junifer 0.0.6.dev389__py3-none-any.whl → 0.0.6.dev407__py3-none-any.whl

junifer/_version.py

@@ -12,5 +12,5 @@ __version__: str
 __version_tuple__: VERSION_TUPLE
 version_tuple: VERSION_TUPLE
 
-__version__ = version = '0.0.6.dev389'
-__version_tuple__ = version_tuple = (0, 0, 6, 'dev389')
+__version__ = version = '0.0.6.dev407'
+__version_tuple__ = version_tuple = (0, 0, 6, 'dev407')

junifer/markers/complexity/tests/test_complexity_base.py

@@ -8,7 +8,7 @@ import pytest
 
 pytest.importorskip("neurokit2")
 
-from junifer.markers.complexity.complexity_base import (  # noqa: E402
+from junifer.markers.complexity.complexity_base import (
     ComplexityBase,
 )
 

junifer/markers/complexity/tests/test_hurst_exponent.py

@@ -12,11 +12,11 @@ import pytest
 pytest.importorskip("neurokit2")
 
 
-from junifer.datareader import DefaultDataReader  # noqa: E402
-from junifer.markers.complexity import HurstExponent  # noqa: E402
-from junifer.pipeline.utils import _check_ants  # noqa: E402
-from junifer.storage import SQLiteFeatureStorage  # noqa: E402
-from junifer.testing.datagrabbers import (  # noqa: E402
+from junifer.datareader import DefaultDataReader
+from junifer.markers.complexity import HurstExponent
+from junifer.pipeline.utils import _check_ants
+from junifer.storage import SQLiteFeatureStorage
+from junifer.testing.datagrabbers import (
     SPMAuditoryTestingDataGrabber,
 )
 

junifer/markers/complexity/tests/test_multiscale_entropy_auc.py

@@ -11,11 +11,11 @@ import pytest
 
 pytest.importorskip("neurokit2")
 
-from junifer.datareader import DefaultDataReader  # noqa: E402
-from junifer.markers.complexity import MultiscaleEntropyAUC  # noqa: E402
-from junifer.pipeline.utils import _check_ants  # noqa: E402
-from junifer.storage import SQLiteFeatureStorage  # noqa: E402
-from junifer.testing.datagrabbers import (  # noqa: E402
+from junifer.datareader import DefaultDataReader
+from junifer.markers.complexity import MultiscaleEntropyAUC
+from junifer.pipeline.utils import _check_ants
+from junifer.storage import SQLiteFeatureStorage
+from junifer.testing.datagrabbers import (
     SPMAuditoryTestingDataGrabber,
 )
 

junifer/markers/complexity/tests/test_perm_entropy.py

@@ -11,11 +11,11 @@ import pytest
 
 pytest.importorskip("neurokit2")
 
-from junifer.datareader import DefaultDataReader  # noqa: E402
-from junifer.markers.complexity import PermEntropy  # noqa: E402
-from junifer.pipeline.utils import _check_ants  # noqa: E402
-from junifer.storage import SQLiteFeatureStorage  # noqa: E402
-from junifer.testing.datagrabbers import (  # noqa: E402
+from junifer.datareader import DefaultDataReader
+from junifer.markers.complexity import PermEntropy
+from junifer.pipeline.utils import _check_ants
+from junifer.storage import SQLiteFeatureStorage
+from junifer.testing.datagrabbers import (
     SPMAuditoryTestingDataGrabber,
 )
 

junifer/markers/complexity/tests/test_range_entropy.py

@@ -12,11 +12,11 @@ import pytest
 pytest.importorskip("neurokit2")
 
 
-from junifer.datareader import DefaultDataReader  # noqa: E402
-from junifer.markers.complexity import RangeEntropy  # noqa: E402
-from junifer.pipeline.utils import _check_ants  # noqa: E402
-from junifer.storage import SQLiteFeatureStorage  # noqa: E402
-from junifer.testing.datagrabbers import (  # noqa: E402
+from junifer.datareader import DefaultDataReader
+from junifer.markers.complexity import RangeEntropy
+from junifer.pipeline.utils import _check_ants
+from junifer.storage import SQLiteFeatureStorage
+from junifer.testing.datagrabbers import (
     SPMAuditoryTestingDataGrabber,
 )
 

junifer/markers/complexity/tests/test_range_entropy_auc.py

@@ -12,11 +12,11 @@ import pytest
 pytest.importorskip("neurokit2")
 
 
-from junifer.datareader import DefaultDataReader  # noqa: E402
-from junifer.markers.complexity import RangeEntropyAUC  # noqa: E402
-from junifer.pipeline.utils import _check_ants  # noqa: E402
-from junifer.storage import SQLiteFeatureStorage  # noqa: E402
-from junifer.testing.datagrabbers import (  # noqa: E402
+from junifer.datareader import DefaultDataReader
+from junifer.markers.complexity import RangeEntropyAUC
+from junifer.pipeline.utils import _check_ants
+from junifer.storage import SQLiteFeatureStorage
+from junifer.testing.datagrabbers import (
     SPMAuditoryTestingDataGrabber,
 )
 

junifer/markers/complexity/tests/test_sample_entropy.py

@@ -11,11 +11,11 @@ import pytest
 
 pytest.importorskip("neurokit2")
 
-from junifer.datareader import DefaultDataReader  # noqa: E402
-from junifer.markers.complexity import SampleEntropy  # noqa: E402
-from junifer.pipeline.utils import _check_ants  # noqa: E402
-from junifer.storage import SQLiteFeatureStorage  # noqa: E402
-from junifer.testing.datagrabbers import (  # noqa: E402
+from junifer.datareader import DefaultDataReader
+from junifer.markers.complexity import SampleEntropy
+from junifer.pipeline.utils import _check_ants
+from junifer.storage import SQLiteFeatureStorage
+from junifer.testing.datagrabbers import (
     SPMAuditoryTestingDataGrabber,
 )
 

junifer/markers/complexity/tests/test_weighted_perm_entropy.py

@@ -11,11 +11,11 @@ import pytest
 
 pytest.importorskip("neurokit2")
 
-from junifer.datareader import DefaultDataReader  # noqa: E402
-from junifer.markers.complexity import WeightedPermEntropy  # noqa: E402
-from junifer.pipeline.utils import _check_ants  # noqa: E402
-from junifer.storage import SQLiteFeatureStorage  # noqa: E402
-from junifer.testing.datagrabbers import (  # noqa: E402
+from junifer.datareader import DefaultDataReader
+from junifer.markers.complexity import WeightedPermEntropy
+from junifer.pipeline.utils import _check_ants
+from junifer.storage import SQLiteFeatureStorage
+from junifer.testing.datagrabbers import (
     SPMAuditoryTestingDataGrabber,
 )
 

junifer/preprocess/confounds/fmriprep_confound_remover.py

@@ -596,6 +596,8 @@ class fMRIPrepConfoundRemover(BasePreprocessor):
             t_r=t_r,
             mask_img=mask_img,
         )
+        # Fix t_r as nilearn messes it up
+        cleaned_img.header["pixdim"][4] = t_r
         # Save deconfounded data
         deconfounded_img_path = element_tempdir / "deconfounded_data.nii.gz"
         nib.save(cleaned_img, deconfounded_img_path)

junifer/preprocess/confounds/tests/test_fmriprep_confound_remover.py

@@ -460,22 +460,32 @@ def test_fMRIPrepConfoundRemover_fit_transform() -> None:
 
     with PartlyCloudyTestingDataGrabber(reduce_confounds=False) as dg:
         element_data = DefaultDataReader().fit_transform(dg["sub-01"])
-        orig_bold = element_data["BOLD"]["data"].get_fdata().copy()
+        # Get original data
+        input_img = element_data["BOLD"]["data"]
+        input_bold = input_img.get_fdata().copy()
+        input_tr = input_img.header.get_zooms()[3]
+        # Fit-transform
         output = confound_remover.fit_transform(element_data)
-        trans_bold = output["BOLD"]["data"].get_fdata()
+        output_img = output["BOLD"]["data"]
+        output_bold = output_img.get_fdata()
+        output_tr = output_img.header.get_zooms()[3]
+
         # Transformation is in place
         assert_array_equal(
-            trans_bold, element_data["BOLD"]["data"].get_fdata()
+            output_bold, element_data["BOLD"]["data"].get_fdata()
         )
 
         # Data should have the same shape
-        assert orig_bold.shape == trans_bold.shape
+        assert input_bold.shape == output_bold.shape
 
         # but be different
         assert_raises(
-            AssertionError, assert_array_equal, orig_bold, trans_bold
+            AssertionError, assert_array_equal, input_bold, output_bold
         )
 
+        # Check t_r
+        assert input_tr == output_tr
+
         assert "meta" in output["BOLD"]
         assert "preprocess" in output["BOLD"]["meta"]
         t_meta = output["BOLD"]["meta"]["preprocess"]
@@ -506,22 +516,32 @@ def test_fMRIPrepConfoundRemover_fit_transform_masks() -> None:
 
     with PartlyCloudyTestingDataGrabber(reduce_confounds=False) as dg:
         element_data = DefaultDataReader().fit_transform(dg["sub-01"])
-        orig_bold = element_data["BOLD"]["data"].get_fdata().copy()
+        # Get original data
+        input_img = element_data["BOLD"]["data"]
+        input_bold = input_img.get_fdata().copy()
+        input_tr = input_img.header.get_zooms()[3]
+        # Fit-transform
         output = confound_remover.fit_transform(element_data)
-        trans_bold = output["BOLD"]["data"].get_fdata()
+        output_img = output["BOLD"]["data"]
+        output_bold = output_img.get_fdata()
+        output_tr = output_img.header.get_zooms()[3]
+
         # Transformation is in place
         assert_array_equal(
-            trans_bold, element_data["BOLD"]["data"].get_fdata()
+            output_bold, element_data["BOLD"]["data"].get_fdata()
         )
 
         # Data should have the same shape
-        assert orig_bold.shape == trans_bold.shape
+        assert input_bold.shape == output_bold.shape
 
         # but be different
         assert_raises(
-            AssertionError, assert_array_equal, orig_bold, trans_bold
+            AssertionError, assert_array_equal, input_bold, output_bold
         )
 
+        # Check t_r
+        assert input_tr == output_tr
+
         assert "meta" in output["BOLD"]
         assert "preprocess" in output["BOLD"]["meta"]
         t_meta = output["BOLD"]["meta"]["preprocess"]

{junifer-0.0.6.dev389.dist-info → junifer-0.0.6.dev407.dist-info}/METADATA

@@ -1,6 +1,6 @@
-Metadata-Version: 2.1
+Metadata-Version: 2.2
 Name: junifer
-Version: 0.0.6.dev389
+Version: 0.0.6.dev407
 Summary: JUelich NeuroImaging FEature extractoR
 Author-email: Fede Raimondo <f.raimondo@fz-juelich.de>, Synchon Mandal <s.mandal@fz-juelich.de>
 Maintainer-email: Fede Raimondo <f.raimondo@fz-juelich.de>, Synchon Mandal <s.mandal@fz-juelich.de>

{junifer-0.0.6.dev389.dist-info → junifer-0.0.6.dev407.dist-info}/RECORD

@@ -1,6 +1,6 @@
 junifer/__init__.py,sha256=2McgH1yNue6Z1V26-uN_mfMjbTcx4CLhym-DMBl5xA4,266
 junifer/__init__.pyi,sha256=SsTvgq2Dod6UqJN96GH1lCphH6hJQQurEJHGNhHjGUI,508
-junifer/_version.py,sha256=X-yXnQlyg2_EwjCw0n4eAgGDkY1QOoPd1RhBaG_xEes,428
+junifer/_version.py,sha256=9rnb3QC8sI_M_VcAt4dvLzjl0PKqZFrt7q4iJxREOEc,428
 junifer/conftest.py,sha256=PWYkkRDU8ly2lYwv7VBKMHje4et6HX7Yey3Md_I2KbA,613
 junifer/py.typed,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 junifer/stats.py,sha256=e9aaagMGtgpRfW3Wdpz9ocpnYld1IWylCDcjFUgX9Mk,6225
@@ -198,14 +198,14 @@ junifer/markers/complexity/range_entropy.py,sha256=4q23tK4T4JCxJsmuNeUAxJ2Eso21z
 junifer/markers/complexity/range_entropy_auc.py,sha256=0jFCiVhfamK4PaXceEJNbiIOepC_CsjHz-BMZYJHlSE,5005
 junifer/markers/complexity/sample_entropy.py,sha256=5hcd8YYHpB5-9he5O_7yq7bI-2KNqzIIdAdc7b6d-jU,4473
 junifer/markers/complexity/weighted_perm_entropy.py,sha256=eNDPLICRcggYSKEsYw4i96-qPjkhb2qhNisweWhOeiA,4525
-junifer/markers/complexity/tests/test_complexity_base.py,sha256=0E0AjjBqenIb6ZzK-EMie24J4vVjWUjAPfkvvognu9Y,453
-junifer/markers/complexity/tests/test_hurst_exponent.py,sha256=s1G8xF5rBc0TgWbe7nKFgcwlAjUb1Yabw3ALEcXYBj0,2311
-junifer/markers/complexity/tests/test_multiscale_entropy_auc.py,sha256=UDScZLPYc1S1kpL04_Rcj2U_dgRhq2VzNOEDv5O8WGE,2382
-junifer/markers/complexity/tests/test_perm_entropy.py,sha256=VHhqXF1r0RbHvZj383bYy_WhN_do7Mt-Pr1NWG0z13Q,2299
-junifer/markers/complexity/tests/test_range_entropy.py,sha256=RXM0jSL32VA37jYe36mmv2WU0xgiNJ-S79hsb-ZfYqQ,2302
-junifer/markers/complexity/tests/test_range_entropy_auc.py,sha256=__uKRJtAuWG-e8JxxfNUjrNfeIqU_uHQDq_RKyERdgk,2338
-junifer/markers/complexity/tests/test_sample_entropy.py,sha256=rfbiguVq7CUwYIvYBYFCSSfH44nqGLSZYFfwFb155KI,2310
-junifer/markers/complexity/tests/test_weighted_perm_entropy.py,sha256=yDWKEaUbxrnrG6J2NlktLfwSBre5OuXd63kEof7t8PM,2373
+junifer/markers/complexity/tests/test_complexity_base.py,sha256=5-JqcADqDx-wDvbCE2Eplw4TUe7q_s9TDcxjLC1j6_Q,439
+junifer/markers/complexity/tests/test_hurst_exponent.py,sha256=HmAK3-k5IugZ8RCgETeqzF3zWStC7rWKBDQqWZ7WYoU,2241
+junifer/markers/complexity/tests/test_multiscale_entropy_auc.py,sha256=M-BmO-gQDlf16tJSdPZ1lsFxefY5Tz0ai0OlpDQvNn4,2312
+junifer/markers/complexity/tests/test_perm_entropy.py,sha256=dXnZZErUmykn0C-P1sEH3hBJVRmDe37frcE2o2cRhuE,2229
+junifer/markers/complexity/tests/test_range_entropy.py,sha256=oUC9ccLJuYsHf2XDIp3qpjTxvr802v71kzkpkBGFCaQ,2232
+junifer/markers/complexity/tests/test_range_entropy_auc.py,sha256=k_FOKL_doreEqDuj8LVSY_IyV7hwoU26bQGEqHS-0j4,2268
+junifer/markers/complexity/tests/test_sample_entropy.py,sha256=4lPQvhAEkp_GW3Q74lrJVj2j9t7l20EPhIFv3c-wJ1E,2240
+junifer/markers/complexity/tests/test_weighted_perm_entropy.py,sha256=ogWOwmD224FtZhFXaxx-lmk4rvJ_OuNr2zi56Ftfjlg,2303
 junifer/markers/falff/__init__.py,sha256=qxdx_3FsVrn7h3gtbocK0ZmvqZwPQZGKuVkPm31ejNM,217
 junifer/markers/falff/__init__.pyi,sha256=X-q2zBjUX0imQ37yN2Cg5gKfDvq8sh_9y2hRH4g5ufY,120
 junifer/markers/falff/_afni_falff.py,sha256=PYkSOFMyaHoGYDvmBjKLW1ALyWBe7yI36JBqZ71ji2c,4223
@@ -280,9 +280,9 @@ junifer/preprocess/base.py,sha256=hARO4Yq9sQ8m2tATeuBmPMbI4BSnwNxLf2prF8Iq_Tk,66
 junifer/preprocess/py.typed,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 junifer/preprocess/confounds/__init__.py,sha256=L3CquKcndFb2b8yVo-XLi-zsNCe8MMKUN41UOVdooWc,270
 junifer/preprocess/confounds/__init__.pyi,sha256=iC70cqcWNMX4JM42RcUgKb9YX8ciK8oVERdWWjo-13c,102
-junifer/preprocess/confounds/fmriprep_confound_remover.py,sha256=Vw0ymmA8QppKY3GHdP8J9K6KyYUSbLGbBnwT-VpwXLw,21527
+junifer/preprocess/confounds/fmriprep_confound_remover.py,sha256=Mf93SKgrfIDcig3R8Pfu_SaK-E6-JCOSITLtITOmFa0,21615
 junifer/preprocess/confounds/py.typed,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-junifer/preprocess/confounds/tests/test_fmriprep_confound_remover.py,sha256=yZxCud9l8bW36Rsk63Fi1qWUpM9L4Wtd2-zZW-DjvZA,19949
+junifer/preprocess/confounds/tests/test_fmriprep_confound_remover.py,sha256=L1L9yllAyneOL3YgcNRf3a2zXGZjjyPMdjSy0fRGpWc,20517
 junifer/preprocess/smoothing/__init__.py,sha256=7aTwvAG522kA76QQwqxwY5zV_6asyPaaH2uSMTaKQls,216
 junifer/preprocess/smoothing/__init__.pyi,sha256=5sjw61Eyon9gE_SWoktND9raw6IkgqcT2rtGNhVV9EA,58
 junifer/preprocess/smoothing/_afni_smoothing.py,sha256=4mdZk9YkA02wZ8rS6sbLnXL_7SIX7M0NwHPLckJgCmI,3325
@@ -341,10 +341,10 @@ junifer/utils/tests/test_config.py,sha256=7ltIXuwb_W4Mv_1dxQWyiyM10XgUAfsWKV6D_i
 junifer/utils/tests/test_fs.py,sha256=WQS7cKlKEZ742CIuiOYYpueeAhY9PqlastfDVpVVtvE,923
 junifer/utils/tests/test_helpers.py,sha256=k5qqfxK8dFyuewTJyR1Qn6-nFaYNuVr0ysc18bfPjyU,929
 junifer/utils/tests/test_logging.py,sha256=duO4ou365hxwa_kwihFtKPLaL6LC5XHiyhOijrrngbA,8009
-junifer-0.0.6.dev389.dist-info/AUTHORS.rst,sha256=rmULKpchpSol4ExWFdm-qu4fkpSZPYqIESVJBZtGb6E,163
-junifer-0.0.6.dev389.dist-info/LICENSE.md,sha256=MqCnOBu8uXsEOzRZWh9EBVfVz-kE9NkXcLCrtGXo2yU,34354
-junifer-0.0.6.dev389.dist-info/METADATA,sha256=EmDLVfbOnEGVxZpLIPhK8S9OJt_1RcpGW6ABx12fIRw,8429
-junifer-0.0.6.dev389.dist-info/WHEEL,sha256=A3WOREP4zgxI0fKrHUG8DC8013e3dK3n7a6HDbcEIwE,91
-junifer-0.0.6.dev389.dist-info/entry_points.txt,sha256=6O8ru0BP-SP7YMUZiizFNoaZ2HvJpadO2G7nKk4PwjI,48
-junifer-0.0.6.dev389.dist-info/top_level.txt,sha256=4bAq1R2QFQ4b3hohjys2JBvxrl0GKk5LNFzYvz9VGcA,8
-junifer-0.0.6.dev389.dist-info/RECORD,,
+junifer-0.0.6.dev407.dist-info/AUTHORS.rst,sha256=rmULKpchpSol4ExWFdm-qu4fkpSZPYqIESVJBZtGb6E,163
+junifer-0.0.6.dev407.dist-info/LICENSE.md,sha256=MqCnOBu8uXsEOzRZWh9EBVfVz-kE9NkXcLCrtGXo2yU,34354
+junifer-0.0.6.dev407.dist-info/METADATA,sha256=I8O2PCytiREuJWEK4zzbC4syBxRM8_aigDyFutDkRKQ,8429
+junifer-0.0.6.dev407.dist-info/WHEEL,sha256=In9FTNxeP60KnTkGw7wk6mJPYd_dQSjEZmXdBdMCI-8,91
+junifer-0.0.6.dev407.dist-info/entry_points.txt,sha256=6O8ru0BP-SP7YMUZiizFNoaZ2HvJpadO2G7nKk4PwjI,48
+junifer-0.0.6.dev407.dist-info/top_level.txt,sha256=4bAq1R2QFQ4b3hohjys2JBvxrl0GKk5LNFzYvz9VGcA,8
+junifer-0.0.6.dev407.dist-info/RECORD,,

{junifer-0.0.6.dev389.dist-info → junifer-0.0.6.dev407.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: setuptools (75.7.0)
+Generator: setuptools (75.8.0)
 Root-Is-Purelib: true
 Tag: py3-none-any