junifer 0.0.5.dev240__py3-none-any.whl → 0.0.6__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 (279) hide show
  1. junifer/__init__.py +2 -31
  2. junifer/__init__.pyi +37 -0
  3. junifer/_version.py +9 -4
  4. junifer/api/__init__.py +3 -5
  5. junifer/api/__init__.pyi +4 -0
  6. junifer/api/decorators.py +14 -19
  7. junifer/api/functions.py +165 -109
  8. junifer/api/py.typed +0 -0
  9. junifer/api/queue_context/__init__.py +2 -4
  10. junifer/api/queue_context/__init__.pyi +5 -0
  11. junifer/api/queue_context/gnu_parallel_local_adapter.py +22 -6
  12. junifer/api/queue_context/htcondor_adapter.py +23 -6
  13. junifer/api/queue_context/py.typed +0 -0
  14. junifer/api/queue_context/tests/test_gnu_parallel_local_adapter.py +3 -3
  15. junifer/api/queue_context/tests/test_htcondor_adapter.py +3 -3
  16. junifer/api/tests/test_functions.py +168 -74
  17. junifer/cli/__init__.py +24 -0
  18. junifer/cli/__init__.pyi +3 -0
  19. junifer/{api → cli}/cli.py +141 -125
  20. junifer/cli/parser.py +235 -0
  21. junifer/cli/py.typed +0 -0
  22. junifer/{api → cli}/tests/test_cli.py +8 -8
  23. junifer/{api/tests/test_api_utils.py → cli/tests/test_cli_utils.py} +5 -4
  24. junifer/{api → cli}/tests/test_parser.py +2 -2
  25. junifer/{api → cli}/utils.py +6 -16
  26. junifer/configs/juseless/__init__.py +2 -2
  27. junifer/configs/juseless/__init__.pyi +3 -0
  28. junifer/configs/juseless/datagrabbers/__init__.py +2 -12
  29. junifer/configs/juseless/datagrabbers/__init__.pyi +13 -0
  30. junifer/configs/juseless/datagrabbers/ixi_vbm.py +2 -2
  31. junifer/configs/juseless/datagrabbers/py.typed +0 -0
  32. junifer/configs/juseless/datagrabbers/tests/test_ucla.py +2 -2
  33. junifer/configs/juseless/datagrabbers/ucla.py +4 -4
  34. junifer/configs/juseless/py.typed +0 -0
  35. junifer/conftest.py +25 -0
  36. junifer/data/__init__.py +2 -42
  37. junifer/data/__init__.pyi +29 -0
  38. junifer/data/_dispatch.py +248 -0
  39. junifer/data/coordinates/__init__.py +9 -0
  40. junifer/data/coordinates/__init__.pyi +5 -0
  41. junifer/data/coordinates/_ants_coordinates_warper.py +104 -0
  42. junifer/data/coordinates/_coordinates.py +385 -0
  43. junifer/data/coordinates/_fsl_coordinates_warper.py +81 -0
  44. junifer/data/{tests → coordinates/tests}/test_coordinates.py +26 -33
  45. junifer/data/masks/__init__.py +9 -0
  46. junifer/data/masks/__init__.pyi +6 -0
  47. junifer/data/masks/_ants_mask_warper.py +177 -0
  48. junifer/data/masks/_fsl_mask_warper.py +106 -0
  49. junifer/data/masks/_masks.py +802 -0
  50. junifer/data/{tests → masks/tests}/test_masks.py +67 -63
  51. junifer/data/parcellations/__init__.py +9 -0
  52. junifer/data/parcellations/__init__.pyi +6 -0
  53. junifer/data/parcellations/_ants_parcellation_warper.py +166 -0
  54. junifer/data/parcellations/_fsl_parcellation_warper.py +89 -0
  55. junifer/data/parcellations/_parcellations.py +1388 -0
  56. junifer/data/{tests → parcellations/tests}/test_parcellations.py +165 -295
  57. junifer/data/pipeline_data_registry_base.py +76 -0
  58. junifer/data/py.typed +0 -0
  59. junifer/data/template_spaces.py +44 -79
  60. junifer/data/tests/test_data_utils.py +1 -2
  61. junifer/data/tests/test_template_spaces.py +8 -4
  62. junifer/data/utils.py +109 -4
  63. junifer/datagrabber/__init__.py +2 -26
  64. junifer/datagrabber/__init__.pyi +27 -0
  65. junifer/datagrabber/aomic/__init__.py +2 -4
  66. junifer/datagrabber/aomic/__init__.pyi +5 -0
  67. junifer/datagrabber/aomic/id1000.py +81 -52
  68. junifer/datagrabber/aomic/piop1.py +83 -55
  69. junifer/datagrabber/aomic/piop2.py +85 -56
  70. junifer/datagrabber/aomic/py.typed +0 -0
  71. junifer/datagrabber/aomic/tests/test_id1000.py +19 -12
  72. junifer/datagrabber/aomic/tests/test_piop1.py +52 -18
  73. junifer/datagrabber/aomic/tests/test_piop2.py +50 -17
  74. junifer/datagrabber/base.py +22 -18
  75. junifer/datagrabber/datalad_base.py +71 -34
  76. junifer/datagrabber/dmcc13_benchmark.py +31 -18
  77. junifer/datagrabber/hcp1200/__init__.py +2 -3
  78. junifer/datagrabber/hcp1200/__init__.pyi +4 -0
  79. junifer/datagrabber/hcp1200/datalad_hcp1200.py +3 -3
  80. junifer/datagrabber/hcp1200/hcp1200.py +26 -15
  81. junifer/datagrabber/hcp1200/py.typed +0 -0
  82. junifer/datagrabber/hcp1200/tests/test_hcp1200.py +8 -2
  83. junifer/datagrabber/multiple.py +14 -9
  84. junifer/datagrabber/pattern.py +132 -96
  85. junifer/datagrabber/pattern_validation_mixin.py +206 -94
  86. junifer/datagrabber/py.typed +0 -0
  87. junifer/datagrabber/tests/test_datalad_base.py +27 -12
  88. junifer/datagrabber/tests/test_dmcc13_benchmark.py +28 -11
  89. junifer/datagrabber/tests/test_multiple.py +48 -2
  90. junifer/datagrabber/tests/test_pattern_datalad.py +1 -1
  91. junifer/datagrabber/tests/test_pattern_validation_mixin.py +6 -6
  92. junifer/datareader/__init__.py +2 -2
  93. junifer/datareader/__init__.pyi +3 -0
  94. junifer/datareader/default.py +6 -6
  95. junifer/datareader/py.typed +0 -0
  96. junifer/external/nilearn/__init__.py +2 -3
  97. junifer/external/nilearn/__init__.pyi +4 -0
  98. junifer/external/nilearn/junifer_connectivity_measure.py +25 -17
  99. junifer/external/nilearn/junifer_nifti_spheres_masker.py +4 -4
  100. junifer/external/nilearn/py.typed +0 -0
  101. junifer/external/nilearn/tests/test_junifer_connectivity_measure.py +17 -16
  102. junifer/external/nilearn/tests/test_junifer_nifti_spheres_masker.py +2 -3
  103. junifer/markers/__init__.py +2 -38
  104. junifer/markers/__init__.pyi +37 -0
  105. junifer/markers/base.py +11 -14
  106. junifer/markers/brainprint.py +12 -14
  107. junifer/markers/complexity/__init__.py +2 -18
  108. junifer/markers/complexity/__init__.pyi +17 -0
  109. junifer/markers/complexity/complexity_base.py +9 -11
  110. junifer/markers/complexity/hurst_exponent.py +7 -7
  111. junifer/markers/complexity/multiscale_entropy_auc.py +7 -7
  112. junifer/markers/complexity/perm_entropy.py +7 -7
  113. junifer/markers/complexity/py.typed +0 -0
  114. junifer/markers/complexity/range_entropy.py +7 -7
  115. junifer/markers/complexity/range_entropy_auc.py +7 -7
  116. junifer/markers/complexity/sample_entropy.py +7 -7
  117. junifer/markers/complexity/tests/test_complexity_base.py +1 -1
  118. junifer/markers/complexity/tests/test_hurst_exponent.py +5 -5
  119. junifer/markers/complexity/tests/test_multiscale_entropy_auc.py +5 -5
  120. junifer/markers/complexity/tests/test_perm_entropy.py +5 -5
  121. junifer/markers/complexity/tests/test_range_entropy.py +5 -5
  122. junifer/markers/complexity/tests/test_range_entropy_auc.py +5 -5
  123. junifer/markers/complexity/tests/test_sample_entropy.py +5 -5
  124. junifer/markers/complexity/tests/test_weighted_perm_entropy.py +5 -5
  125. junifer/markers/complexity/weighted_perm_entropy.py +7 -7
  126. junifer/markers/ets_rss.py +12 -11
  127. junifer/markers/falff/__init__.py +2 -3
  128. junifer/markers/falff/__init__.pyi +4 -0
  129. junifer/markers/falff/_afni_falff.py +38 -45
  130. junifer/markers/falff/_junifer_falff.py +16 -19
  131. junifer/markers/falff/falff_base.py +7 -11
  132. junifer/markers/falff/falff_parcels.py +9 -9
  133. junifer/markers/falff/falff_spheres.py +8 -8
  134. junifer/markers/falff/py.typed +0 -0
  135. junifer/markers/falff/tests/test_falff_spheres.py +3 -1
  136. junifer/markers/functional_connectivity/__init__.py +2 -12
  137. junifer/markers/functional_connectivity/__init__.pyi +13 -0
  138. junifer/markers/functional_connectivity/crossparcellation_functional_connectivity.py +9 -8
  139. junifer/markers/functional_connectivity/edge_functional_connectivity_parcels.py +8 -8
  140. junifer/markers/functional_connectivity/edge_functional_connectivity_spheres.py +7 -7
  141. junifer/markers/functional_connectivity/functional_connectivity_base.py +13 -12
  142. junifer/markers/functional_connectivity/functional_connectivity_parcels.py +8 -8
  143. junifer/markers/functional_connectivity/functional_connectivity_spheres.py +7 -7
  144. junifer/markers/functional_connectivity/py.typed +0 -0
  145. junifer/markers/functional_connectivity/tests/test_edge_functional_connectivity_parcels.py +1 -2
  146. junifer/markers/functional_connectivity/tests/test_edge_functional_connectivity_spheres.py +1 -2
  147. junifer/markers/functional_connectivity/tests/test_functional_connectivity_parcels.py +6 -6
  148. junifer/markers/functional_connectivity/tests/test_functional_connectivity_spheres.py +5 -5
  149. junifer/markers/parcel_aggregation.py +22 -17
  150. junifer/markers/py.typed +0 -0
  151. junifer/markers/reho/__init__.py +2 -3
  152. junifer/markers/reho/__init__.pyi +4 -0
  153. junifer/markers/reho/_afni_reho.py +29 -35
  154. junifer/markers/reho/_junifer_reho.py +13 -14
  155. junifer/markers/reho/py.typed +0 -0
  156. junifer/markers/reho/reho_base.py +7 -11
  157. junifer/markers/reho/reho_parcels.py +10 -10
  158. junifer/markers/reho/reho_spheres.py +9 -9
  159. junifer/markers/sphere_aggregation.py +22 -17
  160. junifer/markers/temporal_snr/__init__.py +2 -3
  161. junifer/markers/temporal_snr/__init__.pyi +4 -0
  162. junifer/markers/temporal_snr/py.typed +0 -0
  163. junifer/markers/temporal_snr/temporal_snr_base.py +11 -10
  164. junifer/markers/temporal_snr/temporal_snr_parcels.py +8 -8
  165. junifer/markers/temporal_snr/temporal_snr_spheres.py +7 -7
  166. junifer/markers/tests/test_ets_rss.py +3 -3
  167. junifer/markers/tests/test_parcel_aggregation.py +24 -24
  168. junifer/markers/tests/test_sphere_aggregation.py +6 -6
  169. junifer/markers/utils.py +3 -3
  170. junifer/onthefly/__init__.py +2 -1
  171. junifer/onthefly/_brainprint.py +138 -0
  172. junifer/onthefly/read_transform.py +5 -8
  173. junifer/pipeline/__init__.py +2 -10
  174. junifer/pipeline/__init__.pyi +13 -0
  175. junifer/{markers/collection.py → pipeline/marker_collection.py} +8 -14
  176. junifer/pipeline/pipeline_component_registry.py +294 -0
  177. junifer/pipeline/pipeline_step_mixin.py +15 -11
  178. junifer/pipeline/py.typed +0 -0
  179. junifer/{markers/tests/test_collection.py → pipeline/tests/test_marker_collection.py} +2 -3
  180. junifer/pipeline/tests/test_pipeline_component_registry.py +200 -0
  181. junifer/pipeline/tests/test_pipeline_step_mixin.py +36 -37
  182. junifer/pipeline/tests/test_update_meta_mixin.py +4 -4
  183. junifer/pipeline/tests/test_workdir_manager.py +43 -0
  184. junifer/pipeline/update_meta_mixin.py +21 -17
  185. junifer/pipeline/utils.py +6 -6
  186. junifer/pipeline/workdir_manager.py +19 -5
  187. junifer/preprocess/__init__.py +2 -10
  188. junifer/preprocess/__init__.pyi +11 -0
  189. junifer/preprocess/base.py +10 -10
  190. junifer/preprocess/confounds/__init__.py +2 -2
  191. junifer/preprocess/confounds/__init__.pyi +3 -0
  192. junifer/preprocess/confounds/fmriprep_confound_remover.py +243 -64
  193. junifer/preprocess/confounds/py.typed +0 -0
  194. junifer/preprocess/confounds/tests/test_fmriprep_confound_remover.py +121 -14
  195. junifer/preprocess/py.typed +0 -0
  196. junifer/preprocess/smoothing/__init__.py +2 -2
  197. junifer/preprocess/smoothing/__init__.pyi +3 -0
  198. junifer/preprocess/smoothing/_afni_smoothing.py +40 -40
  199. junifer/preprocess/smoothing/_fsl_smoothing.py +22 -32
  200. junifer/preprocess/smoothing/_nilearn_smoothing.py +35 -14
  201. junifer/preprocess/smoothing/py.typed +0 -0
  202. junifer/preprocess/smoothing/smoothing.py +11 -13
  203. junifer/preprocess/warping/__init__.py +2 -2
  204. junifer/preprocess/warping/__init__.pyi +3 -0
  205. junifer/preprocess/warping/_ants_warper.py +136 -32
  206. junifer/preprocess/warping/_fsl_warper.py +73 -22
  207. junifer/preprocess/warping/py.typed +0 -0
  208. junifer/preprocess/warping/space_warper.py +39 -11
  209. junifer/preprocess/warping/tests/test_space_warper.py +5 -9
  210. junifer/py.typed +0 -0
  211. junifer/stats.py +5 -5
  212. junifer/storage/__init__.py +2 -10
  213. junifer/storage/__init__.pyi +11 -0
  214. junifer/storage/base.py +47 -13
  215. junifer/storage/hdf5.py +95 -33
  216. junifer/storage/pandas_base.py +12 -11
  217. junifer/storage/py.typed +0 -0
  218. junifer/storage/sqlite.py +11 -11
  219. junifer/storage/tests/test_hdf5.py +86 -4
  220. junifer/storage/tests/test_sqlite.py +2 -2
  221. junifer/storage/tests/test_storage_base.py +5 -2
  222. junifer/storage/tests/test_utils.py +33 -7
  223. junifer/storage/utils.py +95 -9
  224. junifer/testing/__init__.py +2 -3
  225. junifer/testing/__init__.pyi +4 -0
  226. junifer/testing/datagrabbers.py +10 -11
  227. junifer/testing/py.typed +0 -0
  228. junifer/testing/registry.py +4 -7
  229. junifer/testing/tests/test_testing_registry.py +9 -17
  230. junifer/tests/test_stats.py +2 -2
  231. junifer/typing/__init__.py +9 -0
  232. junifer/typing/__init__.pyi +31 -0
  233. junifer/typing/_typing.py +68 -0
  234. junifer/utils/__init__.py +2 -12
  235. junifer/utils/__init__.pyi +18 -0
  236. junifer/utils/_config.py +110 -0
  237. junifer/utils/_yaml.py +16 -0
  238. junifer/utils/helpers.py +6 -6
  239. junifer/utils/logging.py +117 -8
  240. junifer/utils/py.typed +0 -0
  241. junifer/{pipeline → utils}/singleton.py +19 -14
  242. junifer/utils/tests/test_config.py +59 -0
  243. {junifer-0.0.5.dev240.dist-info → junifer-0.0.6.dist-info}/METADATA +43 -38
  244. junifer-0.0.6.dist-info/RECORD +350 -0
  245. {junifer-0.0.5.dev240.dist-info → junifer-0.0.6.dist-info}/WHEEL +1 -1
  246. junifer-0.0.6.dist-info/entry_points.txt +2 -0
  247. junifer/api/parser.py +0 -118
  248. junifer/data/coordinates.py +0 -408
  249. junifer/data/masks.py +0 -670
  250. junifer/data/parcellations.py +0 -1828
  251. junifer/pipeline/registry.py +0 -177
  252. junifer/pipeline/tests/test_registry.py +0 -150
  253. junifer-0.0.5.dev240.dist-info/RECORD +0 -275
  254. junifer-0.0.5.dev240.dist-info/entry_points.txt +0 -2
  255. /junifer/{api → cli}/tests/data/gmd_mean.yaml +0 -0
  256. /junifer/{api → cli}/tests/data/gmd_mean_htcondor.yaml +0 -0
  257. /junifer/{api → cli}/tests/data/partly_cloudy_agg_mean_tian.yml +0 -0
  258. /junifer/data/{VOIs → coordinates/VOIs}/meta/AutobiographicalMemory_VOIs.txt +0 -0
  259. /junifer/data/{VOIs → coordinates/VOIs}/meta/CogAC_VOIs.txt +0 -0
  260. /junifer/data/{VOIs → coordinates/VOIs}/meta/CogAR_VOIs.txt +0 -0
  261. /junifer/data/{VOIs → coordinates/VOIs}/meta/DMNBuckner_VOIs.txt +0 -0
  262. /junifer/data/{VOIs → coordinates/VOIs}/meta/Dosenbach2010_MNI_VOIs.txt +0 -0
  263. /junifer/data/{VOIs → coordinates/VOIs}/meta/Empathy_VOIs.txt +0 -0
  264. /junifer/data/{VOIs → coordinates/VOIs}/meta/Motor_VOIs.txt +0 -0
  265. /junifer/data/{VOIs → coordinates/VOIs}/meta/MultiTask_VOIs.txt +0 -0
  266. /junifer/data/{VOIs → coordinates/VOIs}/meta/PhysioStress_VOIs.txt +0 -0
  267. /junifer/data/{VOIs → coordinates/VOIs}/meta/Power2011_MNI_VOIs.txt +0 -0
  268. /junifer/data/{VOIs → coordinates/VOIs}/meta/Power2013_MNI_VOIs.tsv +0 -0
  269. /junifer/data/{VOIs → coordinates/VOIs}/meta/Rew_VOIs.txt +0 -0
  270. /junifer/data/{VOIs → coordinates/VOIs}/meta/Somatosensory_VOIs.txt +0 -0
  271. /junifer/data/{VOIs → coordinates/VOIs}/meta/ToM_VOIs.txt +0 -0
  272. /junifer/data/{VOIs → coordinates/VOIs}/meta/VigAtt_VOIs.txt +0 -0
  273. /junifer/data/{VOIs → coordinates/VOIs}/meta/WM_VOIs.txt +0 -0
  274. /junifer/data/{VOIs → coordinates/VOIs}/meta/eMDN_VOIs.txt +0 -0
  275. /junifer/data/{VOIs → coordinates/VOIs}/meta/eSAD_VOIs.txt +0 -0
  276. /junifer/data/{VOIs → coordinates/VOIs}/meta/extDMN_VOIs.txt +0 -0
  277. {junifer-0.0.5.dev240.dist-info → junifer-0.0.6.dist-info/licenses}/AUTHORS.rst +0 -0
  278. {junifer-0.0.5.dev240.dist-info → junifer-0.0.6.dist-info/licenses}/LICENSE.md +0 -0
  279. {junifer-0.0.5.dev240.dist-info → junifer-0.0.6.dist-info}/top_level.txt +0 -0