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Mnt deprecate mlab #22920

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41f946e
MNT: deprecate mlab
jklymak Apr 27, 2022
59532ae
FIX: detrends
jklymak Jul 22, 2022
c6b33a6
Fix for 3.7
jklymak Nov 11, 2022
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27 changes: 22 additions & 5 deletions lib/matplotlib/axes/_axes.py
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Original file line number Diff line number Diff line change
Expand Up @@ -1903,7 +1903,7 @@ def acorr(self, x, **kwargs):
----------
x : array-like

detrend : callable, default: `.mlab.detrend_none` (no detrending)
detrend : callable, default: no detrending
A detrending function applied to *x*. It must have the
signature ::

Expand Down Expand Up @@ -1967,7 +1967,7 @@ def acorr(self, x, **kwargs):
return self.xcorr(x, x, **kwargs)

@_preprocess_data(replace_names=["x", "y"], label_namer="y")
def xcorr(self, x, y, normed=True, detrend=mlab.detrend_none,
def xcorr(self, x, y, normed=True, detrend=None,
usevlines=True, maxlags=10, **kwargs):
r"""
Plot the cross correlation between *x* and *y*.
Expand All @@ -1980,7 +1980,7 @@ def xcorr(self, x, y, normed=True, detrend=mlab.detrend_none,
----------
x, y : array-like of length n

detrend : callable, default: `.mlab.detrend_none` (no detrending)
detrend : callable, default: no detrending
A detrending function applied to *x* and *y*. It must have the
signature ::

Expand Down Expand Up @@ -2045,8 +2045,9 @@ def xcorr(self, x, y, normed=True, detrend=mlab.detrend_none,
if Nx != len(y):
raise ValueError('x and y must be equal length')

x = detrend(np.asarray(x))
y = detrend(np.asarray(y))
if detrend is not None:
x = detrend(np.asarray(x))
y = detrend(np.asarray(y))

correls = np.correlate(x, y, mode="full")

Expand Down Expand Up @@ -7016,6 +7017,7 @@ def hist2d(self, x, y, bins=10, range=None, density=False, weights=None,

return h, xedges, yedges, pc

@_api.deprecated("3.7", alternative="scipy.signal.psd and ax.loglog")
@_preprocess_data(replace_names=["x"])
@_docstring.dedent_interpd
def psd(self, x, NFFT=None, Fs=None, Fc=None, detrend=None,
Expand Down Expand Up @@ -7127,6 +7129,7 @@ def psd(self, x, NFFT=None, Fs=None, Fc=None, detrend=None,
else:
return pxx, freqs, line

@_api.deprecated("3.7", alternative="scipy.signal.csd and ax.plot")
@_preprocess_data(replace_names=["x", "y"], label_namer="y")
@_docstring.dedent_interpd
def csd(self, x, y, NFFT=None, Fs=None, Fc=None, detrend=None,
Expand Down Expand Up @@ -7229,6 +7232,9 @@ def csd(self, x, y, NFFT=None, Fs=None, Fc=None, detrend=None,
else:
return pxy, freqs, line

@_api.deprecated(
"3.7",
alternative="scipy.signal.spectrogram(mode='magnitude') and ax.loglog")
@_preprocess_data(replace_names=["x"])
@_docstring.dedent_interpd
def magnitude_spectrum(self, x, Fs=None, Fc=None, window=None,
Expand Down Expand Up @@ -7315,6 +7321,9 @@ def magnitude_spectrum(self, x, Fs=None, Fc=None, window=None,

return spec, freqs, line

@_api.deprecated("3.7",
alternative="scipy.signal.spectrogram(mode='angle') and "
"ax.loglog")
@_preprocess_data(replace_names=["x"])
@_docstring.dedent_interpd
def angle_spectrum(self, x, Fs=None, Fc=None, window=None,
Expand Down Expand Up @@ -7384,6 +7393,9 @@ def angle_spectrum(self, x, Fs=None, Fc=None, window=None,

return spec, freqs, lines[0]

@_api.deprecated("3.7",
alternative="scipy.signal.spectrogram(mode='phase') and "
"ax.loglog")
@_preprocess_data(replace_names=["x"])
@_docstring.dedent_interpd
def phase_spectrum(self, x, Fs=None, Fc=None, window=None,
Expand Down Expand Up @@ -7453,6 +7465,8 @@ def phase_spectrum(self, x, Fs=None, Fc=None, window=None,

return spec, freqs, lines[0]

@_api.deprecated("3.7", alternative="scipy.signal.coherence and "
"ax.semilogx")
@_preprocess_data(replace_names=["x", "y"])
@_docstring.dedent_interpd
def cohere(self, x, y, NFFT=256, Fs=2, Fc=0, detrend=mlab.detrend_none,
Expand Down Expand Up @@ -7517,6 +7531,9 @@ def cohere(self, x, y, NFFT=256, Fs=2, Fc=0, detrend=mlab.detrend_none,

return cxy, freqs

@_api.deprecated("3.7",
alternative="scipy.signal.spectrogram(mode='psd') and "
"ax.loglog")
@_preprocess_data(replace_names=["x"])
@_docstring.dedent_interpd
def specgram(self, x, NFFT=None, Fs=None, Fc=None, detrend=None,
Expand Down
19 changes: 13 additions & 6 deletions lib/matplotlib/mlab.py
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Original file line number Diff line number Diff line change
@@ -1,8 +1,6 @@
"""
Numerical Python functions written for compatibility with MATLAB
commands with the same names. Most numerical Python functions can be found in
the `NumPy`_ and `SciPy`_ libraries. What remains here is code for performing
spectral computations and kernel density estimations.
This module is deprecated in favour of modules that can be found in
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In the long-term, will GaussianKDE live in another module? Or will mlab stay around to host it?

the `NumPy`_ and `SciPy`_ libraries.

.. _NumPy: https://numpy.org
.. _SciPy: https://www.scipy.org
Expand Down Expand Up @@ -58,6 +56,7 @@
from matplotlib import _api, _docstring, cbook


@_api.deprecated("3.7", alternative="np.hanning")
def window_hanning(x):
"""
Return *x* times the Hanning (or Hann) window of len(*x*).
Expand All @@ -69,6 +68,7 @@ def window_hanning(x):
return np.hanning(len(x))*x


@_api.deprecated("3.7")
def window_none(x):
"""
No window function; simply return *x*.
Expand All @@ -80,6 +80,7 @@ def window_none(x):
return x


@_api.deprecated("3.7", alternative="scipy.signal.detrend")
def detrend(x, key=None, axis=None):
"""
Return *x* with its trend removed.
Expand Down Expand Up @@ -129,6 +130,7 @@ def detrend(x, key=None, axis=None):
f"'constant', 'mean', 'linear', or a function")


@_api.deprecated("3.7", alternative="scipy.signal.detrend")
def detrend_mean(x, axis=None):
"""
Return *x* minus the mean(*x*).
Expand Down Expand Up @@ -157,6 +159,7 @@ def detrend_mean(x, axis=None):
return x - x.mean(axis, keepdims=True)


@_api.deprecated("3.7")
def detrend_none(x, axis=None):
"""
Return *x*: no detrending.
Expand All @@ -179,6 +182,7 @@ def detrend_none(x, axis=None):
return x


@_api.deprecated("3.7", alternative="scipy.signal.detrend")
def detrend_linear(y):
"""
Return *x* minus best fit line; 'linear' detrending.
Expand Down Expand Up @@ -213,7 +217,7 @@ def detrend_linear(y):
return y - (b*x + a)


@_api.deprecated("3.6")
@_api.deprecated("3.7")
def stride_windows(x, n, noverlap=None, axis=0):
"""
Get all windows of *x* with length *n* as a single array,
Expand Down Expand Up @@ -531,6 +535,7 @@ def _single_spectrum_helper(
MATLAB compatibility.""")


@_api.deprecated("3.7", alternative="scipy.signal.psd")
@_docstring.dedent_interpd
def psd(x, NFFT=None, Fs=None, detrend=None, window=None,
noverlap=None, pad_to=None, sides=None, scale_by_freq=None):
Expand Down Expand Up @@ -587,6 +592,7 @@ def psd(x, NFFT=None, Fs=None, detrend=None, window=None,
return Pxx.real, freqs


@_api.deprecated("3.7", alternative="scipy.signal.csd")
@_docstring.dedent_interpd
def csd(x, y, NFFT=None, Fs=None, detrend=None, window=None,
noverlap=None, pad_to=None, sides=None, scale_by_freq=None):
Expand Down Expand Up @@ -688,7 +694,6 @@ def csd(x, y, NFFT=None, Fs=None, detrend=None, window=None,
Can return the complex spectrum of segments within the signal.
"""


complex_spectrum = functools.partial(_single_spectrum_helper, "complex")
complex_spectrum.__doc__ = _single_spectrum_docs.format(
quantity="complex-valued frequency spectrum",
Expand All @@ -707,6 +712,7 @@ def csd(x, y, NFFT=None, Fs=None, detrend=None, window=None,
**_docstring.interpd.params)


@_api.deprecated("3.7", alternative="scipy.signal.welch")
@_docstring.dedent_interpd
def specgram(x, NFFT=None, Fs=None, detrend=None, window=None,
noverlap=None, pad_to=None, sides=None, scale_by_freq=None,
Expand Down Expand Up @@ -790,6 +796,7 @@ def specgram(x, NFFT=None, Fs=None, detrend=None, window=None,
return spec, freqs, t


@_api.deprecated("3.7", alternative="scipy.signal.coherence")
@_docstring.dedent_interpd
def cohere(x, y, NFFT=256, Fs=2, detrend=detrend_none, window=window_hanning,
noverlap=0, pad_to=None, sides='default', scale_by_freq=None):
Expand Down
4 changes: 2 additions & 2 deletions lib/matplotlib/pyplot.py
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Original file line number Diff line number Diff line change
Expand Up @@ -3005,8 +3005,8 @@ def vlines(
# Autogenerated by boilerplate.py. Do not edit as changes will be lost.
@_copy_docstring_and_deprecators(Axes.xcorr)
def xcorr(
x, y, normed=True, detrend=mlab.detrend_none, usevlines=True,
maxlags=10, *, data=None, **kwargs):
x, y, normed=True, detrend=None, usevlines=True, maxlags=10,
*, data=None, **kwargs):
return gca().xcorr(
x, y, normed=normed, detrend=detrend, usevlines=usevlines,
maxlags=maxlags,
Expand Down
18 changes: 18 additions & 0 deletions lib/matplotlib/tests/test_axes.py
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Original file line number Diff line number Diff line change
Expand Up @@ -4725,6 +4725,8 @@ def test_subplot_key_hash():
assert ax.get_subplotspec().get_geometry() == (5, 1, 0, 0)


@pytest.mark.filterwarnings(
'ignore::matplotlib._api.deprecation.MatplotlibDeprecationWarning')
@image_comparison(
["specgram_freqs.png", "specgram_freqs_linear.png",
"specgram_noise.png", "specgram_noise_linear.png"],
Expand Down Expand Up @@ -4761,6 +4763,8 @@ def test_specgram():
scale="linear", norm=matplotlib.colors.LogNorm())


@pytest.mark.filterwarnings(
'ignore::matplotlib._api.deprecation.MatplotlibDeprecationWarning')
@image_comparison(
["specgram_magnitude_freqs.png", "specgram_magnitude_freqs_linear.png",
"specgram_magnitude_noise.png", "specgram_magnitude_noise_linear.png"],
Expand Down Expand Up @@ -4798,6 +4802,8 @@ def test_specgram_magnitude():
scale="linear", norm=matplotlib.colors.LogNorm())


@pytest.mark.filterwarnings(
'ignore::matplotlib._api.deprecation.MatplotlibDeprecationWarning')
@image_comparison(
["specgram_angle_freqs.png", "specgram_phase_freqs.png",
"specgram_angle_noise.png", "specgram_phase_noise.png"],
Expand Down Expand Up @@ -4836,13 +4842,17 @@ def test_specgram_angle():
scale="dB")


@pytest.mark.filterwarnings(
'ignore::matplotlib._api.deprecation.MatplotlibDeprecationWarning')
def test_specgram_fs_none():
"""Test axes.specgram when Fs is None, should not throw error."""
spec, freqs, t, im = plt.specgram(np.ones(300), Fs=None, scale='linear')
xmin, xmax, freq0, freq1 = im.get_extent()
assert xmin == 32 and xmax == 96


@pytest.mark.filterwarnings(
'ignore::matplotlib._api.deprecation.MatplotlibDeprecationWarning')
@check_figures_equal(extensions=["png"])
def test_specgram_origin_rcparam(fig_test, fig_ref):
"""Test specgram ignores image.origin rcParam and uses origin 'upper'."""
Expand All @@ -4861,6 +4871,8 @@ def test_specgram_origin_rcparam(fig_test, fig_ref):
fig_test.subplots().specgram(signal)


@pytest.mark.filterwarnings(
'ignore::matplotlib._api.deprecation.MatplotlibDeprecationWarning')
def test_specgram_origin_kwarg():
"""Ensure passing origin as a kwarg raises a TypeError."""
t = np.arange(500)
Expand All @@ -4870,6 +4882,8 @@ def test_specgram_origin_kwarg():
plt.specgram(signal, origin='lower')


@pytest.mark.filterwarnings(
'ignore::matplotlib._api.deprecation.MatplotlibDeprecationWarning')
@image_comparison(
["psd_freqs.png", "csd_freqs.png", "psd_noise.png", "csd_noise.png"],
remove_text=True, tol=0.002)
Expand Down Expand Up @@ -4904,6 +4918,8 @@ def test_psd_csd():
ax.set(xlabel="", ylabel="")


@pytest.mark.filterwarnings(
'ignore::matplotlib._api.deprecation.MatplotlibDeprecationWarning')
@image_comparison(
["magnitude_spectrum_freqs_linear.png",
"magnitude_spectrum_freqs_dB.png",
Expand Down Expand Up @@ -4946,6 +4962,8 @@ def test_spectrum():
ax.set(xlabel="", ylabel="")


@pytest.mark.filterwarnings(
'ignore::matplotlib._api.deprecation.MatplotlibDeprecationWarning')
def test_psd_csd_edge_cases():
# Inverted yaxis or fully zero inputs used to throw exceptions.
axs = plt.figure().subplots(2)
Expand Down
4 changes: 4 additions & 0 deletions lib/matplotlib/tests/test_mlab.py
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Original file line number Diff line number Diff line change
Expand Up @@ -5,6 +5,10 @@

from matplotlib import mlab, _api

# this module is being deprecated as of 3.6, so...
pytestmark = pytest.mark.filterwarnings(
'ignore::matplotlib._api.deprecation.MatplotlibDeprecationWarning')


class TestStride:
def get_base(self, x):
Expand Down