Deprecate read_montage and class Montage#6764
Conversation
d0c3c8e to
d43a8a8
Compare
Codecov Report
@@ Coverage Diff @@
## master #6764 +/- ##
=========================================
- Coverage 89.64% 89.6% -0.05%
=========================================
Files 422 422
Lines 76545 76693 +148
Branches 12509 12549 +40
=========================================
+ Hits 68621 68721 +100
- Misses 5121 5150 +29
- Partials 2803 2822 +19 |
d43a8a8 to
dec9e12
Compare
69283b0 to
7f29c02
Compare
7f29c02 to
67cbb5d
Compare
mne/channels/montage.py
Outdated
| Parameters | ||
| ---------- | ||
| fname : str | ||
| The filepath of Digitization EEGLAB formatted file. |
There was a problem hiding this comment.
| The filepath of Digitization EEGLAB formatted file. | |
| The file containing electrode locations in EEGLAB format. |
|
If I didn't mess up, I think that what we are missing is: The other hpts file https://github.com/mne-tools/mne-python/blob/master/mne/io/edf/tests/data/biosemi.hpts is a biosemi64 but I don't have the format of the original file. I have not checked that the result matches the loc file we have is in I said supposedly because the ch_names are not a subset of the So my plan so far: 1 - allow polhemus to take the hpts file we have |
|
I would make And if we want, we can add an option to return the raw theta/phi values as an |
e233ac5 to
e3212fd
Compare
|
@larsoner the issue is not that it is stored weirdly. The problem is that it returns something closer to |
mne/channels/montage.py
Outdated
|
|
||
|
|
||
| def read_standard_montage(fname, head_size=HEAD_SIZE_DEFAULT, unit='m'): | ||
| """Read a standard montage file containing polar coordinates. |
There was a problem hiding this comment.
can you check if all files you can read now are in polar coordinates?
There was a problem hiding this comment.
The right way to split them would had been well possed formats vs ill-posed formats. In other wourds, if we have xyz or r,theta,phi is well posed + ch_names and types. (and we should allow for head_size=None and recover whatever is in the file with 0 magic). And this should be some kind of reader (brainvision, hpts, ..)
and read_standard_montage should be used for illposed ie not having radius.
But since we were ignoring it everywhere in read_montage. I just decided to stuff everything in read_standard_montage and drive the action with head_size.
mne/channels/tests/test_montage.py
Outdated
| montage = read_montage(op.join(tempdir, kind), transform=True) | ||
|
|
||
| with pytest.deprecated_call(): | ||
| # XXX: This is a regression test that might need to be translated. |
7aab522 to
16ab7dc
Compare
|
I'll be AFK, feel free to push in the PR. |
|
We need to update also https://mne.tools/dev/auto_tutorials/misc/plot_sensor_locations.html?highlight=montage |
ff5e76c to
49d7f5b
Compare
49d7f5b to
d84aacf
Compare
* WIP: deprecate read_montage in test_montage * wip: just to see what crashes. * continue deprecation * WIP: Add read_dig_eeglab * FIX: read_dig_eeglab docstrings and doc * TST: update test * update whatsnew * add read_dig_eeglab to deprecation msg * Its not read_dig_eeglab. * WIP: Add read_dig_polhemus_fastscan * WIP: add read_standard_montage * WIP: circular dep * fix merge * wip * WIP: something is really funky * fix: old montage was not scaled for .loc * TST: I give up trying to understand why they don't get set same * fix? * remove read_dig_eeglab * fix brainvision * some more fixes * TST: make sure we can read everything * fix * FIX: make _pop_montage not depend in n_fid * WIP: add sfp * wip: add matlab * fix eeglab * wip: add asa electrode * wip: add generic theta-phi in degrees files * wip: add hpts * wip: BESA * wip: add brainvision * fix: besa * TST: add some meaningful information * TST: do test something * wip * ups * clarify what's new + fully deprecate read_dig_montage + factorize code * add read_dig_hpts fucntion * coord_frame param in DigMontage was never released * misc * pep8 + cleanup * more cleanup * update documentation * fix doc? * fix fialing test * BUG: Fix linking problems and rename function * DOC: Complete table * FIX: Dep
This PR needs better description 'cos it will have a dependency
This is a list of all the digitization files I could find in my pc
depends on #6765