[MARKER]: ReHo #36

Merged

synchon merged 97 commits from feature/reho into main 2022-12-19 20:45:35 +00:00

Conversation 25 Commits 97 Files changed 20 +1493 -14

2022-12-19

Fede Raimondo

update: fix tests and add missing AFNI ...

docker wrapper

bfd8043852

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2022-12-19 21:24:15 +01:00

Synchon Mandal

fix: update tests in test_reho_estimator.py

08ca39ef4b

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2022-12-19 20:39:59 +01:00

Synchon Mandal

fix: update package versions for install AFNI in ci.yml

bc1218a3e8

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2022-12-19 20:19:51 +01:00

Synchon Mandal

fix: force install AFNI in root in ci.yml

5e133588a0

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2022-12-19 20:02:43 +01:00

Synchon Mandal

chore: clean up install AFNI in ci.yml

92ed281eef

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2022-12-19 20:02:25 +01:00

Synchon Mandal

fix: update libgfortran for AFNI installation in ci.yml

5edbddcf51

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2022-12-19 19:55:28 +01:00

Synchon Mandal

update: improve install AFNI section in ci.yml

938d31a9ba

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2022-12-19 19:44:44 +01:00

Synchon Mandal

fix: change location while installing afni in ci.yml

ee4462c5a6

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2022-12-19 18:47:31 +01:00

Synchon Mandal

fix: reorder AFNI stuff after Python setup in ci.yml

94a463589d

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2022-12-19 18:26:59 +01:00

Synchon Mandal

fix: correct usage of appending path to $GITHUB_PATH

461947bcdb

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2022-12-19 18:07:39 +01:00

Synchon Mandal

update: replace docker usage with precompiled binaries for AFNI in ci.yml

4b17b31d8c

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2022-12-19 17:43:41 +01:00

Synchon Mandal

update: proper silencing of apt-get in ci.yml

28981409b9

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2022-12-19 17:43:20 +01:00

Synchon Mandal

chore: improve docstrings for reho_estimator.py

71a66eb64c

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2022-12-19 13:27:39 +01:00

Synchon Mandal

chore: clean docstrings for markers.utils

1c68a62256

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2022-12-19 13:27:39 +01:00

Synchon Mandal

update: add new tests for ReHoEstimator()

9734acdc1c

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2022-12-19 13:27:39 +01:00

Synchon Mandal

chore: delete test_reho_map_comparison.py

a586901942

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2022-12-19 13:27:39 +01:00

Synchon Mandal

update: remove afni and nifti testing assets for reho

fb43b11e7c

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2022-12-19 13:27:39 +01:00

Synchon Mandal

chore: update latest.inc

ec8cc909f8

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2022-12-19 13:27:39 +01:00

Synchon Mandal

docs: move ReHo-family from planned to available in builtin.rst

47cafeba44

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2022-12-19 13:27:39 +01:00

Synchon Mandal

update: improve ReHoSpheres computation test to include shape check and normalized data check

a7266805c5

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2022-12-19 13:27:39 +01:00

Synchon Mandal

update: improve ReHoParcels computation test to include shape check and normalized data check

0287ee786f

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2022-12-19 13:27:39 +01:00

Synchon Mandal

chore: update reho_params docstring for ReHoSpheres

281848877a

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2022-12-19 13:27:39 +01:00

Synchon Mandal

chore: update reho_params docstring for ReHoParcels

242896aa23

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2022-12-19 13:27:39 +01:00

Synchon Mandal

chore: improve docstring for _compute_reho_python()

535723b8f1

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2022-12-19 13:27:39 +01:00

Synchon Mandal

refactor: remove code duplication and improve handling for 125 neighbours ReHo map

96bd165b6f

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2022-12-19 13:27:39 +01:00

Synchon Mandal

chore: remove unwanted .nii

525ff10446

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2022-12-19 13:27:39 +01:00

Synchon Mandal

fix: remove stdout and stderr from subprocess.run() to bypass file descriptor error

d64f0ad2ba

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2022-12-19 13:27:39 +01:00

Synchon Mandal

update: add test for comparing ReHoSpheres' implementation

87075ee116

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2022-12-19 13:27:39 +01:00

Synchon Mandal

update: add test for comparing ReHoParcels' implementation

c5d6bf1a34

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2022-12-19 13:27:39 +01:00

Synchon Mandal

chore: lint

6a5ea7a923

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2022-12-19 13:27:39 +01:00

Synchon Mandal

chore: improve logging for ReHoSpheres

fcf1d55944

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2022-12-19 13:27:39 +01:00

Synchon Mandal

update: use use_afni for ReHoSpheres parameters

ad6f0783a6

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2022-12-19 13:27:39 +01:00

Synchon Mandal

chore: improve logging for ReHoParcels

3723ff68b3

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2022-12-19 13:27:39 +01:00

Synchon Mandal

update: use use_afni for ReHoParcels parameters

f312c9fdca

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2022-12-19 13:27:39 +01:00

Synchon Mandal

update: adapt use_afni usage for ReHoBase

aa0b53c50c

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2022-12-19 13:27:39 +01:00

Synchon Mandal

chore: update docstring for ReHoEstimator

0a8fb933d0

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2022-12-19 13:27:39 +01:00

Synchon Mandal

update: remove use_afni from ReHoEstimator parameters and use it in _compute() and fit_transform()

c02e300308

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2022-12-19 13:27:39 +01:00

Synchon Mandal

update: skip test for ReHo map comparison

e62ce61ce0

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2022-12-19 13:27:39 +01:00

Synchon Mandal

update: make use_afni part of parameters ReHoBase()

71a797e534

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2022-12-19 13:27:39 +01:00

Synchon Mandal

fix: use string of Nifti1Image for typing.cast() in reho_estimator.py

5de4fa61e3

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2022-12-19 13:27:39 +01:00

Synchon Mandal

update: use SHA256 hash for making output file of 3dReHo

aca16cce7e

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2022-12-19 13:27:39 +01:00

Synchon Mandal

chore: black on reho_estimator.py

d867243dca

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2022-12-19 13:27:39 +01:00

Synchon Mandal

chore: improve typing for computing ReHo maps

c084352423

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2022-12-19 13:27:39 +01:00

Synchon Mandal

fix: cleanup temporary files for 3dReHo

5b17995781

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2022-12-19 13:27:39 +01:00

Synchon Mandal

fix: use string for subprocess.run() command when shell=True for _compute_reho_afni()

efb48ed1b1

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2022-12-19 13:27:39 +01:00

Synchon Mandal

update: add neighbourhood check before calculating Kendall's W for _compute_reho_python()

44ccc64f89

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2022-12-19 13:27:39 +01:00

Synchon Mandal

update: add MNI152 whole brain masking at 0.5 for _compute_reho_python() to handle boundaries

d5dc1ab226

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2022-12-19 13:27:39 +01:00

Synchon Mandal

chore: improve logging for _compute_reho_python()

b464dac91d

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2022-12-19 13:27:39 +01:00

Synchon Mandal

chore: improve docstring for _compute_reho_python()

d8d69b3983

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2022-12-19 13:27:39 +01:00

Synchon Mandal

chore: remove unnecessary code from test_reho_map_comparison.py

b5adc56b5b

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2022-12-19 13:27:39 +01:00

Synchon Mandal

chore: isort reho_estimator.py

c095b1892c

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2022-12-19 13:27:39 +01:00

Synchon Mandal

update: introduce 125 neighbourhoods ReHo map computation

89ce5612a4

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2022-12-19 13:27:39 +01:00

Synchon Mandal

update: improve ReHo map computation for 7, 19 and 25 neighbourhoods

bb5175716d

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2022-12-19 13:27:39 +01:00

Synchon Mandal

update: rename f_kendall() to _kendall_w_reho() and improve code style

f57196154c

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2022-12-19 13:27:38 +01:00

Fede Raimondo

Re-implement (needs to be cleaned)

586f66d8dd

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2022-12-19 13:27:38 +01:00

Fede Raimondo

Fix nties

66796de3c3

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2022-12-19 13:27:38 +01:00

Synchon Mandal

wip: reho_python debugging

ce5439d197

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2022-12-19 13:27:38 +01:00

Synchon Mandal

update: add test for comparing afni and python implementation for reho map computation

2dbb4ff59a

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2022-12-19 13:27:38 +01:00

Synchon Mandal

chore: add logging for ReHoEstimator() cache hit-or-miss

f84770b391

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2022-12-19 13:27:38 +01:00

Synchon Mandal

chore: improve type annotation for ReHoEstimator.fit_transform()

d1abfb9cf7

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2022-12-19 13:27:38 +01:00

Synchon Mandal

chore: use get_fdata() for fetching data from image loaded via nibabel in _compute_reho_python()

5504ec2fa1

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2022-12-19 13:27:38 +01:00

Synchon Mandal

fix: make markers.reho.tests.test_reho_spheres.py work

dcdce7518f

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2022-12-19 13:27:38 +01:00

Synchon Mandal

fix: make markers.reho.tests.test_reho_parcels.py work

30e71e1bea

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2022-12-19 13:27:38 +01:00

Synchon Mandal

fix: extend-ignore for tox.ini to include lru_cache use in method

26c334cbed

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2022-12-19 13:27:38 +01:00

Synchon Mandal

update: improve output for ReHoSpheres.fit_transform()

a0407b8651

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2022-12-19 13:27:38 +01:00

Synchon Mandal

update: improve output for ReHoParcels.fit_transform()

2980ec002e

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2022-12-19 13:27:38 +01:00

Synchon Mandal

chore: improve type hinting for ReHoEstimator._compute()

7cca49ec9a

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2022-12-19 13:27:38 +01:00

Synchon Mandal

update: add Python implementation for ReHo

8e95a2e44a

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2022-12-19 13:27:38 +01:00

Synchon Mandal

refactor: move reho-family tests to markers.reho.tests

5b6da9ac81

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2022-12-19 13:27:38 +01:00

Synchon Mandal

refactor: move reho-family tests to sub-package markers.tests.reho

917c73584d

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2022-12-19 13:27:38 +01:00

Synchon Mandal

update: make ReHoSpheres() a subclass of ReHoBase()

e6458c62c3

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2022-12-19 13:27:38 +01:00

Synchon Mandal

update: make ReHoParcels() a subclass of ReHoBase()

bddb86e0a9

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2022-12-19 13:27:38 +01:00

Synchon Mandal

update: add ReHoBase() as reho-family base class

4c545ed629

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2022-12-19 13:27:38 +01:00

Synchon Mandal

fix: remove "BOLD" key access in ReHoEstimator.fit_transform()

37d3f53cbe

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2022-12-19 13:27:38 +01:00

Synchon Mandal

chore: lint, spellchecks and docstring updates for ReHoEstimator()

31701ec32d

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2022-12-19 13:27:38 +01:00

Synchon Mandal

update: add use_afni argument to ReHoEstimator()

c3b15c8681

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2022-12-19 13:27:38 +01:00

Synchon Mandal

fix: make ReHoEstimator a class

cf66448984

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2022-12-19 13:27:38 +01:00

Synchon Mandal

update: clear temporary directory files when clearing cache for ReHoEstimator()

f2e966b01b

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2022-12-19 13:27:38 +01:00

Synchon Mandal

update: route stdout to subprocess.stdout for 3dAFNItoNIFTI

c0a02cc7d4

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2022-12-19 13:27:38 +01:00

Synchon Mandal

update: improve logging for ReHoEstimator()

7401730e5d

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2022-12-19 13:27:38 +01:00

Synchon Mandal

update: add ReHoEstimator() with initial _compute_reho_afni()

8cafc74fec

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2022-12-19 13:27:38 +01:00

Synchon Mandal

fix: correct imports in test_reho_parcels.py and test_reho_spheres.py

67578b5e5f

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2022-12-19 13:27:38 +01:00

Synchon Mandal

fix: correct relative imports for ReHoSpheres()

c4c8ec5853

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2022-12-19 13:27:38 +01:00

Synchon Mandal

chore: lint

c927988cb5

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2022-12-19 13:27:38 +01:00

Synchon Mandal

refactor: move ReHoParcels() and ReHoSpheres() to reho sub-package

be11fed73e

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2022-12-19 13:27:38 +01:00

Synchon Mandal

update: use in-place processing for sphere aggregation output in reho spheres

2ade0015b2

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2022-12-19 13:27:38 +01:00

Synchon Mandal

update: use in-place processing for parcel aggregation output in reho parcels

e4b992018a

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2022-12-19 13:27:38 +01:00

Synchon Mandal

update: add basic test for ReHoParcels

3d9f69e15f

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2022-12-19 13:27:38 +01:00

Synchon Mandal

update: add basic test for ReHoSpheres

84c3e11844

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2022-12-19 13:27:38 +01:00

Synchon Mandal

update: rename ReHOParcels to ReHoParcels

7c956869b3

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2022-12-19 13:27:38 +01:00

Synchon Mandal

update: rename ReHOSpheres to ReHoSpheres

a985e03fa9

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2022-12-19 13:27:38 +01:00

Synchon Mandal

update: improve docstring for ReHOSpheres.compute()

4db20d7ae5

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2022-12-19 13:27:38 +01:00

Synchon Mandal

update: improve docstring for ReHOParcels.compute()

dacc9f6929

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2022-12-19 13:27:38 +01:00

Synchon Mandal

chore: add ReHOParcels to markers.__init__

9790d666c6

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2022-12-19 13:27:38 +01:00

Synchon Mandal

feature: add ReHOParcels marker

ea91cb48f9

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2022-12-19 13:27:38 +01:00

Synchon Mandal

chore: add ReHOSpheres to markers.__init__

11311d0a56

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2022-12-19 13:27:38 +01:00

Synchon Mandal

feature: add ReHOSpheres marker

f4e1b67e93

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2022-12-19 13:27:38 +01:00