Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

[WIP] Examples for time frequency analysis on SourceEstimates #6673

Closed
wants to merge 130 commits into from
Closed

[WIP] Examples for time frequency analysis on SourceEstimates #6673

wants to merge 130 commits into from

Conversation

DiGyt
Copy link
Contributor

@DiGyt DiGyt commented Aug 18, 2019

Reference issue

Part of GSoC: TFR in Source Space Project (See: Issue #6290 ).

What does this implement/fix?

Add examples on how to compute time frequency analysis in source space,
using functions from mne.time_frequency and SourceEstimates.

Additional information

This branch is forked from DiGyt:plot_source_tfr (PR #6672),
and therefore should be merged after PR #6672 (and PR #6629).

DiGyt added 30 commits June 6, 2019 14:36
@DiGyt
Added SourceTFR
a65932f 
Added Basic SourceTFR structure and Text

Signed-off-by: Dirk Gütlin <[email protected]>
@DiGyt
Added SourceTFR
dcd19e9 
Added Basic SourceTFR structure and Text

Signed-off-by: Dirk Gütlin <[email protected]>
@DiGyt
Added multitaper test
8e657c9 
Added basic tests to load VectorSourceEstimate into tfr_multitaper

Signed-off-by: Dirk Gütlin <[email protected]>
@DiGyt
added test
9858b4f 
added tests for sourceTFR

Signed-off-by: Dirk Gütlin <[email protected]>
@DiGyt
Read SourceEstimates into multitaper
c40b2e2 
First steps to read SourceEstimates into multitapers

Signed-off-by: Dirk Gütlin <[email protected]>
@DiGyt
Merge branch 'SourceTFR' into source_multitaper
171d0c7
@DiGyt
tfr_multitaper now takes VectorSourceEstimates without error
14a5475 
tfr_multitaper now takes VectorSourceEstimates without error
tests were introduced to check whether it works

Signed-off-by: Dirk Gütlin <[email protected]>
@DiGyt
updated SourceTFR with multitaper and morlet
b02bebc 
updated computing tfr funcs with Source TFR
updated tests for this

Signed-off-by: Dirk Gütlin <[email protected]>
@DiGyt
updated source tfr
ca0a206 
- updated source tfr
- added tests

Signed-off-by: Dirk Gütlin <[email protected]>
@DiGyt
Merge https://github.com/mne-tools/mne-python into source_multit_wavelet
3ad3c1a 
Signed-off-by: Dirk Gütlin <[email protected]>

# Conflicts:
#	mne/time_frequency/multitaper.py
@DiGyt
added tests four SourceTFR
636938b 
added tests four SourceTFR

Signed-off-by: Dirk Gütlin <[email protected]>
@DiGyt
fixed some stuff
b762647 
Signed-off-by: Dirk Gütlin <[email protected]>
@DiGyt
Added Tests for source_tfr
357b40d 
- Added tests
- Removed redundant calls in source_tfr.py

Signed-off-by: Dirk Gütlin <[email protected]>
@DiGyt
Made tfr(VectorSourceEstimate) and source_induced_power more equivalent
adab650 
Signed-off-by: Dirk Gütlin <[email protected]>
@DiGyt
Merge https://github.com/mne-tools/mne-python into source_multit_wavelet
e78ba3c 
# Conflicts:
#	mne/io/eeglab/eeglab.py
@DiGyt
Merge https://github.com/mne-tools/mne-python into source_multit_wavelet
6c8fd11
@DiGyt
Tried to improve equivalence between morlet and source_induced_poewr
cce9bd6 
Signed-off-by: Dirk Gütlin <[email protected]>
@DiGyt
made one equivalent case for tfr_morlet and source_induced_power
05450f2 
Signed-off-by: Dirk Gütlin <[email protected]>
@DiGyt
add full_data param to apply_inverse_epochs
da783f2 
Signed-off-by: Dirk Gütlin <[email protected]>
@DiGyt
cleaned up time_frequency
90dbaec 
cleaned up tfr and multitaper

Signed-off-by: Dirk Gütlin <[email protected]>
@DiGyt
updated minimum_norm.time_frequency
0222eec 
..to master level

Signed-off-by: Dirk Gütlin <[email protected]>
@DiGyt
adapted tfr_morlet(SourceEstimate) to source_induced_poewr
06cd6f0 
- introduced coverage for different cases of parameters

Signed-off-by: Dirk Gütlin <[email protected]>
@DiGyt
prepared morlet, multitaper and stockwell for SourceEstimates
3976049 
- made functions accessible to SourceEstimates
- introduced tests for checking
- made sure data is produced correctly

Signed-off-by: Dirk Gütlin <[email protected]>
@DiGyt
enhanced tests for tfr
0d908ef 
Signed-off-by: Dirk Gütlin <[email protected]>
@DiGyt
read stc lists into tfr_functions
bcb1f9f 
Signed-off-by: Dirk Gütlin <[email protected]>
@DiGyt
improved reading lists into tfr
dbf62c1 
Signed-off-by: Dirk Gütlin <[email protected]>
@DiGyt
update to Kernel param for apply inverse branch
64dd51c 
Signed-off-by: Dirk Gütlin <[email protected]>
@DiGyt
tfr_aux works now for everything
f0df882 
- lists/generators/single stcs
- average
- itc
- power/ complex

Signed-off-by: Dirk Gütlin <[email protected]>
@DiGyt
removed unused test
eb1ab63 
Signed-off-by: Dirk Gütlin <[email protected]>
@DiGyt
stockwell works now with lists, itc
bbe2479 
also reverted _get_data

Signed-off-by: Dirk Gütlin <[email protected]>
@DiGyt
changed sourceTFR data docstring/comments
3536af7 
in order to pass build docsa
@DiGyt
added authur + licensing
ba7e8d7
@DiGyt
manually merged what's new / changes
9e98707
@DiGyt
changed indentation in docstring
3ac8e02 
for build docs
@DiGyt
Merge branch 'source_into_tfr' into plot_source_tfr
e60fbff 
# Conflicts:
#	mne/source_tfr.py
@DiGyt
Merge branch 'plot_source_tfr' into source_tfr_example
6a83ced
@DiGyt
Added new SourceTFR tutorials
44366af 
...and removed the old one
@DiGyt
Fixed error for epochs plotting
db91bd8
@DiGyt
Merge branch 'plot_source_tfr' into source_tfr_example
b13bf46
@DiGyt
Made small changes to the examples
e894529
@DiGyt
Improved docstrings
eacc4ff
@DiGyt
Merge branch 'master' into source_into_tfr
9656534 
# Conflicts:
#	doc/changes/latest.inc
@DiGyt
Merge branch 'source_into_tfr' into plot_source_tfr
2d62814
@DiGyt
Merge branch 'plot_source_tfr' into source_tfr_example
84f51be
@DiGyt
adapted paths to actual somato data paths
43a99af
@DiGyt
changed plot_volume_source_tfr_morlet to read data from sample data set
3a4e255 
... since the somato data set lacks a volume inverse operator, or the trans file to create one
@DiGyt
omit warnings
bee4c96
@DiGyt
reduce computation time
11cb0a4
@DiGyt
fix flake
a749047
@DiGyt
removed labels from volume source example
4500a1e 
also restructured the example a little bit
@DiGyt
fixed vertices function in order to avoid __repr__ and plotting error
8e6a9e0
@DiGyt
Merge branch 'source_into_tfr' into plot_source_tfr
64c87a3
@DiGyt
Merge branch 'plot_source_tfr' into source_tfr_example
5ce5295
@DiGyt
Merge branch 'master' into source_into_tfr
7c78010 
# Conflicts:
#	doc/changes/latest.inc
@DiGyt
Merge https://github.com/mne-tools/mne-python into source_into_tfr
3256746
@DiGyt
fix flake
e9ad48c
@DiGyt
Merge branch 'source_into_tfr' into source_tfr_example
bc0a599
Base automatically changed from master to main January 23, 2021 18:26
@DiGyt DiGyt closed this Feb 22, 2021
@DiGyt
Copy link
Contributor Author

DiGyt commented Feb 22, 2021

Closed: See Issue #6290

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Reviewers

@agramfort agramfort agramfort left review comments

@larsoner larsoner Awaiting requested review from larsoner larsoner will be requested when the pull request is marked ready for review larsoner is a code owner

@drammock drammock Awaiting requested review from drammock drammock will be requested when the pull request is marked ready for review drammock is a code owner

@dengemann dengemann Awaiting requested review from dengemann dengemann will be requested when the pull request is marked ready for review dengemann is a code owner

@adam2392 adam2392 Awaiting requested review from adam2392 adam2392 will be requested when the pull request is marked ready for review adam2392 is a code owner

@mscheltienne mscheltienne Awaiting requested review from mscheltienne mscheltienne will be requested when the pull request is marked ready for review mscheltienne is a code owner

Assignees
No one assigned
Labels
None yet
Projects
None yet
Milestone
No milestone
Development

Successfully merging this pull request may close these issues.
3 participants
@DiGyt @agramfort @massich