Plot_00 for testing

.github/workflows/main.yml → .github/workflows/circle_artifacts.yml

@@ -1,7 +1,7 @@
 on: [status]
 jobs:
   circleci_artifacts_redirector_job:
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-20.04
     name: Run CircleCI artifacts redirector
     steps:
       - name: GitHub Action step

.github/workflows/codespell_and_flake.yml

@@ -10,7 +10,7 @@ on:
 jobs:
   style:
     if: "github.repository == 'mne-tools/mne-python' && !contains(github.event.head_commit.message, '[ci skip]') && !contains(github.event.head_commit.message, '[skip ci]') && !contains(github.event.head_commit.message, '[skip github]')"
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-20.04
     env:
       CODESPELL_DIRS: 'mne/ doc/ tutorials/ examples/'
       CODESPELL_SKIPS: 'doc/auto_*,*.fif,*.eve,*.gz,*.tgz,*.zip,*.mat,*.stc,*.label,*.w,*.bz2,*.annot,*.sulc,*.log,*.local-copy,*.orig_avg,*.inflated_avg,*.gii,*.pyc,*.doctree,*.pickle,*.inv,*.png,*.edf,*.touch,*.thickness,*.nofix,*.volume,*.defect_borders,*.mgh,lh.*,rh.*,COR-*,FreeSurferColorLUT.txt,*.examples,.xdebug_mris_calc,bad.segments,BadChannels,*.hist,empty_file,*.orig,*.js,*.map,*.ipynb,searchindex.dat,install_mne_c.rst,plot_*.rst,*.rst.txt,c_EULA.rst*,*.html,gdf_encodes.txt,*.svg'

.github/workflows/compat_minimal.yml

@@ -12,7 +12,7 @@ jobs:
   job:
     if: "github.repository == 'mne-tools/mne-python' && !contains(github.event.head_commit.message, '[ci skip]') && !contains(github.event.head_commit.message, '[skip ci]') && !contains(github.event.head_commit.message, '[skip github]')"
     name: 'py3.7'
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-20.04
     defaults:
       run:
         shell: bash

.github/workflows/compat_old.yml

@@ -12,7 +12,7 @@ jobs:
   job:
     if: "github.repository == 'mne-tools/mne-python' && !contains(github.event.head_commit.message, '[ci skip]') && !contains(github.event.head_commit.message, '[skip ci]') && !contains(github.event.head_commit.message, '[skip github]')"
     name: 'py3.6'
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-18.04
     defaults:
       run:
         shell: bash

.github/workflows/linux_conda.yml

@@ -12,24 +12,22 @@ jobs:
   job:
     if: "github.repository == 'mne-tools/mne-python' && !contains(github.event.head_commit.message, '[ci skip]') && !contains(github.event.head_commit.message, '[skip ci]') && !contains(github.event.head_commit.message, '[skip github]')"
     name: 'py3.8'
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-20.04
     defaults:
       run:
         shell: bash
     env:
       CONDA_ENV: 'environment.yml'
       DISPLAY: ':99.0'
       MNE_LOGGING_LEVEL: 'warning'
-      OPENBLAS_NUM_THREADS: '1'
+      MKL_NUM_THREADS: '1'
       PYTHONUNBUFFERED: '1'
       PYTHON_VERSION: '3.8'
     steps:
       - uses: actions/checkout@v2
         with:
           fetch-depth: 0
-      - run: |
-          sudo apt-get install -y libxkbcommon-x11-0 libxcb-icccm4 libxcb-image0 libxcb-keysyms1 libxcb-randr0 libxcb-render-util0 libxcb-xinerama0 libxcb-xfixes0 libopengl0
-          /sbin/start-stop-daemon --start --quiet --pidfile /tmp/custom_xvfb_99.pid --make-pidfile --background --exec /usr/bin/Xvfb -- :99 -screen 0 1400x900x24 -ac +extension GLX +render -noreset;
+      - run: ./tools/setup_xvfb.sh
         name: 'Setup xvfb'
       - uses: conda-incubator/setup-miniconda@v2
         with:

.github/workflows/linux_pip.yml

@@ -11,8 +11,8 @@ jobs:
   # PIP + non-default stim channel + log level info
   job:
     if: "github.repository == 'mne-tools/mne-python' && !contains(github.event.head_commit.message, '[ci skip]') && !contains(github.event.head_commit.message, '[skip ci]') && !contains(github.event.head_commit.message, '[skip github]')"
-    name: 'py3.8'
-    runs-on: ubuntu-latest
+    name: 'py3.9'
+    runs-on: ubuntu-20.04
     defaults:
       run:
         shell: bash
@@ -22,14 +22,12 @@ jobs:
       MNE_STIM_CHANNEL: 'STI101'
       OPENBLAS_NUM_THREADS: '1'
       PYTHONUNBUFFERED: '1'
-      PYTHON_VERSION: '3.8'
+      PYTHON_VERSION: '3.9'
     steps:
       - uses: actions/checkout@v2
         with:
           fetch-depth: 0
-      - run: |
-          sudo apt-get install -y libxkbcommon-x11-0 libxcb-icccm4 libxcb-image0 libxcb-keysyms1 libxcb-randr0 libxcb-render-util0 libxcb-xinerama0 libxcb-xfixes0 libopengl0
-          /sbin/start-stop-daemon --start --quiet --pidfile /tmp/custom_xvfb_99.pid --make-pidfile --background --exec /usr/bin/Xvfb -- :99 -screen 0 1400x900x24 -ac +extension GLX +render -noreset;
+      - run: ./tools/setup_xvfb.sh
         name: 'Setup xvfb'
       - uses: actions/setup-python@v2
         with:

README.rst

@@ -1,11 +1,14 @@
 .. -*- mode: rst -*-
 
-|Travis|_ |Azure|_ |Circle|_ |Codecov|_ |PyPI|_ |conda-forge|_ |Zenodo|_
+|GH-Linux|_ |GH-macOS|_ |Azure|_ |Circle|_ |Codecov|_ |PyPI|_ |conda-forge|_ |Zenodo|_
 
 |MNE|_
 
-.. |Travis| image:: https://api.travis-ci.org/mne-tools/mne-python.svg?branch=master
-.. _Travis: https://travis-ci.org/mne-tools/mne-python/branches
+.. |GH-Linux| image:: https://github.com/mne-tools/mne-python/workflows/linux%20/%20conda/badge.svg?branch=master
+.. _GH-Linux: https://github.com/mne-tools/mne-python/actions?query=branch:master+event:push
+
+.. |GH-macOS| image:: https://github.com/mne-tools/mne-python/workflows/macos%20/%20conda/badge.svg?branch=master
+.. _GH-macOS: https://github.com/mne-tools/mne-python/actions?query=branch:master+event:push
 
 .. |Azure| image:: https://dev.azure.com/mne-tools/mne-python/_apis/build/status/mne-tools.mne-python?branchName=master
 .. _Azure: https://dev.azure.com/mne-tools/mne-python/_build/latest?definitionId=1&branchName=master

azure-pipelines.yml

@@ -174,7 +174,6 @@ stages:
       OPENBLAS_NUM_THREADS: 1
       PYTHONUNBUFFERED: 1
       PYTHONIOENCODING: 'utf-8'
-      MKL_NUM_THREADS: 1
       AZURE_CI_WINDOWS: 'true'
       PYTHON_ARCH: 'x64'
     strategy:

doc/_includes/data_formats.rst

@@ -72,6 +72,7 @@ EEG           :ref:`Persyst <import-persyst>`               .lay       :func:`mn
 
 NIRS          :ref:`NIRx <import-nirx>`                     directory  :func:`mne.io.read_raw_nirx`
 
+NIRS          :ref:`BOXY <import-boxy>`                     directory  :func:`mne.io.read_raw_boxy`
 ============  ============================================  =========  ===================================
 
 More details are provided in the tutorials in the :ref:`tut-data-formats`

doc/changes/latest.inc

@@ -20,11 +20,15 @@ Current (0.22.dev0)
 
 .. |Victoria Peterson| replace:: **Victoria Peterson**
 
+.. |Jonathan Kuziek| replace:: **Jonathan Kuziek**
+
 
 Enhancements
 ~~~~~~~~~~~~
 - Add :class:`mne.decoding.SSD` for spatial filtering with spatio-spectral-decomposition (:gh:`7070` **by new contributor** |Victoria Peterson|_ and `Denis Engemann`_)
 
+- Add reader for optical imaging data recorded using ISS Imgagent I/II hardware and BOXY recording software in :func:`mne.io.read_raw_boxy` (:gh:`7717` **by new contributor** |Jonathan Kuziek|_ and `Kyle Mathewson`_)
+
 - Add options to use labels in :func:`mne.minimum_norm.get_point_spread` and :func:`mne.minimum_norm.get_cross_talk` (:gh:`8275` by `Olaf Hauk`_)
 
 - Update ``surfaces`` argument in :func:`mne.viz.plot_alignment` to allow dict for transparency values, and set default for sEEG data to have transparency (:gh:`8445` by `Keith Doelling`_)
@@ -35,6 +39,8 @@ Enhancements
 
 - Add ``proj`` argument to :func:`mne.make_fixed_length_epochs` (:gh:`8351` by `Eric Larson`_)
 
+- Add :func:`mne.preprocessing.realign_raw` to realign simultaneous raw recordings in the presence of clock drift (:gh:`8539` by `Eric Larson`_)
+
 - Reduce memory usage of volume source spaces (:gh:`8379` by `Eric Larson`_)
 
 - Speed up heavy use of :meth:`mne.SourceMorph.apply` for volumetric source spaces by use of the method :meth:`mne.SourceMorph.compute_vol_morph_mat` (:gh:`8366` by `Eric Larson`_)

doc/changes/names.inc

@@ -318,6 +318,8 @@
 
 .. _Rahul Nadkarni: https://github.com/rahuln
 
+.. _Jonathan Kuziek:  https://github.com/kuziekj
+
 .. _Lau Møller Andersen: https://github.com/ualsbombe
 
 .. _Martin Schulz: https://github.com/marsipu

doc/conf.py

@@ -677,7 +677,7 @@ def reset_warnings(gallery_conf, fname):
     'n_dipoles_fwd', 'n_picks_ref', 'n_coords',
     # Undocumented (on purpose)
     'RawKIT', 'RawEximia', 'RawEGI', 'RawEEGLAB', 'RawEDF', 'RawCTF', 'RawBTi',
-    'RawBrainVision', 'RawCurry', 'RawNIRX', 'RawGDF', 'RawSNIRF',
+    'RawBrainVision', 'RawCurry', 'RawNIRX', 'RawGDF', 'RawSNIRF', 'RawBOXY',
     'RawPersyst', 'RawNihon',
     # sklearn subclasses
     'mapping', 'to', 'any',

doc/python_reference.rst

@@ -72,6 +72,7 @@ Reading raw data
    read_raw_fif
    read_raw_eximia
    read_raw_fieldtrip
+   read_raw_boxy
    read_raw_persyst
    read_raw_nihon
 
@@ -380,6 +381,7 @@ Projections:
    oversampled_temporal_projection
    peak_finder
    read_ica
+   realign_raw
    regress_artifact
    corrmap
    read_ica_eeglab

environment.yml

@@ -1,6 +1,6 @@
 name: mne
 channels:
-- defaults
+- conda-forge
 dependencies:
 - python>=3.8
 - pip
@@ -24,18 +24,15 @@ dependencies:
 - imageio
 - tqdm
 - spyder-kernels
-- pip:
-  - mne
-  - imageio-ffmpeg>=0.4.1
-  - vtk>=9.0.1
-  - pyvista>=0.24
-  - pyvistaqt>=0.2.0
-  - mayavi
-  - PySurfer[save_movie]
-  - dipy --only-binary dipy
-  - nibabel
-  - nilearn
-  - neo
-  - python-picard
-  - PyQt5>=5.10,<5.14; platform_system == "Darwin"
-  - PyQt5>=5.10; platform_system != "Darwin"
+- imageio-ffmpeg>=0.4.1
+- vtk>=9.0.1
+- pyvista>=0.24
+- pyvistaqt>=0.2.0
+- mayavi
+- PySurfer
+- dipy
+- nibabel
+- nilearn
+- python-picard
+- pyqt
+- mne

examples/visualization/plot_eeglab_head_sphere.py

@@ -99,7 +99,6 @@
 fake_evoked.plot_sensors(sphere=(x, y, z, radius), axes=ax[1], show=False)
 
 # add titles
-fig.texts[0].remove()
 ax[0].set_title('MNE channel projection', fontweight='bold')
 ax[1].set_title('EEGLAB channel projection', fontweight='bold')
 

mne/beamformer/tests/test_lcmv.py

@@ -648,7 +648,7 @@ def test_lcmv_reg_proj(proj, weight_norm):
     (0.05, 'unit-noise-gain', False, None, 83, 86),
     (0.05, 'unit-noise-gain', False, 0.8, 83, 86),  # depth same for wn != None
     # no reg
-    (0.00, 'unit-noise-gain', True, None, 45, 99),  # TODO: Still not stable
+    (0.00, 'unit-noise-gain', True, None, 35, 99),  # TODO: Still not stable
 ])
 def test_localization_bias_fixed(bias_params_fixed, reg, weight_norm, use_cov,
                                  depth, lower, upper):
@@ -687,7 +687,7 @@ def test_localization_bias_fixed(bias_params_fixed, reg, weight_norm, use_cov,
         (0.00, 'vector', 'unit-noise-gain-invariant', True, None, 50, 65),
         (0.00, 'vector', 'unit-noise-gain', True, None, 42, 65),
         (0.00, 'vector', 'nai', True, None, 42, 65),
-        (0.00, 'max-power', None, True, None, 15, 19),
+        (0.00, 'max-power', None, True, None, 13, 19),
         (0.00, 'max-power', 'unit-noise-gain-invariant', True, None, 43, 50),
         (0.00, 'max-power', 'unit-noise-gain', True, None, 43, 50),
         (0.00, 'max-power', 'nai', True, None, 43, 50),

mne/channels/channels.py

@@ -27,7 +27,7 @@
 from ..io.pick import (channel_type, pick_info, pick_types, _picks_by_type,
                        _check_excludes_includes, _contains_ch_type,
                        channel_indices_by_type, pick_channels, _picks_to_idx,
-                       _get_channel_types)
+                       _get_channel_types, get_channel_type_constants)
 from ..io.write import DATE_NONE
 from ..io._digitization import _get_data_as_dict_from_dig
 
@@ -80,7 +80,8 @@ def _get_ch_type(inst, ch_type, allow_ref_meg=False):
     """
     if ch_type is None:
         allowed_types = ['mag', 'grad', 'planar1', 'planar2', 'eeg', 'csd',
-                         'fnirs_cw_amplitude', 'fnirs_od', 'hbo', 'hbr',
+                         'fnirs_cw_amplitude', 'fnirs_fd_ac_amplitude',
+                         'fnirs_fd_phase', 'fnirs_od', 'hbo', 'hbr',
                          'ecog', 'seeg']
         allowed_types += ['ref_meg'] if allow_ref_meg else []
         for type_ in allowed_types:
@@ -275,41 +276,11 @@ def get_montage(self):
         return montage
 
 
-# XXX Eventually de-duplicate with _kind_dict of mne/io/meas_info.py
-_human2fiff = {'ecg': FIFF.FIFFV_ECG_CH,
-               'eeg': FIFF.FIFFV_EEG_CH,
-               'emg': FIFF.FIFFV_EMG_CH,
-               'eog': FIFF.FIFFV_EOG_CH,
-               'exci': FIFF.FIFFV_EXCI_CH,
-               'ias': FIFF.FIFFV_IAS_CH,
-               'misc': FIFF.FIFFV_MISC_CH,
-               'resp': FIFF.FIFFV_RESP_CH,
-               'seeg': FIFF.FIFFV_SEEG_CH,
-               'stim': FIFF.FIFFV_STIM_CH,
-               'syst': FIFF.FIFFV_SYST_CH,
-               'bio': FIFF.FIFFV_BIO_CH,
-               'ecog': FIFF.FIFFV_ECOG_CH,
-               'fnirs_cw_amplitude': FIFF.FIFFV_FNIRS_CH,
-               'fnirs_od': FIFF.FIFFV_FNIRS_CH,
-               'hbo': FIFF.FIFFV_FNIRS_CH,
-               'hbr': FIFF.FIFFV_FNIRS_CH}
-_human2unit = {'ecg': FIFF.FIFF_UNIT_V,
-               'eeg': FIFF.FIFF_UNIT_V,
-               'emg': FIFF.FIFF_UNIT_V,
-               'eog': FIFF.FIFF_UNIT_V,
-               'exci': FIFF.FIFF_UNIT_NONE,
-               'ias': FIFF.FIFF_UNIT_NONE,
-               'misc': FIFF.FIFF_UNIT_V,
-               'resp': FIFF.FIFF_UNIT_NONE,
-               'seeg': FIFF.FIFF_UNIT_V,
-               'stim': FIFF.FIFF_UNIT_NONE,
-               'syst': FIFF.FIFF_UNIT_NONE,
-               'bio': FIFF.FIFF_UNIT_V,
-               'ecog': FIFF.FIFF_UNIT_V,
-               'fnirs_cw_amplitude': FIFF.FIFF_UNIT_V,
-               'fnirs_od': FIFF.FIFF_UNIT_NONE,
-               'hbo': FIFF.FIFF_UNIT_MOL,
-               'hbr': FIFF.FIFF_UNIT_MOL}
+channel_type_constants = get_channel_type_constants()
+_human2fiff = {k: v.get('kind', FIFF.FIFFV_COIL_NONE) for k, v in
+               channel_type_constants.items()}
+_human2unit = {k: v.get('unit', FIFF.FIFF_UNIT_NONE) for k, v in
+               channel_type_constants.items()}
 _unit2human = {FIFF.FIFF_UNIT_V: 'V',
                FIFF.FIFF_UNIT_T: 'T',
                FIFF.FIFF_UNIT_T_M: 'T/m',
@@ -440,7 +411,8 @@ def set_channel_types(self, mapping, verbose=None):
         The following sensor types are accepted:
 
             ecg, eeg, emg, eog, exci, ias, misc, resp, seeg, stim, syst, ecog,
-            hbo, hbr, fnirs_cw_amplitude, fnirs_od
+            hbo, hbr, fnirs_cw_amplitude, fnirs_fd_ac_amplitude,
+            fnirs_fd_phase, fnirs_od
 
         .. versionadded:: 0.9.0
         """
@@ -482,6 +454,10 @@ def set_channel_types(self, mapping, verbose=None):
                 coil_type = FIFF.FIFFV_COIL_FNIRS_HBR
             elif ch_type == 'fnirs_cw_amplitude':
                 coil_type = FIFF.FIFFV_COIL_FNIRS_CW_AMPLITUDE
+            elif ch_type == 'fnirs_fd_ac_amplitude':
+                coil_type = FIFF.FIFFV_COIL_FNIRS_FD_AC_AMPLITUDE
+            elif ch_type == 'fnirs_fd_phase':
+                coil_type = FIFF.FIFFV_COIL_FNIRS_FD_PHASE
             elif ch_type == 'fnirs_od':
                 coil_type = FIFF.FIFFV_COIL_FNIRS_OD
             else:

mne/channels/layout.py

@@ -17,7 +17,7 @@
 import numpy as np
 
 from ..transforms import _pol_to_cart, _cart_to_sph
-from ..io.pick import pick_types, _picks_to_idx
+from ..io.pick import pick_types, _picks_to_idx, _FNIRS_CH_TYPES_SPLIT
 from ..io.constants import FIFF
 from ..io.meas_info import Info
 from ..utils import (_clean_names, warn, _check_ch_locs, fill_doc,
@@ -917,7 +917,7 @@ def _merge_ch_data(data, ch_type, names, method='rms'):
     if ch_type == 'grad':
         data = _merge_grad_data(data, method)
     else:
-        assert ch_type in ('hbo', 'hbr', 'fnirs_cw_amplitude', 'fnirs_od')
+        assert ch_type in _FNIRS_CH_TYPES_SPLIT
         data, names = _merge_nirs_data(data, names)
     return data, names
 

mne/channels/tests/test_channels.py

@@ -114,21 +114,22 @@ def test_set_channel_types():
     # Error Tests
     # Test channel name exists in ch_names
     mapping = {'EEG 160': 'EEG060'}
-    pytest.raises(ValueError, raw.set_channel_types, mapping)
+    with pytest.raises(ValueError, match=r"name \(EEG 160\) doesn't exist"):
+        raw.set_channel_types(mapping)
     # Test change to illegal channel type
     mapping = {'EOG 061': 'xxx'}
-    pytest.raises(ValueError, raw.set_channel_types, mapping)
-    # Test changing type if in proj (avg eeg ref here)
+    with pytest.raises(ValueError, match='cannot change to this channel type'):
+        raw.set_channel_types(mapping)
+    # Test changing type if in proj
     mapping = {'EEG 058': 'ecog', 'EEG 059': 'ecg', 'EEG 060': 'eog',
                'EOG 061': 'seeg', 'MEG 2441': 'eeg', 'MEG 2443': 'eeg',
                'MEG 2442': 'hbo'}
-    pytest.raises(RuntimeError, raw.set_channel_types, mapping)
-    # Test type change
     raw2 = read_raw_fif(raw_fname)
     raw2.info['bads'] = ['EEG 059', 'EEG 060', 'EOG 061']
-    pytest.raises(RuntimeError, raw2.set_channel_types, mapping)  # has prj
+    with pytest.raises(RuntimeError, match='type .* in projector "PCA-v1"'):
+        raw2.set_channel_types(mapping)  # has prj
     raw2.add_proj([], remove_existing=True)
-    with pytest.warns(RuntimeWarning, match='The unit for channel'):
+    with pytest.warns(RuntimeWarning, match='unit for channel.* has changed'):
         raw2 = raw2.set_channel_types(mapping)
     info = raw2.info
     assert info['chs'][372]['ch_name'] == 'EEG 058'