[WIP] - Add explicit {aperiodic, periodic} 'Modes' support

.github/workflows/build.yml

@@ -15,7 +15,7 @@ jobs:
       MODULE_NAME: specparam
     strategy:
       matrix:
-        python-version: ["3.7", "3.8", "3.9", "3.10", "3.11", "3.12"]
+        python-version: ["3.7", "3.8", "3.9", "3.10", "3.11", "3.12", "3.13"]
 
     steps:
     - uses: actions/checkout@v3

README.rst

@@ -2,29 +2,35 @@
 Spectral Parameterization
 =========================
 
-|ProjectStatus|_ |Version|_ |BuildStatus|_ |Coverage|_ |License|_ |PythonVersions|_ |Paper|_
+|ProjectStatus| |Version| |BuildStatus| |Coverage| |License| |PythonVersions| |Publication|
 
 .. |ProjectStatus| image:: http://www.repostatus.org/badges/latest/active.svg
-.. _ProjectStatus: https://www.repostatus.org/#active
+   :target: https://www.repostatus.org/#active
+   :alt: project status
 
 .. |Version| image:: https://img.shields.io/pypi/v/fooof.svg
-.. _Version: https://pypi.python.org/pypi/fooof/
+   :target: https://pypi.python.org/pypi/fooof/
+   :alt: version
 
 .. |BuildStatus| image:: https://github.com/fooof-tools/fooof/actions/workflows/build.yml/badge.svg
-.. _BuildStatus: https://github.com/fooof-tools/fooof/actions/workflows/build.yml
+   :target: https://github.com/fooof-tools/fooof/actions/workflows/build.yml
+   :alt: build status
 
 .. |Coverage| image:: https://codecov.io/gh/fooof-tools/fooof/branch/main/graph/badge.svg
-.. _Coverage: https://codecov.io/gh/fooof-tools/fooof
+   :target: https://codecov.io/gh/fooof-tools/fooof
+   :alt: coverage
 
 .. |License| image:: https://img.shields.io/pypi/l/fooof.svg
-.. _License: https://opensource.org/licenses/Apache-2.0
+   :target: https://opensource.org/licenses/Apache-2.0
+   :alt: license
 
 .. |PythonVersions| image:: https://img.shields.io/pypi/pyversions/fooof.svg
-.. _PythonVersions: https://pypi.python.org/pypi/fooof/
-
-.. |Paper| image:: https://img.shields.io/badge/paper-nn10.1038-informational.svg
-.. _Paper: https://doi.org/10.1038/s41593-020-00744-x
+   :target: https://pypi.python.org/pypi/fooof/
+   :alt: python versions
 
+.. |Publication| image:: https://img.shields.io/badge/paper-nn10.1038-informational.svg
+   :target: https://doi.org/10.1038/s41593-020-00744-x
+   :alt: publication
 
 Spectral parameterization (`specparam`, formerly `fooof`) is a fast, efficient, and physiologically-informed tool to parameterize neural power spectra.
 

setup.py

@@ -45,6 +45,7 @@
         'Programming Language :: Python :: 3.10',
         'Programming Language :: Python :: 3.11',
         'Programming Language :: Python :: 3.12',
+        'Programming Language :: Python :: 3.13',
     ],
     platforms = 'any',
     project_urls = {

specparam/core/funcs.py

@@ -1,19 +1,16 @@
-"""Functions that can be used for model fitting.
-
-NOTES
------
-- Model fitting currently (only) uses the exponential and gaussian functions.
-- Linear & Quadratic functions are from previous versions.
-    - They are left available for easy swapping back in, if desired.
-"""
+"""Functions that can be used for model fitting."""
 
 import numpy as np
+from scipy.special import erf
 
+from specparam.core.utils import normalize
 from specparam.core.errors import InconsistentDataError
 
 ###################################################################################################
 ###################################################################################################
 
+## PEAK FUNCTIONS
+
 def gaussian_function(xs, *params):
     """Gaussian fitting function.
 
@@ -39,6 +36,37 @@ def gaussian_function(xs, *params):
     return ys
 
 
+def skewnorm_function(xs, *params):
+    """Skewed normal distribution fitting function.
+
+    Parameters
+    ----------
+    xs : 1d array
+        Input x-axis values.
+    *params : float
+        Parameters that define the skewed normal distribution function.
+
+    Returns
+    -------
+    ys : 1d array
+        Output values for skewed normal distribution function.
+    """
+
+    ys = np.zeros_like(xs)
+
+    for ii in range(0, len(params), 4):
+
+        ctr, hgt, wid, skew = params[ii:ii+4]
+
+        ts = (xs - ctr) / wid
+        temp = 2 / wid * (1 / np.sqrt(2 * np.pi) * np.exp(-ts**2 / 2)) * \
+            ((1 + erf(skew * ts / np.sqrt(2))) / 2)
+        ys = ys + hgt * normalize(temp)
+
+    return ys
+
+## APERIODIC FUNCTIONS
+
 def expo_function(xs, *params):
     """Exponential fitting function, for fitting aperiodic component with a 'knee'.
 
@@ -89,6 +117,34 @@ def expo_nk_function(xs, *params):
     return ys
 
 
+def double_expo_function(xs, *params):
+    """Double exponential fitting function, for fitting aperiodic component with two exponents and a knee.
+
+    NOTE: this function requires linear frequency (not log).
+
+    Parameters
+    ----------
+    xs : 1d array
+        Input x-axis values.
+    *params : float
+        Parameters (offset, exp0, knee, exp1) that define the function:
+        y = 10^offset * (1/((x**exp0) * (knee + x^exp1))
+
+    Returns
+    -------
+    ys : 1d array
+        Output values for exponential function.
+    """
+
+    ys = np.zeros_like(xs)
+
+    offset, exp0, knee, exp1 = params
+
+    ys = ys + offset - np.log10((xs**exp0) * (knee + xs**exp1))
+
+    return ys
+
+
 def linear_function(xs, *params):
     """Linear fitting function.
 
@@ -133,6 +189,8 @@ def quadratic_function(xs, *params):
     return ys
 
 
+## GETTER FUNCTIONS
+
 def get_pe_func(periodic_mode):
     """Select and return specified function for periodic component.
 

specparam/core/info.py

@@ -75,6 +75,9 @@ def get_ap_indices(aperiodic_mode):
         Mapping of the column labels and indices for the aperiodic parameters.
     """
 
+    # TEMP / TEST:
+    aperiodic_mode = str(aperiodic_mode)
+
     if aperiodic_mode == 'fixed':
         labels = ('offset', 'exponent')
     elif aperiodic_mode == 'knee':
@@ -101,6 +104,9 @@ def get_indices(aperiodic_mode):
         Mapping of the column labels and indices for all parameters.
     """
 
+    # TEMP / TEST:
+    aperiodic_mode = str(aperiodic_mode)
+
     # Get the periodic indices, and then update dictionary with aperiodic ones
     indices = get_peak_indices()
     indices.update(get_ap_indices(aperiodic_mode))

specparam/core/strings.py

@@ -300,7 +300,7 @@ def gen_model_results_str(model, concise=False):
 
         # Aperiodic parameters
         ('Aperiodic Parameters (offset, ' + \
-         ('knee, ' if model.aperiodic_mode == 'knee' else '') + \
+         ('knee, ' if str(model.aperiodic_mode) == 'knee' else '') + \
          'exponent): '),
         ', '.join(['{:2.4f}'] * len(model.aperiodic_params_)).format(*model.aperiodic_params_),
         '',
@@ -357,7 +357,7 @@ def gen_group_results_str(group, concise=False):
     errors = group.get_params('error')
     exps = group.get_params('aperiodic_params', 'exponent')
     kns = group.get_params('aperiodic_params', 'knee') \
-        if group.aperiodic_mode == 'knee' else np.array([0])
+        if str(group.aperiodic_mode) == 'knee' else np.array([0])
 
     str_lst = [
 
@@ -380,12 +380,13 @@ def gen_group_results_str(group, concise=False):
 
         # Aperiodic parameters - knee fit status, and quick exponent description
         'Power spectra were fit {} a knee.'.format(\
-            'with' if group.aperiodic_mode == 'knee' else 'without'),
+            'with' if str(group.aperiodic_mode) == 'knee' else 'without'),
         '',
         'Aperiodic Fit Values:',
         *[el for el in ['    Knees - Min: {:6.2f}, Max: {:6.2f}, Mean: {:5.2f}'
                         .format(*compute_arr_desc(kns)),
                        ] if group.aperiodic_mode == 'knee'],
+
         'Exponents - Min: {:6.3f}, Max: {:6.3f}, Mean: {:5.3f}'
         .format(*compute_arr_desc(exps)),
         '',

specparam/core/utils.py

@@ -27,13 +27,32 @@ def unlog(arr, base=10):
     return np.power(base, arr)
 
 
-def group_three(vec):
-    """Group an array of values into threes.
+def normalize(data):
+    """Normalize an array of numerical data (to the range of 0-1).
+
+    Parameters
+    ----------
+    data : np.ndarray
+        Array of data to normalize.
+
+    Returns
+    -------
+    np.ndarray
+        Normalized data.
+    """
+
+    return (data - np.min(data)) / (np.max(data) - np.min(data))
+
+
+def groupby(vec, groupby):
+    """Group an array of values by a specified number.
 
     Parameters
     ----------
     vec : list or 1d array
         List or array of items to group by 3. Length of array must be divisible by three.
+    num : int
+        Number to group by.
 
     Returns
     -------
@@ -43,17 +62,17 @@ def group_three(vec):
     Raises
     ------
     ValueError
-        If input data cannot be evenly grouped into threes.
+        If input data cannot be evenly grouped into specified number.
     """
 
-    if len(vec) % 3 != 0:
+    if len(vec) % groupby != 0:
         raise ValueError("Wrong size array to group by three.")
 
-    # Reshape, if an array, as it's faster, otherwise asssume lise
+    # Reshape, if an array, as it's faster, otherwise assume list
     if isinstance(vec, np.ndarray):
-        return np.reshape(vec, (-1, 3))
+        return np.reshape(vec, (-1, groupby))
     else:
-        return [list(vec[ii:ii+3]) for ii in range(0, len(vec), 3)]
+        return [list(vec[ii:ii+groupby]) for ii in range(0, len(vec), groupby)]
 
 
 def nearest_ind(array, value):