Merge pull request #336 from neurodsp-tools/sim2

[WIP] - Simulation updates

doc/api.rst

@@ -326,6 +326,7 @@ Multiple Signals
 
     sim_multiple
     sim_across_values
+    sim_multi_across_values
     sim_from_sampler
 
 Simulation Parameters
@@ -370,20 +371,30 @@ The following objects can be used to manage groups of simulated signals:
     :toctree: generated/
 
     Simulations
-    SampledSimulations
+    VariableSimulations
     MultiSimulations
 
-Utilities
-~~~~~~~~~
+Modulate Signals
+~~~~~~~~~~~~~~~~
 
-.. currentmodule:: neurodsp.sim.utils
+.. currentmodule:: neurodsp.sim.modulate
 .. autosummary::
     :toctree: generated/
 
     rotate_spectrum
     rotate_timeseries
     modulate_signal
 
+I/O
+~~~
+
+.. currentmodule:: neurodsp.sim.io
+.. autosummary::
+    :toctree: generated/
+
+    save_sims
+    load_sims
+
 Random Seed
 ~~~~~~~~~~~
 

neurodsp/filt/filter.py

@@ -1,7 +1,5 @@
 """Filter time series."""
 
-from warnings import warn
-
 from neurodsp.filt.fir import filter_signal_fir
 from neurodsp.filt.iir import filter_signal_iir
 from neurodsp.utils.checks import check_param_options

neurodsp/sim/__init__.py

@@ -9,4 +9,4 @@
 from .cycles import sim_cycle
 from .transients import sim_synaptic_kernel, sim_action_potential
 from .combined import sim_combined, sim_peak_oscillation, sim_modulated_signal, sim_combined_peak
-from .multi import sim_multiple, sim_across_values, sim_from_sampler
+from .multi import sim_multiple, sim_across_values, sim_multi_across_values, sim_from_sampler

neurodsp/sim/aperiodic.py

@@ -7,12 +7,12 @@
 from neurodsp.filt import filter_signal, infer_passtype
 from neurodsp.filt.fir import compute_filter_length
 from neurodsp.filt.checks import check_filter_definition
-from neurodsp.utils import remove_nans
+from neurodsp.utils.norm import normalize_sig
+from neurodsp.utils.outliers import remove_nans
+from neurodsp.utils.decorators import normalize
 from neurodsp.utils.checks import check_param_range
 from neurodsp.utils.data import create_times, compute_nsamples
-from neurodsp.utils.decorators import normalize
-from neurodsp.utils.norm import normalize_sig
-from neurodsp.sim.utils import rotate_timeseries
+from neurodsp.sim.modulate import rotate_timeseries
 from neurodsp.sim.transients import sim_synaptic_kernel
 
 ###################################################################################################

neurodsp/sim/combined.py

@@ -6,9 +6,9 @@
 from scipy.linalg import norm
 
 from neurodsp.sim.info import get_sim_func
-from neurodsp.sim.utils import modulate_signal
-from neurodsp.utils.decorators import normalize
+from neurodsp.sim.modulate import modulate_signal
 from neurodsp.utils.data import create_times
+from neurodsp.utils.decorators import normalize
 
 ###################################################################################################
 ###################################################################################################
@@ -63,8 +63,7 @@ def sim_combined(n_seconds, fs, components, component_variances=1):
         raise ValueError('Signal components and variances lengths do not match.')
 
     # Collect the sim function to use, and repeat variance if is single number
-    components = {(get_sim_func(name) if isinstance(name, str) else name) : params \
-                   for name, params in components.items()}
+    components = {get_sim_func(name) : params for name, params in components.items()}
     variances = repeat(component_variances) if \
         isinstance(component_variances, (int, float, np.number)) else iter(component_variances)
 

neurodsp/sim/generators.py

@@ -0,0 +1,77 @@
+"""Generator simulation functions."""
+
+from collections.abc import Sized
+
+from neurodsp.sim.info import get_sim_func
+from neurodsp.utils.core import counter
+
+###################################################################################################
+###################################################################################################
+
+def sig_yielder(function, params, n_sims):
+    """Generator to yield simulated signals from a given simulation function and parameters.
+
+    Parameters
+    ----------
+    function : str or callable
+        Function to create the simulated time series.
+        If string, should be the name of the desired simulation function.
+    params : dict
+        The parameters for the simulated signal, passed into `function`.
+    n_sims : int, optional
+        Number of simulations to set as the max.
+        If None, creates an infinite generator.
+
+    Yields
+    ------
+    sig : 1d array
+        Simulated time series.
+    """
+
+    function = get_sim_func(function)
+    for _ in counter(n_sims):
+        yield function(**params)
+
+
+def sig_sampler(function, params, return_params=False, n_sims=None):
+    """Generator to yield simulated signals from a parameter sampler.
+
+    Parameters
+    ----------
+    function : str or callable
+        Function to create the simulated time series.
+        If string, should be the name of the desired simulation function.
+    params : iterable
+        The parameters for the simulated signal, passed into `function`.
+    return_params : bool, optional, default: False
+        Whether to yield the simulation parameters as well as the simulated time series.
+    n_sims : int, optional
+        Number of simulations to set as the max.
+        If None, length is defined by the length of `params`, and could be infinite.
+
+    Yields
+    ------
+    sig : 1d array
+        Simulated time series.
+    sample_params : dict
+        Simulation parameters for the yielded time series.
+        Only returned if `return_params` is True.
+    """
+
+    function = get_sim_func(function)
+
+    # If `params` has a size, and `n_sims` is defined, check that they are compatible
+    #   To do so, we first check if the iterable has a __len__ attr, and if so check values
+    if isinstance(params, Sized) and len(params) and n_sims and n_sims > len(params):
+        msg = 'Cannot simulate the requested number of sims with the given parameters.'
+        raise ValueError(msg)
+
+    for ind, sample_params in zip(counter(n_sims), params):
+
+        if return_params:
+            yield function(**sample_params), sample_params
+        else:
+            yield function(**sample_params)
+
+        if n_sims and ind >= n_sims:
+            break

neurodsp/sim/info.py

@@ -9,39 +9,40 @@
 
 SIM_MODULES = ['periodic', 'aperiodic', 'cycles', 'transients', 'combined']
 
-def get_sim_funcs(module_name):
+def get_sim_funcs(module):
     """Get the available sim functions from a specified sub-module.
 
     Parameters
     ----------
-    module_name : {'periodic', 'aperiodic', 'cycles', 'transients', 'combined'}
+    module : {'periodic', 'aperiodic', 'cycles', 'transients', 'combined'}
         Simulation sub-module to get sim functions from.
 
     Returns
     -------
-    funcs : dictionary
+    functions : dictionary
         A dictionary containing the available sim functions from the requested sub-module.
     """
 
-    check_param_options(module_name, 'module_name', SIM_MODULES)
+    check_param_options(module, 'module', SIM_MODULES)
 
     # Note: imports done within function to avoid circular import
     from neurodsp.sim import periodic, aperiodic, transients, combined, cycles
 
-    module = eval(module_name)
+    module = eval(module)
 
-    funcs = {name : func for name, func in getmembers(module, isfunction) \
-        if name[0:4] == 'sim_' and func.__module__.split('.')[-1] == module.__name__.split('.')[-1]}
+    module_name = module.__name__.split('.')[-1]
+    functions = {name : function for name, function in getmembers(module, isfunction) \
+        if name[0:4] == 'sim_' and function.__module__.split('.')[-1] == module_name}
 
-    return funcs
+    return functions
 
 
-def get_sim_names(module_name):
+def get_sim_names(module):
     """Get the names of the available sim functions from a specified sub-module.
 
     Parameters
     ----------
-    module_name : {'periodic', 'aperiodic', 'transients', 'combined'}
+    module : {'periodic', 'aperiodic', 'transients', 'combined'}
         Simulation sub-module to get sim functions from.
 
     Returns
@@ -50,33 +51,57 @@ def get_sim_names(module_name):
         The names of the available functions in the requested sub-module.
     """
 
-    return list(get_sim_funcs(module_name).keys())
+    return list(get_sim_funcs(module).keys())
 
 
-def get_sim_func(function_name, modules=SIM_MODULES):
+def get_sim_func(function, modules=SIM_MODULES):
     """Get a specified sim function.
 
     Parameters
     ----------
-    function_name : str
+    function : str or callabe
         Name of the sim function to retrieve.
+        If callable, returns input.
+        If string searches for corresponding callable sim function.
     modules : list of str, optional
         Which sim modules to look for the function in.
 
     Returns
     -------
-    func : callable
+    function : callable
         Requested sim function.
     """
 
+    if callable(function):
+        return function
+
     for module in modules:
         try:
-            func = get_sim_funcs(module)[function_name]
+            function = get_sim_funcs(module)[function]
             break
         except KeyError:
             continue
 
     else:
         raise ValueError('Requested simulation function not found.') from None
 
-    return func
+    return function
+
+
+def get_sim_func_name(function):
+    """Get the name of a simulation function.
+
+    Parameters
+    ----------
+    function : str or callabe
+        Function to get name for.
+
+    Returns
+    -------
+    name : str
+        Name of the function.
+    """
+
+    name = function.__name__ if callable(function) else function
+
+    return name