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MRG, ENH: Speed up NIRx read without preload#7759

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larsoner merged 1 commit intomne-tools:masterfrom
larsoner:nirx
May 12, 2020
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MRG, ENH: Speed up NIRx read without preload#7759
larsoner merged 1 commit intomne-tools:masterfrom
larsoner:nirx

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@larsoner
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@larsoner larsoner commented May 11, 2020

Closes #7744

@rob-luke this code only takes 1 sec now, no idea how long it takes on master because I lost patience waiting after 30 seconds or so:

import time
import mne
fnirs_data_folder = mne.datasets.fnirs_motor.data_path()
fnirs_raw_dir = fnirs_data_folder + '/Participant-1'
raw = mne.io.read_raw_nirx(fnirs_raw_dir)
t0 = time.time()
raw.save('/dev/null', verbose='error')
print(time.time() - t0)

@kylemath
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kylemath commented May 11, 2020

This change is helpful for us and we will add to our import function too (our data files for different blocks sometimes have different sized headers)

@rob-luke
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rob-luke commented May 12, 2020

Thanks @larsoner, I appreciate you fixing this.

@larsoner
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larsoner commented May 12, 2020

Okay, in it goes, thanks for looking @kylemath @rob-luke . In the future feel free to click the green "Review changes" in the upper right of the files-changed page and "Approve" or add some comments and "Request changes" etc., too, if you want. It's always good to get extra eyes (and know that there have been extra eyes) on any code changes...

@larsoner larsoner merged commit 861e825 into mne-tools:master May 12, 2020
@larsoner larsoner deleted the nirx branch May 12, 2020 14:33
@rob-luke
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rob-luke commented May 13, 2020

feel free to click the green "Review changes" in the upper right

Thanks, will do in the future.

larsoner added a commit to larsoner/mne-python that referenced this pull request May 19, 2020
@larsoner
Merge remote-tracking branch 'upstream/master' into refactor
07564e3 
* upstream/master: (74 commits)
  FIX: Correct a bug in find_bads_eog (mne-tools#7797)
  [MRG] split_naming='bids' changes from _part-%d to _split-%d (mne-tools#7794)
  MRG, MAINT, DOC: Remove spyder (mne-tools#7796)
  MAINT: fixes for linkcheck (mne-tools#7762)
  [WIP] Update ieeg data example for ECoG (mne-tools#7768)
  fix examples/tutorials [circle full] (mne-tools#7786)
  MAINT: Clean up VTK and add to pre on Azure (mne-tools#7780)
  ENH: Add matplotlib animation support [skip travis] (mne-tools#7783)
  MRG, API: change out_type default in permutation_cluster_(1samp_)test (mne-tools#7781)
  DOC: docstring fixes (mne-tools#7777)
  MRG, ENH: Add tol_kind option (mne-tools#7736)
  MRG, DOC: Notes about info (mne-tools#7772)
  ENH: Speed up NIRx read without preload (mne-tools#7759)
  Minor plot_raw aes improvement (mne-tools#7770)
  MRG, FIX: Fixes for BEM contours (mne-tools#7763)
  MRG, STY: Fix E741 (mne-tools#7767)
  MRG, ENH - Plot optodes in plot_alignment for fNIRS channels (mne-tools#7747)
  FIX: Update NIH support [skip travis] (mne-tools#7766)
  MAINT: Bump tol for gamma map test (mne-tools#7764)
  MRG, FIX: Fix MRI orientations (mne-tools#7725)
  ...
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Writing NIRS files to FIF is surprisingly slow

3 participants

@larsoner @kylemath @rob-luke