluepyopt/tests/test_lfpy.py function test_lfpy_evaluator (line 20) | def test_lfpy_evaluator(): FILE: bluepyopt/tests/test_neuroml_fcts.py function test_get_nml_mech_dir (line 54) | def test_get_nml_mech_dir(): function test_get_channel_from_param_name (line 84) | def test_get_channel_from_param_name(): function test_format_dist_fun (line 102) | def test_format_dist_fun(): function test_add_nml_channel_to_nml_cell_file (line 110) | def test_add_nml_channel_to_nml_cell_file(): function test_get_arguments (line 149) | def test_get_arguments(): function test_extract_parameter_value (line 225) | def test_extract_parameter_value(): function test_get_density (line 280) | def test_get_density(): function test_get_specific_capacitance (line 306) | def test_get_specific_capacitance(): function test_get_biophys (line 359) | def test_get_biophys(): function test_add_segment_groups (line 382) | def test_add_segment_groups(): function test_neuroml_run (line 407) | def test_neuroml_run(): FILE: bluepyopt/tests/test_parameters.py function test_parameters_init (line 31) | def test_parameters_init(): function test_parameters_fields (line 40) | def test_parameters_fields(): function test_parameters_str (line 56) | def test_parameters_str(): function test_MetaListEqualParameter_init (line 69) | def test_MetaListEqualParameter_init(): function test_MetaListEqualParameter_freeze_unfreeze (line 95) | def test_MetaListEqualParameter_freeze_unfreeze(): function test_MetaListEqualParamete_str (line 123) | def test_MetaListEqualParamete_str(): FILE: bluepyopt/tests/test_simplecell.py class TestSimpleCellClass (line 13) | class TestSimpleCellClass(object): method setup_method (line 16) | def setup_method(self): method test_exec (line 24) | def test_exec(self): method teardown_method (line 35) | def teardown_method(self): class TestSimpleCellArborClass (line 42) | class TestSimpleCellArborClass(object): method setup_method (line 45) | def setup_method(self): method test_exec (line 53) | def test_exec(self): method teardown_method (line 64) | def teardown_method(self): FILE: bluepyopt/tests/test_stochkv.py function compare_strings (line 22) | def compare_strings(s1, s2): function test_import (line 34) | def test_import(): function test_run (line 40) | def test_run(): function test_run_stochkv3 (line 72) | def test_run_stochkv3(): FILE: bluepyopt/tests/test_tools.py function test_load (line 7) | def test_load(): function test_uint32_seed (line 14) | def test_uint32_seed(): FILE: bluepyopt/tools.py function uint32_seed (line 6) | def uint32_seed(string): FILE: cloud-config/config/amazon/gather_config.py function _get_instances_by_tag (line 32) | def _get_instances_by_tag(ec2, tag): function get_head_public_ip (line 40) | def get_head_public_ip(ec2): function get_work_private_ips (line 48) | def get_work_private_ips(ec2, tag=WORKER_INSTANCE_NAME, include_head=True): function get_parser (line 58) | def get_parser(): function main (line 68) | def main(): FILE: examples/expsyn/expsyn.py function create_model (line 13) | def create_model(sim, do_replace_axon, return_locations=False): function main (line 83) | def main(args): FILE: examples/expsyn/generate_acc.py function main (line 25) | def main(): FILE: examples/graupnerbrunelstdp/gbevaluator.py function gbParam (line 9) | def gbParam(params): class GraupnerBrunelEvaluator (line 27) | class GraupnerBrunelEvaluator(bpop.evaluators.Evaluator): method __init__ (line 31) | def __init__(self): method get_param_dict (line 60) | def get_param_dict(self, param_values): method compute_synaptic_gain_with_lists (line 69) | def compute_synaptic_gain_with_lists(self, param_values): method evaluate_with_lists (line 82) | def evaluate_with_lists(self, param_values): FILE: examples/graupnerbrunelstdp/run_fit.py function run_model (line 20) | def run_model(): function plot_log (line 27) | def plot_log(log): function plot_epspamp_discrete (line 72) | def plot_epspamp_discrete(dt, model_sg, sg, stderr): function plot_calcium_transients (line 90) | def plot_calcium_transients(protocols, best_ind_dict): function plot_dt_scan (line 125) | def plot_dt_scan(best_ind_dict, good_solutions, dt, sg, stderr): function analyse (line 174) | def analyse(): function main (line 215) | def main(): FILE: examples/graupnerbrunelstdp/stdputil.py function logging_debug_vec (line 33) | def logging_debug_vec(fmt, vec): function logging_debug (line 39) | def logging_debug(*args): class Protocol (line 81) | class Protocol(object): method __init__ (line 85) | def __init__(self, stim_vec, delta_vec, f, n, prot_id=None): method sort (line 116) | def sort(self): class CalciumTrace (line 139) | class CalciumTrace(object): method __init__ (line 143) | def __init__(self, protocol, model): method materializetrace (line 192) | def materializetrace(self): method event (line 212) | def event(self): method time (line 217) | def time(self): method amplitude (line 222) | def amplitude(self): function load_neviansakmann (line 227) | def load_neviansakmann(): function time_above_threshold (line 252) | def time_above_threshold(protocol, param): function transition_prob (line 338) | def transition_prob(protocol, param=None): function protocol_outcome (line 398) | def protocol_outcome(protocol, param=None): FILE: examples/graupnerbrunelstdp/test_stdputil.py function test_protocol_outcome (line 11) | def test_protocol_outcome(): FILE: examples/l5pc/benchmark/task_stats.py function get_engine_data (line 10) | def get_engine_data(): function plot_usage (line 50) | def plot_usage(tasks, engine_number_map): function plot_duration_histogram (line 70) | def plot_duration_histogram(tasks): function filter_start_time (line 84) | def filter_start_time(start_time, tasks): function calculate_unused_compute (line 93) | def calculate_unused_compute(tasks): function main (line 105) | def main(): FILE: examples/l5pc/convert_params.py function main (line 6) | def main(): FILE: examples/l5pc/create_tables.py function load_json (line 6) | def load_json(filename): function create_feature_fields (line 12) | def create_feature_fields(): function create_param_fields_list (line 44) | def create_param_fields_list(): function create_param_fields_string (line 103) | def create_param_fields_string(): function create_table (line 143) | def create_table(field_content, n_of_cols): function main (line 156) | def main(): FILE: examples/l5pc/generate_acc.py function main (line 26) | def main(): FILE: examples/l5pc/generate_hoc.py function main (line 40) | def main(): FILE: examples/l5pc/hocmodel.py class HocModel (line 12) | class HocModel(object): method __init__ (line 16) | def __init__( method instantiate (line 36) | def instantiate(self): method run_protocol (line 48) | def run_protocol(self, protocol): method destroy (line 69) | def destroy(self): method run_protocols (line 75) | def run_protocols(self, protocols, param_values=None): method __str__ (line 102) | def __str__(self): FILE: examples/l5pc/l5pc_analysis.py function set_rcoptions (line 55) | def set_rcoptions(func): function get_responses (line 67) | def get_responses(cell_evaluator, individuals, filename): function analyse_cp (line 89) | def analyse_cp(opt, cp_filename, responses_filename, figs, sim='nrn'): function plot_log (line 126) | def plot_log(log, fig=None, box=None): function plot_history (line 176) | def plot_history(history): function plot_objectives (line 192) | def plot_objectives(objectives, fig=None, box=None): function plot_responses (line 222) | def plot_responses(responses, fig=None, box=None): function get_slice (line 236) | def get_slice(start, end, data): function plot_multiple_responses (line 241) | def plot_multiple_responses(responses, fig): function plot_recording (line 269) | def plot_recording(recording, fig=None, box=None, xlabel=False): function plot_validation (line 308) | def plot_validation(opt, parameters): function analyse_releasecircuit_model (line 453) | def analyse_releasecircuit_model(opt, figs, box=None, sim='nrn'): function analyse_releasecircuit_hocmodel (line 481) | def analyse_releasecircuit_hocmodel(opt, fig=None, box=None): function plot_individual_params (line 519) | def plot_individual_params( function plot_diversity (line 563) | def plot_diversity(opt, checkpoint_file, fig, param_names): FILE: examples/l5pc/l5pc_evaluator.py function define_protocols (line 38) | def define_protocols(do_replace_axon=True, sim='nrn'): function load_protocols (line 44) | def load_protocols(): function create_protocols (line 53) | def create_protocols(protocol_definitions, do_replace_axon=None, sim='nr... function define_fitness_calculator (line 133) | def define_fitness_calculator(protocols): function create (line 184) | def create(do_replace_axon=True, sim='nrn'): FILE: examples/l5pc/l5pc_model.py function define_mechanisms (line 36) | def define_mechanisms(): function load_mechanisms (line 43) | def load_mechanisms(): function create_mechanisms (line 52) | def create_mechanisms(mech_definitions): function define_parameters (line 70) | def define_parameters(): function load_parameters (line 77) | def load_parameters(): function create_parameters (line 81) | def create_parameters(param_configs): function define_morphology (line 147) | def define_morphology(do_replace_axon): function create (line 157) | def create(do_replace_axon=True): FILE: examples/l5pc/l5pc_validate_neuron_arbor_pm.py function powerset (line 82) | def powerset(mechs): # from itertools docs function get_extra_params (line 89) | def get_extra_params(loc, mechs): FILE: examples/l5pc/opt_l5pc.py function create_optimizer (line 46) | def create_optimizer(args): function get_parser (line 76) | def get_parser(): function main (line 113) | def main(): # pylint: disable=too-many-statements FILE: examples/l5pc/tasks2dataframe.py function _open_db (line 17) | def _open_db(dbfile): function _add_buffers (line 29) | def _add_buffers(df, arg_names=None, result_names=None, delete_buffers=F... function create_df (line 69) | def create_df(db, arg_names=None, result_names=None): FILE: examples/l5pc_lfpy/generate_extra_features.py class NumpyEncoder (line 54) | class NumpyEncoder(json.JSONEncoder): method default (line 55) | def default(self, obj): function dict_to_json (line 82) | def dict_to_json(data, path): function add_extra_objectives (line 88) | def add_extra_objectives(evaluator): function save_extra_efeatures (line 129) | def save_extra_efeatures(efeature_values): FILE: examples/l5pc_lfpy/l5pc_lfpy_evaluator.py function define_protocols (line 43) | def define_protocols(): function get_feature_name (line 81) | def get_feature_name(protocol_name, location, feature): function get_recording_names (line 85) | def get_recording_names(protocol_name, location=None): function define_fitness_calculator (line 89) | def define_fitness_calculator(protocols, feature_file): function create (line 139) | def create(feature_file="extra_features.json", cvode_active=True, dt=None): FILE: examples/l5pc_lfpy/l5pc_lfpy_model.py function define_electrode (line 35) | def define_electrode( function create (line 73) | def create(): FILE: examples/simplecell/generate_acc.py function main (line 26) | def main(): FILE: examples/simplecell/generate_hoc.py function main (line 23) | def main(): FILE: examples/simplecell/simplecell_model.py function define_morphology (line 26) | def define_morphology(do_replace_axon): function define_mechanisms (line 31) | def define_mechanisms(): function define_parameters (line 41) | def define_parameters(): function create (line 66) | def create(do_replace_axon): FILE: examples/stochkv/stochkv3cell.py function stochkv3_hoc_filename (line 13) | def stochkv3_hoc_filename(deterministic=False): function run_stochkv3_model (line 21) | def run_stochkv3_model(deterministic=False): function main (line 128) | def main(): FILE: examples/stochkv/stochkvcell.py function stochkv_hoc_filename (line 13) | def stochkv_hoc_filename(deterministic=False): function run_stochkv_model (line 21) | def run_stochkv_model(deterministic=False): function main (line 128) | def main(): FILE: examples/thalamocortical-cell/CellEvalSetup/evaluator.py function read_step_protocol (line 41) | def read_step_protocol(protocol_name, function read_ramp_protocol (line 73) | def read_ramp_protocol( function define_protocols (line 108) | def define_protocols(protocols_filename, stochkv_det=None, class eFELFeatureExtra (line 157) | class eFELFeatureExtra(eFELFeature): method __init__ (line 165) | def __init__( method get_bpo_score (line 211) | def get_bpo_score(self, responses): method calculate_feature (line 221) | def calculate_feature(self, responses, raise_warnings=False): method calculate_score (line 251) | def calculate_score(self, responses, trace_check=False): class SingletonWeightObjective (line 289) | class SingletonWeightObjective(EFeatureObjective): method __init__ (line 293) | def __init__(self, name, feature, weight): method calculate_score (line 304) | def calculate_score(self, responses): method __str__ (line 309) | def __str__(self): function define_fitness_calculator (line 315) | def define_fitness_calculator(main_protocol, features_filename, prefix=""): function create (line 406) | def create(etype, runopt=False, altmorph=None): FILE: examples/thalamocortical-cell/CellEvalSetup/protocols.py class StepProtocolCustom (line 43) | class StepProtocolCustom(ephys.protocols.StepProtocol): method __init__ (line 47) | def __init__( method run (line 64) | def run(self, cell_model, param_values, sim=None, isolate=None): class RampProtocol (line 83) | class RampProtocol(ephys.protocols.SweepProtocol): method __init__ (line 87) | def __init__( method step_delay (line 116) | def step_delay(self): method step_duration (line 121) | def step_duration(self): FILE: examples/thalamocortical-cell/CellEvalSetup/template.py function multi_locations (line 38) | def multi_locations(sectionlist): function define_mechanisms (line 76) | def define_mechanisms(params_filename): function define_parameters (line 100) | def define_parameters(params_filename): function define_morphology (line 187) | def define_morphology(morphology_filename, do_set_nseg=1e9): function create (line 197) | def create(recipe, etype, altmorph=None): FILE: examples/thalamocortical-cell/CellEvalSetup/tools.py function rename_prot (line 1) | def rename_prot(name): function rename_featpart (line 34) | def rename_featpart(name): function rename_feat (line 63) | def rename_feat(name, sep = " "): FILE: examples/tsodyksmarkramstp/tmevaluator.py class TsodyksMarkramEvaluator (line 31) | class TsodyksMarkramEvaluator(bpop.evaluators.Evaluator): method __init__ (line 32) | def __init__(self, t, v, tstim, params): method generate_model (line 70) | def generate_model(self, individual): method evaluate_with_lists (line 78) | def evaluate_with_lists(self, individual): method init_simulator_and_evaluate_with_lists (line 86) | def init_simulator_and_evaluate_with_lists(self, individual): FILE: examples/tsodyksmarkramstp/tmevaluator_multiplefreqs.py class TsodyksMarkramEvaluator (line 31) | class TsodyksMarkramEvaluator(bpop.evaluators.Evaluator): method __init__ (line 32) | def __init__(self, data, params): method generate_model (line 58) | def generate_model(self, freq, individual): method evaluate_with_lists (line 64) | def evaluate_with_lists(self, individual): method init_simulator_and_evaluate_with_lists (line 73) | def init_simulator_and_evaluate_with_lists(self, individual): FILE: examples/tsodyksmarkramstp/tmodeint.py function integrate (line 35) | def integrate(sampstim, nsamples, dt, vRest, Trec, Tfac, FILE: examples/tsodyksmarkramstp/tmodesolve.py function solve_TM (line 26) | def solve_TM(t_stims, USE, Trec, Tfac, ASE): FILE: misc/github_wiki/creates_publication_list_markdown.py class Style (line 15) | class Style(OriginalStyle): method format_title (line 19) | def format_title(self, e, which_field, as_sentence=True): function put_bullet_points (line 30) | def put_bullet_points(input):