[ENH]: Add space awareness to existing components #268

Merged

synchon merged 86 commits from enh/space-awareness into main 2023-10-26 12:27:58 +00:00

Conversation 21 Commits 86 Files changed 34 +990 -316

2023-10-25

Synchon Mandal

update: modernize run_compute_parcel_mean.py example

02494a7786

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2023-10-25 17:16:17 +02:00

Synchon Mandal

fix: update correct spaces for testing datagrabbers

8b85612b76

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2023-10-25 17:16:17 +02:00

Synchon Mandal

update: only transform final coordinates if target space is native in get_coordinates()

857e79ec23

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2023-10-25 17:16:17 +02:00

Synchon Mandal

update: only warp final parcellation if target space is native in get_parcellation()

5c610b6ef1

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2023-10-25 17:16:17 +02:00

Synchon Mandal

update: only warp final mask if target space is native in get_mask()

eabe5a0674

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2023-10-25 17:16:17 +02:00

Synchon Mandal

update: fix test for error check for get_mask() mulitple

046f3208da

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2023-10-25 17:16:17 +02:00

Synchon Mandal

update: fix tests for get_mask() multiple

19a8b5462c

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2023-10-25 17:16:17 +02:00

Synchon Mandal

fix: correctly raise error when mask spaces don't match in get_mask()

ce362cfb2a

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2023-10-25 17:16:17 +02:00

Synchon Mandal

update: fix tests for SUIT MNI

a55520ec45

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2023-10-25 17:16:17 +02:00

Synchon Mandal

fix: correct space for SUIT MNI

dce62b1b0d

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2023-10-25 17:16:17 +02:00

Synchon Mandal

update: fix tests for Vickery-Patil mask

d1c55bf619

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2023-10-25 17:16:17 +02:00

Synchon Mandal

fix: correct space for Vickery-Patil mask

f49ec60722

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2023-10-25 17:16:17 +02:00

Synchon Mandal

update: fix tests for AICHA

1be3cf3d8d

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2023-10-25 17:16:17 +02:00

Synchon Mandal

fix: correct space for AICHA and issue warning

bc67fb33ec

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2023-10-25 17:16:17 +02:00

Synchon Mandal

fix: correct parcellations for same space get_parcellation() tests

81b3f8c19d

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2023-10-25 17:16:17 +02:00

Synchon Mandal

update: disallow parcellation merging if multiple parcellations are not in the same space in parcellations.py

4a78ff49eb

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2023-10-25 17:16:17 +02:00

Synchon Mandal

update: disallow mask merging if multiple masks are not in the same space in masks.py

8b94ac0d1a

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2023-10-25 17:16:17 +02:00

Synchon Mandal

chore: remove space from PartlyCloudyTestingDataGrabber's BOLD_confounds

44dbfec70c

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2023-10-25 17:16:17 +02:00

Synchon Mandal

fix: complete space name for testing datagrabbers

5d7370244d

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2023-10-25 17:16:17 +02:00

Synchon Mandal

fix: complete space name for AOMIC datagrabbers

0c518904cc

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2023-10-25 17:16:17 +02:00

Synchon Mandal

fix: correct space for tests in test_parcellations.py

0e227bb643

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2023-10-25 17:16:17 +02:00

Synchon Mandal

update: improve space info for existing parcellations

3ca791d871

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2023-10-25 17:16:17 +02:00

Synchon Mandal

fix: correct space for tests in test_masks.py

fedaa1dbd1

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2023-10-25 17:16:17 +02:00

Synchon Mandal

docs: add space info for existing parcellations and masks in builtin.rst

2dbb9d9f71

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2023-10-25 17:16:17 +02:00

Synchon Mandal

update: improve space info for existing masks

cf83c1d91d

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2023-10-25 17:16:17 +02:00

Synchon Mandal

update: add space info to existing parcellations

0d5e434b56

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2023-10-25 17:16:17 +02:00

Synchon Mandal

fix: add space for tests in test_sphere_aggregation.py

321a83324b

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2023-10-25 17:16:17 +02:00

Synchon Mandal

fix: add space for tests in test_parcel_aggregation.py

dfd550452d

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2023-10-25 17:16:17 +02:00

Synchon Mandal

fix: add space for tests in test_ets_rss.py

cd06606f96

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2023-10-25 17:16:17 +02:00

Synchon Mandal

fix: add space for tests in test_temporal_snr_spheres.py

b8119fe3b2

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2023-10-25 17:16:17 +02:00

Synchon Mandal

fix: add space for tests in test_temporal_snr_parcels.py

874bf654cd

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2023-10-25 17:16:17 +02:00

Synchon Mandal

fix: add space for tests in test_reho_spheres.py

528dd745dd

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2023-10-25 17:16:17 +02:00

Synchon Mandal

fix: add space for tests in test_reho_parcels.py

e3974eed17

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2023-10-25 17:16:17 +02:00

Synchon Mandal

fix: add space for tests in test_functional_connectivity_spheres.py

bceaa5611c

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2023-10-25 17:16:17 +02:00

Synchon Mandal

fix: add space for tests in test_functional_connectivity_parcels.py

e2e16a7b1f

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2023-10-25 17:16:17 +02:00

Synchon Mandal

fix: add space for tests in test_edge_functional_connectivity_spheres.py

22b343124e

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2023-10-25 17:16:17 +02:00

Synchon Mandal

fix: add space for tests in test_edge_functional_connectivity_parcels.py

30de67d8aa

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2023-10-25 17:16:17 +02:00

Synchon Mandal

fix: add space for tests in test_crossparcellation_functional_connectivity.py

e92642e7ca

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2023-10-25 17:16:17 +02:00

Synchon Mandal

fix: correct return value count for load_coordinates() in test_coordinates.py

be3ab708f4

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2023-10-25 17:16:17 +02:00

Synchon Mandal

chore: add changelogs 268.change and 268.enh

24b6e3fac3

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2023-10-25 17:16:17 +02:00

Synchon Mandal

chore: improve error messages in data.masks

c75be1f511

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2023-10-25 17:16:17 +02:00

Synchon Mandal

chore: improve commentary in data.masks

dae7e72155

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2023-10-25 17:16:17 +02:00

Synchon Mandal

chore: improve docstrings in data.masks

0ff5f810bc

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2023-10-25 17:16:17 +02:00

Synchon Mandal

chore: improve commentary in DefaultDataReader

06079d98ab

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2023-10-25 17:16:17 +02:00

Synchon Mandal

chore: improve docstring for DefaultDataReader

0db133ee4d

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2023-10-25 17:16:17 +02:00

Synchon Mandal

chore: improve commentary in BaseDataGrabber

15abb52300

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2023-10-25 17:16:17 +02:00

Synchon Mandal

chore: improve commentary in PatternDataGrabber

df84c363c3

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2023-10-25 17:16:17 +02:00

Synchon Mandal

chore: improve docstring for PatternDataGrabber

e4dd7da4c6

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2023-10-25 17:16:17 +02:00

Synchon Mandal

chore: improve commentary in BaseMarker

1f322b36c1

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2023-10-25 17:16:17 +02:00

Synchon Mandal

chore: improve docstrings in data.masks

a99b3a2182

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2023-10-25 17:16:17 +02:00

Synchon Mandal

chore: improve commentary in data.masks

429d104c5d

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2023-10-25 17:16:17 +02:00

Synchon Mandal

update: use WorkDirManager.cleanup_elementdir() in MarkerCollection

982c1ce425

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2023-10-25 17:16:17 +02:00

Synchon Mandal

update: reset the element-specific tempdir in MarkerCollection

996e3cf4a2

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2023-10-25 17:16:17 +02:00

Synchon Mandal

update: add support for cleaning up element-specific tempdirs in MarkerCollection

7450509209

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2023-10-25 17:16:17 +02:00

Synchon Mandal

update: use WorkDirManager in data.parcellations

9f5b500d7b

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2023-10-25 17:16:17 +02:00

Synchon Mandal

update: use WorkDirManager in data.masks

3f024a6a59

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2023-10-25 17:16:17 +02:00

Synchon Mandal

update: use WorkDirManager in data.coordinates

55fa62b04e

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2023-10-25 17:16:17 +02:00

Synchon Mandal

fix: update space for _fetch_icbm_brain_gm_mask

de5b723b3b

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2023-10-25 17:16:17 +02:00

Synchon Mandal

chore: improve error messages for get_*() functions when space is not MNI

51a798c613

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2023-10-25 17:16:17 +02:00

Synchon Mandal

docs: adapt examples/run_compute_parcel_mean.py to allow for space

30867f5d53

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2023-10-25 17:16:17 +02:00

Synchon Mandal

docs: add information about space for extending masks

3356830fae

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2023-10-25 17:16:16 +02:00

Synchon Mandal

docs: add information about space for extending coordinates

836008e86f

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2023-10-25 17:16:16 +02:00

Synchon Mandal

docs: add information about space for extending parcellations

0d74a27d74

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2023-10-25 17:16:16 +02:00

Synchon Mandal

chore: add tests for multi mask fetch in incorrect space via get_mask()

7f423ee785

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2023-10-25 17:16:16 +02:00

Synchon Mandal

update: add mask warping to other space via FSL FLIRT applywarp

b5da8b785d

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2023-10-25 17:16:16 +02:00

Synchon Mandal

chore: add tests for multi parcellation fetch in incorrect space via get_parcellation()

c7199069e1

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2023-10-25 17:16:16 +02:00

Synchon Mandal

update: add parcellation warping to other space via FSL FLIRT applywarp

42e5999f93

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2023-10-25 17:16:16 +02:00

Synchon Mandal

update: add coordinates space transformation via FSL FLIRT std2imgcoord

44f4702cea

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2023-10-25 17:16:16 +02:00

Synchon Mandal

chore: fix tests affected by space compulsion change in test_sphere_aggregation.py

2a7d09240b

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2023-10-25 17:16:16 +02:00

Synchon Mandal

chore: fix tests affected by space compulsion change in test_parcel_aggregation.py

f4d6f6e853

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2023-10-25 17:16:16 +02:00

Synchon Mandal

chore: fix tests affected by space compulsion change in test_parcellations.py

eda957e090

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2023-10-25 17:16:16 +02:00

Synchon Mandal

update: parametrize Vickery-Patil mask tests in test_masks.py

e95672f36b

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2023-10-25 17:16:16 +02:00

Synchon Mandal

chore: fix tests affected by space compulsion change in test_masks.py

f3d79e84ca

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2023-10-25 17:16:16 +02:00

Synchon Mandal

chore: fix tests affected by space compulsion change in test_coordinates.py

573b6c6a0d

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2023-10-25 17:16:16 +02:00

Synchon Mandal

fix: type cast to remove static type check errors in data.masks

5a38b8f997

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2023-10-25 17:16:16 +02:00

Synchon Mandal

update: return space information from load_masks()

621ac914c1

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2023-10-25 17:16:16 +02:00

Synchon Mandal

update: add space parameter to register_masks()

69420eb2d4

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2023-10-25 17:16:16 +02:00

Synchon Mandal

update: add space information to in-built masks

43d0ff2e14

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2023-10-25 17:16:16 +02:00

Synchon Mandal

update: return space information from load_parcellation()

19225e3bff

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2023-10-25 17:16:16 +02:00

Synchon Mandal

update: add space parameter to register_parcellation()

fa16022064

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2023-10-25 17:16:16 +02:00

Synchon Mandal

update: add space information to in-built parcellations

48b0957267

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2023-10-25 17:16:16 +02:00

Synchon Mandal

update: return space information from load_coordinates()

2ad8c11c6f

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2023-10-25 17:16:16 +02:00

Synchon Mandal

update: add space parameter to register_coordinates()

f0869c1e27

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2023-10-25 17:16:16 +02:00

Synchon Mandal

update: add space information to in-built coordinates

037016de5a

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2023-10-25 17:16:16 +02:00

Synchon Mandal

update: add space information to testing datagrabbers

ae0cfe981d

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2023-10-25 17:16:16 +02:00

Synchon Mandal

update: add space information for AOMIC datagrabbers

da5f7e8978

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2023-10-25 17:16:16 +02:00