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MRG: Warn if NIRX directory structure has been modified from original format #7898

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merged 1 commit into from
Jun 15, 2020
Merged

MRG: Warn if NIRX directory structure has been modified from original format #7898

merged 1 commit into from
Jun 15, 2020

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rob-luke
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Reference issue

Fixes #7894. @swy7ch noted that the NIRX file reader checks for a dat file, but it is not used.

What does this implement/fix?

Instead of failing if the .dat is missing this now throws a warning to the user that the file structure has been modified from what the measurement machine saved.

Additional information

We have had some discussion about what the correct behaviour is. See the above linked issue for discussion.

@rob-luke rob-luke force-pushed the nirsdatwarn branch 2 times, most recently from 5fcdad0 to c544ded Compare June 14, 2020 01:57
agramfort
agramfort reviewed Jun 14, 2020
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mne/io/nirx/tests/test_nirx.py Outdated
with pytest.raises(RuntimeWarning, match='A single dat'):
read_raw_nirx(fname, preload=True)
os.rename(fname_nirx_15_2_short + "/NIRS-2019-08-23_001.tmp",
fname_nirx_15_2_short + "/NIRS-2019-08-23_001.dat")
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this is for me dangerous as if the lines above fail you will never revert the renaming.

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Agreed. Could I not have a test for this? It will drop the code coverage :(

Or is there another way you would suggest?

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@rob-luke the way we usually solve this is with the pattern:

def test_whatever(tmpdir):  # pytest builtin tmpdir fixture
    shutuil.copytree(orig_dir, str(tmpdir))
    # mess with files in tmpdir
    ...
    read_raw_nirx(tmpdir.join('whatever.ext'))

pytest takes care of creating and destroying the tmpdir directory

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beautiful. Thanks

@agramfort
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agramfort commented Jun 14, 2020 via email

@rob-luke
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@larsoner @agramfort could you please review, this failure seems due to the Mac CI exceeding its time limit.

@rob-luke rob-luke changed the title WIP: Warn if NIRX directory structure has been modified from original format MRG: Warn if NIRX directory structure has been modified from original format Jun 15, 2020
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a 16 second turn around. Surely that's a record, thanks @agramfort

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agramfort commented Jun 15, 2020 via email

larsoner
larsoner reviewed Jun 15, 2020
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mne/io/nirx/tests/test_nirx.py
os.rename(str(tmpdir) + "/data" + "/NIRS-2019-08-23_001.dat",
str(tmpdir) + "/data" + "/NIRS-2019-08-23_001.tmp")
fname = str(tmpdir) + "/data" + "/NIRS-2019-08-23_001.hdr"
with pytest.raises(RuntimeWarning, match='A single dat'):
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usually we use pytest.warns, but I suppose this works, too

@larsoner larsoner merged commit 6a7636a into mne-tools:master Jun 15, 2020
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Thanks @rob-luke

larsoner added a commit to GuillaumeFavelier/mne-python that referenced this pull request Jun 16, 2020
@larsoner
Merge remote-tracking branch 'upstream/master' into notebook_screencast
c219ac2 
* upstream/master:
  MRG, FIX: Speed up I/O tests, mark some slow (mne-tools#7904)
  Proper attribution for Blender tutorial (mne-tools#7900)
  MAINT: Check usage [ci skip] (mne-tools#7902)
  Allow find_bad_channels_maxwell() to return scores (mne-tools#7845)
  Warn if NIRx directory structure has been modified from original format (mne-tools#7898)
larsoner added a commit to larsoner/mne-python that referenced this pull request Jun 17, 2020
@larsoner
Merge remote-tracking branch 'upstream/master' into refactor
59db30a 
* upstream/master: (24 commits)
  WIP: Fix Travis (mne-tools#7906)
  WIP: Prototype of notebook viz (screencast) (mne-tools#7758)
  MRG, FIX: Speed up I/O tests, mark some slow (mne-tools#7904)
  Proper attribution for Blender tutorial (mne-tools#7900)
  MAINT: Check usage [ci skip] (mne-tools#7902)
  Allow find_bad_channels_maxwell() to return scores (mne-tools#7845)
  Warn if NIRx directory structure has been modified from original format (mne-tools#7898)
  Pin pvyista to 0.24.3 (mne-tools#7899)
  MRG: Add support for reading and writing sufaces to .obj (mne-tools#7824)
  Fix _auto_topomap_coords docstring. (mne-tools#7895)
  MRG, FIX: Ensure Info H5-writeable (mne-tools#7887)
  Website contents (mne-tools#7889)
  MRG, ENH: Add mri_resolution="sparse" (mne-tools#7888)
  MRG, ENH: Allow disabling FXAA (mne-tools#7877)
  remove "and and" [ci skip] (mne-tools#7882)
  fix evoked nave → inverse guidance (mne-tools#7881)
  ENH: Better error messages (mne-tools#7879)
  FIX : EDF+ Annotation Timestamps missing sub-second accuracy (mne-tools#7875)
  FIX: Fix get_channel_types (mne-tools#7878)
  MRG, BUG: Fix combine evokeds (mne-tools#7869)
  ...
larsoner added a commit to larsoner/mne-python that referenced this pull request Jun 25, 2020
@larsoner
Merge remote-tracking branch 'upstream/master' into resize
3f48e4e 
* upstream/master: (23 commits)
  MAINT: Add mne.surface to docstring tests (mne-tools#7930)
  MRG: Add smoothing controller to TimeViewer for the notebook backend (mne-tools#7928)
  MRG: TimeViewer matplotlib figure color (mne-tools#7925)
  fix typos (mne-tools#7924)
  MRG, ENH: Add method to project onto max power ori (mne-tools#7883)
  WIP: Warn if untested NIRX device (mne-tools#7905)
  MRG, BUG: Fix bug with volume morph and subject_to!="fsaverage" (mne-tools#7896)
  MRG, MAINT: Clean up use of bool, float, int (mne-tools#7917)
  ENH: Better error message for incompatible Evoked objects (mne-tools#7910)
  try to fix nullcontext (mne-tools#7908)
  WIP: Fix Travis (mne-tools#7906)
  WIP: Prototype of notebook viz (screencast) (mne-tools#7758)
  MRG, FIX: Speed up I/O tests, mark some slow (mne-tools#7904)
  Proper attribution for Blender tutorial (mne-tools#7900)
  MAINT: Check usage [ci skip] (mne-tools#7902)
  Allow find_bad_channels_maxwell() to return scores (mne-tools#7845)
  Warn if NIRx directory structure has been modified from original format (mne-tools#7898)
  Pin pvyista to 0.24.3 (mne-tools#7899)
  MRG: Add support for reading and writing sufaces to .obj (mne-tools#7824)
  Fix _auto_topomap_coords docstring. (mne-tools#7895)
  ...
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@agramfort agramfort agramfort approved these changes

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[Question][fNIRS] The use of .dat file
3 participants
@rob-luke @agramfort @larsoner