[MRG] FIX Topographic plotting for KIT-UMD data #3349
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Give a sign once it's ready. |
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This is ready as a temporary fix that makes plotting work for UMD data. |
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The travis problem is just the |
christianbrodbeck
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doesn't it break/change the code of people's code using KIT at NYU? |
mne/channels/layout.py
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| layout_name = 'KIT-157' | ||
| # This applies to the KIT systems at NYU and UMD which have different | ||
| # layouts. The 'KIT-157' layout applies to the NYU system. | ||
| return None |
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This doesn't look right. Like this it would never find 'KIT-157'. It's still in use somewhere, right?
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You can still manually specify it.
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@agramfort it will change the looks of topographic plots slightly because the layout will be slightly different. To avoid that (and still make it work for UMD data) I would have to add the proposed guessing of system by sensor positions. |
christianbrodbeck
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Actually I noticed not all topographic plotting functions currently resort to the automatic layout, so we'll need a more involved fix for this... |
christianbrodbeck
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For KIT systems with <=157 channels, create layout based on sensor position
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that's what I feared
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Current coverage is 86.66%@@ master #3349 diff @@
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christianbrodbeck
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This new solution should not break any old code, and can be updated to be more efficient once we have KIT System-IDs in the measurement info. |
mne/channels/layout.py
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| elif n_kit_grads > 0: | ||
| layout_name = _find_kit_system(info, n_kit_grads) | ||
| if layout_name == 'KIT-UMD': | ||
| return _auto_layout(info) |
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why not adding a layout file for KIT-UMD? by doing this we could share the file between software.
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Ho would I create a layout file, using the generate_2d_layout function? And what are the criteria for a good layout? That plot_topo looks good?
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if generate_2d_layout output looks good with plot_topo yes.
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Ok, I generated an automatic layout and then I nudged the rectangles around manually to minimize overlap, which seemed preferable for plot_topo. I noticed though that topomap also uses the same layout where a deterministic arrangement seems preferable?
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There is some, but limited symmetry... here is a raw.plot_sensors() plot and a layout generated with MNE _auto_topomap_coords():
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ok indeed. Then I think you're manually edited version is good enough.
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@agramfort I added a UMD layout. It will be easier to add a test via the KIT_SYSTEM_ID PR because it adds a small UMD raw file. |
* 'master' of git://github.com/mne-tools/mne-python: (48 commits) FIX: Flake fix pep8 [MRG] FIX Topographic plotting for KIT-UMD data (mne-tools#3349) QUICKFIX: logging test Error message for simulate evoked. (mne-tools#3372) Warnings for big bems. (mne-tools#3374) Add test for baseline correction. Use apply_baseline in read_evokeds. Makes (None, 0) the default value baseline in apply_baseline. [FIX] Adds apply_baseline to Evoked fix component inds in ica tutorial (mne-tools#3379) FIX: Xdawn with shuffled epochs (mne-tools#3373) FIX consistency: Epochs.load_data() should always return self (mne-tools#3376) MRG: Build relevant examples (mne-tools#3365) [MRG] set vmin, vmax after smoothing in plot_epochs_image (mne-tools#3360) [FIX] Attempt to fix circle. fixing a bg plotting bug for topo plots Modified test and tutorial. [MRG] convert surface using python. (mne-tools#3273) [MRG] raw.plot_psd() with flat channel (mne-tools#3342) ...
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Related to #3311.
The builtin KIT-157 layout is based on the KIT-NY system and does not apply for KIT-UMD data. This PR distinguishes the two systems based on sensor positions. If in the future the KIT system-identifier is stored in the measurement info this distinction will be more efficient, but the sensor-based distinction will always be useful for legacy FIFF files.