Merge pull request #372 from fooof-tools/algo

TomDonoghue · web-flow · commit bd75cdc0d182 · 2025-11-10T22:31:08.000Z
[ENH] - Update Algorithm Management
diff --git a/specparam/algorithms/algorithm.py b/specparam/algorithms/algorithm.py
@@ -66,7 +66,7 @@ def __init__(self, name, description, public_settings, private_settings=None,
         self.set_debug(debug)
 
 
-    def _fit_prechecks(self):
+    def _fit_prechecks(self, verbose):
         """Pre-checks to run before the fit function - if are some, overload this function."""
 
 
@@ -195,11 +195,17 @@ def _initialize_bounds(self, mode):
              [high_bound_param1, high_bound_param2])
         """
 
-        n_params = getattr(self.modes, mode).n_params
+        # If modes defined, get number of params - otherwise set stores as empty
+        if self.modes is not None:
+            n_params = getattr(self.modes, mode).n_params
+        else:
+            n_params = 0
+
         bounds = (np.array([-np.inf] * n_params), np.array([np.inf] * n_params))
 
         return bounds
 
+
     def _initialize_guess(self, mode):
         """Initialize a guess definition.
 
diff --git a/specparam/algorithms/definitions.py b/specparam/algorithms/definitions.py
@@ -1,5 +1,9 @@
 """Define collection of fitting algorithms."""
 
+from functools import partial
+
+from specparam.utils.checks import check_selection
+from specparam.algorithms.algorithm import Algorithm
 from specparam.algorithms.spectral_fit import SpectralFitAlgorithm
 
 ###################################################################################################
@@ -9,3 +13,15 @@
 ALGORITHMS = {
     'spectral_fit' : SpectralFitAlgorithm,
 }
+
+
+def check_algorithms():
+    """Check the set of available fit algorithms."""
+
+    print('Available algorithms:')
+    for algorithm in ALGORITHMS.values():
+        algorithm = algorithm()
+        print('    {:12s} : {:s}'.format(algorithm.name, algorithm.description))
+
+
+check_algorithm_definition = partial(check_selection, definition=Algorithm)
diff --git a/specparam/algorithms/spectral_fit.py b/specparam/algorithms/spectral_fit.py
@@ -111,7 +111,7 @@ def __init__(self, peak_width_limits=(0.5, 12.0), max_n_peaks=np.inf, min_peak_h
 
         # Initialize base algorithm object with algorithm metadata
         super().__init__(
-            name='spectral fit',
+            name='spectral_fit',
             description='Original parameterizing neural power spectra algorithm.',
             public_settings=SPECTRAL_FIT_SETTINGS_DEF,
             private_settings=SPECTRAL_FIT_PRIVATE_SETTINGS_DEF,
diff --git a/specparam/metrics/definitions.py b/specparam/metrics/definitions.py
@@ -1,9 +1,12 @@
 """Collect together library of available built in metrics."""
 
+from functools import partial
+
 from specparam.metrics.metrics import Metric
 from specparam.metrics.error import (compute_mean_abs_error, compute_mean_squared_error,
                                      compute_root_mean_squared_error, compute_median_abs_error)
 from specparam.metrics.gof import compute_r_squared, compute_adj_r_squared
+from specparam.utils.checks import check_selection
 
 ###################################################################################################
 ## ERROR METRICS
@@ -79,3 +82,6 @@ def check_metrics():
     print('Available metrics:')
     for metric in METRICS.values():
         print('    {:8s} {:12s} : {:s}'.format(metric.category, metric.measure, metric.description))
+
+
+check_metric_definition = partial(check_selection, definition=Metric)
diff --git a/specparam/metrics/metrics.py b/specparam/metrics/metrics.py
@@ -5,6 +5,7 @@
 import numpy as np
 
 from specparam.metrics.metric import Metric
+from specparam.metrics.definitions import METRICS, check_metric_definition
 
 ###################################################################################################
 ###################################################################################################
@@ -61,6 +62,8 @@ def add_metric(self, metric):
         if isinstance(metric, dict):
             metric = Metric(**metric)
 
+        metric = check_metric_definition(metric, METRICS)
+
         self.metrics.append(deepcopy(metric))
 
 
diff --git a/specparam/models/event.py b/specparam/models/event.py
@@ -60,8 +60,8 @@ def __init__(self, *args, **kwargs):
         self.data = Data3D()
 
         self.results = Results3D(modes=self.modes,
-                                     metrics=kwargs.pop('metrics', None),
-                                     bands=kwargs.pop('bands', None))
+                                 metrics=kwargs.pop('metrics', None),
+                                 bands=kwargs.pop('bands', None))
 
         self.algorithm._reset_subobjects(data=self.data, results=self.results)
 
diff --git a/specparam/models/group.py b/specparam/models/group.py
@@ -63,8 +63,8 @@ def __init__(self, *args, **kwargs):
         self.data = Data2D()
 
         self.results = Results2D(modes=self.modes,
-                                     metrics=kwargs.pop('metrics', None),
-                                     bands=kwargs.pop('bands', None))
+                                 metrics=kwargs.pop('metrics', None),
+                                 bands=kwargs.pop('bands', None))
 
         self.algorithm._reset_subobjects(data=self.data, results=self.results)
 
diff --git a/specparam/models/model.py b/specparam/models/model.py
@@ -11,7 +11,10 @@
 from specparam.data.data import Data
 from specparam.data.conversions import model_to_dataframe
 from specparam.results.results import Results
+
 from specparam.algorithms.spectral_fit import SpectralFitAlgorithm, SPECTRAL_FIT_SETTINGS_DEF
+from specparam.algorithms.definitions import ALGORITHMS, check_algorithm_definition
+
 from specparam.reports.save import save_model_report
 from specparam.reports.strings import gen_model_results_str
 from specparam.modutils.errors import NoDataError, FitError
@@ -34,10 +37,14 @@ class SpectralModel(BaseModel):
     Parameters
     ----------
     % copied in from Spectral Fit Algorithm Settings
-    aperiodic_mode : {'fixed', 'knee'}
+    aperiodic_mode : {'fixed', 'knee'} or Mode
         Which approach to take for fitting the aperiodic component.
-    periodic_mode : {'gaussian', 'skewed_gaussian', 'cauchy'}
+    periodic_mode : {'gaussian', 'skewed_gaussian', 'cauchy'} or Mode
         Which approach to take for fitting the periodic component.
+    algorithm : {'spectral_fit'} or Algorithm
+        The fitting algorithm to use.
+    algorithm_settings : dict
+        Setting for the algorithm.
     metrics : Metrics or list of Metric or list or str
         Metrics definition(s) to use to evaluate the model.
     bands : Bands or dict or int or None, optional
@@ -49,6 +56,7 @@ class SpectralModel(BaseModel):
         Verbosity mode. If True, prints out warnings and general status updates.
     **model_kwargs
         Additional model fitting related keyword arguments.
+        These are passed into the algorithm object.
 
     Attributes
     ----------
@@ -71,25 +79,21 @@ class SpectralModel(BaseModel):
       as this will give better model fits.
     """
 
-    def __init__(self, peak_width_limits=(0.5, 12.0), max_n_peaks=np.inf, min_peak_height=0.0,
-                 peak_threshold=2.0, aperiodic_mode='fixed', periodic_mode='gaussian',
+    def __init__(self, aperiodic_mode='fixed', periodic_mode='gaussian',
+                 algorithm='spectral_fit', algorithm_settings=None,
                  metrics=None, bands=None, debug=False, verbose=True, **model_kwargs):
         """Initialize model object."""
 
-        BaseModel.__init__(self,
-                           aperiodic_mode=aperiodic_mode,
-                           periodic_mode=periodic_mode,
-                           verbose=verbose)
+        BaseModel.__init__(self, aperiodic_mode, periodic_mode, verbose)
 
         self.data = Data()
 
         self.results = Results(modes=self.modes, metrics=metrics, bands=bands)
 
-        self.algorithm = SpectralFitAlgorithm(
-            peak_width_limits=peak_width_limits, max_n_peaks=max_n_peaks,
-            min_peak_height=min_peak_height, peak_threshold=peak_threshold,
-            modes=self.modes, data=self.data, results=self.results,
-            debug=debug, **model_kwargs)
+        algorithm_settings = {} if algorithm_settings is None else algorithm_settings
+        self.algorithm = check_algorithm_definition(algorithm, ALGORITHMS)(
+            **algorithm_settings, modes=self.modes, data=self.data,
+            results=self.results, debug=debug, **model_kwargs)
 
 
     @replace_docstring_sections([docs_get_section(Data.add_data.__doc__, 'Parameters'),
diff --git a/specparam/models/time.py b/specparam/models/time.py
@@ -56,8 +56,8 @@ def __init__(self, *args, **kwargs):
         self.data = Data2DT()
 
         self.results = Results2DT(modes=self.modes,
-                                      metrics=kwargs.pop('metrics', None),
-                                      bands=kwargs.pop('bands', None))
+                                  metrics=kwargs.pop('metrics', None),
+                                  bands=kwargs.pop('bands', None))
 
         self.algorithm._reset_subobjects(data=self.data, results=self.results)
 
diff --git a/specparam/models/utils.py b/specparam/models/utils.py
@@ -237,7 +237,8 @@ def combine_model_objs(model_objs):
                                         "or meta data, and so cannot be combined.")
 
     # Initialize group model object, with settings derived from input objects
-    group = SpectralGroupModel(*model_objs[0].algorithm.get_settings(),
+    group = SpectralGroupModel(**model_objs[0].modes.get_modes()._asdict(),
+                               **model_objs[0].algorithm.get_settings()._asdict(),
                                verbose=model_objs[0].verbose)
 
     # Use a temporary store to collect spectra, as we'll only add it if it is consistently present
diff --git a/specparam/modes/definitions.py b/specparam/modes/definitions.py
@@ -1,12 +1,14 @@
 """Define fitting modes."""
 
+from functools import partial
 from collections import OrderedDict
 
 from specparam.modes.mode import Mode
 from specparam.modes.params import ParamDefinition
 from specparam.modes.funcs import (expo_function, expo_nk_function, double_expo_function,
                                    gaussian_function, skewed_gaussian_function, cauchy_function)
 from specparam.modes.jacobians import jacobian_gauss
+from specparam.utils.checks import check_selection
 
 ###################################################################################################
 ## APERIODIC MODES
@@ -184,3 +186,6 @@ def check_modes(component, check_params=False):
             print('\n{:s}'.format(mode.name))
             print('    {:s}'.format(mode.description))
             mode.check_params()
+
+
+check_mode_definition = partial(check_selection, definition=Mode)
diff --git a/specparam/modes/modes.py b/specparam/modes/modes.py
@@ -1,8 +1,8 @@
 """Modes object."""
 
 from specparam.data import ModelModes
-from specparam.modes.mode import Mode, VALID_COMPONENTS
-from specparam.modes.definitions import AP_MODES, PE_MODES
+from specparam.modes.mode import VALID_COMPONENTS
+from specparam.modes.definitions import check_mode_definition, AP_MODES, PE_MODES
 
 ###################################################################################################
 ###################################################################################################
@@ -49,36 +49,3 @@ def get_modes(self):
 
         return ModelModes(aperiodic_mode=self.aperiodic.name if self.aperiodic else None,
                           periodic_mode=self.periodic.name if self.periodic else None)
-
-
-def check_mode_definition(mode, options):
-    """Check a mode specification.
-
-    Parameters
-    ----------
-    mode : str or None or Mode
-        Fit mode. If str, should be a label corresponding to an entry in `options`.
-    options : dict
-        Available modes.
-
-    Returns
-    -------
-    mode : Mode or None
-        Mode object, if defined, or None if not defined.
-
-    Raises
-    ------
-    ValueError
-        If the mode definition is not found / understood.
-    """
-
-    if isinstance(mode, str):
-        assert mode in list(options.keys()), 'Specific Mode not found.'
-        mode = options[mode]
-
-    if mode is None:
-        mode = None
-    elif not isinstance(mode, Mode):
-        raise ValueError('Mode input not understood.')
-
-    return mode
diff --git a/specparam/results/results.py b/specparam/results/results.py
@@ -125,17 +125,18 @@ def add_metrics(self, metrics):
 
         Parameters
         ----------
-        metrics : Metrics or list of Metric or list or str
+        metrics : Metrics or list of Metric or list of str or None
             Metrics definition(s) to add to object.
+            If None, initialized with default metrics.
         """
 
+        if metrics is None:
+            metrics = DEFAULT_METRICS
+
         if isinstance(metrics, Metrics):
             self.metrics = deepcopy(metrics)
-        elif isinstance(metrics, list):
-            self.metrics = Metrics(\
-                [METRICS[metric] if isinstance(metric, str) else metric for metric in metrics])
         else:
-            self.metrics = Metrics([METRICS[metric] for metric in DEFAULT_METRICS])
+            self.metrics = Metrics(metrics)
 
 
     def add_results(self, results):
diff --git a/specparam/tests/algorithms/test_definitions.py b/specparam/tests/algorithms/test_definitions.py
@@ -0,0 +1,25 @@
+"""Tests for specparam.algorithms.definitions."""
+
+from specparam.algorithms.algorithm import Algorithm
+
+from specparam.algorithms.definitions import *
+
+###################################################################################################
+###################################################################################################
+
+def test_algorithms_library():
+
+    for key, algorithm in ALGORITHMS.items():
+        algorithm = algorithm()
+        assert isinstance(algorithm, Algorithm)
+        assert algorithm.name == key
+
+def test_check_algorithms():
+
+    check_algorithms()
+
+def test_check_algorithm_definition():
+
+    for algorithm in ALGORITHMS.keys():
+        algorithm = check_algorithm_definition(algorithm, ALGORITHMS)
+        assert issubclass(algorithm, Algorithm)
diff --git a/specparam/tests/metrics/test_definitions.py b/specparam/tests/metrics/test_definitions.py
@@ -9,5 +9,10 @@
 
 def test_metrics_library():
 
-    for key in METRICS:
-        assert isinstance(METRICS[key], Metric)
+    for key, metric in METRICS.items():
+        assert isinstance(metric, Metric)
+        assert metric.label == key
+
+def test_check_metrics():
+
+    check_metrics()
diff --git a/specparam/tests/modes/test_definitions.py b/specparam/tests/modes/test_definitions.py
@@ -1,11 +1,30 @@
 """Tests for specparam.modes.definitions."""
 
+from specparam.modes.mode import Mode, VALID_COMPONENTS
+
 from specparam.modes.definitions import *
 
 ###################################################################################################
 ###################################################################################################
 
+def test_modes_library():
+
+    for component in VALID_COMPONENTS:
+        for key, mode in MODES[component].items():
+            assert isinstance(mode, Mode)
+            assert mode.name == key
+
 def test_check_modes():
 
     check_modes('aperiodic')
     check_modes('periodic')
+
+def test_check_mode_definition():
+
+    for ap_mode in AP_MODES.keys():
+        mode = check_mode_definition(ap_mode, AP_MODES)
+        assert isinstance(mode, Mode)
+
+    for pe_mode in PE_MODES.keys():
+        mode = check_mode_definition(pe_mode, PE_MODES)
+        assert isinstance(mode, Mode)
diff --git a/specparam/tests/modes/test_modes.py b/specparam/tests/modes/test_modes.py
@@ -1,6 +1,7 @@
 """Tests for specparam.modes.modes."""
 
 from specparam.data import ModelModes
+from specparam.modes.mode import Mode
 from specparam.modes.definitions import AP_MODES, PE_MODES
 
 from specparam.modes.modes import *
@@ -26,13 +27,3 @@ def test_modes_get_modes():
     assert isinstance(mode_names, ModelModes)
     assert mode_names.aperiodic_mode == ap_mode_name
     assert mode_names.periodic_mode == pe_mode_name
-
-def test_check_mode_definition():
-
-    for ap_mode in AP_MODES.keys():
-        mode = check_mode_definition(ap_mode, AP_MODES)
-        assert isinstance(mode, Mode)
-
-    for pe_mode in PE_MODES.keys():
-        mode = check_mode_definition(pe_mode, PE_MODES)
-        assert isinstance(mode, Mode)
diff --git a/specparam/tests/utils/test_checks.py b/specparam/tests/utils/test_checks.py
diff --git a/specparam/utils/checks.py b/specparam/utils/checks.py
