niwrap-afni 0.6.3__py3-none-any.whl → 0.7.0__py3-none-any.whl

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Files changed (573) hide show
  1. niwrap_afni/afni/__init__.py +601 -18
  2. niwrap_afni/afni/abids_json_info_py.py +35 -51
  3. niwrap_afni/afni/abids_json_tool_py.py +48 -59
  4. niwrap_afni/afni/{abids_tool.py → abids_tool_py.py} +60 -78
  5. niwrap_afni/afni/adjunct_apqc_tsnr_general.py +83 -84
  6. niwrap_afni/afni/adjunct_aw_tableize_roi_info_py.py +31 -50
  7. niwrap_afni/afni/adjunct_calc_mont_dims_py.py +20 -43
  8. niwrap_afni/afni/adjunct_combine_str_py.py +29 -51
  9. niwrap_afni/afni/adjunct_is_label_py.py +22 -44
  10. niwrap_afni/afni/adjunct_make_script_and_rst_py.py +35 -55
  11. niwrap_afni/afni/adjunct_select_str_py.py +24 -45
  12. niwrap_afni/afni/{adjunct_simplify_cost.py → adjunct_simplify_cost_py.py} +49 -70
  13. niwrap_afni/afni/adjunct_suma_fs_mask_and_qc.py +36 -55
  14. niwrap_afni/afni/adjunct_suma_fs_roi_info.py +28 -48
  15. niwrap_afni/afni/adjunct_tort_plot_dp_align.py +38 -58
  16. niwrap_afni/afni/adwarp.py +43 -59
  17. niwrap_afni/afni/afni.py +77 -77
  18. niwrap_afni/afni/afni_batch_r.py +28 -47
  19. niwrap_afni/afni/afni_check_omp.py +21 -44
  20. niwrap_afni/afni/afni_history.py +72 -75
  21. niwrap_afni/afni/afni_open.py +49 -58
  22. niwrap_afni/afni/afni_proc_py.py +50 -64
  23. niwrap_afni/afni/afni_run_r.py +22 -44
  24. niwrap_afni/afni/afni_system_check_py.py +43 -57
  25. niwrap_afni/afni/aiv.py +33 -51
  26. niwrap_afni/afni/{align_epi_anat.py → align_epi_anat_py.py} +84 -92
  27. niwrap_afni/afni/analyze_trace.py +48 -61
  28. niwrap_afni/afni/{ap_run_simple_rest.py → ap_run_simple_rest_tcsh.py} +72 -90
  29. niwrap_afni/afni/{apqc_make_html.py → apqc_make_html_py.py} +45 -68
  30. niwrap_afni/afni/apqc_make_tcsh_py.py +34 -53
  31. niwrap_afni/afni/apsearch.py +26 -48
  32. niwrap_afni/afni/auto_warp_py.py +98 -89
  33. niwrap_afni/afni/balloon.py +33 -51
  34. niwrap_afni/afni/bayes_view.py +29 -50
  35. niwrap_afni/afni/bayesian_group_ana_py.py +57 -68
  36. niwrap_afni/afni/brain_skin.py +64 -76
  37. niwrap_afni/afni/build_afni_py.py +62 -71
  38. niwrap_afni/afni/cat_matvec.py +26 -46
  39. niwrap_afni/afni/ccalc.py +23 -45
  40. niwrap_afni/afni/cifti_tool.py +42 -58
  41. niwrap_afni/afni/cjpeg.py +34 -52
  42. niwrap_afni/afni/clust_exp_hist_table_py.py +33 -54
  43. niwrap_afni/afni/clust_exp_stat_parse_py.py +57 -69
  44. niwrap_afni/afni/column_cat.py +32 -54
  45. niwrap_afni/afni/compare_surfaces.py +58 -68
  46. niwrap_afni/afni/{convert_cdiflist_to_grads.py → convert_cdiflist_to_grads_py.py} +60 -78
  47. niwrap_afni/afni/convert_dset.py +73 -77
  48. niwrap_afni/afni/convert_surface.py +47 -62
  49. niwrap_afni/afni/convex_hull.py +68 -77
  50. niwrap_afni/afni/count.py +56 -66
  51. niwrap_afni/afni/create_icosahedron.py +44 -58
  52. niwrap_afni/afni/dcm2niix_afni.py +102 -98
  53. niwrap_afni/afni/dicom_hdr.py +39 -53
  54. niwrap_afni/afni/dicom_hinfo.py +31 -49
  55. niwrap_afni/afni/dicom_to_raw.py +21 -45
  56. niwrap_afni/afni/dimon.py +45 -64
  57. niwrap_afni/afni/djpeg.py +34 -52
  58. niwrap_afni/afni/drive_suma.py +99 -92
  59. niwrap_afni/afni/dsetstat2p.py +30 -49
  60. niwrap_afni/afni/dtistudio_fiberto_segments.py +26 -48
  61. niwrap_afni/afni/{epi_b0_correct.py → epi_b0_correct_py.py} +110 -111
  62. niwrap_afni/afni/examine_xmat.py +45 -62
  63. niwrap_afni/afni/fat_mat2d_plot_py.py +88 -86
  64. niwrap_afni/afni/fat_mat_sel_py.py +87 -89
  65. niwrap_afni/afni/{fat_mat_tableize.py → fat_mat_tableize_py.py} +72 -87
  66. niwrap_afni/afni/fat_mvm_gridconv_py.py +24 -51
  67. niwrap_afni/afni/{fat_mvm_prep.py → fat_mvm_prep_py.py} +61 -79
  68. niwrap_afni/afni/fat_mvm_scripter_py.py +53 -65
  69. niwrap_afni/afni/fat_proc_align_anat_pair.py +50 -63
  70. niwrap_afni/afni/fat_proc_axialize_anat.py +76 -79
  71. niwrap_afni/afni/fat_proc_connec_vis.py +56 -70
  72. niwrap_afni/afni/fat_proc_convert_dcm_anat.py +44 -59
  73. niwrap_afni/afni/fat_proc_convert_dcm_dwis.py +74 -79
  74. niwrap_afni/afni/fat_proc_decmap.py +51 -65
  75. niwrap_afni/afni/fat_proc_dwi_to_dt.py +94 -93
  76. niwrap_afni/afni/fat_proc_filter_dwis.py +47 -61
  77. niwrap_afni/afni/fat_proc_imit2w_from_t1w.py +41 -62
  78. niwrap_afni/afni/fat_proc_map_to_dti.py +53 -65
  79. niwrap_afni/afni/fat_proc_select_vols.py +38 -55
  80. niwrap_afni/afni/{fat_roi_row.py → fat_roi_row_py.py} +58 -79
  81. niwrap_afni/afni/fatcat_matplot.py +22 -44
  82. niwrap_afni/afni/fdrval.py +34 -51
  83. niwrap_afni/afni/fftest.py +26 -46
  84. niwrap_afni/afni/file_tool.py +111 -94
  85. niwrap_afni/afni/fim2.py +85 -87
  86. niwrap_afni/afni/{find_variance_lines.py → find_variance_lines_tcsh.py} +90 -109
  87. niwrap_afni/afni/firdesign.py +33 -51
  88. niwrap_afni/afni/float_scan.py +27 -48
  89. niwrap_afni/afni/from3d.py +42 -60
  90. niwrap_afni/afni/fsread_annot.py +52 -66
  91. niwrap_afni/afni/gen_epi_review_py.py +47 -61
  92. niwrap_afni/afni/{gen_group_command.py → gen_group_command_py.py} +82 -95
  93. niwrap_afni/afni/{gen_ss_review_scripts.py → gen_ss_review_scripts_py.py} +100 -106
  94. niwrap_afni/afni/gen_ss_review_table_py.py +55 -66
  95. niwrap_afni/afni/get_afni_model_prf.py +26 -46
  96. niwrap_afni/afni/get_afni_model_prf_6.py +32 -49
  97. niwrap_afni/afni/get_afni_model_prf_6_bad.py +30 -48
  98. niwrap_afni/afni/gifti_tool.py +77 -80
  99. niwrap_afni/afni/gltsymtest.py +28 -49
  100. niwrap_afni/afni/help_format.py +20 -44
  101. niwrap_afni/afni/im2niml.py +24 -48
  102. niwrap_afni/afni/images_equal.py +24 -46
  103. niwrap_afni/afni/imand.py +30 -52
  104. niwrap_afni/afni/imaver.py +32 -54
  105. niwrap_afni/afni/imcalc.py +30 -51
  106. niwrap_afni/afni/imcat.py +89 -87
  107. niwrap_afni/afni/imcutup.py +35 -55
  108. niwrap_afni/afni/imdump.py +20 -44
  109. niwrap_afni/afni/immask.py +35 -53
  110. niwrap_afni/afni/imreg.py +70 -75
  111. niwrap_afni/afni/imrotate.py +33 -51
  112. niwrap_afni/afni/imstack.py +28 -50
  113. niwrap_afni/afni/imstat.py +29 -50
  114. niwrap_afni/afni/imupsam.py +27 -48
  115. niwrap_afni/afni/init_user_dotfiles_py.py +59 -66
  116. niwrap_afni/afni/inspec.py +37 -54
  117. niwrap_afni/afni/iso_surface.py +56 -67
  118. niwrap_afni/afni/make_color_map.py +77 -82
  119. niwrap_afni/afni/make_pq_script_py.py +27 -48
  120. niwrap_afni/afni/make_random_timing_py.py +85 -88
  121. niwrap_afni/afni/make_stim_times_py.py +49 -62
  122. niwrap_afni/afni/map_icosahedron.py +51 -62
  123. niwrap_afni/afni/map_track_id.py +35 -52
  124. niwrap_afni/afni/mba.py +62 -72
  125. niwrap_afni/afni/meica_py.py +38 -55
  126. niwrap_afni/afni/myget.py +26 -48
  127. niwrap_afni/afni/neuro_deconvolve_py.py +51 -66
  128. niwrap_afni/afni/nicat.py +27 -47
  129. niwrap_afni/afni/niccc.py +50 -63
  130. niwrap_afni/afni/nifti_tool.py +52 -65
  131. niwrap_afni/afni/niml_feedme.py +36 -53
  132. niwrap_afni/afni/nsize.py +23 -46
  133. niwrap_afni/afni/p2dsetstat.py +34 -51
  134. niwrap_afni/afni/parse_fs_lt_log_py.py +29 -48
  135. niwrap_afni/afni/plugout_drive.py +56 -65
  136. niwrap_afni/afni/plugout_ijk.py +46 -59
  137. niwrap_afni/afni/plugout_tt.py +48 -60
  138. niwrap_afni/afni/plugout_tta.py +49 -63
  139. niwrap_afni/afni/prompt_popup.py +35 -53
  140. niwrap_afni/afni/prompt_user.py +26 -47
  141. niwrap_afni/afni/pta.py +44 -61
  142. niwrap_afni/afni/qdelaunay.py +100 -91
  143. niwrap_afni/afni/qhull.py +63 -67
  144. niwrap_afni/afni/quick_alpha_vals_py.py +23 -46
  145. niwrap_afni/afni/quickspec.py +41 -59
  146. niwrap_afni/afni/quickspec_sl.py +46 -63
  147. niwrap_afni/afni/quotize.py +25 -47
  148. niwrap_afni/afni/r_pkgs_install.py +30 -50
  149. niwrap_afni/afni/rba.py +93 -92
  150. niwrap_afni/afni/rbox.py +68 -71
  151. niwrap_afni/afni/read_matlab_files_py.py +32 -51
  152. niwrap_afni/afni/{realtime_receiver.py → realtime_receiver_py.py} +76 -88
  153. niwrap_afni/afni/retro_ts_py.py +84 -84
  154. niwrap_afni/afni/rmz.py +27 -47
  155. niwrap_afni/afni/roi2dataset.py +47 -60
  156. niwrap_afni/afni/roigrow.py +38 -55
  157. niwrap_afni/afni/rotcom.py +27 -50
  158. niwrap_afni/afni/rsfgen.py +53 -65
  159. niwrap_afni/afni/rtfeedme.py +47 -60
  160. niwrap_afni/afni/samp_bias.py +42 -60
  161. niwrap_afni/afni/scale_to_map.py +98 -90
  162. niwrap_afni/afni/serial_helper.py +48 -60
  163. niwrap_afni/afni/sfim.py +31 -54
  164. niwrap_afni/afni/slow_surf_clustsim_py.py +44 -57
  165. niwrap_afni/afni/spharm_deco.py +47 -68
  166. niwrap_afni/afni/spharm_reco.py +38 -54
  167. niwrap_afni/afni/stimband.py +34 -53
  168. niwrap_afni/afni/strblast.py +38 -55
  169. niwrap_afni/afni/suma_change_spec.py +34 -53
  170. niwrap_afni/afni/suma_glxdino.py +24 -47
  171. niwrap_afni/afni/surf2_vol_coord.py +46 -60
  172. niwrap_afni/afni/surf_clust.py +113 -99
  173. niwrap_afni/afni/surf_dist.py +37 -54
  174. niwrap_afni/afni/surf_dset_info.py +59 -64
  175. niwrap_afni/afni/surf_extrema.py +43 -60
  176. niwrap_afni/afni/surf_fwhm.py +59 -70
  177. niwrap_afni/afni/surf_info.py +67 -72
  178. niwrap_afni/afni/surf_layers.py +49 -70
  179. niwrap_afni/afni/surf_localstat.py +33 -52
  180. niwrap_afni/afni/surf_measures.py +64 -71
  181. niwrap_afni/afni/surf_mesh.py +37 -54
  182. niwrap_afni/afni/surf_patch.py +68 -72
  183. niwrap_afni/afni/surf_qual.py +38 -57
  184. niwrap_afni/afni/surf_retino_map.py +32 -52
  185. niwrap_afni/afni/surf_smooth.py +63 -72
  186. niwrap_afni/afni/surf_to_surf.py +55 -67
  187. niwrap_afni/afni/surface_metrics.py +68 -69
  188. niwrap_afni/afni/tedana_wrapper_py.py +51 -63
  189. niwrap_afni/afni/tfim.py +39 -57
  190. niwrap_afni/afni/timing_tool_py.py +72 -78
  191. niwrap_afni/afni/to3d.py +125 -110
  192. niwrap_afni/afni/tokens.py +24 -46
  193. niwrap_afni/afni/trr.py +70 -77
  194. niwrap_afni/afni/uber_align_test_py.py +41 -55
  195. niwrap_afni/afni/uber_proc_py.py +21 -44
  196. niwrap_afni/afni/{uber_skel.py → uber_skel_py.py} +72 -85
  197. niwrap_afni/afni/uber_subject_py.py +143 -124
  198. niwrap_afni/afni/un_warp_epi_py.py +34 -50
  199. niwrap_afni/afni/uniq_images.py +26 -50
  200. niwrap_afni/afni/v_1d_apar2mat.py +42 -54
  201. niwrap_afni/afni/v_1d_astrip.py +20 -44
  202. niwrap_afni/afni/v_1d_bandpass.py +34 -51
  203. niwrap_afni/afni/v_1d_bport.py +47 -60
  204. niwrap_afni/afni/v_1d_correlate.py +42 -57
  205. niwrap_afni/afni/v_1d_dw_grad_o_mat__.py +72 -76
  206. niwrap_afni/afni/v_1d_flag_motion.py +30 -52
  207. niwrap_afni/afni/v_1d_marry.py +25 -47
  208. niwrap_afni/afni/v_1d_nlfit.py +29 -49
  209. niwrap_afni/afni/v_1d_rplot.py +72 -78
  210. niwrap_afni/afni/v_1d_sem.py +60 -69
  211. niwrap_afni/afni/v_1d_tool_py.py +53 -65
  212. niwrap_afni/afni/v_1d_tsort.py +31 -49
  213. niwrap_afni/afni/v_1d_upsample.py +24 -46
  214. niwrap_afni/afni/v_1dcat.py +38 -54
  215. niwrap_afni/afni/v_1ddot.py +34 -51
  216. niwrap_afni/afni/v_1deval.py +44 -61
  217. niwrap_afni/afni/v_1dfft.py +40 -56
  218. niwrap_afni/afni/v_1dgen_arma11.py +57 -70
  219. niwrap_afni/afni/v_1dgrayplot.py +38 -53
  220. niwrap_afni/afni/v_1dmatcalc.py +25 -49
  221. niwrap_afni/afni/v_1dnorm.py +31 -50
  222. niwrap_afni/afni/v_1dplot.py +191 -155
  223. niwrap_afni/afni/v_1dplot_py.py +110 -103
  224. niwrap_afni/afni/v_1dsound.py +44 -58
  225. niwrap_afni/afni/v_1dsum.py +36 -53
  226. niwrap_afni/afni/v_1dsvd.py +45 -59
  227. niwrap_afni/afni/v_1dtranspose.py +24 -47
  228. niwrap_afni/afni/v_24swap.py +25 -46
  229. niwrap_afni/afni/v_2d_im_reg.py +55 -68
  230. niwrap_afni/afni/v_2dcat.py +86 -86
  231. niwrap_afni/afni/v_2perm.py +35 -54
  232. niwrap_afni/afni/v_2swap.py +22 -44
  233. niwrap_afni/afni/v_3d_aboverlap.py +32 -51
  234. niwrap_afni/afni/v_3d_acost.py +28 -49
  235. niwrap_afni/afni/v_3d_afnito3_d.py +28 -49
  236. niwrap_afni/afni/v_3d_afnito_analyze.py +31 -52
  237. niwrap_afni/afni/v_3d_afnito_nifti.py +36 -53
  238. niwrap_afni/afni/v_3d_afnito_niml.py +27 -47
  239. niwrap_afni/afni/v_3d_afnito_raw.py +25 -46
  240. niwrap_afni/afni/v_3d_allineate.py +63 -74
  241. niwrap_afni/afni/v_3d_amp_to_rsfc.py +39 -58
  242. niwrap_afni/afni/v_3d_anhist.py +41 -56
  243. niwrap_afni/afni/v_3d_anova.py +64 -75
  244. niwrap_afni/afni/v_3d_anova2.py +101 -100
  245. niwrap_afni/afni/v_3d_anova3.py +138 -126
  246. niwrap_afni/afni/v_3d_attribute.py +40 -55
  247. niwrap_afni/afni/v_3d_auto_tcorrelate.py +52 -64
  248. niwrap_afni/afni/v_3d_autobox.py +56 -66
  249. niwrap_afni/afni/v_3d_automask.py +40 -58
  250. niwrap_afni/afni/v_3d_ball_match.py +38 -56
  251. niwrap_afni/afni/v_3d_bandpass.py +66 -74
  252. niwrap_afni/afni/v_3d_blur_in_mask.py +45 -59
  253. niwrap_afni/afni/v_3d_blur_to_fwhm.py +41 -58
  254. niwrap_afni/afni/v_3d_brain_sync.py +40 -58
  255. niwrap_afni/afni/v_3d_brain_voyagerto_afni.py +52 -63
  256. niwrap_afni/afni/v_3d_brick_stat.py +83 -78
  257. niwrap_afni/afni/v_3d_clip_level.py +32 -52
  258. niwrap_afni/afni/v_3d_clust_count.py +30 -51
  259. niwrap_afni/afni/v_3d_clust_sim.py +85 -88
  260. niwrap_afni/afni/v_3d_clusterize.py +81 -82
  261. niwrap_afni/afni/v_3d_cm.py +43 -59
  262. niwrap_afni/afni/v_3d_compare_affine.py +31 -53
  263. niwrap_afni/afni/v_3d_conformist.py +24 -46
  264. niwrap_afni/afni/v_3d_convolve.py +26 -48
  265. niwrap_afni/afni/v_3d_cruiseto_afni.py +48 -60
  266. niwrap_afni/afni/v_3d_deconvolve.py +68 -78
  267. niwrap_afni/afni/v_3d_degree_centrality.py +49 -66
  268. niwrap_afni/afni/v_3d_depth_map.py +53 -65
  269. niwrap_afni/afni/v_3d_despike.py +28 -51
  270. niwrap_afni/afni/v_3d_detrend.py +24 -47
  271. niwrap_afni/afni/v_3d_dft.py +40 -58
  272. niwrap_afni/afni/v_3d_diff.py +37 -54
  273. niwrap_afni/afni/v_3d_dteig.py +35 -55
  274. niwrap_afni/afni/v_3d_dtto_dwi.py +37 -54
  275. niwrap_afni/afni/v_3d_dtto_noisy_dwi.py +45 -60
  276. niwrap_afni/afni/v_3d_dwito_dt.py +84 -86
  277. niwrap_afni/afni/v_3d_dwuncert.py +43 -59
  278. niwrap_afni/afni/v_3d_ecm.py +65 -73
  279. niwrap_afni/afni/v_3d_edu_01_scale.py +28 -53
  280. niwrap_afni/afni/v_3d_eigs_to_dt.py +38 -55
  281. niwrap_afni/afni/v_3d_empty.py +31 -52
  282. niwrap_afni/afni/v_3d_entropy.py +22 -44
  283. niwrap_afni/afni/v_3d_errts_cormat.py +39 -58
  284. niwrap_afni/afni/v_3d_exchange.py +30 -50
  285. niwrap_afni/afni/v_3d_extract_group_in_corr.py +28 -51
  286. niwrap_afni/afni/v_3d_extrema.py +67 -72
  287. niwrap_afni/afni/v_3d_fdr.py +54 -65
  288. niwrap_afni/afni/v_3d_fft.py +52 -65
  289. niwrap_afni/afni/v_3d_friedman.py +30 -53
  290. niwrap_afni/afni/v_3d_fwhmx.py +51 -63
  291. niwrap_afni/afni/v_3d_gen_feature_dist.py +50 -63
  292. niwrap_afni/afni/v_3d_gen_priors.py +87 -86
  293. niwrap_afni/afni/v_3d_getrow.py +34 -54
  294. niwrap_afni/afni/v_3d_grayplot.py +58 -69
  295. niwrap_afni/afni/v_3d_group_in_corr.py +87 -84
  296. niwrap_afni/afni/v_3d_hist.py +74 -78
  297. niwrap_afni/afni/v_3d_icc.py +55 -66
  298. niwrap_afni/afni/v_3d_intracranial.py +41 -57
  299. niwrap_afni/afni/v_3d_inv_fmri.py +48 -62
  300. niwrap_afni/afni/v_3d_isc.py +43 -59
  301. niwrap_afni/afni/v_3d_kruskal_wallis.py +31 -51
  302. niwrap_afni/afni/v_3d_lfcd.py +47 -63
  303. niwrap_afni/afni/v_3d_lme.py +97 -92
  304. niwrap_afni/afni/v_3d_lmer.py +77 -80
  305. niwrap_afni/afni/v_3d_local_acf.py +35 -55
  306. niwrap_afni/afni/v_3d_local_bistat.py +50 -63
  307. niwrap_afni/afni/v_3d_local_histog.py +46 -61
  308. niwrap_afni/afni/v_3d_local_pv.py +50 -64
  309. niwrap_afni/afni/v_3d_local_svd.py +38 -54
  310. niwrap_afni/afni/v_3d_local_unifize.py +46 -62
  311. niwrap_afni/afni/v_3d_localstat.py +76 -81
  312. niwrap_afni/afni/v_3d_lomb_scargle.py +42 -59
  313. niwrap_afni/afni/v_3d_lrflip.py +35 -55
  314. niwrap_afni/afni/v_3d_lss.py +39 -56
  315. niwrap_afni/afni/v_3d_mann_whitney.py +30 -54
  316. niwrap_afni/afni/v_3d_mask_to_ascii.py +25 -47
  317. niwrap_afni/afni/v_3d_match.py +49 -65
  318. niwrap_afni/afni/v_3d_mean.py +64 -70
  319. niwrap_afni/afni/v_3d_median_filter.py +39 -58
  320. niwrap_afni/afni/v_3d_mema.py +89 -87
  321. niwrap_afni/afni/v_3d_mepfm.py +43 -63
  322. niwrap_afni/afni/v_3d_mse.py +44 -60
  323. niwrap_afni/afni/v_3d_mss.py +66 -73
  324. niwrap_afni/afni/v_3d_multi_thresh.py +47 -61
  325. niwrap_afni/afni/v_3d_mvm.py +62 -72
  326. niwrap_afni/afni/v_3d_mvm_validator.py +23 -49
  327. niwrap_afni/afni/v_3d_net_corr.py +67 -72
  328. niwrap_afni/afni/v_3d_nlfim.py +134 -122
  329. niwrap_afni/afni/v_3d_normality_test.py +27 -48
  330. niwrap_afni/afni/v_3d_notes.py +36 -53
  331. niwrap_afni/afni/v_3d_nwarp_adjust.py +34 -56
  332. niwrap_afni/afni/v_3d_nwarp_apply.py +59 -73
  333. niwrap_afni/afni/v_3d_nwarp_cat.py +42 -58
  334. niwrap_afni/afni/v_3d_nwarp_funcs.py +35 -54
  335. niwrap_afni/afni/v_3d_nwarp_xyz.py +31 -52
  336. niwrap_afni/afni/v_3d_overlap.py +27 -49
  337. niwrap_afni/afni/{v_3d_par2_afni.py → v_3d_par2_afni_pl.py} +65 -80
  338. niwrap_afni/afni/v_3d_periodogram.py +35 -56
  339. niwrap_afni/afni/v_3d_pfm.py +62 -72
  340. niwrap_afni/afni/v_3d_polyfit.py +62 -73
  341. niwrap_afni/afni/v_3d_pval.py +32 -51
  342. niwrap_afni/afni/v_3d_pvmap.py +31 -52
  343. niwrap_afni/afni/v_3d_qwarp.py +64 -67
  344. niwrap_afni/afni/v_3d_rank.py +30 -51
  345. niwrap_afni/afni/v_3d_rankizer.py +37 -56
  346. niwrap_afni/afni/v_3d_re_ho.py +65 -76
  347. niwrap_afni/afni/v_3d_reg_ana.py +58 -68
  348. niwrap_afni/afni/v_3d_remlfit.py +64 -74
  349. niwrap_afni/afni/v_3d_retino_phase.py +71 -80
  350. niwrap_afni/afni/{v_3_droimaker.py → v_3d_roimaker.py} +100 -105
  351. niwrap_afni/afni/v_3d_roistats.py +52 -62
  352. niwrap_afni/afni/v_3d_row_fillin.py +33 -53
  353. niwrap_afni/afni/v_3d_rprog_demo.py +43 -57
  354. niwrap_afni/afni/v_3d_rsfc.py +78 -79
  355. niwrap_afni/afni/v_3d_seg.py +80 -86
  356. niwrap_afni/afni/v_3d_setup_group_in_corr.py +46 -60
  357. niwrap_afni/afni/v_3d_sharpen.py +30 -52
  358. niwrap_afni/afni/v_3d_signatures.py +33 -52
  359. niwrap_afni/afni/v_3d_skull_strip.py +27 -49
  360. niwrap_afni/afni/v_3d_slice_ndice.py +36 -54
  361. niwrap_afni/afni/v_3d_space_time_corr.py +36 -54
  362. niwrap_afni/afni/v_3d_spat_norm.py +40 -56
  363. niwrap_afni/afni/v_3d_stat_clust.py +44 -60
  364. niwrap_afni/afni/v_3d_surf2_vol.py +84 -87
  365. niwrap_afni/afni/v_3d_surf_mask.py +44 -60
  366. niwrap_afni/afni/v_3d_synthesize.py +34 -51
  367. niwrap_afni/afni/v_3d_tagalign.py +54 -64
  368. niwrap_afni/afni/v_3d_tcat.py +34 -53
  369. niwrap_afni/afni/v_3d_tcorr1_d.py +40 -57
  370. niwrap_afni/afni/v_3d_tcorr_map.py +66 -73
  371. niwrap_afni/afni/v_3d_tcorrelate.py +59 -68
  372. niwrap_afni/afni/v_3d_tfilter.py +29 -51
  373. niwrap_afni/afni/v_3d_tfitter.py +71 -78
  374. niwrap_afni/afni/v_3d_threeto_rgb.py +41 -58
  375. niwrap_afni/afni/v_3d_tnorm.py +37 -54
  376. niwrap_afni/afni/v_3d_tortoiseto_here.py +36 -55
  377. niwrap_afni/afni/v_3d_toutcount.py +44 -59
  378. niwrap_afni/afni/v_3d_toy_prog.py +54 -62
  379. niwrap_afni/afni/v_3d_tproject.py +77 -83
  380. niwrap_afni/afni/v_3d_tqual.py +36 -53
  381. niwrap_afni/afni/v_3d_track_id.py +139 -120
  382. niwrap_afni/afni/v_3d_trfix.py +33 -53
  383. niwrap_afni/afni/v_3d_tsgen.py +55 -66
  384. niwrap_afni/afni/v_3d_tshift.py +59 -71
  385. niwrap_afni/afni/v_3d_tsmooth.py +58 -69
  386. niwrap_afni/afni/v_3d_tsort.py +43 -57
  387. niwrap_afni/afni/v_3d_tsplit4_d.py +27 -51
  388. niwrap_afni/afni/v_3d_tstat.py +151 -115
  389. niwrap_afni/afni/v_3d_tto1_d.py +34 -53
  390. niwrap_afni/afni/v_3d_twoto_complex.py +35 -54
  391. niwrap_afni/afni/v_3d_undump.py +65 -72
  392. niwrap_afni/afni/v_3d_unifize.py +56 -67
  393. niwrap_afni/afni/v_3d_upsample.py +34 -53
  394. niwrap_afni/afni/v_3d_vec_rgb_to_hsl.py +33 -54
  395. niwrap_afni/afni/v_3d_vol2_surf.py +125 -108
  396. niwrap_afni/afni/v_3d_warp.py +71 -73
  397. niwrap_afni/afni/v_3d_warp_drive.py +108 -95
  398. niwrap_afni/afni/v_3d_wilcoxon.py +35 -53
  399. niwrap_afni/afni/v_3d_winsor.py +45 -61
  400. niwrap_afni/afni/v_3d_xclust_sim.py +64 -74
  401. niwrap_afni/afni/v_3d_xyzcat.py +30 -51
  402. niwrap_afni/afni/v_3d_zcat.py +36 -54
  403. niwrap_afni/afni/v_3d_zcutup.py +27 -49
  404. niwrap_afni/afni/v_3d_zeropad.py +62 -72
  405. niwrap_afni/afni/v_3d_zipper_zapper.py +63 -72
  406. niwrap_afni/afni/v_3d_zregrid.py +36 -55
  407. niwrap_afni/afni/v_3danisosmooth.py +72 -75
  408. niwrap_afni/afni/v_3daxialize.py +41 -56
  409. niwrap_afni/afni/v_3dbucket.py +43 -57
  410. niwrap_afni/afni/v_3dcalc.py +46 -61
  411. niwrap_afni/afni/v_3dclust.py +64 -69
  412. niwrap_afni/afni/v_3dcopy.py +32 -49
  413. niwrap_afni/afni/v_3ddelay.py +83 -84
  414. niwrap_afni/afni/v_3ddot.py +50 -60
  415. niwrap_afni/afni/v_3ddot_beta.py +28 -49
  416. niwrap_afni/afni/v_3dedge3.py +40 -56
  417. niwrap_afni/afni/v_3dedgedog.py +59 -72
  418. niwrap_afni/afni/v_3dfim_.py +60 -73
  419. niwrap_afni/afni/v_3dfractionize.py +36 -54
  420. niwrap_afni/afni/v_3dhistog.py +63 -70
  421. niwrap_afni/afni/v_3dinfill.py +48 -63
  422. niwrap_afni/afni/v_3dinfo.py +250 -161
  423. niwrap_afni/afni/v_3dkmeans.py +73 -79
  424. niwrap_afni/afni/v_3dmask_svd.py +46 -62
  425. niwrap_afni/afni/v_3dmask_tool.py +53 -65
  426. niwrap_afni/afni/v_3dmaskave.py +36 -56
  427. niwrap_afni/afni/v_3dmaskdump.py +73 -78
  428. niwrap_afni/afni/v_3dmatcalc.py +29 -50
  429. niwrap_afni/afni/v_3dmatmult.py +31 -51
  430. niwrap_afni/afni/v_3dmaxdisp.py +30 -50
  431. niwrap_afni/afni/v_3dmaxima.py +68 -70
  432. niwrap_afni/afni/v_3dmerge.py +48 -61
  433. niwrap_afni/afni/v_3dnewid.py +37 -53
  434. niwrap_afni/afni/v_3dnvals.py +24 -45
  435. niwrap_afni/afni/v_3dpc.py +58 -68
  436. niwrap_afni/afni/v_3drefit.py +65 -73
  437. niwrap_afni/afni/v_3drename.py +22 -44
  438. niwrap_afni/afni/v_3dresample.py +38 -56
  439. niwrap_afni/afni/v_3dretroicor.py +51 -67
  440. niwrap_afni/afni/v_3drotate.py +83 -83
  441. niwrap_afni/afni/v_3dsvm.py +90 -88
  442. niwrap_afni/afni/v_3dsvm_linpredict.py +25 -47
  443. niwrap_afni/afni/v_3dto_xdataset.py +25 -47
  444. niwrap_afni/afni/v_3dttest__.py +77 -81
  445. niwrap_afni/afni/v_3dvolreg.py +60 -70
  446. niwrap_afni/afni/v_4swap.py +22 -44
  447. niwrap_afni/afni/v__1d_diff_mag.py +20 -44
  448. niwrap_afni/afni/v__2dwarper.py +20 -44
  449. niwrap_afni/afni/v__2dwarper_allin.py +28 -50
  450. niwrap_afni/afni/v__4_daverage.py +22 -44
  451. niwrap_afni/afni/v__add_edge.py +59 -69
  452. niwrap_afni/afni/v__afni_env.py +42 -56
  453. niwrap_afni/afni/v__afni_orient2_raimap.py +20 -43
  454. niwrap_afni/afni/v__afni_orient_sign.py +21 -45
  455. niwrap_afni/afni/v__afni_r_package_install.py +34 -52
  456. niwrap_afni/afni/v__afni_refacer_make_master.py +20 -44
  457. niwrap_afni/afni/v__afni_refacer_make_onebig_a12.py +21 -45
  458. niwrap_afni/afni/v__afni_refacer_run.py +55 -67
  459. niwrap_afni/afni/v__afni_run_me.py +24 -45
  460. niwrap_afni/afni/v__align_centers.py +57 -68
  461. niwrap_afni/afni/v__align_partial_oblique.py +42 -58
  462. niwrap_afni/afni/v__anaticor.py +50 -61
  463. niwrap_afni/afni/v__animal_warper.py +113 -104
  464. niwrap_afni/afni/v__atlasize.py +67 -74
  465. niwrap_afni/afni/v__auto_tlrc.py +119 -105
  466. niwrap_afni/afni/v__build_afni_xlib.py +30 -48
  467. niwrap_afni/afni/v__center_distance.py +22 -45
  468. niwrap_afni/afni/v__chauffeur_afni.py +68 -75
  469. niwrap_afni/afni/v__check_for_afni_dset.py +21 -45
  470. niwrap_afni/afni/v__clip_volume.py +71 -78
  471. niwrap_afni/afni/v__clust_exp_cat_lab.py +25 -47
  472. niwrap_afni/afni/v__clust_exp_run_shiny.py +22 -44
  473. niwrap_afni/afni/v__command_globb.py +27 -51
  474. niwrap_afni/afni/v__compute_gcor.py +38 -56
  475. niwrap_afni/afni/v__compute_oc_weights.py +47 -62
  476. niwrap_afni/afni/v__deblank_file_names.py +35 -51
  477. niwrap_afni/afni/v__demo_prompt.py +20 -44
  478. niwrap_afni/afni/v__dice_metric.py +48 -59
  479. niwrap_afni/afni/v__diff_files.py +47 -58
  480. niwrap_afni/afni/v__diff_tree.py +61 -67
  481. niwrap_afni/afni/v__djunct_4d_imager.py +37 -58
  482. niwrap_afni/afni/v__djunct_4d_slices_to_3d_vol.py +20 -44
  483. niwrap_afni/afni/v__djunct_anonymize.py +28 -48
  484. niwrap_afni/afni/v__djunct_dwi_selector_tcsh.py +170 -0
  485. niwrap_afni/afni/v__djunct_edgy_align_check.py +88 -86
  486. niwrap_afni/afni/v__djunct_modal_smoothing_with_rep.py +43 -60
  487. niwrap_afni/afni/v__djunct_montage_coordinator.py +36 -54
  488. niwrap_afni/afni/v__djunct_overlap_check.py +80 -80
  489. niwrap_afni/afni/v__djunct_ssw_intermed_edge_imgs.py +54 -63
  490. niwrap_afni/afni/v__do_examples.py +20 -44
  491. niwrap_afni/afni/v__electro_grid.py +35 -54
  492. niwrap_afni/afni/v__examine_gen_feat_dists.py +42 -57
  493. niwrap_afni/afni/v__extract_meica_ortvec.py +36 -55
  494. niwrap_afni/afni/v__fast_roi.py +41 -56
  495. niwrap_afni/afni/v__fat_tract_colorize.py +37 -55
  496. niwrap_afni/afni/v__find_afni_dset_path.py +30 -48
  497. niwrap_afni/afni/v__fix_fssphere.py +32 -51
  498. niwrap_afni/afni/v__float_fix.py +24 -47
  499. niwrap_afni/afni/v__from_rai.py +22 -44
  500. niwrap_afni/afni/v__fs_roi_label.py +45 -60
  501. niwrap_afni/afni/v__fslabel2dset.py +33 -52
  502. niwrap_afni/afni/v__get_afni_dims.py +20 -44
  503. niwrap_afni/afni/v__get_afni_id.py +20 -44
  504. niwrap_afni/afni/v__get_afni_orient.py +23 -46
  505. niwrap_afni/afni/v__get_afni_prefix.py +23 -45
  506. niwrap_afni/afni/v__get_afni_res.py +23 -45
  507. niwrap_afni/afni/v__get_afni_version.py +21 -45
  508. niwrap_afni/afni/v__get_afni_view.py +20 -44
  509. niwrap_afni/afni/v__grad_flip_test.py +58 -69
  510. niwrap_afni/afni/v__grayplot.py +33 -53
  511. niwrap_afni/afni/v__help_afni.py +31 -49
  512. niwrap_afni/afni/v__is_oblique.py +20 -44
  513. niwrap_afni/afni/v__iso_masks.py +23 -45
  514. niwrap_afni/afni/v__make_label_table.py +116 -106
  515. niwrap_afni/afni/v__make_plug_diff.py +32 -49
  516. niwrap_afni/afni/v__measure_bb_thick.py +59 -72
  517. niwrap_afni/afni/v__measure_erosion_thick.py +45 -60
  518. niwrap_afni/afni/v__measure_in2out.py +50 -63
  519. niwrap_afni/afni/v__move_to_series_dirs.py +41 -57
  520. niwrap_afni/afni/v__no_ext.py +23 -46
  521. niwrap_afni/afni/v__no_pound.py +20 -43
  522. niwrap_afni/afni/v__noisy_skull_strip.py +29 -51
  523. niwrap_afni/afni/v__np.py +28 -50
  524. niwrap_afni/afni/v__parse_afni_name.py +24 -48
  525. niwrap_afni/afni/v__purify_1_d.py +26 -47
  526. niwrap_afni/afni/v__quiet_talkers.py +38 -54
  527. niwrap_afni/afni/v__radial_correlate.py +74 -79
  528. niwrap_afni/afni/v__rename_panga.py +43 -58
  529. niwrap_afni/afni/v__reorder.py +38 -56
  530. niwrap_afni/afni/v__retino_proc.py +130 -114
  531. niwrap_afni/afni/v__roi_corr_mat.py +42 -57
  532. niwrap_afni/afni/v__roi_decluster.py +40 -57
  533. niwrap_afni/afni/v__roi_modal_grow.py +39 -56
  534. niwrap_afni/afni/v__scale_volume.py +38 -55
  535. niwrap_afni/afni/v__script_check.py +25 -47
  536. niwrap_afni/afni/v__shift_volume.py +36 -55
  537. niwrap_afni/afni/v__show_dynamic_range.py +26 -50
  538. niwrap_afni/afni/v__simulate_motion.py +58 -67
  539. niwrap_afni/afni/v__skull_strip_touch_up.py +36 -55
  540. niwrap_afni/afni/v__snapshot_volreg.py +29 -50
  541. niwrap_afni/afni/v__spharm_examples.py +31 -49
  542. niwrap_afni/afni/v__sswarper.py +89 -89
  543. niwrap_afni/afni/v__statauxcode.py +20 -44
  544. niwrap_afni/afni/v__suma_acknowledge.py +40 -58
  545. niwrap_afni/afni/v__suma_align_to_experiment.py +75 -78
  546. niwrap_afni/afni/v__suma_fsvol_to_brik.py +24 -47
  547. niwrap_afni/afni/v__suma_make_spec_caret.py +35 -54
  548. niwrap_afni/afni/v__suma_make_spec_fs.py +60 -69
  549. niwrap_afni/afni/v__suma_make_spec_sf.py +28 -50
  550. niwrap_afni/afni/v__suma_renumber_fs.py +29 -53
  551. niwrap_afni/afni/v__suma_reprefixize_spec.py +28 -51
  552. niwrap_afni/afni/v__surf_smooth_heat_07_examples.py +20 -43
  553. niwrap_afni/afni/v__surf_to_vol_spackle.py +57 -68
  554. niwrap_afni/afni/v__t1scale.py +50 -61
  555. niwrap_afni/afni/v__thickness_master.py +28 -50
  556. niwrap_afni/afni/v__time_diff.py +22 -44
  557. niwrap_afni/afni/v__to_mni_awarp.py +22 -48
  558. niwrap_afni/afni/v__to_mni_qwarpar.py +23 -46
  559. niwrap_afni/afni/v__to_rai.py +22 -44
  560. niwrap_afni/afni/v__update_afni_binaries.py +73 -73
  561. niwrap_afni/afni/v__vol_center.py +23 -45
  562. niwrap_afni/afni/v__xyz_to_ijk.py +30 -50
  563. niwrap_afni/afni/vecwarp.py +41 -59
  564. niwrap_afni/afni/waver.py +80 -83
  565. niwrap_afni/afni/whirlgif.py +42 -60
  566. niwrap_afni/afni/xmat_tool_py.py +66 -70
  567. niwrap_afni-0.7.0.dist-info/METADATA +8 -0
  568. niwrap_afni-0.7.0.dist-info/RECORD +569 -0
  569. niwrap_afni-0.7.0.dist-info/WHEEL +4 -0
  570. niwrap_afni/afni/v__djunct_dwi_selector.py +0 -192
  571. niwrap_afni-0.6.3.dist-info/METADATA +0 -8
  572. niwrap_afni-0.6.3.dist-info/RECORD +0 -569
  573. niwrap_afni-0.6.3.dist-info/WHEEL +0 -4
@@ -6,7 +6,7 @@ import pathlib
6
6
  from styxdefs import *
7
7
 
8
8
  V_3D_AMP_TO_RSFC_METADATA = Metadata(
9
- id="322ec34577168f15edf52a084c3d09223b534b09.boutiques",
9
+ id="d93e2359a57d357c7b1980a76378dde19262abcb.boutiques",
10
10
  name="3dAmpToRSFC",
11
11
  package="afni",
12
12
  container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,7 +14,16 @@ V_3D_AMP_TO_RSFC_METADATA = Metadata(
14
14
 
15
15
 
16
16
  V3dAmpToRsfcParameters = typing.TypedDict('V3dAmpToRsfcParameters', {
17
- "__STYXTYPE__": typing.Literal["3dAmpToRSFC"],
17
+ "@type": typing.NotRequired[typing.Literal["afni/3dAmpToRSFC"]],
18
+ "in_amp": typing.NotRequired[InputPathType | None],
19
+ "in_pow": typing.NotRequired[InputPathType | None],
20
+ "prefix": str,
21
+ "band": list[float],
22
+ "mask": typing.NotRequired[InputPathType | None],
23
+ "nifti": bool,
24
+ })
25
+ V3dAmpToRsfcParametersTagged = typing.TypedDict('V3dAmpToRsfcParametersTagged', {
26
+ "@type": typing.Literal["afni/3dAmpToRSFC"],
18
27
  "in_amp": typing.NotRequired[InputPathType | None],
19
28
  "in_pow": typing.NotRequired[InputPathType | None],
20
29
  "prefix": str,
@@ -22,43 +31,11 @@ V3dAmpToRsfcParameters = typing.TypedDict('V3dAmpToRsfcParameters', {
22
31
  "mask": typing.NotRequired[InputPathType | None],
23
32
  "nifti": bool,
24
33
  })
25
-
26
-
27
- def dyn_cargs(
28
- t: str,
29
- ) -> typing.Any:
30
- """
31
- Get build cargs function by command type.
32
-
33
- Args:
34
- t: Command type.
35
- Returns:
36
- Build cargs function.
37
- """
38
- return {
39
- "3dAmpToRSFC": v_3d_amp_to_rsfc_cargs,
40
- }.get(t)
41
-
42
-
43
- def dyn_outputs(
44
- t: str,
45
- ) -> typing.Any:
46
- """
47
- Get build outputs function by command type.
48
-
49
- Args:
50
- t: Command type.
51
- Returns:
52
- Build outputs function.
53
- """
54
- return {
55
- "3dAmpToRSFC": v_3d_amp_to_rsfc_outputs,
56
- }.get(t)
57
34
 
58
35
 
59
36
  class V3dAmpToRsfcOutputs(typing.NamedTuple):
60
37
  """
61
- Output object returned when calling `v_3d_amp_to_rsfc(...)`.
38
+ Output object returned when calling `V3dAmpToRsfcParameters(...)`.
62
39
  """
63
40
  root: OutputPathType
64
41
  """Output root folder. This is the root folder for all outputs."""
@@ -85,7 +62,7 @@ def v_3d_amp_to_rsfc_params(
85
62
  in_pow: InputPathType | None = None,
86
63
  mask: InputPathType | None = None,
87
64
  nifti: bool = False,
88
- ) -> V3dAmpToRsfcParameters:
65
+ ) -> V3dAmpToRsfcParametersTagged:
89
66
  """
90
67
  Build parameters.
91
68
 
@@ -104,7 +81,7 @@ def v_3d_amp_to_rsfc_params(
104
81
  Parameter dictionary
105
82
  """
106
83
  params = {
107
- "__STYXTYPE__": "3dAmpToRSFC",
84
+ "@type": "afni/3dAmpToRSFC",
108
85
  "prefix": prefix,
109
86
  "band": band,
110
87
  "nifti": nifti,
@@ -133,30 +110,30 @@ def v_3d_amp_to_rsfc_cargs(
133
110
  """
134
111
  cargs = []
135
112
  cargs.append("3dAmpToRSFC")
136
- if params.get("in_amp") is not None:
113
+ if params.get("in_amp", None) is not None:
137
114
  cargs.extend([
138
115
  "-in_amp",
139
- execution.input_file(params.get("in_amp"))
116
+ execution.input_file(params.get("in_amp", None))
140
117
  ])
141
- if params.get("in_pow") is not None:
118
+ if params.get("in_pow", None) is not None:
142
119
  cargs.extend([
143
120
  "-in_pow",
144
- execution.input_file(params.get("in_pow"))
121
+ execution.input_file(params.get("in_pow", None))
145
122
  ])
146
123
  cargs.extend([
147
124
  "-prefix",
148
- params.get("prefix")
125
+ params.get("prefix", None)
149
126
  ])
150
127
  cargs.extend([
151
128
  "-band",
152
- *map(str, params.get("band"))
129
+ *map(str, params.get("band", None))
153
130
  ])
154
- if params.get("mask") is not None:
131
+ if params.get("mask", None) is not None:
155
132
  cargs.extend([
156
133
  "-mask",
157
- execution.input_file(params.get("mask"))
134
+ execution.input_file(params.get("mask", None))
158
135
  ])
159
- if params.get("nifti"):
136
+ if params.get("nifti", False):
160
137
  cargs.append("-nifti")
161
138
  return cargs
162
139
 
@@ -176,21 +153,23 @@ def v_3d_amp_to_rsfc_outputs(
176
153
  """
177
154
  ret = V3dAmpToRsfcOutputs(
178
155
  root=execution.output_file("."),
179
- output_alff=execution.output_file(params.get("prefix") + "_ALFF*"),
180
- output_malff=execution.output_file(params.get("prefix") + "_MALFF*"),
181
- output_falff=execution.output_file(params.get("prefix") + "_FALFF*"),
182
- output_rsfa=execution.output_file(params.get("prefix") + "_RSFA*"),
183
- output_mrsfa=execution.output_file(params.get("prefix") + "_MRSFA*"),
184
- output_frsfa=execution.output_file(params.get("prefix") + "_FRSFA*"),
156
+ output_alff=execution.output_file(params.get("prefix", None) + "_ALFF"),
157
+ output_malff=execution.output_file(params.get("prefix", None) + "_MALFF"),
158
+ output_falff=execution.output_file(params.get("prefix", None) + "_FALFF"),
159
+ output_rsfa=execution.output_file(params.get("prefix", None) + "_RSFA"),
160
+ output_mrsfa=execution.output_file(params.get("prefix", None) + "_MRSFA"),
161
+ output_frsfa=execution.output_file(params.get("prefix", None) + "_FRSFA"),
185
162
  )
186
163
  return ret
187
164
 
188
165
 
189
166
  def v_3d_amp_to_rsfc_execute(
190
167
  params: V3dAmpToRsfcParameters,
191
- execution: Execution,
168
+ runner: Runner | None = None,
192
169
  ) -> V3dAmpToRsfcOutputs:
193
170
  """
171
+ 3dAmpToRSFC
172
+
194
173
  Convert spectral amplitudes into standard RSFC parameters.
195
174
 
196
175
  Author: AFNI Developers
@@ -199,10 +178,12 @@ def v_3d_amp_to_rsfc_execute(
199
178
 
200
179
  Args:
201
180
  params: The parameters.
202
- execution: The execution object.
181
+ runner: Command runner.
203
182
  Returns:
204
183
  NamedTuple of outputs (described in `V3dAmpToRsfcOutputs`).
205
184
  """
185
+ runner = runner or get_global_runner()
186
+ execution = runner.start_execution(V_3D_AMP_TO_RSFC_METADATA)
206
187
  params = execution.params(params)
207
188
  cargs = v_3d_amp_to_rsfc_cargs(params, execution)
208
189
  ret = v_3d_amp_to_rsfc_outputs(params, execution)
@@ -220,6 +201,8 @@ def v_3d_amp_to_rsfc(
220
201
  runner: Runner | None = None,
221
202
  ) -> V3dAmpToRsfcOutputs:
222
203
  """
204
+ 3dAmpToRSFC
205
+
223
206
  Convert spectral amplitudes into standard RSFC parameters.
224
207
 
225
208
  Author: AFNI Developers
@@ -241,8 +224,6 @@ def v_3d_amp_to_rsfc(
241
224
  Returns:
242
225
  NamedTuple of outputs (described in `V3dAmpToRsfcOutputs`).
243
226
  """
244
- runner = runner or get_global_runner()
245
- execution = runner.start_execution(V_3D_AMP_TO_RSFC_METADATA)
246
227
  params = v_3d_amp_to_rsfc_params(
247
228
  in_amp=in_amp,
248
229
  in_pow=in_pow,
@@ -251,13 +232,13 @@ def v_3d_amp_to_rsfc(
251
232
  mask=mask,
252
233
  nifti=nifti,
253
234
  )
254
- return v_3d_amp_to_rsfc_execute(params, execution)
235
+ return v_3d_amp_to_rsfc_execute(params, runner)
255
236
 
256
237
 
257
238
  __all__ = [
258
239
  "V3dAmpToRsfcOutputs",
259
- "V3dAmpToRsfcParameters",
260
240
  "V_3D_AMP_TO_RSFC_METADATA",
261
241
  "v_3d_amp_to_rsfc",
242
+ "v_3d_amp_to_rsfc_execute",
262
243
  "v_3d_amp_to_rsfc_params",
263
244
  ]
@@ -6,7 +6,7 @@ import pathlib
6
6
  from styxdefs import *
7
7
 
8
8
  V_3D_ANHIST_METADATA = Metadata(
9
- id="0c0bd91348202d1b0045fb9d1e10c4cafea33971.boutiques",
9
+ id="c40972f414c2d5996b16432a9c6b6450fc0e7b2a.boutiques",
10
10
  name="3dAnhist",
11
11
  package="afni",
12
12
  container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,7 +14,18 @@ V_3D_ANHIST_METADATA = Metadata(
14
14
 
15
15
 
16
16
  V3dAnhistParameters = typing.TypedDict('V3dAnhistParameters', {
17
- "__STYXTYPE__": typing.Literal["3dAnhist"],
17
+ "@type": typing.NotRequired[typing.Literal["afni/3dAnhist"]],
18
+ "dataset": InputPathType,
19
+ "quiet": bool,
20
+ "dump_histogram": bool,
21
+ "no_scurve": bool,
22
+ "winsorize": typing.NotRequired[str | None],
23
+ "top_2peaks": bool,
24
+ "label": typing.NotRequired[str | None],
25
+ "filename": typing.NotRequired[str | None],
26
+ })
27
+ V3dAnhistParametersTagged = typing.TypedDict('V3dAnhistParametersTagged', {
28
+ "@type": typing.Literal["afni/3dAnhist"],
18
29
  "dataset": InputPathType,
19
30
  "quiet": bool,
20
31
  "dump_histogram": bool,
@@ -24,43 +35,11 @@ V3dAnhistParameters = typing.TypedDict('V3dAnhistParameters', {
24
35
  "label": typing.NotRequired[str | None],
25
36
  "filename": typing.NotRequired[str | None],
26
37
  })
27
-
28
-
29
- def dyn_cargs(
30
- t: str,
31
- ) -> typing.Any:
32
- """
33
- Get build cargs function by command type.
34
-
35
- Args:
36
- t: Command type.
37
- Returns:
38
- Build cargs function.
39
- """
40
- return {
41
- "3dAnhist": v_3d_anhist_cargs,
42
- }.get(t)
43
-
44
-
45
- def dyn_outputs(
46
- t: str,
47
- ) -> typing.Any:
48
- """
49
- Get build outputs function by command type.
50
-
51
- Args:
52
- t: Command type.
53
- Returns:
54
- Build outputs function.
55
- """
56
- return {
57
- "3dAnhist": v_3d_anhist_outputs,
58
- }.get(t)
59
38
 
60
39
 
61
40
  class V3dAnhistOutputs(typing.NamedTuple):
62
41
  """
63
- Output object returned when calling `v_3d_anhist(...)`.
42
+ Output object returned when calling `V3dAnhistParameters(...)`.
64
43
  """
65
44
  root: OutputPathType
66
45
  """Output root folder. This is the root folder for all outputs."""
@@ -79,7 +58,7 @@ def v_3d_anhist_params(
79
58
  top_2peaks: bool = False,
80
59
  label: str | None = None,
81
60
  filename: str | None = None,
82
- ) -> V3dAnhistParameters:
61
+ ) -> V3dAnhistParametersTagged:
83
62
  """
84
63
  Build parameters.
85
64
 
@@ -99,7 +78,7 @@ def v_3d_anhist_params(
99
78
  Parameter dictionary
100
79
  """
101
80
  params = {
102
- "__STYXTYPE__": "3dAnhist",
81
+ "@type": "afni/3dAnhist",
103
82
  "dataset": dataset,
104
83
  "quiet": quiet,
105
84
  "dump_histogram": dump_histogram,
@@ -130,29 +109,29 @@ def v_3d_anhist_cargs(
130
109
  """
131
110
  cargs = []
132
111
  cargs.append("3dAnhist")
133
- cargs.append(execution.input_file(params.get("dataset")))
134
- if params.get("quiet"):
112
+ cargs.append(execution.input_file(params.get("dataset", None)))
113
+ if params.get("quiet", False):
135
114
  cargs.append("-q")
136
- if params.get("dump_histogram"):
115
+ if params.get("dump_histogram", False):
137
116
  cargs.append("-h")
138
- if params.get("no_scurve"):
117
+ if params.get("no_scurve", False):
139
118
  cargs.append("-F")
140
- if params.get("winsorize") is not None:
119
+ if params.get("winsorize", None) is not None:
141
120
  cargs.extend([
142
121
  "-w",
143
- params.get("winsorize")
122
+ params.get("winsorize", None)
144
123
  ])
145
- if params.get("top_2peaks"):
124
+ if params.get("top_2peaks", False):
146
125
  cargs.append("-2")
147
- if params.get("label") is not None:
126
+ if params.get("label", None) is not None:
148
127
  cargs.extend([
149
128
  "-label",
150
- params.get("label")
129
+ params.get("label", None)
151
130
  ])
152
- if params.get("filename") is not None:
131
+ if params.get("filename", None) is not None:
153
132
  cargs.extend([
154
133
  "-fname",
155
- params.get("filename")
134
+ params.get("filename", None)
156
135
  ])
157
136
  return cargs
158
137
 
@@ -180,10 +159,13 @@ def v_3d_anhist_outputs(
180
159
 
181
160
  def v_3d_anhist_execute(
182
161
  params: V3dAnhistParameters,
183
- execution: Execution,
162
+ runner: Runner | None = None,
184
163
  ) -> V3dAnhistOutputs:
185
164
  """
186
- Tool to analyze histogram peaks in a T1-weighted high-res brain image dataset.
165
+ 3dAnhist
166
+
167
+ Tool to analyze histogram peaks in a T1-weighted high-res brain image
168
+ dataset.
187
169
 
188
170
  Author: AFNI Developers
189
171
 
@@ -191,10 +173,12 @@ def v_3d_anhist_execute(
191
173
 
192
174
  Args:
193
175
  params: The parameters.
194
- execution: The execution object.
176
+ runner: Command runner.
195
177
  Returns:
196
178
  NamedTuple of outputs (described in `V3dAnhistOutputs`).
197
179
  """
180
+ runner = runner or get_global_runner()
181
+ execution = runner.start_execution(V_3D_ANHIST_METADATA)
198
182
  params = execution.params(params)
199
183
  cargs = v_3d_anhist_cargs(params, execution)
200
184
  ret = v_3d_anhist_outputs(params, execution)
@@ -214,7 +198,10 @@ def v_3d_anhist(
214
198
  runner: Runner | None = None,
215
199
  ) -> V3dAnhistOutputs:
216
200
  """
217
- Tool to analyze histogram peaks in a T1-weighted high-res brain image dataset.
201
+ 3dAnhist
202
+
203
+ Tool to analyze histogram peaks in a T1-weighted high-res brain image
204
+ dataset.
218
205
 
219
206
  Author: AFNI Developers
220
207
 
@@ -236,8 +223,6 @@ def v_3d_anhist(
236
223
  Returns:
237
224
  NamedTuple of outputs (described in `V3dAnhistOutputs`).
238
225
  """
239
- runner = runner or get_global_runner()
240
- execution = runner.start_execution(V_3D_ANHIST_METADATA)
241
226
  params = v_3d_anhist_params(
242
227
  dataset=dataset,
243
228
  quiet=quiet,
@@ -248,13 +233,13 @@ def v_3d_anhist(
248
233
  label=label,
249
234
  filename=filename,
250
235
  )
251
- return v_3d_anhist_execute(params, execution)
236
+ return v_3d_anhist_execute(params, runner)
252
237
 
253
238
 
254
239
  __all__ = [
255
240
  "V3dAnhistOutputs",
256
- "V3dAnhistParameters",
257
241
  "V_3D_ANHIST_METADATA",
258
242
  "v_3d_anhist",
243
+ "v_3d_anhist_execute",
259
244
  "v_3d_anhist_params",
260
245
  ]
@@ -6,7 +6,7 @@ import pathlib
6
6
  from styxdefs import *
7
7
 
8
8
  V_3D_ANOVA_METADATA = Metadata(
9
- id="e6105d0203eca902c2a3bd514ee2ed3729772721.boutiques",
9
+ id="d6eed026bc71b24760c5cfa681faaf549200477b.boutiques",
10
10
  name="3dANOVA",
11
11
  package="afni",
12
12
  container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,7 +14,24 @@ V_3D_ANOVA_METADATA = Metadata(
14
14
 
15
15
 
16
16
  V3dAnovaParameters = typing.TypedDict('V3dAnovaParameters', {
17
- "__STYXTYPE__": typing.Literal["3dANOVA"],
17
+ "@type": typing.NotRequired[typing.Literal["afni/3dANOVA"]],
18
+ "levels": int,
19
+ "datasets": list[str],
20
+ "voxel": typing.NotRequired[int | None],
21
+ "diskspace": bool,
22
+ "mask": typing.NotRequired[InputPathType | None],
23
+ "debug": typing.NotRequired[int | None],
24
+ "ftr": typing.NotRequired[str | None],
25
+ "mean": typing.NotRequired[str | None],
26
+ "diff": typing.NotRequired[str | None],
27
+ "contr": typing.NotRequired[str | None],
28
+ "old_method": bool,
29
+ "ok": bool,
30
+ "assume_sph": bool,
31
+ "bucket": typing.NotRequired[str | None],
32
+ })
33
+ V3dAnovaParametersTagged = typing.TypedDict('V3dAnovaParametersTagged', {
34
+ "@type": typing.Literal["afni/3dANOVA"],
18
35
  "levels": int,
19
36
  "datasets": list[str],
20
37
  "voxel": typing.NotRequired[int | None],
@@ -30,43 +47,11 @@ V3dAnovaParameters = typing.TypedDict('V3dAnovaParameters', {
30
47
  "assume_sph": bool,
31
48
  "bucket": typing.NotRequired[str | None],
32
49
  })
33
-
34
-
35
- def dyn_cargs(
36
- t: str,
37
- ) -> typing.Any:
38
- """
39
- Get build cargs function by command type.
40
-
41
- Args:
42
- t: Command type.
43
- Returns:
44
- Build cargs function.
45
- """
46
- return {
47
- "3dANOVA": v_3d_anova_cargs,
48
- }.get(t)
49
-
50
-
51
- def dyn_outputs(
52
- t: str,
53
- ) -> typing.Any:
54
- """
55
- Get build outputs function by command type.
56
-
57
- Args:
58
- t: Command type.
59
- Returns:
60
- Build outputs function.
61
- """
62
- return {
63
- "3dANOVA": v_3d_anova_outputs,
64
- }.get(t)
65
50
 
66
51
 
67
52
  class V3dAnovaOutputs(typing.NamedTuple):
68
53
  """
69
- Output object returned when calling `v_3d_anova(...)`.
54
+ Output object returned when calling `V3dAnovaParameters(...)`.
70
55
  """
71
56
  root: OutputPathType
72
57
  """Output root folder. This is the root folder for all outputs."""
@@ -107,7 +92,7 @@ def v_3d_anova_params(
107
92
  ok: bool = False,
108
93
  assume_sph: bool = False,
109
94
  bucket: str | None = None,
110
- ) -> V3dAnovaParameters:
95
+ ) -> V3dAnovaParametersTagged:
111
96
  """
112
97
  Build parameters.
113
98
 
@@ -131,7 +116,7 @@ def v_3d_anova_params(
131
116
  Parameter dictionary
132
117
  """
133
118
  params = {
134
- "__STYXTYPE__": "3dANOVA",
119
+ "@type": "afni/3dANOVA",
135
120
  "levels": levels,
136
121
  "datasets": datasets,
137
122
  "diskspace": diskspace,
@@ -175,59 +160,59 @@ def v_3d_anova_cargs(
175
160
  cargs.append("3dANOVA")
176
161
  cargs.extend([
177
162
  "-levels",
178
- str(params.get("levels"))
163
+ str(params.get("levels", None))
179
164
  ])
180
165
  cargs.extend([
181
166
  "-dset",
182
- *params.get("datasets")
167
+ *params.get("datasets", None)
183
168
  ])
184
- if params.get("voxel") is not None:
169
+ if params.get("voxel", None) is not None:
185
170
  cargs.extend([
186
171
  "-voxel",
187
- str(params.get("voxel"))
172
+ str(params.get("voxel", None))
188
173
  ])
189
- if params.get("diskspace"):
174
+ if params.get("diskspace", False):
190
175
  cargs.append("-diskspace")
191
- if params.get("mask") is not None:
176
+ if params.get("mask", None) is not None:
192
177
  cargs.extend([
193
178
  "-mask",
194
- execution.input_file(params.get("mask"))
179
+ execution.input_file(params.get("mask", None))
195
180
  ])
196
- if params.get("debug") is not None:
181
+ if params.get("debug", None) is not None:
197
182
  cargs.extend([
198
183
  "-debug",
199
- str(params.get("debug"))
184
+ str(params.get("debug", None))
200
185
  ])
201
- if params.get("ftr") is not None:
186
+ if params.get("ftr", None) is not None:
202
187
  cargs.extend([
203
188
  "-ftr",
204
- params.get("ftr")
189
+ params.get("ftr", None)
205
190
  ])
206
- if params.get("mean") is not None:
191
+ if params.get("mean", None) is not None:
207
192
  cargs.extend([
208
193
  "-mean",
209
- params.get("mean")
194
+ params.get("mean", None)
210
195
  ])
211
- if params.get("diff") is not None:
196
+ if params.get("diff", None) is not None:
212
197
  cargs.extend([
213
198
  "-diff",
214
- params.get("diff")
199
+ params.get("diff", None)
215
200
  ])
216
- if params.get("contr") is not None:
201
+ if params.get("contr", None) is not None:
217
202
  cargs.extend([
218
203
  "-contr",
219
- params.get("contr")
204
+ params.get("contr", None)
220
205
  ])
221
- if params.get("old_method"):
206
+ if params.get("old_method", False):
222
207
  cargs.append("-old_method")
223
- if params.get("ok"):
208
+ if params.get("ok", False):
224
209
  cargs.append("-OK")
225
- if params.get("assume_sph"):
210
+ if params.get("assume_sph", False):
226
211
  cargs.append("-assume_sph")
227
- if params.get("bucket") is not None:
212
+ if params.get("bucket", None) is not None:
228
213
  cargs.extend([
229
214
  "-bucket",
230
- params.get("bucket")
215
+ params.get("bucket", None)
231
216
  ])
232
217
  return cargs
233
218
 
@@ -247,25 +232,27 @@ def v_3d_anova_outputs(
247
232
  """
248
233
  ret = V3dAnovaOutputs(
249
234
  root=execution.output_file("."),
250
- ftr_output=execution.output_file(params.get("ftr") + ".HEAD") if (params.get("ftr") is not None) else None,
251
- ftr_brick_output=execution.output_file(params.get("ftr") + ".BRIK") if (params.get("ftr") is not None) else None,
252
- mean_output=execution.output_file(params.get("mean") + "_mean.HEAD") if (params.get("mean") is not None) else None,
253
- mean_brick_output=execution.output_file(params.get("mean") + "_mean.BRIK") if (params.get("mean") is not None) else None,
254
- diff_output=execution.output_file(params.get("diff") + "_diff.HEAD") if (params.get("diff") is not None) else None,
255
- diff_brick_output=execution.output_file(params.get("diff") + "_diff.BRIK") if (params.get("diff") is not None) else None,
256
- contr_output=execution.output_file(params.get("contr") + "_contr.HEAD") if (params.get("contr") is not None) else None,
257
- contr_brick_output=execution.output_file(params.get("contr") + "_contr.BRIK") if (params.get("contr") is not None) else None,
258
- bucket_output=execution.output_file(params.get("bucket") + ".HEAD") if (params.get("bucket") is not None) else None,
259
- bucket_brick_output=execution.output_file(params.get("bucket") + ".BRIK") if (params.get("bucket") is not None) else None,
235
+ ftr_output=execution.output_file(params.get("ftr", None) + ".HEAD") if (params.get("ftr") is not None) else None,
236
+ ftr_brick_output=execution.output_file(params.get("ftr", None) + ".BRIK") if (params.get("ftr") is not None) else None,
237
+ mean_output=execution.output_file(params.get("mean", None) + "_mean.HEAD") if (params.get("mean") is not None) else None,
238
+ mean_brick_output=execution.output_file(params.get("mean", None) + "_mean.BRIK") if (params.get("mean") is not None) else None,
239
+ diff_output=execution.output_file(params.get("diff", None) + "_diff.HEAD") if (params.get("diff") is not None) else None,
240
+ diff_brick_output=execution.output_file(params.get("diff", None) + "_diff.BRIK") if (params.get("diff") is not None) else None,
241
+ contr_output=execution.output_file(params.get("contr", None) + "_contr.HEAD") if (params.get("contr") is not None) else None,
242
+ contr_brick_output=execution.output_file(params.get("contr", None) + "_contr.BRIK") if (params.get("contr") is not None) else None,
243
+ bucket_output=execution.output_file(params.get("bucket", None) + ".HEAD") if (params.get("bucket") is not None) else None,
244
+ bucket_brick_output=execution.output_file(params.get("bucket", None) + ".BRIK") if (params.get("bucket") is not None) else None,
260
245
  )
261
246
  return ret
262
247
 
263
248
 
264
249
  def v_3d_anova_execute(
265
250
  params: V3dAnovaParameters,
266
- execution: Execution,
251
+ runner: Runner | None = None,
267
252
  ) -> V3dAnovaOutputs:
268
253
  """
254
+ 3dANOVA
255
+
269
256
  Performs single-factor Analysis of Variance (ANOVA) on 3D datasets.
270
257
 
271
258
  Author: AFNI Developers
@@ -274,10 +261,12 @@ def v_3d_anova_execute(
274
261
 
275
262
  Args:
276
263
  params: The parameters.
277
- execution: The execution object.
264
+ runner: Command runner.
278
265
  Returns:
279
266
  NamedTuple of outputs (described in `V3dAnovaOutputs`).
280
267
  """
268
+ runner = runner or get_global_runner()
269
+ execution = runner.start_execution(V_3D_ANOVA_METADATA)
281
270
  params = execution.params(params)
282
271
  cargs = v_3d_anova_cargs(params, execution)
283
272
  ret = v_3d_anova_outputs(params, execution)
@@ -303,6 +292,8 @@ def v_3d_anova(
303
292
  runner: Runner | None = None,
304
293
  ) -> V3dAnovaOutputs:
305
294
  """
295
+ 3dANOVA
296
+
306
297
  Performs single-factor Analysis of Variance (ANOVA) on 3D datasets.
307
298
 
308
299
  Author: AFNI Developers
@@ -329,8 +320,6 @@ def v_3d_anova(
329
320
  Returns:
330
321
  NamedTuple of outputs (described in `V3dAnovaOutputs`).
331
322
  """
332
- runner = runner or get_global_runner()
333
- execution = runner.start_execution(V_3D_ANOVA_METADATA)
334
323
  params = v_3d_anova_params(
335
324
  levels=levels,
336
325
  datasets=datasets,
@@ -347,13 +336,13 @@ def v_3d_anova(
347
336
  assume_sph=assume_sph,
348
337
  bucket=bucket,
349
338
  )
350
- return v_3d_anova_execute(params, execution)
339
+ return v_3d_anova_execute(params, runner)
351
340
 
352
341
 
353
342
  __all__ = [
354
343
  "V3dAnovaOutputs",
355
- "V3dAnovaParameters",
356
344
  "V_3D_ANOVA_METADATA",
357
345
  "v_3d_anova",
346
+ "v_3d_anova_execute",
358
347
  "v_3d_anova_params",
359
348
  ]