MRG, BUG: Fix alpha for volumes #8663
Merged
+42
−22
Conversation
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
GuillaumeFavelier
reviewed
Dec 15, 2020
There was a problem hiding this comment.
Awesome! LGTM. And don't worry about the conflicts, I'll fix these in #8335
GuillaumeFavelier
approved these changes
Dec 15, 2020
|
Thanks for the quick review @GuillaumeFavelier ! |
larsoner
added a commit
to agramfort/mne-python
that referenced
this pull request
Dec 16, 2020
* upstream/master: (42 commits) MRG, ENH: Add DICS bias tests (mne-tools#8610) MRG, BUG, ENH: Add window option (mne-tools#8662) BUG: Fix alpha for volumes (mne-tools#8663) MRG, BUG: Fix bugs with envcorr (mne-tools#8658) MRG, ENH: Progressbar for csd_morlet (mne-tools#8608) Render is necessary now (mne-tools#8657) VIZ: Fix head size (mne-tools#8651) MRG, MAINT: bump sphinxcontrib-bitex version (mne-tools#8653) MRG, MAINT: Improve server env (mne-tools#8656) BUG: Mayavi center (mne-tools#8644) VIZ, ENH: allow show/hide annotations by label (mne-tools#8624) Add regression test for EEGLAB data with a chanlocs struct (mne-tools#8647) FIX: scalar_bar (mne-tools#8643) MRG: Small fix to tutorial; rename plot_events ordinate label to "Event id"; improve some SSP docstrings (mne-tools#8612) MRG, ENH: make plot alignment use defaults for colors (mne-tools#8553) BUG: Fix passing of channel type (mne-tools#8638) FIX: fixed loop over norm PSF/CTF options (mne-tools#8636) MRG, BUG: Pass kwargs (mne-tools#8630) DOC: Clearer error message (mne-tools#8631) BUG: Fix number of labels (mne-tools#8629) ...
larsoner
added a commit
to wmvanvliet/mne-python
that referenced
this pull request
Dec 16, 2020
* upstream/master: (38 commits) MRG, ENH: Add DICS bias tests (mne-tools#8610) MRG, BUG, ENH: Add window option (mne-tools#8662) BUG: Fix alpha for volumes (mne-tools#8663) MRG, BUG: Fix bugs with envcorr (mne-tools#8658) MRG, ENH: Progressbar for csd_morlet (mne-tools#8608) Render is necessary now (mne-tools#8657) VIZ: Fix head size (mne-tools#8651) MRG, MAINT: bump sphinxcontrib-bitex version (mne-tools#8653) MRG, MAINT: Improve server env (mne-tools#8656) BUG: Mayavi center (mne-tools#8644) VIZ, ENH: allow show/hide annotations by label (mne-tools#8624) Add regression test for EEGLAB data with a chanlocs struct (mne-tools#8647) FIX: scalar_bar (mne-tools#8643) MRG: Small fix to tutorial; rename plot_events ordinate label to "Event id"; improve some SSP docstrings (mne-tools#8612) MRG, ENH: make plot alignment use defaults for colors (mne-tools#8553) BUG: Fix passing of channel type (mne-tools#8638) FIX: fixed loop over norm PSF/CTF options (mne-tools#8636) MRG, BUG: Pass kwargs (mne-tools#8630) DOC: Clearer error message (mne-tools#8631) BUG: Fix number of labels (mne-tools#8629) ...
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Some simple code to plot with
hot_rwithtransparent=Trueandalpha=1.(should yield an opaque volume where values are large) looks like this onmaster:And on this PR it's correct:
The key was the opacity and color transfer functions both need to yield floats between 0 and 1, so we just need to divide both by 255 (ctable is
np.int8) rather than doing whatever silly gymnastics we were doing before where the colors ranged from 0 to 255 and the alphas 0 to 1/255 (effectively).While I was messing around with this I noticed
add_datacould not usecolormap='mne'so I refactored ourget_cmapcalls. I also added a simple test totest_brainto make sure ourctableis correct.@GuillaumeFavelier can you take a quick look? Not sure if this or #8335 should go in first, but I think they're going to conflict.