junifer 0.0.6.dev299__py3-none-any.whl → 0.0.6.dev302__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.dev299'
-__version_tuple__ = version_tuple = (0, 0, 6, 'dev299')
+__version__ = version = '0.0.6.dev302'
+__version_tuple__ = version_tuple = (0, 0, 6, 'dev302')

junifer/data/coordinates/_fsl_coordinates_warper.py

@@ -69,7 +69,7 @@ class FSLCoordinatesWarper:
             f"{pretransform_coordinates_path.resolve()}",
             "| img2imgcoord -mm",
             f"-src {target_data['path'].resolve()}",
-            f"-dest {target_data['reference_path'].resolve()}",
+            f"-dest {target_data['reference']['path'].resolve()}",
             f"-warp {warp_data['path'].resolve()}",
             f"> {transformed_coords_path.resolve()};",
             f"sed -i 1d {transformed_coords_path.resolve()}",

junifer/data/masks/_ants_mask_warper.py

@@ -49,9 +49,10 @@ class ANTsMaskWarper:
             It should be empty string if ``dst="T1w"``.
         dst : str
             The data type or template space to warp to.
-            `"T1w"` is the only allowed data type and it uses the resampled T1w
-            found in ``target_data.reference_path``. The ``"reference_path"``
-            key is added when :class:`.SpaceWarper` is used.
+            `"native"` is the only allowed data type and it uses the resampled
+            T1w found in ``target_data.reference``. The
+            ``"reference"`` key is added when :class:`.SpaceWarper` is
+            used or if the data is provided native space.
         target_data : dict
             The corresponding item of the data object to which the mask
             will be applied.
@@ -87,6 +88,10 @@ class ANTsMaskWarper:
             # Warp data check
             if warp_data is None:
                 raise_error("No `warp_data` provided")
+            if "reference" not in target_data:
+                raise_error("No `reference` provided")
+            if "path" not in target_data["reference"]:
+                raise_error("No `path` provided in `reference`")
 
             logger.debug("Using ANTs for mask transformation")
 
@@ -104,7 +109,7 @@ class ANTsMaskWarper:
                 "-n 'GenericLabel[NearestNeighbor]'",
                 f"-i {prewarp_mask_path.resolve()}",
                 # use resampled reference
-                f"-r {target_data['reference_path'].resolve()}",
+                f"-r {target_data['reference']['path'].resolve()}",
                 f"-t {warp_data['path'].resolve()}",
                 f"-o {warped_mask_path.resolve()}",
             ]

junifer/data/masks/_fsl_mask_warper.py

@@ -74,7 +74,7 @@ class FSLMaskWarper:
             "--interp=nn",
             f"-i {prewarp_mask_path.resolve()}",
             # use resampled reference
-            f"-r {target_data['reference_path'].resolve()}",
+            f"-r {target_data['reference']['path'].resolve()}",
             f"-w {warp_data['path'].resolve()}",
             f"-o {warped_mask_path.resolve()}",
         ]

junifer/data/parcellations/_ants_parcellation_warper.py

@@ -50,8 +50,9 @@ class ANTsParcellationWarper:
         dst : str
             The data type or template space to warp to.
             `"T1w"` is the only allowed data type and it uses the resampled T1w
-            found in ``target_data.reference_path``. The ``"reference_path"``
-            key is added when :class:`.SpaceWarper` is used.
+            found in ``target_data.reference``. The ``"reference"``
+            key is added if the :class:`.SpaceWarper` is used or if the
+            data is provided in native space.
         target_data : dict
             The corresponding item of the data object to which the parcellation
             will be applied.
@@ -87,6 +88,10 @@ class ANTsParcellationWarper:
             # Warp data check
             if warp_data is None:
                 raise_error("No `warp_data` provided")
+            if "reference" not in target_data:
+                raise_error("No `reference` provided")
+            if "path" not in target_data["reference"]:
+                raise_error("No `path` provided in `reference`")
 
             logger.debug("Using ANTs for parcellation transformation")
 
@@ -108,7 +113,7 @@ class ANTsParcellationWarper:
                 "-n 'GenericLabel[NearestNeighbor]'",
                 f"-i {prewarp_parcellation_path.resolve()}",
                 # use resampled reference
-                f"-r {target_data['reference_path'].resolve()}",
+                f"-r {target_data['reference']['path'].resolve()}",
                 f"-t {warp_data['path'].resolve()}",
                 f"-o {warped_parcellation_path.resolve()}",
             ]

junifer/data/parcellations/_fsl_parcellation_warper.py

@@ -78,7 +78,7 @@ class FSLParcellationWarper:
             "--interp=nn",
             f"-i {prewarp_parcellation_path.resolve()}",
             # use resampled reference
-            f"-r {target_data['reference_path'].resolve()}",
+            f"-r {target_data['reference']['path'].resolve()}",
             f"-w {warp_data['path'].resolve()}",
             f"-o {warped_parcellation_path.resolve()}",
         ]

junifer/datagrabber/pattern_validation_mixin.py

@@ -33,6 +33,8 @@ PATTERNS_SCHEMA = {
                 "mandatory": ["pattern", "format"],
                 "optional": ["mappings"],
             },
+            "reference": {"mandatory": ["pattern"], "optional": []},
+            "prewarp_space": {"mandatory": [], "optional": []},
         },
     },
     "Warp": {

junifer/preprocess/warping/_ants_warper.py

@@ -59,7 +59,7 @@ class ANTsWarper:
         -------
         dict
             The ``input`` dictionary with modified ``data`` and ``space`` key
-            values and new ``reference_path`` key whose value points to the
+            values and new ``reference`` key whose value points to the
             reference file used for warping.
 
         Raises
@@ -129,7 +129,7 @@ class ANTsWarper:
             # Load nifti
             input["data"] = nib.load(apply_transforms_out_path)
             # Save resampled reference path
-            input["reference_path"] = resample_image_out_path
+            input["reference"] = {"path": resample_image_out_path}
             # Keep pre-warp space for further operations
             input["prewarp_space"] = input["space"]
             # Use reference input's space as warped input's space

junifer/preprocess/warping/_fsl_warper.py

@@ -55,7 +55,7 @@ class FSLWarper:
         -------
         dict
             The ``input`` dictionary with modified ``data`` and ``space`` key
-            values and new ``reference_path`` key whose value points to the
+            values and new ``reference`` key whose value points to the
             reference file used for warping.
 
         Raises
@@ -116,7 +116,7 @@ class FSLWarper:
         # Load nifti
         input["data"] = nib.load(applywarp_out_path)
         # Save resampled reference path
-        input["reference_path"] = flirt_out_path
+        input["reference"] = {"path": flirt_out_path}
         # Keep pre-warp space for further operations
         input["prewarp_space"] = input["space"]
         # Use reference input's space as warped input's space

{junifer-0.0.6.dev299.dist-info → junifer-0.0.6.dev302.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: junifer
-Version: 0.0.6.dev299
+Version: 0.0.6.dev302
 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.dev299.dist-info → junifer-0.0.6.dev302.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=725_F3dOAgOL9Sw-MMC-B_RSYBVTStBAyk4cmIorMWI,428
+junifer/_version.py,sha256=6ivRaEJnq1nwi7sNAqQwwarVpyzKReHtuarvntATZ2E,428
 junifer/conftest.py,sha256=PWYkkRDU8ly2lYwv7VBKMHje4et6HX7Yey3Md_I2KbA,613
 junifer/py.typed,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 junifer/stats.py,sha256=e9aaagMGtgpRfW3Wdpz9ocpnYld1IWylCDcjFUgX9Mk,6225
@@ -81,7 +81,7 @@ junifer/data/coordinates/__init__.py,sha256=ffM8rwcHLgHAWixJbKrATrbUKzX940V1UF6R
 junifer/data/coordinates/__init__.pyi,sha256=Z-Ti5XD3HigkZ8uYN6oYsLqw40-F1GvTVQ5QAy08Wng,88
 junifer/data/coordinates/_ants_coordinates_warper.py,sha256=5RWDC-nI3VG9lkSJ-_y_hlDtjPctKSJokQOp3v8ozwY,2956
 junifer/data/coordinates/_coordinates.py,sha256=fBXVvuTxYLTNBSrQiTCiQsxpT0SdbQze3DYuGGgz_mY,12501
-junifer/data/coordinates/_fsl_coordinates_warper.py,sha256=GI0SrkNyAuRsoRSxI5WNvQmtPXQ3MlXvPx9lrd3NYB4,2406
+junifer/data/coordinates/_fsl_coordinates_warper.py,sha256=5h7rwiPMYBQlA3sMZUImcpnNLLWvIp2-bAEaaHtzX9c,2409
 junifer/data/coordinates/VOIs/meta/AutobiographicalMemory_VOIs.txt,sha256=9af38naeL18Tlt_gy_ep6vyTAxOB336JYjbo5FvP8PQ,686
 junifer/data/coordinates/VOIs/meta/CogAC_VOIs.txt,sha256=Sr5_E712OLdeQRyUcDNM0wLBvZIyO6gc9Q7KkyJHX1A,398
 junifer/data/coordinates/VOIs/meta/CogAR_VOIs.txt,sha256=t3NLwEVUZTPP34p15SaB3UInLrQyK-7Qc4iLBuQlZu8,189
@@ -104,8 +104,8 @@ 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=yGjC-b6Ui-MpPG3FpRnI8pEAxjMUfSSuUGVIeazjN7I,5078
-junifer/data/masks/_fsl_mask_warper.py,sha256=_7UkX3-wFXQs4KwxopO-QjMyB6aeq1GAkiGSGpG-OzM,2412
+junifer/data/masks/_ants_mask_warper.py,sha256=6ex2jxxKI5yA4G1rebSpcAYGGisflVK-DwhtUtWY964,5348
+junifer/data/masks/_fsl_mask_warper.py,sha256=VApp-ofGBKePNmCdgTg1HoEA66lMQiAPT0ihkhB2ezY,2415
 junifer/data/masks/_masks.py,sha256=96NKsSSosD6r03Jb2N1xQoyOc2Vl5miokcQdSeuM6SY,20729
 junifer/data/masks/tests/test_masks.py,sha256=1Zm09ZSdUlR278DTCZeVuxuQntryefsnYYPP02MttVE,16120
 junifer/data/masks/ukb/UKB_15K_GM_template.nii.gz,sha256=jcX1pDOrDsoph8cPMNFVKH5gZYio5G4rJNpOFXm9wJI,946636
@@ -114,8 +114,8 @@ 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=UBjO9W8jWcM8GK80pbIzORir60ZFAhLTttGtaaDNT2g,5530
-junifer/data/parcellations/_fsl_parcellation_warper.py,sha256=pUsLbR34Ry3e_0_5KxngI-jU06YmXTU795k-SjJHmig,2676
+junifer/data/parcellations/_ants_parcellation_warper.py,sha256=4CYieBer6ow4i8o4NjKsfufc96XdtsMGwfBbMF-Kw78,5802
+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
@@ -128,7 +128,7 @@ junifer/datagrabber/dmcc13_benchmark.py,sha256=VMyiwvkr4qSvzBICSksPPKOI2w_WVo06H
 junifer/datagrabber/multiple.py,sha256=4tCOzojs3hoG7daHJJ7HUsx15atWR5nTmyP0S0__aig,6666
 junifer/datagrabber/pattern.py,sha256=UwJQ0MObBIS6eHH9FfoM_sBYuNM9n5NAX7DA0HdtL1A,18709
 junifer/datagrabber/pattern_datalad.py,sha256=QPWXIToYHDU4mvm9lz_hy8BjdqqoCXiGiJKCcATrT-w,4568
-junifer/datagrabber/pattern_validation_mixin.py,sha256=MlcQIDyPHtqPcq1eHkwvrp-m5MhZaxTG1l2j3JM6FOc,19236
+junifer/datagrabber/pattern_validation_mixin.py,sha256=6IlL5EMbr-XEtiiXs_buD3DJkujjs335BmAgAiWGZ3M,19369
 junifer/datagrabber/py.typed,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 junifer/datagrabber/aomic/__init__.py,sha256=ATxzXq9NBPmWowTMuL77zqrmIbbnk0Wd1iXtXCP3XDg,266
 junifer/datagrabber/aomic/__init__.pyi,sha256=Rp6C075fZDdKY8VIq508_g4NhVj8bWzR6zb9yln761Q,189
@@ -294,8 +294,8 @@ 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=oJrTW_YG-VJ-piq_L1CX5fEoERyRtsMpFEQQ-0fUFMg,6502
-junifer/preprocess/warping/_fsl_warper.py,sha256=IV_vkn3TGDPWM_N-hEQv1YC4LYMTfZfDmuYu5MW_TQ8,3798
+junifer/preprocess/warping/_ants_warper.py,sha256=BHfweLDtq3J8NmgUFvA7bfWIN4kDvo0RiB1fNDJ71qw,6502
+junifer/preprocess/warping/_fsl_warper.py,sha256=yilHysV9t9bkBDK_eQzjROzlwhXStVzflCaEkxkwjlY,3798
 junifer/preprocess/warping/py.typed,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 junifer/preprocess/warping/space_warper.py,sha256=mf7SDu574R3TXNt82fqGl_hcEYx7SjXwz2TcmWObHQA,7706
 junifer/preprocess/warping/tests/test_space_warper.py,sha256=amFHtt-q7L7v9uL4cOvrmHEbUOGDhmoMHkLnKJ0dF7A,5543
@@ -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.dev299.dist-info/AUTHORS.rst,sha256=rmULKpchpSol4ExWFdm-qu4fkpSZPYqIESVJBZtGb6E,163
-junifer-0.0.6.dev299.dist-info/LICENSE.md,sha256=MqCnOBu8uXsEOzRZWh9EBVfVz-kE9NkXcLCrtGXo2yU,34354
-junifer-0.0.6.dev299.dist-info/METADATA,sha256=BJYB-ABLfZGsNi7s6U-r36VN0lNHYn83wbqsdQX-DbU,8429
-junifer-0.0.6.dev299.dist-info/WHEEL,sha256=PZUExdf71Ui_so67QXpySuHtCi3-J3wvF4ORK6k_S8U,91
-junifer-0.0.6.dev299.dist-info/entry_points.txt,sha256=6O8ru0BP-SP7YMUZiizFNoaZ2HvJpadO2G7nKk4PwjI,48
-junifer-0.0.6.dev299.dist-info/top_level.txt,sha256=4bAq1R2QFQ4b3hohjys2JBvxrl0GKk5LNFzYvz9VGcA,8
-junifer-0.0.6.dev299.dist-info/RECORD,,
+junifer-0.0.6.dev302.dist-info/AUTHORS.rst,sha256=rmULKpchpSol4ExWFdm-qu4fkpSZPYqIESVJBZtGb6E,163
+junifer-0.0.6.dev302.dist-info/LICENSE.md,sha256=MqCnOBu8uXsEOzRZWh9EBVfVz-kE9NkXcLCrtGXo2yU,34354
+junifer-0.0.6.dev302.dist-info/METADATA,sha256=-xzY1LfIMeHg8ism1hOUBXsfcyjaW58Mu1VuATPtKXY,8429
+junifer-0.0.6.dev302.dist-info/WHEEL,sha256=PZUExdf71Ui_so67QXpySuHtCi3-J3wvF4ORK6k_S8U,91
+junifer-0.0.6.dev302.dist-info/entry_points.txt,sha256=6O8ru0BP-SP7YMUZiizFNoaZ2HvJpadO2G7nKk4PwjI,48
+junifer-0.0.6.dev302.dist-info/top_level.txt,sha256=4bAq1R2QFQ4b3hohjys2JBvxrl0GKk5LNFzYvz9VGcA,8
+junifer-0.0.6.dev302.dist-info/RECORD,,