bmtk.simulator.filternet package

Subpackages

• bmtk.simulator.filternet.default_setters package
  • Submodules
  • bmtk.simulator.filternet.default_setters.cell_loaders module
    • createOneUnitOfTwoSubunitFilter()
    • create_two_sub_cell()
    • default_cell_loader()
    • get_sigma()
    • get_tf_params()
    • get_wavelet_params()
  • Module contents
• bmtk.simulator.filternet.lgnmodel package
  • Submodules
  • bmtk.simulator.filternet.lgnmodel.cellmetrics module
    • SubclassMetricsCache
      • SubclassMetricsCache.get_metrics()
      • SubclassMetricsCache.load_dir()
      • SubclassMetricsCache.saved_metrics_dir
    • get_data_metrics_for_each_subclass()
  • bmtk.simulator.filternet.lgnmodel.cellmodel module
    • LGNOnOffCell
    • OffUnit
    • OnUnit
    • TwoSubfieldLinearCell
  • bmtk.simulator.filternet.lgnmodel.cursor module
    • FilterCursor
    • KernelCursor
      • KernelCursor.apply_dot_product()
      • KernelCursor.col_range
      • KernelCursor.evaluate()
      • KernelCursor.frame_rate
      • KernelCursor.row_range
      • KernelCursor.t_range
    • LNUnitCursor
    • MultiLNUnitCursor
      • MultiLNUnitCursor.evaluate()
    • MultiLNUnitMultiMovieCursor
    • SeparableKernelCursor
      • SeparableKernelCursor.evaluate()
    • SeparableLNUnitCursor
      • SeparableLNUnitCursor.evaluate()
    • SeparableMultiLNUnitCursor
      • SeparableMultiLNUnitCursor.evaluate()
    • SeparableSpatioTemporalFilterCursor
    • kernel_dot_product()
  • bmtk.simulator.filternet.lgnmodel.fitfuns module
    • ff()
    • invnl()
    • makeBasis_StimKernel()
    • makeBasis_StimKernel_exp()
    • makeFitStruct_GLM()
    • nlin()
    • normalizecols()
    • sameconv()
  • bmtk.simulator.filternet.lgnmodel.gaborfilter module
    • GaborFilter
      • GaborFilter.get_kernel()
      • GaborFilter.imshow()
      • GaborFilter.to_dict()
  • bmtk.simulator.filternet.lgnmodel.kernel module
    • Kernel1D
      • Kernel1D.full()
      • Kernel1D.imshow()
      • Kernel1D.normalize()
      • Kernel1D.rescale()
    • Kernel2D
      • Kernel2D.apply_threshold()
      • Kernel2D.copy()
      • Kernel2D.from_dense()
      • Kernel2D.full()
      • Kernel2D.imshow()
      • Kernel2D.normalize()
      • Kernel2D.normalize2()
      • Kernel2D.rescale()
    • Kernel3D
      • Kernel3D.apply_threshold()
      • Kernel3D.copy()
      • Kernel3D.full()
      • Kernel3D.imshow()
      • Kernel3D.normalize()
      • Kernel3D.rescale()
      • Kernel3D.t_slice()
    • find_l_r_in_t_range()
    • get_contour()
    • merge_spatial_temporal()
    • plot_single_contour()
  • bmtk.simulator.filternet.lgnmodel.lattice_unit_constructor module
    • make_lattice_unit()
    • make_overlapping_onoff_cell_list()
    • make_sOFF_cell_list()
    • make_sON_cell_list()
    • make_separate_onoff_cell_list()
    • make_tOFF_cell_list()
    • make_tON_cell_list()
  • bmtk.simulator.filternet.lgnmodel.lgnmodel1 module
    • LGNModel
      • LGNModel.evaluate()
    • heat_plot()
    • line_plot()
  • bmtk.simulator.filternet.lgnmodel.linearfilter module
    • SpatioTemporalFilter
      • SpatioTemporalFilter.get_spatiotemporal_kernel()
      • SpatioTemporalFilter.show_spatial_filter()
      • SpatioTemporalFilter.show_temporal_filter()
      • SpatioTemporalFilter.t_slice()
      • SpatioTemporalFilter.to_dict()
    • SpectroTemporalFilter
      • SpectroTemporalFilter.get_spectrotemporal_kernel()
      • SpectroTemporalFilter.show_spatial_filter()
      • SpectroTemporalFilter.show_temporal_filter()
      • SpectroTemporalFilter.t_slice()
      • SpectroTemporalFilter.to_dict()
  • bmtk.simulator.filternet.lgnmodel.lnunit module
    • LNUnit
      • LNUnit.evaluate()
      • LNUnit.get_cursor()
      • LNUnit.get_spatiotemporal_kernel()
      • LNUnit.get_spectrotemporal_kernel()
      • LNUnit.show_spatial_filter()
      • LNUnit.show_temporal_filter()
      • LNUnit.to_dict()
    • MultiLNUnit
      • MultiLNUnit.evaluate()
      • MultiLNUnit.get_cursor()
      • MultiLNUnit.get_spatiotemporal_kernel()
      • MultiLNUnit.show_spatial_filter()
      • MultiLNUnit.show_temporal_filter()
  • bmtk.simulator.filternet.lgnmodel.make_cell_list module
    • evaluate_cell_and_plot()
    • make_on_off_cell_list()
    • make_single_unit_cell_list()
    • multi_cell_random_generator()
  • bmtk.simulator.filternet.lgnmodel.movie module
    • FullFieldFlashMovie
    • FullFieldMovie
      • FullFieldMovie.create_movie()
      • FullFieldMovie.data
      • FullFieldMovie.frame_rate
      • FullFieldMovie.full()
    • GratingMovie
      • GratingMovie.create_movie()
    • LoomingMovie
      • LoomingMovie.create_movie()
    • Movie
      • Movie.imshow()
      • Movie.imshow_summary()
      • Movie.normalize_matrix()
      • Movie.play()
      • Movie.ranges
  • bmtk.simulator.filternet.lgnmodel.poissongeneration module
    • generate_inhomogenous_poisson()
    • generate_poisson_process()
    • generate_poisson_rescaling()
    • generate_poisson_rescaling_function()
    • generate_renewal_process()
  • bmtk.simulator.filternet.lgnmodel.singleunitcell module
  • bmtk.simulator.filternet.lgnmodel.spatialfilter module
    • ArrayFilter
      • ArrayFilter.get_kernel()
      • ArrayFilter.imshow()
    • GaussianSpatialFilter
      • GaussianSpatialFilter.get_kernel()
      • GaussianSpatialFilter.imshow()
      • GaussianSpatialFilter.to_dict()
  • bmtk.simulator.filternet.lgnmodel.temporalfilter module
    • ArrayTemporalFilter
      • ArrayTemporalFilter.get_default_t_grid()
    • TemporalFilter
      • TemporalFilter.get_default_t_grid()
      • TemporalFilter.get_kernel()
      • TemporalFilter.imshow()
      • TemporalFilter.to_dict()
    • TemporalFilterCosineBump
      • TemporalFilterCosineBump.get_default_t_grid()
      • TemporalFilterCosineBump.to_dict()
  • bmtk.simulator.filternet.lgnmodel.transferfunction module
    • MultiTransferFunction
      • MultiTransferFunction.to_dict()
    • ScalarTransferFunction
      • ScalarTransferFunction.imshow()
      • ScalarTransferFunction.to_dict()
  • bmtk.simulator.filternet.lgnmodel.util_fns module
    • check_optim_results_against_bounds()
    • chunks()
    • compute_FFT_OneCycle()
    • create_ff_mov()
    • create_grating_movie_list()
    • cross_from_above()
    • get_tcross_from_temporal_kernel()
  • bmtk.simulator.filternet.lgnmodel.utilities module
    • apply_transformation_matrix()
    • convert_tmin_tmax_framerate_to_trange()
    • get_convolution()
    • get_convolution_ind()
    • get_rotation_matrix()
    • get_scale_matrix()
    • get_translation_matrix()
    • get_vanhateren()
  • bmtk.simulator.filternet.lgnmodel.waveletfilter module
    • WaveletFilter
      • WaveletFilter.get_kernel()
      • WaveletFilter.imshow()
      • WaveletFilter.to_dict()
  • Module contents
• bmtk.simulator.filternet.modules package
  • Submodules
  • bmtk.simulator.filternet.modules.base module
    • SimModule
      • SimModule.finalize()
      • SimModule.initialize()
      • SimModule.save()
  • bmtk.simulator.filternet.modules.create_spikes module
    • SpikesGenerator
      • SpikesGenerator.finalize()
      • SpikesGenerator.save()
    • f_rate_to_spike_train()
  • bmtk.simulator.filternet.modules.record_rates module
    • RecordRates
      • RecordRates.finalize()
      • RecordRates.initialize()
      • RecordRates.save()
  • Module contents

Submodules

bmtk.simulator.filternet.auditory_processing module

class bmtk.simulator.filternet.auditory_processing.AuditoryInput(aud_fn, low_lim=50.0, hi_lim=8000.0, sample_factor=4, downsample=None)

Bases: object

get_cochleagram(desired_sr=1000, interp_to_freq=False)

bmtk.simulator.filternet.cell module

class bmtk.simulator.filternet.cell.Cell(node, population=None)

Bases: object

build()

property default_jitter

get(item, default)

property gid

property lgn_cell_obj

property population

bmtk.simulator.filternet.cell_models module

bmtk.simulator.filternet.config module

class bmtk.simulator.filternet.config.Config(*args, **kwargs)

Bases: SimulationConfig

property io

property jitter

bmtk.simulator.filternet.filternetwork module

class bmtk.simulator.filternet.filternetwork.FilterNetwork

Bases: SimNetwork

build()

build_nodes()

cells()

property jitter

set_default_processing(processing_fnc)

bmtk.simulator.filternet.filters module

bmtk.simulator.filternet.filtersimulator module

class bmtk.simulator.filternet.filtersimulator.FilterSimulator(network, dt, tstop)

Bases: Simulator

add_audio(audio_type, params)

add_movie(movie_type, params)

property dt

static find_params(param_names, **kwargs)

classmethod from_config(config, network)

property io

local_cells()

run()

bmtk.simulator.filternet.io_tools module

class bmtk.simulator.filternet.io_tools.FilterNetIOUtils

Bases: IOUtils

barrier()

MPI Barrier call

log_debug(message, all_ranks=False)

log_info(message, all_ranks=False)

bmtk.simulator.filternet.pyfunction_cache module

bmtk.simulator.filternet.pyfunction_cache.add_cell_processor(func, name=None, overwrite=True)

bmtk.simulator.filternet.pyfunction_cache.cell_processor(*wargs, **wkwargs)

A decorator for registering NEURON cell loader functions.

bmtk.simulator.filternet.pyfunction_cache.load_py_modules(cell_processors)

bmtk.simulator.filternet.sonata_adaptors module

class bmtk.simulator.filternet.sonata_adaptors.FilterNode(node, prop_adaptor)

Bases: SonataBaseNode

property amplitude

property b_t

property delay

property delays

property delays_non_dom

property direction

property jitter

property kpeaks

property kpeaks_non_dom

property non_dom_params

property order_t

property predefined_jitter

property psi

property sf_sep

property sigma_f

property sp_mod_freq

property t_mod_freq

property tuning_angle

property weights

property weights_non_dom

class bmtk.simulator.filternet.sonata_adaptors.FilterNodeAdaptor(network)

Bases: NodeAdaptor

get_node(sonata_node)

classmethod patch_adaptor(adaptor, node_group, network)

static preprocess_node_types(network, node_population)

bmtk.simulator.filternet.sonata_adaptors.find_delays_params(node_group, node_adaptor)

bmtk.simulator.filternet.sonata_adaptors.find_kpeaks_params(node_group, node_adaptor)

bmtk.simulator.filternet.sonata_adaptors.find_nondom_delays_params(node_group, node_adaptor)

bmtk.simulator.filternet.sonata_adaptors.find_nondom_kpeaks_params(node_group, node_adaptor)

bmtk.simulator.filternet.sonata_adaptors.find_nondom_weight_params(node_group, node_adaptor)

bmtk.simulator.filternet.sonata_adaptors.find_spectrotemporal_params(node_group, node_adaptor)

bmtk.simulator.filternet.sonata_adaptors.find_weight_params(node_group, node_adaptor)

bmtk.simulator.filternet.sonata_adaptors.non_dom_params(self, node)

bmtk.simulator.filternet.sonata_adaptors.return_none(self, node)

bmtk.simulator.filternet.sonata_adaptors.tuning_angle_preset(self, node)

bmtk.simulator.filternet.sonata_adaptors.tuning_angle_rand(self, node)

bmtk.simulator.filternet.sonata_adaptors.weights(self, node)

bmtk.simulator.filternet.transfer_functions module

bmtk.simulator.filternet.utils module

Module contents