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chore: clarify datagrabber parameters
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-45
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9 files changed

+37
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‎junifer/configs/juseless/datagrabbers/ixi_vbm.py‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -42,7 +42,7 @@ class JuselessDataladIXIVBM(PatternDataladDataGrabber):
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That path where the datalad dataset will be cloned.
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If not specified, the datalad dataset will be cloned into a temporary
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directory.
45-
sites : :enum:`.IXISite` or list of variants, optional
45+
sites : {"Guys", "HH", "IOP"} or list of the options, optional
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IXI sites.
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By default, all available sites are selected.
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‎junifer/configs/juseless/datagrabbers/ucla.py‎

Lines changed: 5 additions & 4 deletions
Original file line numberDiff line numberDiff line change
@@ -63,11 +63,12 @@ class JuselessUCLA(PatternDataGrabber):
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datadir : Path, optional
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The directory where the dataset is stored.
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(default "/data/project/psychosis_thalamus/data/fmriprep").
66-
types: {``DataType.BOLD``, ``DataType.T1w``, \
67-
``DataType.VBM_CSF``, ``DataType.VBM_GM``, ``DataType.VBM_WM``} \
68-
or list of them, optional
66+
types: {"BOLD", "T1w", "VBM_CSF", "VBM_GM", "VBM_WM"} or \
67+
list of the options, optional
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The data type(s) to grab.
70-
tasks : :enum:`.UCLATask` or list of variants, optional
69+
tasks : {"rest", "bart", "bht", "pamenc", "pamret", \
70+
"scap", "taskswitch", "stopsignal"} or \
71+
list of the options, optional
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UCLA task sessions.
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By default, all available task are selected.
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‎junifer/datagrabber/aomic/id1000.py‎

Lines changed: 3 additions & 5 deletions
Original file line numberDiff line numberDiff line change
@@ -40,16 +40,14 @@ class DataladAOMICID1000(PatternDataladDataGrabber):
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Parameters
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----------
43-
types : {``DataType.BOLD``, ``DataType.T1w``, \
44-
``DataType.VBM_CSF``, ``DataType.VBM_GM``, ``DataType.VBM_WM``, \
45-
``DataType.DWI``, ``DataType.FreeSurfer``, ``DataType.Warp``} \
46-
or list of them, optional
43+
types : {"BOLD", "T1w", "VBM_CSF", "VBM_GM", "VBM_WM", "DWI", \
44+
"FreeSurfer", "Warp"} or list of the options, optional
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The data type(s) to grab.
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datadir : pathlib.Path, optional
4947
That path where the datalad dataset will be cloned.
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If not specified, the datalad dataset will be cloned into a temporary
5149
directory.
52-
space : :enum:`.AOMICSpace`, optional
50+
space : {"native", "MNI152NLin2009cAsym"}, optional
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AOMIC space (default ``AOMICSpace.MNI152NLin2009cAsym``).
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"""

‎junifer/datagrabber/aomic/piop1.py‎

Lines changed: 5 additions & 9 deletions
Original file line numberDiff line numberDiff line change
@@ -50,22 +50,18 @@ class DataladAOMICPIOP1(PatternDataladDataGrabber):
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Parameters
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----------
53-
types : {``DataType.BOLD``, ``DataType.T1w``, \
54-
``DataType.VBM_CSF``, ``DataType.VBM_GM``, ``DataType.VBM_WM``, \
55-
``DataType.DWI``, ``DataType.FreeSurfer``, ``DataType.Warp``} \
56-
or list of them, optional
53+
types : {"BOLD", "T1w", "VBM_CSF", "VBM_GM", "VBM_WM", "DWI", \
54+
"FreeSurfer", "Warp"} or list of the options, optional
5755
The data type(s) to grab.
5856
datadir : pathlib.Path, optional
5957
That path where the datalad dataset will be cloned.
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If not specified, the datalad dataset will be cloned into a temporary
6159
directory.
62-
tasks : {``AOMICTask.RestingState``, ``AOMICTask.Anticipation``, \
63-
``AOMICTask.EmoMatching``, ``AOMICTask.Faces``, \
64-
``AOMICTask.Gstroop``, ``AOMICTask.WorkingMemory``} or \
65-
list of them, optional
60+
tasks : {"restingstate", "anticipation", "emomatching", "faces", \
61+
"gstroop", "workingmemory"} or list of the options, optional
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AOMIC PIOP1 task sessions.
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By default, all available task sessions are selected.
68-
space : :enum:`.AOMICSpace`, optional
64+
space : {"native", "MNI152NLin2009cAsym"}, optional
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AOMIC space (default ``AOMICSpace.MNI152NLin2009cAsym``).
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"""

‎junifer/datagrabber/aomic/piop2.py‎

Lines changed: 5 additions & 8 deletions
Original file line numberDiff line numberDiff line change
@@ -48,21 +48,18 @@ class DataladAOMICPIOP2(PatternDataladDataGrabber):
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Parameters
5050
----------
51-
types : {``DataType.BOLD``, ``DataType.T1w``, \
52-
``DataType.VBM_CSF``, ``DataType.VBM_GM``, ``DataType.VBM_WM``, \
53-
``DataType.DWI``, ``DataType.FreeSurfer``, ``DataType.Warp``} \
54-
or list of them, optional
51+
types : {"BOLD", "T1w", "VBM_CSF", "VBM_GM", "VBM_WM", "DWI", \
52+
"FreeSurfer", "Warp"} or list of the options, optional
5553
The data type(s) to grab.
5654
datadir : pathlib.Path, optional
5755
That path where the datalad dataset will be cloned.
5856
If not specified, the datalad dataset will be cloned into a temporary
5957
directory.
60-
tasks : list of {``AOMICTask.RestingState``, ``AOMICTask.StopSignal``, \
61-
``AOMICTask.WorkingMemory``, ``AOMICTask.EmoMatching``} or \
62-
list of them, optional
58+
tasks : {"restingstate", "stopsignal", "workingmemory", "emomatching"} or \
59+
list of the options, optional
6360
AOMIC PIOP2 task sessions.
6461
By default, all available task sessions are selected.
65-
space : :enum:`.AOMICSpace`, optional
62+
space : {"native", "MNI152NLin2009cAsym"}, optional
6663
AOMIC space (default ``AOMICSpace.MNI152NLin2009cAsym``).
6764
6865
"""

‎junifer/datagrabber/dmcc13_benchmark.py‎

Lines changed: 8 additions & 7 deletions
Original file line numberDiff line numberDiff line change
@@ -98,24 +98,25 @@ class DMCC13Benchmark(PatternDataladDataGrabber):
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Parameters
100100
----------
101-
types : {``DataType.BOLD``, ``DataType.T1w``, \
102-
``DataType.VBM_CSF``, ``DataType.VBM_GM``, ``DataType.VBM_WM``, \
103-
``DataType.Warp``} or list of them, optional
101+
types : {"BOLD", "T1w", "VBM_CSF", "VBM_GM", "VBM_WM", "Warp"} or \
102+
list of the options, optional
104103
The data type(s) to grab.
105104
datadir : pathlib.Path, optional
106105
That path where the datalad dataset will be cloned.
107106
If not specified, the datalad dataset will be cloned into a temporary
108107
directory.
109-
sessions : :enum:`.DMCCSession` or list of variants, optional
108+
sessions : {"ses-wave1bas", "ses-wave1pro", "ses-wave1rea"} or \
109+
list of the options, optional
110110
DMCC sessions.
111111
By default, all available sessions are selected.
112-
tasks : :enum:`.DMCCTask` or list of variants, optional
112+
tasks : {"Rest", "Axcpt", "Cuedts", "Stern", "Stroop"} or \
113+
list of the options, optional
113114
DMCC tasks.
114115
By default, all available tasks are selected.
115-
phase_encodings : :enum:`.DMCCPhaseEncoding` or list of variants, optional
116+
phase_encodings : {"AP", "PA"} or list of the options, optional
116117
DMCC phase encoding directions.
117118
By default, all available phase encodings are selected.
118-
runs : :enum:`.DMCCRun` or list of variants, optional
119+
runs : {"1", "2"} or list of the options, optional
119120
DMCC runs.
120121
By default, all available runs are selected.
121122
native_t1w : bool, optional

‎junifer/datagrabber/hcp1200/datalad_hcp1200.py‎

Lines changed: 4 additions & 4 deletions
Original file line numberDiff line numberDiff line change
@@ -29,17 +29,17 @@ class DataladHCP1200(DataladDataGrabber, HCP1200):
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Parameters
3131
----------
32-
types : {``DataType.BOLD``, ``DataType.T1w``, ``DataType.Warp``} \
33-
or list of them, optional
32+
types : {"BOLD", "T1w", "Warp"} or list of the options, optional
3433
The data type(s) to grab.
3534
datadir : pathlib.Path, optional
3635
That path where the datalad dataset will be cloned.
3736
If not specified, the datalad dataset will be cloned into a temporary
3837
directory.
39-
tasks : list of :enum:`.HCP1200Task`, optional
38+
tasks : {"REST1", "REST2", "SOCIAL", "WM", "RELATIONAL", "EMOTION", \
39+
"LANGUAGE", "GAMBLING", "MOTOR"} or list of the options, optional
4040
HCP task sessions.
4141
By default, all available task sessions are selected.
42-
phase_encodings : list of :enum:`.HCP1200PhaseEncoding`, optional
42+
phase_encodings : {"LR", "RL"} or list of the options, optional
4343
HCP phase encoding directions.
4444
By default, all are used.
4545
ica_fix : bool, optional

‎junifer/datagrabber/hcp1200/hcp1200.py‎

Lines changed: 4 additions & 5 deletions
Original file line numberDiff line numberDiff line change
@@ -68,16 +68,15 @@ class HCP1200(PatternDataGrabber):
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Parameters
7070
----------
71-
types : {``DataType.BOLD``, ``DataType.T1w``, ``DataType.Warp``} \
72-
or list of them, optional
71+
types : {"BOLD", "T1w", "Warp"} or list of the options, optional
7372
The data type(s) to grab.
7473
datadir : pathlib.Path
7574
The path where the data is stored.
76-
tasks : :enum:`.HCP1200Task` or list of variants, optional
75+
tasks : {"REST1", "REST2", "SOCIAL", "WM", "RELATIONAL", "EMOTION", \
76+
"LANGUAGE", "GAMBLING", "MOTOR"} or list of the options, optional
7777
HCP task sessions.
7878
By default, all available task sessions are selected.
79-
phase_encodings : :enum:`.HCP1200PhaseEncoding` or list of variants, \
80-
optional
79+
phase_encodings : {"LR", "RL"} or list of the options, optional
8180
HCP phase encoding directions.
8281
By default, all are used.
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ica_fix : bool, optional

‎junifer/testing/datagrabbers.py‎

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -179,8 +179,8 @@ class PartlyCloudyTestingDataGrabber(BaseDataGrabber):
179179
purpose of having realistic examples. Depending on your research
180180
question, other confounds might be more appropriate.
181181
If False, returns all :term:`fMRIPrep` confounds (default True).
182-
age_group : :enum:`.PartlyCloudyAgeGroup`, optional
183-
Age group to fetch (default PartlyCloudyAgeGroup.Both).
182+
age_group : {"adult", "child", "both"}, optional
183+
Age group to fetch (default ``PartlyCloudyAgeGroup.Both``).
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"""
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