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Time-frequency in Source Space #6629

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DiGyt wants to merge 101 commits into mne-tools:main from DiGyt:source_into_tfr

Contributor

DiGyt commented Aug 5, 2019

Reference issue

This is the main PR for the GSoC TFR in Source Space Project (See: Issue #6290 ).

What does this implement/fix?

This PR will allow SourceEstimates or lists/generators of SourceEstimates to be passed into time_frequency functions. This means that the functions tfr_morlet, tfr_multitaper and tfr_stockwell will accept all types of SourceEstimates, and compute the correct time-frequency representation of source level data. It should work for all possible arguments of the respective functions (except n_jobs, which is ignored for morlet/multitaper, if a list is passed).

Additional information

Note that the PR #6543 will be further maintained within this pull, as the SourceTFR class and changes in time_frequency/tfr often depend on each other.

There are also some things that still should be implemented:

economic computation, if stcs with a (kernel, sens_data) data field is passed
economic computation of lists for tfr_stockwell
frequency plotting in source space.

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>

Contributor Author

DiGyt commented Aug 18, 2019

Is #6674 taking over this one?
Sorry #6673

@massich
No, I just opened #6673 and #6672 up as draft PRs, to be merged after this one. I think this pull should really be the priority, and the other stuff can be added later.

DiGyt added 25 commits

August 18, 2019 17:44


          fix flake

6298fb1


          Enable tfr_stockwell to process lists/generators subsequently

c601c31


          enabling tfr_stockwell to compute lists/gens subsequently

c8e1cb6

- made lists and single stcs work
- introduced checks
- added to test


          changed tests to also cover kernelized data

b03b858


          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


          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 'master' into source_into_tfr

# Conflicts:
#	doc/changes/latest.inc


          fixed vertices function in order to avoid __repr__ and plotting error

8e6a9e0


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

966af7a


          migrated source_tfr...

c25dc4c

...from mne/ to mne/time_frequency


          not load SourceTFR in time_frequency.__init__

b8daad8

... to prevent a deep circular import reference.

Contributor Author

DiGyt commented Sep 3, 2019

@agramfort
I tried to migrate the source_tfr.py module from mne/ to mne/time_frequency as you mentioned in #6673 (comment) (I also think that this idea makes a lot of sense). However this is causing a very nasty circular import reference, if we include in in time_frequency.__init__ and I'm not sure how to handle it in the best manner.
I thought, as you also would like to factorize everything with _BaseSourceEstimate ( #6673 (comment) ), we might just add the SourceTFR class to source_estimate.py, in order to keep everything together. But obviously, it would also make sense to keep SourceTFR in mne/time_frequency.

However, @agramfort @massich
The SourceTFR class does currently allow the possibility of storing data in the (kernel, sensor_data) form. But for now, this option is not even used, as the full tfr source time course is computed inside the time_frequency functions (in order to cope with the nonlinear steps that need to be performed after np.dot(kernel, sensor_data) ). So at the moment, the question is if we want to maintain the unused (kernel, sensor_data) representation for SourceTFRs.
If we do, I think it makes sense to make SourceTFR inherit stuff from _BaseSourceEstimate, and add it to the mne/source_estimate.py file as mentioned above. If we don't want to maintain this functionality, there will be less stuff to inherit from _BaseSourceEstimate, and therefore it would eventually be better to keep it a separate class.

So 2 questions, where i'd like to hear your opinions:

Should we maintain the functionality of SourceTFRs supporting (kernel, sensor_data) type data?
Should we add SourceTFR to mne/source_estimate.py or try to put it in mne/time_frequency/source_tfr.py?

Base automatically changed from master to main

January 23, 2021 18:26

DiGyt closed this

Contributor Author

DiGyt commented Feb 22, 2021

Closed: See Issue #6290

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