From edad62e90aaea2424469054db79dc09f8bef2ba3 Mon Sep 17 00:00:00 2001 From: AmaiaBA Date: Tue, 30 Jan 2024 10:36:49 -0500 Subject: [PATCH 1/4] include OPM channels as megmag under .pick/get_coil_types() --- mne_bids/pick.py | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/mne_bids/pick.py b/mne_bids/pick.py index c9b4baad6..f83b09d46 100644 --- a/mne_bids/pick.py +++ b/mne_bids/pick.py @@ -45,6 +45,11 @@ def get_coil_types(): FIFF.FIFFV_COIL_NM_122, FIFF.FIFFV_COIL_MAGNES_MAG, FIFF.FIFFV_COIL_BABY_MAG, + # support for OPM data + FIFF.FIFFV_COIL_QUSPIN_ZFOPM_MAG, # QuSpin v1 + FIFF.FIFFV_COIL_QUSPIN_ZFOPM_MAG2, # QuSpin v2 + FIFF.FIFFV_COIL_FIELDLINE_OPM_MAG_GEN1, # FieldLine v1 + FIFF.FIFFV_COIL_KERNEL_OPM_MAG_GEN1, # Kernel ), megrefmag=( FIFF.FIFFV_COIL_KIT_REF_MAG, From b6686b74135455289c323c909e4dfeddc24cf591 Mon Sep 17 00:00:00 2001 From: "pre-commit-ci[bot]" <66853113+pre-commit-ci[bot]@users.noreply.github.com> Date: Wed, 31 Jan 2024 21:57:28 +0000 Subject: [PATCH 2/4] [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci --- mne_bids/pick.py | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/mne_bids/pick.py b/mne_bids/pick.py index f83b09d46..1fd3ab925 100644 --- a/mne_bids/pick.py +++ b/mne_bids/pick.py @@ -46,10 +46,10 @@ def get_coil_types(): FIFF.FIFFV_COIL_MAGNES_MAG, FIFF.FIFFV_COIL_BABY_MAG, # support for OPM data - FIFF.FIFFV_COIL_QUSPIN_ZFOPM_MAG, # QuSpin v1 - FIFF.FIFFV_COIL_QUSPIN_ZFOPM_MAG2, # QuSpin v2 - FIFF.FIFFV_COIL_FIELDLINE_OPM_MAG_GEN1, # FieldLine v1 - FIFF.FIFFV_COIL_KERNEL_OPM_MAG_GEN1, # Kernel + FIFF.FIFFV_COIL_QUSPIN_ZFOPM_MAG, # QuSpin v1 + FIFF.FIFFV_COIL_QUSPIN_ZFOPM_MAG2, # QuSpin v2 + FIFF.FIFFV_COIL_FIELDLINE_OPM_MAG_GEN1, # FieldLine v1 + FIFF.FIFFV_COIL_KERNEL_OPM_MAG_GEN1, # Kernel ), megrefmag=( FIFF.FIFFV_COIL_KIT_REF_MAG, From f101984827f89505c59da365c800c3aa9897b5c7 Mon Sep 17 00:00:00 2001 From: AmaiaBA Date: Tue, 30 Jul 2024 10:11:52 -0400 Subject: [PATCH 3/4] logging contributions --- CITATION.cff | 4 ++++ doc/authors.rst | 1 + doc/whats_new.rst | 2 ++ 3 files changed, 7 insertions(+) diff --git a/CITATION.cff b/CITATION.cff index f17d661fd..bbfe44e45 100644 --- a/CITATION.cff +++ b/CITATION.cff @@ -57,6 +57,10 @@ authors: family-names: Rockhill affiliation: 'University of Oregon, Eugene OR, USA' orcid: 'https://orcid.org/0000-0003-3868-7453' + - given-names: Amaia + family-names: Benitez + affiliation: 'Magnetoencephalography Core, National Institutes of Health, Bethesda, Maryland, USA' + orcid: 'https://orcid.org/0000-0001-6364-7272' - given-names: Eric family-names: Larson affiliation: 'Institute for Learning and Brain Sciences, University of Washington, Seattle, WA, USA' diff --git a/doc/authors.rst b/doc/authors.rst index efad72dbf..17854a354 100644 --- a/doc/authors.rst +++ b/doc/authors.rst @@ -45,3 +45,4 @@ .. _Ford McDonald: https://github.com/fordmcdonald .. _Pierre Guetschel: https://github.com/PierreGtch .. _Mara Wolter: https://github.com/marakw +.. _Amaia Benitez: https://github.com/AmaiaBA diff --git a/doc/whats_new.rst b/doc/whats_new.rst index 66eea1fc8..c294ac457 100644 --- a/doc/whats_new.rst +++ b/doc/whats_new.rst @@ -19,6 +19,7 @@ The following authors contributed for the first time. Thank you so much! 🤩 * `Daniel McCloy`_ * `Mara Wolter`_ +* `Amaia Benitez`_ The following authors had contributed before. Thank you for sticking around! 🤘 @@ -64,6 +65,7 @@ Detailed list of changes when renaming the files of a .ds folder, by `Mara Wolter`_ (:gh:`1230`) - We fixed handling of time zones when reading ``*_scans.tsv`` files; specifically, non-UTC timestamps are now processed correctly, by `Stefan Appelhoff`_ and `Richard Höchenberger`_ (:gh:`1240`) +- Fixed KeyError in ``write_raw_bids()`` for OPM data by including additional OPM channels in ``get_coil_types()`` by `Amaia Benitez`_ (:gh:`1222`) ⚕️ Code health ^^^^^^^^^^^^^^ From bc5da97e4d9228976fb6b8e1b13735ff7f322bc6 Mon Sep 17 00:00:00 2001 From: Stefan Appelhoff Date: Tue, 30 Jul 2024 16:32:28 +0200 Subject: [PATCH 4/4] clean merge main --- CITATION.cff | 8 ++++---- doc/authors.rst | 2 +- doc/whats_new.rst | 9 --------- 3 files changed, 5 insertions(+), 14 deletions(-) diff --git a/CITATION.cff b/CITATION.cff index da7f1ebf8..29e9e1aef 100644 --- a/CITATION.cff +++ b/CITATION.cff @@ -57,10 +57,6 @@ authors: family-names: Rockhill affiliation: 'University of Oregon, Eugene OR, USA' orcid: 'https://orcid.org/0000-0003-3868-7453' - - given-names: Amaia - family-names: Benitez - affiliation: 'Magnetoencephalography Core, National Institutes of Health, Bethesda, Maryland, USA' - orcid: 'https://orcid.org/0000-0001-6364-7272' - given-names: Eric family-names: Larson affiliation: 'Institute for Learning and Brain Sciences, University of Washington, Seattle, WA, USA' @@ -183,6 +179,10 @@ authors: family-names: Welzel affiliation: 'Department of Neurology, Kiel University, Germany' orcid: 'https://orcid.org/0000-0003-4782-5360' + - given-names: Amaia + family-names: Benitez + affiliation: 'Magnetoencephalography Core, National Institutes of Health, Bethesda, Maryland, USA' + orcid: 'https://orcid.org/0000-0001-6364-7272' - given-names: Alexandre family-names: Gramfort affiliation: 'Université Paris-Saclay, Inria, CEA, Palaiseau, France' diff --git a/doc/authors.rst b/doc/authors.rst index 3dddf2c60..fe8ae8881 100644 --- a/doc/authors.rst +++ b/doc/authors.rst @@ -45,5 +45,5 @@ .. _Ford McDonald: https://github.com/fordmcdonald .. _Pierre Guetschel: https://github.com/PierreGtch .. _Mara Wolter: https://github.com/marakw -.. _Amaia Benitez: https://github.com/AmaiaBA .. _Julius Welzel: https://github.com/JuliusWelzel +.. _Amaia Benitez: https://github.com/AmaiaBA diff --git a/doc/whats_new.rst b/doc/whats_new.rst index 655ca862b..d8f0798dc 100644 --- a/doc/whats_new.rst +++ b/doc/whats_new.rst @@ -18,9 +18,6 @@ Version 0.16 (unreleased) The following authors contributed for the first time. Thank you so much! 🤩 * `Amaia Benitez`_ -* `Daniel McCloy`_ -* `Mara Wolter`_ - The following authors had contributed before. Thank you for sticking around! 🤘 @@ -50,12 +47,6 @@ Detailed list of changes 🪲 Bug fixes ^^^^^^^^^^^^ -- The datatype in the dataframe returned by :func:`mne_bids.stats.count_events` is now - ``pandas.Int64Dtype`` instead of ``float64``, by `Eric Larson`_ (:gh:`1227`) -- The :func:`mne_bids.copyfiles.copyfile_ctf` now accounts for files with ``.{integer}_meg4`` extension, instead of only .meg4, - when renaming the files of a .ds folder, by `Mara Wolter`_ (:gh:`1230`) -- We fixed handling of time zones when reading ``*_scans.tsv`` files; specifically, non-UTC timestamps are now processed correctly, - by `Stefan Appelhoff`_ and `Richard Höchenberger`_ (:gh:`1240`) - When anonymizing the date of a recording, MNE-BIDS will no longer error during `~mne_bids.write_raw_bids` if passing a `~mne.io.Raw` instance to ``empty_room``, by `Daniel McCloy`_ (:gh:`1270`) ⚕️ Code health