add jacobian funcs

Author: TomDonoghue

fooof/core/jacobians.py

@@ -0,0 +1,51 @@
+""""Functions for computing Jacobian matrices to be used during fitting."""
+
+import numpy as np
+
+###################################################################################################
+###################################################################################################
+
+## Periodic fit functions
+
+def jacobian_gauss(xs, *params):
+    """Create the Jacobian matrix for the Guassian function."""
+
+    jacobians = []
+    for a, b, c in zip(*[iter(params)] * 3):
+
+        sub = b * np.exp((-(((-a + xs)**2) / (2 * c**2))))
+
+        jacobian = np.hstack([
+            (sub * (-a + xs) / c**2).reshape(-1, 1),
+            np.exp(-(-a + xs)**2 / (2 * c**2)).reshape(-1, 1),
+            (sub * (-a + xs)**2 / c**3).reshape(-1, 1),
+        ])
+        jacobians.append(jacobian)
+
+    return np.hstack(jacobians)
+
+
+## Aperiodic fit functions
+
+def jacobian_expo(xs, *params):
+    """Create the Jacobian matrix for the exponential function."""
+
+    a, b, c = params
+    jacobian = np.hstack([
+        np.ones([len(xs), 1]),
+        - (1 / (b + xs**c)).reshape(-1, 1),
+        -((xs**c * np.log10(xs)) / (b + xs**c)).reshape(-1, 1),
+    ])
+
+    return jacobian
+
+
+def jacobian_expo_nk(xs, *params):
+    """Create the Jacobian matrix for the exponential no-knee function."""
+
+    jacobian = np.hstack([
+        np.ones([len(xs), 1]),
+        (-np.log10(xs) / np.log10(10)).reshape(-1, 1),
+    ])
+
+    return jacobian

fooof/tests/core/test_jacobians.py

@@ -0,0 +1,34 @@
+"""Tests for fooof.core.jacobians."""
+
+
+from fooof.core.jacobians import *
+
+###################################################################################################
+###################################################################################################
+
+def test_jacobian_gauss():
+
+    xs = np.arange(1, 100)
+    ctr, hgt, wid = 50, 5, 10
+
+    jacobian = jacobian_gauss(xs, ctr, hgt, wid)
+    assert isinstance(jacobian, np.ndarray)
+    assert jacobian.shape == (len(xs), 3)
+
+def test_jacobian_expo():
+
+    xs = np.arange(1, 100)
+    off, knee, exp = 10, 5, 2
+
+    jacobian = jacobian_expo(xs, off, knee, exp)
+    assert isinstance(jacobian, np.ndarray)
+    assert jacobian.shape == (len(xs), 3)
+
+def test_jacobian_expo_nk():
+
+    xs = np.arange(1, 100)
+    off, exp = 10, 2
+
+    jacobian = jacobian_expo_nk(xs, off, exp)
+    assert isinstance(jacobian, np.ndarray)
+    assert jacobian.shape == (len(xs), 2)