niwrap-afni 0.6.2__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 +73 -75
  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-0.6.2.dist-info/METADATA +0 -8
  572. niwrap_afni-0.6.2.dist-info/RECORD +0 -569
  573. niwrap_afni-0.6.2.dist-info/WHEEL +0 -4
@@ -6,7 +6,7 @@ import pathlib
6
6
  from styxdefs import *
7
7
 
8
8
  V__DJUNCT_EDGY_ALIGN_CHECK_METADATA = Metadata(
9
- id="aa6a4a0022ad0531d548adba7cc36b0a1b5b39ae.boutiques",
9
+ id="263194bcd65e1cbac2926808163efba80932de8e.boutiques",
10
10
  name="@djunct_edgy_align_check",
11
11
  package="afni",
12
12
  container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,7 +14,36 @@ V__DJUNCT_EDGY_ALIGN_CHECK_METADATA = Metadata(
14
14
 
15
15
 
16
16
  VDjunctEdgyAlignCheckParameters = typing.TypedDict('VDjunctEdgyAlignCheckParameters', {
17
- "__STYXTYPE__": typing.Literal["@djunct_edgy_align_check"],
17
+ "@type": typing.NotRequired[typing.Literal["afni/@djunct_edgy_align_check"]],
18
+ "ULAY": str,
19
+ "OLAY": str,
20
+ "PREFIX": str,
21
+ "set_dicom_xyz": typing.NotRequired[list[float] | None],
22
+ "box_focus_slices": typing.NotRequired[str | None],
23
+ "montgap": typing.NotRequired[float | None],
24
+ "montcolor": typing.NotRequired[str | None],
25
+ "cbar": typing.NotRequired[str | None],
26
+ "save_ftype": typing.NotRequired[str | None],
27
+ "umin_fac": typing.NotRequired[float | None],
28
+ "montx": typing.NotRequired[float | None],
29
+ "monty": typing.NotRequired[float | None],
30
+ "use_olay_grid": typing.NotRequired[str | None],
31
+ "label_mode": typing.NotRequired[str | None],
32
+ "help_flag": bool,
33
+ "ver_flag": bool,
34
+ "echo_flag": bool,
35
+ "sharpen_ulay_off_flag": bool,
36
+ "mask_olay_edges_flag": bool,
37
+ "no_cor_flag": bool,
38
+ "no_sag_flag": bool,
39
+ "no_axi_flag": bool,
40
+ "no_clean_flag": bool,
41
+ "ulay_range": typing.NotRequired[list[float] | None],
42
+ "ulay_range_nz": typing.NotRequired[list[float] | None],
43
+ "ulay_range_am": typing.NotRequired[list[float] | None],
44
+ })
45
+ VDjunctEdgyAlignCheckParametersTagged = typing.TypedDict('VDjunctEdgyAlignCheckParametersTagged', {
46
+ "@type": typing.Literal["afni/@djunct_edgy_align_check"],
18
47
  "ULAY": str,
19
48
  "OLAY": str,
20
49
  "PREFIX": str,
@@ -42,42 +71,11 @@ VDjunctEdgyAlignCheckParameters = typing.TypedDict('VDjunctEdgyAlignCheckParamet
42
71
  "ulay_range_nz": typing.NotRequired[list[float] | None],
43
72
  "ulay_range_am": typing.NotRequired[list[float] | None],
44
73
  })
45
-
46
-
47
- def dyn_cargs(
48
- t: str,
49
- ) -> typing.Any:
50
- """
51
- Get build cargs function by command type.
52
-
53
- Args:
54
- t: Command type.
55
- Returns:
56
- Build cargs function.
57
- """
58
- return {
59
- "@djunct_edgy_align_check": v__djunct_edgy_align_check_cargs,
60
- }.get(t)
61
-
62
-
63
- def dyn_outputs(
64
- t: str,
65
- ) -> typing.Any:
66
- """
67
- Get build outputs function by command type.
68
-
69
- Args:
70
- t: Command type.
71
- Returns:
72
- Build outputs function.
73
- """
74
- return {
75
- }.get(t)
76
74
 
77
75
 
78
76
  class VDjunctEdgyAlignCheckOutputs(typing.NamedTuple):
79
77
  """
80
- Output object returned when calling `v__djunct_edgy_align_check(...)`.
78
+ Output object returned when calling `VDjunctEdgyAlignCheckParameters(...)`.
81
79
  """
82
80
  root: OutputPathType
83
81
  """Output root folder. This is the root folder for all outputs."""
@@ -110,7 +108,7 @@ def v__djunct_edgy_align_check_params(
110
108
  ulay_range: list[float] | None = None,
111
109
  ulay_range_nz: list[float] | None = None,
112
110
  ulay_range_am: list[float] | None = None,
113
- ) -> VDjunctEdgyAlignCheckParameters:
111
+ ) -> VDjunctEdgyAlignCheckParametersTagged:
114
112
  """
115
113
  Build parameters.
116
114
 
@@ -145,7 +143,7 @@ def v__djunct_edgy_align_check_params(
145
143
  Parameter dictionary
146
144
  """
147
145
  params = {
148
- "__STYXTYPE__": "@djunct_edgy_align_check",
146
+ "@type": "afni/@djunct_edgy_align_check",
149
147
  "ULAY": ulay,
150
148
  "OLAY": olay,
151
149
  "PREFIX": prefix,
@@ -205,55 +203,55 @@ def v__djunct_edgy_align_check_cargs(
205
203
  """
206
204
  cargs = []
207
205
  cargs.append("@djunct_edgy_align_check")
208
- cargs.append(params.get("ULAY"))
209
- cargs.append(params.get("OLAY"))
210
- cargs.append(params.get("PREFIX"))
211
- if params.get("set_dicom_xyz") is not None:
212
- cargs.extend(map(str, params.get("set_dicom_xyz")))
213
- if params.get("box_focus_slices") is not None:
214
- cargs.append(params.get("box_focus_slices"))
215
- if params.get("montgap") is not None:
216
- cargs.append(str(params.get("montgap")))
217
- if params.get("montcolor") is not None:
218
- cargs.append(params.get("montcolor"))
219
- if params.get("cbar") is not None:
220
- cargs.append(params.get("cbar"))
221
- if params.get("save_ftype") is not None:
222
- cargs.append(params.get("save_ftype"))
223
- if params.get("umin_fac") is not None:
224
- cargs.append(str(params.get("umin_fac")))
225
- if params.get("montx") is not None:
226
- cargs.append(str(params.get("montx")))
227
- if params.get("monty") is not None:
228
- cargs.append(str(params.get("monty")))
229
- if params.get("use_olay_grid") is not None:
230
- cargs.append(params.get("use_olay_grid"))
231
- if params.get("label_mode") is not None:
232
- cargs.append(params.get("label_mode"))
233
- if params.get("help_flag"):
206
+ cargs.append(params.get("ULAY", None))
207
+ cargs.append(params.get("OLAY", None))
208
+ cargs.append(params.get("PREFIX", None))
209
+ if params.get("set_dicom_xyz", None) is not None:
210
+ cargs.extend(map(str, params.get("set_dicom_xyz", None)))
211
+ if params.get("box_focus_slices", None) is not None:
212
+ cargs.append(params.get("box_focus_slices", None))
213
+ if params.get("montgap", None) is not None:
214
+ cargs.append(str(params.get("montgap", None)))
215
+ if params.get("montcolor", None) is not None:
216
+ cargs.append(params.get("montcolor", None))
217
+ if params.get("cbar", None) is not None:
218
+ cargs.append(params.get("cbar", None))
219
+ if params.get("save_ftype", None) is not None:
220
+ cargs.append(params.get("save_ftype", None))
221
+ if params.get("umin_fac", None) is not None:
222
+ cargs.append(str(params.get("umin_fac", None)))
223
+ if params.get("montx", None) is not None:
224
+ cargs.append(str(params.get("montx", None)))
225
+ if params.get("monty", None) is not None:
226
+ cargs.append(str(params.get("monty", None)))
227
+ if params.get("use_olay_grid", None) is not None:
228
+ cargs.append(params.get("use_olay_grid", None))
229
+ if params.get("label_mode", None) is not None:
230
+ cargs.append(params.get("label_mode", None))
231
+ if params.get("help_flag", False):
234
232
  cargs.append("-help")
235
- if params.get("ver_flag"):
233
+ if params.get("ver_flag", False):
236
234
  cargs.append("-ver")
237
- if params.get("echo_flag"):
235
+ if params.get("echo_flag", False):
238
236
  cargs.append("-echo")
239
- if params.get("sharpen_ulay_off_flag"):
237
+ if params.get("sharpen_ulay_off_flag", False):
240
238
  cargs.append("-sharpen_ulay_off")
241
- if params.get("mask_olay_edges_flag"):
239
+ if params.get("mask_olay_edges_flag", False):
242
240
  cargs.append("-mask_olay_edges")
243
- if params.get("no_cor_flag"):
241
+ if params.get("no_cor_flag", False):
244
242
  cargs.append("-no_cor")
245
- if params.get("no_sag_flag"):
243
+ if params.get("no_sag_flag", False):
246
244
  cargs.append("-no_sag")
247
- if params.get("no_axi_flag"):
245
+ if params.get("no_axi_flag", False):
248
246
  cargs.append("-no_axi")
249
- if params.get("no_clean_flag"):
247
+ if params.get("no_clean_flag", False):
250
248
  cargs.append("-no_clean")
251
- if params.get("ulay_range") is not None:
252
- cargs.extend(map(str, params.get("ulay_range")))
253
- if params.get("ulay_range_nz") is not None:
254
- cargs.extend(map(str, params.get("ulay_range_nz")))
255
- if params.get("ulay_range_am") is not None:
256
- cargs.extend(map(str, params.get("ulay_range_am")))
249
+ if params.get("ulay_range", None) is not None:
250
+ cargs.extend(map(str, params.get("ulay_range", None)))
251
+ if params.get("ulay_range_nz", None) is not None:
252
+ cargs.extend(map(str, params.get("ulay_range_nz", None)))
253
+ if params.get("ulay_range_am", None) is not None:
254
+ cargs.extend(map(str, params.get("ulay_range_am", None)))
257
255
  return cargs
258
256
 
259
257
 
@@ -278,11 +276,13 @@ def v__djunct_edgy_align_check_outputs(
278
276
 
279
277
  def v__djunct_edgy_align_check_execute(
280
278
  params: VDjunctEdgyAlignCheckParameters,
281
- execution: Execution,
279
+ runner: Runner | None = None,
282
280
  ) -> VDjunctEdgyAlignCheckOutputs:
283
281
  """
284
- Helper script for various tasks, heavily modeled on RW Cox's '@snapshot_volreg'
285
- script.
282
+ @djunct_edgy_align_check
283
+
284
+ Helper script for various tasks, heavily modeled on RW Cox's
285
+ '@snapshot_volreg' script.
286
286
 
287
287
  Author: AFNI Developers
288
288
 
@@ -290,10 +290,12 @@ def v__djunct_edgy_align_check_execute(
290
290
 
291
291
  Args:
292
292
  params: The parameters.
293
- execution: The execution object.
293
+ runner: Command runner.
294
294
  Returns:
295
295
  NamedTuple of outputs (described in `VDjunctEdgyAlignCheckOutputs`).
296
296
  """
297
+ runner = runner or get_global_runner()
298
+ execution = runner.start_execution(V__DJUNCT_EDGY_ALIGN_CHECK_METADATA)
297
299
  params = execution.params(params)
298
300
  cargs = v__djunct_edgy_align_check_cargs(params, execution)
299
301
  ret = v__djunct_edgy_align_check_outputs(params, execution)
@@ -331,8 +333,10 @@ def v__djunct_edgy_align_check(
331
333
  runner: Runner | None = None,
332
334
  ) -> VDjunctEdgyAlignCheckOutputs:
333
335
  """
334
- Helper script for various tasks, heavily modeled on RW Cox's '@snapshot_volreg'
335
- script.
336
+ @djunct_edgy_align_check
337
+
338
+ Helper script for various tasks, heavily modeled on RW Cox's
339
+ '@snapshot_volreg' script.
336
340
 
337
341
  Author: AFNI Developers
338
342
 
@@ -369,8 +373,6 @@ def v__djunct_edgy_align_check(
369
373
  Returns:
370
374
  NamedTuple of outputs (described in `VDjunctEdgyAlignCheckOutputs`).
371
375
  """
372
- runner = runner or get_global_runner()
373
- execution = runner.start_execution(V__DJUNCT_EDGY_ALIGN_CHECK_METADATA)
374
376
  params = v__djunct_edgy_align_check_params(
375
377
  ulay=ulay,
376
378
  olay=olay,
@@ -399,13 +401,13 @@ def v__djunct_edgy_align_check(
399
401
  ulay_range_nz=ulay_range_nz,
400
402
  ulay_range_am=ulay_range_am,
401
403
  )
402
- return v__djunct_edgy_align_check_execute(params, execution)
404
+ return v__djunct_edgy_align_check_execute(params, runner)
403
405
 
404
406
 
405
407
  __all__ = [
406
408
  "VDjunctEdgyAlignCheckOutputs",
407
- "VDjunctEdgyAlignCheckParameters",
408
409
  "V__DJUNCT_EDGY_ALIGN_CHECK_METADATA",
409
410
  "v__djunct_edgy_align_check",
411
+ "v__djunct_edgy_align_check_execute",
410
412
  "v__djunct_edgy_align_check_params",
411
413
  ]
@@ -6,7 +6,7 @@ import pathlib
6
6
  from styxdefs import *
7
7
 
8
8
  V__DJUNCT_MODAL_SMOOTHING_WITH_REP_METADATA = Metadata(
9
- id="0a3436dc5db4b133e39a70c1855022a5b90e8a73.boutiques",
9
+ id="549d26acfd55eb2936295a593b7935e86b19dc28.boutiques",
10
10
  name="@djunct_modal_smoothing_with_rep",
11
11
  package="afni",
12
12
  container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,7 +14,18 @@ V__DJUNCT_MODAL_SMOOTHING_WITH_REP_METADATA = Metadata(
14
14
 
15
15
 
16
16
  VDjunctModalSmoothingWithRepParameters = typing.TypedDict('VDjunctModalSmoothingWithRepParameters', {
17
- "__STYXTYPE__": typing.Literal["@djunct_modal_smoothing_with_rep"],
17
+ "@type": typing.NotRequired[typing.Literal["afni/@djunct_modal_smoothing_with_rep"]],
18
+ "input_file": InputPathType,
19
+ "output_prefix": str,
20
+ "modesmooth": typing.NotRequired[float | None],
21
+ "help_view": bool,
22
+ "help": bool,
23
+ "version": bool,
24
+ "overwrite": bool,
25
+ "no_clean": bool,
26
+ })
27
+ VDjunctModalSmoothingWithRepParametersTagged = typing.TypedDict('VDjunctModalSmoothingWithRepParametersTagged', {
28
+ "@type": typing.Literal["afni/@djunct_modal_smoothing_with_rep"],
18
29
  "input_file": InputPathType,
19
30
  "output_prefix": str,
20
31
  "modesmooth": typing.NotRequired[float | None],
@@ -24,43 +35,11 @@ VDjunctModalSmoothingWithRepParameters = typing.TypedDict('VDjunctModalSmoothing
24
35
  "overwrite": bool,
25
36
  "no_clean": bool,
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
- "@djunct_modal_smoothing_with_rep": v__djunct_modal_smoothing_with_rep_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
- "@djunct_modal_smoothing_with_rep": v__djunct_modal_smoothing_with_rep_outputs,
58
- }.get(t)
59
38
 
60
39
 
61
40
  class VDjunctModalSmoothingWithRepOutputs(typing.NamedTuple):
62
41
  """
63
- Output object returned when calling `v__djunct_modal_smoothing_with_rep(...)`.
42
+ Output object returned when calling `VDjunctModalSmoothingWithRepParameters(...)`.
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__djunct_modal_smoothing_with_rep_params(
79
58
  version: bool = False,
80
59
  overwrite: bool = False,
81
60
  no_clean: bool = False,
82
- ) -> VDjunctModalSmoothingWithRepParameters:
61
+ ) -> VDjunctModalSmoothingWithRepParametersTagged:
83
62
  """
84
63
  Build parameters.
85
64
 
@@ -96,7 +75,7 @@ def v__djunct_modal_smoothing_with_rep_params(
96
75
  Parameter dictionary
97
76
  """
98
77
  params = {
99
- "__STYXTYPE__": "@djunct_modal_smoothing_with_rep",
78
+ "@type": "afni/@djunct_modal_smoothing_with_rep",
100
79
  "input_file": input_file,
101
80
  "output_prefix": output_prefix,
102
81
  "help_view": help_view,
@@ -125,22 +104,22 @@ def v__djunct_modal_smoothing_with_rep_cargs(
125
104
  """
126
105
  cargs = []
127
106
  cargs.append("@djunct_modal_smoothing_with_rep")
128
- cargs.append(execution.input_file(params.get("input_file")))
129
- cargs.append(params.get("output_prefix"))
130
- if params.get("modesmooth") is not None:
107
+ cargs.append(execution.input_file(params.get("input_file", None)))
108
+ cargs.append(params.get("output_prefix", None))
109
+ if params.get("modesmooth", None) is not None:
131
110
  cargs.extend([
132
111
  "-modesmooth",
133
- str(params.get("modesmooth"))
112
+ str(params.get("modesmooth", None))
134
113
  ])
135
- if params.get("help_view"):
114
+ if params.get("help_view", False):
136
115
  cargs.append("-hview")
137
- if params.get("help"):
116
+ if params.get("help", False):
138
117
  cargs.append("-help")
139
- if params.get("version"):
118
+ if params.get("version", False):
140
119
  cargs.append("-ver")
141
- if params.get("overwrite"):
120
+ if params.get("overwrite", False):
142
121
  cargs.append("-overwrite")
143
- if params.get("no_clean"):
122
+ if params.get("no_clean", False):
144
123
  cargs.append("-no_clean")
145
124
  return cargs
146
125
 
@@ -160,20 +139,22 @@ def v__djunct_modal_smoothing_with_rep_outputs(
160
139
  """
161
140
  ret = VDjunctModalSmoothingWithRepOutputs(
162
141
  root=execution.output_file("."),
163
- output_file_head=execution.output_file(params.get("output_prefix") + "+tlrc.HEAD"),
164
- output_file_brik=execution.output_file(params.get("output_prefix") + "+tlrc.BRIK"),
142
+ output_file_head=execution.output_file(params.get("output_prefix", None) + "+tlrc.HEAD"),
143
+ output_file_brik=execution.output_file(params.get("output_prefix", None) + "+tlrc.BRIK"),
165
144
  )
166
145
  return ret
167
146
 
168
147
 
169
148
  def v__djunct_modal_smoothing_with_rep_execute(
170
149
  params: VDjunctModalSmoothingWithRepParameters,
171
- execution: Execution,
150
+ runner: Runner | None = None,
172
151
  ) -> VDjunctModalSmoothingWithRepOutputs:
173
152
  """
174
- A script to perform modal smoothing of ROI maps and check for eliminated ROIs.
175
- If any ROIs are eliminated during smoothing, they are restored, potentially in a
176
- degraded form.
153
+ @djunct_modal_smoothing_with_rep
154
+
155
+ A script to perform modal smoothing of ROI maps and check for eliminated
156
+ ROIs. If any ROIs are eliminated during smoothing, they are restored,
157
+ potentially in a degraded form.
177
158
 
178
159
  Author: AFNI Developers
179
160
 
@@ -181,10 +162,12 @@ def v__djunct_modal_smoothing_with_rep_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 `VDjunctModalSmoothingWithRepOutputs`).
187
168
  """
169
+ runner = runner or get_global_runner()
170
+ execution = runner.start_execution(V__DJUNCT_MODAL_SMOOTHING_WITH_REP_METADATA)
188
171
  params = execution.params(params)
189
172
  cargs = v__djunct_modal_smoothing_with_rep_cargs(params, execution)
190
173
  ret = v__djunct_modal_smoothing_with_rep_outputs(params, execution)
@@ -204,9 +187,11 @@ def v__djunct_modal_smoothing_with_rep(
204
187
  runner: Runner | None = None,
205
188
  ) -> VDjunctModalSmoothingWithRepOutputs:
206
189
  """
207
- A script to perform modal smoothing of ROI maps and check for eliminated ROIs.
208
- If any ROIs are eliminated during smoothing, they are restored, potentially in a
209
- degraded form.
190
+ @djunct_modal_smoothing_with_rep
191
+
192
+ A script to perform modal smoothing of ROI maps and check for eliminated
193
+ ROIs. If any ROIs are eliminated during smoothing, they are restored,
194
+ potentially in a degraded form.
210
195
 
211
196
  Author: AFNI Developers
212
197
 
@@ -225,8 +210,6 @@ def v__djunct_modal_smoothing_with_rep(
225
210
  Returns:
226
211
  NamedTuple of outputs (described in `VDjunctModalSmoothingWithRepOutputs`).
227
212
  """
228
- runner = runner or get_global_runner()
229
- execution = runner.start_execution(V__DJUNCT_MODAL_SMOOTHING_WITH_REP_METADATA)
230
213
  params = v__djunct_modal_smoothing_with_rep_params(
231
214
  input_file=input_file,
232
215
  output_prefix=output_prefix,
@@ -237,13 +220,13 @@ def v__djunct_modal_smoothing_with_rep(
237
220
  overwrite=overwrite,
238
221
  no_clean=no_clean,
239
222
  )
240
- return v__djunct_modal_smoothing_with_rep_execute(params, execution)
223
+ return v__djunct_modal_smoothing_with_rep_execute(params, runner)
241
224
 
242
225
 
243
226
  __all__ = [
244
227
  "VDjunctModalSmoothingWithRepOutputs",
245
- "VDjunctModalSmoothingWithRepParameters",
246
228
  "V__DJUNCT_MODAL_SMOOTHING_WITH_REP_METADATA",
247
229
  "v__djunct_modal_smoothing_with_rep",
230
+ "v__djunct_modal_smoothing_with_rep_execute",
248
231
  "v__djunct_modal_smoothing_with_rep_params",
249
232
  ]
@@ -6,7 +6,7 @@ import pathlib
6
6
  from styxdefs import *
7
7
 
8
8
  V__DJUNCT_MONTAGE_COORDINATOR_METADATA = Metadata(
9
- id="64d756e8e5ea73bbb91b5d094f44148b8d947acd.boutiques",
9
+ id="543baf357b03cf37f54ec8393a57595187a3d63b.boutiques",
10
10
  name="@djunct_montage_coordinator",
11
11
  package="afni",
12
12
  container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -14,7 +14,17 @@ V__DJUNCT_MONTAGE_COORDINATOR_METADATA = Metadata(
14
14
 
15
15
 
16
16
  VDjunctMontageCoordinatorParameters = typing.TypedDict('VDjunctMontageCoordinatorParameters', {
17
- "__STYXTYPE__": typing.Literal["@djunct_montage_coordinator"],
17
+ "@type": typing.NotRequired[typing.Literal["afni/@djunct_montage_coordinator"]],
18
+ "input_file": InputPathType,
19
+ "montx": float,
20
+ "monty": float,
21
+ "out_ijk": bool,
22
+ "out_xyz": bool,
23
+ "help": bool,
24
+ "version": bool,
25
+ })
26
+ VDjunctMontageCoordinatorParametersTagged = typing.TypedDict('VDjunctMontageCoordinatorParametersTagged', {
27
+ "@type": typing.Literal["afni/@djunct_montage_coordinator"],
18
28
  "input_file": InputPathType,
19
29
  "montx": float,
20
30
  "monty": float,
@@ -23,43 +33,11 @@ VDjunctMontageCoordinatorParameters = typing.TypedDict('VDjunctMontageCoordinato
23
33
  "help": bool,
24
34
  "version": bool,
25
35
  })
26
-
27
-
28
- def dyn_cargs(
29
- t: str,
30
- ) -> typing.Any:
31
- """
32
- Get build cargs function by command type.
33
-
34
- Args:
35
- t: Command type.
36
- Returns:
37
- Build cargs function.
38
- """
39
- return {
40
- "@djunct_montage_coordinator": v__djunct_montage_coordinator_cargs,
41
- }.get(t)
42
-
43
-
44
- def dyn_outputs(
45
- t: str,
46
- ) -> typing.Any:
47
- """
48
- Get build outputs function by command type.
49
-
50
- Args:
51
- t: Command type.
52
- Returns:
53
- Build outputs function.
54
- """
55
- return {
56
- "@djunct_montage_coordinator": v__djunct_montage_coordinator_outputs,
57
- }.get(t)
58
36
 
59
37
 
60
38
  class VDjunctMontageCoordinatorOutputs(typing.NamedTuple):
61
39
  """
62
- Output object returned when calling `v__djunct_montage_coordinator(...)`.
40
+ Output object returned when calling `VDjunctMontageCoordinatorParameters(...)`.
63
41
  """
64
42
  root: OutputPathType
65
43
  """Output root folder. This is the root folder for all outputs."""
@@ -75,7 +53,7 @@ def v__djunct_montage_coordinator_params(
75
53
  out_xyz: bool = False,
76
54
  help_: bool = False,
77
55
  version: bool = False,
78
- ) -> VDjunctMontageCoordinatorParameters:
56
+ ) -> VDjunctMontageCoordinatorParametersTagged:
79
57
  """
80
58
  Build parameters.
81
59
 
@@ -93,7 +71,7 @@ def v__djunct_montage_coordinator_params(
93
71
  Parameter dictionary
94
72
  """
95
73
  params = {
96
- "__STYXTYPE__": "@djunct_montage_coordinator",
74
+ "@type": "afni/@djunct_montage_coordinator",
97
75
  "input_file": input_file,
98
76
  "montx": montx,
99
77
  "monty": monty,
@@ -122,23 +100,23 @@ def v__djunct_montage_coordinator_cargs(
122
100
  cargs.append("@djunct_montage_coordinator")
123
101
  cargs.extend([
124
102
  "-inset",
125
- execution.input_file(params.get("input_file"))
103
+ execution.input_file(params.get("input_file", None))
126
104
  ])
127
105
  cargs.extend([
128
106
  "-montx",
129
- str(params.get("montx"))
107
+ str(params.get("montx", None))
130
108
  ])
131
109
  cargs.extend([
132
110
  "-monty",
133
- str(params.get("monty"))
111
+ str(params.get("monty", None))
134
112
  ])
135
- if params.get("out_ijk"):
113
+ if params.get("out_ijk", False):
136
114
  cargs.append("-out_ijk")
137
- if params.get("out_xyz"):
115
+ if params.get("out_xyz", False):
138
116
  cargs.append("-out_xyz")
139
- if params.get("help"):
117
+ if params.get("help", False):
140
118
  cargs.append("-help")
141
- if params.get("version"):
119
+ if params.get("version", False):
142
120
  cargs.append("-ver")
143
121
  return cargs
144
122
 
@@ -165,11 +143,13 @@ def v__djunct_montage_coordinator_outputs(
165
143
 
166
144
  def v__djunct_montage_coordinator_execute(
167
145
  params: VDjunctMontageCoordinatorParameters,
168
- execution: Execution,
146
+ runner: Runner | None = None,
169
147
  ) -> VDjunctMontageCoordinatorOutputs:
170
148
  """
171
- Small program to calculate how to evenly space a certain number of slices within
172
- each view plane of a dataset.
149
+ @djunct_montage_coordinator
150
+
151
+ Small program to calculate how to evenly space a certain number of slices
152
+ within each view plane of a dataset.
173
153
 
174
154
  Author: AFNI Developers
175
155
 
@@ -177,10 +157,12 @@ def v__djunct_montage_coordinator_execute(
177
157
 
178
158
  Args:
179
159
  params: The parameters.
180
- execution: The execution object.
160
+ runner: Command runner.
181
161
  Returns:
182
162
  NamedTuple of outputs (described in `VDjunctMontageCoordinatorOutputs`).
183
163
  """
164
+ runner = runner or get_global_runner()
165
+ execution = runner.start_execution(V__DJUNCT_MONTAGE_COORDINATOR_METADATA)
184
166
  params = execution.params(params)
185
167
  cargs = v__djunct_montage_coordinator_cargs(params, execution)
186
168
  ret = v__djunct_montage_coordinator_outputs(params, execution)
@@ -199,8 +181,10 @@ def v__djunct_montage_coordinator(
199
181
  runner: Runner | None = None,
200
182
  ) -> VDjunctMontageCoordinatorOutputs:
201
183
  """
202
- Small program to calculate how to evenly space a certain number of slices within
203
- each view plane of a dataset.
184
+ @djunct_montage_coordinator
185
+
186
+ Small program to calculate how to evenly space a certain number of slices
187
+ within each view plane of a dataset.
204
188
 
205
189
  Author: AFNI Developers
206
190
 
@@ -220,8 +204,6 @@ def v__djunct_montage_coordinator(
220
204
  Returns:
221
205
  NamedTuple of outputs (described in `VDjunctMontageCoordinatorOutputs`).
222
206
  """
223
- runner = runner or get_global_runner()
224
- execution = runner.start_execution(V__DJUNCT_MONTAGE_COORDINATOR_METADATA)
225
207
  params = v__djunct_montage_coordinator_params(
226
208
  input_file=input_file,
227
209
  montx=montx,
@@ -231,13 +213,13 @@ def v__djunct_montage_coordinator(
231
213
  help_=help_,
232
214
  version=version,
233
215
  )
234
- return v__djunct_montage_coordinator_execute(params, execution)
216
+ return v__djunct_montage_coordinator_execute(params, runner)
235
217
 
236
218
 
237
219
  __all__ = [
238
220
  "VDjunctMontageCoordinatorOutputs",
239
- "VDjunctMontageCoordinatorParameters",
240
221
  "V__DJUNCT_MONTAGE_COORDINATOR_METADATA",
241
222
  "v__djunct_montage_coordinator",
223
+ "v__djunct_montage_coordinator_execute",
242
224
  "v__djunct_montage_coordinator_params",
243
225
  ]