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agramfort merged 12 commits into from
Aug 29, 2022
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[ENH, MRG] Add time-frequency epoch source estimation #11095

agramfort merged 12 commits into from
Aug 29, 2022

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@alexrockhill alexrockhill commented Aug 26, 2022

The MNE methods part of #10920.

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agramfort commented Aug 26, 2022 via email

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alexrockhill commented Aug 26, 2022 •
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do you understand why?
…
Message ID: @.***>

No, it was much larger than just rounding error which is odd. The time stamps were off by several ms.

>>> stcs[0][0].times
array([0.        , 0.00332992, 0.00665984, 0.00998976, 0.01331968,
       0.0166496 , 0.01997952, 0.02330944, 0.02663936, 0.02996928,
       0.0332992 , 0.03662912, 0.03995904, 0.04328896, 0.04661888,
       0.0499488 , 0.05327872, 0.05660864, 0.05993856, 0.06326848,
       0.0665984 , 0.06992832, 0.07325824, 0.07658817, 0.07991809,
       0.08324801, 0.08657793, 0.08990785, 0.09323777, 0.09656769,
       0.09989761, 0.10322753, 0.10655745, 0.10988737, 0.11321729,
       0.11654721, 0.11987713, 0.12320705, 0.12653697, 0.12986689,
       0.13319681, 0.13652673, 0.13985665, 0.14318657, 0.14651649,
       0.14984641, 0.15317633, 0.15650625, 0.15983617, 0.16316609,
       0.16649601, 0.16982593, 0.17315585, 0.17648577, 0.17981569,
       0.18314561, 0.18647553, 0.18980545, 0.19313537, 0.19646529,
       0.19979521, 0.20312513, 0.20645505, 0.20978497, 0.21311489,
       0.21644481, 0.21977473, 0.22310465, 0.22643457, 0.2297645 ,
       0.23309442, 0.23642434, 0.23975426, 0.24308418, 0.2464141 ,
       0.24974402, 0.25307394, 0.25640386, 0.25973378, 0.2630637 ,
       0.26639362, 0.26972354, 0.27305346, 0.27638338, 0.2797133 ,
       0.28304322, 0.28637314, 0.28970306, 0.29303298, 0.2963629 ,
       0.29969282, 0.30302274, 0.30635266, 0.30968258, 0.3130125 ,
       0.31634242, 0.31967234, 0.32300226, 0.32633218, 0.3296621 ,
       0.33299202, 0.33632194, 0.33965186, 0.34298178, 0.3463117 ,
       0.34964162, 0.35297154, 0.35630146, 0.35963138, 0.3629613 ,
       0.36629122, 0.36962114, 0.37295106, 0.37628098, 0.37961091,
       0.38294083, 0.38627075, 0.38960067, 0.39293059, 0.39626051,
       0.39959043, 0.40292035, 0.40625027, 0.40958019, 0.41291011,
       0.41624003, 0.41956995, 0.42289987, 0.42622979, 0.42955971,
       0.43288963, 0.43621955, 0.43954947, 0.44287939, 0.44620931,
       0.44953923, 0.45286915, 0.45619907, 0.45952899, 0.46285891,
       0.46618883, 0.46951875, 0.47284867, 0.47617859, 0.47950851,
       0.48283843, 0.48616835, 0.48949827, 0.49282819, 0.49615811,
       0.49948803, 0.50281795, 0.50614787, 0.50947779, 0.51280771,
       0.51613763, 0.51946755, 0.52279747, 0.52612739, 0.52945731,
       0.53278724, 0.53611716, 0.53944708, 0.542777  , 0.54610692,
       0.54943684, 0.55276676, 0.55609668, 0.5594266 , 0.56275652,
       0.56608644, 0.56941636, 0.57274628, 0.5760762 , 0.57940612,
       0.58273604, 0.58606596, 0.58939588, 0.5927258 , 0.59605572,
       0.59938564, 0.60271556, 0.60604548, 0.6093754 , 0.61270532,
       0.61603524, 0.61936516, 0.62269508, 0.626025  , 0.62935492,
       0.63268484, 0.63601476, 0.63934468, 0.6426746 , 0.64600452,
       0.64933444, 0.65266436, 0.65599428, 0.6593242 , 0.66265412,
       0.66598404, 0.66931396, 0.67264388, 0.6759738 , 0.67930372,
       0.68263364, 0.68596357, 0.68929349, 0.69262341, 0.69595333,
       0.69928325, 0.70261317, 0.70594309, 0.70927301, 0.71260293,
       0.71593285, 0.71926277, 0.72259269, 0.72592261, 0.72925253,
       0.73258245, 0.73591237, 0.73924229, 0.74257221, 0.74590213,
       0.74923205, 0.75256197, 0.75589189, 0.75922181, 0.76255173,
       0.76588165, 0.76921157, 0.77254149, 0.77587141, 0.77920133,
       0.78253125, 0.78586117, 0.78919109, 0.79252101, 0.79585093,
       0.79918085, 0.80251077, 0.80584069, 0.80917061, 0.81250053,
       0.81583045, 0.81916037, 0.82249029, 0.82582021, 0.82915013,
       0.83248005, 0.83580998, 0.8391399 , 0.84246982, 0.84579974,
       0.84912966, 0.85245958, 0.8557895 , 0.85911942, 0.86244934,
       0.86577926, 0.86910918, 0.8724391 , 0.87576902, 0.87909894,
       0.88242886, 0.88575878, 0.8890887 , 0.89241862, 0.89574854,
       0.89907846, 0.90240838, 0.9057383 , 0.90906822, 0.91239814,
       0.91572806, 0.91905798, 0.9223879 , 0.92571782, 0.92904774,
       0.93237766, 0.93570758, 0.9390375 , 0.94236742, 0.94569734,
       0.94902726, 0.95235718, 0.9556871 , 0.95901702, 0.96234694,
       0.96567686, 0.96900678, 0.9723367 , 0.97566662, 0.97899654,
       0.98232646, 0.98565638, 0.98898631, 0.99231623, 0.99564615])

>>> epochs_tfr.times
array([0.        , 0.00334448, 0.00668896, 0.01003344, 0.01337793,
       0.01672241, 0.02006689, 0.02341137, 0.02675585, 0.03010033,
       0.03344482, 0.0367893 , 0.04013378, 0.04347826, 0.04682274,
       0.05016722, 0.05351171, 0.05685619, 0.06020067, 0.06354515,
       0.06688963, 0.07023411, 0.0735786 , 0.07692308, 0.08026756,
       0.08361204, 0.08695652, 0.090301  , 0.09364548, 0.09698997,
       0.10033445, 0.10367893, 0.10702341, 0.11036789, 0.11371237,
       0.11705686, 0.12040134, 0.12374582, 0.1270903 , 0.13043478,
       0.13377926, 0.13712375, 0.14046823, 0.14381271, 0.14715719,
       0.15050167, 0.15384615, 0.15719064, 0.16053512, 0.1638796 ,
       0.16722408, 0.17056856, 0.17391304, 0.17725753, 0.18060201,
       0.18394649, 0.18729097, 0.19063545, 0.19397993, 0.19732441,
       0.2006689 , 0.20401338, 0.20735786, 0.21070234, 0.21404682,
       0.2173913 , 0.22073579, 0.22408027, 0.22742475, 0.23076923,
       0.23411371, 0.23745819, 0.24080268, 0.24414716, 0.24749164,
       0.25083612, 0.2541806 , 0.25752508, 0.26086957, 0.26421405,
       0.26755853, 0.27090301, 0.27424749, 0.27759197, 0.28093645,
       0.28428094, 0.28762542, 0.2909699 , 0.29431438, 0.29765886,
       0.30100334, 0.30434783, 0.30769231, 0.31103679, 0.31438127,
       0.31772575, 0.32107023, 0.32441472, 0.3277592 , 0.33110368,
       0.33444816, 0.33779264, 0.34113712, 0.34448161, 0.34782609,
       0.35117057, 0.35451505, 0.35785953, 0.36120401, 0.36454849,
       0.36789298, 0.37123746, 0.37458194, 0.37792642, 0.3812709 ,
       0.38461538, 0.38795987, 0.39130435, 0.39464883, 0.39799331,
       0.40133779, 0.40468227, 0.40802676, 0.41137124, 0.41471572,
       0.4180602 , 0.42140468, 0.42474916, 0.42809365, 0.43143813,
       0.43478261, 0.43812709, 0.44147157, 0.44481605, 0.44816054,
       0.45150502, 0.4548495 , 0.45819398, 0.46153846, 0.46488294,
       0.46822742, 0.47157191, 0.47491639, 0.47826087, 0.48160535,
       0.48494983, 0.48829431, 0.4916388 , 0.49498328, 0.49832776,
       0.50167224, 0.50501672, 0.5083612 , 0.51170569, 0.51505017,
       0.51839465, 0.52173913, 0.52508361, 0.52842809, 0.53177258,
       0.53511706, 0.53846154, 0.54180602, 0.5451505 , 0.54849498,
       0.55183946, 0.55518395, 0.55852843, 0.56187291, 0.56521739,
       0.56856187, 0.57190635, 0.57525084, 0.57859532, 0.5819398 ,
       0.58528428, 0.58862876, 0.59197324, 0.59531773, 0.59866221,
       0.60200669, 0.60535117, 0.60869565, 0.61204013, 0.61538462,
       0.6187291 , 0.62207358, 0.62541806, 0.62876254, 0.63210702,
       0.63545151, 0.63879599, 0.64214047, 0.64548495, 0.64882943,
       0.65217391, 0.65551839, 0.65886288, 0.66220736, 0.66555184,
       0.66889632, 0.6722408 , 0.67558528, 0.67892977, 0.68227425,
       0.68561873, 0.68896321, 0.69230769, 0.69565217, 0.69899666,
       0.70234114, 0.70568562, 0.7090301 , 0.71237458, 0.71571906,
       0.71906355, 0.72240803, 0.72575251, 0.72909699, 0.73244147,
       0.73578595, 0.73913043, 0.74247492, 0.7458194 , 0.74916388,
       0.75250836, 0.75585284, 0.75919732, 0.76254181, 0.76588629,
       0.76923077, 0.77257525, 0.77591973, 0.77926421, 0.7826087 ,
       0.78595318, 0.78929766, 0.79264214, 0.79598662, 0.7993311 ,
       0.80267559, 0.80602007, 0.80936455, 0.81270903, 0.81605351,
       0.81939799, 0.82274247, 0.82608696, 0.82943144, 0.83277592,
       0.8361204 , 0.83946488, 0.84280936, 0.84615385, 0.84949833,
       0.85284281, 0.85618729, 0.85953177, 0.86287625, 0.86622074,
       0.86956522, 0.8729097 , 0.87625418, 0.87959866, 0.88294314,
       0.88628763, 0.88963211, 0.89297659, 0.89632107, 0.89966555,
       0.90301003, 0.90635452, 0.909699  , 0.91304348, 0.91638796,
       0.91973244, 0.92307692, 0.9264214 , 0.92976589, 0.93311037,
       0.93645485, 0.93979933, 0.94314381, 0.94648829, 0.94983278,
       0.95317726, 0.95652174, 0.95986622, 0.9632107 , 0.96655518,
       0.96989967, 0.97324415, 0.97658863, 0.97993311, 0.98327759,
       0.98662207, 0.98996656, 0.99331104, 0.99665552, 1.        ])

Both are the same length though...

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agramfort commented Aug 26, 2022 •
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@alexrockhill can I replicate easily?

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alexrockhill commented Aug 26, 2022

@alexrockhill can I replicate easily?

Yes, you can just uncomment it from the test.

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agramfort commented Aug 29, 2022 via email

agramfort
agramfort reviewed Aug 29, 2022
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@agramfort agramfort enabled auto-merge (squash) August 29, 2022 14:05
@agramfort agramfort merged commit 0faabfb into mne-tools:main Aug 29, 2022
@alexrockhill alexrockhill deleted the tfr branch August 29, 2022 17:10
larsoner added a commit to larsoner/mne-python that referenced this pull request Aug 29, 2022
@larsoner
Merge remote-tracking branch 'upstream/main' into openmeeg
d78f2e9 
* upstream/main:
  BUG: Spectrum deprecation cleanup [circle deploy] (mne-tools#11115)
  Add API entry list and map (mne-tools#10999)
  Add legacy decorator (mne-tools#11097)
  [ENH, MRG] Add time-frequency epoch source estimation (mne-tools#11095)
larsoner added a commit to larsoner/mne-python that referenced this pull request Aug 29, 2022
@larsoner
Merge remote-tracking branch 'upstream/main' into skip
99fa0c1 
* upstream/main: (366 commits)
  BUG: Spectrum deprecation cleanup [circle deploy] (mne-tools#11115)
  Add API entry list and map (mne-tools#10999)
  Add legacy decorator (mne-tools#11097)
  [ENH, MRG] Add time-frequency epoch source estimation (mne-tools#11095)
  Revert "Add error message when conversion of EEG locs to [circle deploy] (mne-tools#11104)
  MRG: Fixes for mne-tools#11090 (mne-tools#11108)
  add test for edf units param (mne-tools#11105)
  BUG: Improve logic for bti (mne-tools#11102)
  add spectrum class (mne-tools#10184)
  ENH : add units parameter to read_raw_edf in case units is missing from the file (mne-tools#11099)
  ENH: Add temperature and galvanic (mne-tools#11090)
  Add error message when conversion of EEG locs to head space fails (mne-tools#11080)
  DOC: removed unnecessary line in PSF example (mne-tools#11085)
  FIX: Update helmet during ICP (mne-tools#11084)
  Fix various typos (mne-tools#11086)
  DOC: Rel
  BUG: don't assume that channel info contains particular keys (mne-tools#11074)
  [BUG] Fix plot_topomap with sphere="eeglab" (mne-tools#11081)
  Add `vmin` and `vmax` specification to `mne.Evoked.animate_topomap` (mne-tools#11073)
  Add _on_missing functionality to UpdateChannelsMixin (mne-tools#11077)
  ...
larsoner added a commit to larsoner/mne-python that referenced this pull request Aug 30, 2022
@larsoner
Merge remote-tracking branch 'upstream/main' into volpc
4bac62a 
* upstream/main: (25 commits)
  DOC: Exclude some implicit refs in doc build (mne-tools#10433)
  MAINT: Better issue forms (mne-tools#11101)
  [FIX] Typo in example (mne-tools#11118)
  [MRG] Improve interpolation of bridged electrodes (mne-tools#11094)
  BUG: Spectrum deprecation cleanup [circle deploy] (mne-tools#11115)
  Add API entry list and map (mne-tools#10999)
  Add legacy decorator (mne-tools#11097)
  [ENH, MRG] Add time-frequency epoch source estimation (mne-tools#11095)
  Revert "Add error message when conversion of EEG locs to [circle deploy] (mne-tools#11104)
  MRG: Fixes for mne-tools#11090 (mne-tools#11108)
  add test for edf units param (mne-tools#11105)
  BUG: Improve logic for bti (mne-tools#11102)
  add spectrum class (mne-tools#10184)
  ENH : add units parameter to read_raw_edf in case units is missing from the file (mne-tools#11099)
  ENH: Add temperature and galvanic (mne-tools#11090)
  Add error message when conversion of EEG locs to head space fails (mne-tools#11080)
  DOC: removed unnecessary line in PSF example (mne-tools#11085)
  FIX: Update helmet during ICP (mne-tools#11084)
  Fix various typos (mne-tools#11086)
  DOC: Rel
  ...
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