Updates for v2.0.0

README.md

@@ -8,7 +8,7 @@
 [![Supported Python Versions](https://img.shields.io/pypi/pyversions/neurodsp.svg)](https://pypi.python.org/pypi/neurodsp/)
 [![Binder](https://mybinder.org/badge.svg)](https://mybinder.org/v2/gh/neurodsp-tools/neurodsp/master)
 
-A package of tools to process, analyze, and simulate neural recordings as individual voltage time series, with specific focus on time and frequency domain analyses.
+A package of tools to process, analyze, and simulate neural time series, with specific focus on time and frequency domain analyses.
 
 ## Documentation
 
@@ -64,15 +64,14 @@ Please use the [Github issue tracker](https://github.com/neurodsp-tools/neurodsp
 
 ## Modules
 
-NeuroDSP includes the following modules:
+Available modules in NeuroDSP include:
 
 - ```filt``` : Filter data with bandpass, highpass, lowpass, or notch filters
 - ```burst``` : Detect bursting oscillations in neural signals
-- ```laggedcoherence``` : Estimate rhythmicity using the lagged coherence measure
+- ```rhythm``` : Find and analyze rhythmic and recurrent patterns in time series
 - ```spectral``` : Compute spectral domain features such as power spectra
-- ```swm``` : Identify recurrent patterns in signals using sliding window matching
 - ```timefrequency``` : Estimate instantaneous measures of oscillatory activity
-- ```sim``` : Simulate periodic and aperiodic signal components
+- ```sim``` : Simulate time series, including periodic and aperiodic signal components
 - ```plts``` : Plotting functions
 
 ## Contribute

doc/Makefile

@@ -29,6 +29,7 @@ clean:
 ## make install:
 # Build the html site, and push it to gh-pages branch of repo to deploy
 install:
+	make clean
 	rm -rf _build/doctrees _build/tmp_html
 	# Clone, specifically, the gh-pages branch:
 	#   --no-checkout just fetches the root folder without content

doc/api.rst

@@ -16,79 +16,170 @@ Table of Contents
 Filtering
 ---------
 
-.. currentmodule:: neurodsp.filt
+Functions and utilities for filtering time series.
 
-Design & Apply Filters
-~~~~~~~~~~~~~~~~~~~~~~
+General Filter Function
+~~~~~~~~~~~~~~~~~~~~~~~
+
+.. currentmodule:: neurodsp.filt.filter
 
 .. autosummary::
   :toctree: generated/
 
   filter_signal
+
+
+FIR Filters
+~~~~~~~~~~~
+
+.. currentmodule:: neurodsp.filt.fir
+
+.. autosummary::
+  :toctree: generated/
+
   filter_signal_fir
-  filter_signal_iir
   design_fir_filter
+
+IIR Filters
+~~~~~~~~~~~
+
+.. currentmodule:: neurodsp.filt.iir
+
+.. autosummary::
+  :toctree: generated/
+
+  filter_signal_iir
   design_iir_filter
 
-Filter Properties
-~~~~~~~~~~~~~~~~~
+Check Filter Properties
+~~~~~~~~~~~~~~~~~~~~~~~
+
+.. currentmodule:: neurodsp.filt.checks
 
 .. autosummary::
   :toctree: generated/
 
   check_filter_definition
   check_filter_properties
+
+Filter Utilities
+~~~~~~~~~~~~~~~~
+
+.. currentmodule:: neurodsp.filt.utils
+
+.. autosummary::
+  :toctree: generated/
+
   compute_frequency_response
   compute_pass_band
-  compute_trans_band
+  compute_transition_band
   compute_nyquist
+  remove_filter_edges
 
 Time-Frequency analysis
 -----------------------
 
-.. currentmodule:: neurodsp.timefrequency
+Functions and utilities for time-frequency analyses.
+
+Hilbert Methods
+~~~~~~~~~~~~~~~
+
+.. currentmodule:: neurodsp.timefrequency.hilbert
 
 .. autosummary::
   :toctree: generated/
 
+  robust_hilbert
   phase_by_time
   amp_by_time
   freq_by_time
 
+Wavelet Methods
+~~~~~~~~~~~~~~~
+
+.. currentmodule:: neurodsp.timefrequency.wavelets
+
+.. autosummary::
+  :toctree: generated/
+
+  morlet_transform
+  morlet_convolve
+
 Spectral analysis
 -----------------
 
-.. currentmodule:: neurodsp.spectral
+Functions and utilities for spectral analyses.
+
+Spectral Power Measures
+~~~~~~~~~~~~~~~~~~~~~~~
+
+.. currentmodule:: neurodsp.spectral.spectral
 
 .. autosummary::
    :toctree: generated/
 
-   compute_spectrum
-   compute_scv
-   compute_scv_rs
-   spectral_hist
-   morlet_transform
-   morlet_convolve
-   rotate_powerlaw
+  compute_spectrum
+  compute_spectrum_welch
+  compute_spectrum_wavelet
+  compute_spectrum_medfilt
 
-Rhythmic analysis
------------------
+Spectral Variance Measures
+~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+.. currentmodule:: neurodsp.spectral.spectral
+
+.. autosummary::
+   :toctree: generated/
+
+  compute_scv
+  compute_scv_rs
+  compute_spectral_hist
+
+Spectral Utilities
+~~~~~~~~~~~~~~~~~~
+
+.. currentmodule:: neurodsp.spectral.utils
+
+.. autosummary::
+   :toctree: generated/
+
+  trim_spectrum
+  rotate_powerlaw
 
 Burst Detection
-~~~~~~~~~~~~~~~
+---------------
+
+Functions and utilities for detection bursts in time series.
+
+Burst Detection Algorithms
+~~~~~~~~~~~~~~~~~~~~~~~~~~
 
 .. currentmodule:: neurodsp.burst
 
 .. autosummary::
   :toctree: generated/
 
   detect_bursts_dual_threshold
+
+Burst Utilities
+~~~~~~~~~~~~~~~
+
+.. currentmodule:: neurodsp.burst.utils
+
+.. autosummary::
+  :toctree: generated/
+
   compute_burst_stats
 
+Rhythm Analysis
+---------------
+
+Functions and utilities for finding and analyzing rhythmic and recurring patterns in time series.
+
 Sliding Window Matching
 ~~~~~~~~~~~~~~~~~~~~~~~
 
-.. currentmodule:: neurodsp.swm
+.. currentmodule:: neurodsp.rhythm.swm
 
 .. autosummary::
   :toctree: generated/
@@ -98,47 +189,115 @@ Sliding Window Matching
 Lagged Coherence
 ~~~~~~~~~~~~~~~~
 
-.. currentmodule:: neurodsp.laggedcoherence
+.. currentmodule:: neurodsp.rhythm.lc
 
 .. autosummary::
   :toctree: generated/
 
   lagged_coherence
 
-Signal simulation
------------------
-
-.. currentmodule:: neurodsp.sim
+Simulations
+-----------
 
-.. autosummary::
-  :toctree: generated/
+Functions and utilities for simulating time series.
 
 Periodic Signals
 ~~~~~~~~~~~~~~~~
 
+.. currentmodule:: neurodsp.sim.periodic
+
 .. autosummary::
   :toctree: generated/
 
-  sim_oscillator
-  sim_bursty_oscillator
-  sim_jittered_oscillator
+  sim_oscillation
+  sim_bursty_oscillation
+  sim_bursty_oscillation_features
+  sim_jittered_oscillation
 
 Aperiodic Signals
 ~~~~~~~~~~~~~~~~~
 
+.. currentmodule:: neurodsp.sim.aperiodic
+
 .. autosummary::
   :toctree: generated/
 
-  sim_filtered_noise
-  sim_synaptic_noise
-  sim_ou_process
-  sim_variable_powerlaw
+  sim_powerlaw
+  sim_poisson_pop
+  sim_synaptic_current
+  sim_random_walk
+
+Transients
+~~~~~~~~~~
+
+.. currentmodule:: neurodsp.sim.transients
+
+.. autosummary::
+  :toctree: generated/
+
+  sim_osc_cycle
+  sim_synaptic_kernel
 
 Combined Signals
 ~~~~~~~~~~~~~~~~
 
+.. currentmodule:: neurodsp.sim.combined
+
+.. autosummary::
+  :toctree: generated/
+
+  sim_combined
+
+Plots
+-----
+
+Functions for plotting time series and analysis outputs.
+
+Time Series
+~~~~~~~~~~~
+
+.. currentmodule:: neurodsp.plts.time_series
+
+.. autosummary::
+  :toctree: generated/
+
+  plot_time_series
+  plot_instantaneous_measure
+  plot_bursts
+
+Spectral
+~~~~~~~~
+
+.. currentmodule:: neurodsp.plts.spectral
+
+.. autosummary::
+  :toctree: generated/
+
+  plot_power_spectra
+  plot_scv
+  plot_scv_rs_lines
+  plot_scv_rs_matrix
+  plot_spectral_hist
+
+Filter
+~~~~~~
+
+.. currentmodule:: neurodsp.plts.filt
+
+.. autosummary::
+  :toctree: generated/
+
+  plot_filter_properties
+  plot_frequency_response
+  plot_impulse_response
+
+Rhythm
+~~~~~~
+
+.. currentmodule:: neurodsp.plts.rhythm
+
 .. autosummary::
   :toctree: generated/
 
-  sim_noisy_oscillator
-  sim_noisy_bursty_oscillator
+  plot_swm_pattern
+  plot_lagged_coherence