From 1c23bdd8bfadb23acb20189d06a894e73ed52353 Mon Sep 17 00:00:00 2001 From: Synchon Mandal Date: Thu, 13 Apr 2023 22:12:01 +0200 Subject: [PATCH 01/11] refactor: consistent datagrabber naming for OasisVBMTestingDataGrabber --- junifer/testing/datagrabbers.py | 12 ++++++++---- 1 file changed, 8 insertions(+), 4 deletions(-) diff --git a/junifer/testing/datagrabbers.py b/junifer/testing/datagrabbers.py index 0594eb93d..4bb51cb6b 100644 --- a/junifer/testing/datagrabbers.py +++ b/junifer/testing/datagrabbers.py @@ -14,8 +14,12 @@ from nilearn import datasets, image from ..datagrabber.base import BaseDataGrabber -class OasisVBMTestingDatagrabber(BaseDataGrabber): - """Data Grabber for Oasis VBM testing data.""" +class OasisVBMTestingDataGrabber(BaseDataGrabber): + """Data Grabber for Oasis VBM testing data. + + Wrapper for :func:`nilearn.datasets.fetch_oasis_vbm` + + """ def __init__(self) -> None: # Create temporary directory @@ -55,12 +59,12 @@ class OasisVBMTestingDatagrabber(BaseDataGrabber): return out - def __enter__(self) -> "OasisVBMTestingDatagrabber": + def __enter__(self) -> "OasisVBMTestingDataGrabber": """Implement context entry. Returns ------- - OasisVBMTestingDatagrabber + OasisVBMTestingDataGrabber """ self._dataset = datasets.fetch_oasis_vbm(n_subjects=10) -- 2.52.0 From 29db8e7973fb74cc41aa0e422c48fe782fd8d859 Mon Sep 17 00:00:00 2001 From: Synchon Mandal Date: Thu, 13 Apr 2023 22:12:50 +0200 Subject: [PATCH 02/11] refactor: consistent datagrabber naming for SPMAuditoryTestingDataGrabber --- junifer/testing/datagrabbers.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/junifer/testing/datagrabbers.py b/junifer/testing/datagrabbers.py index 4bb51cb6b..6005e69d9 100644 --- a/junifer/testing/datagrabbers.py +++ b/junifer/testing/datagrabbers.py @@ -82,7 +82,7 @@ class OasisVBMTestingDataGrabber(BaseDataGrabber): return [f"sub-{x:02d}" for x in list(range(1, 11))] -class SPMAuditoryTestingDatagrabber(BaseDataGrabber): +class SPMAuditoryTestingDataGrabber(BaseDataGrabber): """Data Grabber for SPM Auditory dataset. Wrapper for :func:`nilearn.datasets.fetch_spm_auditory`. -- 2.52.0 From 470ffd94ad0d2667f53dc23bfe6ba08ec8e1de24 Mon Sep 17 00:00:00 2001 From: Synchon Mandal Date: Thu, 13 Apr 2023 22:13:24 +0200 Subject: [PATCH 03/11] refactor: update datagrabber naming in testing.registry --- junifer/testing/registry.py | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/junifer/testing/registry.py b/junifer/testing/registry.py index d5e4a57d5..9ecf668fb 100644 --- a/junifer/testing/registry.py +++ b/junifer/testing/registry.py @@ -6,23 +6,23 @@ from ..pipeline.registry import register from .datagrabbers import ( - OasisVBMTestingDatagrabber, + OasisVBMTestingDataGrabber, + SPMAuditoryTestingDataGrabber, PartlyCloudyTestingDataGrabber, - SPMAuditoryTestingDatagrabber, ) # Register testing datagrabber register( step="datagrabber", - name="OasisVBMTestingDatagrabber", - klass=OasisVBMTestingDatagrabber, + name="OasisVBMTestingDataGrabber", + klass=OasisVBMTestingDataGrabber, ) register( step="datagrabber", - name="SPMAuditoryTestingDatagrabber", - klass=SPMAuditoryTestingDatagrabber, + name="SPMAuditoryTestingDataGrabber", + klass=SPMAuditoryTestingDataGrabber, ) register( -- 2.52.0 From 2d6e5ee92422b172cf8e3154085cb9d01780b6c2 Mon Sep 17 00:00:00 2001 From: Synchon Mandal Date: Fri, 14 Apr 2023 10:27:15 +0200 Subject: [PATCH 04/11] refactor: consistent datagrabber naming for SPMAuditoryTestingDataGrabber tests --- junifer/testing/tests/test_oasisvmbtesting_datagrabber.py | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/junifer/testing/tests/test_oasisvmbtesting_datagrabber.py b/junifer/testing/tests/test_oasisvmbtesting_datagrabber.py index 283be2716..2ae15d348 100644 --- a/junifer/testing/tests/test_oasisvmbtesting_datagrabber.py +++ b/junifer/testing/tests/test_oasisvmbtesting_datagrabber.py @@ -3,10 +3,10 @@ # Authors: Federico Raimondo # License: AGPL -from junifer.testing.datagrabbers import OasisVBMTestingDatagrabber +from junifer.testing.datagrabbers import OasisVBMTestingDataGrabber -def test_OasisVBMTestingDatagrabber() -> None: +def test_OasisVBMTestingDataGrabber() -> None: """Test Oasis VBM Testing datagrabber.""" expected_elements = [ "sub-01", @@ -20,7 +20,7 @@ def test_OasisVBMTestingDatagrabber() -> None: "sub-09", "sub-10", ] - with OasisVBMTestingDatagrabber() as dg: + with OasisVBMTestingDataGrabber() as dg: all_elements = dg.get_elements() assert set(all_elements) == set(expected_elements) out = dg["sub-01"] -- 2.52.0 From 81f0718bfb15447dd8aee22ad987c0107255cd3f Mon Sep 17 00:00:00 2001 From: Synchon Mandal Date: Fri, 14 Apr 2023 10:27:28 +0200 Subject: [PATCH 05/11] refactor: consistent datagrabber naming for SPMAuditoryTestingDataGrabber tests --- junifer/testing/tests/test_spmauditory_datagrabber.py | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/junifer/testing/tests/test_spmauditory_datagrabber.py b/junifer/testing/tests/test_spmauditory_datagrabber.py index 711712f85..f1da02636 100644 --- a/junifer/testing/tests/test_spmauditory_datagrabber.py +++ b/junifer/testing/tests/test_spmauditory_datagrabber.py @@ -3,10 +3,10 @@ # Authors: Federico Raimondo # License: AGPL -from junifer.testing.datagrabbers import SPMAuditoryTestingDatagrabber +from junifer.testing.datagrabbers import SPMAuditoryTestingDataGrabber -def test_SPMAuditoryTestingDatagrabber() -> None: +def test_SPMAuditoryTestingDataGrabber() -> None: """Test SPM Auditory datagrabber.""" expected_elements = [ "sub001", @@ -20,7 +20,7 @@ def test_SPMAuditoryTestingDatagrabber() -> None: "sub009", "sub010", ] - with SPMAuditoryTestingDatagrabber() as dg: + with SPMAuditoryTestingDataGrabber() as dg: all_elements = dg.get_elements() assert set(all_elements) == set(expected_elements) out = dg["sub001"] -- 2.52.0 From 643233ad45e34a0f88f57793c0f72558ecd566d2 Mon Sep 17 00:00:00 2001 From: Synchon Mandal Date: Fri, 14 Apr 2023 10:27:42 +0200 Subject: [PATCH 06/11] update: add PartlyCloudyTestingDataGrabber to testing registry tests --- junifer/testing/tests/test_testing_registry.py | 10 ++++++---- 1 file changed, 6 insertions(+), 4 deletions(-) diff --git a/junifer/testing/tests/test_testing_registry.py b/junifer/testing/tests/test_testing_registry.py index d72e63336..1c2e2d467 100644 --- a/junifer/testing/tests/test_testing_registry.py +++ b/junifer/testing/tests/test_testing_registry.py @@ -12,9 +12,11 @@ def test_testing_registry() -> None: importlib.reload(junifer.pipeline.registry) importlib.reload(junifer) - assert "OasisVBMTestingDatagrabber" not in get_step_names("datagrabber") - assert "SPMAuditoryTestingDatagrabber" not in get_step_names("datagrabber") + assert "OasisVBMTestingDataGrabber" not in get_step_names("datagrabber") + assert "SPMAuditoryTestingDataGrabber" not in get_step_names("datagrabber") + assert "PartlyCloudyTestingDataGrabber" not in get_step_names("datagrabber") importlib.reload(junifer.testing.registry) # type: ignore - assert "OasisVBMTestingDatagrabber" in get_step_names("datagrabber") - assert "SPMAuditoryTestingDatagrabber" in get_step_names("datagrabber") + assert "OasisVBMTestingDataGrabber" in get_step_names("datagrabber") + assert "SPMAuditoryTestingDataGrabber" in get_step_names("datagrabber") + assert "PartlyCloudyTestingDataGrabber" in get_step_names("datagrabber") -- 2.52.0 From 20aa38fb3bf8b15a964a8cb788951a89e47258f2 Mon Sep 17 00:00:00 2001 From: Synchon Mandal Date: Tue, 18 Apr 2023 17:43:09 +0200 Subject: [PATCH 07/11] chore: isort --- junifer/testing/registry.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/junifer/testing/registry.py b/junifer/testing/registry.py index 9ecf668fb..c0935ddab 100644 --- a/junifer/testing/registry.py +++ b/junifer/testing/registry.py @@ -7,8 +7,8 @@ from ..pipeline.registry import register from .datagrabbers import ( OasisVBMTestingDataGrabber, - SPMAuditoryTestingDataGrabber, PartlyCloudyTestingDataGrabber, + SPMAuditoryTestingDataGrabber, ) -- 2.52.0 From 98234fc574ed1ea4d48bfb4f0db9ea3125c31422 Mon Sep 17 00:00:00 2001 From: Synchon Mandal Date: Tue, 18 Apr 2023 17:43:17 +0200 Subject: [PATCH 08/11] chore: black --- junifer/testing/tests/test_testing_registry.py | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/junifer/testing/tests/test_testing_registry.py b/junifer/testing/tests/test_testing_registry.py index 1c2e2d467..d67858f1e 100644 --- a/junifer/testing/tests/test_testing_registry.py +++ b/junifer/testing/tests/test_testing_registry.py @@ -14,7 +14,9 @@ def test_testing_registry() -> None: assert "OasisVBMTestingDataGrabber" not in get_step_names("datagrabber") assert "SPMAuditoryTestingDataGrabber" not in get_step_names("datagrabber") - assert "PartlyCloudyTestingDataGrabber" not in get_step_names("datagrabber") + assert "PartlyCloudyTestingDataGrabber" not in get_step_names( + "datagrabber" + ) importlib.reload(junifer.testing.registry) # type: ignore assert "OasisVBMTestingDataGrabber" in get_step_names("datagrabber") -- 2.52.0 From f52310bd346cb60cff658c5713d40987202d1364 Mon Sep 17 00:00:00 2001 From: Synchon Mandal Date: Tue, 18 Apr 2023 18:43:28 +0200 Subject: [PATCH 09/11] chore: rename remaining instances of Datagrabber to DataGrabber for consistency --- docs/understanding/data.rst | 10 +++++----- docs/using/codeless.rst | 4 ++-- examples/run_ets_rss_marker.py | 2 +- examples/run_junifer_julearn.py | 2 +- examples/run_run_gmd_mean.py | 2 +- examples/yamls/gmd_mean.yaml | 5 ++--- examples/yamls/gmd_mean_htcondor.yaml | 6 +++--- junifer/api/tests/data/gmd_mean.yaml | 5 ++--- junifer/api/tests/data/gmd_mean_htcondor.yaml | 6 +++--- junifer/api/tests/test_functions.py | 2 +- junifer/data/tests/test_masks.py | 16 ++++++++-------- ..._crossparcellation_functional_connectivity.py | 6 +++--- junifer/markers/reho/tests/test_reho_parcels.py | 8 ++++---- junifer/markers/reho/tests/test_reho_spheres.py | 8 ++++---- junifer/markers/tests/test_collection.py | 6 +++--- junifer/markers/tests/test_ets_rss.py | 6 +++--- .../tests/test_fmriprep_confound_remover.py | 4 ++-- 17 files changed, 48 insertions(+), 50 deletions(-) diff --git a/docs/understanding/data.rst b/docs/understanding/data.rst index 15dca78d9..2961ab107 100644 --- a/docs/understanding/data.rst +++ b/docs/understanding/data.rst @@ -26,12 +26,12 @@ step only contains information about the datagrabber used. .. code-block:: python - {'BOLD': {'meta': {'datagrabber': {'class': 'SPMAuditoryTestingDatagrabber', + {'BOLD': {'meta': {'datagrabber': {'class': 'SPMAuditoryTestingDataGrabber', 'types': ['BOLD', 'T1w']}, 'dependencies': set(), 'element': {'subject': 'sub001'}}, 'path': PosixPath('/var/folders/dv/2lbr8f8j0q12zrx3mz3ll5m40000gp/T/tmpgxcyjfo1/sub001_bold.nii.gz')}, - 'T1w': {'meta': {'datagrabber': {'class': 'SPMAuditoryTestingDatagrabber', + 'T1w': {'meta': {'datagrabber': {'class': 'SPMAuditoryTestingDataGrabber', 'types': ['BOLD', 'T1w']}, 'dependencies': set(), 'element': {'subject': 'sub001'}}, @@ -44,14 +44,14 @@ adds information about the datareader used to read the data. .. code-block:: python {'BOLD': {'data': , - 'meta': {'datagrabber': {'class': 'SPMAuditoryTestingDatagrabber', + 'meta': {'datagrabber': {'class': 'SPMAuditoryTestingDataGrabber', 'types': ['BOLD', 'T1w']}, 'datareader': {'class': 'DefaultDataReader'}, 'dependencies': {'nilearn'}, 'element': {'subject': 'sub001'}}, 'path': PosixPath('/var/folders/dv/2lbr8f8j0q12zrx3mz3ll5m40000gp/T/tmpe49321ce/sub001_bold.nii.gz')}, 'T1w': {'data': , - 'meta': {'datagrabber': {'class': 'SPMAuditoryTestingDatagrabber', + 'meta': {'datagrabber': {'class': 'SPMAuditoryTestingDataGrabber', 'types': ['BOLD', 'T1w']}, 'datareader': {'class': 'DefaultDataReader'}, 'dependencies': set(), @@ -70,7 +70,7 @@ and adds further keys needed for the storage, for example, ``col_names``. {'BOLD': {'col_names': ['root_sum_of_squares_ets'], 'data': ..., - 'meta': {'datagrabber': {'class': 'SPMAuditoryTestingDatagrabber', + 'meta': {'datagrabber': {'class': 'SPMAuditoryTestingDataGrabber', 'types': ['BOLD', 'T1w']}, 'datareader': {'class': 'DefaultDataReader'}, 'dependencies': {'nilearn'}, diff --git a/docs/using/codeless.rst b/docs/using/codeless.rst index 2ae7398dd..f053209ba 100644 --- a/docs/using/codeless.rst +++ b/docs/using/codeless.rst @@ -100,7 +100,7 @@ In the ``Oasis VBM Testing dataset`` example, the section will look like this: .. code-block:: yaml datagrabber: - kind: OasisVBMTestingDatagrabber + kind: OasisVBMTestingDataGrabber Data Reader @@ -212,7 +212,7 @@ looks like: workdir: /tmp datagrabber: - kind: OasisVBMTestingDatagrabber + kind: OasisVBMTestingDataGrabber markers: - name: Schaefer100x7_mean diff --git a/examples/run_ets_rss_marker.py b/examples/run_ets_rss_marker.py index c364eec60..5a8cfa74e 100644 --- a/examples/run_ets_rss_marker.py +++ b/examples/run_ets_rss_marker.py @@ -27,7 +27,7 @@ configure_logging(level="INFO") ############################################################################## # Define the datagrabber interface datagrabber = { - "kind": "SPMAuditoryTestingDatagrabber", + "kind": "SPMAuditoryTestingDataGrabber", } ############################################################################### diff --git a/examples/run_junifer_julearn.py b/examples/run_junifer_julearn.py index c2437ccf2..aec3bbbaf 100644 --- a/examples/run_junifer_julearn.py +++ b/examples/run_junifer_julearn.py @@ -75,7 +75,7 @@ with tempfile.TemporaryDirectory() as tmpdir: # run the defined junifer feature extraction pipeline run( workdir="/tmp", - datagrabber={"kind": "OasisVBMTestingDatagrabber"}, + datagrabber={"kind": "OasisVBMTestingDataGrabber"}, markers=marker_dicts, storage=storage, ) diff --git a/examples/run_run_gmd_mean.py b/examples/run_run_gmd_mean.py index 16b56e6b6..277ba8f42 100644 --- a/examples/run_run_gmd_mean.py +++ b/examples/run_run_gmd_mean.py @@ -13,7 +13,7 @@ from junifer.api import run datagrabber = { - "kind": "OasisVBMTestingDatagrabber", + "kind": "OasisVBMTestingDataGrabber", } markers = [ diff --git a/examples/yamls/gmd_mean.yaml b/examples/yamls/gmd_mean.yaml index 447a2fc47..9b944b407 100644 --- a/examples/yamls/gmd_mean.yaml +++ b/examples/yamls/gmd_mean.yaml @@ -2,7 +2,7 @@ with: junifer.testing.registry workdir: /tmp datagrabber: - kind: OasisVBMTestingDatagrabber + kind: OasisVBMTestingDataGrabber elements: markers: - name: Schaefer1000x7_TrimMean80 @@ -19,7 +19,6 @@ markers: kind: ParcelAggregation parcellation: Schaefer1000x7 method: std -storage: +storage: kind: SQLiteFeatureStorage uri: /Users/fraimondo/dev/tbox/junifer/scratch/db/test.sqlite - diff --git a/examples/yamls/gmd_mean_htcondor.yaml b/examples/yamls/gmd_mean_htcondor.yaml index 62ad14329..f29be473c 100644 --- a/examples/yamls/gmd_mean_htcondor.yaml +++ b/examples/yamls/gmd_mean_htcondor.yaml @@ -2,13 +2,13 @@ with: junifer.testing.registry workdir: /tmp datagrabber: - kind: OasisVBMTestingDatagrabber + kind: OasisVBMTestingDataGrabber markers: - name: Schaefer1000x7_Mean kind: ParcelAggregation parcellation: Schaefer1000x7 method: mean -storage: +storage: kind: SQLiteFeatureStorage uri: /data/group/appliedml/fraimondo/junifer_test/test.sqlite queue: @@ -17,4 +17,4 @@ queue: env: kind: conda name: junifer - mem: 8G \ No newline at end of file + mem: 8G diff --git a/junifer/api/tests/data/gmd_mean.yaml b/junifer/api/tests/data/gmd_mean.yaml index c5e954c7e..4ee9319cf 100644 --- a/junifer/api/tests/data/gmd_mean.yaml +++ b/junifer/api/tests/data/gmd_mean.yaml @@ -2,14 +2,13 @@ with: junifer.testing.registry workdir: /tmp datagrabber: - kind: OasisVBMTestingDatagrabber + kind: OasisVBMTestingDataGrabber elements: [1, 2] markers: - name: Schaefer1000x7_Mean kind: ParcelAggregation parcellation: Schaefer1000x7 method: mean -storage: +storage: kind: SQLiteFeatureStorage uri: /Users/fraimondo/dev/tbox/junifer/scratch/db/test.sqlite - diff --git a/junifer/api/tests/data/gmd_mean_htcondor.yaml b/junifer/api/tests/data/gmd_mean_htcondor.yaml index 1b5db62b8..892efb48d 100644 --- a/junifer/api/tests/data/gmd_mean_htcondor.yaml +++ b/junifer/api/tests/data/gmd_mean_htcondor.yaml @@ -2,13 +2,13 @@ with: junifer.testing.registry workdir: /tmp datagrabber: - kind: OasisVBMTestingDatagrabber + kind: OasisVBMTestingDataGrabber markers: - name: Schaefer1000x7_Mean kind: ParcelAggregation parcellation: Schaefer1000x7 method: mean -storage: +storage: kind: SQLiteFeatureStorage uri: /Users/fraimondo/dev/tbox/junifer/scratch/db/test.sqlite queue: @@ -17,4 +17,4 @@ queue: env: kind: conda name: junifer - mem: 8G \ No newline at end of file + mem: 8G diff --git a/junifer/api/tests/test_functions.py b/junifer/api/tests/test_functions.py index 8beed2243..79c4dd9e5 100644 --- a/junifer/api/tests/test_functions.py +++ b/junifer/api/tests/test_functions.py @@ -21,7 +21,7 @@ from junifer.pipeline.registry import build # Define datagrabber datagrabber = { - "kind": "OasisVBMTestingDatagrabber", + "kind": "OasisVBMTestingDataGrabber", } # Define markers diff --git a/junifer/data/tests/test_masks.py b/junifer/data/tests/test_masks.py index 7de819096..9f28688cc 100644 --- a/junifer/data/tests/test_masks.py +++ b/junifer/data/tests/test_masks.py @@ -30,8 +30,8 @@ from junifer.data.masks import ( ) from junifer.datareader import DefaultDataReader from junifer.testing.datagrabbers import ( - OasisVBMTestingDatagrabber, - SPMAuditoryTestingDatagrabber, + OasisVBMTestingDataGrabber, + SPMAuditoryTestingDataGrabber, ) @@ -181,7 +181,7 @@ def test_vickery_patil() -> None: def test_get_mask() -> None: """Test the get_mask function.""" reader = DefaultDataReader() - with OasisVBMTestingDatagrabber() as dg: + with OasisVBMTestingDataGrabber() as dg: input = dg["sub-01"] input = reader.fit_transform(input) vbm_gm = input["VBM_GM"] @@ -209,7 +209,7 @@ def test_mask_callable() -> None: _available_masks["identity"] = {"family": "Callable", "func": ident} reader = DefaultDataReader() - with OasisVBMTestingDatagrabber() as dg: + with OasisVBMTestingDataGrabber() as dg: input = dg["sub-01"] input = reader.fit_transform(input) vbm_gm = input["VBM_GM"] @@ -224,7 +224,7 @@ def test_mask_callable() -> None: def test_get_mask_errors() -> None: """Test passing wrong parameters to get_mask.""" reader = DefaultDataReader() - with OasisVBMTestingDatagrabber() as dg: + with OasisVBMTestingDataGrabber() as dg: input = dg["sub-01"] input = reader.fit_transform(input) vbm_gm = input["VBM_GM"] @@ -306,7 +306,7 @@ def test_nilearn_compute_masks( Whether to resample the mask to the target data. """ reader = DefaultDataReader() - with SPMAuditoryTestingDatagrabber() as dg: + with SPMAuditoryTestingDataGrabber() as dg: input = dg["sub001"] input = reader.fit_transform(input) bold = input["BOLD"] @@ -339,7 +339,7 @@ def test_nilearn_compute_masks( def test_get_mask_inherit() -> None: """Test using the inherit mask functionality.""" reader = DefaultDataReader() - with SPMAuditoryTestingDatagrabber() as dg: + with SPMAuditoryTestingDataGrabber() as dg: input = dg["sub001"] input = reader.fit_transform(input) # Compute brain mask using nilearn @@ -394,7 +394,7 @@ def test_get_mask_multiple( Parameters to pass to the intersect_masks function. """ reader = DefaultDataReader() - with SPMAuditoryTestingDatagrabber() as dg: + with SPMAuditoryTestingDataGrabber() as dg: input = dg["sub001"] input = reader.fit_transform(input) if not isinstance(masks, list): diff --git a/junifer/markers/functional_connectivity/tests/test_crossparcellation_functional_connectivity.py b/junifer/markers/functional_connectivity/tests/test_crossparcellation_functional_connectivity.py index 608897482..137fb8277 100644 --- a/junifer/markers/functional_connectivity/tests/test_crossparcellation_functional_connectivity.py +++ b/junifer/markers/functional_connectivity/tests/test_crossparcellation_functional_connectivity.py @@ -11,7 +11,7 @@ from nilearn import image from junifer.markers.functional_connectivity import CrossParcellationFC from junifer.storage import SQLiteFeatureStorage -from junifer.testing.datagrabbers import SPMAuditoryTestingDatagrabber +from junifer.testing.datagrabbers import SPMAuditoryTestingDataGrabber parcellation_ONE = "Schaefer100x17" @@ -21,7 +21,7 @@ parcellation_TWO = "Schaefer200x17" def test_compute() -> None: """Test CrossParcellationFC compute().""" - with SPMAuditoryTestingDatagrabber() as dg: + with SPMAuditoryTestingDataGrabber() as dg: out = dg["sub001"] niimg = image.load_img(str(out["BOLD"]["path"].absolute())) input_dict = { @@ -53,7 +53,7 @@ def test_store(tmp_path: Path) -> None: """ - with SPMAuditoryTestingDatagrabber() as dg: + with SPMAuditoryTestingDataGrabber() as dg: input_dict = dg["sub001"] niimg = image.load_img(str(input_dict["BOLD"]["path"].absolute())) diff --git a/junifer/markers/reho/tests/test_reho_parcels.py b/junifer/markers/reho/tests/test_reho_parcels.py index 4b427def7..285560cff 100644 --- a/junifer/markers/reho/tests/test_reho_parcels.py +++ b/junifer/markers/reho/tests/test_reho_parcels.py @@ -12,7 +12,7 @@ from scipy.stats import pearsonr from junifer.markers.reho.reho_parcels import ReHoParcels from junifer.pipeline.utils import _check_afni from junifer.storage.sqlite import SQLiteFeatureStorage -from junifer.testing.datagrabbers import SPMAuditoryTestingDatagrabber +from junifer.testing.datagrabbers import SPMAuditoryTestingDataGrabber PARCELLATION = "Schaefer100x7" @@ -20,7 +20,7 @@ PARCELLATION = "Schaefer100x7" def test_reho_parcels_computation() -> None: """Test ReHoParcels fit-transform.""" - with SPMAuditoryTestingDatagrabber() as dg: + with SPMAuditoryTestingDataGrabber() as dg: # Use first subject subject_data = dg["sub001"] # Load image to memory @@ -51,7 +51,7 @@ def test_reho_parcels_computation() -> None: ) def test_reho_parcels_computation_comparison() -> None: """Test ReHoParcels fit-transform implementation comparison..""" - with SPMAuditoryTestingDatagrabber() as dg: + with SPMAuditoryTestingDataGrabber() as dg: # Use first subject subject_data = dg["sub001"] # Load image to memory @@ -96,7 +96,7 @@ def test_reho_parcels_storage(tmp_path: Path) -> None: The path to the test directory. """ - with SPMAuditoryTestingDatagrabber() as dg: + with SPMAuditoryTestingDataGrabber() as dg: # Use first subject subject_data = dg["sub001"] # Load image to memory diff --git a/junifer/markers/reho/tests/test_reho_spheres.py b/junifer/markers/reho/tests/test_reho_spheres.py index 4bd42a2b5..3026bc9f5 100644 --- a/junifer/markers/reho/tests/test_reho_spheres.py +++ b/junifer/markers/reho/tests/test_reho_spheres.py @@ -12,7 +12,7 @@ from scipy.stats import pearsonr from junifer.markers.reho.reho_spheres import ReHoSpheres from junifer.pipeline.utils import _check_afni from junifer.storage.sqlite import SQLiteFeatureStorage -from junifer.testing.datagrabbers import SPMAuditoryTestingDatagrabber +from junifer.testing.datagrabbers import SPMAuditoryTestingDataGrabber COORDINATES = "DMNBuckner" @@ -20,7 +20,7 @@ COORDINATES = "DMNBuckner" def test_reho_spheres_computation() -> None: """Test ReHoSpheres fit-transform.""" - with SPMAuditoryTestingDatagrabber() as dg: + with SPMAuditoryTestingDataGrabber() as dg: # Use first subject subject_data = dg["sub001"] # Load image to memory @@ -51,7 +51,7 @@ def test_reho_spheres_computation() -> None: ) def test_reho_spheres_computation_comparison() -> None: """Test ReHoSpheres fit-transform implementation comparison..""" - with SPMAuditoryTestingDatagrabber() as dg: + with SPMAuditoryTestingDataGrabber() as dg: # Use first subject subject_data = dg["sub001"] # Load image to memory @@ -96,7 +96,7 @@ def test_reho_spheres_storage(tmp_path: Path) -> None: The path to the test directory. """ - with SPMAuditoryTestingDatagrabber() as dg: + with SPMAuditoryTestingDataGrabber() as dg: # Use first subject subject_data = dg["sub001"] # Load image to memory diff --git a/junifer/markers/tests/test_collection.py b/junifer/markers/tests/test_collection.py index 804d9e3ff..ebea847f9 100644 --- a/junifer/markers/tests/test_collection.py +++ b/junifer/markers/tests/test_collection.py @@ -19,7 +19,7 @@ from junifer.pipeline import PipelineStepMixin from junifer.preprocess import fMRIPrepConfoundRemover from junifer.storage import SQLiteFeatureStorage from junifer.testing.datagrabbers import ( - OasisVBMTestingDatagrabber, + OasisVBMTestingDataGrabber, PartlyCloudyTestingDataGrabber, ) @@ -69,7 +69,7 @@ def test_marker_collection() -> None: assert isinstance(mc._datareader, DefaultDataReader) # Create testing datagrabber - dg = OasisVBMTestingDatagrabber() + dg = OasisVBMTestingDataGrabber() mc.validate(dg) with dg: @@ -168,7 +168,7 @@ def test_marker_collection_storage(tmp_path: Path) -> None: ), ] # Test storage - dg = OasisVBMTestingDatagrabber() + dg = OasisVBMTestingDataGrabber() uri = tmp_path / "test_marker_collection_storage.sqlite" storage = SQLiteFeatureStorage(uri=uri) diff --git a/junifer/markers/tests/test_ets_rss.py b/junifer/markers/tests/test_ets_rss.py index d18ff4a81..0c6c872c4 100644 --- a/junifer/markers/tests/test_ets_rss.py +++ b/junifer/markers/tests/test_ets_rss.py @@ -14,7 +14,7 @@ from nilearn.maskers import NiftiLabelsMasker from junifer.data import load_parcellation from junifer.markers.ets_rss import RSSETSMarker from junifer.storage import SQLiteFeatureStorage -from junifer.testing.datagrabbers import SPMAuditoryTestingDatagrabber +from junifer.testing.datagrabbers import SPMAuditoryTestingDataGrabber # Set parcellation @@ -23,7 +23,7 @@ PARCELLATION = "Schaefer100x17" def test_compute() -> None: """Test RSS ETS compute().""" - with SPMAuditoryTestingDatagrabber() as dg: + with SPMAuditoryTestingDataGrabber() as dg: # Fetch element out = dg["sub001"] # Load BOLD image @@ -61,7 +61,7 @@ def test_store(tmp_path: Path) -> None: The path to the test directory. """ - with SPMAuditoryTestingDatagrabber() as dg: + with SPMAuditoryTestingDataGrabber() as dg: # Fetch element elem = dg["sub001"] # Load BOLD image diff --git a/junifer/preprocess/confounds/tests/test_fmriprep_confound_remover.py b/junifer/preprocess/confounds/tests/test_fmriprep_confound_remover.py index f16c01132..2ab4a6b6f 100644 --- a/junifer/preprocess/confounds/tests/test_fmriprep_confound_remover.py +++ b/junifer/preprocess/confounds/tests/test_fmriprep_confound_remover.py @@ -19,7 +19,7 @@ from junifer.datareader import DefaultDataReader from junifer.preprocess.confounds import fMRIPrepConfoundRemover from junifer.testing import get_testing_data from junifer.testing.datagrabbers import ( - OasisVBMTestingDatagrabber, + OasisVBMTestingDataGrabber, PartlyCloudyTestingDataGrabber, ) @@ -327,7 +327,7 @@ def test_fMRIPrepConfoundRemover__validate_data() -> None: """Test fMRIPrepConfoundRemover validate data.""" confound_remover = fMRIPrepConfoundRemover(strategy={"wm_csf": "full"}) reader = DefaultDataReader() - with OasisVBMTestingDatagrabber() as dg: + with OasisVBMTestingDataGrabber() as dg: input = dg["sub-01"] input = reader.fit_transform(input) new_input = input["VBM_GM"] -- 2.52.0 From 0ee68a95bbd6c105f08e4bf592e2366888da46fc Mon Sep 17 00:00:00 2001 From: Synchon Mandal Date: Tue, 18 Apr 2023 18:54:05 +0200 Subject: [PATCH 10/11] chore: change final Datagrabber to DataGrabber in docs/whats_new.rst --- docs/whats_new.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/whats_new.rst b/docs/whats_new.rst index 90f575319..e4afcfec1 100644 --- a/docs/whats_new.rst +++ b/docs/whats_new.rst @@ -220,7 +220,7 @@ Enhancements Features ^^^^^^^^ -- Implement :class:`.SPMAuditoryTestingDatagrabber` datagrabber by +- Implement :class:`.SPMAuditoryTestingDataGrabber` datagrabber by `Fede Raimondo`_ (:gh:`52`) - Implement matrix storage in SQliteFeatureStorage by `Fede Raimondo`_ -- 2.52.0 From e03d4cd4f97efbcbc4eb92e00aa05bd1b8f0e0e3 Mon Sep 17 00:00:00 2001 From: Synchon Mandal Date: Wed, 19 Apr 2023 12:39:00 +0200 Subject: [PATCH 11/11] chore: add changelogs 222.change and 222.enh --- docs/changes/newsfragments/222.change | 1 + docs/changes/newsfragments/222.enh | 1 + 2 files changed, 2 insertions(+) create mode 100644 docs/changes/newsfragments/222.change create mode 100644 docs/changes/newsfragments/222.enh diff --git a/docs/changes/newsfragments/222.change b/docs/changes/newsfragments/222.change new file mode 100644 index 000000000..3a64c2eb8 --- /dev/null +++ b/docs/changes/newsfragments/222.change @@ -0,0 +1 @@ +Rename ``junifer.testing.datagrabbers.SPMAuditoryTestingDatagrabber`` to :class:`.SPMAuditoryTestingDataGrabber` and ``junifer.testing.datagrabbers.OasisVBMTestingDatagrabber`` to :class:`.OasisVBMTestingDataGrabber` by `Synchon Mandal`_ \ No newline at end of file diff --git a/docs/changes/newsfragments/222.enh b/docs/changes/newsfragments/222.enh new file mode 100644 index 000000000..fd3f4a8ed --- /dev/null +++ b/docs/changes/newsfragments/222.enh @@ -0,0 +1 @@ +Rename instances of "Datagrabber" to "DataGrabber" especially in ``junifer.testing`` to be consistent by `Synchon Mandal`_ \ No newline at end of file -- 2.52.0