Merge pull request #142 from florisvb/make-spectral-freq-cutoff-right-scale

realized one of the params of spectraldiff was scaled oddly

Author: pavelkomarov

examples/1_basic_tutorial.ipynb

@@ -263,7 +263,7 @@ def spectraldiff(x, dt, params=None, options=None, high_freq_cutoff=None, even_e
     :param dict options: (**deprecated**, prefer :code:`even_extension`
             and :code:`pad_to_zero_dxdt`) a dictionary consisting of {'even_extension': (bool), 'pad_to_zero_dxdt': (bool)}
     :param float high_freq_cutoff: The high frequency cutoff as a multiple of the Nyquist frequency: Should be between 0
-            and 0.5. Frequencies below this threshold will be kept, and above will be zeroed.
+            and 1. Frequencies below this threshold will be kept, and above will be zeroed.
     :param bool even_extension: if True, extend the data with an even extension so signal starts and ends at the same value.
     :param bool pad_to_zero_dxdt: if True, extend the data with extra regions that smoothly force the derivative to
             zero before taking FFT.
@@ -310,7 +310,7 @@ def spectraldiff(x, dt, params=None, options=None, high_freq_cutoff=None, even_e
     omega = k*2*np.pi/(dt*N) # turn wavenumbers into frequencies in radians/s
 
     # Frequency based smoothing: remove signals with a frequency higher than high_freq_cutoff
-    discrete_cutoff = int(high_freq_cutoff*N)
+    discrete_cutoff = int(high_freq_cutoff*N/2) # Nyquist is at N/2 location, and we're cutting off as a fraction of that
     omega[discrete_cutoff:N-discrete_cutoff] = 0
 
     # Derivative = 90 deg phase shift

examples/2a_optimizing_parameters_with_dxdt_known.ipynb

@@ -34,7 +34,7 @@ def iterated_first_order(*args, **kwargs): return first_order(*args, **kwargs)
     (lineardiff, {'order':3, 'gamma':5, 'window_size':11, 'solver':'CLARABEL'}), (lineardiff, [3, 5, 11], {'solver':'CLARABEL'}),
     (polydiff, {'poly_order':2, 'window_size':3}), (polydiff, [2, 3]),
     (savgoldiff, {'poly_order':2, 'window_size':5, 'smoothing_win':5}), (savgoldiff, [2, 5, 5]),
-    (spectraldiff, {'high_freq_cutoff':0.1}), (spectraldiff, [0.1]),
+    (spectraldiff, {'high_freq_cutoff':0.2}), (spectraldiff, [0.2]),
     (mediandiff, {'window_size':3, 'num_iterations':2}), (mediandiff, [3, 2], {'iterate':True}),
     (meandiff, {'window_size':3, 'num_iterations':2}), (meandiff, [3, 2], {'iterate':True}),
     (gaussiandiff, {'window_size':5}), (gaussiandiff, [5]),

examples/2b_optimizing_parameters_with_dxdt_unknown.ipynb

@@ -83,8 +83,8 @@ def test_savgoldiff():
 def test_spectraldiff():
     params1, val1 = optimize(spectraldiff, x, dt, dxdt_truth=dxdt_truth, padding='auto')
     params2, val2 = optimize(spectraldiff, x, dt, tvgamma=tvgamma, padding='auto')
-    np.testing.assert_almost_equal(params1['high_freq_cutoff'], 0.0975, decimal=3)
-    np.testing.assert_almost_equal(params2['high_freq_cutoff'], 0.10, decimal=2)
+    np.testing.assert_almost_equal(params1['high_freq_cutoff'], 0.105, decimal=2)
+    np.testing.assert_almost_equal(params2['high_freq_cutoff'], 0.105, decimal=2)
 
 def test_polydiff():
     params1, val1 = optimize(polydiff, x, dt, search_space={'step_size':1}, dxdt_truth=dxdt_truth, padding='auto')