junifer 0.0.4.dev782__py3-none-any.whl → 0.0.4.dev810__py3-none-any.whl
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- junifer/_version.py +2 -2
- junifer/configs/juseless/datagrabbers/aomic_id1000_vbm.py +6 -1
- junifer/configs/juseless/datagrabbers/camcan_vbm.py +6 -1
- junifer/configs/juseless/datagrabbers/ixi_vbm.py +6 -1
- junifer/configs/juseless/datagrabbers/ucla.py +42 -24
- junifer/configs/juseless/datagrabbers/ukb_vbm.py +6 -1
- junifer/datagrabber/aomic/id1000.py +98 -91
- junifer/datagrabber/aomic/piop1.py +97 -73
- junifer/datagrabber/aomic/piop2.py +97 -73
- junifer/datagrabber/base.py +6 -4
- junifer/datagrabber/datalad_base.py +0 -2
- junifer/datagrabber/dmcc13_benchmark.py +87 -50
- junifer/datagrabber/hcp1200/hcp1200.py +21 -19
- junifer/datagrabber/pattern.py +124 -25
- junifer/datagrabber/pattern_datalad.py +111 -13
- junifer/datagrabber/tests/test_base.py +0 -6
- junifer/datagrabber/tests/test_datagrabber_utils.py +204 -76
- junifer/datagrabber/tests/test_datalad_base.py +0 -6
- junifer/datagrabber/tests/test_multiple.py +43 -10
- junifer/datagrabber/tests/test_pattern.py +125 -178
- junifer/datagrabber/tests/test_pattern_datalad.py +44 -25
- junifer/datagrabber/utils.py +141 -21
- junifer/datareader/default.py +6 -7
- {junifer-0.0.4.dev782.dist-info → junifer-0.0.4.dev810.dist-info}/METADATA +1 -1
- {junifer-0.0.4.dev782.dist-info → junifer-0.0.4.dev810.dist-info}/RECORD +30 -30
- {junifer-0.0.4.dev782.dist-info → junifer-0.0.4.dev810.dist-info}/AUTHORS.rst +0 -0
- {junifer-0.0.4.dev782.dist-info → junifer-0.0.4.dev810.dist-info}/LICENSE.md +0 -0
- {junifer-0.0.4.dev782.dist-info → junifer-0.0.4.dev810.dist-info}/WHEEL +0 -0
- {junifer-0.0.4.dev782.dist-info → junifer-0.0.4.dev810.dist-info}/entry_points.txt +0 -0
- {junifer-0.0.4.dev782.dist-info → junifer-0.0.4.dev810.dist-info}/top_level.txt +0 -0
junifer/_version.py
CHANGED
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@@ -12,5 +12,5 @@ __version__: str
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__version_tuple__: VERSION_TUPLE
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version_tuple: VERSION_TUPLE
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__version__ = version = '0.0.4.
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__version_tuple__ = version_tuple = (0, 0, 4, '
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__version__ = version = '0.0.4.dev810'
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__version_tuple__ = version_tuple = (0, 0, 4, 'dev810')
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@@ -31,7 +31,12 @@ class JuselessDataladAOMICID1000VBM(PatternDataladDataGrabber):
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types = ["VBM_GM"]
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replacements = ["subject"]
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patterns = {
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"VBM_GM":
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"VBM_GM": {
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"pattern": (
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"sub-{subject}/mri/mwp1sub-{subject}_run-2_T1w.nii.gz"
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),
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"space": "IXI549Space",
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},
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}
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super().__init__(
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types=types,
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)
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types = ["VBM_GM"]
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replacements = ["subject"]
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patterns = {
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patterns = {
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"VBM_GM": {
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"pattern": "sub-{subject}/mri/m0wp1sub-{subject}.nii.gz",
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"space": "IXI549Space",
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},
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}
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super().__init__(
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types=types,
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datadir=datadir,
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@@ -43,7 +43,12 @@ class JuselessDataladIXIVBM(PatternDataladDataGrabber):
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types = ["VBM_GM"]
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replacements = ["site", "subject"]
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patterns = {
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"VBM_GM":
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"VBM_GM": {
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"pattern": (
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"{site}/sub-{subject}/mri/m0wp1sub-{subject}.nii.gz"
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"space": "IXI549Space",
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# validate and/or transform 'site' input
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self.tasks = tasks
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# The patterns
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patterns = {
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"MNI152NLin2009cAsym_preproc.nii.gz"
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"space": "MNI152NLin2009cAsym",
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},
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"BOLD_confounds": {
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"pattern": (
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"space": "fmriprep",
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},
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"T1w": {
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"pattern": (
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"space": "MNI152NLin2009cAsym",
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},
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"probseg_CSF": {
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"pattern": (
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"sub-{subject}/anat/sub-{subject}_T1w_space-"
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"space": "MNI152NLin2009cAsym",
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},
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"probseg_GM": {
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"pattern": (
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"sub-{subject}/anat/sub-{subject}_T1w_space-"
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"MNI152NLin2009cAsym_class-GM_probtissue.nii.gz"
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"space": "MNI152NLin2009cAsym",
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},
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"probseg_WM": {
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"pattern": (
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"sub-{subject}/anat/sub-{subject}_T1w_space"
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"-MNI152NLin2009cAsym_class-WM_probtissue.nii.gz"
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"space": "MNI152NLin2009cAsym",
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},
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# Set default types
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if types is None:
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rootdir = "m0wp1"
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types = ["VBM_GM"]
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replacements = ["subject", "session"]
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patterns = {
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patterns = {
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"VBM_GM": {
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"pattern": "m0wp1sub-{subject}_ses-{session}_T1w.nii.gz",
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"space": "IXI549Space",
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},
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}
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super().__init__(
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datadir=datadir,
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# License: AGPL
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from pathlib import Path
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from typing import
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from typing import List, Union
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from ...api.decorators import register_datagrabber
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from ..pattern_datalad import PatternDataladDataGrabber
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# The patterns
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# Set default types
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# Use native T1w assets
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self.native_t1w = False
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@@ -128,19 +156,30 @@ class DataladAOMICPIOP1(PatternDataladDataGrabber):
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{
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),
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},
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}
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)
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|
# Set default types
|
|
@@ -192,22 +231,7 @@ class DataladAOMICPIOP1(PatternDataladDataGrabber):
|
|
|
192
231
|
acq = task_acqs[task]
|
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193
232
|
new_task = f"{task}_acq-{acq}"
|
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194
233
|
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|
-
|
|
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|
-
if out.get("BOLD"):
|
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|
-
out["BOLD"]["mask_item"] = "BOLD_mask"
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|
-
# Add space information
|
|
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|
-
out["BOLD"].update({"space": "MNI152NLin2009cAsym"})
|
|
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|
-
if out.get("T1w"):
|
|
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|
-
out["T1w"]["mask_item"] = "T1w_mask"
|
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|
-
# Add space information
|
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|
-
if self.native_t1w:
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204
|
-
out["T1w"].update({"space": "native"})
|
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205
|
-
else:
|
|
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|
-
out["T1w"].update({"space": "MNI152NLin2009cAsym"})
|
|
207
|
-
if out.get("Warp"):
|
|
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|
-
# Add source space information
|
|
209
|
-
out["Warp"].update({"src": "MNI152NLin2009cAsym"})
|
|
210
|
-
return out
|
|
234
|
+
return super().get_item(subject=subject, task=new_task)
|
|
211
235
|
|
|
212
236
|
def get_elements(self) -> List:
|
|
213
237
|
"""Implement fetching list of subjects in the dataset.
|