Compile

README.md

@@ -15,7 +15,7 @@
 
 | Package | Status | Version | API Coverage |
 | --- | --- | --- | --- |
-| [AFNI](https://afni.nimh.nih.gov/) | In progress | [`24.2.06`](https://hub.docker.com/r/afni/afni_make_build) | 532/658 (80.9%) |
+| [AFNI](https://afni.nimh.nih.gov/) | In progress | [`24.2.06`](https://hub.docker.com/r/afni/afni_make_build) | 565/611 (92.5%) |
 | [ANTs](https://github.com/ANTsX/ANTs) | In progress | [`2.5.3`](https://hub.docker.com/r/antsx/ants) | 71/113 (62.8%) |
 | [Connectome Workbench](https://github.com/Washington-University/workbench) | Testing | [`1.5.0`](https://hub.docker.com/r/brainlife/connectome_workbench) | 202/202 (100% 🎉) |
 | [Convert3D](http://www.itksnap.org/pmwiki/pmwiki.php?n=Convert3D.Convert3D) | In progress | [`1.1.0`](https://hub.docker.com/r/pyushkevich/itksnap) | 2/4 (50.0%) |

python/README.md

@@ -41,14 +41,14 @@ pip install -e "git+https://github.com/childmindresearch/niwrap.git/#egg=niwrap&
 
 | Package | Status | Version | API Coverage |
 | --- | --- | --- | --- |
-| [AFNI](https://afni.nimh.nih.gov/) | In progress | [`24.2.06`](https://hub.docker.com/r/afni/afni_make_build) | 532/658 (80.9%) |
+| [AFNI](https://afni.nimh.nih.gov/) | In progress | [`24.2.06`](https://hub.docker.com/r/afni/afni_make_build) | 565/611 (92.5%) |
 | [ANTs](https://github.com/ANTsX/ANTs) | In progress | [`2.5.3`](https://hub.docker.com/r/antsx/ants) | 71/113 (62.8%) |
 | [Connectome Workbench](https://github.com/Washington-University/workbench) | Testing | [`1.5.0`](https://hub.docker.com/r/brainlife/connectome_workbench) | 202/202 (100% 🎉) |
 | [Convert3D](http://www.itksnap.org/pmwiki/pmwiki.php?n=Convert3D.Convert3D) | In progress | [`1.1.0`](https://hub.docker.com/r/pyushkevich/itksnap) | 2/4 (50.0%) |
 | [FSL](https://fsl.fmrib.ox.ac.uk/fsl/fslwiki) | In progress | [`6.0.5`](https://hub.docker.com/r/brainlife/fsl) | 241/312 (77.2%) |
 | [FreeSurfer](https://github.com/freesurfer/freesurfer) | In progress | [`7.4.1`](https://hub.docker.com/r/freesurfer/freesurfer) | 713/806 (88.5%) |
 | [Greedy](https://sites.google.com/view/greedyreg/about) | In progress | [`1.0.1`](https://hub.docker.com/r/pyushkevich/itksnap) | 1/1 (100% 🎉) |
-| [MRTrix3](https://www.mrtrix.org/) | Testing | [`3.0.4`](https://hub.docker.com/r/mrtrix3/mrtrix3) | 115/121 (95.0%) |
+| [MRTrix3](https://www.mrtrix.org/) | Testing | [`3.0.4`](https://hub.docker.com/r/mrtrix3/mrtrix3) | 117/123 (95.1%) |
 | [MRTrix3Tissue](https://3tissue.github.io/) | Testing | [`5.2.8`](https://hub.docker.com/r/brainlife/3tissue) | 1/1 (100% 🎉) |
 | [NiftyReg](http://cmictig.cs.ucl.ac.uk/wiki/index.php/NiftyReg) | In progress | [`1.4.0`](https://hub.docker.com/r/vnmd/niftyreg_1.4.0) | 7/7 (100% 🎉) |
 

python/src/niwrap/afni/__init__.py

@@ -22,30 +22,21 @@
 from .adjunct_aw_tableize_roi_info_py import *
 from .adjunct_calc_mont_dims_py import *
 from .adjunct_combine_str_py import *
-from .adjunct_glue_imgs_vert import *
 from .adjunct_is_label_py import *
-from .adjunct_json_value import *
 from .adjunct_make_script_and_rst_py import *
 from .adjunct_select_str_py import *
 from .adjunct_simplify_cost import *
-from .adjunct_slice_space import *
 from .adjunct_suma_fs_mask_and_qc import *
 from .adjunct_suma_fs_roi_info import *
 from .adjunct_tort_plot_dp_align import *
-from .adjunct_tort_read_dp_align import *
-from .adjunct_vol_3slice_select import *
 from .adwarp import *
 from .afni import *
 from .afni_batch_r import *
 from .afni_check_omp import *
 from .afni_history import *
 from .afni_open import *
-from .afni_orient_sign import *
 from .afni_proc_py import *
-from .afni_python_wrapper import *
-from .afni_refacer_make_master_addendum import *
 from .afni_run_r import *
-from .afni_skeleton import *
 from .afni_system_check_py import *
 from .aiv import *
 from .align_epi_anat import *
@@ -57,22 +48,21 @@
 from .auto_warp_py import *
 from .balloon import *
 from .bayes_view import *
-from .bayesian_group_ana import *
+from .bayesian_group_ana_py import *
 from .brain_skin import *
 from .build_afni_py import *
 from .cat_matvec import *
 from .ccalc import *
 from .cifti_tool import *
 from .cjpeg import *
-from .clip_volume import *
 from .clust_exp_hist_table_py import *
 from .clust_exp_stat_parse_py import *
 from .column_cat import *
 from .compare_surfaces import *
 from .convert_cdiflist_to_grads import *
 from .convert_dset import *
 from .convert_surface import *
-from .convex_hull_triangulation import *
+from .convex_hull import *
 from .count import *
 from .create_icosahedron import *
 from .dcm2niix_afni import *
@@ -81,17 +71,11 @@
 from .dicom_to_raw import *
 from .dimon import *
 from .djpeg import *
-from .djunct_4d_imager import *
-from .djunct_modal_smoothing_with_rep import *
-from .drive_afni import *
 from .drive_suma import *
 from .dsetstat2p import *
 from .dtistudio_fiberto_segments import *
-from .eg_main_chrono import *
 from .epi_b0_correct import *
-from .escape import *
 from .examine_xmat import *
-from .fast_roi import *
 from .fat_mat2d_plot_py import *
 from .fat_mat_sel_py import *
 from .fat_mat_tableize import *
@@ -124,13 +108,10 @@
 from .gen_group_command import *
 from .gen_ss_review_scripts import *
 from .gen_ss_review_table_py import *
-from .get_afni_dims import *
-from .get_afni_id import *
 from .get_afni_model_prf import *
 from .get_afni_model_prf_6 import *
 from .get_afni_model_prf_6_bad import *
 from .gifti_tool import *
-from .global_parse import *
 from .gltsymtest import *
 from .help_format import *
 from .im2niml import *
@@ -149,18 +130,6 @@
 from .imupsam import *
 from .init_user_dotfiles_py import *
 from .inspec import *
-from .install_3d_pfm_demo import *
-from .install_dbsproc import *
-from .install_fatcat_demo import *
-from .install_ibt_datasets import *
-from .install_insta_corr_demo import *
-from .install_macaque_demo import *
-from .install_macaque_demo_rest import *
-from .install_mbm_marmoset import *
-from .install_meica_demo import *
-from .install_nih_marmoset import *
-from .install_nmt import *
-from .install_rsfmri_motion_group_demo import *
 from .iso_surface import *
 from .make_color_map import *
 from .make_pq_script_py import *
@@ -179,23 +148,19 @@
 from .nsize import *
 from .p2dsetstat import *
 from .parse_fs_lt_log_py import *
-from .parse_name import *
-from .parse_name import *
 from .plugout_drive import *
 from .plugout_ijk import *
 from .plugout_tt import *
 from .plugout_tta import *
 from .prompt_popup import *
 from .prompt_user import *
 from .pta import *
-from .python_module_test import *
 from .qdelaunay import *
 from .qhull import *
 from .quick_alpha_vals_py import *
 from .quickspec import *
 from .quickspec_sl import *
 from .quotize import *
-from .r_funclist import *
 from .r_pkgs_install import *
 from .rba import *
 from .rbox import *
@@ -204,33 +169,21 @@
 from .retro_ts_py import *
 from .rmz import *
 from .roi2dataset import *
-from .roi_decluster import *
-from .roi_modal_grow import *
 from .roigrow import *
-from .roimaker import *
 from .rotcom import *
 from .rsfgen import *
 from .rtfeedme import *
 from .samp_bias import *
 from .scale_to_map import *
-from .script_checker import *
 from .serial_helper import *
 from .sfim import *
-from .shift_volume import *
-from .show_dynamic_range import *
 from .slow_surf_clustsim_py import *
 from .spharm_deco import *
-from .spherical_harmonics_reconstruction import *
-from .statauxcode import *
+from .spharm_reco import *
 from .stimband import *
 from .strblast import *
-from .suma import *
-from .suma_acknowledge import *
-from .suma_align_to_experiment import *
 from .suma_change_spec import *
-from .suma_fsvol_to_brik import *
 from .suma_glxdino import *
-from .suma_reprefixize_spec import *
 from .surf2_vol_coord import *
 from .surf_clust import *
 from .surf_dist import *
@@ -239,7 +192,7 @@
 from .surf_fwhm import *
 from .surf_info import *
 from .surf_layers import *
-from .surf_local_stat import *
+from .surf_localstat import *
 from .surf_measures import *
 from .surf_mesh import *
 from .surf_patch import *
@@ -248,7 +201,6 @@
 from .surf_smooth import *
 from .surf_to_surf import *
 from .surface_metrics import *
-from .t1scale import *
 from .tedana_wrapper_py import *
 from .tfim import *
 from .timing_tool_py import *
@@ -259,7 +211,6 @@
 from .uber_proc_py import *
 from .uber_skel import *
 from .uber_subject_py import *
-from .uber_ttest import *
 from .un_warp_epi_py import *
 from .uniq_images import *
 from .v_1d_apar2mat import *
@@ -293,9 +244,9 @@
 from .v_24swap import *
 from .v_2d_im_reg import *
 from .v_2dcat import *
-from .v_2dwarper import *
 from .v_2perm import *
 from .v_2swap import *
+from .v_3_droimaker import *
 from .v_3d_aboverlap import *
 from .v_3d_acost import *
 from .v_3d_afnito3_d import *
@@ -456,7 +407,7 @@
 from .v_3d_undump import *
 from .v_3d_unifize import *
 from .v_3d_upsample import *
-from .v_3d_vec_rgbto_hsl import *
+from .v_3d_vec_rgb_to_hsl import *
 from .v_3d_vol2_surf import *
 from .v_3d_warp import *
 from .v_3d_warp_drive import *
@@ -510,11 +461,13 @@
 from .v_3dvolreg import *
 from .v_4swap import *
 from .v__1d_diff_mag import *
+from .v__2dwarper import *
 from .v__2dwarper_allin import *
 from .v__4_daverage import *
 from .v__add_edge import *
 from .v__afni_env import *
 from .v__afni_orient2_raimap import *
+from .v__afni_orient_sign import *
 from .v__afni_r_package_install import *
 from .v__afni_refacer_make_master import *
 from .v__afni_refacer_make_onebig_a12 import *
@@ -530,6 +483,7 @@
 from .v__center_distance import *
 from .v__chauffeur_afni import *
 from .v__check_for_afni_dset import *
+from .v__clip_volume import *
 from .v__clust_exp_cat_lab import *
 from .v__clust_exp_run_shiny import *
 from .v__command_globb import *
@@ -540,26 +494,29 @@
 from .v__dice_metric import *
 from .v__diff_files import *
 from .v__diff_tree import *
+from .v__djunct_4d_imager import *
 from .v__djunct_4d_slices_to_3d_vol import *
 from .v__djunct_anonymize import *
 from .v__djunct_dwi_selector import *
 from .v__djunct_edgy_align_check import *
+from .v__djunct_modal_smoothing_with_rep import *
 from .v__djunct_montage_coordinator import *
 from .v__djunct_overlap_check import *
 from .v__djunct_ssw_intermed_edge_imgs import *
 from .v__do_examples import *
-from .v__drive_suma import *
 from .v__electro_grid import *
 from .v__examine_gen_feat_dists import *
 from .v__extract_meica_ortvec import *
+from .v__fast_roi import *
 from .v__fat_tract_colorize import *
 from .v__find_afni_dset_path import *
 from .v__fix_fssphere import *
 from .v__float_fix import *
 from .v__from_rai import *
 from .v__fs_roi_label import *
 from .v__fslabel2dset import *
-from .v__full_path import *
+from .v__get_afni_dims import *
+from .v__get_afni_id import *
 from .v__get_afni_orient import *
 from .v__get_afni_prefix import *
 from .v__get_afni_res import *
@@ -568,12 +525,6 @@
 from .v__grad_flip_test import *
 from .v__grayplot import *
 from .v__help_afni import *
-from .v__install_afni_retino_demo import *
-from .v__install_apmulti_demo1_rest import *
-from .v__install_apmulti_demo2_realtime import *
-from .v__install_d99_macaque import *
-from .v__install_fatcat_demo2 import *
-from .v__install_surflayers_demo1 import *
 from .v__is_oblique import *
 from .v__iso_masks import *
 from .v__make_label_table import *
@@ -594,18 +545,29 @@
 from .v__reorder import *
 from .v__retino_proc import *
 from .v__roi_corr_mat import *
+from .v__roi_decluster import *
+from .v__roi_modal_grow import *
 from .v__scale_volume import *
+from .v__script_check import *
+from .v__shift_volume import *
+from .v__show_dynamic_range import *
 from .v__simulate_motion import *
 from .v__skull_strip_touch_up import *
 from .v__snapshot_volreg import *
 from .v__spharm_examples import *
 from .v__sswarper import *
+from .v__statauxcode import *
+from .v__suma_acknowledge import *
+from .v__suma_align_to_experiment import *
+from .v__suma_fsvol_to_brik import *
 from .v__suma_make_spec_caret import *
 from .v__suma_make_spec_fs import *
 from .v__suma_make_spec_sf import *
 from .v__suma_renumber_fs import *
+from .v__suma_reprefixize_spec import *
 from .v__surf_smooth_heat_07_examples import *
 from .v__surf_to_vol_spackle import *
+from .v__t1scale import *
 from .v__thickness_master import *
 from .v__time_diff import *
 from .v__to_mni_awarp import *

python/src/niwrap/afni/abids_tool.py

@@ -7,7 +7,7 @@
 import dataclasses
 
 ABIDS_TOOL_METADATA = Metadata(
-    id="98dc76918d7cdf3c8fc51ace8cb8e94abe757b0e.boutiques",
+    id="be4cc3dea9c1ff2c94a88b9126da6ad487f347ca.boutiques",
     name="abids_tool",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -47,7 +47,7 @@ def abids_tool(
     runner = runner or get_global_runner()
     execution = runner.start_execution(ABIDS_TOOL_METADATA)
     cargs = []
-    cargs.append("abids_tool")
+    cargs.append("abids_tool.py")
     cargs.extend([execution.input_file(f) for f in input_files])
     if copy_prefix is not None:
         cargs.extend([