Merge pull request #407 from fooof-tools/convcheck

[MNT] - Update organization and consistency of `check_options` functions

Author: TomDonoghue

specparam/algorithms/__init__.py

@@ -1 +1,6 @@
 """Algorithms sub-module."""
+
+from .algorithm import Algorithm
+
+# Link in report function to list available algorithms
+from specparam.reports.options import check_algorithms

specparam/algorithms/algorithm.py

@@ -2,6 +2,7 @@
 
 import numpy as np
 
+from specparam.data.data import DATA_FORMATS
 from specparam.utils.checks import check_input_options
 from specparam.algorithms.settings import SettingsDefinition, SettingsValues
 from specparam.modutils.docs import docs_get_section, replace_docstring_sections
@@ -10,17 +11,18 @@
 ###################################################################################################
 ###################################################################################################
 
-DATA_FORMATS = ['spectrum', 'spectra', 'spectrogram', 'spectrograms']
-
 class Algorithm():
     """Template object for defining a fit algorithm.
 
-    Parameters
+    Attributes
     ----------
     name : str
         Name of the fitting algorithm.
     description : str
         Description of the fitting algorithm.
+
+    Parameters
+    ----------
     public_settings : SettingsDefinition or dict
         Name and description of public settings for the fitting algorithm.
     private_settings :  SettingsDefinition or dict, optional
@@ -39,13 +41,12 @@ class Algorithm():
         Whether to run in debug state, raising an error if encountered during fitting.
     """
 
-    def __init__(self, name, description, public_settings, private_settings=None,
-                 data_format='spectrum', modes=None, data=None, results=None, model=None,
-                 debug=False):
-        """Initialize Algorithm object."""
+    name = None
+    description = None
 
-        self.name = name
-        self.description = description
+    def __init__(self, public_settings, private_settings=None, data_format='spectrum',
+                 modes=None, data=None, results=None, model=None, debug=False):
+        """Initialize Algorithm object."""
 
         if not isinstance(public_settings, SettingsDefinition):
             public_settings = SettingsDefinition(public_settings)
@@ -182,15 +183,13 @@ class AlgorithmCF(Algorithm):
     % copied in from Algorithm
     """
 
-    def __init__(self, name, description, public_settings, private_settings=None,
-                 data_format='spectrum', modes=None, data=None, results=None,
-                 model=None, debug=False):
+    def __init__(self, public_settings, private_settings=None, data_format='spectrum',
+                 modes=None, data=None, results=None, model=None, debug=False):
         """Initialize Algorithm object."""
 
-        Algorithm.__init__(self, name=name, description=description,
-                           public_settings=public_settings, private_settings=private_settings,
-                           data_format=data_format, modes=modes, data=data, results=results,
-                           model=model, debug=debug)
+        Algorithm.__init__(self, public_settings, private_settings=private_settings,
+                           data_format=data_format, modes=modes, data=data,
+                           results=results, model=model, debug=debug)
 
         self._cf_settings_desc = CURVE_FIT_SETTINGS
         self._cf_settings = SettingsValues(self._cf_settings_desc.names)

specparam/algorithms/definitions.py

@@ -14,14 +14,4 @@
     '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)

specparam/algorithms/spectral_fit.py

@@ -103,6 +103,9 @@ class SpectralFitAlgorithm(AlgorithmCF):
     """
     # pylint: disable=attribute-defined-outside-init
 
+    name = 'spectral_fit'
+    description = 'Original parameterizing neural power spectra algorithm.'
+
     def __init__(self, peak_width_limits=(0.5, 12.0), max_n_peaks=np.inf, min_peak_height=0.0,
                  peak_threshold=2.0, ap_percentile_thresh=0.025, ap_guess=None, ap_bounds=None,
                  cf_bound=1.5, bw_std_edge=1.0, gauss_overlap_thresh=0.75, maxfev=5000,
@@ -111,8 +114,6 @@ 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',
-            description='Original parameterizing neural power spectra algorithm.',
             public_settings=SPECTRAL_FIT_SETTINGS_DEF,
             private_settings=SPECTRAL_FIT_PRIVATE_SETTINGS_DEF,
             modes=modes, data=data, results=results, model=model, debug=debug)

specparam/data/data.py

@@ -21,9 +21,10 @@
 ###################################################################################################
 
 # Define set of data fields
-DATA_FIELDS = ['power_spectrum', 'freq_range', 'freq_res']
 META_DATA_FIELDS = ['freq_range', 'freq_res']
-FORMATS = ['power']
+DATA_FORMATS = ['spectrum', 'spectra', 'spectrogram', 'spectrograms']
+DATA_FIELDS = ['power_spectrum', 'freq_range', 'freq_res']
+DATA_UNITS = ['power']
 
 
 class Data():
@@ -58,7 +59,7 @@ class Data():
     All power values are stored internally in log10 scale.
     """
 
-    def __init__(self, check_freqs=True, check_data=True, format='power', model=None):
+    def __init__(self, check_freqs=True, check_data=True, units='power', model=None):
         """Initialize Data object."""
 
         self._reset_data(True, True)
@@ -70,8 +71,8 @@ def __init__(self, check_freqs=True, check_data=True, format='power', model=None
             'data' : check_data,
         }
 
-        check_input_options(format, FORMATS, 'format')
-        self.format = format
+        check_input_options(units, DATA_UNITS, 'units')
+        self.units = units
 
         self._model = model
 

specparam/metrics/__init__.py

@@ -1,4 +1,6 @@
 """Metrics sub-module."""
 
 from .metric import Metric
-from .check import check_metrics
+
+# Link in report function to list available metrics
+from specparam.reports.options import check_metrics

specparam/metrics/check.py

@@ -1,5 +1,8 @@
 """Functionality related to definining fit modes."""
 
 from .mode import Mode
-from .check import check_modes
 from .paramdef import ParamDefinition
+
+# Link in report function to list available modes
+from specparam.reports.options import check_modes
+

specparam/modes/__init__.py

@@ -1 +1,7 @@
 """Sub-module for functionality related to parameters and parameter conversions."""
+
+from .converter import AperiodicParamConverter, PeriodicParamConverter
+
+# Link in report function to list available parameter converters
+from specparam.reports.options import check_converters
+