junifer 0.0.6.dev330__py3-none-any.whl → 0.0.6.dev335__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.dev330'
-__version_tuple__ = version_tuple = (0, 0, 6, 'dev330')
+__version__ = version = '0.0.6.dev335'
+__version_tuple__ = version_tuple = (0, 0, 6, 'dev335')

junifer/data/masks/_ants_mask_warper.py

@@ -125,7 +125,7 @@ class ANTsMaskWarper:
             # Get template space image
             template_space_img = get_template(
                 space=dst,
-                target_data=target_data,
+                target_img=mask_img,
                 extra_input=None,
             )
             # Save template to a tempfile

junifer/data/masks/_masks.py

@@ -106,15 +106,15 @@ def compute_brain_mask(
             if entry["dst"] == "native":
                 target_std_space = entry["src"]
 
+    target_img = target_data["data"]
     # Fetch template in closest resolution
     template = get_template(
         space=target_std_space,
-        target_data=target_data,
+        target_img=target_img,
         extra_input=extra_input,
         template_type=mask_type,
     )
     # Resample template to target image
-    target_img = target_data["data"]
     resampled_template = resample_to_img(
         source_img=template, target_img=target_img
     )

junifer/data/parcellations/_ants_parcellation_warper.py

@@ -131,7 +131,7 @@ class ANTsParcellationWarper:
             # Get template space image
             template_space_img = get_template(
                 space=dst,
-                target_data=target_data,
+                target_img=parcellation_img,
                 extra_input=None,
             )
             # Save template to a tempfile

junifer/data/template_spaces.py

@@ -122,7 +122,7 @@ def get_xfm(
 
 def get_template(
     space: str,
-    target_data: dict[str, Any],
+    target_img: nib.Nifti1Image,
     extra_input: Optional[dict[str, Any]] = None,
     template_type: str = "T1w",
 ) -> nib.Nifti1Image:
@@ -132,9 +132,9 @@ def get_template(
     ----------
     space : str
         The name of the template space.
-    target_data : dict
-        The corresponding item of the data object for which the template space
-        will be loaded.
+    target_img : Nifti1Image
+        The corresponding image for which the template space will be loaded.
+        This is used to obtain the best matching resolution.
     extra_input : dict, optional
         The other fields in the data object. Useful for accessing other data
         types (default None).
@@ -163,7 +163,6 @@ def get_template(
         raise_error(f"Unknown template type: {template_type}")
 
     # Get the min of the voxels sizes and use it as the resolution
-    target_img = target_data["data"]
     resolution = np.min(target_img.header.get_zooms()[:3]).astype(int)
 
     # Fetch available resolutions for the template

junifer/data/tests/test_template_spaces.py

@@ -61,7 +61,9 @@ def test_get_template(template_type: str) -> None:
         bold = element_data["BOLD"]
         # Get tailored parcellation
         tailored_template = get_template(
-            space=bold["space"], target_data=bold, template_type=template_type
+            space=bold["space"],
+            target_img=bold["data"],
+            template_type=template_type,
         )
         assert isinstance(tailored_template, nib.Nifti1Image)
 
@@ -74,7 +76,7 @@ def test_get_template_invalid_space() -> None:
         vbm_gm = element_data["VBM_GM"]
         # Get tailored parcellation
         with pytest.raises(ValueError, match="Unknown template space:"):
-            get_template(space="andromeda", target_data=vbm_gm)
+            get_template(space="andromeda", target_img=vbm_gm["data"])
 
 
 def test_get_template_invalid_template_type() -> None:
@@ -87,7 +89,7 @@ def test_get_template_invalid_template_type() -> None:
         with pytest.raises(ValueError, match="Unknown template type:"):
             get_template(
                 space=vbm_gm["space"],
-                target_data=vbm_gm,
+                target_img=vbm_gm["data"],
                 template_type="xenon",
             )
 
@@ -100,5 +102,7 @@ def test_get_template_closest_resolution() -> None:
         vbm_gm = element_data["VBM_GM"]
         # Change header resolution to fetch closest resolution
         element_data["VBM_GM"]["data"].header.set_zooms((3, 3, 3))
-        template = get_template(space=vbm_gm["space"], target_data=vbm_gm)
+        template = get_template(
+            space=vbm_gm["space"], target_img=vbm_gm["data"]
+        )
         assert isinstance(template, nib.Nifti1Image)

junifer/preprocess/warping/_ants_warper.py

@@ -189,7 +189,7 @@ class ANTsWarper:
             # Get template space image
             template_space_img = get_template(
                 space=reference,
-                target_data=input,
+                target_img=input["data"],
                 extra_input=None,
             )
             # Save template

{junifer-0.0.6.dev330.dist-info → junifer-0.0.6.dev335.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: junifer
-Version: 0.0.6.dev330
+Version: 0.0.6.dev335
 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.dev330.dist-info → junifer-0.0.6.dev335.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=ib7p2sRvl9n6dHPTqNlqVwUPPOKf5EKIksHMk7EQqno,428
+junifer/_version.py,sha256=wpXWesraPrhb_cofYpN1ctRb0HDonccBP0feD-Khgm0,428
 junifer/conftest.py,sha256=PWYkkRDU8ly2lYwv7VBKMHje4et6HX7Yey3Md_I2KbA,613
 junifer/py.typed,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 junifer/stats.py,sha256=e9aaagMGtgpRfW3Wdpz9ocpnYld1IWylCDcjFUgX9Mk,6225
@@ -75,7 +75,7 @@ junifer/data/__init__.pyi,sha256=qYszjUYcbFi_2zO23MnbA2HhTW-Ad2oh1pqPQYd6yt0,542
 junifer/data/_dispatch.py,sha256=O524U1R4MtbGhGJsL0HSh9EqisapBFJWK7uupXrJuMg,6158
 junifer/data/pipeline_data_registry_base.py,sha256=G8bE3WTj4D_rKC4ZKZe6E48Sd96CGea1PS3SxmTgGK4,2010
 junifer/data/py.typed,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-junifer/data/template_spaces.py,sha256=AVNuXuCqY0w7dSrVOZURjCPFIkg0wzQsAV2ggtQFpJU,6504
+junifer/data/template_spaces.py,sha256=JPsrGyfbaVgZ75uB3ci2CUuVxUg3NDi6HhO_VTIHeOE,6508
 junifer/data/utils.py,sha256=5r-0QGQCNZvDM1tVcl9xyrIdgAO85mww0plpM1RUaGA,3247
 junifer/data/coordinates/__init__.py,sha256=ffM8rwcHLgHAWixJbKrATrbUKzX940V1UF6RAxZdUMg,186
 junifer/data/coordinates/__init__.pyi,sha256=Z-Ti5XD3HigkZ8uYN6oYsLqw40-F1GvTVQ5QAy08Wng,88
@@ -104,9 +104,9 @@ junifer/data/coordinates/VOIs/meta/extDMN_VOIs.txt,sha256=Ogx1QvqZcnXDM3ncF2ha78
 junifer/data/coordinates/tests/test_coordinates.py,sha256=_c2P4oaDGpsmui5gJBe_jN6HLGiKxONkYPR69sRBUlU,4219
 junifer/data/masks/__init__.py,sha256=eEEhHglyVEx1LrqwXjq3cOmjf4sTsgBstRx5-k7zIQU,180
 junifer/data/masks/__init__.pyi,sha256=lcgr8gmWDPibC4RxnWBXb8DDpIkO73Aax09u6VXiJJI,114
-junifer/data/masks/_ants_mask_warper.py,sha256=6ex2jxxKI5yA4G1rebSpcAYGGisflVK-DwhtUtWY964,5348
+junifer/data/masks/_ants_mask_warper.py,sha256=CLZ6f8jp2PE1F8uHSrSYZ5wW8Nz0aeg84vStIpz0L2Y,5344
 junifer/data/masks/_fsl_mask_warper.py,sha256=VApp-ofGBKePNmCdgTg1HoEA66lMQiAPT0ihkhB2ezY,2415
-junifer/data/masks/_masks.py,sha256=96NKsSSosD6r03Jb2N1xQoyOc2Vl5miokcQdSeuM6SY,20729
+junifer/data/masks/_masks.py,sha256=W-vl1CTr5MHg5mvm51sObE4mqKR5f6RD6eE2wzCHRVc,20727
 junifer/data/masks/tests/test_masks.py,sha256=1Zm09ZSdUlR278DTCZeVuxuQntryefsnYYPP02MttVE,16120
 junifer/data/masks/ukb/UKB_15K_GM_template.nii.gz,sha256=jcX1pDOrDsoph8cPMNFVKH5gZYio5G4rJNpOFXm9wJI,946636
 junifer/data/masks/vickery-patil/CAT12_IXI555_MNI152_TMP_GS_GMprob0.2_clean.nii.gz,sha256=j6EY8EtRnUuRxeKgD65Q6B0GPEPIALKDJEIje1TfnAU,88270
@@ -114,12 +114,12 @@ junifer/data/masks/vickery-patil/CAT12_IXI555_MNI152_TMP_GS_GMprob0.2_clean_3mm.
 junifer/data/masks/vickery-patil/GMprob0.2_cortex_3mm_NA_rm.nii.gz,sha256=jfMe_4H9XEnArYms5bSQbqS2V1_HbLHTfI5amQa_Pes,8700
 junifer/data/parcellations/__init__.py,sha256=6-Ysil3NyZ69V6rWx4RO15_d-iDKizfbHuxSjsHNt24,188
 junifer/data/parcellations/__init__.pyi,sha256=lhBHTbMDizzqUqVHrx2eyfPFodrTBgMFeTgxfESSkQ8,140
-junifer/data/parcellations/_ants_parcellation_warper.py,sha256=4CYieBer6ow4i8o4NjKsfufc96XdtsMGwfBbMF-Kw78,5802
+junifer/data/parcellations/_ants_parcellation_warper.py,sha256=YUCJC0_wutGw7j_n9JRU3LCwm9Ttg5PIlJUgqejfRhs,5806
 junifer/data/parcellations/_fsl_parcellation_warper.py,sha256=JfJ022flg5OR48P4OAALVHHQgTVxdMBXT-fAqBl3nUM,2679
 junifer/data/parcellations/_parcellations.py,sha256=uOqoucoynv--iEftrhdnOd3jBcqq9PSDgs9DYhbeN24,65611
 junifer/data/parcellations/tests/test_parcellations.py,sha256=crluGgUjocVZ0ZIkMpUVol27A-Px6oc2eflY5g0C4BY,38315
 junifer/data/tests/test_data_utils.py,sha256=136iGPjGecCxyqgUwU8VZMHoE6imcYJ0WNC32PDGK4g,1063
-junifer/data/tests/test_template_spaces.py,sha256=PJulN7xHpAcSOTY-UzTG_WPywZEBSlAZGiNG4gzk1_8,3144
+junifer/data/tests/test_template_spaces.py,sha256=ZEicEcLqOJ-NpuBZ5SYh4yZ0xZRkhYHnYXiC_YSxjrY,3219
 junifer/datagrabber/__init__.py,sha256=EHIK-lbjuvkt0V8ypFvLSt85OAAXSkaxBmVlCbNNz8M,323
 junifer/datagrabber/__init__.pyi,sha256=zOQE4TaCKXBTHnNqgmECtsszWIOHYiQ1CUEeXXFU9F4,832
 junifer/datagrabber/base.py,sha256=a3_fUZIN5Bqhq2f4ldpwk_eWeSVRDpDmx2QGIKzCtkg,6761
@@ -294,7 +294,7 @@ junifer/preprocess/smoothing/tests/test_smoothing.py,sha256=t1j3zEvJk5XLO4fzcb-w
 junifer/preprocess/tests/test_preprocess_base.py,sha256=-0rpe8QjqYES36H6MHuDs3cv_6upHBdVHnFMgQsmEX4,2571
 junifer/preprocess/warping/__init__.py,sha256=rzUUP7-6H_nygQ7a7TBZ4_RY7p0ELacosYsWQbSdVZk,214
 junifer/preprocess/warping/__init__.pyi,sha256=Drbqp8N3uprvXcKSxqdfj90fesz9XYVLgivhPnKAYcc,65
-junifer/preprocess/warping/_ants_warper.py,sha256=Qk6piCuGPlfgGbH3zMVC5UHCoQ7iddYuc2vgsrqncGg,10163
+junifer/preprocess/warping/_ants_warper.py,sha256=8-YzQmevZ_9vh4QnHDJgsXoEgitDtFV_atOZrVLQNtI,10170
 junifer/preprocess/warping/_fsl_warper.py,sha256=dH1xd3jTRPREzgdh98Dz_4o2gwdrOgc0h5wbARSSB98,5226
 junifer/preprocess/warping/py.typed,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 junifer/preprocess/warping/space_warper.py,sha256=mf7SDu574R3TXNt82fqGl_hcEYx7SjXwz2TcmWObHQA,7706
@@ -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.dev330.dist-info/AUTHORS.rst,sha256=rmULKpchpSol4ExWFdm-qu4fkpSZPYqIESVJBZtGb6E,163
-junifer-0.0.6.dev330.dist-info/LICENSE.md,sha256=MqCnOBu8uXsEOzRZWh9EBVfVz-kE9NkXcLCrtGXo2yU,34354
-junifer-0.0.6.dev330.dist-info/METADATA,sha256=LkxGgT6R7p-H0fZTaFoWi71TBNqAnRpuXVa9w6DUhZ4,8429
-junifer-0.0.6.dev330.dist-info/WHEEL,sha256=PZUExdf71Ui_so67QXpySuHtCi3-J3wvF4ORK6k_S8U,91
-junifer-0.0.6.dev330.dist-info/entry_points.txt,sha256=6O8ru0BP-SP7YMUZiizFNoaZ2HvJpadO2G7nKk4PwjI,48
-junifer-0.0.6.dev330.dist-info/top_level.txt,sha256=4bAq1R2QFQ4b3hohjys2JBvxrl0GKk5LNFzYvz9VGcA,8
-junifer-0.0.6.dev330.dist-info/RECORD,,
+junifer-0.0.6.dev335.dist-info/AUTHORS.rst,sha256=rmULKpchpSol4ExWFdm-qu4fkpSZPYqIESVJBZtGb6E,163
+junifer-0.0.6.dev335.dist-info/LICENSE.md,sha256=MqCnOBu8uXsEOzRZWh9EBVfVz-kE9NkXcLCrtGXo2yU,34354
+junifer-0.0.6.dev335.dist-info/METADATA,sha256=WeHldE8PQXwyXQvgchca6TTVSjFOCWYuPql8YVCDmwo,8429
+junifer-0.0.6.dev335.dist-info/WHEEL,sha256=PZUExdf71Ui_so67QXpySuHtCi3-J3wvF4ORK6k_S8U,91
+junifer-0.0.6.dev335.dist-info/entry_points.txt,sha256=6O8ru0BP-SP7YMUZiizFNoaZ2HvJpadO2G7nKk4PwjI,48
+junifer-0.0.6.dev335.dist-info/top_level.txt,sha256=4bAq1R2QFQ4b3hohjys2JBvxrl0GKk5LNFzYvz9VGcA,8
+junifer-0.0.6.dev335.dist-info/RECORD,,