junifer 0.0.4.dev824__py3-none-any.whl → 0.0.4.dev831__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.
Files changed (25) hide show
  1. junifer/_version.py +2 -2
  2. junifer/configs/juseless/datagrabbers/aomic_id1000_vbm.py +1 -1
  3. junifer/configs/juseless/datagrabbers/camcan_vbm.py +1 -1
  4. junifer/configs/juseless/datagrabbers/ixi_vbm.py +1 -1
  5. junifer/configs/juseless/datagrabbers/ucla.py +6 -6
  6. junifer/configs/juseless/datagrabbers/ukb_vbm.py +1 -1
  7. junifer/data/tests/test_masks.py +2 -2
  8. junifer/datagrabber/aomic/id1000.py +24 -24
  9. junifer/datagrabber/aomic/piop1.py +25 -25
  10. junifer/datagrabber/aomic/piop2.py +25 -25
  11. junifer/datagrabber/aomic/tests/test_id1000.py +7 -7
  12. junifer/datagrabber/aomic/tests/test_piop1.py +7 -7
  13. junifer/datagrabber/aomic/tests/test_piop2.py +7 -7
  14. junifer/datagrabber/dmcc13_benchmark.py +45 -45
  15. junifer/datagrabber/tests/test_dmcc13_benchmark.py +33 -33
  16. junifer/preprocess/ants/tests/test_ants_apply_transforms_warper.py +2 -2
  17. junifer/preprocess/tests/test_bold_warper.py +6 -6
  18. junifer/preprocess/warping/tests/test_space_warper.py +6 -6
  19. {junifer-0.0.4.dev824.dist-info → junifer-0.0.4.dev831.dist-info}/METADATA +1 -1
  20. {junifer-0.0.4.dev824.dist-info → junifer-0.0.4.dev831.dist-info}/RECORD +25 -25
  21. {junifer-0.0.4.dev824.dist-info → junifer-0.0.4.dev831.dist-info}/AUTHORS.rst +0 -0
  22. {junifer-0.0.4.dev824.dist-info → junifer-0.0.4.dev831.dist-info}/LICENSE.md +0 -0
  23. {junifer-0.0.4.dev824.dist-info → junifer-0.0.4.dev831.dist-info}/WHEEL +0 -0
  24. {junifer-0.0.4.dev824.dist-info → junifer-0.0.4.dev831.dist-info}/entry_points.txt +0 -0
  25. {junifer-0.0.4.dev824.dist-info → junifer-0.0.4.dev831.dist-info}/top_level.txt +0 -0
junifer/_version.py CHANGED
@@ -12,5 +12,5 @@ __version__: str
12
12
  __version_tuple__: VERSION_TUPLE
13
13
  version_tuple: VERSION_TUPLE
14
14
 
15
- __version__ = version = '0.0.4.dev824'
16
- __version_tuple__ = version_tuple = (0, 0, 4, 'dev824')
15
+ __version__ = version = '0.0.4.dev831'
16
+ __version_tuple__ = version_tuple = (0, 0, 4, 'dev831')
junifer/configs/juseless/datagrabbers/aomic_id1000_vbm.py CHANGED
@@ -33,7 +33,7 @@ class JuselessDataladAOMICID1000VBM(PatternDataladDataGrabber):
33
33
  patterns = {
34
34
  "VBM_GM": {
35
35
  "pattern": (
36
- "sub-{subject}/mri/mwp1sub-{subject}_run-2_T1w.nii.gz"
36
+ "{subject}/mri/mwp1{subject}_run-2_T1w.nii.gz"
37
37
  ),
38
38
  "space": "IXI549Space",
39
39
  },
junifer/configs/juseless/datagrabbers/camcan_vbm.py CHANGED
@@ -36,7 +36,7 @@ class JuselessDataladCamCANVBM(PatternDataladDataGrabber):
36
36
  replacements = ["subject"]
37
37
  patterns = {
38
38
  "VBM_GM": {
39
- "pattern": "sub-{subject}/mri/m0wp1sub-{subject}.nii.gz",
39
+ "pattern": "{subject}/mri/m0wp1{subject}.nii.gz",
40
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  "space": "IXI549Space",
41
41
  },
42
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  }
junifer/configs/juseless/datagrabbers/ixi_vbm.py CHANGED
@@ -45,7 +45,7 @@ class JuselessDataladIXIVBM(PatternDataladDataGrabber):
45
45
  patterns = {
46
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  "VBM_GM": {
47
47
  "pattern": (
48
- "{site}/sub-{subject}/mri/m0wp1sub-{subject}.nii.gz"
48
+ "{site}/{subject}/mri/m0wp1{subject}.nii.gz"
49
49
  ),
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  "space": "IXI549Space",
51
51
  },
junifer/configs/juseless/datagrabbers/ucla.py CHANGED
@@ -72,42 +72,42 @@ class JuselessUCLA(PatternDataGrabber):
72
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  patterns = {
73
73
  "BOLD": {
74
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  "pattern": (
75
- "sub-{subject}/func/sub-{subject}_task-{task}_bold_space-"
75
+ "{subject}/func/{subject}_task-{task}_bold_space-"
76
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  "MNI152NLin2009cAsym_preproc.nii.gz"
77
77
  ),
78
78
  "space": "MNI152NLin2009cAsym",
79
79
  },
80
80
  "BOLD_confounds": {
81
81
  "pattern": (
82
- "sub-{subject}/func/sub-{subject}_"
82
+ "{subject}/func/{subject}_"
83
83
  "task-{task}_bold_confounds.tsv"
84
84
  ),
85
85
  "space": "fmriprep",
86
86
  },
87
87
  "T1w": {
88
88
  "pattern": (
89
- "sub-{subject}/anat/sub-{subject}_"
89
+ "{subject}/anat/{subject}_"
90
90
  "T1w_space-MNI152NLin2009cAsym_preproc.nii.gz"
91
91
  ),
92
92
  "space": "MNI152NLin2009cAsym",
93
93
  },
94
94
  "VBM_CSF": {
95
95
  "pattern": (
96
- "sub-{subject}/anat/sub-{subject}_T1w_space-"
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+ "{subject}/anat/{subject}_T1w_space-"
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  "MNI152NLin2009cAsym_class-CSF_probtissue.nii.gz"
98
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  ),
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  "space": "MNI152NLin2009cAsym",
100
100
  },
101
101
  "VBM_GM": {
102
102
  "pattern": (
103
- "sub-{subject}/anat/sub-{subject}_T1w_space-"
103
+ "{subject}/anat/{subject}_T1w_space-"
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  "MNI152NLin2009cAsym_class-GM_probtissue.nii.gz"
105
105
  ),
106
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  "space": "MNI152NLin2009cAsym",
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  },
108
108
  "VBM_WM": {
109
109
  "pattern": (
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- "sub-{subject}/anat/sub-{subject}_T1w_space"
110
+ "{subject}/anat/{subject}_T1w_space"
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  "-MNI152NLin2009cAsym_class-WM_probtissue.nii.gz"
112
112
  ),
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  "space": "MNI152NLin2009cAsym",
junifer/configs/juseless/datagrabbers/ukb_vbm.py CHANGED
@@ -34,7 +34,7 @@ class JuselessDataladUKBVBM(PatternDataladDataGrabber):
34
34
  replacements = ["subject", "session"]
35
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  patterns = {
36
36
  "VBM_GM": {
37
- "pattern": "m0wp1sub-{subject}_ses-{session}_T1w.nii.gz",
37
+ "pattern": "m0wp1{subject}_ses-{session}_T1w.nii.gz",
38
38
  "space": "IXI549Space",
39
39
  },
40
40
  }
junifer/data/tests/test_masks.py CHANGED
@@ -96,14 +96,14 @@ def test_compute_brain_mask_for_native(mask_type: str) -> None:
96
96
  """
97
97
  with DMCC13Benchmark(
98
98
  types=["BOLD"],
99
- sessions=["wave1bas"],
99
+ sessions=["ses-wave1bas"],
100
100
  tasks=["Rest"],
101
101
  phase_encodings=["AP"],
102
102
  runs=["1"],
103
103
  native_t1w=True,
104
104
  ) as dg:
105
105
  element_data = DefaultDataReader().fit_transform(
106
- dg[("f1031ax", "wave1bas", "Rest", "AP", "1")]
106
+ dg[("sub-f1031ax", "ses-wave1bas", "Rest", "AP", "1")]
107
107
  )
108
108
  mask = compute_brain_mask(
109
109
  target_data=element_data["BOLD"],
junifer/datagrabber/aomic/id1000.py CHANGED
@@ -43,8 +43,8 @@ class DataladAOMICID1000(PatternDataladDataGrabber):
43
43
  patterns = {
44
44
  "BOLD": {
45
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  "pattern": (
46
- "derivatives/fmriprep/sub-{subject}/func/"
47
- "sub-{subject}_task-moviewatching_"
46
+ "derivatives/fmriprep/{subject}/func/"
47
+ "{subject}_task-moviewatching_"
48
48
  "space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz"
49
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  ),
50
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  "space": "MNI152NLin2009cAsym",
@@ -52,16 +52,16 @@ class DataladAOMICID1000(PatternDataladDataGrabber):
52
52
  },
53
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  "BOLD_confounds": {
54
54
  "pattern": (
55
- "derivatives/fmriprep/sub-{subject}/func/"
56
- "sub-{subject}_task-moviewatching_"
55
+ "derivatives/fmriprep/{subject}/func/"
56
+ "{subject}_task-moviewatching_"
57
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  "desc-confounds_regressors.tsv"
58
58
  ),
59
59
  "format": "fmriprep",
60
60
  },
61
61
  "BOLD_mask": {
62
62
  "pattern": (
63
- "derivatives/fmriprep/sub-{subject}/func/"
64
- "sub-{subject}_task-moviewatching_"
63
+ "derivatives/fmriprep/{subject}/func/"
64
+ "{subject}_task-moviewatching_"
65
65
  "space-MNI152NLin2009cAsym_"
66
66
  "desc-brain_mask.nii.gz"
67
67
  ),
@@ -69,8 +69,8 @@ class DataladAOMICID1000(PatternDataladDataGrabber):
69
69
  },
70
70
  "T1w": {
71
71
  "pattern": (
72
- "derivatives/fmriprep/sub-{subject}/anat/"
73
- "sub-{subject}_space-MNI152NLin2009cAsym_"
72
+ "derivatives/fmriprep/{subject}/anat/"
73
+ "{subject}_space-MNI152NLin2009cAsym_"
74
74
  "desc-preproc_T1w.nii.gz"
75
75
  ),
76
76
  "space": "MNI152NLin2009cAsym",
@@ -78,40 +78,40 @@ class DataladAOMICID1000(PatternDataladDataGrabber):
78
78
  },
79
79
  "T1w_mask": {
80
80
  "pattern": (
81
- "derivatives/fmriprep/sub-{subject}/anat/"
82
- "sub-{subject}_space-MNI152NLin2009cAsym_"
81
+ "derivatives/fmriprep/{subject}/anat/"
82
+ "{subject}_space-MNI152NLin2009cAsym_"
83
83
  "desc-brain_mask.nii.gz"
84
84
  ),
85
85
  "space": "MNI152NLin2009cAsym",
86
86
  },
87
87
  "VBM_CSF": {
88
88
  "pattern": (
89
- "derivatives/fmriprep/sub-{subject}/anat/"
90
- "sub-{subject}_space-MNI152NLin2009cAsym_label-"
89
+ "derivatives/fmriprep/{subject}/anat/"
90
+ "{subject}_space-MNI152NLin2009cAsym_label-"
91
91
  "CSF_probseg.nii.gz"
92
92
  ),
93
93
  "space": "MNI152NLin2009cAsym",
94
94
  },
95
95
  "VBM_GM": {
96
96
  "pattern": (
97
- "derivatives/fmriprep/sub-{subject}/anat/"
98
- "sub-{subject}_space-MNI152NLin2009cAsym_label-"
97
+ "derivatives/fmriprep/{subject}/anat/"
98
+ "{subject}_space-MNI152NLin2009cAsym_label-"
99
99
  "GM_probseg.nii.gz"
100
100
  ),
101
101
  "space": "MNI152NLin2009cAsym",
102
102
  },
103
103
  "VBM_WM": {
104
104
  "pattern": (
105
- "derivatives/fmriprep/sub-{subject}/anat/"
106
- "sub-{subject}_space-MNI152NLin2009cAsym_label-"
105
+ "derivatives/fmriprep/{subject}/anat/"
106
+ "{subject}_space-MNI152NLin2009cAsym_label-"
107
107
  "WM_probseg.nii.gz"
108
108
  ),
109
109
  "space": "MNI152NLin2009cAsym",
110
110
  },
111
111
  "DWI": {
112
112
  "pattern": (
113
- "derivatives/dwipreproc/sub-{subject}/dwi/"
114
- "sub-{subject}_desc-preproc_dwi.nii.gz"
113
+ "derivatives/dwipreproc/{subject}/dwi/"
114
+ "{subject}_desc-preproc_dwi.nii.gz"
115
115
  ),
116
116
  },
117
117
  }
@@ -123,23 +123,23 @@ class DataladAOMICID1000(PatternDataladDataGrabber):
123
123
  {
124
124
  "T1w": {
125
125
  "pattern": (
126
- "derivatives/fmriprep/sub-{subject}/anat/"
127
- "sub-{subject}_desc-preproc_T1w.nii.gz"
126
+ "derivatives/fmriprep/{subject}/anat/"
127
+ "{subject}_desc-preproc_T1w.nii.gz"
128
128
  ),
129
129
  "space": "native",
130
130
  "mask_item": "T1w_mask",
131
131
  },
132
132
  "T1w_mask": {
133
133
  "pattern": (
134
- "derivatives/fmriprep/sub-{subject}/anat/"
135
- "sub-{subject}_desc-brain_mask.nii.gz"
134
+ "derivatives/fmriprep/{subject}/anat/"
135
+ "{subject}_desc-brain_mask.nii.gz"
136
136
  ),
137
137
  "space": "native",
138
138
  },
139
139
  "Warp": {
140
140
  "pattern": (
141
- "derivatives/fmriprep/sub-{subject}/anat/"
142
- "sub-{subject}_from-MNI152NLin2009cAsym_to-T1w_"
141
+ "derivatives/fmriprep/{subject}/anat/"
142
+ "{subject}_from-MNI152NLin2009cAsym_to-T1w_"
143
143
  "mode-image_xfm.h5"
144
144
  ),
145
145
  "src": "MNI152NLin2009cAsym",
junifer/datagrabber/aomic/piop1.py CHANGED
@@ -79,8 +79,8 @@ class DataladAOMICPIOP1(PatternDataladDataGrabber):
79
79
  patterns = {
80
80
  "BOLD": {
81
81
  "pattern": (
82
- "derivatives/fmriprep/sub-{subject}/func/"
83
- "sub-{subject}_task-{task}_"
82
+ "derivatives/fmriprep/{subject}/func/"
83
+ "{subject}_task-{task}_"
84
84
  "space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz"
85
85
  ),
86
86
  "space": "MNI152NLin2009cAsym",
@@ -88,24 +88,24 @@ class DataladAOMICPIOP1(PatternDataladDataGrabber):
88
88
  },
89
89
  "BOLD_confounds": {
90
90
  "pattern": (
91
- "derivatives/fmriprep/sub-{subject}/func/"
92
- "sub-{subject}_task-{task}_"
91
+ "derivatives/fmriprep/{subject}/func/"
92
+ "{subject}_task-{task}_"
93
93
  "desc-confounds_regressors.tsv"
94
94
  ),
95
95
  "format": "fmriprep",
96
96
  },
97
97
  "BOLD_mask": {
98
98
  "pattern": (
99
- "derivatives/fmriprep/sub-{subject}/func/"
100
- "sub-{subject}_task-{task}_"
99
+ "derivatives/fmriprep/{subject}/func/"
100
+ "{subject}_task-{task}_"
101
101
  "space-MNI152NLin2009cAsym_desc-brain_mask.nii.gz"
102
102
  ),
103
103
  "space": "MNI152NLin2009cAsym",
104
104
  },
105
105
  "T1w": {
106
106
  "pattern": (
107
- "derivatives/fmriprep/sub-{subject}/anat/"
108
- "sub-{subject}_space-MNI152NLin2009cAsym_"
107
+ "derivatives/fmriprep/{subject}/anat/"
108
+ "{subject}_space-MNI152NLin2009cAsym_"
109
109
  "desc-preproc_T1w.nii.gz"
110
110
  ),
111
111
  "space": "MNI152NLin2009cAsym",
@@ -113,40 +113,40 @@ class DataladAOMICPIOP1(PatternDataladDataGrabber):
113
113
  },
114
114
  "T1w_mask": {
115
115
  "pattern": (
116
- "derivatives/fmriprep/sub-{subject}/anat/"
117
- "sub-{subject}_space-MNI152NLin2009cAsym_"
116
+ "derivatives/fmriprep/{subject}/anat/"
117
+ "{subject}_space-MNI152NLin2009cAsym_"
118
118
  "desc-brain_mask.nii.gz"
119
119
  ),
120
120
  "space": "MNI152NLin2009cAsym",
121
121
  },
122
122
  "VBM_CSF": {
123
123
  "pattern": (
124
- "derivatives/fmriprep/sub-{subject}/anat/"
125
- "sub-{subject}_space-MNI152NLin2009cAsym_label-"
124
+ "derivatives/fmriprep/{subject}/anat/"
125
+ "{subject}_space-MNI152NLin2009cAsym_label-"
126
126
  "CSF_probseg.nii.gz"
127
127
  ),
128
128
  "space": "MNI152NLin2009cAsym",
129
129
  },
130
130
  "VBM_GM": {
131
131
  "pattern": (
132
- "derivatives/fmriprep/sub-{subject}/anat/"
133
- "sub-{subject}_space-MNI152NLin2009cAsym_label-"
132
+ "derivatives/fmriprep/{subject}/anat/"
133
+ "{subject}_space-MNI152NLin2009cAsym_label-"
134
134
  "GM_probseg.nii.gz"
135
135
  ),
136
136
  "space": "MNI152NLin2009cAsym",
137
137
  },
138
138
  "VBM_WM": {
139
139
  "pattern": (
140
- "derivatives/fmriprep/sub-{subject}/anat/"
141
- "sub-{subject}_space-MNI152NLin2009cAsym_label-"
140
+ "derivatives/fmriprep/{subject}/anat/"
141
+ "{subject}_space-MNI152NLin2009cAsym_label-"
142
142
  "WM_probseg.nii.gz"
143
143
  ),
144
144
  "space": "MNI152NLin2009cAsym",
145
145
  },
146
146
  "DWI": {
147
147
  "pattern": (
148
- "derivatives/dwipreproc/sub-{subject}/dwi/"
149
- "sub-{subject}_desc-preproc_dwi.nii.gz"
148
+ "derivatives/dwipreproc/{subject}/dwi/"
149
+ "{subject}_desc-preproc_dwi.nii.gz"
150
150
  ),
151
151
  },
152
152
  }
@@ -158,23 +158,23 @@ class DataladAOMICPIOP1(PatternDataladDataGrabber):
158
158
  {
159
159
  "T1w": {
160
160
  "pattern": (
161
- "derivatives/fmriprep/sub-{subject}/anat/"
162
- "sub-{subject}_desc-preproc_T1w.nii.gz"
161
+ "derivatives/fmriprep/{subject}/anat/"
162
+ "{subject}_desc-preproc_T1w.nii.gz"
163
163
  ),
164
164
  "space": "native",
165
165
  "mask_item": "T1w_mask",
166
166
  },
167
167
  "T1w_mask": {
168
168
  "pattern": (
169
- "derivatives/fmriprep/sub-{subject}/anat/"
170
- "sub-{subject}_desc-brain_mask.nii.gz"
169
+ "derivatives/fmriprep/{subject}/anat/"
170
+ "{subject}_desc-brain_mask.nii.gz"
171
171
  ),
172
172
  "space": "native",
173
173
  },
174
174
  "Warp": {
175
175
  "pattern": (
176
- "derivatives/fmriprep/sub-{subject}/anat/"
177
- "sub-{subject}_from-MNI152NLin2009cAsym_to-T1w_"
176
+ "derivatives/fmriprep/{subject}/anat/"
177
+ "{subject}_from-MNI152NLin2009cAsym_to-T1w_"
178
178
  "mode-image_xfm.h5"
179
179
  ),
180
180
  "src": "MNI152NLin2009cAsym",
@@ -242,7 +242,7 @@ class DataladAOMICPIOP1(PatternDataladDataGrabber):
242
242
  The list of subjects in the dataset.
243
243
 
244
244
  """
245
- subjects = [f"{x:04d}" for x in range(1, 217)]
245
+ subjects = [f"sub-{x:04d}" for x in range(1, 217)]
246
246
  elems = []
247
247
  for subject, task in product(subjects, self.tasks):
248
248
  elems.append((subject, task))
junifer/datagrabber/aomic/piop2.py CHANGED
@@ -76,8 +76,8 @@ class DataladAOMICPIOP2(PatternDataladDataGrabber):
76
76
  patterns = {
77
77
  "BOLD": {
78
78
  "pattern": (
79
- "derivatives/fmriprep/sub-{subject}/func/"
80
- "sub-{subject}_task-{task}_"
79
+ "derivatives/fmriprep/{subject}/func/"
80
+ "{subject}_task-{task}_"
81
81
  "space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz"
82
82
  ),
83
83
  "space": "MNI152NLin2009cAsym",
@@ -85,24 +85,24 @@ class DataladAOMICPIOP2(PatternDataladDataGrabber):
85
85
  },
86
86
  "BOLD_confounds": {
87
87
  "pattern": (
88
- "derivatives/fmriprep/sub-{subject}/func/"
89
- "sub-{subject}_task-{task}_"
88
+ "derivatives/fmriprep/{subject}/func/"
89
+ "{subject}_task-{task}_"
90
90
  "desc-confounds_regressors.tsv"
91
91
  ),
92
92
  "format": "fmriprep",
93
93
  },
94
94
  "BOLD_mask": {
95
95
  "pattern": (
96
- "derivatives/fmriprep/sub-{subject}/func/"
97
- "sub-{subject}_task-{task}_"
96
+ "derivatives/fmriprep/{subject}/func/"
97
+ "{subject}_task-{task}_"
98
98
  "space-MNI152NLin2009cAsym_desc-brain_mask.nii.gz"
99
99
  ),
100
100
  "space": "MNI152NLin2009cAsym",
101
101
  },
102
102
  "T1w": {
103
103
  "pattern": (
104
- "derivatives/fmriprep/sub-{subject}/anat/"
105
- "sub-{subject}_space-MNI152NLin2009cAsym_"
104
+ "derivatives/fmriprep/{subject}/anat/"
105
+ "{subject}_space-MNI152NLin2009cAsym_"
106
106
  "desc-preproc_T1w.nii.gz"
107
107
  ),
108
108
  "space": "MNI152NLin2009cAsym",
@@ -110,40 +110,40 @@ class DataladAOMICPIOP2(PatternDataladDataGrabber):
110
110
  },
111
111
  "T1w_mask": {
112
112
  "pattern": (
113
- "derivatives/fmriprep/sub-{subject}/anat/"
114
- "sub-{subject}_space-MNI152NLin2009cAsym_"
113
+ "derivatives/fmriprep/{subject}/anat/"
114
+ "{subject}_space-MNI152NLin2009cAsym_"
115
115
  "desc-brain_mask.nii.gz"
116
116
  ),
117
117
  "space": "MNI152NLin2009cAsym",
118
118
  },
119
119
  "VBM_CSF": {
120
120
  "pattern": (
121
- "derivatives/fmriprep/sub-{subject}/anat/"
122
- "sub-{subject}_space-MNI152NLin2009cAsym_label-"
121
+ "derivatives/fmriprep/{subject}/anat/"
122
+ "{subject}_space-MNI152NLin2009cAsym_label-"
123
123
  "CSF_probseg.nii.gz"
124
124
  ),
125
125
  "space": "MNI152NLin2009cAsym",
126
126
  },
127
127
  "VBM_GM": {
128
128
  "pattern": (
129
- "derivatives/fmriprep/sub-{subject}/anat/"
130
- "sub-{subject}_space-MNI152NLin2009cAsym_label-"
129
+ "derivatives/fmriprep/{subject}/anat/"
130
+ "{subject}_space-MNI152NLin2009cAsym_label-"
131
131
  "GM_probseg.nii.gz"
132
132
  ),
133
133
  "space": "MNI152NLin2009cAsym",
134
134
  },
135
135
  "VBM_WM": {
136
136
  "pattern": (
137
- "derivatives/fmriprep/sub-{subject}/anat/"
138
- "sub-{subject}_space-MNI152NLin2009cAsym_label-"
137
+ "derivatives/fmriprep/{subject}/anat/"
138
+ "{subject}_space-MNI152NLin2009cAsym_label-"
139
139
  "WM_probseg.nii.gz"
140
140
  ),
141
141
  "space": "MNI152NLin2009cAsym",
142
142
  },
143
143
  "DWI": {
144
144
  "pattern": (
145
- "derivatives/dwipreproc/sub-{subject}/dwi/"
146
- "sub-{subject}_desc-preproc_dwi.nii.gz"
145
+ "derivatives/dwipreproc/{subject}/dwi/"
146
+ "{subject}_desc-preproc_dwi.nii.gz"
147
147
  ),
148
148
  },
149
149
  }
@@ -155,23 +155,23 @@ class DataladAOMICPIOP2(PatternDataladDataGrabber):
155
155
  {
156
156
  "T1w": {
157
157
  "pattern": (
158
- "derivatives/fmriprep/sub-{subject}/anat/"
159
- "sub-{subject}_desc-preproc_T1w.nii.gz"
158
+ "derivatives/fmriprep/{subject}/anat/"
159
+ "{subject}_desc-preproc_T1w.nii.gz"
160
160
  ),
161
161
  "space": "native",
162
162
  "mask_item": "T1w_mask",
163
163
  },
164
164
  "T1w_mask": {
165
165
  "pattern": (
166
- "derivatives/fmriprep/sub-{subject}/anat/"
167
- "sub-{subject}_desc-brain_mask.nii.gz"
166
+ "derivatives/fmriprep/{subject}/anat/"
167
+ "{subject}_desc-brain_mask.nii.gz"
168
168
  ),
169
169
  "space": "native",
170
170
  },
171
171
  "Warp": {
172
172
  "pattern": (
173
- "derivatives/fmriprep/sub-{subject}/anat/"
174
- "sub-{subject}_from-MNI152NLin2009cAsym_to-T1w_"
173
+ "derivatives/fmriprep/{subject}/anat/"
174
+ "{subject}_from-MNI152NLin2009cAsym_to-T1w_"
175
175
  "mode-image_xfm.h5"
176
176
  ),
177
177
  "src": "MNI152NLin2009cAsym",
@@ -208,7 +208,7 @@ class DataladAOMICPIOP2(PatternDataladDataGrabber):
208
208
  imposing constraints based on specified tasks.
209
209
 
210
210
  """
211
- subjects = [f"{x:04d}" for x in range(1, 227)]
211
+ subjects = [f"sub-{x:04d}" for x in range(1, 227)]
212
212
  elems = []
213
213
  for subject, task in product(subjects, self.tasks):
214
214
  elems.append((subject, task))
junifer/datagrabber/aomic/tests/test_id1000.py CHANGED
@@ -34,7 +34,7 @@ def test_DataladAOMICID1000() -> None:
34
34
 
35
35
  assert (
36
36
  out["BOLD"]["path"].name
37
- == f"sub-{test_element}_task-moviewatching_"
37
+ == f"{test_element}_task-moviewatching_"
38
38
  "space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz"
39
39
  )
40
40
 
@@ -46,7 +46,7 @@ def test_DataladAOMICID1000() -> None:
46
46
 
47
47
  assert (
48
48
  out["BOLD_confounds"]["path"].name
49
- == f"sub-{test_element}_task-moviewatching_"
49
+ == f"{test_element}_task-moviewatching_"
50
50
  "desc-confounds_regressors.tsv"
51
51
  )
52
52
 
@@ -61,7 +61,7 @@ def test_DataladAOMICID1000() -> None:
61
61
 
62
62
  assert (
63
63
  out["T1w"]["path"].name
64
- == f"sub-{test_element}_space-MNI152NLin2009cAsym_"
64
+ == f"{test_element}_space-MNI152NLin2009cAsym_"
65
65
  "desc-preproc_T1w.nii.gz"
66
66
  )
67
67
 
@@ -76,7 +76,7 @@ def test_DataladAOMICID1000() -> None:
76
76
 
77
77
  assert (
78
78
  out["VBM_CSF"]["path"].name
79
- == f"sub-{test_element}_space-MNI152NLin2009cAsym_label-"
79
+ == f"{test_element}_space-MNI152NLin2009cAsym_label-"
80
80
  "CSF_probseg.nii.gz"
81
81
  )
82
82
 
@@ -88,7 +88,7 @@ def test_DataladAOMICID1000() -> None:
88
88
 
89
89
  assert (
90
90
  out["VBM_GM"]["path"].name
91
- == f"sub-{test_element}_space-MNI152NLin2009cAsym_label-"
91
+ == f"{test_element}_space-MNI152NLin2009cAsym_label-"
92
92
  "GM_probseg.nii.gz"
93
93
  )
94
94
 
@@ -100,7 +100,7 @@ def test_DataladAOMICID1000() -> None:
100
100
 
101
101
  assert (
102
102
  out["VBM_WM"]["path"].name
103
- == f"sub-{test_element}_space-MNI152NLin2009cAsym_label-"
103
+ == f"{test_element}_space-MNI152NLin2009cAsym_label-"
104
104
  "WM_probseg.nii.gz"
105
105
  )
106
106
 
@@ -112,7 +112,7 @@ def test_DataladAOMICID1000() -> None:
112
112
 
113
113
  assert (
114
114
  out["DWI"]["path"].name
115
- == f"sub-{test_element}_desc-preproc_dwi.nii.gz"
115
+ == f"{test_element}_desc-preproc_dwi.nii.gz"
116
116
  )
117
117
 
118
118
  assert out["DWI"]["path"].exists()
junifer/datagrabber/aomic/tests/test_piop1.py CHANGED
@@ -56,7 +56,7 @@ def test_DataladAOMICPIOP1(tasks: Optional[str]) -> None:
56
56
  acq = task_acqs[task]
57
57
  new_task = f"{task}_acq-{acq}"
58
58
  assert (
59
- out["BOLD"]["path"].name == f"sub-{sub}_task-{new_task}_"
59
+ out["BOLD"]["path"].name == f"{sub}_task-{new_task}_"
60
60
  "space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz"
61
61
  )
62
62
 
@@ -67,7 +67,7 @@ def test_DataladAOMICPIOP1(tasks: Optional[str]) -> None:
67
67
  assert "BOLD_confounds" in out
68
68
 
69
69
  assert (
70
- out["BOLD_confounds"]["path"].name == f"sub-{sub}_task-{new_task}_"
70
+ out["BOLD_confounds"]["path"].name == f"{sub}_task-{new_task}_"
71
71
  "desc-confounds_regressors.tsv"
72
72
  )
73
73
 
@@ -81,7 +81,7 @@ def test_DataladAOMICPIOP1(tasks: Optional[str]) -> None:
81
81
  assert "T1w" in out
82
82
 
83
83
  assert (
84
- out["T1w"]["path"].name == f"sub-{sub}_space-MNI152NLin2009cAsym_"
84
+ out["T1w"]["path"].name == f"{sub}_space-MNI152NLin2009cAsym_"
85
85
  "desc-preproc_T1w.nii.gz"
86
86
  )
87
87
 
@@ -96,7 +96,7 @@ def test_DataladAOMICPIOP1(tasks: Optional[str]) -> None:
96
96
 
97
97
  assert (
98
98
  out["VBM_CSF"]["path"].name
99
- == f"sub-{sub}_space-MNI152NLin2009cAsym_label-"
99
+ == f"{sub}_space-MNI152NLin2009cAsym_label-"
100
100
  "CSF_probseg.nii.gz"
101
101
  )
102
102
 
@@ -108,7 +108,7 @@ def test_DataladAOMICPIOP1(tasks: Optional[str]) -> None:
108
108
 
109
109
  assert (
110
110
  out["VBM_GM"]["path"].name
111
- == f"sub-{sub}_space-MNI152NLin2009cAsym_label-"
111
+ == f"{sub}_space-MNI152NLin2009cAsym_label-"
112
112
  "GM_probseg.nii.gz"
113
113
  )
114
114
 
@@ -120,7 +120,7 @@ def test_DataladAOMICPIOP1(tasks: Optional[str]) -> None:
120
120
 
121
121
  assert (
122
122
  out["VBM_WM"]["path"].name
123
- == f"sub-{sub}_space-MNI152NLin2009cAsym_label-"
123
+ == f"{sub}_space-MNI152NLin2009cAsym_label-"
124
124
  "WM_probseg.nii.gz"
125
125
  )
126
126
 
@@ -130,7 +130,7 @@ def test_DataladAOMICPIOP1(tasks: Optional[str]) -> None:
130
130
  # asserts type "DWI"
131
131
  assert "DWI" in out
132
132
 
133
- assert out["DWI"]["path"].name == f"sub-{sub}_desc-preproc_dwi.nii.gz"
133
+ assert out["DWI"]["path"].name == f"{sub}_desc-preproc_dwi.nii.gz"
134
134
 
135
135
  assert out["DWI"]["path"].exists()
136
136
  assert out["DWI"]["path"].is_file()
junifer/datagrabber/aomic/tests/test_piop2.py CHANGED
@@ -50,7 +50,7 @@ def test_DataladAOMICPIOP2(tasks: Optional[str]) -> None:
50
50
 
51
51
  new_task = f"{task}_acq-seq"
52
52
  assert (
53
- out["BOLD"]["path"].name == f"sub-{sub}_task-{new_task}_"
53
+ out["BOLD"]["path"].name == f"{sub}_task-{new_task}_"
54
54
  "space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz"
55
55
  )
56
56
 
@@ -61,7 +61,7 @@ def test_DataladAOMICPIOP2(tasks: Optional[str]) -> None:
61
61
  assert "BOLD_confounds" in out
62
62
 
63
63
  assert (
64
- out["BOLD_confounds"]["path"].name == f"sub-{sub}_task-{new_task}_"
64
+ out["BOLD_confounds"]["path"].name == f"{sub}_task-{new_task}_"
65
65
  "desc-confounds_regressors.tsv"
66
66
  )
67
67
 
@@ -75,7 +75,7 @@ def test_DataladAOMICPIOP2(tasks: Optional[str]) -> None:
75
75
  assert "T1w" in out
76
76
 
77
77
  assert (
78
- out["T1w"]["path"].name == f"sub-{sub}_space-MNI152NLin2009cAsym_"
78
+ out["T1w"]["path"].name == f"{sub}_space-MNI152NLin2009cAsym_"
79
79
  "desc-preproc_T1w.nii.gz"
80
80
  )
81
81
 
@@ -90,7 +90,7 @@ def test_DataladAOMICPIOP2(tasks: Optional[str]) -> None:
90
90
 
91
91
  assert (
92
92
  out["VBM_CSF"]["path"].name
93
- == f"sub-{sub}_space-MNI152NLin2009cAsym_label-"
93
+ == f"{sub}_space-MNI152NLin2009cAsym_label-"
94
94
  "CSF_probseg.nii.gz"
95
95
  )
96
96
 
@@ -102,7 +102,7 @@ def test_DataladAOMICPIOP2(tasks: Optional[str]) -> None:
102
102
 
103
103
  assert (
104
104
  out["VBM_GM"]["path"].name
105
- == f"sub-{sub}_space-MNI152NLin2009cAsym_label-"
105
+ == f"{sub}_space-MNI152NLin2009cAsym_label-"
106
106
  "GM_probseg.nii.gz"
107
107
  )
108
108
 
@@ -114,7 +114,7 @@ def test_DataladAOMICPIOP2(tasks: Optional[str]) -> None:
114
114
 
115
115
  assert (
116
116
  out["VBM_WM"]["path"].name
117
- == f"sub-{sub}_space-MNI152NLin2009cAsym_label-"
117
+ == f"{sub}_space-MNI152NLin2009cAsym_label-"
118
118
  "WM_probseg.nii.gz"
119
119
  )
120
120
 
@@ -124,7 +124,7 @@ def test_DataladAOMICPIOP2(tasks: Optional[str]) -> None:
124
124
  # asserts type "DWI"
125
125
  assert "DWI" in out
126
126
 
127
- assert out["DWI"]["path"].name == f"sub-{sub}_desc-preproc_dwi.nii.gz"
127
+ assert out["DWI"]["path"].name == f"{sub}_desc-preproc_dwi.nii.gz"
128
128
 
129
129
  assert out["DWI"]["path"].exists()
130
130
  assert out["DWI"]["path"].is_file()
junifer/datagrabber/dmcc13_benchmark.py CHANGED
@@ -29,8 +29,8 @@ class DMCC13Benchmark(PatternDataladDataGrabber):
29
29
  "VBM_WM"} or a list of the options, optional
30
30
  DMCC data types. If None, all available data types are selected.
31
31
  (default None).
32
- sessions: {"wave1bas", "wave1pro", "wave1rea"} or list of the options, \
33
- optional
32
+ sessions: {"ses-wave1bas", "ses-wave1pro", "ses-wave1rea"} or list of \
33
+ the options, optional
34
34
  DMCC sessions. If None, all available sessions are selected
35
35
  (default None).
36
36
  tasks: {"Rest", "Axcpt", "Cuedts", "Stern", "Stroop"} or \
@@ -68,9 +68,9 @@ class DMCC13Benchmark(PatternDataladDataGrabber):
68
68
  ) -> None:
69
69
  # Declare all sessions
70
70
  all_sessions = [
71
- "wave1bas",
72
- "wave1pro",
73
- "wave1rea",
71
+ "ses-wave1bas",
72
+ "ses-wave1pro",
73
+ "ses-wave1rea",
74
74
  ]
75
75
  # Set default sessions
76
76
  if sessions is None:
@@ -141,8 +141,8 @@ class DMCC13Benchmark(PatternDataladDataGrabber):
141
141
  patterns = {
142
142
  "BOLD": {
143
143
  "pattern": (
144
- "derivatives/fmriprep-1.3.2/sub-{subject}/ses-{session}/"
145
- "func/sub-{subject}_ses-{session}_task-{task}_acq-mb4"
144
+ "derivatives/fmriprep-1.3.2/{subject}/{session}/"
145
+ "func/{subject}_{session}_task-{task}_acq-mb4"
146
146
  "{phase_encoding}_run-{run}_"
147
147
  "space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz"
148
148
  ),
@@ -151,16 +151,16 @@ class DMCC13Benchmark(PatternDataladDataGrabber):
151
151
  },
152
152
  "BOLD_confounds": {
153
153
  "pattern": (
154
- "derivatives/fmriprep-1.3.2/sub-{subject}/ses-{session}/"
155
- "func/sub-{subject}_ses-{session}_task-{task}_acq-mb4"
154
+ "derivatives/fmriprep-1.3.2/{subject}/{session}/"
155
+ "func/{subject}_{session}_task-{task}_acq-mb4"
156
156
  "{phase_encoding}_run-{run}_desc-confounds_regressors.tsv"
157
157
  ),
158
158
  "format": "fmriprep",
159
159
  },
160
160
  "BOLD_mask": {
161
161
  "pattern": (
162
- "derivatives/fmriprep-1.3.2/sub-{subject}/ses-{session}/"
163
- "/func/sub-{subject}_ses-{session}_task-{task}_acq-mb4"
162
+ "derivatives/fmriprep-1.3.2/{subject}/{session}/"
163
+ "/func/{subject}_{session}_task-{task}_acq-mb4"
164
164
  "{phase_encoding}_run-{run}_"
165
165
  "space-MNI152NLin2009cAsym_desc-brain_mask.nii.gz"
166
166
  ),
@@ -168,37 +168,37 @@ class DMCC13Benchmark(PatternDataladDataGrabber):
168
168
  },
169
169
  "T1w": {
170
170
  "pattern": (
171
- "derivatives/fmriprep-1.3.2/sub-{subject}/anat/"
172
- "sub-{subject}_space-MNI152NLin2009cAsym_desc-preproc_T1w.nii.gz"
171
+ "derivatives/fmriprep-1.3.2/{subject}/anat/"
172
+ "{subject}_space-MNI152NLin2009cAsym_desc-preproc_T1w.nii.gz"
173
173
  ),
174
174
  "space": "MNI152NLin2009cAsym",
175
175
  "mask_item": "T1w_mask",
176
176
  },
177
177
  "T1w_mask": {
178
178
  "pattern": (
179
- "derivatives/fmriprep-1.3.2/sub-{subject}/anat/"
180
- "sub-{subject}_space-MNI152NLin2009cAsym_desc-brain_mask.nii.gz"
179
+ "derivatives/fmriprep-1.3.2/{subject}/anat/"
180
+ "{subject}_space-MNI152NLin2009cAsym_desc-brain_mask.nii.gz"
181
181
  ),
182
182
  "space": "MNI152NLin2009cAsym",
183
183
  },
184
184
  "VBM_CSF": {
185
185
  "pattern": (
186
- "derivatives/fmriprep-1.3.2/sub-{subject}/anat/"
187
- "sub-{subject}_space-MNI152NLin2009cAsym_label-CSF_probseg.nii.gz"
186
+ "derivatives/fmriprep-1.3.2/{subject}/anat/"
187
+ "{subject}_space-MNI152NLin2009cAsym_label-CSF_probseg.nii.gz"
188
188
  ),
189
189
  "space": "MNI152NLin2009cAsym",
190
190
  },
191
191
  "VBM_GM": {
192
192
  "pattern": (
193
- "derivatives/fmriprep-1.3.2/sub-{subject}/anat/"
194
- "sub-{subject}_space-MNI152NLin2009cAsym_label-GM_probseg.nii.gz"
193
+ "derivatives/fmriprep-1.3.2/{subject}/anat/"
194
+ "{subject}_space-MNI152NLin2009cAsym_label-GM_probseg.nii.gz"
195
195
  ),
196
196
  "space": "MNI152NLin2009cAsym",
197
197
  },
198
198
  "VBM_WM": {
199
199
  "pattern": (
200
- "derivatives/fmriprep-1.3.2/sub-{subject}/anat/"
201
- "sub-{subject}_space-MNI152NLin2009cAsym_label-WM_probseg.nii.gz"
200
+ "derivatives/fmriprep-1.3.2/{subject}/anat/"
201
+ "{subject}_space-MNI152NLin2009cAsym_label-WM_probseg.nii.gz"
202
202
  ),
203
203
  "space": "MNI152NLin2009cAsym",
204
204
  },
@@ -211,23 +211,23 @@ class DMCC13Benchmark(PatternDataladDataGrabber):
211
211
  {
212
212
  "T1w": {
213
213
  "pattern": (
214
- "derivatives/fmriprep-1.3.2/sub-{subject}/anat/"
215
- "sub-{subject}_desc-preproc_T1w.nii.gz"
214
+ "derivatives/fmriprep-1.3.2/{subject}/anat/"
215
+ "{subject}_desc-preproc_T1w.nii.gz"
216
216
  ),
217
217
  "space": "native",
218
218
  "mask_item": "T1w_mask",
219
219
  },
220
220
  "T1w_mask": {
221
221
  "pattern": (
222
- "derivatives/fmriprep-1.3.2/sub-{subject}/anat/"
223
- "sub-{subject}_desc-brain_mask.nii.gz"
222
+ "derivatives/fmriprep-1.3.2/{subject}/anat/"
223
+ "{subject}_desc-brain_mask.nii.gz"
224
224
  ),
225
225
  "space": "native",
226
226
  },
227
227
  "Warp": {
228
228
  "pattern": (
229
- "derivatives/fmriprep-1.3.2/sub-{subject}/anat/"
230
- "sub-{subject}_from-MNI152NLin2009cAsym_to-T1w_"
229
+ "derivatives/fmriprep-1.3.2/{subject}/anat/"
230
+ "{subject}_from-MNI152NLin2009cAsym_to-T1w_"
231
231
  "mode-image_xfm.h5"
232
232
  ),
233
233
  "src": "MNI152NLin2009cAsym",
@@ -268,7 +268,7 @@ class DMCC13Benchmark(PatternDataladDataGrabber):
268
268
  ----------
269
269
  subject : str
270
270
  The subject ID.
271
- session : {"wave1bas", "wave1pro", "wave1rea"}
271
+ session : {"ses-wave1bas", "ses-wave1pro", "ses-wave1rea"}
272
272
  The session to get.
273
273
  task : {"Rest", "Axcpt", "Cuedts", "Stern", "Stroop"}
274
274
  The task to get.
@@ -323,25 +323,25 @@ class DMCC13Benchmark(PatternDataladDataGrabber):
323
323
 
324
324
  """
325
325
  subjects = [
326
- "f1031ax",
327
- "f1552xo",
328
- "f1659oa",
329
- "f1670rz",
330
- "f1951tt",
331
- "f3300jh",
332
- "f3720ca",
333
- "f5004cr",
334
- "f5407sl",
335
- "f5416zj",
336
- "f8113do",
337
- "f8570ui",
338
- "f9057kp",
326
+ "sub-f1031ax",
327
+ "sub-f1552xo",
328
+ "sub-f1659oa",
329
+ "sub-f1670rz",
330
+ "sub-f1951tt",
331
+ "sub-f3300jh",
332
+ "sub-f3720ca",
333
+ "sub-f5004cr",
334
+ "sub-f5407sl",
335
+ "sub-f5416zj",
336
+ "sub-f8113do",
337
+ "sub-f8570ui",
338
+ "sub-f9057kp",
339
339
  ]
340
340
  elems = []
341
341
  # For wave1bas session
342
342
  for subject, session, task, phase_encoding in product(
343
343
  subjects,
344
- ["wave1bas"],
344
+ ["ses-wave1bas"],
345
345
  self.tasks,
346
346
  self.phase_encodings,
347
347
  ):
@@ -350,13 +350,13 @@ class DMCC13Benchmark(PatternDataladDataGrabber):
350
350
  else:
351
351
  run = "2"
352
352
  # Bypass for f1951tt not having run 2 for Rest
353
- if subject == "f1951tt" and task == "Rest" and run == "2":
353
+ if subject == "sub-f1951tt" and task == "Rest" and run == "2":
354
354
  continue
355
355
  elems.append((subject, session, task, phase_encoding, run))
356
356
  # For other sessions
357
357
  for subject, session, task, phase_encoding in product(
358
358
  subjects,
359
- ["wave1pro", "wave1rea"],
359
+ ["ses-wave1pro", "ses-wave1rea"],
360
360
  ["Rest"],
361
361
  self.phase_encodings,
362
362
  ):
@@ -365,7 +365,7 @@ class DMCC13Benchmark(PatternDataladDataGrabber):
365
365
  else:
366
366
  run = "2"
367
367
  # Bypass for f5416zj for not having wave1rea session
368
- if subject == "f5416zj" and session == "wave1rea":
368
+ if subject == "sub-f5416zj" and session == "ses-wave1rea":
369
369
  continue
370
370
  elems.append((subject, session, task, phase_encoding, run))
371
371
 
junifer/datagrabber/tests/test_dmcc13_benchmark.py CHANGED
@@ -17,34 +17,34 @@ URI = "https://gin.g-node.org/synchon/datalad-example-dmcc13-benchmark"
17
17
  "sessions, tasks, phase_encodings, runs, native_t1w",
18
18
  [
19
19
  (None, None, None, None, False),
20
- ("wave1bas", "Rest", "AP", "1", False),
21
- ("wave1bas", "Axcpt", "AP", "1", False),
22
- ("wave1bas", "Cuedts", "AP", "1", False),
23
- ("wave1bas", "Stern", "AP", "1", False),
24
- ("wave1bas", "Stroop", "AP", "1", False),
25
- ("wave1bas", "Rest", "PA", "2", False),
26
- ("wave1bas", "Axcpt", "PA", "2", False),
27
- ("wave1bas", "Cuedts", "PA", "2", False),
28
- ("wave1bas", "Stern", "PA", "2", False),
29
- ("wave1bas", "Stroop", "PA", "2", False),
30
- ("wave1bas", "Rest", "AP", "1", True),
31
- ("wave1bas", "Axcpt", "AP", "1", True),
32
- ("wave1bas", "Cuedts", "AP", "1", True),
33
- ("wave1bas", "Stern", "AP", "1", True),
34
- ("wave1bas", "Stroop", "AP", "1", True),
35
- ("wave1bas", "Rest", "PA", "2", True),
36
- ("wave1bas", "Axcpt", "PA", "2", True),
37
- ("wave1bas", "Cuedts", "PA", "2", True),
38
- ("wave1bas", "Stern", "PA", "2", True),
39
- ("wave1bas", "Stroop", "PA", "2", True),
40
- ("wave1pro", "Rest", "AP", "1", False),
41
- ("wave1pro", "Rest", "PA", "2", False),
42
- ("wave1pro", "Rest", "AP", "1", True),
43
- ("wave1pro", "Rest", "PA", "2", True),
44
- ("wave1rea", "Rest", "AP", "1", False),
45
- ("wave1rea", "Rest", "PA", "2", False),
46
- ("wave1rea", "Rest", "AP", "1", True),
47
- ("wave1rea", "Rest", "PA", "2", True),
20
+ ("ses-wave1bas", "Rest", "AP", "1", False),
21
+ ("ses-wave1bas", "Axcpt", "AP", "1", False),
22
+ ("ses-wave1bas", "Cuedts", "AP", "1", False),
23
+ ("ses-wave1bas", "Stern", "AP", "1", False),
24
+ ("ses-wave1bas", "Stroop", "AP", "1", False),
25
+ ("ses-wave1bas", "Rest", "PA", "2", False),
26
+ ("ses-wave1bas", "Axcpt", "PA", "2", False),
27
+ ("ses-wave1bas", "Cuedts", "PA", "2", False),
28
+ ("ses-wave1bas", "Stern", "PA", "2", False),
29
+ ("ses-wave1bas", "Stroop", "PA", "2", False),
30
+ ("ses-wave1bas", "Rest", "AP", "1", True),
31
+ ("ses-wave1bas", "Axcpt", "AP", "1", True),
32
+ ("ses-wave1bas", "Cuedts", "AP", "1", True),
33
+ ("ses-wave1bas", "Stern", "AP", "1", True),
34
+ ("ses-wave1bas", "Stroop", "AP", "1", True),
35
+ ("ses-wave1bas", "Rest", "PA", "2", True),
36
+ ("ses-wave1bas", "Axcpt", "PA", "2", True),
37
+ ("ses-wave1bas", "Cuedts", "PA", "2", True),
38
+ ("ses-wave1bas", "Stern", "PA", "2", True),
39
+ ("ses-wave1bas", "Stroop", "PA", "2", True),
40
+ ("ses-wave1pro", "Rest", "AP", "1", False),
41
+ ("ses-wave1pro", "Rest", "PA", "2", False),
42
+ ("ses-wave1pro", "Rest", "AP", "1", True),
43
+ ("ses-wave1pro", "Rest", "PA", "2", True),
44
+ ("ses-wave1rea", "Rest", "AP", "1", False),
45
+ ("ses-wave1rea", "Rest", "PA", "2", False),
46
+ ("ses-wave1rea", "Rest", "AP", "1", True),
47
+ ("ses-wave1rea", "Rest", "PA", "2", True),
48
48
  ],
49
49
  )
50
50
  def test_DMCC13Benchmark(
@@ -88,7 +88,7 @@ def test_DMCC13Benchmark(
88
88
  # Get test element's access values
89
89
  _, ses, task, phase, run = test_element
90
90
  # Access data
91
- out = dg[("01", ses, task, phase, run)]
91
+ out = dg[("sub-01", ses, task, phase, run)]
92
92
 
93
93
  # Available data types
94
94
  data_types = [
@@ -108,15 +108,15 @@ def test_DMCC13Benchmark(
108
108
  # Data type file name formats
109
109
  data_file_names = [
110
110
  (
111
- f"sub-01_ses-{ses}_task-{task}_acq-mb4{phase}_run-{run}_"
111
+ f"sub-01_{ses}_task-{task}_acq-mb4{phase}_run-{run}_"
112
112
  "space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz"
113
113
  ),
114
114
  (
115
- f"sub-01_ses-{ses}_task-{task}_acq-mb4{phase}_run-{run}_"
115
+ f"sub-01_{ses}_task-{task}_acq-mb4{phase}_run-{run}_"
116
116
  "desc-confounds_regressors.tsv"
117
117
  ),
118
118
  (
119
- f"sub-01_ses-{ses}_task-{task}_acq-mb4{phase}_run-{run}_"
119
+ f"sub-01_{ses}_task-{task}_acq-mb4{phase}_run-{run}_"
120
120
  "space-MNI152NLin2009cAsym_desc-brain_mask.nii.gz"
121
121
  ),
122
122
  "sub-01_space-MNI152NLin2009cAsym_label-CSF_probseg.nii.gz",
@@ -199,7 +199,7 @@ def test_DMCC13Benchmark_partial_data_access(
199
199
  # Get test element's access values
200
200
  _, ses, task, phase, run = test_element
201
201
  # Access data
202
- out = dg[("01", ses, task, phase, run)]
202
+ out = dg[("sub-01", ses, task, phase, run)]
203
203
  # Assert data type
204
204
  if isinstance(types, list):
205
205
  for type_ in types:
junifer/preprocess/ants/tests/test_ants_apply_transforms_warper.py CHANGED
@@ -35,7 +35,7 @@ def test_AntsApplyTransformsWarper_preprocess() -> None:
35
35
  """Test AntsApplyTransformsWarper preprocess."""
36
36
  with DMCC13Benchmark(
37
37
  types=["BOLD", "T1w", "Warp"],
38
- sessions=["wave1bas"],
38
+ sessions=["ses-wave1bas"],
39
39
  tasks=["Rest"],
40
40
  phase_encodings=["AP"],
41
41
  runs=["1"],
@@ -43,7 +43,7 @@ def test_AntsApplyTransformsWarper_preprocess() -> None:
43
43
  ) as dg:
44
44
  # Read data
45
45
  element_data = DefaultDataReader().fit_transform(
46
- dg[("f9057kp", "wave1bas", "Rest", "AP", "1")]
46
+ dg[("sub-f9057kp", "ses-wave1bas", "Rest", "AP", "1")]
47
47
  )
48
48
  # Preprocess data
49
49
  data_type, data = _AntsApplyTransformsWarper(
junifer/preprocess/tests/test_bold_warper.py CHANGED
@@ -43,13 +43,13 @@ def test_BOLDWarper_get_output_type() -> None:
43
43
  [
44
44
  DMCC13Benchmark(
45
45
  types=["BOLD", "T1w", "Warp"],
46
- sessions=["wave1bas"],
46
+ sessions=["ses-wave1bas"],
47
47
  tasks=["Rest"],
48
48
  phase_encodings=["AP"],
49
49
  runs=["1"],
50
50
  native_t1w=True,
51
51
  ),
52
- ("f9057kp", "wave1bas", "Rest", "AP", "1"),
52
+ ("sub-f9057kp", "ses-wave1bas", "Rest", "AP", "1"),
53
53
  ],
54
54
  [
55
55
  DataladHCP1200(
@@ -99,25 +99,25 @@ def test_BOLDWarper_preprocess_to_native(
99
99
  [
100
100
  DMCC13Benchmark(
101
101
  types=["BOLD"],
102
- sessions=["wave1bas"],
102
+ sessions=["ses-wave1bas"],
103
103
  tasks=["Rest"],
104
104
  phase_encodings=["AP"],
105
105
  runs=["1"],
106
106
  native_t1w=False,
107
107
  ),
108
- ("f9057kp", "wave1bas", "Rest", "AP", "1"),
108
+ ("sub-f9057kp", "ses-wave1bas", "Rest", "AP", "1"),
109
109
  "MNI152NLin2009aAsym",
110
110
  ],
111
111
  [
112
112
  DMCC13Benchmark(
113
113
  types=["BOLD"],
114
- sessions=["wave1bas"],
114
+ sessions=["ses-wave1bas"],
115
115
  tasks=["Rest"],
116
116
  phase_encodings=["AP"],
117
117
  runs=["1"],
118
118
  native_t1w=False,
119
119
  ),
120
- ("f9057kp", "wave1bas", "Rest", "AP", "1"),
120
+ ("sub-f9057kp", "ses-wave1bas", "Rest", "AP", "1"),
121
121
  "MNI152NLin6Asym",
122
122
  ],
123
123
  ],
junifer/preprocess/warping/tests/test_space_warper.py CHANGED
@@ -70,13 +70,13 @@ def test_SpaceWarper_errors(
70
70
  [
71
71
  DMCC13Benchmark(
72
72
  types=["BOLD", "T1w", "Warp"],
73
- sessions=["wave1bas"],
73
+ sessions=["ses-wave1bas"],
74
74
  tasks=["Rest"],
75
75
  phase_encodings=["AP"],
76
76
  runs=["1"],
77
77
  native_t1w=True,
78
78
  ),
79
- ("f9057kp", "wave1bas", "Rest", "AP", "1"),
79
+ ("sub-f9057kp", "ses-wave1bas", "Rest", "AP", "1"),
80
80
  "ants",
81
81
  ],
82
82
  [
@@ -135,25 +135,25 @@ def test_SpaceWarper_native(
135
135
  [
136
136
  DMCC13Benchmark(
137
137
  types=["T1w"],
138
- sessions=["wave1bas"],
138
+ sessions=["ses-wave1bas"],
139
139
  tasks=["Rest"],
140
140
  phase_encodings=["AP"],
141
141
  runs=["1"],
142
142
  native_t1w=False,
143
143
  ),
144
- ("f9057kp", "wave1bas", "Rest", "AP", "1"),
144
+ ("sub-f9057kp", "ses-wave1bas", "Rest", "AP", "1"),
145
145
  "MNI152NLin2009aAsym",
146
146
  ],
147
147
  [
148
148
  DMCC13Benchmark(
149
149
  types=["T1w"],
150
- sessions=["wave1bas"],
150
+ sessions=["ses-wave1bas"],
151
151
  tasks=["Rest"],
152
152
  phase_encodings=["AP"],
153
153
  runs=["1"],
154
154
  native_t1w=False,
155
155
  ),
156
- ("f9057kp", "wave1bas", "Rest", "AP", "1"),
156
+ ("sub-f9057kp", "ses-wave1bas", "Rest", "AP", "1"),
157
157
  "MNI152NLin6Asym",
158
158
  ],
159
159
  ],
{junifer-0.0.4.dev824.dist-info → junifer-0.0.4.dev831.dist-info}/METADATA RENAMED
@@ -1,6 +1,6 @@
1
1
  Metadata-Version: 2.1
2
2
  Name: junifer
3
- Version: 0.0.4.dev824
3
+ Version: 0.0.4.dev831
4
4
  Summary: JUelich NeuroImaging FEature extractoR
5
5
  Author-email: Fede Raimondo <f.raimondo@fz-juelich.de>, Synchon Mandal <s.mandal@fz-juelich.de>
6
6
  Maintainer-email: Fede Raimondo <f.raimondo@fz-juelich.de>, Synchon Mandal <s.mandal@fz-juelich.de>
{junifer-0.0.4.dev824.dist-info → junifer-0.0.4.dev831.dist-info}/RECORD RENAMED
@@ -1,5 +1,5 @@
1
1
  junifer/__init__.py,sha256=x1UR2jUcrUdm2HNl-3Qvyi4UUrU6ms5qm2qcmNY7zZk,391
2
- junifer/_version.py,sha256=UagWSi-zHoGa6KS0dHcXrPxUENdONGC6fscTIQ6HMn8,428
2
+ junifer/_version.py,sha256=49QCIbmjequispHfWYN5Texe7FGM_le9CtB5yJ62hJg,428
3
3
  junifer/stats.py,sha256=sU5IZ2qFZWbzgSutQS_z42miIVItpSGmQYBn6KkD5fA,6162
4
4
  junifer/api/__init__.py,sha256=YILu9M7SC0Ri4CVd90fELH2OnK_gvCYAXCoqBNCFE8E,257
5
5
  junifer/api/cli.py,sha256=_fC35jp0YzqNIpO5yvTb_5QBmUpw6sRFgVjBeoRbhO8,13627
@@ -39,11 +39,11 @@ junifer/api/tests/data/partly_cloudy_agg_mean_tian.yml,sha256=nS8K_R1hEuV71Vv-i9
39
39
  junifer/configs/__init__.py,sha256=r6BU6vW7FVapSD81j24QeQiZe1oKspsJJRRPjXnCk00,120
40
40
  junifer/configs/juseless/__init__.py,sha256=Ws98DvlLEMHfwW6BjmvHQmqTlFRDps9r4pLAfNjfEiM,149
41
41
  junifer/configs/juseless/datagrabbers/__init__.py,sha256=tqCLmelWqB1xfElvknnaJ5oVRPp9XVXtZLzIpxYIghg,452
42
- junifer/configs/juseless/datagrabbers/aomic_id1000_vbm.py,sha256=HNyfxjU_D7hkwnaeSW1r_PllOlc3phBq2LP25zZGziE,1474
43
- junifer/configs/juseless/datagrabbers/camcan_vbm.py,sha256=PtzjrfL2b6nxXLQ4TU8cKftHnD4g7nk4bf2ib6WLqGg,1505
44
- junifer/configs/juseless/datagrabbers/ixi_vbm.py,sha256=OE2D311Sfey0DrfoKqWB_hFIBApzP3-r1M9sliKZPC4,2309
45
- junifer/configs/juseless/datagrabbers/ucla.py,sha256=QtCA1X2JGv3EJE7kDbmSwkEvAjTm5XwpACPazBXhFqQ,4891
46
- junifer/configs/juseless/datagrabbers/ukb_vbm.py,sha256=lb9pLXFnlMOeQUX-BBFD9dKECdaU2bEIHA-iD9KkOAQ,1489
42
+ junifer/configs/juseless/datagrabbers/aomic_id1000_vbm.py,sha256=vY4xfZA1v_6zdCELoG9hHpe6BHfumEJGTvLxMUaX9Uw,1466
43
+ junifer/configs/juseless/datagrabbers/camcan_vbm.py,sha256=GXnDML55kKEGSb38olRUWL_AFdN9IvPViEGP9CaDTUQ,1497
44
+ junifer/configs/juseless/datagrabbers/ixi_vbm.py,sha256=HvRQWGIdoNX47Sr13GCyhNFG318Ii1GUktvePNyVN6o,2301
45
+ junifer/configs/juseless/datagrabbers/ucla.py,sha256=C14OW7eI2kruJIqgAsd_PtJTyW5R8wp9lDOpQOnfarM,4843
46
+ junifer/configs/juseless/datagrabbers/ukb_vbm.py,sha256=d2N3X1OVrcmkKNVkruNDKzU2iqBH9oGUnhfxkg0-7aw,1485
47
47
  junifer/configs/juseless/datagrabbers/tests/test_aomic_id1000_vbm.py,sha256=Y_npFmmj0MN0TYv8jaxVMgFHLMQLZ8vXl8lWQKvOYbc,1001
48
48
  junifer/configs/juseless/datagrabbers/tests/test_camcan_vbm.py,sha256=o0dzptS97pxrWaY7I1m0dpJtsnAwmIXNqdU9ABTWCqI,975
49
49
  junifer/configs/juseless/datagrabbers/tests/test_ixi_vbm.py,sha256=8jxpNZelXwpJGvA5LOfpso2X8yt1chvERAYmv76hS_g,1252
@@ -79,24 +79,24 @@ junifer/data/masks/vickery-patil/CAT12_IXI555_MNI152_TMP_GS_GMprob0.2_clean_3mm.
79
79
  junifer/data/masks/vickery-patil/GMprob0.2_cortex_3mm_NA_rm.nii.gz,sha256=jfMe_4H9XEnArYms5bSQbqS2V1_HbLHTfI5amQa_Pes,8700
80
80
  junifer/data/tests/test_coordinates.py,sha256=BNkz9qFbnwAI0oVlIm_XrT-z4Vsia_rMtMVaoFXT6mU,4328
81
81
  junifer/data/tests/test_data_utils.py,sha256=_DaiC8K79gs9HFHxr-udNeE2YTM6JA0-1i-K2cqK9qA,1087
82
- junifer/data/tests/test_masks.py,sha256=cZmj6UZmuyqXI-8zMqAkuim6DWYecjaMCPo00cr_J5g,16160
82
+ junifer/data/tests/test_masks.py,sha256=hJAvwPElhzvHYN15-6n98ABgCD-3lBY5WwHFuhImRe0,16172
83
83
  junifer/data/tests/test_parcellations.py,sha256=ZEU1VHIK0AyxpclcJhG_0rQU0phaBU_dHP7Erfi3mN8,38222
84
84
  junifer/data/tests/test_template_spaces.py,sha256=PJulN7xHpAcSOTY-UzTG_WPywZEBSlAZGiNG4gzk1_8,3144
85
85
  junifer/datagrabber/__init__.py,sha256=pZHJIY8nAlbVngsyRScE6a6GKbytiwjJB7SdJNqIbl4,680
86
86
  junifer/datagrabber/base.py,sha256=KgMSKfkwd4yLW4PhoJDoWMgcDkGmDoIs6jkgKyOJd9A,6303
87
87
  junifer/datagrabber/datalad_base.py,sha256=SsGUJdefdDgAJARBG5kHcbLK2CvvnoEto0TpGZUgnWE,10659
88
- junifer/datagrabber/dmcc13_benchmark.py,sha256=vXpMWSFbqAIUm9tNCSrpMZeOzOEjls6YAyoCR0kLZlA,12872
88
+ junifer/datagrabber/dmcc13_benchmark.py,sha256=K7-TnVRCDQwL6IIaFofJABKr2Jho0loewAavzdmBjK0,12869
89
89
  junifer/datagrabber/multiple.py,sha256=eXQIsvSNvD8GuEITjMaMoi1GwoeyWXXbQMRi-f2qgc4,4923
90
90
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- junifer/datagrabber/aomic/tests/test_piop2.py,sha256=E2F-jAVFUYcJLoUZ7mfw8ittBhk_KwxzBKSONnVsFuw,5293
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+ junifer/datagrabber/aomic/id1000.py,sha256=hvi-25NWeakUX4Pu1YDjxfKbo6U4WUjw-I9c2kGmgnk,6005
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+ junifer/datagrabber/aomic/piop1.py,sha256=ivQ1wjYAR1qb-fN13NWA-69iS8XvgMMUCwQR5fBh2n0,8428
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+ junifer/datagrabber/aomic/piop2.py,sha256=LuYQL4t4k-K_74Gd8zVnV7Y5W6tt1krBpk0a7D5LQ9Q,8047
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+ junifer/datagrabber/aomic/tests/test_id1000.py,sha256=Rk14VsWOp36D2_JXxFswKXNYQfc1UbVAQxDpq5qJHCs,4712
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+ junifer/datagrabber/aomic/tests/test_piop1.py,sha256=Faqmya-OisThPom1nooxlacaCD4afLFSw03Wn58gK6g,5466
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- junifer/datagrabber/tests/test_dmcc13_benchmark.py,sha256=5aTfsjfOK1cvhDm2Qb9UtHdkFJbzOezB7czCX6xjsg0,8063
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+ junifer/datagrabber/tests/test_dmcc13_benchmark.py,sha256=m1_ODoGAvSiFeGS-tyTaK1YHTveQRDeCWBsNjdknh04,8171
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@@ -205,20 +205,20 @@ junifer/preprocess/base.py,sha256=Bn1VdonQ1f_DDPwFMpdaeyfLfNSnROulr-U8HuGQ81A,66
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+ junifer/preprocess/ants/tests/test_ants_apply_transforms_warper.py,sha256=IIwzo7iTFR2xy00S59ubXb0JSPukdPiRv6mdd25oeBA,1678
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- junifer/preprocess/tests/test_bold_warper.py,sha256=sPS8Xd9Ix5TIvxiTCkfRDcA_zxk-2UUteIt68Rv6JGw,4600
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+ junifer/preprocess/tests/test_bold_warper.py,sha256=U_r7DwPWoO_it1LIkhuQWBe20a-6X5c8o0AvTOnWKEc,4636
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- junifer/preprocess/warping/tests/test_space_warper.py,sha256=ph92dIDOr9ih9tkqT0yo5tnQL3UkOgQRXG3WzP5QLSE,5586
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+ junifer/preprocess/warping/tests/test_space_warper.py,sha256=hHF97XUrMeAu8pIPBUrqD77PijbSv5_dAj9-Zte7UZM,5622
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@@ -248,10 +248,10 @@ junifer/utils/logging.py,sha256=furcU3XIUpUvnpe4PEwzWWIWgmH4j2ZA4MQdvSGWjj0,9216
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- junifer-0.0.4.dev824.dist-info/AUTHORS.rst,sha256=rmULKpchpSol4ExWFdm-qu4fkpSZPYqIESVJBZtGb6E,163
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- junifer-0.0.4.dev824.dist-info/LICENSE.md,sha256=MqCnOBu8uXsEOzRZWh9EBVfVz-kE9NkXcLCrtGXo2yU,34354
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- junifer-0.0.4.dev824.dist-info/METADATA,sha256=fGHhDFaE8INr9IaHX8WoX-C_RP2Y52kl8Lx5lizlYPM,8235
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- junifer-0.0.4.dev824.dist-info/WHEEL,sha256=GJ7t_kWBFywbagK5eo9IoUwLW6oyOeTKmQ-9iHFVNxQ,92
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- junifer-0.0.4.dev824.dist-info/entry_points.txt,sha256=DxFvKq0pOqRunAK0FxwJcoDfV1-dZvsFDpD5HRqSDhw,48
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- junifer-0.0.4.dev824.dist-info/top_level.txt,sha256=4bAq1R2QFQ4b3hohjys2JBvxrl0GKk5LNFzYvz9VGcA,8
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- junifer-0.0.4.dev824.dist-info/RECORD,,
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+ junifer-0.0.4.dev831.dist-info/AUTHORS.rst,sha256=rmULKpchpSol4ExWFdm-qu4fkpSZPYqIESVJBZtGb6E,163
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+ junifer-0.0.4.dev831.dist-info/LICENSE.md,sha256=MqCnOBu8uXsEOzRZWh9EBVfVz-kE9NkXcLCrtGXo2yU,34354
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+ junifer-0.0.4.dev831.dist-info/METADATA,sha256=Jd7BAiWWLytawTNB3q4m5LVdTrhyY3RzRY6xEVjqNRE,8235
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+ junifer-0.0.4.dev831.dist-info/WHEEL,sha256=GJ7t_kWBFywbagK5eo9IoUwLW6oyOeTKmQ-9iHFVNxQ,92
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+ junifer-0.0.4.dev831.dist-info/entry_points.txt,sha256=DxFvKq0pOqRunAK0FxwJcoDfV1-dZvsFDpD5HRqSDhw,48
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+ junifer-0.0.4.dev831.dist-info/top_level.txt,sha256=4bAq1R2QFQ4b3hohjys2JBvxrl0GKk5LNFzYvz9VGcA,8
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+ junifer-0.0.4.dev831.dist-info/RECORD,,