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_TFITTER_METADATA = Metadata(
9
- id="5551f704047c1d65ffe2a71f1785e21d42693265.boutiques",
9
+ id="823720eb849f313e116601e7d8bf16a32c9a2615.boutiques",
10
10
  name="3dTfitter",
11
11
  package="afni",
12
12
  container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,7 +14,28 @@ V_3D_TFITTER_METADATA = Metadata(
14
14
 
15
15
 
16
16
  V3dTfitterParameters = typing.TypedDict('V3dTfitterParameters', {
17
- "__STYXTYPE__": typing.Literal["3dTfitter"],
17
+ "@type": typing.NotRequired[typing.Literal["afni/3dTfitter"]],
18
+ "RHS": str,
19
+ "LHS": typing.NotRequired[list[str] | None],
20
+ "polort": typing.NotRequired[float | None],
21
+ "vthr": typing.NotRequired[float | None],
22
+ "FALTUNG": typing.NotRequired[list[str] | None],
23
+ "lsqfit": bool,
24
+ "l1fit": bool,
25
+ "l2lasso": typing.NotRequired[list[str] | None],
26
+ "lasso_centro_block": typing.NotRequired[list[str] | None],
27
+ "l2sqrtlasso": typing.NotRequired[list[str] | None],
28
+ "consign": typing.NotRequired[list[str] | None],
29
+ "consFAL": typing.NotRequired[str | None],
30
+ "prefix": typing.NotRequired[str | None],
31
+ "label": typing.NotRequired[list[str] | None],
32
+ "fitts": typing.NotRequired[str | None],
33
+ "errsum": typing.NotRequired[str | None],
34
+ "mask": typing.NotRequired[str | None],
35
+ "quiet": bool,
36
+ })
37
+ V3dTfitterParametersTagged = typing.TypedDict('V3dTfitterParametersTagged', {
38
+ "@type": typing.Literal["afni/3dTfitter"],
18
39
  "RHS": str,
19
40
  "LHS": typing.NotRequired[list[str] | None],
20
41
  "polort": typing.NotRequired[float | None],
@@ -34,43 +55,11 @@ V3dTfitterParameters = typing.TypedDict('V3dTfitterParameters', {
34
55
  "mask": typing.NotRequired[str | None],
35
56
  "quiet": bool,
36
57
  })
37
-
38
-
39
- def dyn_cargs(
40
- t: str,
41
- ) -> typing.Any:
42
- """
43
- Get build cargs function by command type.
44
-
45
- Args:
46
- t: Command type.
47
- Returns:
48
- Build cargs function.
49
- """
50
- return {
51
- "3dTfitter": v_3d_tfitter_cargs,
52
- }.get(t)
53
-
54
-
55
- def dyn_outputs(
56
- t: str,
57
- ) -> typing.Any:
58
- """
59
- Get build outputs function by command type.
60
-
61
- Args:
62
- t: Command type.
63
- Returns:
64
- Build outputs function.
65
- """
66
- return {
67
- "3dTfitter": v_3d_tfitter_outputs,
68
- }.get(t)
69
58
 
70
59
 
71
60
  class V3dTfitterOutputs(typing.NamedTuple):
72
61
  """
73
- Output object returned when calling `v_3d_tfitter(...)`.
62
+ Output object returned when calling `V3dTfitterParameters(...)`.
74
63
  """
75
64
  root: OutputPathType
76
65
  """Output root folder. This is the root folder for all outputs."""
@@ -101,7 +90,7 @@ def v_3d_tfitter_params(
101
90
  errsum: str | None = None,
102
91
  mask: str | None = None,
103
92
  quiet: bool = False,
104
- ) -> V3dTfitterParameters:
93
+ ) -> V3dTfitterParametersTagged:
105
94
  """
106
95
  Build parameters.
107
96
 
@@ -140,7 +129,7 @@ def v_3d_tfitter_params(
140
129
  Parameter dictionary
141
130
  """
142
131
  params = {
143
- "__STYXTYPE__": "3dTfitter",
132
+ "@type": "afni/3dTfitter",
144
133
  "RHS": rhs,
145
134
  "lsqfit": lsqfit,
146
135
  "l1fit": l1fit,
@@ -194,83 +183,83 @@ def v_3d_tfitter_cargs(
194
183
  cargs.append("3dTfitter")
195
184
  cargs.extend([
196
185
  "-RHS",
197
- params.get("RHS")
186
+ params.get("RHS", None)
198
187
  ])
199
- if params.get("LHS") is not None:
188
+ if params.get("LHS", None) is not None:
200
189
  cargs.extend([
201
190
  "-LHS",
202
- *params.get("LHS")
191
+ *params.get("LHS", None)
203
192
  ])
204
- if params.get("polort") is not None:
193
+ if params.get("polort", None) is not None:
205
194
  cargs.extend([
206
195
  "-polort",
207
- str(params.get("polort"))
196
+ str(params.get("polort", None))
208
197
  ])
209
- if params.get("vthr") is not None:
198
+ if params.get("vthr", None) is not None:
210
199
  cargs.extend([
211
200
  "-vthr",
212
- str(params.get("vthr"))
201
+ str(params.get("vthr", None))
213
202
  ])
214
- if params.get("FALTUNG") is not None:
203
+ if params.get("FALTUNG", None) is not None:
215
204
  cargs.extend([
216
205
  "-FALTUNG",
217
- *params.get("FALTUNG")
206
+ *params.get("FALTUNG", None)
218
207
  ])
219
- if params.get("lsqfit"):
208
+ if params.get("lsqfit", False):
220
209
  cargs.append("-lsqfit")
221
- if params.get("l1fit"):
210
+ if params.get("l1fit", False):
222
211
  cargs.append("-l1fit")
223
- if params.get("l2lasso") is not None:
212
+ if params.get("l2lasso", None) is not None:
224
213
  cargs.extend([
225
214
  "-l2lasso",
226
- *params.get("l2lasso")
215
+ *params.get("l2lasso", None)
227
216
  ])
228
- if params.get("lasso_centro_block") is not None:
217
+ if params.get("lasso_centro_block", None) is not None:
229
218
  cargs.extend([
230
219
  "-lasso_centro_block",
231
- *params.get("lasso_centro_block")
220
+ *params.get("lasso_centro_block", None)
232
221
  ])
233
- if params.get("l2sqrtlasso") is not None:
222
+ if params.get("l2sqrtlasso", None) is not None:
234
223
  cargs.extend([
235
224
  "-l2sqrtlasso",
236
- *params.get("l2sqrtlasso")
225
+ *params.get("l2sqrtlasso", None)
237
226
  ])
238
- if params.get("consign") is not None:
227
+ if params.get("consign", None) is not None:
239
228
  cargs.extend([
240
229
  "-consign",
241
- *params.get("consign")
230
+ *params.get("consign", None)
242
231
  ])
243
- if params.get("consFAL") is not None:
232
+ if params.get("consFAL", None) is not None:
244
233
  cargs.extend([
245
234
  "-consFAL",
246
- params.get("consFAL")
235
+ params.get("consFAL", None)
247
236
  ])
248
- if params.get("prefix") is not None:
237
+ if params.get("prefix", None) is not None:
249
238
  cargs.extend([
250
239
  "-prefix",
251
- params.get("prefix")
240
+ params.get("prefix", None)
252
241
  ])
253
- if params.get("label") is not None:
242
+ if params.get("label", None) is not None:
254
243
  cargs.extend([
255
244
  "-label",
256
- *params.get("label")
245
+ *params.get("label", None)
257
246
  ])
258
- if params.get("fitts") is not None:
247
+ if params.get("fitts", None) is not None:
259
248
  cargs.extend([
260
249
  "-fitts",
261
- params.get("fitts")
250
+ params.get("fitts", None)
262
251
  ])
263
- if params.get("errsum") is not None:
252
+ if params.get("errsum", None) is not None:
264
253
  cargs.extend([
265
254
  "-errsum",
266
- params.get("errsum")
255
+ params.get("errsum", None)
267
256
  ])
268
- if params.get("mask") is not None:
257
+ if params.get("mask", None) is not None:
269
258
  cargs.extend([
270
259
  "-mask",
271
- params.get("mask")
260
+ params.get("mask", None)
272
261
  ])
273
- if params.get("quiet"):
262
+ if params.get("quiet", False):
274
263
  cargs.append("-quiet")
275
264
  return cargs
276
265
 
@@ -290,18 +279,20 @@ def v_3d_tfitter_outputs(
290
279
  """
291
280
  ret = V3dTfitterOutputs(
292
281
  root=execution.output_file("."),
293
- output_prefix=execution.output_file(params.get("prefix") + ".nii.gz") if (params.get("prefix") is not None) else None,
294
- fitted_time_series=execution.output_file(params.get("fitts") + ".nii.gz") if (params.get("fitts") is not None) else None,
295
- error_sums=execution.output_file(params.get("errsum") + ".nii.gz") if (params.get("errsum") is not None) else None,
282
+ output_prefix=execution.output_file(params.get("prefix", None) + ".nii.gz") if (params.get("prefix") is not None) else None,
283
+ fitted_time_series=execution.output_file(params.get("fitts", None) + ".nii.gz") if (params.get("fitts") is not None) else None,
284
+ error_sums=execution.output_file(params.get("errsum", None) + ".nii.gz") if (params.get("errsum") is not None) else None,
296
285
  )
297
286
  return ret
298
287
 
299
288
 
300
289
  def v_3d_tfitter_execute(
301
290
  params: V3dTfitterParameters,
302
- execution: Execution,
291
+ runner: Runner | None = None,
303
292
  ) -> V3dTfitterOutputs:
304
293
  """
294
+ 3dTfitter
295
+
305
296
  * At each voxel, assembles and solves a set of linear equations.
306
297
  ++ The matrix at each voxel may be the same or may be different.
307
298
  ++ This flexibility (for voxel-wise regressors) is one feature
@@ -316,10 +307,12 @@ def v_3d_tfitter_execute(
316
307
 
317
308
  Args:
318
309
  params: The parameters.
319
- execution: The execution object.
310
+ runner: Command runner.
320
311
  Returns:
321
312
  NamedTuple of outputs (described in `V3dTfitterOutputs`).
322
313
  """
314
+ runner = runner or get_global_runner()
315
+ execution = runner.start_execution(V_3D_TFITTER_METADATA)
323
316
  params = execution.params(params)
324
317
  cargs = v_3d_tfitter_cargs(params, execution)
325
318
  ret = v_3d_tfitter_outputs(params, execution)
@@ -349,6 +342,8 @@ def v_3d_tfitter(
349
342
  runner: Runner | None = None,
350
343
  ) -> V3dTfitterOutputs:
351
344
  """
345
+ 3dTfitter
346
+
352
347
  * At each voxel, assembles and solves a set of linear equations.
353
348
  ++ The matrix at each voxel may be the same or may be different.
354
349
  ++ This flexibility (for voxel-wise regressors) is one feature
@@ -396,8 +391,6 @@ def v_3d_tfitter(
396
391
  Returns:
397
392
  NamedTuple of outputs (described in `V3dTfitterOutputs`).
398
393
  """
399
- runner = runner or get_global_runner()
400
- execution = runner.start_execution(V_3D_TFITTER_METADATA)
401
394
  params = v_3d_tfitter_params(
402
395
  rhs=rhs,
403
396
  lhs=lhs,
@@ -418,13 +411,13 @@ def v_3d_tfitter(
418
411
  mask=mask,
419
412
  quiet=quiet,
420
413
  )
421
- return v_3d_tfitter_execute(params, execution)
414
+ return v_3d_tfitter_execute(params, runner)
422
415
 
423
416
 
424
417
  __all__ = [
425
418
  "V3dTfitterOutputs",
426
- "V3dTfitterParameters",
427
419
  "V_3D_TFITTER_METADATA",
428
420
  "v_3d_tfitter",
421
+ "v_3d_tfitter_execute",
429
422
  "v_3d_tfitter_params",
430
423
  ]
@@ -6,7 +6,7 @@ import pathlib
6
6
  from styxdefs import *
7
7
 
8
8
  V_3D_THREETO_RGB_METADATA = Metadata(
9
- id="9e2d64e118fc6f51565e791f8cb22a6510ace6f5.boutiques",
9
+ id="f4ddee1d7e220b57e9ab948d804be5fbf2aecce3.boutiques",
10
10
  name="3dThreetoRGB",
11
11
  package="afni",
12
12
  container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,7 +14,18 @@ V_3D_THREETO_RGB_METADATA = Metadata(
14
14
 
15
15
 
16
16
  V3dThreetoRgbParameters = typing.TypedDict('V3dThreetoRgbParameters', {
17
- "__STYXTYPE__": typing.Literal["3dThreetoRGB"],
17
+ "@type": typing.NotRequired[typing.Literal["afni/3dThreetoRGB"]],
18
+ "output_prefix": typing.NotRequired[str | None],
19
+ "scale_factor": typing.NotRequired[float | None],
20
+ "mask_dataset": typing.NotRequired[InputPathType | None],
21
+ "fim": bool,
22
+ "anat": bool,
23
+ "input_dataset": InputPathType,
24
+ "input_dataset2": typing.NotRequired[InputPathType | None],
25
+ "input_dataset3": typing.NotRequired[InputPathType | None],
26
+ })
27
+ V3dThreetoRgbParametersTagged = typing.TypedDict('V3dThreetoRgbParametersTagged', {
28
+ "@type": typing.Literal["afni/3dThreetoRGB"],
18
29
  "output_prefix": typing.NotRequired[str | None],
19
30
  "scale_factor": typing.NotRequired[float | None],
20
31
  "mask_dataset": typing.NotRequired[InputPathType | None],
@@ -24,43 +35,11 @@ V3dThreetoRgbParameters = typing.TypedDict('V3dThreetoRgbParameters', {
24
35
  "input_dataset2": typing.NotRequired[InputPathType | None],
25
36
  "input_dataset3": typing.NotRequired[InputPathType | 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
- "3dThreetoRGB": v_3d_threeto_rgb_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
- "3dThreetoRGB": v_3d_threeto_rgb_outputs,
58
- }.get(t)
59
38
 
60
39
 
61
40
  class V3dThreetoRgbOutputs(typing.NamedTuple):
62
41
  """
63
- Output object returned when calling `v_3d_threeto_rgb(...)`.
42
+ Output object returned when calling `V3dThreetoRgbParameters(...)`.
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_threeto_rgb_params(
79
58
  anat: bool = False,
80
59
  input_dataset2: InputPathType | None = None,
81
60
  input_dataset3: InputPathType | None = None,
82
- ) -> V3dThreetoRgbParameters:
61
+ ) -> V3dThreetoRgbParametersTagged:
83
62
  """
84
63
  Build parameters.
85
64
 
@@ -100,7 +79,7 @@ def v_3d_threeto_rgb_params(
100
79
  Parameter dictionary
101
80
  """
102
81
  params = {
103
- "__STYXTYPE__": "3dThreetoRGB",
82
+ "@type": "afni/3dThreetoRGB",
104
83
  "fim": fim,
105
84
  "anat": anat,
106
85
  "input_dataset": input_dataset,
@@ -133,30 +112,30 @@ def v_3d_threeto_rgb_cargs(
133
112
  """
134
113
  cargs = []
135
114
  cargs.append("3dThreetoRGB")
136
- if params.get("output_prefix") is not None:
115
+ if params.get("output_prefix", None) is not None:
137
116
  cargs.extend([
138
117
  "-prefix",
139
- params.get("output_prefix")
118
+ params.get("output_prefix", None)
140
119
  ])
141
- if params.get("scale_factor") is not None:
120
+ if params.get("scale_factor", None) is not None:
142
121
  cargs.extend([
143
122
  "-scale",
144
- str(params.get("scale_factor"))
123
+ str(params.get("scale_factor", None))
145
124
  ])
146
- if params.get("mask_dataset") is not None:
125
+ if params.get("mask_dataset", None) is not None:
147
126
  cargs.extend([
148
127
  "-mask",
149
- execution.input_file(params.get("mask_dataset"))
128
+ execution.input_file(params.get("mask_dataset", None))
150
129
  ])
151
- if params.get("fim"):
130
+ if params.get("fim", False):
152
131
  cargs.append("-fim")
153
- if params.get("anat"):
132
+ if params.get("anat", False):
154
133
  cargs.append("-anat")
155
- cargs.append(execution.input_file(params.get("input_dataset")))
156
- if params.get("input_dataset2") is not None:
157
- cargs.append(execution.input_file(params.get("input_dataset2")))
158
- if params.get("input_dataset3") is not None:
159
- cargs.append(execution.input_file(params.get("input_dataset3")))
134
+ cargs.append(execution.input_file(params.get("input_dataset", None)))
135
+ if params.get("input_dataset2", None) is not None:
136
+ cargs.append(execution.input_file(params.get("input_dataset2", None)))
137
+ if params.get("input_dataset3", None) is not None:
138
+ cargs.append(execution.input_file(params.get("input_dataset3", None)))
160
139
  return cargs
161
140
 
162
141
 
@@ -175,17 +154,19 @@ def v_3d_threeto_rgb_outputs(
175
154
  """
176
155
  ret = V3dThreetoRgbOutputs(
177
156
  root=execution.output_file("."),
178
- output_dataset_head=execution.output_file(params.get("output_prefix") + "+rgb.HEAD") if (params.get("output_prefix") is not None) else None,
179
- output_dataset_brik=execution.output_file(params.get("output_prefix") + "+rgb.BRIK") if (params.get("output_prefix") is not None) else None,
157
+ output_dataset_head=execution.output_file(params.get("output_prefix", None) + "+rgb.HEAD") if (params.get("output_prefix") is not None) else None,
158
+ output_dataset_brik=execution.output_file(params.get("output_prefix", None) + "+rgb.BRIK") if (params.get("output_prefix") is not None) else None,
180
159
  )
181
160
  return ret
182
161
 
183
162
 
184
163
  def v_3d_threeto_rgb_execute(
185
164
  params: V3dThreetoRgbParameters,
186
- execution: Execution,
165
+ runner: Runner | None = None,
187
166
  ) -> V3dThreetoRgbOutputs:
188
167
  """
168
+ 3dThreetoRGB
169
+
189
170
  Converts 3 sub-bricks of input to an RGB-valued dataset.
190
171
 
191
172
  Author: AFNI Developers
@@ -194,10 +175,12 @@ def v_3d_threeto_rgb_execute(
194
175
 
195
176
  Args:
196
177
  params: The parameters.
197
- execution: The execution object.
178
+ runner: Command runner.
198
179
  Returns:
199
180
  NamedTuple of outputs (described in `V3dThreetoRgbOutputs`).
200
181
  """
182
+ runner = runner or get_global_runner()
183
+ execution = runner.start_execution(V_3D_THREETO_RGB_METADATA)
201
184
  params = execution.params(params)
202
185
  cargs = v_3d_threeto_rgb_cargs(params, execution)
203
186
  ret = v_3d_threeto_rgb_outputs(params, execution)
@@ -217,6 +200,8 @@ def v_3d_threeto_rgb(
217
200
  runner: Runner | None = None,
218
201
  ) -> V3dThreetoRgbOutputs:
219
202
  """
203
+ 3dThreetoRGB
204
+
220
205
  Converts 3 sub-bricks of input to an RGB-valued dataset.
221
206
 
222
207
  Author: AFNI Developers
@@ -240,8 +225,6 @@ def v_3d_threeto_rgb(
240
225
  Returns:
241
226
  NamedTuple of outputs (described in `V3dThreetoRgbOutputs`).
242
227
  """
243
- runner = runner or get_global_runner()
244
- execution = runner.start_execution(V_3D_THREETO_RGB_METADATA)
245
228
  params = v_3d_threeto_rgb_params(
246
229
  output_prefix=output_prefix,
247
230
  scale_factor=scale_factor,
@@ -252,13 +235,13 @@ def v_3d_threeto_rgb(
252
235
  input_dataset2=input_dataset2,
253
236
  input_dataset3=input_dataset3,
254
237
  )
255
- return v_3d_threeto_rgb_execute(params, execution)
238
+ return v_3d_threeto_rgb_execute(params, runner)
256
239
 
257
240
 
258
241
  __all__ = [
259
242
  "V3dThreetoRgbOutputs",
260
- "V3dThreetoRgbParameters",
261
243
  "V_3D_THREETO_RGB_METADATA",
262
244
  "v_3d_threeto_rgb",
245
+ "v_3d_threeto_rgb_execute",
263
246
  "v_3d_threeto_rgb_params",
264
247
  ]
@@ -6,7 +6,7 @@ import pathlib
6
6
  from styxdefs import *
7
7
 
8
8
  V_3D_TNORM_METADATA = Metadata(
9
- id="25b9e3edcf15c98bfac019a6df8102a76fdaa6a1.boutiques",
9
+ id="7f2e7dc2e7d52489c9bd56c37e8353d2ad4b12ba.boutiques",
10
10
  name="3dTnorm",
11
11
  package="afni",
12
12
  container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,7 +14,18 @@ V_3D_TNORM_METADATA = Metadata(
14
14
 
15
15
 
16
16
  V3dTnormParameters = typing.TypedDict('V3dTnormParameters', {
17
- "__STYXTYPE__": typing.Literal["3dTnorm"],
17
+ "@type": typing.NotRequired[typing.Literal["afni/3dTnorm"]],
18
+ "prefix": typing.NotRequired[str | None],
19
+ "norm2": bool,
20
+ "normR": bool,
21
+ "norm1": bool,
22
+ "normx": bool,
23
+ "polort": typing.NotRequired[float | None],
24
+ "L1fit": bool,
25
+ "input_dataset": InputPathType,
26
+ })
27
+ V3dTnormParametersTagged = typing.TypedDict('V3dTnormParametersTagged', {
28
+ "@type": typing.Literal["afni/3dTnorm"],
18
29
  "prefix": typing.NotRequired[str | None],
19
30
  "norm2": bool,
20
31
  "normR": bool,
@@ -24,43 +35,11 @@ V3dTnormParameters = typing.TypedDict('V3dTnormParameters', {
24
35
  "L1fit": bool,
25
36
  "input_dataset": InputPathType,
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
- "3dTnorm": v_3d_tnorm_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
- "3dTnorm": v_3d_tnorm_outputs,
58
- }.get(t)
59
38
 
60
39
 
61
40
  class V3dTnormOutputs(typing.NamedTuple):
62
41
  """
63
- Output object returned when calling `v_3d_tnorm(...)`.
42
+ Output object returned when calling `V3dTnormParameters(...)`.
64
43
  """
65
44
  root: OutputPathType
66
45
  """Output root folder. This is the root folder for all outputs."""
@@ -77,7 +56,7 @@ def v_3d_tnorm_params(
77
56
  normx: bool = False,
78
57
  polort: float | None = None,
79
58
  l1fit: bool = False,
80
- ) -> V3dTnormParameters:
59
+ ) -> V3dTnormParametersTagged:
81
60
  """
82
61
  Build parameters.
83
62
 
@@ -94,7 +73,7 @@ def v_3d_tnorm_params(
94
73
  Parameter dictionary
95
74
  """
96
75
  params = {
97
- "__STYXTYPE__": "3dTnorm",
76
+ "@type": "afni/3dTnorm",
98
77
  "norm2": norm2,
99
78
  "normR": norm_r,
100
79
  "norm1": norm1,
@@ -124,27 +103,27 @@ def v_3d_tnorm_cargs(
124
103
  """
125
104
  cargs = []
126
105
  cargs.append("3dTnorm")
127
- if params.get("prefix") is not None:
106
+ if params.get("prefix", None) is not None:
128
107
  cargs.extend([
129
108
  "-prefix",
130
- params.get("prefix")
109
+ params.get("prefix", None)
131
110
  ])
132
- if params.get("norm2"):
111
+ if params.get("norm2", False):
133
112
  cargs.append("-norm2")
134
- if params.get("normR"):
113
+ if params.get("normR", False):
135
114
  cargs.append("-normR")
136
- if params.get("norm1"):
115
+ if params.get("norm1", False):
137
116
  cargs.append("-norm1")
138
- if params.get("normx"):
117
+ if params.get("normx", False):
139
118
  cargs.append("-normx")
140
- if params.get("polort") is not None:
119
+ if params.get("polort", None) is not None:
141
120
  cargs.extend([
142
121
  "-polort",
143
- str(params.get("polort"))
122
+ str(params.get("polort", None))
144
123
  ])
145
- if params.get("L1fit"):
124
+ if params.get("L1fit", False):
146
125
  cargs.append("-L1fit")
147
- cargs.append(execution.input_file(params.get("input_dataset")))
126
+ cargs.append(execution.input_file(params.get("input_dataset", None)))
148
127
  return cargs
149
128
 
150
129
 
@@ -163,16 +142,18 @@ def v_3d_tnorm_outputs(
163
142
  """
164
143
  ret = V3dTnormOutputs(
165
144
  root=execution.output_file("."),
166
- output_dataset=execution.output_file(params.get("prefix") + ".nii") if (params.get("prefix") is not None) else None,
145
+ output_dataset=execution.output_file(params.get("prefix", None) + ".nii") if (params.get("prefix") is not None) else None,
167
146
  )
168
147
  return ret
169
148
 
170
149
 
171
150
  def v_3d_tnorm_execute(
172
151
  params: V3dTnormParameters,
173
- execution: Execution,
152
+ runner: Runner | None = None,
174
153
  ) -> V3dTnormOutputs:
175
154
  """
155
+ 3dTnorm
156
+
176
157
  Normalizes each voxel time series by multiplicative scaling.
177
158
 
178
159
  Author: AFNI Developers
@@ -181,10 +162,12 @@ def v_3d_tnorm_execute(
181
162
 
182
163
  Args:
183
164
  params: The parameters.
184
- execution: The execution object.
165
+ runner: Command runner.
185
166
  Returns:
186
167
  NamedTuple of outputs (described in `V3dTnormOutputs`).
187
168
  """
169
+ runner = runner or get_global_runner()
170
+ execution = runner.start_execution(V_3D_TNORM_METADATA)
188
171
  params = execution.params(params)
189
172
  cargs = v_3d_tnorm_cargs(params, execution)
190
173
  ret = v_3d_tnorm_outputs(params, execution)
@@ -204,6 +187,8 @@ def v_3d_tnorm(
204
187
  runner: Runner | None = None,
205
188
  ) -> V3dTnormOutputs:
206
189
  """
190
+ 3dTnorm
191
+
207
192
  Normalizes each voxel time series by multiplicative scaling.
208
193
 
209
194
  Author: AFNI Developers
@@ -223,8 +208,6 @@ def v_3d_tnorm(
223
208
  Returns:
224
209
  NamedTuple of outputs (described in `V3dTnormOutputs`).
225
210
  """
226
- runner = runner or get_global_runner()
227
- execution = runner.start_execution(V_3D_TNORM_METADATA)
228
211
  params = v_3d_tnorm_params(
229
212
  prefix=prefix,
230
213
  norm2=norm2,
@@ -235,13 +218,13 @@ def v_3d_tnorm(
235
218
  l1fit=l1fit,
236
219
  input_dataset=input_dataset,
237
220
  )
238
- return v_3d_tnorm_execute(params, execution)
221
+ return v_3d_tnorm_execute(params, runner)
239
222
 
240
223
 
241
224
  __all__ = [
242
225
  "V3dTnormOutputs",
243
- "V3dTnormParameters",
244
226
  "V_3D_TNORM_METADATA",
245
227
  "v_3d_tnorm",
228
+ "v_3d_tnorm_execute",
246
229
  "v_3d_tnorm_params",
247
230
  ]