junifer 0.0.4.dev831__py3-none-any.whl → 0.0.5__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 (206) hide show
  1. junifer/__init__.py +17 -0
  2. junifer/_version.py +2 -2
  3. junifer/api/__init__.py +4 -1
  4. junifer/api/cli.py +91 -1
  5. junifer/api/decorators.py +9 -0
  6. junifer/api/functions.py +56 -10
  7. junifer/api/parser.py +3 -0
  8. junifer/api/queue_context/__init__.py +4 -1
  9. junifer/api/queue_context/gnu_parallel_local_adapter.py +16 -6
  10. junifer/api/queue_context/htcondor_adapter.py +16 -5
  11. junifer/api/queue_context/tests/test_gnu_parallel_local_adapter.py +41 -12
  12. junifer/api/queue_context/tests/test_htcondor_adapter.py +48 -15
  13. junifer/api/res/afni/run_afni_docker.sh +1 -1
  14. junifer/api/res/ants/run_ants_docker.sh +1 -1
  15. junifer/api/res/freesurfer/mri_binarize +3 -0
  16. junifer/api/res/freesurfer/mri_mc +3 -0
  17. junifer/api/res/freesurfer/mri_pretess +3 -0
  18. junifer/api/res/freesurfer/mris_convert +3 -0
  19. junifer/api/res/freesurfer/run_freesurfer_docker.sh +61 -0
  20. junifer/api/res/fsl/run_fsl_docker.sh +1 -1
  21. junifer/api/res/{run_conda.sh → run_conda.bash} +1 -1
  22. junifer/api/res/run_conda.zsh +23 -0
  23. junifer/api/res/run_venv.bash +22 -0
  24. junifer/api/res/{run_venv.sh → run_venv.zsh} +1 -1
  25. junifer/api/tests/test_api_utils.py +4 -2
  26. junifer/api/tests/test_cli.py +83 -0
  27. junifer/api/tests/test_functions.py +27 -2
  28. junifer/configs/__init__.py +1 -1
  29. junifer/configs/juseless/__init__.py +4 -1
  30. junifer/configs/juseless/datagrabbers/__init__.py +10 -1
  31. junifer/configs/juseless/datagrabbers/aomic_id1000_vbm.py +4 -3
  32. junifer/configs/juseless/datagrabbers/camcan_vbm.py +3 -0
  33. junifer/configs/juseless/datagrabbers/ixi_vbm.py +4 -3
  34. junifer/configs/juseless/datagrabbers/tests/test_ucla.py +1 -3
  35. junifer/configs/juseless/datagrabbers/ucla.py +12 -9
  36. junifer/configs/juseless/datagrabbers/ukb_vbm.py +3 -0
  37. junifer/data/__init__.py +21 -1
  38. junifer/data/coordinates.py +10 -19
  39. junifer/data/masks/ukb/UKB_15K_GM_template.nii.gz +0 -0
  40. junifer/data/masks.py +58 -87
  41. junifer/data/parcellations.py +14 -3
  42. junifer/data/template_spaces.py +4 -1
  43. junifer/data/tests/test_masks.py +26 -37
  44. junifer/data/utils.py +3 -0
  45. junifer/datagrabber/__init__.py +18 -1
  46. junifer/datagrabber/aomic/__init__.py +3 -0
  47. junifer/datagrabber/aomic/id1000.py +70 -37
  48. junifer/datagrabber/aomic/piop1.py +69 -36
  49. junifer/datagrabber/aomic/piop2.py +71 -38
  50. junifer/datagrabber/aomic/tests/test_id1000.py +44 -100
  51. junifer/datagrabber/aomic/tests/test_piop1.py +65 -108
  52. junifer/datagrabber/aomic/tests/test_piop2.py +45 -102
  53. junifer/datagrabber/base.py +13 -6
  54. junifer/datagrabber/datalad_base.py +13 -1
  55. junifer/datagrabber/dmcc13_benchmark.py +36 -53
  56. junifer/datagrabber/hcp1200/__init__.py +3 -0
  57. junifer/datagrabber/hcp1200/datalad_hcp1200.py +3 -0
  58. junifer/datagrabber/hcp1200/hcp1200.py +4 -1
  59. junifer/datagrabber/multiple.py +45 -6
  60. junifer/datagrabber/pattern.py +170 -62
  61. junifer/datagrabber/pattern_datalad.py +25 -12
  62. junifer/datagrabber/pattern_validation_mixin.py +388 -0
  63. junifer/datagrabber/tests/test_datalad_base.py +4 -4
  64. junifer/datagrabber/tests/test_dmcc13_benchmark.py +46 -19
  65. junifer/datagrabber/tests/test_multiple.py +161 -84
  66. junifer/datagrabber/tests/test_pattern.py +45 -0
  67. junifer/datagrabber/tests/test_pattern_datalad.py +4 -4
  68. junifer/datagrabber/tests/test_pattern_validation_mixin.py +249 -0
  69. junifer/datareader/__init__.py +4 -1
  70. junifer/datareader/default.py +95 -43
  71. junifer/external/BrainPrint/brainprint/__init__.py +4 -0
  72. junifer/external/BrainPrint/brainprint/_version.py +3 -0
  73. junifer/external/BrainPrint/brainprint/asymmetry.py +91 -0
  74. junifer/external/BrainPrint/brainprint/brainprint.py +441 -0
  75. junifer/external/BrainPrint/brainprint/surfaces.py +258 -0
  76. junifer/external/BrainPrint/brainprint/utils/__init__.py +1 -0
  77. junifer/external/BrainPrint/brainprint/utils/_config.py +112 -0
  78. junifer/external/BrainPrint/brainprint/utils/utils.py +188 -0
  79. junifer/external/__init__.py +1 -1
  80. junifer/external/nilearn/__init__.py +5 -1
  81. junifer/external/nilearn/junifer_connectivity_measure.py +483 -0
  82. junifer/external/nilearn/junifer_nifti_spheres_masker.py +23 -9
  83. junifer/external/nilearn/tests/test_junifer_connectivity_measure.py +1089 -0
  84. junifer/external/nilearn/tests/test_junifer_nifti_spheres_masker.py +76 -1
  85. junifer/markers/__init__.py +23 -1
  86. junifer/markers/base.py +68 -28
  87. junifer/markers/brainprint.py +459 -0
  88. junifer/markers/collection.py +10 -2
  89. junifer/markers/complexity/__init__.py +10 -0
  90. junifer/markers/complexity/complexity_base.py +26 -43
  91. junifer/markers/complexity/hurst_exponent.py +3 -0
  92. junifer/markers/complexity/multiscale_entropy_auc.py +3 -0
  93. junifer/markers/complexity/perm_entropy.py +3 -0
  94. junifer/markers/complexity/range_entropy.py +3 -0
  95. junifer/markers/complexity/range_entropy_auc.py +3 -0
  96. junifer/markers/complexity/sample_entropy.py +3 -0
  97. junifer/markers/complexity/tests/test_hurst_exponent.py +11 -3
  98. junifer/markers/complexity/tests/test_multiscale_entropy_auc.py +11 -3
  99. junifer/markers/complexity/tests/test_perm_entropy.py +11 -3
  100. junifer/markers/complexity/tests/test_range_entropy.py +11 -3
  101. junifer/markers/complexity/tests/test_range_entropy_auc.py +11 -3
  102. junifer/markers/complexity/tests/test_sample_entropy.py +11 -3
  103. junifer/markers/complexity/tests/test_weighted_perm_entropy.py +11 -3
  104. junifer/markers/complexity/weighted_perm_entropy.py +3 -0
  105. junifer/markers/ets_rss.py +27 -42
  106. junifer/markers/falff/__init__.py +3 -0
  107. junifer/markers/falff/_afni_falff.py +5 -2
  108. junifer/markers/falff/_junifer_falff.py +3 -0
  109. junifer/markers/falff/falff_base.py +20 -46
  110. junifer/markers/falff/falff_parcels.py +56 -27
  111. junifer/markers/falff/falff_spheres.py +60 -29
  112. junifer/markers/falff/tests/test_falff_parcels.py +39 -23
  113. junifer/markers/falff/tests/test_falff_spheres.py +39 -23
  114. junifer/markers/functional_connectivity/__init__.py +9 -0
  115. junifer/markers/functional_connectivity/crossparcellation_functional_connectivity.py +63 -60
  116. junifer/markers/functional_connectivity/edge_functional_connectivity_parcels.py +45 -32
  117. junifer/markers/functional_connectivity/edge_functional_connectivity_spheres.py +49 -36
  118. junifer/markers/functional_connectivity/functional_connectivity_base.py +71 -70
  119. junifer/markers/functional_connectivity/functional_connectivity_parcels.py +34 -25
  120. junifer/markers/functional_connectivity/functional_connectivity_spheres.py +40 -30
  121. junifer/markers/functional_connectivity/tests/test_crossparcellation_functional_connectivity.py +11 -7
  122. junifer/markers/functional_connectivity/tests/test_edge_functional_connectivity_parcels.py +27 -7
  123. junifer/markers/functional_connectivity/tests/test_edge_functional_connectivity_spheres.py +28 -12
  124. junifer/markers/functional_connectivity/tests/test_functional_connectivity_parcels.py +35 -11
  125. junifer/markers/functional_connectivity/tests/test_functional_connectivity_spheres.py +36 -62
  126. junifer/markers/parcel_aggregation.py +47 -61
  127. junifer/markers/reho/__init__.py +3 -0
  128. junifer/markers/reho/_afni_reho.py +5 -2
  129. junifer/markers/reho/_junifer_reho.py +4 -1
  130. junifer/markers/reho/reho_base.py +8 -27
  131. junifer/markers/reho/reho_parcels.py +28 -17
  132. junifer/markers/reho/reho_spheres.py +27 -18
  133. junifer/markers/reho/tests/test_reho_parcels.py +8 -3
  134. junifer/markers/reho/tests/test_reho_spheres.py +8 -3
  135. junifer/markers/sphere_aggregation.py +43 -59
  136. junifer/markers/temporal_snr/__init__.py +3 -0
  137. junifer/markers/temporal_snr/temporal_snr_base.py +23 -32
  138. junifer/markers/temporal_snr/temporal_snr_parcels.py +9 -6
  139. junifer/markers/temporal_snr/temporal_snr_spheres.py +9 -6
  140. junifer/markers/temporal_snr/tests/test_temporal_snr_parcels.py +6 -3
  141. junifer/markers/temporal_snr/tests/test_temporal_snr_spheres.py +6 -3
  142. junifer/markers/tests/test_brainprint.py +58 -0
  143. junifer/markers/tests/test_collection.py +9 -8
  144. junifer/markers/tests/test_ets_rss.py +15 -9
  145. junifer/markers/tests/test_markers_base.py +17 -18
  146. junifer/markers/tests/test_parcel_aggregation.py +93 -32
  147. junifer/markers/tests/test_sphere_aggregation.py +72 -19
  148. junifer/onthefly/__init__.py +4 -1
  149. junifer/onthefly/read_transform.py +3 -0
  150. junifer/pipeline/__init__.py +9 -1
  151. junifer/pipeline/pipeline_step_mixin.py +21 -4
  152. junifer/pipeline/registry.py +3 -0
  153. junifer/pipeline/singleton.py +3 -0
  154. junifer/pipeline/tests/test_registry.py +1 -1
  155. junifer/pipeline/update_meta_mixin.py +3 -0
  156. junifer/pipeline/utils.py +67 -1
  157. junifer/pipeline/workdir_manager.py +3 -0
  158. junifer/preprocess/__init__.py +10 -2
  159. junifer/preprocess/base.py +6 -3
  160. junifer/preprocess/confounds/__init__.py +3 -0
  161. junifer/preprocess/confounds/fmriprep_confound_remover.py +47 -60
  162. junifer/preprocess/confounds/tests/test_fmriprep_confound_remover.py +72 -113
  163. junifer/preprocess/smoothing/__init__.py +9 -0
  164. junifer/preprocess/smoothing/_afni_smoothing.py +119 -0
  165. junifer/preprocess/smoothing/_fsl_smoothing.py +116 -0
  166. junifer/preprocess/smoothing/_nilearn_smoothing.py +69 -0
  167. junifer/preprocess/smoothing/smoothing.py +174 -0
  168. junifer/preprocess/smoothing/tests/test_smoothing.py +94 -0
  169. junifer/preprocess/warping/__init__.py +3 -0
  170. junifer/preprocess/warping/_ants_warper.py +3 -0
  171. junifer/preprocess/warping/_fsl_warper.py +3 -0
  172. junifer/stats.py +4 -1
  173. junifer/storage/__init__.py +9 -1
  174. junifer/storage/base.py +40 -1
  175. junifer/storage/hdf5.py +71 -9
  176. junifer/storage/pandas_base.py +3 -0
  177. junifer/storage/sqlite.py +3 -0
  178. junifer/storage/tests/test_hdf5.py +82 -10
  179. junifer/storage/utils.py +9 -0
  180. junifer/testing/__init__.py +4 -1
  181. junifer/testing/datagrabbers.py +13 -6
  182. junifer/testing/tests/test_partlycloudytesting_datagrabber.py +7 -7
  183. junifer/testing/utils.py +3 -0
  184. junifer/utils/__init__.py +13 -2
  185. junifer/utils/fs.py +3 -0
  186. junifer/utils/helpers.py +32 -1
  187. junifer/utils/logging.py +33 -4
  188. junifer/utils/tests/test_logging.py +8 -0
  189. {junifer-0.0.4.dev831.dist-info → junifer-0.0.5.dist-info}/METADATA +17 -16
  190. junifer-0.0.5.dist-info/RECORD +275 -0
  191. {junifer-0.0.4.dev831.dist-info → junifer-0.0.5.dist-info}/WHEEL +1 -1
  192. junifer/datagrabber/tests/test_datagrabber_utils.py +0 -218
  193. junifer/datagrabber/utils.py +0 -230
  194. junifer/preprocess/ants/__init__.py +0 -4
  195. junifer/preprocess/ants/ants_apply_transforms_warper.py +0 -185
  196. junifer/preprocess/ants/tests/test_ants_apply_transforms_warper.py +0 -56
  197. junifer/preprocess/bold_warper.py +0 -265
  198. junifer/preprocess/fsl/__init__.py +0 -4
  199. junifer/preprocess/fsl/apply_warper.py +0 -179
  200. junifer/preprocess/fsl/tests/test_apply_warper.py +0 -45
  201. junifer/preprocess/tests/test_bold_warper.py +0 -159
  202. junifer-0.0.4.dev831.dist-info/RECORD +0 -257
  203. {junifer-0.0.4.dev831.dist-info → junifer-0.0.5.dist-info}/AUTHORS.rst +0 -0
  204. {junifer-0.0.4.dev831.dist-info → junifer-0.0.5.dist-info}/LICENSE.md +0 -0
  205. {junifer-0.0.4.dev831.dist-info → junifer-0.0.5.dist-info}/entry_points.txt +0 -0
  206. {junifer-0.0.4.dev831.dist-info → junifer-0.0.5.dist-info}/top_level.txt +0 -0
junifer-0.0.4.dev831.dist-info/RECORD DELETED
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- junifer/configs/juseless/datagrabbers/aomic_id1000_vbm.py,sha256=vY4xfZA1v_6zdCELoG9hHpe6BHfumEJGTvLxMUaX9Uw,1466
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- junifer/configs/juseless/datagrabbers/ixi_vbm.py,sha256=HvRQWGIdoNX47Sr13GCyhNFG318Ii1GUktvePNyVN6o,2301
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