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plot SourceTFR #6672

Closed

DiGyt wants to merge 113 commits into mne-tools:main from DiGyt:plot_source_tfr

Contributor

DiGyt commented Aug 18, 2019

Reference issue

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

What does this implement/fix?

Allow simple 3D plotting for SourceTFR objects.

Additional information

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

DiGyt added 30 commits

June 6, 2019 14:36


          Added SourceTFR

a65932f

Added Basic SourceTFR structure and Text

Signed-off-by: Dirk Gütlin <dirk.guetlin@stud.sbg.ac.at>


          Added SourceTFR

dcd19e9

Added Basic SourceTFR structure and Text

Signed-off-by: Dirk Gütlin <dirk.guetlin@stud.sbg.ac.at>


          Added multitaper test

8e657c9

Added basic tests to load VectorSourceEstimate into tfr_multitaper

Signed-off-by: Dirk Gütlin <dirk.guetlin@stud.sbg.ac.at>


          added test

9858b4f

added tests for sourceTFR

Signed-off-by: Dirk Gütlin <dirk.guetlin@stud.sbg.ac.at>


          Read SourceEstimates into multitaper

c40b2e2

First steps to read SourceEstimates into multitapers

Signed-off-by: Dirk Gütlin <dirk.guetlin@stud.sbg.ac.at>


          Merge branch 'SourceTFR' into source_multitaper

171d0c7


          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 <dirk.guetlin@stud.sbg.ac.at>


          updated SourceTFR with multitaper and morlet

b02bebc

updated computing tfr funcs with Source TFR
updated tests for this

Signed-off-by: Dirk Gütlin <dirk.guetlin@stud.sbg.ac.at>


          updated source tfr

ca0a206

- updated source tfr
- added tests

Signed-off-by: Dirk Gütlin <dirk.guetlin@stud.sbg.ac.at>


          Merge https://github.com/mne-tools/mne-python into source_multit_wavelet

3ad3c1a

Signed-off-by: Dirk Gütlin <dirk.guetlin@stud.sbg.ac.at>

# Conflicts:
#	mne/time_frequency/multitaper.py


          added tests four SourceTFR

636938b

added tests four SourceTFR

Signed-off-by: Dirk Gütlin <dirk.guetlin@stud.sbg.ac.at>


          fixed some stuff

b762647

Signed-off-by: Dirk Gütlin <dirk.guetlin@stud.sbg.ac.at>


          Added Tests for source_tfr

357b40d

- Added tests
- Removed redundant calls in source_tfr.py

Signed-off-by: Dirk Gütlin <dirk.guetlin@stud.sbg.ac.at>


          Made tfr(VectorSourceEstimate) and source_induced_power more equivalent

adab650

Signed-off-by: Dirk Gütlin <dirk.guetlin@stud.sbg.ac.at>


          Merge https://github.com/mne-tools/mne-python into source_multit_wavelet

e78ba3c

# Conflicts:
#	mne/io/eeglab/eeglab.py


          Merge https://github.com/mne-tools/mne-python into source_multit_wavelet

6c8fd11


          Tried to improve equivalence between morlet and source_induced_poewr

cce9bd6

Signed-off-by: Dirk Gütlin <dirk.guetlin@stud.sbg.ac.at>


          made one equivalent case for tfr_morlet and source_induced_power

05450f2

Signed-off-by: Dirk Gütlin <dirk.guetlin@stud.sbg.ac.at>


          add full_data param to apply_inverse_epochs

da783f2

Signed-off-by: Dirk Gütlin <dirk.guetlin@stud.sbg.ac.at>


          cleaned up time_frequency

90dbaec

cleaned up tfr and multitaper

Signed-off-by: Dirk Gütlin <dirk.guetlin@stud.sbg.ac.at>


          updated minimum_norm.time_frequency

0222eec

..to master level

Signed-off-by: Dirk Gütlin <dirk.guetlin@stud.sbg.ac.at>


          adapted tfr_morlet(SourceEstimate) to source_induced_poewr

06cd6f0

- introduced coverage for different cases of parameters

Signed-off-by: Dirk Gütlin <dirk.guetlin@stud.sbg.ac.at>


          prepared morlet, multitaper and stockwell for SourceEstimates

- made functions accessible to SourceEstimates
- introduced tests for checking
- made sure data is produced correctly

Signed-off-by: Dirk Gütlin <dirk.guetlin@stud.sbg.ac.at>


          enhanced tests for tfr

0d908ef

Signed-off-by: Dirk Gütlin <dirk.guetlin@stud.sbg.ac.at>


          read stc lists into tfr_functions

bcb1f9f

Signed-off-by: Dirk Gütlin <dirk.guetlin@stud.sbg.ac.at>


          improved reading lists into tfr

dbf62c1

Signed-off-by: Dirk Gütlin <dirk.guetlin@stud.sbg.ac.at>


          update to Kernel param for apply inverse branch

64dd51c

Signed-off-by: Dirk Gütlin <dirk.guetlin@stud.sbg.ac.at>


          tfr_aux works now for everything

f0df882

- lists/generators/single stcs
- average
- itc
- power/ complex

Signed-off-by: Dirk Gütlin <dirk.guetlin@stud.sbg.ac.at>


          removed unused test

eb1ab63

Signed-off-by: Dirk Gütlin <dirk.guetlin@stud.sbg.ac.at>


          stockwell works now with lists, itc

bbe2479

also reverted _get_data

Signed-off-by: Dirk Gütlin <dirk.guetlin@stud.sbg.ac.at>

DiGyt added 9 commits

August 20, 2019 12:38


          removed delayed tests from test_morlet_induced_power...

9593f12

... as this is now covered in test_stfr_equivalence


          compute tfr_stockwell only on sensor data

e43619c

stockwell is computed on sensor data to save time, and the full stc data is computed afterwards


          flake, pydocstyle

a34d150


          refactor stockwell functions

114d31d


          small improvements

1ae38ec

to make stuff more comprehensible


          more small improvements

65090e3


          renamed testing check function

c673a9d

to better suit


          Merge https://github.com/mne-tools/mne-python into source_into_tfr

f04eca5


          Merge branch 'source_into_tfr' into plot_source_tfr

f0c4d34

codecov bot commented Aug 22, 2019 •

edited

Loading

Codecov Report

Merging #6672 into master will increase coverage by 6.77%.
The diff coverage is 92.13%.

@@            Coverage Diff             @@
##           master    #6672      +/-   ##
==========================================
+ Coverage    82.7%   89.47%   +6.77%     
==========================================
  Files         420      422       +2     
  Lines       75601    76116     +515     
  Branches    12382    12474      +92     
==========================================
+ Hits        62525    68104    +5579     
+ Misses      10479     5187    -5292     
- Partials     2597     2825     +228

DiGyt added 15 commits

August 22, 2019 09:57


          use random state instead of random seed

fb5b733


          changed sourceTFR data docstring/comments

3536af7

in order to pass build docsa


          added authur + licensing

ba7e8d7


          manually merged what's new / changes

9e98707


          changed indentation in docstring

3ac8e02

for build docs


          Merge branch 'source_into_tfr' into plot_source_tfr

e60fbff

# Conflicts:
#	mne/source_tfr.py


          Fixed error for epochs plotting

db91bd8


          Merge branch 'master' into source_into_tfr

# Conflicts:
#	doc/changes/latest.inc


          Merge branch 'source_into_tfr' into plot_source_tfr

2d62814


          fixed vertices function in order to avoid __repr__ and plotting error

8e6a9e0


          Merge branch 'source_into_tfr' into plot_source_tfr

64c87a3


          Merge branch 'master' into source_into_tfr

7c78010

# Conflicts:
#	doc/changes/latest.inc


          Merge https://github.com/mne-tools/mne-python into source_into_tfr


          fix flake

e9ad48c


          Merge branch 'source_into_tfr' into plot_source_tfr

05725c5

Base automatically changed from master to main

January 23, 2021 18:26

DiGyt closed this

Member

larsoner commented Feb 22, 2021

Sorry for the slow uptake on this @DiGyt , there is good stuff in here ! Hopefully in the future we can use your commits as a base and start a new PR

Contributor Author

DiGyt commented Feb 22, 2021

Closed: See Issue #6290

Contributor Author

DiGyt commented Mar 10, 2021 •

edited

Loading

Sorry for the slow uptake on this @DiGyt , there is good stuff in here ! Hopefully in the future we can use your commits as a base and start a new PR

No need to be sorry about that at all! I'm sorry for not being able to take the time and push this further 😕

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