junifer 0.0.6.dev227__py3-none-any.whl → 0.0.6.dev248__py3-none-any.whl
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- junifer/_version.py +2 -2
- junifer/data/coordinates/_ants_coordinates_warper.py +4 -6
- junifer/data/coordinates/_coordinates.py +28 -15
- junifer/data/coordinates/_fsl_coordinates_warper.py +4 -6
- junifer/data/masks/_ants_mask_warper.py +16 -9
- junifer/data/masks/_fsl_mask_warper.py +4 -6
- junifer/data/masks/_masks.py +21 -25
- junifer/data/parcellations/_ants_parcellation_warper.py +16 -9
- junifer/data/parcellations/_fsl_parcellation_warper.py +4 -6
- junifer/data/parcellations/_parcellations.py +20 -24
- junifer/data/utils.py +67 -3
- junifer/datagrabber/aomic/id1000.py +22 -9
- junifer/datagrabber/aomic/piop1.py +22 -9
- junifer/datagrabber/aomic/piop2.py +22 -9
- junifer/datagrabber/base.py +6 -1
- junifer/datagrabber/datalad_base.py +15 -8
- junifer/datagrabber/dmcc13_benchmark.py +23 -10
- junifer/datagrabber/hcp1200/hcp1200.py +18 -7
- junifer/datagrabber/pattern.py +65 -35
- junifer/datagrabber/pattern_validation_mixin.py +197 -87
- junifer/datagrabber/tests/test_dmcc13_benchmark.py +26 -9
- junifer/pipeline/pipeline_step_mixin.py +8 -4
- junifer/pipeline/update_meta_mixin.py +21 -17
- junifer/preprocess/warping/_ants_warper.py +23 -2
- junifer/preprocess/warping/_fsl_warper.py +19 -3
- junifer/preprocess/warping/space_warper.py +31 -4
- {junifer-0.0.6.dev227.dist-info → junifer-0.0.6.dev248.dist-info}/METADATA +1 -1
- {junifer-0.0.6.dev227.dist-info → junifer-0.0.6.dev248.dist-info}/RECORD +33 -33
- {junifer-0.0.6.dev227.dist-info → junifer-0.0.6.dev248.dist-info}/WHEEL +1 -1
- {junifer-0.0.6.dev227.dist-info → junifer-0.0.6.dev248.dist-info}/AUTHORS.rst +0 -0
- {junifer-0.0.6.dev227.dist-info → junifer-0.0.6.dev248.dist-info}/LICENSE.md +0 -0
- {junifer-0.0.6.dev227.dist-info → junifer-0.0.6.dev248.dist-info}/entry_points.txt +0 -0
- {junifer-0.0.6.dev227.dist-info → junifer-0.0.6.dev248.dist-info}/top_level.txt +0 -0
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@@ -24,11 +24,12 @@ class SpaceWarper(BasePreprocessor):
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Parameters
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----------
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using : {"fsl", "ants"}
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using : {"fsl", "ants", "auto"}
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Implementation to use for warping:
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* "fsl" : Use FSL's ``applywarp``
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* "ants" : Use ANTs' ``antsApplyTransforms``
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* "auto" : Auto-select tool when ``reference="T1w"``
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reference : str
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The data type to use as reference for warping, can be either a data
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@@ -56,6 +57,10 @@ class SpaceWarper(BasePreprocessor):
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"using": "ants",
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"depends_on": ANTsWarper,
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},
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{
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"using": "auto",
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"depends_on": [FSLWarper, ANTsWarper],
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},
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]
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def __init__(
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@@ -156,14 +161,16 @@ class SpaceWarper(BasePreprocessor):
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If ``extra_input`` is None when transforming to native space
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i.e., using ``"T1w"`` as reference.
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RuntimeError
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If
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If warper could not be found in ``extra_input`` when
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``using="auto"`` or
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if the data is in the correct space and does not require
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warping or
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if FSL is used
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if FSL is used when ``reference="T1w"``.
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"""
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logger.info(f"Warping to {self.reference} space using SpaceWarper")
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# Transform to native space
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if self.using in ["fsl", "ants"] and self.reference == "T1w":
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if self.using in ["fsl", "ants", "auto"] and self.reference == "T1w":
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# Check for extra inputs
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if extra_input is None:
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raise_error(
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@@ -182,6 +189,26 @@ class SpaceWarper(BasePreprocessor):
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extra_input=extra_input,
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reference=self.reference,
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)
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elif self.using == "auto":
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warper = None
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for entry in extra_input["Warp"]:
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if entry["dst"] == "native":
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warper = entry["warper"]
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if warper is None:
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raise_error(
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klass=RuntimeError, msg="Could not find correct warper"
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)
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if warper == "fsl":
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input = FSLWarper().preprocess(
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input=input,
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extra_input=extra_input,
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)
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elif warper == "ants":
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input = ANTsWarper().preprocess(
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input=input,
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extra_input=extra_input,
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reference=self.reference,
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)
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# Transform to template space with ANTs possible
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elif self.using == "ants" and self.reference != "T1w":
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# Check pre-requirements for space manipulation
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@@ -1,6 +1,6 @@
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Metadata-Version: 2.1
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Name: junifer
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Version: 0.0.6.
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Version: 0.0.6.dev248
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Summary: JUelich NeuroImaging FEature extractoR
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Author-email: Fede Raimondo <f.raimondo@fz-juelich.de>, Synchon Mandal <s.mandal@fz-juelich.de>
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Maintainer-email: Fede Raimondo <f.raimondo@fz-juelich.de>, Synchon Mandal <s.mandal@fz-juelich.de>
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junifer/__init__.py,sha256=2McgH1yNue6Z1V26-uN_mfMjbTcx4CLhym-DMBl5xA4,266
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junifer/__init__.pyi,sha256=SsTvgq2Dod6UqJN96GH1lCphH6hJQQurEJHGNhHjGUI,508
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junifer/_version.py,sha256=
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junifer/_version.py,sha256=c9at3dTDJliiVXJD4N375bgGPl2MVMwHVvZh9Sx-SO0,428
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junifer/conftest.py,sha256=PWYkkRDU8ly2lYwv7VBKMHje4et6HX7Yey3Md_I2KbA,613
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junifer/py.typed,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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junifer/stats.py,sha256=BjQb2lfTGDP9l4UuQYmJFcJJNRfbJDGlNvC06SJaDDE,6237
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@@ -76,12 +76,12 @@ junifer/data/_dispatch.py,sha256=_hmlIXuuuLJBbY5VH6lohJzhbMB7KEhFkVFwRDEdR_E,618
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junifer/data/pipeline_data_registry_base.py,sha256=8UyrkXHVr7JdeVfD2xgIRQlrlH3lR2RLHUfnqbw0EyI,1989
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junifer/data/py.typed,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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junifer/data/template_spaces.py,sha256=9uZuFztBGNZk3mhUI2h0oQMajjx6Wv31Fx11pGlDI20,6510
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junifer/data/utils.py,sha256=
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junifer/data/utils.py,sha256=hfzx4QZRuP4JLADU13LWYFRPEsTz6Kg5XDCLxlWZ6kQ,3232
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junifer/data/coordinates/__init__.py,sha256=ffM8rwcHLgHAWixJbKrATrbUKzX940V1UF6RAxZdUMg,186
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junifer/data/coordinates/__init__.pyi,sha256=Z-Ti5XD3HigkZ8uYN6oYsLqw40-F1GvTVQ5QAy08Wng,88
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junifer/data/coordinates/_ants_coordinates_warper.py,sha256=
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junifer/data/coordinates/_coordinates.py,sha256=
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junifer/data/coordinates/_fsl_coordinates_warper.py,sha256=
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junifer/data/coordinates/_ants_coordinates_warper.py,sha256=Jhvw8Mzi53U5a_74s5y7RCgcrIGv-WDX4s7hlAUqupc,2660
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junifer/data/coordinates/_coordinates.py,sha256=t2yflc1aJ_xXPRfyfxcF0V9_AjAYPMPSyIS_jAzek-8,12512
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junifer/data/coordinates/_fsl_coordinates_warper.py,sha256=4L-82CEka58PxTJxQ6H_17xvow9w8EQ9Id04zo8c-cs,2412
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junifer/data/coordinates/VOIs/meta/AutobiographicalMemory_VOIs.txt,sha256=9af38naeL18Tlt_gy_ep6vyTAxOB336JYjbo5FvP8PQ,686
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junifer/data/coordinates/VOIs/meta/CogAC_VOIs.txt,sha256=Sr5_E712OLdeQRyUcDNM0wLBvZIyO6gc9Q7KkyJHX1A,398
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junifer/data/coordinates/VOIs/meta/CogAR_VOIs.txt,sha256=t3NLwEVUZTPP34p15SaB3UInLrQyK-7Qc4iLBuQlZu8,189
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junifer/data/coordinates/tests/test_coordinates.py,sha256=_c2P4oaDGpsmui5gJBe_jN6HLGiKxONkYPR69sRBUlU,4219
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junifer/data/masks/__init__.py,sha256=eEEhHglyVEx1LrqwXjq3cOmjf4sTsgBstRx5-k7zIQU,180
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junifer/data/masks/__init__.pyi,sha256=lcgr8gmWDPibC4RxnWBXb8DDpIkO73Aax09u6VXiJJI,114
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junifer/data/masks/_ants_mask_warper.py,sha256=CkvNZobIQLepvN7PJEEqr0sSM69wSLkXduH3Z0kS-XI,5084
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junifer/data/masks/_fsl_mask_warper.py,sha256=t6dovcUi6grYxv9nW4uo5vqebuyNXJLWikRmYWUUQA4,2418
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junifer/data/masks/_masks.py,sha256=fTudLOKXDweqPjt2sIMk8iWHACgi89HA2JK2z83vkdA,20760
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junifer/data/masks/tests/test_masks.py,sha256=RDYe8Z46M_hHdZn3hOvdqQXqiMlxJ6454gD3d1ee3zM,16132
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junifer/data/masks/ukb/UKB_15K_GM_template.nii.gz,sha256=jcX1pDOrDsoph8cPMNFVKH5gZYio5G4rJNpOFXm9wJI,946636
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junifer/data/masks/vickery-patil/CAT12_IXI555_MNI152_TMP_GS_GMprob0.2_clean.nii.gz,sha256=j6EY8EtRnUuRxeKgD65Q6B0GPEPIALKDJEIje1TfnAU,88270
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junifer/data/masks/vickery-patil/GMprob0.2_cortex_3mm_NA_rm.nii.gz,sha256=jfMe_4H9XEnArYms5bSQbqS2V1_HbLHTfI5amQa_Pes,8700
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junifer/data/parcellations/__init__.py,sha256=6-Ysil3NyZ69V6rWx4RO15_d-iDKizfbHuxSjsHNt24,188
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junifer/data/parcellations/__init__.pyi,sha256=lhBHTbMDizzqUqVHrx2eyfPFodrTBgMFeTgxfESSkQ8,140
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junifer/data/parcellations/_ants_parcellation_warper.py,sha256=KMvweP7BnTEd3RiGHr3GTzNo0Ui7kAdIQS19cwLALss,5536
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junifer/data/parcellations/_fsl_parcellation_warper.py,sha256=9CwDczMswxzRK5eQICm0Tgvfy1xDNmdEWAe5yC3zbr0,2682
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junifer/data/parcellations/_parcellations.py,sha256=ReJAxkdR6Nn8LHKaHvk3NyC_GuMX4SOL8tolZon_JhM,65630
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junifer/data/parcellations/tests/test_parcellations.py,sha256=43h7lR7nEvo9vTK-AeUDMk0XdGTqyzQI8isYl8dWw6s,38339
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junifer/data/tests/test_data_utils.py,sha256=_DaiC8K79gs9HFHxr-udNeE2YTM6JA0-1i-K2cqK9qA,1087
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junifer/data/tests/test_template_spaces.py,sha256=PJulN7xHpAcSOTY-UzTG_WPywZEBSlAZGiNG4gzk1_8,3144
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junifer/datagrabber/__init__.py,sha256=EHIK-lbjuvkt0V8ypFvLSt85OAAXSkaxBmVlCbNNz8M,323
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junifer/datagrabber/__init__.pyi,sha256=zOQE4TaCKXBTHnNqgmECtsszWIOHYiQ1CUEeXXFU9F4,832
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junifer/datagrabber/base.py,sha256=Bvuj01FBg-p9z_0WYdrIo91lhQBh99k94ccoYlWtNdI,6753
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junifer/datagrabber/datalad_base.py,sha256=Pi9lFSfjwJpLd5ej_vhG1lP1fSQDyOJ_UCevIgjPqJ8,11428
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junifer/datagrabber/dmcc13_benchmark.py,sha256=wByHdLJRhTVWbWbVSKFT5g0hxz_joNrZwapnRQCUw10,12831
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junifer/datagrabber/multiple.py,sha256=OgGKMQCyET4R_19s0DYNXrzvXIWYoNCktZivE1SeTAI,6524
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junifer/datagrabber/pattern_datalad.py,sha256=QPWXIToYHDU4mvm9lz_hy8BjdqqoCXiGiJKCcATrT-w,4568
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junifer/datagrabber/pattern_validation_mixin.py,sha256=1r7OcsR0W6AgHjTQD-LzRMfwwhyunEUravQ9poepOOQ,19302
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junifer/datagrabber/aomic/__init__.py,sha256=ATxzXq9NBPmWowTMuL77zqrmIbbnk0Wd1iXtXCP3XDg,266
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junifer/datagrabber/aomic/__init__.pyi,sha256=Rp6C075fZDdKY8VIq508_g4NhVj8bWzR6zb9yln761Q,189
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junifer/datagrabber/aomic/id1000.py,sha256=n7Y9As2W-yhpmKE930yM7YOhCdMmJhDENPDHDB7Zz14,7820
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junifer/datagrabber/aomic/piop1.py,sha256=S3G68Ayo0QbZ6VNrc0aEm-xb7TV1czRQ2-O1DlKRr30,10238
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junifer/datagrabber/aomic/piop2.py,sha256=30oo1qBuOAYlXJ8LO8tTJ6EcjDb-xormVJu3iBtIjgg,9899
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junifer/datagrabber/aomic/tests/test_id1000.py,sha256=AWacDroSxvRjzozFjyRlDpiJpPflYRfhDm_RANrYAKM,3283
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junifer/datagrabber/hcp1200/datalad_hcp1200.py,sha256=hngQYLv4b8tC9Ep2X5A5R_L2sFM3ZJ8dmWTr_OlRLAA,2463
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