From 856fbbf8afbff25c68c193bbe98ad765be794e67 Mon Sep 17 00:00:00 2001 From: Circle Ci Date: Sun, 28 Jul 2024 08:32:08 +0000 Subject: [PATCH] doc updates [skip ci] --- dev/.buildinfo | 2 +- .../auto_examples_python.zip | Bin 100040 -> 100203 bytes .../convert_group_studies.py | 3 +- .../convert_group_studies.ipynb | 2 +- .../read_bids_datasets.zip | Bin 19837 -> 19850 bytes .../mark_bad_channels.zip | Bin 16506 -> 16499 bytes .../mark_bad_channels.py | 2 +- .../convert_mne_sample.zip | Bin 20498 -> 20493 bytes .../rename_brainvision_files.py | 2 +- .../bidspath.py | 2 +- .../convert_nirs_to_bids.zip | Bin 16287 -> 16296 bytes .../convert_group_studies.zip | Bin 11165 -> 11192 bytes .../read_bids_datasets.py | 3 +- .../rename_brainvision_files.zip | Bin 8920 -> 8931 bytes .../auto_examples_jupyter.zip | Bin 154559 -> 154556 bytes .../bidspath.zip | Bin 17536 -> 17550 bytes .../convert_ieeg_to_bids.zip | Bin 47941 -> 47945 bytes .../convert_mne_sample.py | 2 +- .../update_bids_datasets.py | 2 +- .../update_bids_datasets.zip | Bin 11243 -> 11262 bytes .../convert_nirs_to_bids.py | 3 +- .../convert_ieeg_to_bids.py | 3 +- .../convert_mri_and_trans.py | 3 +- .../create_bids_folder.zip | Bin 5670 -> 5694 bytes .../create_bids_folder.py | 2 +- .../convert_eeg_to_bids.py | 3 +- .../mark_bad_channels.ipynb | 2 +- .../anonymize_dataset.zip | Bin 18580 -> 18580 bytes .../convert_eeg_to_bids.zip | Bin 21342 -> 21351 bytes .../convert_mri_and_trans.zip | Bin 27363 -> 27386 bytes .../convert_empty_room.py | 2 +- .../convert_empty_room.zip | Bin 11975 -> 11994 bytes dev/_modules/index.html | 6 +- dev/_modules/mne_bids/copyfiles.html | 6 +- dev/_modules/mne_bids/dig.html | 6 +- dev/_modules/mne_bids/inspect.html | 6 +- dev/_modules/mne_bids/path.html | 14 ++-- dev/_modules/mne_bids/read.html | 8 +-- dev/_modules/mne_bids/report/_report.html | 10 +-- dev/_modules/mne_bids/sidecar_updates.html | 6 +- dev/_modules/mne_bids/stats.html | 6 +- dev/_modules/mne_bids/utils.html | 10 +-- dev/_modules/mne_bids/write.html | 8 +-- dev/_static/documentation_options.js | 2 +- dev/api.html | 6 +- dev/authors.html | 6 +- dev/auto_examples/anonymize_dataset.html | 68 +++++++++--------- dev/auto_examples/bidspath.html | 6 +- dev/auto_examples/convert_eeg_to_bids.html | 8 +-- dev/auto_examples/convert_empty_room.html | 8 +-- dev/auto_examples/convert_group_studies.html | 20 +++--- dev/auto_examples/convert_ieeg_to_bids.html | 20 +++--- dev/auto_examples/convert_mne_sample.html | 54 +++++++------- dev/auto_examples/convert_mri_and_trans.html | 8 +-- dev/auto_examples/convert_nirs_to_bids.html | 8 +-- dev/auto_examples/create_bids_folder.html | 6 +- dev/auto_examples/mark_bad_channels.html | 10 +-- dev/auto_examples/read_bids_datasets.html | 48 ++++++------- .../rename_brainvision_files.html | 8 +-- dev/auto_examples/sg_execution_times.html | 32 ++++----- dev/auto_examples/update_bids_datasets.html | 8 +-- dev/contribute.html | 6 +- dev/generated/cli.html | 6 +- dev/generated/mne_bids.BIDSPath.html | 10 +-- dev/generated/mne_bids.anonymize_dataset.html | 6 +- .../mne_bids.convert_montage_to_mri.html | 6 +- .../mne_bids.convert_montage_to_ras.html | 6 +- ...e_bids.copyfiles.copyfile_brainvision.html | 6 +- .../mne_bids.copyfiles.copyfile_bti.html | 6 +- .../mne_bids.copyfiles.copyfile_ctf.html | 6 +- .../mne_bids.copyfiles.copyfile_edf.html | 6 +- .../mne_bids.copyfiles.copyfile_eeglab.html | 6 +- .../mne_bids.copyfiles.copyfile_kit.html | 6 +- .../mne_bids.find_matching_paths.html | 6 +- .../mne_bids.get_anat_landmarks.html | 6 +- .../mne_bids.get_anonymization_daysback.html | 8 +-- .../mne_bids.get_bids_path_from_fname.html | 6 +- dev/generated/mne_bids.get_datatypes.html | 6 +- .../mne_bids.get_entities_from_fname.html | 6 +- dev/generated/mne_bids.get_entity_vals.html | 6 +- .../mne_bids.get_head_mri_trans.html | 6 +- dev/generated/mne_bids.inspect_dataset.html | 8 +-- .../mne_bids.make_dataset_description.html | 6 +- dev/generated/mne_bids.make_report.html | 8 +-- dev/generated/mne_bids.mark_channels.html | 8 +-- dev/generated/mne_bids.print_dir_tree.html | 8 +-- dev/generated/mne_bids.read_raw_bids.html | 8 +-- .../mne_bids.search_folder_for_text.html | 6 +- .../mne_bids.stats.count_events.html | 8 +-- dev/generated/mne_bids.template_to_head.html | 6 +- .../mne_bids.update_anat_landmarks.html | 6 +- .../mne_bids.update_sidecar_json.html | 6 +- dev/generated/mne_bids.write_anat.html | 6 +- .../mne_bids.write_meg_calibration.html | 6 +- .../mne_bids.write_meg_crosstalk.html | 6 +- dev/generated/mne_bids.write_raw_bids.html | 10 +-- dev/genindex.html | 6 +- dev/index.html | 6 +- dev/install.html | 6 +- dev/objects.inv | Bin 3759 -> 3759 bytes dev/py-modindex.html | 6 +- dev/search.html | 6 +- dev/searchindex.js | 2 +- dev/sg_execution_times.html | 32 ++++----- dev/use.html | 10 +-- dev/whats_new.html | 7 +- dev/whats_new_previous_releases.html | 6 +- 107 files changed, 381 insertions(+), 388 deletions(-) diff --git a/dev/.buildinfo b/dev/.buildinfo index 19714783a..09dfb3142 100644 --- a/dev/.buildinfo +++ b/dev/.buildinfo @@ -1,4 +1,4 @@ # Sphinx build info version 1 # This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done. -config: ea9cba626ef42c051e3ea60f81fcb445 +config: 260e07dd1f774787c78be8eca66e450a tags: 645f666f9bcd5a90fca523b33c5a78b7 diff --git a/dev/_downloads/07fcc19ba03226cd3d83d4e40ec44385/auto_examples_python.zip b/dev/_downloads/07fcc19ba03226cd3d83d4e40ec44385/auto_examples_python.zip index d415e0e6f242acc37556933e8ca4ee0604f96b3a..4ebf984b0799b8bc465578bdc5bb20569a84b8f1 100644 GIT binary patch delta 1275 zcma)*TS!xJ9LN8^%}eIayv=QS+0I-kD2o~G!Kesbp{NuiQ7H+={c z;Sm3P>B$7`g7ZH-&_%mJl0IZmkWrD@LqzmeQCj_u(wQg2`XBxehx7g2zQ50z?1}l% z8>1<8siSm6I!#-h@*va)#I$~XB= z)NJE-JM8(qbBo=RXuSxMvv9Gt^#HS4K#kSiK%zN9z>>$w4BL(C=Dm z=4JWk#!;*=Dt__6gOw$e+=%GG2*=G~jbU$4v=|7nh*J&l4*qMYA};llPBmLZ69TYn zX>~Hk)Ej^TvjRzM2n~`?*xyOR0m$JM^dW(%vV@SZKglgDRvPk3U7*sbm;am9NJb*U z{#Lpp2%F3b#1OOP&}CuR@1*`9Sb3>GnKmR2(UDKse>x;ohcXqVSA!<&vDaHv(*+yN zN|gQ_=rKKrBDVq>^d&x$2s0Vp5>k8Y$f@R@mY+0e{IJ_v}me@AQ@;%U=fA275n^W>BEx++k2)F#IlZHzyizz)S-v0e^|Y+X zouA};Gj=Q|A|Mo@H@gyCHX9}gMMAr;v!yBpPxwz3@U1|fKXU&rw;dslHb(teGuJE9 z_d}z3N!^wYH{x6t>kY(8)3pC*i3z_;oEgucKG~g--3TP**5QhG`3SKC8Xt#1g{PgU>oyoWkp}3BIo37*-Oe|~CQ}JU&%QHaTOy`Q; zgpgje&aWgN8Tscs{>Y%QeaC|Y>paI#Xj5SnJ O8#&aEOLRDh;r1WZ5kH^+ diff --git a/dev/_downloads/1eed244ec75de0e6a9392a728e24219b/convert_group_studies.py b/dev/_downloads/1eed244ec75de0e6a9392a728e24219b/convert_group_studies.py index 0990762e0..1b40010fc 100644 --- a/dev/_downloads/1eed244ec75de0e6a9392a728e24219b/convert_group_studies.py +++ b/dev/_downloads/1eed244ec75de0e6a9392a728e24219b/convert_group_studies.py @@ -2,13 +2,14 @@ ===================================== 05. BIDS conversion for group studies ===================================== + Here, we show how to do BIDS conversion for group studies. We will use the `EEG Motor Movement/Imagery Dataset `_ available on the PhysioBank database. We recommend that you go through the more basic BIDS conversion example before checking out this group conversion example: :ref:`ex-convert-mne-sample` -""" +""" # noqa: E501 D205 D400 # Authors: The MNE-BIDS developers # SPDX-License-Identifier: BSD-3-Clause diff --git a/dev/_downloads/241c30601b8e062b34a8b85829a39a45/convert_group_studies.ipynb b/dev/_downloads/241c30601b8e062b34a8b85829a39a45/convert_group_studies.ipynb index e75f4781e..ff8d256a2 100644 --- a/dev/_downloads/241c30601b8e062b34a8b85829a39a45/convert_group_studies.ipynb +++ b/dev/_downloads/241c30601b8e062b34a8b85829a39a45/convert_group_studies.ipynb @@ -4,7 +4,7 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "\n# 05. BIDS conversion for group studies\nHere, we show how to do BIDS conversion for group studies.\nWe will use the\n[EEG Motor Movement/Imagery Dataset](https://doi.org/10.13026/C28G6P)\navailable on the PhysioBank database.\nWe recommend that you go through the more basic BIDS conversion example before\nchecking out this group conversion example: `ex-convert-mne-sample`\n" + "\n# 05. BIDS conversion for group studies\n\nHere, we show how to do BIDS conversion for group studies.\nWe will use the\n[EEG Motor Movement/Imagery Dataset](https://doi.org/10.13026/C28G6P)\navailable on the PhysioBank database.\nWe recommend that you go through the more basic BIDS conversion example before\nchecking out this group conversion example: `ex-convert-mne-sample`\n" ] }, { diff --git a/dev/_downloads/268d987293d4ee80f1e0d3ca84cf1bd4/read_bids_datasets.zip b/dev/_downloads/268d987293d4ee80f1e0d3ca84cf1bd4/read_bids_datasets.zip index 1d2464cdb76424c925066f5cd03f65441de7012c..d278ca2b7b901ac7ac3c0809a5283799d597158a 100644 GIT binary patch delta 109 zcmex6i?M4qqj-QfGm8iV2<&qH6R~WWLdipE28M?l#jTlzm6Vhe6qFV6@(UBK6kJRU y47j)^+bJk*u40}p!L-+Tv#`u{16~wulfV0z0c9rZ`^qqiO!o2BW_#@eG8+IERv~Ku delta 109 zcmeC0&G>f~qjZ2bGm8iV2t-@|i7?QcXLLoHfdPa?C+o|IZ8TJ5X5&&)QsUy8?5&`* vxt)2s1XF_bW(Aq+2D~UbCbRgO0c9rJ_{uP`%S<+qk(ylME5LTo2V^z?9=9Av diff --git a/dev/_downloads/2d16cae3d55264a4b7d58ed70766e580/mark_bad_channels.zip b/dev/_downloads/2d16cae3d55264a4b7d58ed70766e580/mark_bad_channels.zip index 2609122ce0b49d3df094793d0a5629caa1ace8d1..ee50837e02384b9fb09c23ca82384e7454b8f406 100644 GIT binary patch delta 145 zcmey>!1%d=Q98hznMH&F1P(g?iI6(9w2MI!$N^%J$^Md}8x0Z}8FeQgl``0Tgt1DT z_c%~dIjfgjz8V8V{$_8<5}@qnqf#oWyeQfyf3r7LKv4@+FAlZ_LTqU?lAIhMDLFaC LL4fU=JxCA$+Vdvv delta 160 zcmey|!1$|yQ98hznMH&F1d^=(L`ctHx`0WNfdPa?CNnySZ#0T$WPa2zdGbCfgUyE+ ztHcE}fy$g#?6xUUV_*PbaiB8M%}J8cjBGKbMh1q)oA*hnsPdwiHu=51sRD*Zu&oec VOQVV8WIsvC$*~RsY`. .. _BrainVision data format: https://www.brainproducts.com/support-resources/brainvision-core-data-format-1-0/ -""" # noqa:E501 +""" # noqa: E501 D205 D400 # Authors: The MNE-BIDS developers # SPDX-License-Identifier: BSD-3-Clause diff --git a/dev/_downloads/4b11a3ce6cfd9d8cf2b976f8386a2f8f/bidspath.py b/dev/_downloads/4b11a3ce6cfd9d8cf2b976f8386a2f8f/bidspath.py index 943821398..0430e4c72 100644 --- a/dev/_downloads/4b11a3ce6cfd9d8cf2b976f8386a2f8f/bidspath.py +++ b/dev/_downloads/4b11a3ce6cfd9d8cf2b976f8386a2f8f/bidspath.py @@ -7,7 +7,7 @@ BIDSPath is MNE-BIDS's working horse when it comes to file and folder operations. Learn here how to use it. -""" +""" # noqa: D400 # Authors: The MNE-BIDS developers # SPDX-License-Identifier: BSD-3-Clause diff --git a/dev/_downloads/4c4fb656ad2ed5296dbabd0c14fa2b02/convert_nirs_to_bids.zip b/dev/_downloads/4c4fb656ad2ed5296dbabd0c14fa2b02/convert_nirs_to_bids.zip index a44f388a31f19a8374ae0b634acf385c1be8a43e..43cdee1a513d2582652a19be544e6aa99a4937c1 100644 GIT binary patch delta 120 zcmbPVzoK3yz?+#xgaHH|Isb`R71Od^QJjGRgvA*q=h};JG(O2Ft)!%+prEXfmtUA@ zrQm96V5s0?WMHb`Vq##hnUBd+lbxjsOcu4b0Lo1Ex0hiIo19~>%f@OC GvIqdS+8`(Z delta 115 zcmZ2cKfhi&z?+#xgaHJat^Y*mebU@4AZz?+#xgaHIjIRA;*c4=KkBtHWK2uno#yeIeaZ`y1ta9j#33^#VN fpthv~ib9}bAcBJ}js5%+Wh5pyX^XN6YlDOVMI|em delta 148 zcmdlHJ~v!Cz?+#xgaHIHt^Y)DJ&OPAz|X({!V;71w52DSm2F%b!nj$IsexB83#j70 zlcK+;Gy?+&O9NF%PCm>(b>dp9%~J%rrFc=yn5?61seqveY!`&s(pbhn*>@?33E JwjWv`K>$tdC=CDr diff --git a/dev/_downloads/5eebd75ee4f8ffd30e34a83e87d0e28b/read_bids_datasets.py b/dev/_downloads/5eebd75ee4f8ffd30e34a83e87d0e28b/read_bids_datasets.py index 00263d3b8..995c8c661 100644 --- a/dev/_downloads/5eebd75ee4f8ffd30e34a83e87d0e28b/read_bids_datasets.py +++ b/dev/_downloads/5eebd75ee4f8ffd30e34a83e87d0e28b/read_bids_datasets.py @@ -22,8 +22,7 @@ In this tutorial, we show how ``read_raw_bids`` can be used to load and inspect BIDS-formatted data. - -""" +""" # noqa: D400 # Authors: The MNE-BIDS developers # SPDX-License-Identifier: BSD-3-Clause diff --git a/dev/_downloads/6a5f0c10c42d095fdc0217cd0f22c214/rename_brainvision_files.zip b/dev/_downloads/6a5f0c10c42d095fdc0217cd0f22c214/rename_brainvision_files.zip index ebf186c86c3e942818f683ffc706951e562b1b8a..966d0cd54e518f12f8fcfbac4690472e93e86826 100644 GIT binary patch delta 128 zcmccN`q))Gz?+#xgaHIjIRA;*rxm_|mydygccZvAtDu6bsez$_i;;n;f{TfP0TSPpDBgxJ#PHhH0vA)AE~ Ghz|e;gCYa~ delta 96 zcmaFtdc##Zz?+#xgaHJytp7wP-R%6s#K*t@!qSry`D8YlbF;Fzni?2x4rKk$!IWja iIf(C*FfWSQ$$?5XK$*$?N-~Vrlh-I2vgs;;352e diff --git a/dev/_downloads/6f1e7a639e0699d6164445b55e6c116d/auto_examples_jupyter.zip b/dev/_downloads/6f1e7a639e0699d6164445b55e6c116d/auto_examples_jupyter.zip index c3bb22b39581371b6770a2b4e292a55ad9c28018..18de2d4d70f5131effbf662b07b3f2add764951b 100644 GIT binary patch delta 511 zcmdnLopaB2PM!d7W)=|!5P0Ogkw;UD>6-IqbFH~{yeFLhL>O3xGkQxiFnCXXn6YW| z#LS~oOb4AeN3^gQGM#YV9JlqSq0n)lvT{~0w|q4Q1`rl!m>w6&Bsu-YYR2@*FQ30> z)ZKjVg_0^z{dOik#t*_wd!4s`QDnSoz;w%b`{^LYFg_4NIg#<8Hi+@8hw+FU(@p2? zYgRLIW`abvi!c>QGd*(Nu5G}yULDAoekYvC8R*REiV;lisLq^T8o^{Ee-P-T1x|hY zFBmW|fUpGEdk|tvqu=xk5lrep_e}p8!6d^JvUPIaR_W=I(M&w@n0`U%+|uYjJvNd_ zO&%03^}BW@ZWCr;0AV?V8ip;6pQkU1WYPtCa{9$cCK<-3)89ohsVm+B>Y4e)iA{-* zfdPb3U9=~Nar&JgM#<^^QA|8QFHet+0%{eRUKPb83*ycMaj#F`76o+nP3P(NLEO31 x|3ooq%7YAE|7lgG4KR{GSPI24E2g_dGiic?EI%5kM`n6YG?Omd>2M~XDgb$YpWpxh delta 517 zcmdn9opb+oPM!d7W)=|!5NNjE$fK#nRBpZ5Tx+f!Z}@@4{+Ijz`jQ=-PeP_jAgc?lz1OsSE9q4DP1FO*c7 zvaGlN=VkmL%#>ig{i7n|RRgAK>+L6k7{mBL4249-gW4d*;~vH%a!i%h+gGk;2eWF?x?PtUKGJ(19aK+4G~N-j6T!PMlh)> zfE+gczasw;Lk0#AmIQkeLTqUa+B&<MqjJNG2Y66fXe1A&#QbcY0JLlbSpzIO=!p zO57&QzyQK>D2l#KpC8Gj3-sjlbCEzNyqNwvl1W{@8mMRH7bi9)J_ZI5mO#<7f4X55 zlRD6^)1#t*dc>!fM={BQ^;`~+ES~_h0EAKX+?u`_q^Ht)`W=v-1=D{MJtpBts m(*_t-AS{Jq&+6%p(M+145X^}N>XDz`8O@~2b}pO=s0siBca~}Z diff --git a/dev/_downloads/701f5b32d08455f1c1e98b7ab1715881/bidspath.zip b/dev/_downloads/701f5b32d08455f1c1e98b7ab1715881/bidspath.zip index fa41dc4931a5d5f333d7f2057eed93f629b8db8c..45ba27e57fac27d15450601a487f441413b7034c 100644 GIT binary patch delta 99 zcmZqZWbEr?6c6xbW)Wckfm_ahB6L016o^YOFo;hS|I4SKpsbLWUzlj6;9_E6uvvsr nL!9ZB^JY7V!`i$kiYN2A=m2FV+qlRuI!umqQDkFw0htH@JVP1* delta 91 zcmeC{WNheU6c6xbW)WckfokhN5rKCL|8hz&FmO&3|I5V1HCa(gX|o$6i#SuY^=2Q5 f!`i$kiYCjr=m2FVd%4Ik8cj}jQDpn-3^EA-hu0YX diff --git a/dev/_downloads/7d2e2f052d27d212228870d603a1aca7/convert_ieeg_to_bids.zip b/dev/_downloads/7d2e2f052d27d212228870d603a1aca7/convert_ieeg_to_bids.zip index 95a41df45c9de5cc708cadd2808a85a8b304abe8..517dd0a6b2346674a035f43d2ef9fac536155ff9 100644 GIT binary patch delta 144 zcmX^5jp^h!Cg}igW)=|!5V+?2C!%*{bzE8?0|N+)Pd>X#YNP2vRxu?dB?Sd#g}nU2 zL@NbXQv*W<7ZU@6%^Ykqy_s%0Z(bb8oym)$d-CpG7790k=Dm){&A*(%zyQKhU|S%> Wmd4qElh5rEpRBc8lx^8AkRSjOjC JwrFjTRRE`HC|>{o delta 83 zcmewt{yJPdz?+#xgaHJqt^Y)X|F|kYpPzwY{zma5jGNyvGV?K2TW|i%Un0$mB0af8 Y+X5&vd7ZWlV6}Qzi)o1!aZ2{K7;l1y@r8Lj@Nj z15*VT69a?IzD#dem~J_5wq}pu<3rUrd7-E&P-^lGQ5hz8_Q~GtQj-P51lZ<_g6seQ D-jW^c delta 85 zcmdm|vrI=Kz?+#xgaHJqt^Y(ESTX0+A2tStKWrN%Oqn*PGQDA8sH4VYVrqB8AkodykgpH?V=!40K}skI{*Lx diff --git a/dev/_downloads/b637816c94a7cf4caf2ce4be824a809e/create_bids_folder.py b/dev/_downloads/b637816c94a7cf4caf2ce4be824a809e/create_bids_folder.py index b050b97b6..cdca659f0 100644 --- a/dev/_downloads/b637816c94a7cf4caf2ce4be824a809e/create_bids_folder.py +++ b/dev/_downloads/b637816c94a7cf4caf2ce4be824a809e/create_bids_folder.py @@ -11,7 +11,7 @@ You may automatically convert Raw objects to BIDS-compatible files with ``write_raw_bids``. This example is for manually creating files/folders. -""" +""" # noqa: E501 D205 D400 # Authors: The MNE-BIDS developers # SPDX-License-Identifier: BSD-3-Clause diff --git a/dev/_downloads/b7d549fc992398180d012ad4f3a73e8d/convert_eeg_to_bids.py b/dev/_downloads/b7d549fc992398180d012ad4f3a73e8d/convert_eeg_to_bids.py index b3191bf8c..1ad26448f 100644 --- a/dev/_downloads/b7d549fc992398180d012ad4f3a73e8d/convert_eeg_to_bids.py +++ b/dev/_downloads/b7d549fc992398180d012ad4f3a73e8d/convert_eeg_to_bids.py @@ -19,8 +19,7 @@ .. _BrainVision format: https://www.brainproducts.com/support-resources/brainvision-core-data-format-1-0/ .. _CapTrak: https://www.fieldtriptoolbox.org/faq/coordsys/#details-of-the-captrak-coordinate-system - -""" # noqa: E501 +""" # noqa: E501 D205 D400 # Authors: The MNE-BIDS developers # SPDX-License-Identifier: BSD-3-Clause diff --git a/dev/_downloads/bcdfe0d0e220cf6da56beb8f9163c326/mark_bad_channels.ipynb b/dev/_downloads/bcdfe0d0e220cf6da56beb8f9163c326/mark_bad_channels.ipynb index ed5ca3dc5..991489411 100644 --- a/dev/_downloads/bcdfe0d0e220cf6da56beb8f9163c326/mark_bad_channels.ipynb +++ b/dev/_downloads/bcdfe0d0e220cf6da56beb8f9163c326/mark_bad_channels.ipynb @@ -4,7 +4,7 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "\n# 03. Interactive data inspection and bad channel selection\n\nYou can use MNE-BIDS interactively inspect your MEG or (i)EEG data.\nProblematic channels can be marked as \"bad\", for example if the connected\nsensor produced mostly noise \u2013 or no signal at all. Similarly, you can declare\nchannels as \"good\", should you discover they were incorrectly marked as bad.\nBad channel selection can also be performed non-interactively.\n\nFurthermore, you can view and edit the experimental events and mark time\nsegments as \"bad\".\n\n" + "\n# 03. Interactive data inspection and bad channel selection\n\nYou can use MNE-BIDS interactively inspect your MEG or (i)EEG data.\nProblematic channels can be marked as \"bad\", for example if the connected\nsensor produced mostly noise - or no signal at all. Similarly, you can declare\nchannels as \"good\", should you discover they were incorrectly marked as bad.\nBad channel selection can also be performed non-interactively.\n\nFurthermore, you can view and edit the experimental events and mark time\nsegments as \"bad\".\n\n" ] }, { diff --git a/dev/_downloads/bdc50d7de6c227351cc05fc714c0362c/anonymize_dataset.zip b/dev/_downloads/bdc50d7de6c227351cc05fc714c0362c/anonymize_dataset.zip index 33709a5fd018c4c5ff84538e372fdbf951b00df0..7ea1f79f59c7c2a984fbfd83b1a6ddcf071bd321 100644 GIT binary patch delta 45 ycmbO-k#WjIMxFp~W)=|!5V+;Mk>`{w(d zVWO3StEqwEW<%yBvP_xQo3AVUHsnRoIr)B&IZ$S@M6e9wp~8{0|N+4FihT%C9%=u8jG}&l9GagvO->d zVWO3StEqvZf{T%Xse+4%fx%`z*4b)I*PJ)6)}C+2i(hPKzslU-6)L! delta 109 zcmex$mGSXaM(F@=W)=|!5XiFr6QRpqC6lSmzyQJ$lP_vZZZx^Z!p5bfq{PKFxyw*# vvnOl08dJIT=0n=^?RZgiOwP-)1jv diff --git a/dev/_downloads/f336dfe6a8ab84474813b87342e0c0a3/convert_empty_room.py b/dev/_downloads/f336dfe6a8ab84474813b87342e0c0a3/convert_empty_room.py index 2c6767d77..09c496bad 100644 --- a/dev/_downloads/f336dfe6a8ab84474813b87342e0c0a3/convert_empty_room.py +++ b/dev/_downloads/f336dfe6a8ab84474813b87342e0c0a3/convert_empty_room.py @@ -7,7 +7,7 @@ This example demonstrates how to store empty room data "manually" in the BIDS format and how to retrieve them. -""" +""" # noqa: E501 D400 # Authors: The MNE-BIDS developers # SPDX-License-Identifier: BSD-3-Clause diff --git a/dev/_downloads/f6baa7da9ece655f45f704c75843a8ff/convert_empty_room.zip b/dev/_downloads/f6baa7da9ece655f45f704c75843a8ff/convert_empty_room.zip index d8d67da135e888d53ed0984c92a776a3394228a8..a182dad6ab86393bd46da55a912eed682f1fb42d 100644 GIT binary patch delta 120 zcmX>edn;Bvz?+#xgaHI@I{%4S>y}jK#LvLsv{77+QCLAiSs^dKFwsiE)zrXH!NtVD zV6!QsIUmz4=goQi$K-fXv`lu?GXu&@uGEuZD&?PC$1f!o;LXYgGMWhpJAt&d9*743 D+d>_? delta 96 zcmcZ=dpuS;z?+#xgaHI9t^Y)vJ{;kz&(FXB!lIKW@QZCUWMSOw!D!CMRBgSvk^h(+ iFN(6sA$n#&naMqRGE7PQlPB^^O+KP0z^0)GG7tbCY8n~< diff --git a/dev/_modules/index.html b/dev/_modules/index.html index c5de895b9..0b375a1d7 100644 --- a/dev/_modules/index.html +++ b/dev/_modules/index.html @@ -7,7 +7,7 @@ - Overview: module code — MNE-BIDS 0.16.0.dev17+g91655260 documentation + Overview: module code — MNE-BIDS 0.16.0.dev18+g1c9361cc documentation @@ -40,7 +40,7 @@ - + @@ -147,7 +147,7 @@ -

MNE-BIDS 0.16.0.dev17+g91655260 documentation

+

MNE-BIDS 0.16.0.dev18+g1c9361cc documentation

diff --git a/dev/_modules/mne_bids/copyfiles.html b/dev/_modules/mne_bids/copyfiles.html index 8fd45d164..5f8f61390 100644 --- a/dev/_modules/mne_bids/copyfiles.html +++ b/dev/_modules/mne_bids/copyfiles.html @@ -7,7 +7,7 @@ - mne_bids.copyfiles — MNE-BIDS 0.16.0.dev17+g91655260 documentation + mne_bids.copyfiles — MNE-BIDS 0.16.0.dev18+g1c9361cc documentation @@ -40,7 +40,7 @@ - + @@ -147,7 +147,7 @@ -

MNE-BIDS 0.16.0.dev17+g91655260 documentation

+

MNE-BIDS 0.16.0.dev18+g1c9361cc documentation

diff --git a/dev/_modules/mne_bids/dig.html b/dev/_modules/mne_bids/dig.html index c0a428a3d..9d893207f 100644 --- a/dev/_modules/mne_bids/dig.html +++ b/dev/_modules/mne_bids/dig.html @@ -7,7 +7,7 @@ - mne_bids.dig — MNE-BIDS 0.16.0.dev17+g91655260 documentation + mne_bids.dig — MNE-BIDS 0.16.0.dev18+g1c9361cc documentation @@ -40,7 +40,7 @@ - + @@ -147,7 +147,7 @@ -

MNE-BIDS 0.16.0.dev17+g91655260 documentation

+

MNE-BIDS 0.16.0.dev18+g1c9361cc documentation

diff --git a/dev/_modules/mne_bids/inspect.html b/dev/_modules/mne_bids/inspect.html index 510f92f12..236652f00 100644 --- a/dev/_modules/mne_bids/inspect.html +++ b/dev/_modules/mne_bids/inspect.html @@ -7,7 +7,7 @@ - mne_bids.inspect — MNE-BIDS 0.16.0.dev17+g91655260 documentation + mne_bids.inspect — MNE-BIDS 0.16.0.dev18+g1c9361cc documentation @@ -40,7 +40,7 @@ - + @@ -147,7 +147,7 @@ -

MNE-BIDS 0.16.0.dev17+g91655260 documentation

+

MNE-BIDS 0.16.0.dev18+g1c9361cc documentation

diff --git a/dev/_modules/mne_bids/path.html b/dev/_modules/mne_bids/path.html index b71ed693c..7a8d35b0e 100644 --- a/dev/_modules/mne_bids/path.html +++ b/dev/_modules/mne_bids/path.html @@ -7,7 +7,7 @@ - mne_bids.path — MNE-BIDS 0.16.0.dev17+g91655260 documentation + mne_bids.path — MNE-BIDS 0.16.0.dev18+g1c9361cc documentation @@ -40,7 +40,7 @@ - + @@ -147,7 +147,7 @@ -

MNE-BIDS 0.16.0.dev17+g91655260 documentation

+

MNE-BIDS 0.16.0.dev18+g1c9361cc documentation

@@ -2420,13 +2420,13 @@

Source code for mne_bids.path

     """
     # Take all possible data types from "entity" table
     # (Appendix in BIDS spec)
-    # https://bids-specification.readthedocs.io/en/latest/appendices/entity-table.html  # noqa
+    # https://bids-specification.readthedocs.io/en/latest/appendices/entity-table.html
     datatype_list = ("anat", "func", "dwi", "fmap", "beh", "meg", "eeg", "ieeg", "nirs")
     datatypes = list()
     for root, dirs, files in os.walk(root):
-        for dir in dirs:
-            if dir in datatype_list and dir not in datatypes:
-                datatypes.append(dir)
+        for _dir in dirs:
+            if _dir in datatype_list and _dir not in datatypes:
+                datatypes.append(_dir)
 
     return datatypes
diff --git a/dev/_modules/mne_bids/read.html b/dev/_modules/mne_bids/read.html index 6ce052513..223162386 100644 --- a/dev/_modules/mne_bids/read.html +++ b/dev/_modules/mne_bids/read.html @@ -7,7 +7,7 @@ - mne_bids.read — MNE-BIDS 0.16.0.dev17+g91655260 documentation + mne_bids.read — MNE-BIDS 0.16.0.dev18+g1c9361cc documentation @@ -40,7 +40,7 @@ - + @@ -147,7 +147,7 @@ -

MNE-BIDS 0.16.0.dev17+g91655260 documentation

+

MNE-BIDS 0.16.0.dev18+g1c9361cc documentation

@@ -1140,7 +1140,7 @@

Source code for mne_bids.read

 
         if updated_ch_type is None:
             # XXX Try again with uppercase spelling – this should be removed
-            # XXX once https://github.com/bids-standard/bids-validator/issues/1018  # noqa:E501
+            # XXX once https://github.com/bids-standard/bids-validator/issues/1018
             # XXX has been resolved.
             # XXX x-ref https://github.com/mne-tools/mne-bids/issues/481
             updated_ch_type = bids_to_mne_ch_types.get(ch_type.upper(), None)
diff --git a/dev/_modules/mne_bids/report/_report.html b/dev/_modules/mne_bids/report/_report.html
index d793b8106..2d0d1f3b1 100644
--- a/dev/_modules/mne_bids/report/_report.html
+++ b/dev/_modules/mne_bids/report/_report.html
@@ -7,7 +7,7 @@
   
     
     
-    mne_bids.report._report — MNE-BIDS 0.16.0.dev17+g91655260 documentation
+    mne_bids.report._report — MNE-BIDS 0.16.0.dev18+g1c9361cc documentation
   
   
   
@@ -40,7 +40,7 @@
 
   
 
-    
+    
     
     
     
@@ -147,7 +147,7 @@
   
   
   
-    
MNE-BIDS 0.16.0.dev17+g91655260 documentation

+    
MNE-BIDS 0.16.0.dev18+g1c9361cc documentation
@@ -559,12 +559,12 @@

Source code for mne_bids.report._report

     return "{}, and {}".format(", ".join(listed[:-1]), listed[-1])
 
 
-def _range_str(minval, maxval, meanval, stdval, n_unknown, type):
+def _range_str(minval, maxval, meanval, stdval, n_unknown, typ):
     if minval == "n/a":
         return "ages all unknown"
 
     if n_unknown > 0:
-        unknown_str = f"; {n_unknown} with unknown {type}"
+        unknown_str = f"; {n_unknown} with unknown {typ}"
     else:
         unknown_str = ""
     return (
diff --git a/dev/_modules/mne_bids/sidecar_updates.html b/dev/_modules/mne_bids/sidecar_updates.html
index 0296ecb96..137258bdc 100644
--- a/dev/_modules/mne_bids/sidecar_updates.html
+++ b/dev/_modules/mne_bids/sidecar_updates.html
@@ -7,7 +7,7 @@
   
     
     
-    mne_bids.sidecar_updates — MNE-BIDS 0.16.0.dev17+g91655260 documentation
+    mne_bids.sidecar_updates — MNE-BIDS 0.16.0.dev18+g1c9361cc documentation
   
   
   
@@ -40,7 +40,7 @@
 
   
 
-    
+    
     
     
     
@@ -147,7 +147,7 @@
   
   
   
-    
MNE-BIDS 0.16.0.dev17+g91655260 documentation

+    
MNE-BIDS 0.16.0.dev18+g1c9361cc documentation
diff --git a/dev/_modules/mne_bids/stats.html b/dev/_modules/mne_bids/stats.html index 75341d2dd..ca81c15ca 100644 --- a/dev/_modules/mne_bids/stats.html +++ b/dev/_modules/mne_bids/stats.html @@ -7,7 +7,7 @@ - mne_bids.stats — MNE-BIDS 0.16.0.dev17+g91655260 documentation + mne_bids.stats — MNE-BIDS 0.16.0.dev18+g1c9361cc documentation @@ -40,7 +40,7 @@ - + @@ -147,7 +147,7 @@ -

MNE-BIDS 0.16.0.dev17+g91655260 documentation

+

MNE-BIDS 0.16.0.dev18+g1c9361cc documentation

diff --git a/dev/_modules/mne_bids/utils.html b/dev/_modules/mne_bids/utils.html index 73b1c0ead..9f0953d6e 100644 --- a/dev/_modules/mne_bids/utils.html +++ b/dev/_modules/mne_bids/utils.html @@ -7,7 +7,7 @@ - mne_bids.utils — MNE-BIDS 0.16.0.dev17+g91655260 documentation + mne_bids.utils — MNE-BIDS 0.16.0.dev18+g1c9361cc documentation @@ -40,7 +40,7 @@ - + @@ -147,7 +147,7 @@ -

MNE-BIDS 0.16.0.dev17+g91655260 documentation

+

MNE-BIDS 0.16.0.dev18+g1c9361cc documentation

@@ -1030,7 +1030,7 @@

Source code for mne_bids.utils

 
 def _import_nibabel(why="work with MRI data"):
     try:
-        import nibabel  # noqa
+        import nibabel
     except ImportError as exc:
         raise exc.__class__(
             f"nibabel is required to {why} but could not be imported, " f"got: {exc}"
@@ -1044,7 +1044,7 @@ 
Source code for mne_bids.utils
     category=RuntimeWarning,
     module="mne_bids",
     ignore_namespaces=("mne", "mne_bids"),
-):  # noqa: D103
+):
     """Emit a warning."""
     _warn(
         message,
diff --git a/dev/_modules/mne_bids/write.html b/dev/_modules/mne_bids/write.html
index a85ff8b82..97c8ebc28 100644
--- a/dev/_modules/mne_bids/write.html
+++ b/dev/_modules/mne_bids/write.html
@@ -7,7 +7,7 @@
   
     
     
-    mne_bids.write — MNE-BIDS 0.16.0.dev17+g91655260 documentation
+    mne_bids.write — MNE-BIDS 0.16.0.dev18+g1c9361cc documentation
   
   
   
@@ -40,7 +40,7 @@
 
   
 
-    
+    
     
     
     
@@ -147,7 +147,7 @@
   
   
   
-    
MNE-BIDS 0.16.0.dev17+g91655260 documentation

+    
MNE-BIDS 0.16.0.dev18+g1c9361cc documentation

   
 

     
@@ -3209,7 +3209,7 @@ 
Source code for mne_bids.write
     ...                      root=op.join(data_path, 'mne_bids')) # doctest: +SKIP
     >>> write_meg_crosstalk(crosstalk_fname, bids_path) # doctest: +SKIP
     Writing crosstalk file to ...sub-01_ses-test_acq-crosstalk_meg.fif
-    """  # noqa: E501
+    """
     if bids_path.root is None or bids_path.subject is None:
         raise ValueError("bids_path must have root and subject set.")
     if bids_path.datatype not in (None, "meg"):
diff --git a/dev/_static/documentation_options.js b/dev/_static/documentation_options.js
index 1311470b6..9f263cf71 100644
--- a/dev/_static/documentation_options.js
+++ b/dev/_static/documentation_options.js
@@ -1,5 +1,5 @@
 const DOCUMENTATION_OPTIONS = {
-    VERSION: '0.16.0.dev17+g91655260',
+    VERSION: '0.16.0.dev18+g1c9361cc',
     LANGUAGE: 'en',
     COLLAPSE_INDEX: false,
     BUILDER: 'html',
diff --git a/dev/api.html b/dev/api.html
index abbf4bcd8..41fc9bd1c 100644
--- a/dev/api.html
+++ b/dev/api.html
@@ -8,7 +8,7 @@
     
     
 
-    API Documentation — MNE-BIDS 0.16.0.dev17+g91655260 documentation
+    API Documentation — MNE-BIDS 0.16.0.dev18+g1c9361cc documentation
   
   
   
@@ -41,7 +41,7 @@
 
   
 
-    
+    
     
     
     
@@ -150,7 +150,7 @@
   
   
   
-    
MNE-BIDS 0.16.0.dev17+g91655260 documentation

+    
MNE-BIDS 0.16.0.dev18+g1c9361cc documentation

   
 

     
diff --git a/dev/authors.html b/dev/authors.html
index 9c173cd70..31758d981 100644
--- a/dev/authors.html
+++ b/dev/authors.html
@@ -8,7 +8,7 @@
     
     
 
-    <no title> — MNE-BIDS 0.16.0.dev17+g91655260 documentation
+    <no title> — MNE-BIDS 0.16.0.dev18+g1c9361cc documentation
   
   
   
@@ -41,7 +41,7 @@
 
   
 
-    
+    
     
     
     
@@ -148,7 +148,7 @@
   
   
   
-    
MNE-BIDS 0.16.0.dev17+g91655260 documentation

+    
MNE-BIDS 0.16.0.dev18+g1c9361cc documentation
diff --git a/dev/auto_examples/anonymize_dataset.html b/dev/auto_examples/anonymize_dataset.html index ce652081e..d617db874 100644 --- a/dev/auto_examples/anonymize_dataset.html +++ b/dev/auto_examples/anonymize_dataset.html @@ -8,7 +8,7 @@ - 13. Anonymizing a BIDS dataset — MNE-BIDS 0.16.0.dev17+g91655260 documentation + 13. Anonymizing a BIDS dataset — MNE-BIDS 0.16.0.dev18+g1c9361cc documentation @@ -41,7 +41,7 @@ - + @@ -151,7 +151,7 @@ -

MNE-BIDS 0.16.0.dev17+g91655260 documentation

+

MNE-BIDS 0.16.0.dev18+g1c9361cc documentation

@@ -675,7 +675,7 @@

Basic anonymizationSpecifying subject IDsSpecifying subject IDsSpecifying subject IDs @@ -930,9 +930,9 @@

ReproducibilityTotal running time of the script: (0 minutes 11.825 seconds)

+

Total running time of the script: (0 minutes 11.702 seconds)

 @@ -1127,7 +1127,7 @@

Cite mne-bidshttps://bids-standard.github.io/bids-validator/

Command line tool: https://www.npmjs.com/package/bids-validator

-

Total running time of the script: (0 minutes 0.353 seconds)

+

Total running time of the script: (0 minutes 0.358 seconds)

-

Total running time of the script: (0 minutes 2.324 seconds)

+

Total running time of the script: (0 minutes 2.134 seconds)

-

Total running time of the script: (0 minutes 1.253 seconds)

+

Total running time of the script: (0 minutes 1.281 seconds)

This should be very similar to the ds000248 dataset_description.json!

-

Total running time of the script: (0 minutes 3.865 seconds)

+

Total running time of the script: (0 minutes 3.889 seconds)

-

Total running time of the script: (0 minutes 12.813 seconds)

+

Total running time of the script: (0 minutes 13.098 seconds)