ALLEN INSTITUTE

# 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