[WIP] add plot_anat_landmarks function #824
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add plot_anat_landmarks function
Codecov Report
@@ Coverage Diff @@
## main #824 +/- ##
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- Coverage 95.20% 94.67% -0.54%
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Files 24 25 +1
Lines 3860 3887 +27
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+ Hits 3675 3680 +5
- Misses 185 207 +22
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ok this one should be good for review. See rendered doc: https://4812-89170358-gh.circle-artifacts.com/0/dev/auto_examples/convert_mri_and_trans.html I will add a what's new entry at the end. |
examples/convert_mri_and_trans.py
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| print_dir_tree(output_path) | ||
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| plot_anat_landmarks(t1w_bids_path, vmax=160) | ||
| plt.suptitle('T1 MRI') |
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Can this be moved into plot_anat_landmarks? It would be nice if the figure came with a sensible title by default
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Would also be good to briefly explain what vmax is doing here?
examples/convert_mri_and_trans.py
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| # landmarks Nasion, LPA, and RPA onto the brain image. For that, we can | ||
| # extract the location of Nasion, LPA, and RPA from the MEG file, apply our | ||
| # transformation matrix :code:`trans`, and plot the results. |
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Wondering if we should start off this paragraph differently or put it into a new subsection. The first sentence made me think, "umm, but we just DID that??" until I got to the point where it says, " ... from the MEG file"
| vmax : float | ||
| Maximum colormap value. |
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Should we limit the acceptable range, e.g. to the interval [0, 255]?
mne_bids/viz.py
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| fig : matplotlib.figure.Figure | None | ||
| The figure object containing the plot. None if no landmarks | ||
| are avaiable. |
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Shouldn't we raise an exception if there are no landmarks?
mne_bids/viz.py
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| ) | ||
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| if show: | ||
| plt.show() |
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Should this better be fig.show()?
Co-authored-by: Richard Höchenberger <richard.hoechenberger@gmail.com>
…into plot_landmarks
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@sappelhoff it's ok for me if we don't merge this. It was a very convenient tool for debugging recently and I see this as being potentially useful to check some existing dataset. but It's ok if we don't merge this. Maybe it's not useful in the end... |
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Okay, I'll leave the decision to you and @hoechenberger - I am 50-50 |
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I would say let's wait.... it also adds new dependencies on nilearn and
matplotlib which is not great....
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sappelhoff
changed the title
let me know what you think