neurotools package

Subpackages

• neurotools.graphics package
  • Submodules
    • neurotools.graphics.color module
      • rgb2hex()
      • hex2rgb()
      • hsv2rgb()
      • lightness()
      • luminance_matrix()
      • match_luminance()
      • rotate()
      • RGBtoHCL()
      • hue_angle()
      • hcl2rgb()
      • circularly_smooth_colormap()
      • isoluminance1()
      • isoluminance2()
      • isoluminance3()
      • isoluminance4()
      • lighthues()
      • darkhues()
      • medhues()
      • radl2rgb()
      • radl2rgbLUT()
      • complexHLArr2RGB()
      • color_boxplot()
      • hex_pack_BGR()
      • code_to_16bit()
      • bit16_RGB_to_tuple()
      • enumerate_fast_colors()
      • tuple_to_bit16()
      • tuple_to_bit24()
      • bit16_print_color()
      • show_fast_pallet()
      • show_complete_fast_pallet()
      • show_complete_fastest_pallet()
      • show_hex_pallet()
      • lighten()
      • darken()
    • neurotools.graphics.colormaps module
      • register_phasor_map()
      • test_colormaps()
    • neurotools.graphics.dendron module
      • list_like()
      • get_depth()
      • count_nodes()
      • inorder_traversal()
      • plot_brackets()
      • plot_brackets_polar()
    • neurotools.graphics.fabio_maps module
    • neurotools.graphics.image module
      • median_center()
      • mean_center()
      • unitize()
      • visualize_derivatives()
    • neurotools.graphics.matplotlib module
      • hide_toolbar()
      • start()
      • draw_array()
    • neurotools.graphics.plot module
      • simpleaxis()
      • rightaxis()
      • simpleraxis()
      • simplerright()
      • noaxis()
      • nicey()
      • nicex()
      • nicexy()
      • roundx()
      • roundy()
      • positivex()
      • positivey()
      • positivexy()
      • xylim()
      • noclip()
      • notick()
      • nox()
      • noy()
      • noxyaxes()
      • noxlabels()
      • noylabels()
      • nolabels()
      • righty()
      • unity()
      • unitx()
      • fsize()
      • force_aspect()
      • square_compare()
      • get_aspect()
      • match_image_aspect()
      • unitaxes()
      • adjustmap()
      • get_ax_size()
      • get_ax_pixel()
      • get_ax_pixel_ratio()
      • pixels_to_xunits()
      • yunits_to_pixels()
      • xunits_to_pixels()
      • pixels_to_yunits()
      • pixels_to_xfigureunits()
      • px2x()
      • px2y()
      • pixels_to_yfigureunits()
      • xfigureunits_to_pixels()
      • yfigureunits_to_pixels()
      • adjust_ylabel_space()
      • adjust_xlabel_space()
      • get_bbox()
      • nudge_axis_y_pixels()
      • adjust_axis_height_pixels()
      • nudge_axis_y()
      • nudge_axis_up()
      • nudge_axis_down()
      • nudge_axis_x()
      • expand_axis_x()
      • expand_axis_y()
      • nudge_axis_baseline()
      • nudge_axis_top()
      • nudge_axis_left()
      • nudge_axis_right()
      • expand_axis_outward()
      • fudgex()
      • fudgey()
      • fudgexy()
      • vtwin()
      • zoombox()
      • shade_edges()
      • ybartext()
      • xbartext()
      • nice_legend()
      • right_legend()
      • left_legend()
      • base_legend()
      • top_legend()
      • rangeto()
      • rangeover()
      • cleartop()
      • plotCWT()
      • plotWTPhase()
      • wtpshow()
      • plotWTPhaseFig()
      • domask()
      • HandlerSquare
      • plot_complex()
      • animate_complex()
      • good_colorbar()
      • complex_axis()
      • subfigurelabel()
      • sigbar()
      • hsigbar()
      • savefigure()
      • clean_y_range()
      • round_to_precision()
      • ceil_to_precision()
      • floor_to_precision()
      • expand_y_range()
      • Gaussian2D_covellipse()
      • stderrplot()
      • yscalebar()
      • xscalebar()
      • addspikes()
      • unit_crosshairs()
      • covariance_crosshairs()
      • draw_circle()
      • simple_arrow()
      • inhibition_arrow()
      • figurebox()
      • more_xticks()
      • more_yticks()
      • border_width()
      • broken_step()
      • label()
      • flathist()
      • barcompare()
      • shellmean()
      • trendline()
      • shellplot()
      • arrow_between()
      • splitz()
      • plotz()
      • save_limits()
      • restore_limits()
      • mock_legend()
      • xtickpad()
      • ytickpad()
      • xticklen()
      • yticklen()
      • xin()
      • yin()
      • lighten()
      • darken()
      • axvstripe()
      • axvbands()
      • zerohline()
      • zerovline()
      • plot_circular_histogram()
      • plot_quadrant()
      • quadrant_axes()
      • nicebp()
      • colored_violin()
      • colored_boxplot()
      • boxplot_significance()
      • simplestem()
      • pike()
      • confidencebox()
      • anatomy_axis()
      • vpaired_histogram()
      • hollow_polygon()
      • add_polygon()
      • linscale_polar_plot()
      • vonmises_ring()
      • disk_axis()
    • neurotools.graphics.pygame module
      • enable_vsync()
      • start()
      • draw_array()
    • neurotools.graphics.ztransform_plot_helpers module
      • configure_matplotlib()
      • add_circle()
      • label_complex_axes()
      • add_complex_axes()
      • add_colorbar()
      • phase_magnitude_figure()
      • joint_phase_magnitude_plot()
      • do_bode_z()
      • do_nyquist()
      • do_bode_and_nyquist()
      • do_bode_s()
  • Module contents
• neurotools.jobs package
  • Submodules
    • neurotools.jobs.cache module
      • get_source()
      • function_hash_no_subroutines()
      • function_signature()
      • signature_to_file_string()
      • file_string_to_signature()
      • human_encode()
      • human_decode()
      • get_cache_path()
      • locate_cached()
      • validate_for_matfile()
      • validate_for_numpy()
      • read_cache_entry()
      • disk_cacher()
      • hierarchical_cacher()
      • scan_cachedir()
      • hashit()
      • base64hash()
      • base64hash10bytes()
      • function_hash_with_subroutines()
      • combine_caches()
      • exists()
    • neurotools.jobs.closure module
      • is_immutable()
      • is_probably_safe()
      • csv()
      • inspect_function_closure()
      • verify_function_closure()
      • get_subroutines()
    • neurotools.jobs.filenames module
      • validate_argument_signature()
      • is_dangerous_filename()
      • check_filename()
    • neurotools.jobs.initialize_system_cache module
      • purge_ram_cache()
      • purge_ssd_cache()
      • du()
      • reset_ramdisk()
      • launch_cache_synchronizers()
      • initialize_caches()
      • cache_test()
    • neurotools.jobs.ndecorator module
      • listit()
      • tupleit()
      • sanitize()
      • summarize_function()
      • argument_signature()
      • print_signature()
      • timed()
      • clear_memoized()
      • memoize()
      • unwrap()
    • neurotools.jobs.parallel module
      • parmap()
      • pararraymap()
      • parmap_dict()
      • function_fingerprint()
      • eval_from_cached()
      • parallel_indirect_wrapper()
      • parallel_cached_wrapper()
      • parimap()
      • close_pool()
      • reset_pool()
      • parallel_error_handling()
      • limit_cores()
      • parcontext()
  • Module contents
• neurotools.linalg package
  • Submodules
    • neurotools.linalg.arguments module
      • issquare()
      • iscolumn()
      • isrow()
      • asrow()
      • ascolumn()
      • assquare()
      • assertsquare()
      • assertcolumn()
      • assertrow()
      • assertvector()
      • asvector()
      • scalar()
      • assertfinite()
      • assertreal()
      • assertfinitereal()
      • assertshape()
    • neurotools.linalg.matrix module
      • triu_elements()
      • tril_elements()
      • column()
      • row()
      • rcond()
      • check_finite_real()
      • check_covmat()
      • check_covmat_fast()
      • real_eig()
      • psd_eig()
      • logdet()
      • solt()
      • rsolt()
      • rsolve()
      • qf()
      • abserr()
      • errmx()
      • cholupdate()
      • cholupdate_eye()
      • cartesian_product()
      • nearPDHigham()
      • nearPSDRebonatoJackel()
      • cinv()
      • csolve()
      • wheremax()
      • wheremin()
      • reglstsq()
      • Ldistance()
      • Llasso()
      • rmatrix()
      • ldiv()
      • rdiv()
      • autopredict()
      • kronsum()
      • top_v()
      • normedcovariance()
      • maxeig()
      • selector_matrix()
      • laplace_kernel()
      • match_covariance()
      • get_whitener()
    • neurotools.linalg.operators module
      • adjacency1D()
      • laplacian1D_circular()
      • adjacency2D()
      • laplacian2D()
      • adjacency2D_circular()
      • adjacency2d_rotational()
      • laplacian1D()
      • laplacianFT1D()
      • wienerFT1D()
      • diffuseFT1D()
      • flatcov()
      • delta()
      • dirichlet_derivative_operator()
      • neumann_derivative_operator()
      • circular_derivative_operator()
      • circular_derivative_fourier()
      • truncated_derivative_operator()
      • terminated_derivative_operator()
      • truncated_derivative()
      • pad1up()
      • spaced_derivative_operator()
      • integrator()
      • covfrom()
      • oucov()
      • gaussian1DblurOperator()
      • circular1DblurOperator()
      • separable_guassian_blur()
      • gaussian2DblurOperator()
      • cosine_kernel()
      • log_cosine_basis()
      • make_cosine_basis()
  • Module contents
• neurotools.obsolete package
  • Subpackages
    • neurotools.obsolete.encoding package
      • Submodules
      • Module contents
    • neurotools.obsolete.gpu package
      • Subpackages
      • Module contents
    • neurotools.obsolete.models package
      • Submodules
      • Module contents
  • Submodules
    • neurotools.obsolete.opto module
      • opto_get_events_passive()
      • opto_get_all_lfp_quick()
      • opto_get_map()
      • opto_get_laser()
      • opto_get_lfp()
      • opto_get_lfp_filtered()
      • opto_get_all_lfp_analytic_quick()
      • opto_get_all_lfp_analytic_quick_parallel()
      • opto_get_lfp_analytic()
      • opto_get_Fs()
  • Module contents
• neurotools.signal package
  • Submodules
    • neurotools.signal.coherence module
      • morlet_population_synchrony_spectrum()
      • population_eigencoherence()
      • population_coherence_matrix()
      • multitaper_coherence()
      • sliding_multitaper_coherence()
      • sliding_multitaper_coherence_parallel()
      • coherence_pvalue()
      • multitaper_multitrial_coherence()
    • neurotools.signal.conv module
      • reflect2D()
      • reflect2D_1()
      • mirror2d()
      • convolve2dct()
      • separable2d()
      • gausskern2d()
      • gausskern1d()
    • neurotools.signal.morlet module
      • normalized_morlet()
      • prepare_wavelet_fft_basis()
      • fft_cwt()
      • geometric_window()
      • logfreqs()
      • prepare_wavelet_fft_basis_logspace()
      • population_synchrony_spectrum()
      • fft_cwt_transposed()
      • fft_cwt_transposed_logspaced()
      • convenient_morlet()
      • get_gentle_morlets_ft()
      • gentle_morlet_psd()
    • neurotools.signal.multitaper module
      • dpss_cached()
      • spectrum()
      • population_coherence()
      • population_eigencoherence()
    • neurotools.signal.phase module
      • amp()
      • ifreq()
      • unwrapped_angle()
      • pdiff()
      • rewrap()
      • pghilbert()
      • unwrap()
      • ang()
      • fix_derivative()
      • phase_rotate()
      • randband()
      • phase_randomize()
      • phase_randomize_from_amplitudes()
      • sign_preserving_amplitude_demodulate()
    • neurotools.signal.savitskygolay module
      • SGOrd()
      • SGKern()
      • SGKernV()
      • SGKernA()
      • SGKernJ()
      • SGfilt()
      • SGfiltV()
      • SGfiltA()
      • SGfiltJ()
      • SGsmooth()
      • SGdifferentiate()
      • SGaccelerate()
      • SGjerk()
    • neurotools.signal.sde module
      • sample_wiener_process()
      • sample_ou_process()
  • Module contents
    • gaussian_kernel()
    • gaussian_smooth()
    • circular_gaussian_smooth()
    • mirrored_gaussian_smooth()
    • circular_gaussian_smooth_2D()
    • nonnegative_bandpass_filter()
    • bandpass_filter()
    • box_filter()
    • median_filter()
    • percentile_filter()
    • variance_filter()
    • stats_block()
    • mean_block()
    • var_block()
    • median_block()
    • linfilter()
    • padout()
    • padin()
    • estimate_padding()
    • lowpass_filter()
    • highpass_filter()
    • fdiff()
    • arenear()
    • aresafe()
    • get_edges()
    • set_edges()
    • remove_gaps()
    • remove_short()
    • pieces()
    • interpolate_NaN()
    • interpolate_NaN_quadratic()
    • killSpikes()
    • drop_nonfinite()
    • virtual_reference_line_noise_removal()
    • band_stop_line_noise_removal()
    • local_peak_within()
    • local_maxima()
    • local_minima()
    • peak_within()
    • interpmax1d()
    • peak_fwhm()
    • PeakInfoResult
      • PeakInfoResult.index
      • PeakInfoResult.height
      • PeakInfoResult.inflection_below
      • PeakInfoResult.inflection_above
      • PeakInfoResult.trough_below
      • PeakInfoResult.trough_above
      • PeakInfoResult.qfit
    • quadratic_peakinfo()
    • unitscale()
    • topercentiles()
    • zeromean()
    • zeromedian()
    • zscore()
    • unitsum()
    • gaussianize()
    • uniformize()
    • normalize()
    • invert_uniformize()
    • deltaovermean()
    • span()
    • mintomax()
    • unit_length()
    • spaced_derivative()
    • upsample()
    • nice_interp()
    • autocorrelation()
    • fftacorr1d()
    • zgrid()
    • make_lagged()
    • linear_cosine_basis()
    • circular_cosine_basis()
• neurotools.spatial package
  • Submodules
    • neurotools.spatial.array module
      • array_average_amplitude()
      • array_kuramoto()
      • array_synchrony()
      • array_kuramoto_standard_deviation()
      • array_synchrony_standard_deviation()
      • array_phase_gradient()
      • array_count_centers()
      • array_count_critical()
      • array_phasegradient_local()
      • array_phasegradient_planar()
      • array_phasegradient_magnitude_sigma()
      • array_phasegradient_magnitude_cv()
      • array_phasegradient_pgd_threshold()
      • array_wavelength_pgd_threshold()
      • array_wavelength_local_pgd_threshold()
      • array_speed_pgd_threshold()
      • array_speed_local()
      • array_wavelength_local()
      • array_wavelength_planar()
      • array_synchrony_pgd()
      • array_synchrony_pgd_standard_deviation()
      • array_kuramoto_pgd()
      • array_kuramoto_pgd_standard_deviation()
      • trim_array()
      • trim_array_as_if()
      • pack_array_data()
    • neurotools.spatial.dct module
      • get_mask_antialiased()
      • get_mask()
      • dct_cut()
      • outer_complex()
      • dct_cut_antialias()
      • dct_cut_downsampled()
      • dct_upsample()
      • iterated_upsample()
      • dct_upsample_notrim()
    • neurotools.spatial.distance module
      • get_pair_distance()
      • distance_angular_deviation()
      • get_averaged_angular_distance()
      • get_length_constant_trial()
      • get_average_synchrony_length_constant_parallel()
      • synchrony_length_constant_areas_summary()
    • neurotools.spatial.fftzeros module
      • plot_phase_gradient()
      • plot_phase_direction()
      • dPhidx()
      • dPhidy()
      • get_phase_gradient_as_complex()
      • getpeaks2d()
      • coalesce()
      • coalesce_points()
      • find_critical_points()
      • plot_critical_points()
      • find_critical_potential_points()
      • grad()
      • quickgrad()
      • getp()
      • get_critical_spectra()
      • plot_critical_spectra()
      • cut_array_data()
      • mirror2D()
    • neurotools.spatial.geometry module
      • p2z()
      • z2p()
      • polar_smooth_contour()
      • convex_hull()
      • convex_hull_from_mask()
      • resample_convex_hull()
      • in_hull()
    • neurotools.spatial.kernels module
      • laplace_kernel()
      • laplacian()
      • gaussian_2D_kernel()
      • absorbing_gaussian()
      • absorbing_laplacian()
      • magicsharp()
      • magickernel()
      • continuum_kernel()
      • log_spline_basis()
      • cosine_kernel()
      • log_cosine_basis()
      • make_cosine_basis()
      • exponential_basis()
      • diffusion_basis()
      • iterative_orthogonalize_basis()
    • neurotools.spatial.masking module
      • as_mask()
      • mask_to_points()
      • extend_mask()
      • pgrid()
      • nan_mask()
      • maskout()
      • trim_mask()
      • mask_crop()
      • to_image()
    • neurotools.spatial.peaks module
      • blurkernel()
      • blurkernel2D()
      • conv()
      • blur()
      • findpeaks()
      • dx_op()
      • hessian_2D()
      • circle_mask()
      • fft_upsample_2D()
      • interpolate_peaks()
      • bin_spikes()
      • get_peak_density()
      • brute_force_local_2d_maxima()
    • neurotools.spatial.phase module
      • population_kuramoto()
      • population_synchrony()
      • population_polar_std()
      • population_average_amplitude()
      • population_signal_dispersion()
      • population_signal_concentration()
      • population_signal_precision()
      • population_signal_phase_dispersion()
      • population_signal_phase_std()
      • population_signal_amplitude_std()
      • population_signal_amplitude_dispersion()
      • population_signal_phase_precision()
      • population_signal_amplitude_precision()
      • population_signal_description()
      • population_synchrony_linear()
      • population_phase_coherence()
      • analytic_signal_coherence()
      • population_sliding_signal_coherence()
      • sliding_population_signal_coherence()
      • population_normalized_sliding_signal_coherence()
      • population_phase_relative_sliding_kuramoto()
      • population_median_phase_velocity()
      • population_median_frequency()
    • neurotools.spatial.points module
      • p2c()
      • c2p()
      • to_xypoint()
      • closest()
      • pair_neighbors()
      • paired_distances()
      • assign_to_regions()
      • collect_in_regions()
      • gaussian_from_points()
      • collect_gaussians()
    • neurotools.spatial.spiking module
      • interp_bin()
    • neurotools.spatial.triangulation module
      • z2xy()
      • uniquerow()
      • trianglesToEdges()
      • edgesNearby()
      • coalesce()
      • plot_edges()
      • plot_triangles()
      • mergeNearby()
  • Module contents
• neurotools.spikes package
  • Submodules
    • neurotools.spikes.convolutional module
      • ccor()
      • ccm()
      • blockccm()
      • sta()
      • blocksta()
      • reconstruct()
      • cspect()
      • cspectm()
      • spike_lfp_filters()
      • spectreconstruct()
      • create_spectral_model()
      • construct_lowpass_operator()
      • autocorrelation_bayes()
    • neurotools.spikes.ppc module
      • phase_randomize()
      • fftppc_biased()
      • fftppc()
      • fftppc_biased_multitaper()
      • fftppc_multitaper()
      • discard_spikes_closer_than_delta()
      • pairwise_phase_consistancy()
      • estimate_bias_in_uncorrected_ppc()
      • phase_randomized_bias_correction()
      • ppc_chance_level()
      • ppc_phase_randomize_chance_level_sample()
    • neurotools.spikes.sta module
      • get_snips()
      • triggered_average()
      • get_triggered_stats()
      • fftsta()
    • neurotools.spikes.waveform module
      • realign()
      • getFWHM()
      • getPVT()
      • getWAHP()
      • getPT()
      • getPTHW()
      • getPHP()
      • normalized_waveform()
      • is_thin()
      • is_thin_pvt()
      • process()
  • Module contents
    • pp_xcorr()
    • txcorr()
    • pack_cross_correlation_matrix()
    • cut_spikes()
    • times_to_raster()
    • bin_spikes_raster()
    • bin_spike_times()
• neurotools.stats package
  • Submodules
    • neurotools.stats.circular module
      • logpolar_gaussian()
      • complex_gaussian()
      • logpolar_stats()
      • abspolar_stats()
      • squared_first_circular_moment()
      • fit_vonmises()
      • wrapped_circular_linear_error()
      • asunit()
      • circvar()
      • circwrap()
      • circmce()
      • circdelta()
      • circmean()
      • circcenter()
      • circcorr()
      • circabsdelta()
      • degrees_to_survey_format()
    • neurotools.stats.covalign module
      • keeprank()
      • expected_intersection_rank1()
      • expected_intersection()
      • expected_intersection_enormed()
      • expected_intersection_enormed_chance()
      • rebuild_unit_quality_caches()
      • orthnormedcovariance()
      • get_orthogonal_alignment()
      • alignment_angle()
      • sample_alignment_angle()
      • sample_alignment_self()
      • sample_alignment_cross()
      • sample_alignment_complement()
      • alignment_angle_unnormalized()
      • alignment_angle_normalized()
      • sample_alignment_angle_unnormalized()
      • sample_alignment_angle_normalized()
      • sample_alignment_self_unnormalized()
      • sample_alignment_self_unnormalized_nounit()
      • sample_alignment_self_normalized()
      • sample_alignment_cross_normalized()
      • sample_alignment_complement_normalized()
      • new_alignment_normalized()
    • neurotools.stats.density module
      • kdepeak()
      • knn_1d_density()
      • adaptive_density_grid()
      • gridhist()
    • neurotools.stats.distributions module
      • poisson_logpdf()
      • poisson_pdf()
      • gaussian_logpdf()
      • gaussian_pdf()
      • explogpdf()
      • sample_categorical()
    • neurotools.stats.fastkde module
      • fast_kde()
      • image_cov()
    • neurotools.stats.gaussian module
      • gaussian_quadrature()
      • gaussian_quadrature_logarithmic()
      • Gaussian
      • MVG_check()
      • MVG_logPDF()
      • MVG_PDF()
      • MVG_sample()
      • MVG_multiply()
      • MVG_multiply_C()
      • MVG_divide()
      • MVG_projection()
      • MVG_entropy()
      • MVG_DKL()
      • MVG_DKL_CP()
      • MVG_conditional()
      • MVG_kalman()
      • MVG_kalman_P_inverseA()
      • MVG_kalman_joint()
      • MVG_kalman_joint_P()
    • neurotools.stats.glm module
      • GLMPenaltyPoisson()
      • sexp()
      • sigmoid()
      • GLMPenaltyBernoulli()
      • GLMPenaltyL2()
      • ppglmfit()
      • fitGLM()
      • crossvalidatedAUC()
      • gradientglmfit()
      • cosine_kernel()
      • log_cosine_basis()
      • make_cosine_basis()
      • numeric_grad()
      • numeric_hess()
    • neurotools.stats.gridsearch module
      • grid_search()
    • neurotools.stats.hmm module
      • poisson_parameter_guess()
      • poisson_baum_welch()
      • viterbi()
      • viterbi_log()
      • hasNaN()
      • poisson_viterbi_state_infer()
      • forward_backward()
      • jump()
      • sample()
      • log_likelihood()
      • baum_welch()
      • forward_abstract()
      • backward_abstract()
      • forward_backward_abstract()
      • DiffusionGaussian
      • LogGaussianCoxApproximator
      • LogGaussianCoxModel
      • GaussianCoxApproximator
      • GaussianCoxModel
      • ChisquareCoxApproximator
      • ChisquareCoxModel
      • BernoulliObservationApproximator
      • BernoulliObservationModel
      • TruncatedLogGaussianCoxApproximator
      • TruncatedLogGaussianCoxModel
      • MVGaussian
      • MVGUpdate
      • lgcp_observation_minimizer()
      • MVLogGaussianCox
      • OUGaussian
      • MVGOUUpdate
      • PoissonObservationApproximator
      • PoissonObservationModel
      • TruncatedPoissonObservationApproximator
      • TruncatedPoissonObservationModel
    • neurotools.stats.information module
      • discrete
      • poisson_entropy_nats()
      • betapr()
      • beta_regularized_histogram_mutual_information()
      • JointCategoricalDistribution
      • joint()
      • dirichlet_density
    • neurotools.stats.kalman module
      • multiply_gaussian()
      • kalman_forward()
      • kalman_backward()
      • kalman_measure()
      • kalman_smooth()
    • neurotools.stats.mcint module
      • monte_carlo_expectation()
      • monte_carlo_moments()
    • neurotools.stats.minimize module
      • FailureError
      • minimize_retry()
    • neurotools.stats.mixtures module
      • two_class_poisson_mixture_model()
    • neurotools.stats.modefind module
      • modefind()
      • logmodeplot()
      • logmode()
      • peakfinder5()
    • neurotools.stats.pvalues module
      • benjamini_hochberg_positive_correlations()
      • correct_pvalues_positive_dependent()
      • correct_pvalues()
      • bootstrap_statistic()
      • bootstrap_statistic_two_sided()
      • bootstrap_median()
      • bootstrap_mean()
      • bootstrap_compare_statistic_two_sided()
      • bootstrap_compare_statistic_two_sided_parallel()
      • bootstrap_compare_median()
      • bootstrap_compare_mean()
      • bootstrap_in_blocks()
      • nancorrect()
      • atac()
    • neurotools.stats.regressions module
      • damped_cosine()
      • weighted_least_squares()
      • power_law()
      • gaussian_function()
      • half_gaussian_function()
      • exponential_decay()
      • robust_line()
      • cubic_spline_regression()
      • CircregressResult
      • circregress()
    • neurotools.stats.shuffleL2explore module
      • hess()
      • MSE()
      • error_covariance()
      • reglstq_moments()
      • reglstsq_MSE()
      • regroup()
      • ungroup()
      • scov()
      • xy_moments()
      • reglstq_xy()
      • group_moments()
      • group_mse()
      • group_error_covariance()
      • get_whiten()
      • group_R2_matrix()
      • regsweep_r2()
      • regsweep_MSE()
      • shuffle_variable()
      • adaptive_shuffle()
      • AdaptiveShuffleResult
      • adaptive_shuffle_pvalue()
      • joint_reglstsq_MSE()
      • best_rho()
      • joint_best_rho_gradient()
      • lfit()
      • leave_one_out()
      • linear_regression_shuffle()
      • beta()
      • binomial()
      • bytes()
      • chisquare()
      • choice()
      • dirichlet()
      • exponential()
      • f()
      • gamma()
      • geometric()
      • get_state()
      • gumbel()
      • hypergeometric()
      • laplace()
      • logistic()
      • lognormal()
      • logseries()
      • multinomial()
      • multivariate_normal()
      • negative_binomial()
      • noncentral_chisquare()
      • noncentral_f()
      • normal()
      • pareto()
      • permutation()
      • poisson()
      • power()
      • rand()
      • randint()
      • randn()
      • random()
      • random_integers()
      • random_sample()
      • rayleigh()
      • set_state()
      • shuffle()
      • standard_cauchy()
      • standard_exponential()
      • standard_gamma()
      • standard_normal()
      • standard_t()
      • triangular()
      • uniform()
      • vonmises()
      • wald()
      • weibull()
      • zipf()
    • neurotools.stats.tests module
      • two_tailed_sampled_test()
      • ZTestResult
      • ztest_from_moments()
      • WeightedTtestResult
      • weighted_ttest_1samp()
      • beta_propotion_test()
      • cohen_d()
  • Module contents
    • partition_data()
    • partition_trials_for_crossvalidation()
    • add_constant()
    • trial_crossvalidated_least_squares()
    • partition_data_for_crossvalidation()
    • block_shuffle()
    • crossvalidated_least_squares()
    • fraction_explained_deviance()
    • nrmse()
    • weighted_avg_and_std()
    • print_stats()
    • outliers()
    • reject_outliers()
    • Description
      • Description.short()
    • glmfit()
    • pca()
    • covariance()
    • get_factor_analysis()
    • project_factors()
    • predict_latent()
    • factor_predict()
    • nanrankdata()
    • mean_confidence_interval()
    • minmax()
• neurotools.util package
  • Submodules
    • neurotools.util.array module
      • lmap()
      • slist()
      • amap()
      • lap()
      • aap()
      • sls()
      • arraymap()
      • find()
      • ezip()
      • asiterable()
      • invert_permutation()
      • ndargmax()
      • complex_to_nan()
      • verify_axes()
      • axes_complement()
      • reslice()
      • make_rebroadcast_slice()
      • deep_tuple()
      • deep_map()
      • to_indices()
      • onehot()
      • zeroslike()
      • oneslike()
      • split_into_groups()
      • maybe_integer()
      • widths_to_edges()
      • widths_to_limits()
      • centers()
      • widths_to_centers()
      • extract()
      • binspace()
      • binto()
      • remove_nonincreasing()
      • remove_nans()
      • allclose_recursive()
    • neurotools.util.functions module
      • slog()
      • sexp()
      • sigmoid()
      • inversesigmoid()
      • dsigmoid()
      • g()
      • f()
      • f1()
      • f2()
      • npdf()
      • log_factorial()
    • neurotools.util.getfftw module
      • ftwthr()
    • neurotools.util.hdfmat module
      • getHDFvalue()
      • getHDF()
      • hdf2dict()
      • printmatHDF5()
      • recursive_printmatHDF5()
      • matversion()
      • matstrip()
      • mat5todict()
    • neurotools.util.pandas module
      • get()
      • is_empty_col()
      • from_hierarchical_columns()
      • to_ndarray()
      • camelcase_columns()
      • snakecase_columns()
      • ndarray_from_mat()
      • read_mat()
      • to_mat()
      • conform()
      • add_column_from_dict()
      • dfhcat()
      • dfvcat()
      • check_column_signs()
    • neurotools.util.string module
      • hcat()
      • wordwrap()
      • incolumns()
      • percent()
      • shortscientific()
      • eformat()
      • v2str()
      • v2str_long()
      • nicetable()
      • isInt()
      • camel_to_snake()
      • snake_to_camel()
    • neurotools.util.system module
      • execfile()
      • query_yes_no()
    • neurotools.util.time module
      • current_milli_time()
      • today()
      • now()
      • tic()
      • toc()
      • waitfor()
      • outputlimiter()
    • neurotools.util.tools module
      • varexists()
      • nowarn()
      • okwarn()
      • dowarn()
      • warn()
      • debug()
      • wait()
      • matlab()
      • history()
      • p2c()
      • c2p()
      • emitter
      • piper
      • globalize()
      • exists()
      • metaloadmat()
      • find_all_extension()
      • setinrange()
      • mapdict()
      • getdict()
      • ensure_dir()
      • getsize()
      • saveContext()
      • clear()
      • restoreContext()
      • getVariable()
      • TolerantDict
      • yank()
  • Module contents

Submodules

• neurotools.nlab module
  • random()
  • beta()
  • binomial()
  • chisquare()
  • choice()
  • dirichlet()
  • exponential()
  • f()
  • gamma()
  • geometric()
  • get_state()
  • gumbel()
  • hypergeometric()
  • laplace()
  • logistic()
  • lognormal()
  • logseries()
  • multinomial()
  • multivariate_normal()
  • negative_binomial()
  • noncentral_chisquare()
  • noncentral_f()
  • normal()
  • pareto()
  • permutation()
  • poisson()
  • power()
  • rand()
  • randint()
  • randn()
  • random_integers()
  • random_sample()
  • rayleigh()
  • set_state()
  • shuffle()
  • standard_cauchy()
  • standard_exponential()
  • standard_gamma()
  • standard_normal()
  • standard_t()
  • triangular()
  • uniform()
  • vonmises()
  • wald()
  • weibull()
  • zipf()

Module contents