junifer 0.0.5__py3-none-any.whl → 0.0.5.dev24__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 (194) hide show
  1. junifer/__init__.py +0 -17
  2. junifer/_version.py +2 -2
  3. junifer/api/__init__.py +1 -4
  4. junifer/api/cli.py +1 -91
  5. junifer/api/decorators.py +0 -9
  6. junifer/api/functions.py +10 -56
  7. junifer/api/parser.py +0 -3
  8. junifer/api/queue_context/__init__.py +1 -4
  9. junifer/api/res/afni/run_afni_docker.sh +1 -1
  10. junifer/api/res/ants/run_ants_docker.sh +1 -1
  11. junifer/api/res/fsl/run_fsl_docker.sh +1 -1
  12. junifer/api/tests/test_api_utils.py +2 -4
  13. junifer/api/tests/test_cli.py +0 -83
  14. junifer/api/tests/test_functions.py +2 -27
  15. junifer/configs/__init__.py +1 -1
  16. junifer/configs/juseless/__init__.py +1 -4
  17. junifer/configs/juseless/datagrabbers/__init__.py +1 -10
  18. junifer/configs/juseless/datagrabbers/aomic_id1000_vbm.py +0 -3
  19. junifer/configs/juseless/datagrabbers/camcan_vbm.py +0 -3
  20. junifer/configs/juseless/datagrabbers/ixi_vbm.py +0 -3
  21. junifer/configs/juseless/datagrabbers/tests/test_ucla.py +3 -1
  22. junifer/configs/juseless/datagrabbers/ucla.py +9 -12
  23. junifer/configs/juseless/datagrabbers/ukb_vbm.py +0 -3
  24. junifer/data/__init__.py +1 -21
  25. junifer/data/coordinates.py +19 -10
  26. junifer/data/masks.py +87 -58
  27. junifer/data/parcellations.py +3 -14
  28. junifer/data/template_spaces.py +1 -4
  29. junifer/data/tests/test_masks.py +37 -26
  30. junifer/data/utils.py +0 -3
  31. junifer/datagrabber/__init__.py +1 -18
  32. junifer/datagrabber/aomic/__init__.py +0 -3
  33. junifer/datagrabber/aomic/id1000.py +37 -70
  34. junifer/datagrabber/aomic/piop1.py +36 -69
  35. junifer/datagrabber/aomic/piop2.py +38 -71
  36. junifer/datagrabber/aomic/tests/test_id1000.py +99 -44
  37. junifer/datagrabber/aomic/tests/test_piop1.py +108 -65
  38. junifer/datagrabber/aomic/tests/test_piop2.py +102 -45
  39. junifer/datagrabber/base.py +6 -13
  40. junifer/datagrabber/datalad_base.py +1 -13
  41. junifer/datagrabber/dmcc13_benchmark.py +53 -36
  42. junifer/datagrabber/hcp1200/__init__.py +0 -3
  43. junifer/datagrabber/hcp1200/datalad_hcp1200.py +0 -3
  44. junifer/datagrabber/hcp1200/hcp1200.py +1 -4
  45. junifer/datagrabber/multiple.py +6 -45
  46. junifer/datagrabber/pattern.py +62 -170
  47. junifer/datagrabber/pattern_datalad.py +12 -25
  48. junifer/datagrabber/tests/test_datagrabber_utils.py +218 -0
  49. junifer/datagrabber/tests/test_datalad_base.py +4 -4
  50. junifer/datagrabber/tests/test_dmcc13_benchmark.py +19 -46
  51. junifer/datagrabber/tests/test_multiple.py +84 -161
  52. junifer/datagrabber/tests/test_pattern.py +0 -45
  53. junifer/datagrabber/tests/test_pattern_datalad.py +4 -4
  54. junifer/datagrabber/utils.py +230 -0
  55. junifer/datareader/__init__.py +1 -4
  56. junifer/datareader/default.py +43 -95
  57. junifer/external/__init__.py +1 -1
  58. junifer/external/nilearn/__init__.py +1 -5
  59. junifer/external/nilearn/junifer_nifti_spheres_masker.py +9 -23
  60. junifer/external/nilearn/tests/test_junifer_nifti_spheres_masker.py +1 -76
  61. junifer/markers/__init__.py +1 -23
  62. junifer/markers/base.py +28 -68
  63. junifer/markers/collection.py +2 -10
  64. junifer/markers/complexity/__init__.py +0 -10
  65. junifer/markers/complexity/complexity_base.py +43 -26
  66. junifer/markers/complexity/hurst_exponent.py +0 -3
  67. junifer/markers/complexity/multiscale_entropy_auc.py +0 -3
  68. junifer/markers/complexity/perm_entropy.py +0 -3
  69. junifer/markers/complexity/range_entropy.py +0 -3
  70. junifer/markers/complexity/range_entropy_auc.py +0 -3
  71. junifer/markers/complexity/sample_entropy.py +0 -3
  72. junifer/markers/complexity/tests/test_hurst_exponent.py +3 -11
  73. junifer/markers/complexity/tests/test_multiscale_entropy_auc.py +3 -11
  74. junifer/markers/complexity/tests/test_perm_entropy.py +3 -11
  75. junifer/markers/complexity/tests/test_range_entropy.py +3 -11
  76. junifer/markers/complexity/tests/test_range_entropy_auc.py +3 -11
  77. junifer/markers/complexity/tests/test_sample_entropy.py +3 -11
  78. junifer/markers/complexity/tests/test_weighted_perm_entropy.py +3 -11
  79. junifer/markers/complexity/weighted_perm_entropy.py +0 -3
  80. junifer/markers/ets_rss.py +42 -27
  81. junifer/markers/falff/__init__.py +0 -3
  82. junifer/markers/falff/_afni_falff.py +2 -5
  83. junifer/markers/falff/_junifer_falff.py +0 -3
  84. junifer/markers/falff/falff_base.py +46 -20
  85. junifer/markers/falff/falff_parcels.py +27 -56
  86. junifer/markers/falff/falff_spheres.py +29 -60
  87. junifer/markers/falff/tests/test_falff_parcels.py +23 -39
  88. junifer/markers/falff/tests/test_falff_spheres.py +23 -39
  89. junifer/markers/functional_connectivity/__init__.py +0 -9
  90. junifer/markers/functional_connectivity/crossparcellation_functional_connectivity.py +60 -63
  91. junifer/markers/functional_connectivity/edge_functional_connectivity_parcels.py +32 -45
  92. junifer/markers/functional_connectivity/edge_functional_connectivity_spheres.py +36 -49
  93. junifer/markers/functional_connectivity/functional_connectivity_base.py +70 -71
  94. junifer/markers/functional_connectivity/functional_connectivity_parcels.py +25 -34
  95. junifer/markers/functional_connectivity/functional_connectivity_spheres.py +30 -40
  96. junifer/markers/functional_connectivity/tests/test_crossparcellation_functional_connectivity.py +7 -11
  97. junifer/markers/functional_connectivity/tests/test_edge_functional_connectivity_parcels.py +7 -27
  98. junifer/markers/functional_connectivity/tests/test_edge_functional_connectivity_spheres.py +12 -28
  99. junifer/markers/functional_connectivity/tests/test_functional_connectivity_parcels.py +11 -35
  100. junifer/markers/functional_connectivity/tests/test_functional_connectivity_spheres.py +62 -36
  101. junifer/markers/parcel_aggregation.py +61 -47
  102. junifer/markers/reho/__init__.py +0 -3
  103. junifer/markers/reho/_afni_reho.py +2 -5
  104. junifer/markers/reho/_junifer_reho.py +1 -4
  105. junifer/markers/reho/reho_base.py +27 -8
  106. junifer/markers/reho/reho_parcels.py +17 -28
  107. junifer/markers/reho/reho_spheres.py +18 -27
  108. junifer/markers/reho/tests/test_reho_parcels.py +3 -8
  109. junifer/markers/reho/tests/test_reho_spheres.py +3 -8
  110. junifer/markers/sphere_aggregation.py +59 -43
  111. junifer/markers/temporal_snr/__init__.py +0 -3
  112. junifer/markers/temporal_snr/temporal_snr_base.py +32 -23
  113. junifer/markers/temporal_snr/temporal_snr_parcels.py +6 -9
  114. junifer/markers/temporal_snr/temporal_snr_spheres.py +6 -9
  115. junifer/markers/temporal_snr/tests/test_temporal_snr_parcels.py +3 -6
  116. junifer/markers/temporal_snr/tests/test_temporal_snr_spheres.py +3 -6
  117. junifer/markers/tests/test_collection.py +8 -9
  118. junifer/markers/tests/test_ets_rss.py +9 -15
  119. junifer/markers/tests/test_markers_base.py +18 -17
  120. junifer/markers/tests/test_parcel_aggregation.py +32 -93
  121. junifer/markers/tests/test_sphere_aggregation.py +19 -72
  122. junifer/onthefly/__init__.py +1 -4
  123. junifer/onthefly/read_transform.py +0 -3
  124. junifer/pipeline/__init__.py +1 -9
  125. junifer/pipeline/pipeline_step_mixin.py +4 -21
  126. junifer/pipeline/registry.py +0 -3
  127. junifer/pipeline/singleton.py +0 -3
  128. junifer/pipeline/tests/test_registry.py +1 -1
  129. junifer/pipeline/update_meta_mixin.py +0 -3
  130. junifer/pipeline/utils.py +1 -67
  131. junifer/pipeline/workdir_manager.py +0 -3
  132. junifer/preprocess/__init__.py +2 -9
  133. junifer/preprocess/ants/__init__.py +4 -0
  134. junifer/preprocess/ants/ants_apply_transforms_warper.py +185 -0
  135. junifer/preprocess/ants/tests/test_ants_apply_transforms_warper.py +56 -0
  136. junifer/preprocess/base.py +3 -6
  137. junifer/preprocess/bold_warper.py +265 -0
  138. junifer/preprocess/confounds/__init__.py +0 -3
  139. junifer/preprocess/confounds/fmriprep_confound_remover.py +60 -47
  140. junifer/preprocess/confounds/tests/test_fmriprep_confound_remover.py +113 -72
  141. junifer/preprocess/fsl/__init__.py +4 -0
  142. junifer/preprocess/fsl/apply_warper.py +179 -0
  143. junifer/preprocess/fsl/tests/test_apply_warper.py +45 -0
  144. junifer/preprocess/smoothing/__init__.py +0 -3
  145. junifer/preprocess/smoothing/_afni_smoothing.py +1 -1
  146. junifer/preprocess/tests/test_bold_warper.py +159 -0
  147. junifer/preprocess/warping/__init__.py +0 -3
  148. junifer/preprocess/warping/_ants_warper.py +0 -3
  149. junifer/preprocess/warping/_fsl_warper.py +0 -3
  150. junifer/stats.py +1 -4
  151. junifer/storage/__init__.py +1 -9
  152. junifer/storage/base.py +1 -40
  153. junifer/storage/hdf5.py +9 -71
  154. junifer/storage/pandas_base.py +0 -3
  155. junifer/storage/sqlite.py +0 -3
  156. junifer/storage/tests/test_hdf5.py +10 -82
  157. junifer/storage/utils.py +0 -9
  158. junifer/testing/__init__.py +1 -4
  159. junifer/testing/datagrabbers.py +6 -13
  160. junifer/testing/tests/test_partlycloudytesting_datagrabber.py +7 -7
  161. junifer/testing/utils.py +0 -3
  162. junifer/utils/__init__.py +2 -13
  163. junifer/utils/fs.py +0 -3
  164. junifer/utils/helpers.py +1 -32
  165. junifer/utils/logging.py +4 -33
  166. junifer/utils/tests/test_logging.py +0 -8
  167. {junifer-0.0.5.dist-info → junifer-0.0.5.dev24.dist-info}/METADATA +16 -17
  168. junifer-0.0.5.dev24.dist-info/RECORD +265 -0
  169. {junifer-0.0.5.dist-info → junifer-0.0.5.dev24.dist-info}/WHEEL +1 -1
  170. junifer/api/res/freesurfer/mri_binarize +0 -3
  171. junifer/api/res/freesurfer/mri_mc +0 -3
  172. junifer/api/res/freesurfer/mri_pretess +0 -3
  173. junifer/api/res/freesurfer/mris_convert +0 -3
  174. junifer/api/res/freesurfer/run_freesurfer_docker.sh +0 -61
  175. junifer/data/masks/ukb/UKB_15K_GM_template.nii.gz +0 -0
  176. junifer/datagrabber/pattern_validation_mixin.py +0 -388
  177. junifer/datagrabber/tests/test_pattern_validation_mixin.py +0 -249
  178. junifer/external/BrainPrint/brainprint/__init__.py +0 -4
  179. junifer/external/BrainPrint/brainprint/_version.py +0 -3
  180. junifer/external/BrainPrint/brainprint/asymmetry.py +0 -91
  181. junifer/external/BrainPrint/brainprint/brainprint.py +0 -441
  182. junifer/external/BrainPrint/brainprint/surfaces.py +0 -258
  183. junifer/external/BrainPrint/brainprint/utils/__init__.py +0 -1
  184. junifer/external/BrainPrint/brainprint/utils/_config.py +0 -112
  185. junifer/external/BrainPrint/brainprint/utils/utils.py +0 -188
  186. junifer/external/nilearn/junifer_connectivity_measure.py +0 -483
  187. junifer/external/nilearn/tests/test_junifer_connectivity_measure.py +0 -1089
  188. junifer/markers/brainprint.py +0 -459
  189. junifer/markers/tests/test_brainprint.py +0 -58
  190. junifer-0.0.5.dist-info/RECORD +0 -275
  191. {junifer-0.0.5.dist-info → junifer-0.0.5.dev24.dist-info}/AUTHORS.rst +0 -0
  192. {junifer-0.0.5.dist-info → junifer-0.0.5.dev24.dist-info}/LICENSE.md +0 -0
  193. {junifer-0.0.5.dist-info → junifer-0.0.5.dev24.dist-info}/entry_points.txt +0 -0
  194. {junifer-0.0.5.dist-info → junifer-0.0.5.dev24.dist-info}/top_level.txt +0 -0
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- junifer/configs/juseless/datagrabbers/aomic_id1000_vbm.py,sha256=dhOeIQg-IVDatJu2Y1ObuAANdMoYDgACtMOu-9SHzh8,1474
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- junifer/configs/juseless/datagrabbers/camcan_vbm.py,sha256=_d_nMmKQbGEK644wCMmVfHaI2ioTmDmg5ypr_Ik3hDI,1538
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