bmtk.simulator.filternet.lgnmodel package¶
Submodules¶
bmtk.simulator.filternet.lgnmodel.cellmetrics module¶
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class
bmtk.simulator.filternet.lgnmodel.cellmetrics.
SubclassMetricsCache
(saved_metrics_dir=None)[source]¶ Bases:
object
Used to calc optimized parameteres for different types of cells using existing data that contains cell responses to different types of stimulus. The existing data should be stored in a single directory with a csv file for reach cell type.
- usage:
- subcell_metrics = SubclassMetricsCache(‘/path/to/observations/’)
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get_metrics
(subclass_type)[source]¶ Calculates various parameters for a given cell class, using observations stored in saved_metrics_dir
Parameters: subclass_type – name of cell subclass types Returns: A dictionary of parameters for various types of inputs
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saved_metrics_dir
¶
bmtk.simulator.filternet.lgnmodel.cellmodel module¶
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class
bmtk.simulator.filternet.lgnmodel.cellmodel.
LGNOnOffCell
(on_filter, off_filter, transfer_function=<bmtk.simulator.filternet.lgnmodel.transferfunction.MultiTransferFunction object>)[source]¶ Bases:
bmtk.simulator.filternet.lgnmodel.lnunit.MultiLNUnit
A cell model for a OnOff cell
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class
bmtk.simulator.filternet.lgnmodel.cellmodel.
OffUnit
(linear_filter, transfer_function)[source]¶
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class
bmtk.simulator.filternet.lgnmodel.cellmodel.
TwoSubfieldLinearCell
(dominant_filter, nondominant_filter, subfield_separation=10, onoff_axis_angle=45, dominant_subfield_location=(30, 40), transfer_function=<bmtk.simulator.filternet.lgnmodel.transferfunction.MultiTransferFunction object>)[source]¶
bmtk.simulator.filternet.lgnmodel.cursor module¶
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class
bmtk.simulator.filternet.lgnmodel.cursor.
FilterCursor
(spatiotemporal_filter, movie, threshold=0)[source]¶ Bases:
bmtk.simulator.filternet.lgnmodel.cursor.KernelCursor
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class
bmtk.simulator.filternet.lgnmodel.cursor.
KernelCursor
(kernel, movie)[source]¶ Bases:
object
A class that takes care of the convolution of the (non-separable) spatial-temporal linear filter with the move.
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col_range
¶
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frame_rate
¶
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row_range
¶
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t_range
¶
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-
class
bmtk.simulator.filternet.lgnmodel.cursor.
LNUnitCursor
(lnunit, movie, threshold=0)[source]¶ Bases:
bmtk.simulator.filternet.lgnmodel.cursor.KernelCursor
A class that takes care of applying a linear-nonlinear filter to a movie. Parent class is used to apply the spatial-termporal filter convolution to the movie, when then the lnunit non-linear transfer function is applied.
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class
bmtk.simulator.filternet.lgnmodel.cursor.
MultiLNUnitCursor
(multi_lnunit, movie, threshold=0)[source]¶ Bases:
object
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class
bmtk.simulator.filternet.lgnmodel.cursor.
MultiLNUnitMultiMovieCursor
(multi_lnunit, movie_list, threshold=0.0)[source]¶ Bases:
bmtk.simulator.filternet.lgnmodel.cursor.MultiLNUnitCursor
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class
bmtk.simulator.filternet.lgnmodel.cursor.
SeparableKernelCursor
(spatial_kernel, temporal_kernel, movie)[source]¶ Bases:
object
A class for applying a spatial-temporal convolution to a movie. Unlike the KernelCursor the spatial-temporal filter is broken up into its components, spatial filter is applied then followed by a temporal filter convolution.
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class
bmtk.simulator.filternet.lgnmodel.cursor.
SeparableLNUnitCursor
(lnunit, movie)[source]¶ Bases:
bmtk.simulator.filternet.lgnmodel.cursor.SeparableSpatioTemporalFilterCursor
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class
bmtk.simulator.filternet.lgnmodel.cursor.
SeparableMultiLNUnitCursor
(multilnunit, movie)[source]¶ Bases:
object
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class
bmtk.simulator.filternet.lgnmodel.cursor.
SeparableSpatioTemporalFilterCursor
(spatiotemporal_filter, movie)[source]¶ Bases:
bmtk.simulator.filternet.lgnmodel.cursor.SeparableKernelCursor
bmtk.simulator.filternet.lgnmodel.fitfuns module¶
bmtk.simulator.filternet.lgnmodel.kernel module¶
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class
bmtk.simulator.filternet.lgnmodel.kernel.
Kernel1D
(t_range, kernel_array, threshold=0.0, reverse=False)[source]¶ Bases:
object
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class
bmtk.simulator.filternet.lgnmodel.kernel.
Kernel2D
(row_range, col_range, row_inds, col_inds, kernel)[source]¶ Bases:
object
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class
bmtk.simulator.filternet.lgnmodel.kernel.
Kernel3D
(row_range, col_range, t_range, row_inds, col_inds, t_inds, kernel)[source]¶ Bases:
object
bmtk.simulator.filternet.lgnmodel.lattice_unit_constructor module¶
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bmtk.simulator.filternet.lgnmodel.lattice_unit_constructor.
make_lattice_unit
(lattice_unit_center=None)[source]¶
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bmtk.simulator.filternet.lgnmodel.lattice_unit_constructor.
make_overlapping_onoff_cell_list
(lattice_unit_center)[source]¶
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bmtk.simulator.filternet.lgnmodel.lattice_unit_constructor.
make_sOFF_cell_list
(lattice_unit_center)[source]¶
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bmtk.simulator.filternet.lgnmodel.lattice_unit_constructor.
make_sON_cell_list
(lattice_unit_center)[source]¶
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bmtk.simulator.filternet.lgnmodel.lattice_unit_constructor.
make_separate_onoff_cell_list
(lattice_unit_center)[source]¶
bmtk.simulator.filternet.lgnmodel.lgnmodel1 module¶
bmtk.simulator.filternet.lgnmodel.linearfilter module¶
bmtk.simulator.filternet.lgnmodel.lnunit module¶
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class
bmtk.simulator.filternet.lgnmodel.lnunit.
LNUnit
(linear_filter, transfer_function, amplitude=1.0)[source]¶ Bases:
object
bmtk.simulator.filternet.lgnmodel.make_cell_list module¶
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bmtk.simulator.filternet.lgnmodel.make_cell_list.
evaluate_cell_and_plot
(input_cell, input_movie, ax, show=False)[source]¶
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bmtk.simulator.filternet.lgnmodel.make_cell_list.
make_on_off_cell_list
(number_of_cells=None, lattice_unit_center=None, weights_on=None, weights_off=None, kpeaks_on=None, kpeaks_off=None, delays_on=None, delays_off=None, amplitude_on=None, amplitude_off=None, sigma_on=None, sigma_off=None, subfield_separation=None, ang=None, dominant_subunit=None, width=5, transfer_function_str='Heaviside(x)*x + Heaviside(y)*y')[source]¶
bmtk.simulator.filternet.lgnmodel.movie module¶
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class
bmtk.simulator.filternet.lgnmodel.movie.
FullFieldFlashMovie
(row_range, col_range, t_on, t_off, max_intensity=1, frame_rate=24)[source]¶ Bases:
bmtk.simulator.filternet.lgnmodel.movie.FullFieldMovie
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class
bmtk.simulator.filternet.lgnmodel.movie.
FullFieldMovie
(f, rows, cols, frame_rate=24.0)[source]¶ Bases:
bmtk.simulator.filternet.lgnmodel.movie.Movie
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data
¶
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frame_rate
¶
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-
class
bmtk.simulator.filternet.lgnmodel.movie.
GratingMovie
(row_size, col_size, frame_rate=1000.0)[source]¶ Bases:
bmtk.simulator.filternet.lgnmodel.movie.Movie
-
create_movie
(t_min=0, t_max=1, gray_screen_dur=0, cpd=0.05, temporal_f=4, theta=45, phase=0.0, contrast=1.0, row_size_new=None, col_size_new=None)[source]¶ Create the grating movie with the desired parameters
Parameters: - t_min – start time in seconds
- t_max – end time in seconds
- gray_screen_dur – Duration of gray screen before grating stimulus starts
- cpd – cycles per degree
- temporal_f – in Hz
- theta – orientation angle, in degrees
- phase – temporal phase, in degrees
- contrast – the maximum constrast, must be between 0 and 1.0
- row_size_new – Use to truncate screen, by default leaves original row dimension
- col_size_new – Use to truncate screen, by default leaves original col dimension
Returns: Movie object of grating with desired parameters
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class
bmtk.simulator.filternet.lgnmodel.movie.
LoomingMovie
(row_size, col_size, frame_rate=1000.0)[source]¶
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class
bmtk.simulator.filternet.lgnmodel.movie.
Movie
(data, row_range=None, col_range=None, labels=('time', 'y', 'x'), units=('second', 'pixel', 'pixel'), frame_rate=None, t_range=None)[source]¶ Bases:
object
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play
(interval=None, skip=None, playback_speed=1.0, cmap=None, vmin=-1.0, vmax=1.0, save_as=None, show=True)[source]¶ Parameters: - interval –
- skip – skip every Nth frame, useful for very large data sets
- playback_speed –
- cmap – color map, default to gray
- save_as – If set to a valid (mp4 file) path animation will be saved. Otherwise it won’t
- show – display the animation, default True
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ranges
¶
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bmtk.simulator.filternet.lgnmodel.poissongeneration module¶
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bmtk.simulator.filternet.lgnmodel.poissongeneration.
generate_inhomogenous_poisson
(t_range, y_range, seed=None)[source]¶
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bmtk.simulator.filternet.lgnmodel.poissongeneration.
generate_poisson_rescaling
(t, y, seed=None)[source]¶
bmtk.simulator.filternet.lgnmodel.singleunitcell module¶
bmtk.simulator.filternet.lgnmodel.spatialfilter module¶
-
class
bmtk.simulator.filternet.lgnmodel.spatialfilter.
GaussianSpatialFilter
(translate=(0.0, 0.0), sigma=(1.0, 1.0), rotation=0, origin='center')[source]¶ Bases:
object
bmtk.simulator.filternet.lgnmodel.temporalfilter module¶
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class
bmtk.simulator.filternet.lgnmodel.temporalfilter.
ArrayTemporalFilter
(mask, t_support)[source]¶ Bases:
bmtk.simulator.filternet.lgnmodel.temporalfilter.TemporalFilter
bmtk.simulator.filternet.lgnmodel.transferfunction module¶
bmtk.simulator.filternet.lgnmodel.util_fns module¶
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bmtk.simulator.filternet.lgnmodel.util_fns.
check_optim_results_against_bounds
(bounds, opt_wts, opt_kpeaks)[source]¶
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bmtk.simulator.filternet.lgnmodel.util_fns.
chunks
(l, n)[source]¶ Yield successive n-sized chunks from l.
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bmtk.simulator.filternet.lgnmodel.util_fns.
create_ff_mov
(frame_rate, tst, tend, xrng, yrng)[source]¶
bmtk.simulator.filternet.lgnmodel.utilities module¶
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bmtk.simulator.filternet.lgnmodel.utilities.
convert_tmin_tmax_framerate_to_trange
(t_min, t_max, frame_rate)[source]¶
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bmtk.simulator.filternet.lgnmodel.utilities.
get_convolution
(t, frame_rate, flipped_t_inds, kernel, data)[source]¶
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bmtk.simulator.filternet.lgnmodel.utilities.
get_convolution_ind
(curr_fi, flipped_t_inds, kernel, data)[source]¶