Merge pull request #128 from yarikoptic/enh-examples-gen

Primarily to make more reproducible -- sort files

Author: bclenet

.github/workflows/parsers_test_on_nidmexamples.yml

@@ -23,65 +23,8 @@ jobs:
           sudo apt-get install graphviz
       - name: SPM/FSL/AFNI parsing on nidm-examples
         run: |
-          mkdir -p nidmresults-examples
-          wget https://raw.githubusercontent.com/incf-nidash/nidmresults-examples/master/spm_group_ols/batch.m -O nidmresults-examples/spm_group_ols_batch.m
-          wget https://raw.githubusercontent.com/incf-nidash/nidmresults-examples/master/spm_thr_voxelunct4/batch.m -O nidmresults-examples/spm_thr_voxelunct4_batch.m
-          wget https://raw.githubusercontent.com/incf-nidash/nidmresults-examples/master/spm_thr_clustfwep05/batch.m -O nidmresults-examples/spm_thr_clustfwep05_batch.m
-          wget https://raw.githubusercontent.com/incf-nidash/nidmresults-examples/master/spm_covariate/batch.m -O nidmresults-examples/spm_covariate_batch.m
-          wget https://raw.githubusercontent.com/incf-nidash/nidmresults-examples/master/spm_group_wls/batch.m -O nidmresults-examples/spm_group_wls_batch.m
-          wget https://raw.githubusercontent.com/incf-nidash/nidmresults-examples/master/spm_contrast_mask/batch.m -O nidmresults-examples/spm_contrast_mask_batch.m
-          wget https://raw.githubusercontent.com/incf-nidash/nidmresults-examples/master/spm_thr_clustunck10/batch.m -O nidmresults-examples/spm_thr_clustunck10_batch.m
-          wget https://raw.githubusercontent.com/incf-nidash/nidmresults-examples/master/spm_thr_voxelfwep05/batch.m -O nidmresults-examples/spm_thr_voxelfwep05_batch.m
-          wget https://raw.githubusercontent.com/incf-nidash/nidmresults-examples/master/spm_hrf_fir/batch.m -O nidmresults-examples/spm_hrf_fir_batch.m
-          wget https://raw.githubusercontent.com/incf-nidash/nidmresults-examples/master/spm_explicit_mask/batch.m -O nidmresults-examples/spm_explicit_mask_batch.m
-          wget https://raw.githubusercontent.com/incf-nidash/nidmresults-examples/master/spm_2_t_test/batch.m -O nidmresults-examples/spm_2_t_test_batch.m
-          wget https://raw.githubusercontent.com/incf-nidash/nidmresults-examples/master/spm_conjunction/batch.m -O nidmresults-examples/spm_conjunction_batch.m
-          wget https://raw.githubusercontent.com/incf-nidash/nidmresults-examples/master/spm_con_f/batch.m -O nidmresults-examples/spm_con_f_batch.m
-          wget https://raw.githubusercontent.com/incf-nidash/nidmresults-examples/master/spm_default/batch.m -O nidmresults-examples/spm_default_batch.m
-          wget https://raw.githubusercontent.com/incf-nidash/nidmresults-examples/master/spm_HRF_informed_basis/batch.m -O nidmresults-examples/spm_HRF_informed_basis_batch.m
-          wget https://raw.githubusercontent.com/incf-nidash/nidmresults-examples/master/spm_partial_conjunction/batch.m -O nidmresults-examples/spm_partial_conjunction_batch.m
-          wget https://raw.githubusercontent.com/incf-nidash/nidmresults-examples/master/spm_thr_voxelfdrp05/batch.m -O nidmresults-examples/spm_thr_voxelfdrp05_batch.m
-          wget https://raw.githubusercontent.com/incf-nidash/nidmresults-examples/master/spm_temporal_derivative/batch.m -O nidmresults-examples/spm_temporal_derivative_batch.m
-          wget https://raw.githubusercontent.com/incf-nidash/nidmresults-examples/master/spm_non_sphericity/batch.m -O nidmresults-examples/spm_non_sphericity_batch.m
-          
-          wget https://raw.githubusercontent.com/incf-nidash/nidmresults-examples/master/fsl_con_f/report_log.html -O nidmresults-examples/fsl_con_f_report_log.html
-          wget https://raw.githubusercontent.com/incf-nidash/nidmresults-examples/master/fsl_con_f_multiple/report_log.html -O nidmresults-examples/fsl_con_f_multiple_report_log.html
-          wget https://raw.githubusercontent.com/incf-nidash/nidmresults-examples/master/fsl_contrast_mask/report_log.html -O nidmresults-examples/fsl_contrast_mask_report_log.html
-          wget https://raw.githubusercontent.com/incf-nidash/nidmresults-examples/master/fsl_default/report_log.html -O nidmresults-examples/fsl_default_report_log.html
-          wget https://raw.githubusercontent.com/incf-nidash/nidmresults-examples/master/fsl_full_examples001/report_log.html -O nidmresults-examples/fsl_full_examples001_report_log.html
-          wget https://raw.githubusercontent.com/incf-nidash/nidmresults-examples/master/fsl_gamma_basis/report_log.html -O nidmresults-examples/fsl_gamma_basis_report_log.html
-          wget https://raw.githubusercontent.com/incf-nidash/nidmresults-examples/master/fsl_gaussian/report_log.html -O nidmresults-examples/fsl_gaussian_report_log.html
-          wget https://raw.githubusercontent.com/incf-nidash/nidmresults-examples/master/fsl_group_btw/report_log.html -O nidmresults-examples/fsl_group_btw_report_log.html
-          wget https://raw.githubusercontent.com/incf-nidash/nidmresults-examples/master/fsl_group_ols/report_log.html -O nidmresults-examples/fsl_group_ols_report_log.html
-          wget https://raw.githubusercontent.com/incf-nidash/nidmresults-examples/master/fsl_group_wls/report_log.html -O nidmresults-examples/fsl_group_wls_report_log.html
-          wget https://raw.githubusercontent.com/incf-nidash/nidmresults-examples/master/fsl_hrf_fir/report_log.html -O nidmresults-examples/fsl_hrf_fir_report_log.html
-          wget https://raw.githubusercontent.com/incf-nidash/nidmresults-examples/master/fsl_hrf_gammadiff/report_log.html -O nidmresults-examples/fsl_hrf_gammadiff_report_log.html
-          wget https://raw.githubusercontent.com/incf-nidash/nidmresults-examples/master/fsl_motion_reg/report_log.html -O nidmresults-examples/fsl_motion_reg_report_log.html
-          wget https://raw.githubusercontent.com/incf-nidash/nidmresults-examples/master/fsl_motion_reg_der/report_log.html -O nidmresults-examples/fsl_motion_reg_der_report_log.html
-          wget https://raw.githubusercontent.com/incf-nidash/nidmresults-examples/master/fsl_thr_clustfwep05/report_log.html -O nidmresults-examples/fsl_thr_clustfwep05_report_log.html
-          wget https://raw.githubusercontent.com/incf-nidash/nidmresults-examples/master/fsl_thr_voxelfwep05/report_log.html -O nidmresults-examples/fsl_thr_voxelfwep05_report_log.html
-
-          wget https://raw.githubusercontent.com/incf-nidash/nidmresults-examples/master/afni_default/subject_results/group.DS0011/subj.sub_001/proc.sub_001 -O nidmresults-examples/afni_default_proc.sub_001
-          wget https://raw.githubusercontent.com/incf-nidash/nidmresults-examples/master/afni_hrf_gammadiff/subject_results/group.DS0011/subj.sub_001/proc.sub_001 -O nidmresults-examples/afni_hrf_gammadiff_proc.sub_001
-          wget https://raw.githubusercontent.com/incf-nidash/nidmresults-examples/master/afni_hrf_tent/subject_results/group.DS0011/subj.sub_001/proc.sub_001 -O nidmresults-examples/afni_hrf_tent_proc.sub_001
-          wget https://raw.githubusercontent.com/incf-nidash/nidmresults-examples/master/afni_thr_clustfwep05/proc.sub_001 -O nidmresults-examples/afni_thr_clustfwep05_proc.sub_001
-          wget https://raw.githubusercontent.com/incf-nidash/nidmresults-examples/master/afni_other_template/subject_results/group.DS0011/subj.sub_001/proc.sub_001 -O nidmresults-examples/afni_other_template_proc.sub_001
-          wget https://raw.githubusercontent.com/incf-nidash/nidmresults-examples/master/afni_gam/subject_results/group.DS000011/subj.sub_001/proc.sub_001 -O nidmresults-examples/afni_gam_proc.sub_001
-          wget https://raw.githubusercontent.com/incf-nidash/nidmresults-examples/master/afni_clustconn_18/proc.sub_001 -O nidmresults-examples/afni_clustconn_18_proc.sub_001
-          wget https://raw.githubusercontent.com/incf-nidash/nidmresults-examples/master/afni_clustconn_26/proc.sub_001 -O nidmresults-examples/afni_clustconn_26_proc.sub_001
-          wget https://raw.githubusercontent.com/incf-nidash/nidmresults-examples/master/afni_con_f/proc.sub_001 -O nidmresults-examples/afni_con_f_proc.sub_001
-          wget https://raw.githubusercontent.com/incf-nidash/nidmresults-examples/master/afni_thr_clustunck10/proc.sub_001 -O nidmresults-examples/afni_thr_clustunck10_proc.sub_001
-          wget https://raw.githubusercontent.com/incf-nidash/nidmresults-examples/master/afni_thr_voxelfdrp05/proc.sub_001 -O nidmresults-examples/afni_thr_voxelfdrp05_proc.sub_001
-          wget https://raw.githubusercontent.com/incf-nidash/nidmresults-examples/master/afni_alt_onesided/proc.sub_001 -O nidmresults-examples/afni_alt_onesided_proc.sub_001
-          wget https://raw.githubusercontent.com/incf-nidash/nidmresults-examples/master/afni_bi_sided_t_test/proc.sub_001 -O nidmresults-examples/afni_bi_sided_t_test_proc.sub_001
-          wget https://raw.githubusercontent.com/incf-nidash/nidmresults-examples/master/afni_thr_voxelunct4/proc.sub_001 -O nidmresults-examples/afni_thr_voxelunct4_proc.sub_001
-
-          wget https://raw.githubusercontent.com/afni/apaper_highlight_narps/main/scripts_suppl_proc_vox/do_13_view_zoom.tcsh -O nidmresults-examples/narps_do_13_view_zoom.tcsh
-          wget https://raw.githubusercontent.com/afni/apaper_highlight_narps/main/scripts_suppl_proc_teams/do_04_make_imgs_A.tcsh -O nidmresults-examples/narps_do_04_make_imgs_A.tcsh
-          wget https://raw.githubusercontent.com/afni/apaper_highlight_narps/main/scripts_suppl_proc_teams/do_02_pc_with_sign0.tcsh -O nidmresults-examples/narps_do_02_pc_with_sign0.tcsh
-          
-          python launch_parser_on_nidm.py --input_dir nidmresults-examples --output_dir examples/from_parsers
-
+          ./fetch_nidmresults-examples
+          ./launch_parser_on_nidm.py --input_dir nidmresults-examples --output_dir examples/from_parsers
       - name: push on the repo the dir "examples/from_parsers"
         run: |
           git config user.name "GitHub Actions Bot"

fetch_nidmresults-examples

@@ -0,0 +1,60 @@
+#!/bin/sh
+
+set -eu
+
+mkdir -p nidmresults-examples
+wget https://raw.githubusercontent.com/incf-nidash/nidmresults-examples/master/spm_group_ols/batch.m -O nidmresults-examples/spm_group_ols_batch.m
+wget https://raw.githubusercontent.com/incf-nidash/nidmresults-examples/master/spm_thr_voxelunct4/batch.m -O nidmresults-examples/spm_thr_voxelunct4_batch.m
+wget https://raw.githubusercontent.com/incf-nidash/nidmresults-examples/master/spm_thr_clustfwep05/batch.m -O nidmresults-examples/spm_thr_clustfwep05_batch.m
+wget https://raw.githubusercontent.com/incf-nidash/nidmresults-examples/master/spm_covariate/batch.m -O nidmresults-examples/spm_covariate_batch.m
+wget https://raw.githubusercontent.com/incf-nidash/nidmresults-examples/master/spm_group_wls/batch.m -O nidmresults-examples/spm_group_wls_batch.m
+wget https://raw.githubusercontent.com/incf-nidash/nidmresults-examples/master/spm_contrast_mask/batch.m -O nidmresults-examples/spm_contrast_mask_batch.m
+wget https://raw.githubusercontent.com/incf-nidash/nidmresults-examples/master/spm_thr_clustunck10/batch.m -O nidmresults-examples/spm_thr_clustunck10_batch.m
+wget https://raw.githubusercontent.com/incf-nidash/nidmresults-examples/master/spm_thr_voxelfwep05/batch.m -O nidmresults-examples/spm_thr_voxelfwep05_batch.m
+wget https://raw.githubusercontent.com/incf-nidash/nidmresults-examples/master/spm_hrf_fir/batch.m -O nidmresults-examples/spm_hrf_fir_batch.m
+wget https://raw.githubusercontent.com/incf-nidash/nidmresults-examples/master/spm_explicit_mask/batch.m -O nidmresults-examples/spm_explicit_mask_batch.m
+wget https://raw.githubusercontent.com/incf-nidash/nidmresults-examples/master/spm_2_t_test/batch.m -O nidmresults-examples/spm_2_t_test_batch.m
+wget https://raw.githubusercontent.com/incf-nidash/nidmresults-examples/master/spm_conjunction/batch.m -O nidmresults-examples/spm_conjunction_batch.m
+wget https://raw.githubusercontent.com/incf-nidash/nidmresults-examples/master/spm_con_f/batch.m -O nidmresults-examples/spm_con_f_batch.m
+wget https://raw.githubusercontent.com/incf-nidash/nidmresults-examples/master/spm_default/batch.m -O nidmresults-examples/spm_default_batch.m
+wget https://raw.githubusercontent.com/incf-nidash/nidmresults-examples/master/spm_HRF_informed_basis/batch.m -O nidmresults-examples/spm_HRF_informed_basis_batch.m
+wget https://raw.githubusercontent.com/incf-nidash/nidmresults-examples/master/spm_partial_conjunction/batch.m -O nidmresults-examples/spm_partial_conjunction_batch.m
+wget https://raw.githubusercontent.com/incf-nidash/nidmresults-examples/master/spm_thr_voxelfdrp05/batch.m -O nidmresults-examples/spm_thr_voxelfdrp05_batch.m
+wget https://raw.githubusercontent.com/incf-nidash/nidmresults-examples/master/spm_temporal_derivative/batch.m -O nidmresults-examples/spm_temporal_derivative_batch.m
+wget https://raw.githubusercontent.com/incf-nidash/nidmresults-examples/master/spm_non_sphericity/batch.m -O nidmresults-examples/spm_non_sphericity_batch.m
+
+wget https://raw.githubusercontent.com/incf-nidash/nidmresults-examples/master/fsl_con_f/report_log.html -O nidmresults-examples/fsl_con_f_report_log.html
+wget https://raw.githubusercontent.com/incf-nidash/nidmresults-examples/master/fsl_con_f_multiple/report_log.html -O nidmresults-examples/fsl_con_f_multiple_report_log.html
+wget https://raw.githubusercontent.com/incf-nidash/nidmresults-examples/master/fsl_contrast_mask/report_log.html -O nidmresults-examples/fsl_contrast_mask_report_log.html
+wget https://raw.githubusercontent.com/incf-nidash/nidmresults-examples/master/fsl_default/report_log.html -O nidmresults-examples/fsl_default_report_log.html
+wget https://raw.githubusercontent.com/incf-nidash/nidmresults-examples/master/fsl_full_examples001/report_log.html -O nidmresults-examples/fsl_full_examples001_report_log.html
+wget https://raw.githubusercontent.com/incf-nidash/nidmresults-examples/master/fsl_gamma_basis/report_log.html -O nidmresults-examples/fsl_gamma_basis_report_log.html
+wget https://raw.githubusercontent.com/incf-nidash/nidmresults-examples/master/fsl_gaussian/report_log.html -O nidmresults-examples/fsl_gaussian_report_log.html
+wget https://raw.githubusercontent.com/incf-nidash/nidmresults-examples/master/fsl_group_btw/report_log.html -O nidmresults-examples/fsl_group_btw_report_log.html
+wget https://raw.githubusercontent.com/incf-nidash/nidmresults-examples/master/fsl_group_ols/report_log.html -O nidmresults-examples/fsl_group_ols_report_log.html
+wget https://raw.githubusercontent.com/incf-nidash/nidmresults-examples/master/fsl_group_wls/report_log.html -O nidmresults-examples/fsl_group_wls_report_log.html
+wget https://raw.githubusercontent.com/incf-nidash/nidmresults-examples/master/fsl_hrf_fir/report_log.html -O nidmresults-examples/fsl_hrf_fir_report_log.html
+wget https://raw.githubusercontent.com/incf-nidash/nidmresults-examples/master/fsl_hrf_gammadiff/report_log.html -O nidmresults-examples/fsl_hrf_gammadiff_report_log.html
+wget https://raw.githubusercontent.com/incf-nidash/nidmresults-examples/master/fsl_motion_reg/report_log.html -O nidmresults-examples/fsl_motion_reg_report_log.html
+wget https://raw.githubusercontent.com/incf-nidash/nidmresults-examples/master/fsl_motion_reg_der/report_log.html -O nidmresults-examples/fsl_motion_reg_der_report_log.html
+wget https://raw.githubusercontent.com/incf-nidash/nidmresults-examples/master/fsl_thr_clustfwep05/report_log.html -O nidmresults-examples/fsl_thr_clustfwep05_report_log.html
+wget https://raw.githubusercontent.com/incf-nidash/nidmresults-examples/master/fsl_thr_voxelfwep05/report_log.html -O nidmresults-examples/fsl_thr_voxelfwep05_report_log.html
+
+wget https://raw.githubusercontent.com/incf-nidash/nidmresults-examples/master/afni_default/subject_results/group.DS0011/subj.sub_001/proc.sub_001 -O nidmresults-examples/afni_default_proc.sub_001
+wget https://raw.githubusercontent.com/incf-nidash/nidmresults-examples/master/afni_hrf_gammadiff/subject_results/group.DS0011/subj.sub_001/proc.sub_001 -O nidmresults-examples/afni_hrf_gammadiff_proc.sub_001
+wget https://raw.githubusercontent.com/incf-nidash/nidmresults-examples/master/afni_hrf_tent/subject_results/group.DS0011/subj.sub_001/proc.sub_001 -O nidmresults-examples/afni_hrf_tent_proc.sub_001
+wget https://raw.githubusercontent.com/incf-nidash/nidmresults-examples/master/afni_thr_clustfwep05/proc.sub_001 -O nidmresults-examples/afni_thr_clustfwep05_proc.sub_001
+wget https://raw.githubusercontent.com/incf-nidash/nidmresults-examples/master/afni_other_template/subject_results/group.DS0011/subj.sub_001/proc.sub_001 -O nidmresults-examples/afni_other_template_proc.sub_001
+wget https://raw.githubusercontent.com/incf-nidash/nidmresults-examples/master/afni_gam/subject_results/group.DS000011/subj.sub_001/proc.sub_001 -O nidmresults-examples/afni_gam_proc.sub_001
+wget https://raw.githubusercontent.com/incf-nidash/nidmresults-examples/master/afni_clustconn_18/proc.sub_001 -O nidmresults-examples/afni_clustconn_18_proc.sub_001
+wget https://raw.githubusercontent.com/incf-nidash/nidmresults-examples/master/afni_clustconn_26/proc.sub_001 -O nidmresults-examples/afni_clustconn_26_proc.sub_001
+wget https://raw.githubusercontent.com/incf-nidash/nidmresults-examples/master/afni_con_f/proc.sub_001 -O nidmresults-examples/afni_con_f_proc.sub_001
+wget https://raw.githubusercontent.com/incf-nidash/nidmresults-examples/master/afni_thr_clustunck10/proc.sub_001 -O nidmresults-examples/afni_thr_clustunck10_proc.sub_001
+wget https://raw.githubusercontent.com/incf-nidash/nidmresults-examples/master/afni_thr_voxelfdrp05/proc.sub_001 -O nidmresults-examples/afni_thr_voxelfdrp05_proc.sub_001
+wget https://raw.githubusercontent.com/incf-nidash/nidmresults-examples/master/afni_alt_onesided/proc.sub_001 -O nidmresults-examples/afni_alt_onesided_proc.sub_001
+wget https://raw.githubusercontent.com/incf-nidash/nidmresults-examples/master/afni_bi_sided_t_test/proc.sub_001 -O nidmresults-examples/afni_bi_sided_t_test_proc.sub_001
+wget https://raw.githubusercontent.com/incf-nidash/nidmresults-examples/master/afni_thr_voxelunct4/proc.sub_001 -O nidmresults-examples/afni_thr_voxelunct4_proc.sub_001
+
+wget https://raw.githubusercontent.com/afni/apaper_highlight_narps/main/scripts_suppl_proc_vox/do_13_view_zoom.tcsh -O nidmresults-examples/narps_do_13_view_zoom.tcsh
+wget https://raw.githubusercontent.com/afni/apaper_highlight_narps/main/scripts_suppl_proc_teams/do_04_make_imgs_A.tcsh -O nidmresults-examples/narps_do_04_make_imgs_A.tcsh
+wget https://raw.githubusercontent.com/afni/apaper_highlight_narps/main/scripts_suppl_proc_teams/do_02_pc_with_sign0.tcsh -O nidmresults-examples/narps_do_02_pc_with_sign0.tcsh

launch_parser_on_nidm.py

@@ -1,3 +1,5 @@
+#!/usr/bin/env python
+
 import argparse
 import os
 import random
@@ -79,8 +81,8 @@ def main():
     context_write.write("Processing files...\n")
 
     # Iteration on each example
-    for root, _, files in os.walk(opt.input_dir):
-        for file in files:
+    for root, _, files in sorted(os.walk(opt.input_dir)):
+        for file in sorted(files):
 
             if file.endswith("batch.m"):  # spm
                 filename_ss_ext = file.split(".m")[0]