Hello community,
here is the log from the commit of package python-tensorpac for
openSUSE:Factory checked in at 2020-04-07 10:30:26
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
Comparing /work/SRC/openSUSE:Factory/python-tensorpac (Old)
and /work/SRC/openSUSE:Factory/.python-tensorpac.new.3248 (New)
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
Package is "python-tensorpac"
Tue Apr 7 10:30:26 2020 rev:2 rq:791712 version:0.6.3
Changes:
--------
--- /work/SRC/openSUSE:Factory/python-tensorpac/python-tensorpac.changes
2019-12-10 22:41:48.745822712 +0100
+++
/work/SRC/openSUSE:Factory/.python-tensorpac.new.3248/python-tensorpac.changes
2020-04-07 10:31:59.846551431 +0200
@@ -1,0 +2,6 @@
+Mon Apr 6 07:42:03 UTC 2020 - Tomáš Chvátal <[email protected]>
+
+- Update to 0.6.3:
+ * no upstream changelog
+
+-------------------------------------------------------------------
Old:
----
tensorpac-0.6.2.tar.gz
New:
----
tensorpac-0.6.3.tar.gz
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
Other differences:
------------------
++++++ python-tensorpac.spec ++++++
--- /var/tmp/diff_new_pack.GarRk9/_old 2020-04-07 10:32:01.526553619 +0200
+++ /var/tmp/diff_new_pack.GarRk9/_new 2020-04-07 10:32:01.530553624 +0200
@@ -1,7 +1,7 @@
#
# spec file for package python-tensorpac
#
-# Copyright (c) 2019 SUSE LINUX GmbH, Nuernberg, Germany.
+# Copyright (c) 2020 SUSE LLC
#
# All modifications and additions to the file contributed by third parties
# remain the property of their copyright owners, unless otherwise agreed
@@ -17,8 +17,9 @@
%{?!python_module:%define python_module() python-%{**} python3-%{**}}
+%define skip_python2 1
Name: python-tensorpac
-Version: 0.6.2
+Version: 0.6.3
Release: 0
Summary: Tensor-based phase-Amplitude coupling package
License: BSD-3-Clause
@@ -35,9 +36,12 @@
BuildArch: noarch
# SECTION test requirements
BuildRequires: %{python_module joblib}
+BuildRequires: %{python_module matplotlib}
BuildRequires: %{python_module numpy >= 1.12}
+BuildRequires: %{python_module pandas}
BuildRequires: %{python_module pytest}
BuildRequires: %{python_module scipy}
+BuildRequires: %{python_module statsmodels}
# /SECTION
%python_subpackages
@@ -48,6 +52,9 @@
%prep
%setup -q -n tensorpac-%{version}
chmod a-x LICENSE README.rst
+# upstream tarball contains py3.7 cache files
+rm -rf */__pycache__
+rm -rf */*/__pycache__
%build
%python_build
@@ -55,13 +62,11 @@
%install
%python_install
%python_expand chmod a-x %{buildroot}%{$python_sitelib}/*egg-info/*
+%python_expand rm -r
%{buildroot}%{$python_sitelib}/tensorpac/{tests,methods/tests}
%python_expand %fdupes %{buildroot}%{$python_sitelib}
-# Tests missing and no recent tags to download from github. See:
-# https://github.com/EtienneCmb/tensorpac/issues/4
-# https://github.com/EtienneCmb/tensorpac/pull/5
-# %%check
-# %%pytest
+%check
+%pytest
%files %{python_files}
%doc README.rst
++++++ tensorpac-0.6.2.tar.gz -> tensorpac-0.6.3.tar.gz ++++++
diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn'
'--exclude=.svnignore' old/tensorpac-0.6.2/MANIFEST.in
new/tensorpac-0.6.3/MANIFEST.in
--- old/tensorpac-0.6.2/MANIFEST.in 2019-02-06 21:52:32.000000000 +0100
+++ new/tensorpac-0.6.3/MANIFEST.in 2020-03-18 17:25:40.000000000 +0100
@@ -1,3 +1,5 @@
include README.rst
include LICENSE
-include requirements.txt
\ No newline at end of file
+include requirements.txt
+
+recursive-include tensorpac *.*
diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn'
'--exclude=.svnignore' old/tensorpac-0.6.2/PKG-INFO new/tensorpac-0.6.3/PKG-INFO
--- old/tensorpac-0.6.2/PKG-INFO 2019-09-10 11:51:54.000000000 +0200
+++ new/tensorpac-0.6.3/PKG-INFO 2020-03-25 07:57:28.000000000 +0100
@@ -1,13 +1,13 @@
Metadata-Version: 1.2
Name: tensorpac
-Version: 0.6.2
+Version: 0.6.3
Summary: Tensor-based Phase-Amplitude Coupling
Home-page: http://etiennecmb.github.io/tensorpac/
Author: Etienne Combrisson
Author-email: [email protected]
Maintainer: Etienne Combrisson
License: BSD 3-Clause License
-Download-URL: https://github.com/EtienneCmb/tensorpac/archive/v0.6.2.tar.gz
+Download-URL: https://github.com/EtienneCmb/tensorpac/archive/v0.6.3.tar.gz
Description: =========
Tensorpac
=========
@@ -78,18 +78,6 @@
.. figure::
https://github.com/EtienneCmb/tensorpac/blob/master/docs/source/picture/readme.png
:align: center
- Contributors
- ------------
-
- * `Etienne Combrisson <http://etiennecmb.github.io>`_
- * `Karim Jerbi <http://www.karimjerbi.com>`_
- * Juan L.P. Soto
- * Timothy C. Nest
- * `Robin Ince <http://www.robinince.net/about.html>`_
- * `Andrea Brovelli <http://andrea-brovelli.net/>`_
- * `Aymeric Guillot
<https://libm.univ-st-etienne.fr/fr/les-membres-du-libm/les-enseignants-chercheurs/guillot-aymeric.html>`_
-
-
Keywords: phase-amplitude coupling pac tensor oscillation meg eeg python
Platform: any
Classifier: Development Status :: 5 - Production/Stable
diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn'
'--exclude=.svnignore' old/tensorpac-0.6.2/README.rst
new/tensorpac-0.6.3/README.rst
--- old/tensorpac-0.6.2/README.rst 2019-08-06 14:20:40.000000000 +0200
+++ new/tensorpac-0.6.3/README.rst 2020-03-25 07:53:16.000000000 +0100
@@ -67,15 +67,3 @@
.. figure::
https://github.com/EtienneCmb/tensorpac/blob/master/docs/source/picture/readme.png
:align: center
-
-Contributors
-------------
-
-* `Etienne Combrisson <http://etiennecmb.github.io>`_
-* `Karim Jerbi <http://www.karimjerbi.com>`_
-* Juan L.P. Soto
-* Timothy C. Nest
-* `Robin Ince <http://www.robinince.net/about.html>`_
-* `Andrea Brovelli <http://andrea-brovelli.net/>`_
-* `Aymeric Guillot
<https://libm.univ-st-etienne.fr/fr/les-membres-du-libm/les-enseignants-chercheurs/guillot-aymeric.html>`_
-
diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn'
'--exclude=.svnignore' old/tensorpac-0.6.2/setup.py new/tensorpac-0.6.3/setup.py
--- old/tensorpac-0.6.2/setup.py 2019-09-10 11:39:55.000000000 +0200
+++ new/tensorpac-0.6.3/setup.py 2020-03-25 07:56:30.000000000 +0100
@@ -4,7 +4,7 @@
import os
from setuptools import setup, find_packages
-__version__ = "0.6.2"
+__version__ = "0.6.3"
NAME = 'tensorpac'
AUTHOR = "Etienne Combrisson"
MAINTAINER = "Etienne Combrisson"
diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn'
'--exclude=.svnignore' old/tensorpac-0.6.2/tensorpac/__init__.py
new/tensorpac-0.6.3/tensorpac/__init__.py
--- old/tensorpac-0.6.2/tensorpac/__init__.py 2019-09-10 11:40:03.000000000
+0200
+++ new/tensorpac-0.6.3/tensorpac/__init__.py 2020-03-25 07:56:41.000000000
+0100
@@ -14,4 +14,4 @@
logger = logging.getLogger('brainets')
set_log_level('info')
-__version__ = "0.6.2"
+__version__ = "0.6.3"
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diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn'
'--exclude=.svnignore' old/tensorpac-0.6.2/tensorpac/methods/meth_pac.py
new/tensorpac-0.6.3/tensorpac/methods/meth_pac.py
--- old/tensorpac-0.6.2/tensorpac/methods/meth_pac.py 2019-08-26
09:29:35.000000000 +0200
+++ new/tensorpac-0.6.3/tensorpac/methods/meth_pac.py 2020-03-23
08:12:50.000000000 +0100
@@ -172,7 +172,7 @@
return pac
-def _kl_hr(pha, amp, n_bins):
+def _kl_hr(pha, amp, n_bins, mean_bins=True):
"""Binarize the amplitude according to phase values.
This function is shared by the Kullback-Leibler Distance and the
@@ -185,8 +185,9 @@
for i in np.unique(phad):
# Find where phase take vecbin values :
idx = phad == i
+ m = idx.sum() if mean_bins else 1.
# Take the sum of amplitude inside the bin :
- abin_pha = np.einsum('i...j, k...j->ik...', amp, idx) / idx.sum()
+ abin_pha = np.einsum('i...j, k...j->ik...', amp, idx) / m
abin.append(abin_pha)
return np.array(abin)
@@ -201,7 +202,9 @@
Respectively the arrays of phases of shape (n_pha, ..., n_times) and
the array of amplitudes of shape (n_amp, ..., n_times).
p : float | .05
- P-value to use for thresholding
+ P-value to use for thresholding. Sub-threshold PAC values
+ will be set to 0. To disable this behavior (no masking), use ``p=1`` or
+ ``p=None``.
Returns
-------
@@ -216,35 +219,42 @@
"""
npts = amp.shape[-1]
# Normalize amplitude :
- np.subtract(amp, np.mean(amp, axis=-1, keepdims=True), out=amp)
- np.divide(amp, np.std(amp, axis=-1, keepdims=True), out=amp)
+ # Use the sample standard deviation, as in original Matlab code from author
+ amp = np.subtract(amp, np.mean(amp, axis=-1, keepdims=True))
+ amp = np.divide(amp, np.std(amp, ddof=1, axis=-1, keepdims=True))
# Compute pac :
pac = np.abs(np.einsum('i...j, k...j->ik...', amp, np.exp(1j * pha)))
- pac *= pac / npts
+
+ if p == 1. or p is None:
+ # No thresholding
+ return pac / npts
+
+ s = pac**2
+ pac /= npts
# Set to zero non-significant values:
- xlim = erfinv(1 - p)**2
- pac[pac <= 2 * xlim] = 0.
+ xlim = npts * erfinv(1 - p)**2
+ pac[s <= 2 * xlim] = 0.
return pac
-def ps(pha, amp):
+def ps(pha, pha_amp):
"""Phase Synchrony (Penny, 2008; Cohen, 2008).
- In order to measure the phase synchrony, the phase of the amplitude must be
- provided.
+ In order to measure the phase synchrony, the phase of the amplitude of the
+ higher-frequency signal must be provided, and not the amplitude as in most
+ other PAC functions.
Parameters
----------
- pha, amp : array_like
- Respectively the arrays of phases of shape (n_pha, ..., n_times) and
- the array of amplitudes of shape (n_amp, ..., n_times).
- n_bins : int | 18
- Number of bins to binarize the amplitude according to phase intervals
+ pha, pha_amp : array_like
+ Respectively the arrays of phases of shape (n_pha, ..., n_times) for
+ the lower frequency and the array of phase of the amplitude signal of
+ shape (n_pha_amp, ..., n_times) for the higher frequency.
Returns
-------
pac : array_like
- Array of phase amplitude coupling of shape (n_amp, n_pha, ...)
+ Array of phase amplitude coupling of shape (n_pha_amp, n_pha, ...)
References
----------
@@ -254,7 +264,8 @@
coupling in the human medial frontal cortex during decision making. Journal
of cognitive neuroscience 21:390–402.
"""
- pac = np.einsum('i...j, k...j->ik...', np.exp(-1j * amp), np.exp(1j * pha))
+ pac = np.einsum('i...j, k...j->ik...', np.exp(-1j * pha_amp),
+ np.exp(1j * pha))
return np.abs(pac) / pha.shape[-1]
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old/tensorpac-0.6.2/tensorpac/methods/tests/test_pac_methods.py
new/tensorpac-0.6.3/tensorpac/methods/tests/test_pac_methods.py
--- old/tensorpac-0.6.2/tensorpac/methods/tests/test_pac_methods.py
1970-01-01 01:00:00.000000000 +0100
+++ new/tensorpac-0.6.3/tensorpac/methods/tests/test_pac_methods.py
2020-03-23 08:12:50.000000000 +0100
@@ -0,0 +1,112 @@
+"""Test PAC methods."""
+import numpy as np
+from tensorpac.methods.meth_pac import get_pac_fcn, pacstr
+from tensorpac.methods.meth_surrogates import compute_surrogates, normalize
+from tensorpac.methods.meth_pp import preferred_phase
+from tensorpac.methods.meth_erpac import erpac, ergcpac, _ergcpac_perm
+
+n_pac_range = range(1, 7)
+n_sur_range = range(4)
+n_norm_range = range(1, 5)
+
+n_epochs = 5
+n_times = 1000
+n_pha_freqs = 2
+n_amp_freqs = 3
+n_bins = 18
+pval = .05
+n_perm = 2
+
+pha = np.random.uniform(-np.pi, np.pi, (n_pha_freqs, n_epochs, n_times))
+amp = np.random.rand(n_amp_freqs, n_epochs, n_times)
+
+
+class TestMethods(object):
+ """Test individual pac methods."""
+
+ @staticmethod
+ def _get_methods():
+ meths = []
+ q = 1
+ while q is not None:
+ try:
+ meths += [get_pac_fcn(q, n_bins, pval)]
+ q += 1
+ except ValueError as e: # noqa
+ q = None
+ return meths
+
+ def test_pacstr(self):
+ """Test getting pas string name."""
+ for p in n_pac_range:
+ for s in n_sur_range:
+ for n in n_norm_range:
+ names = pacstr((p, s, n))
+ assert all([isinstance(k, str) for k in names])
+ # test assert error
+ try:
+ pacstr((p + 1, s, n))
+ except ValueError as e: # noqa
+ pass
+ try:
+ pacstr((p, s + 1, n))
+ except ValueError as e: # noqa
+ pass
+ try:
+ pacstr((p, s, n + 1))
+ except ValueError as e: # noqa
+ pass
+
+ def test_pac_methods(self):
+ """Test individual pac methods."""
+ for n, meth in enumerate(self._get_methods()):
+ if n + 1 == 6: # gc pac need additional multivariate axis
+ _pha = np.stack([np.sin(pha), np.cos(pha)], axis=-2)
+ _amp = amp[..., np.newaxis, :]
+ pac = meth(_pha, _amp)
+ elif n + 1 == 4: # Try with different values of p for coverage
+ pac = meth(pha, amp, p=0.5)
+ pac = meth(pha, amp, p=1)
+ pac = meth(pha, amp, p=None)
+ else:
+ pac = meth(pha, amp)
+ assert pac.shape == (n_amp_freqs, n_pha_freqs, n_epochs)
+
+ def test_surrogates(self):
+ """Test computing surrogates."""
+ fcn = get_pac_fcn(1, n_bins, pval)
+ s_shape = (n_perm, n_amp_freqs, n_pha_freqs, n_epochs)
+ for s in n_sur_range:
+ surro = compute_surrogates(pha, amp, s, fcn, n_perm, 1)
+ assert (surro is None) or (surro.shape == s_shape)
+
+ def test_normalize(self):
+ """Test normalization."""
+ for k in n_norm_range:
+ true_pac = np.random.rand(n_amp_freqs, n_pha_freqs)
+ perm_pac = np.random.rand(n_perm, n_amp_freqs, n_pha_freqs)
+ normalize(k, true_pac, perm_pac)
+
+ def test_erpac(self):
+ """Test event-related PAC."""
+ er_pha, er_amp = np.moveaxis(pha, -2, -1), np.moveaxis(amp, -2, -1)
+ # circular
+ er_circ, pv_circ = erpac(er_pha, er_amp)
+ assert er_circ.shape == pv_circ.shape
+ assert er_circ.shape == (n_amp_freqs, n_pha_freqs, n_times)
+ # gaussian copula
+ _pha = np.stack([np.sin(er_pha), np.cos(er_pha)], axis=-2)
+ _amp = er_amp[..., np.newaxis, :]
+ ergc_circ = ergcpac(_pha, _amp, smooth=None)
+ assert ergc_circ.shape == (n_amp_freqs, n_pha_freqs, n_times)
+ ergcpac(_pha, _amp, smooth=5)
+ # test erpac permutations
+ ergc_perm = _ergcpac_perm(_pha, _amp, smooth=None, n_perm=n_perm)
+ assert ergc_perm.shape == (n_perm, n_amp_freqs, n_pha_freqs, n_times)
+
+ def test_preferred_phase(self):
+ """Test preferred phase method."""
+ bin_amp, pp, fvec = preferred_phase(pha, amp, n_bins)
+ assert bin_amp.shape == (n_bins, n_amp_freqs, n_pha_freqs, n_epochs)
+ assert pp.shape == (n_amp_freqs, n_pha_freqs, n_epochs)
+ assert fvec.shape == (n_bins,)
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diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn'
'--exclude=.svnignore' old/tensorpac-0.6.2/tensorpac/tests/test_gcmi.py
new/tensorpac-0.6.3/tensorpac/tests/test_gcmi.py
--- old/tensorpac-0.6.2/tensorpac/tests/test_gcmi.py 1970-01-01
01:00:00.000000000 +0100
+++ new/tensorpac-0.6.3/tensorpac/tests/test_gcmi.py 2019-10-07
16:13:11.000000000 +0200
@@ -0,0 +1,28 @@
+"""Test gcmi related functions."""
+import numpy as np
+
+from tensorpac.gcmi import copnorm, nd_mi_gg
+from tensorpac.config import CONFIG
+
+
+class TestGcmi(object):
+ """Test GCMI functions."""
+
+ def test_copnorm(self):
+ """Test Gaussian-copula normalization."""
+ x = np.random.rand(10, 20, 30)
+ copnorm(x)
+
+ def test_mi(self):
+ """Test computing MI."""
+ rng = np.random.RandomState(0)
+ x = rng.rand(100, 1, 100)
+ y = rng.rand(100, 1, 100)
+ # basic config
+ nd_mi_gg(x, y)
+ # modified config
+ CONFIG['MI_DEMEAN'] = True
+ CONFIG['MI_BIASCORRECT'] = True
+ nd_mi_gg(x, y)
+ CONFIG['MI_BIASCORRECT'] = False
+ CONFIG['MI_DEMEAN'] = False
diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn'
'--exclude=.svnignore' old/tensorpac-0.6.2/tensorpac/tests/test_io.py
new/tensorpac-0.6.3/tensorpac/tests/test_io.py
--- old/tensorpac-0.6.2/tensorpac/tests/test_io.py 1970-01-01
01:00:00.000000000 +0100
+++ new/tensorpac-0.6.3/tensorpac/tests/test_io.py 2019-10-07
16:13:11.000000000 +0200
@@ -0,0 +1,42 @@
+"""Test I/O."""
+import logging
+
+from tensorpac.io import (set_log_level, is_pandas_installed,
+ is_statsmodels_installed, progress_bar)
+
+logger = logging.getLogger('tensorpac')
+
+
+levels = ['profiler', 'debug', 'info', 'warning', 'error', 'critical']
+
+
+class TestIO(object):
+ """Test statistical functions."""
+
+ def test_log_level(self):
+ """Test setting the log level."""
+ for l in levels:
+ set_log_level(l)
+ set_log_level(False)
+ set_log_level(True)
+ set_log_level(match="ok")
+ logger.info("show me ok")
+ logger.info("show me")
+
+ def test_logger(self):
+ """Test logger levels."""
+ set_log_level("profiler")
+ logger.profiler("profiler")
+ logger.debug("debug")
+ logger.info("info")
+ logger.warning("warning")
+ logger.critical("critical")
+
+ def test_progress_bar(self):
+ """Test progress bar."""
+ progress_bar(5, 10)
+
+ def test_dependance(self):
+ """Test dependancies."""
+ is_statsmodels_installed()
+ is_pandas_installed()
diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn'
'--exclude=.svnignore' old/tensorpac-0.6.2/tensorpac/tests/test_pac.py
new/tensorpac-0.6.3/tensorpac/tests/test_pac.py
--- old/tensorpac-0.6.2/tensorpac/tests/test_pac.py 1970-01-01
01:00:00.000000000 +0100
+++ new/tensorpac-0.6.3/tensorpac/tests/test_pac.py 2019-10-07
16:13:11.000000000 +0200
@@ -0,0 +1,174 @@
+"""Test tensorpac functions."""
+import numpy as np
+import matplotlib
+
+from tensorpac import Pac, EventRelatedPac, PreferredPhase
+from tensorpac.utils import pac_trivec
+
+
+class TestPac(object):
+ """Tests for Pac, Erpac and Preferred phase."""
+
+ def test_id_pac_definition(self):
+ """Test Pac object definition."""
+ nmeth, nsuro, nnorm = 6, 4, 5
+ for k in range(nmeth):
+ for i in range(nsuro):
+ for j in range(nnorm):
+ p = Pac(idpac=(k + 1, i, j))
+ str(p)
+
+ def test_filtering_definition(self):
+ """Test filtering defintion."""
+ dcomplex = ['hilbert', 'wavelet']
+ cycle = (12, 24)
+ width = 12
+ for k in dcomplex:
+ Pac(dcomplex=k, cycle=cycle, width=width)
+
+ def test_spectral(self):
+ """Test filtering using the provided filters."""
+ data = np.random.rand(3, 1000)
+ p = Pac()
+ dcomplex = ['hilbert', 'wavelet']
+ for k in dcomplex:
+ p.dcomplex = k
+ p.filter(1024, data, n_jobs=1)
+
+ def test_filter(self):
+ """Test filter method."""
+ data = np.random.rand(2, 1000)
+ p = Pac()
+ p.filter(256, data, 'phase')
+ p.filter(256, data, 'phase', edges=2)
+ p.filter(256, data, 'amplitude')
+
+ def test_fit(self):
+ """Test all Pac methods."""
+ pha = np.random.rand(2, 7, 1024)
+ amp = np.random.rand(3, 7, 1024)
+ nmeth, nsuro, nnorm = 5, 4, 5
+ p = Pac()
+ for k in range(nmeth):
+ for i in range(nsuro):
+ for j in range(nnorm):
+ p.idpac = (k + 1, i, j)
+ p.fit(pha, amp, n_jobs=1, n_perm=10)
+
+ def test_filterfit(self):
+ """Test filtering test computing PAC."""
+ data = np.random.rand(2, 1024)
+ p = Pac(idpac=(4, 0, 0))
+ p.filterfit(1024, data, n_jobs=1)
+ p.idpac = (1, 1, 1)
+ p.filterfit(1024, data, data, n_jobs=1, n_perm=2)
+ p.dcomplex = 'wavelet'
+ p.filter(1024, data, n_jobs=1)
+
+ def test_properties(self):
+ """Test Pac properties."""
+ p = Pac()
+ # Idpac :
+ p.idpac
+ p.idpac = (2, 1, 1)
+ # Dcomplex :
+ p.dcomplex
+ p.dcomplex = 'wavelet'
+ # Cycle :
+ p.cycle
+ p.cycle = (12, 24)
+ # Width :
+ p.width
+ p.width = 12
+
+ def test_pac_comodulogram(self):
+ """Test Pac object definition.
+
+ This test works locally but failed on travis...
+ """
+ matplotlib.use('agg')
+ f, tridx = pac_trivec()
+ pac = np.random.rand(20, 10)
+ pval = np.random.rand(20, 10)
+ p = Pac(f_pha=np.arange(11), f_amp=np.arange(21))
+ p.comodulogram(np.random.rand(10, 10, 20))
+ p.comodulogram(pac, rmaxis=True, dpaxis=True, interp=(.1, .1))
+ p.comodulogram(pac, plotas='contour', pvalues=pval)
+ p.comodulogram(pac, plotas='pcolor', pvalues=pval, levels=[.5, .7],
+ under='gray', over='red', bad='orange')
+ p = Pac(f_pha=np.arange(11), f_amp=f)
+ pac = np.random.rand(len(f))
+ p.triplot(pac, f, tridx)
+ p.savefig('test_savefig.png')
+ p.show()
+ matplotlib.pyplot.close('all')
+
+
+class TestErpac(object):
+ """Test EventRelatedPac class."""
+
+ def test_filter(self):
+ """Test function filter."""
+ data = np.random.rand(7, 1000)
+ p = EventRelatedPac()
+ p.filter(256, data, 'phase')
+ p.filter(256, data, 'amplitude')
+
+ def test_fit(self):
+ """Test function fit."""
+ data = np.random.rand(100, 1000)
+ p = EventRelatedPac()
+ pha = p.filter(256, data, 'phase')
+ amp = p.filter(256, data, 'amplitude')
+ p.fit(pha, amp, method='circular')
+ p.fit(pha, amp, method='gc')
+ p.fit(pha, amp, method='gc', n_perm=2)
+ p.fit(pha, amp, method='gc', smooth=5)
+ p.surrogates, p.pvalues
+
+ def test_filterfit(self):
+ """Test function filterfit."""
+ p = EventRelatedPac()
+ x_pha = np.random.rand(100, 1000)
+ x_amp = np.random.rand(100, 1000)
+ p.filterfit(256, x_pha, x_amp=x_amp, method='circular')
+ p.filterfit(256, x_pha, x_amp=x_amp, method='gc')
+
+
+class TestPreferredPhase(object):
+ """Test EventRelatedPac class."""
+
+ def test_filter(self):
+ """Test function filter."""
+ data = np.random.rand(7, 1000)
+ p = PreferredPhase()
+ p.filter(256, data, 'phase')
+ p.filter(256, data, 'amplitude')
+
+ def test_fit(self):
+ """Test function fit."""
+ data = np.random.rand(100, 1000)
+ p = PreferredPhase()
+ pha = p.filter(256, data, 'phase')
+ amp = p.filter(256, data, 'amplitude')
+ p.fit(pha, amp)
+
+ def test_filterfit(self):
+ """Test function filterfit."""
+ p = PreferredPhase()
+ x_pha = np.random.rand(100, 1000)
+ x_amp = np.random.rand(100, 1000)
+ p.filterfit(256, x_pha, x_amp=x_amp)
+
+ def test_polar_plot(self):
+ """Test the polar plot."""
+ matplotlib.use('agg')
+ p = PreferredPhase(f_pha=[5, 7], f_amp=(60, 200, 10, 1))
+ x_pha = np.random.rand(100, 1000)
+ x_amp = np.random.rand(100, 1000)
+ ampbin, pp, vecbin = p.filterfit(256, x_pha, x_amp=x_amp)
+ pp = np.squeeze(pp).T
+ ampbin = np.squeeze(ampbin).mean(-1)
+ p.polar(ampbin.T, vecbin, p.yvec, cmap='RdBu_r', interp=.1,
+ cblabel='Amplitude bins')
+ matplotlib.pyplot.close('all')
diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn'
'--exclude=.svnignore' old/tensorpac-0.6.2/tensorpac/tests/test_signals.py
new/tensorpac-0.6.3/tensorpac/tests/test_signals.py
--- old/tensorpac-0.6.2/tensorpac/tests/test_signals.py 1970-01-01
01:00:00.000000000 +0100
+++ new/tensorpac-0.6.3/tensorpac/tests/test_signals.py 2019-10-07
16:13:11.000000000 +0200
@@ -0,0 +1,25 @@
+"""Test random signals generation."""
+import numpy as np
+
+from tensorpac.signals import pac_signals_wavelet, pac_signals_tort
+
+
+class TestSignals(object):
+ """Test random signals generation."""
+
+ def test_pac_signals_dtrials(self):
+ """Definition of artificially coupled signals using dPha/dAmp."""
+ assert pac_signals_tort(f_pha=5, f_amp=130, sf=512, n_epochs=23,
+ chi=0.9, noise=2, dpha=35, damp=46)
+
+ def test_pac_signals_bandwidth(self):
+ """Definition of artificially coupled signals using bandwidth."""
+ assert pac_signals_tort(f_pha=[5, 7], f_amp=[30, 60], sf=200.,
+ n_epochs=100, chi=0.5, noise=3., n_times=1000)
+ assert pac_signals_wavelet(f_pha=10, f_amp=57., n_times=1240, sf=256,
+ noise=.7, n_epochs=33, pp=np.pi / 4,
+ rnd_state=23)
+
+ def test_default_args(self):
+ """Test default aurguments for pac_vec."""
+ assert pac_signals_tort(chi=2., noise=11., dpha=120., damp=200.)
diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn'
'--exclude=.svnignore' old/tensorpac-0.6.2/tensorpac/tests/test_stats.py
new/tensorpac-0.6.3/tensorpac/tests/test_stats.py
--- old/tensorpac-0.6.2/tensorpac/tests/test_stats.py 1970-01-01
01:00:00.000000000 +0100
+++ new/tensorpac-0.6.3/tensorpac/tests/test_stats.py 2019-10-07
16:13:11.000000000 +0200
@@ -0,0 +1,19 @@
+"""Test stastical functions."""
+import numpy as np
+
+from tensorpac.stats import test_stationarity as stats_stationarity
+
+n_epochs = 8
+n_times = 200
+sf = 128.
+pval = .05
+rng = np.random.RandomState(1)
+data = rng.rand(n_epochs, n_times)
+
+
+class TestStats(object):
+ """Test statistical functions."""
+
+ def test_stats_stationarity(self):
+ """Test the stationarity."""
+ stats_stationarity(data, p=pval)
diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn'
'--exclude=.svnignore' old/tensorpac-0.6.2/tensorpac/tests/test_utils.py
new/tensorpac-0.6.3/tensorpac/tests/test_utils.py
--- old/tensorpac-0.6.2/tensorpac/tests/test_utils.py 1970-01-01
01:00:00.000000000 +0100
+++ new/tensorpac-0.6.3/tensorpac/tests/test_utils.py 2019-10-07
16:13:11.000000000 +0200
@@ -0,0 +1,68 @@
+"""Test tensorpac utils."""
+import numpy as np
+import matplotlib
+
+from tensorpac.utils import pac_vec, pac_trivec, PSD, BinAmplitude, PLV
+
+
+class TestUtils(object):
+ """Test utility functions."""
+
+ def test_pac_vec(self):
+ """Definition of PAC vectors."""
+ assert pac_vec()
+ assert pac_vec(f_pha=(1, 30, 2, 2), f_amp=(60, 200, 10, 5))
+ assert pac_vec(f_pha=[1, 2], f_amp=np.arange(50))
+ assert pac_vec(f_pha=np.array([[2, 4], [5, 7], [9, 10]]),
+ f_amp=np.array([[30, 60], [60, 90], [100, 200]]).T)
+ assert pac_vec(f_pha=[[1, 2], [5, 7]], f_amp=[60, 150])
+ assert pac_vec(f_pha='lres', f_amp='lres')
+ assert pac_vec(f_pha='mres', f_amp='mres')
+ assert pac_vec(f_pha='hres', f_amp='hres')
+
+ def test_trivec(self):
+ """Definition of triangular vectors."""
+ assert pac_trivec(2, 200, 10)
+
+ def test_psd(self):
+ """Test PSD."""
+ # test definition
+ x = np.random.rand(10, 200)
+ psd = PSD(x, 128)
+ # test properties
+ psd.freqs
+ psd.psd
+ # test plotting
+ matplotlib.use('agg')
+ psd.plot(confidence=None, log=True, grid=True, interp=.1)
+ psd.plot(confidence=.95, log=False, grid=False, interp=None)
+ psd.show()
+ matplotlib.pyplot.close('all')
+
+ def test_binned_amplitude(self):
+ """Test binned amplitude."""
+ # test definition
+ x = np.random.rand(10, 200)
+ binamp = BinAmplitude(x, 128)
+ # test plot
+ binamp.plot(unit='rad')
+ binamp.plot(unit='deg')
+ binamp.show()
+ matplotlib.pyplot.close('all')
+ # test properties
+ binamp.phase
+ binamp.amplitude
+
+ def test_plv(self):
+ """Test Phase-locking Value."""
+ # test definition
+ x = np.random.rand(10, 200)
+ plv_1d = PLV(x, 128, f_pha=[2, 4])
+ plv_2d = PLV(x, 128, f_pha=[[2, 4], [5, 7]])
+ # test properties
+ plv_1d.plv
+ # test plot
+ plv_1d.plot()
+ plv_2d.plot()
+ plv_1d.show()
+ matplotlib.pyplot.close('all')
diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn'
'--exclude=.svnignore' old/tensorpac-0.6.2/tensorpac/utils.py
new/tensorpac-0.6.3/tensorpac/utils.py
--- old/tensorpac-0.6.2/tensorpac/utils.py 2019-08-20 12:20:55.000000000
+0200
+++ new/tensorpac-0.6.3/tensorpac/utils.py 2019-10-16 10:45:09.000000000
+0200
@@ -264,7 +264,7 @@
pha = self.filter(sf, x, 'phase', **kw)
amp = self.filter(sf, x, 'amplitude', **kw)
# binarize amplitude according to phase
- self._amplitude = _kl_hr(pha, amp, n_bins).squeeze()
+ self._amplitude = _kl_hr(pha, amp, n_bins, mean_bins=False).squeeze()
self.n_bins = n_bins
def plot(self, unit='rad', **kw):
diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn'
'--exclude=.svnignore' old/tensorpac-0.6.2/tensorpac/visu.py
new/tensorpac-0.6.3/tensorpac/visu.py
--- old/tensorpac-0.6.2/tensorpac/visu.py 2019-08-20 12:21:59.000000000
+0200
+++ new/tensorpac-0.6.3/tensorpac/visu.py 2019-10-16 11:00:33.000000000
+0200
@@ -172,8 +172,9 @@
if polar:
ax.grid(True)
ax.set_rlabel_position(0)
- ax.set_thetamin(0)
- ax.set_thetamax(360)
+ ax.set_thetamin(-180)
+ ax.set_thetamax(180)
+ ax.set_thetagrids([-135, -90, -45, 0, 45, 90, 135, 180])
return plt.gca()
diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn'
'--exclude=.svnignore' old/tensorpac-0.6.2/tensorpac.egg-info/PKG-INFO
new/tensorpac-0.6.3/tensorpac.egg-info/PKG-INFO
--- old/tensorpac-0.6.2/tensorpac.egg-info/PKG-INFO 2019-09-10
11:51:54.000000000 +0200
+++ new/tensorpac-0.6.3/tensorpac.egg-info/PKG-INFO 2020-03-25
07:57:27.000000000 +0100
@@ -1,13 +1,13 @@
Metadata-Version: 1.2
Name: tensorpac
-Version: 0.6.2
+Version: 0.6.3
Summary: Tensor-based Phase-Amplitude Coupling
Home-page: http://etiennecmb.github.io/tensorpac/
Author: Etienne Combrisson
Author-email: [email protected]
Maintainer: Etienne Combrisson
License: BSD 3-Clause License
-Download-URL: https://github.com/EtienneCmb/tensorpac/archive/v0.6.2.tar.gz
+Download-URL: https://github.com/EtienneCmb/tensorpac/archive/v0.6.3.tar.gz
Description: =========
Tensorpac
=========
@@ -78,18 +78,6 @@
.. figure::
https://github.com/EtienneCmb/tensorpac/blob/master/docs/source/picture/readme.png
:align: center
- Contributors
- ------------
-
- * `Etienne Combrisson <http://etiennecmb.github.io>`_
- * `Karim Jerbi <http://www.karimjerbi.com>`_
- * Juan L.P. Soto
- * Timothy C. Nest
- * `Robin Ince <http://www.robinince.net/about.html>`_
- * `Andrea Brovelli <http://andrea-brovelli.net/>`_
- * `Aymeric Guillot
<https://libm.univ-st-etienne.fr/fr/les-membres-du-libm/les-enseignants-chercheurs/guillot-aymeric.html>`_
-
-
Keywords: phase-amplitude coupling pac tensor oscillation meg eeg python
Platform: any
Classifier: Development Status :: 5 - Production/Stable
diff -urN '--exclude=CVS' '--exclude=.cvsignore' '--exclude=.svn'
'--exclude=.svnignore' old/tensorpac-0.6.2/tensorpac.egg-info/SOURCES.txt
new/tensorpac-0.6.3/tensorpac.egg-info/SOURCES.txt
--- old/tensorpac-0.6.2/tensorpac.egg-info/SOURCES.txt 2019-09-10
11:51:54.000000000 +0200
+++ new/tensorpac-0.6.3/tensorpac.egg-info/SOURCES.txt 2020-03-25
07:57:27.000000000 +0100
@@ -18,8 +18,43 @@
tensorpac.egg-info/dependency_links.txt
tensorpac.egg-info/requires.txt
tensorpac.egg-info/top_level.txt
+tensorpac/__pycache__/__init__.cpython-37.pyc
+tensorpac/__pycache__/config.cpython-37.pyc
+tensorpac/__pycache__/filtering.cpython-37.pyc
+tensorpac/__pycache__/gcmi.cpython-37.pyc
+tensorpac/__pycache__/io.cpython-37.pyc
+tensorpac/__pycache__/memory.cpython-37.pyc
+tensorpac/__pycache__/methods.cpython-37.pyc
+tensorpac/__pycache__/normalize.cpython-37.pyc
+tensorpac/__pycache__/pac.cpython-37.pyc
+tensorpac/__pycache__/pacstr.cpython-37.pyc
+tensorpac/__pycache__/signals.cpython-37.pyc
+tensorpac/__pycache__/spectral.cpython-37.pyc
+tensorpac/__pycache__/stats.cpython-37.pyc
+tensorpac/__pycache__/surrogates.cpython-37.pyc
+tensorpac/__pycache__/utils.cpython-37.pyc
+tensorpac/__pycache__/visu.cpython-37.pyc
tensorpac/methods/__init__.py
tensorpac/methods/meth_erpac.py
tensorpac/methods/meth_pac.py
tensorpac/methods/meth_pp.py
-tensorpac/methods/meth_surrogates.py
\ No newline at end of file
+tensorpac/methods/meth_surrogates.py
+tensorpac/methods/__pycache__/__init__.cpython-37.pyc
+tensorpac/methods/__pycache__/meth_erpac.cpython-37.pyc
+tensorpac/methods/__pycache__/meth_pac.cpython-37.pyc
+tensorpac/methods/__pycache__/meth_pp.cpython-37.pyc
+tensorpac/methods/__pycache__/meth_surrogates.cpython-37.pyc
+tensorpac/methods/tests/test_pac_methods.py
+tensorpac/methods/tests/__pycache__/test_pac_methods.cpython-37-PYTEST.pyc
+tensorpac/tests/test_gcmi.py
+tensorpac/tests/test_io.py
+tensorpac/tests/test_pac.py
+tensorpac/tests/test_signals.py
+tensorpac/tests/test_stats.py
+tensorpac/tests/test_utils.py
+tensorpac/tests/__pycache__/test_gcmi.cpython-37-PYTEST.pyc
+tensorpac/tests/__pycache__/test_io.cpython-37-PYTEST.pyc
+tensorpac/tests/__pycache__/test_pac.cpython-37-PYTEST.pyc
+tensorpac/tests/__pycache__/test_signals.cpython-37-PYTEST.pyc
+tensorpac/tests/__pycache__/test_stats.cpython-37-PYTEST.pyc
+tensorpac/tests/__pycache__/test_utils.cpython-37-PYTEST.pyc
\ No newline at end of file
