Started Running as brainvisa ---------------------------------------- $ /usr/bin/python3 /home_local/a-sac-ns-brainvisa/bbi-daily/soma-env-0.0/src/brainvisa-cmake/bin/bv_run_pixi_env.py bv_maker name=soma-env-0.0 -- sources ---------------------------------------- Updating git repository /home_local/a-sac-ns-brainvisa/bbi-daily/soma-env-0.0/src/aims-free $ git fetch --tags --prune origin '+refs/heads/*:refs/remotes/origin/*' Depuis https://github.com/brainvisa/aims-free 037bba77..9e78763c master -> origin/master 6a2ac96b..5a790aa9 sip-6-15 -> origin/sip-6-15 084f3953..e2e77a64 soma-env-6.0 -> origin/soma-env-6.0 $ git update-ref --no-deref refs/bv_head refs/remotes/origin/master $ git -c remote.origin.skipDefaultUpdate remote update $ git merge --ff-only refs/bv_head Mise à jour 037bba77..9e78763c Fast-forward CMakeLists.txt | 10 ++ aimsdata/shared/plugins/aimsdata.plugins | 3 +- aimsdata/sphinx/user_doc/changelog.md | 16 ++ aimsdata/src/CMakeLists.txt | 5 + aimsdata/src/aimsdata/fibers/bundles.cc | 175 +++++++++++++-------- aimsdata/src/aimsdata/fibers/bundles.h | 24 ++- aimsdata/src/aimsdata/fibers/mrtrixbundlereader.cc | 9 +- aimsdata/src/aimsdata/fibers/mrtrixbundlereader.h | 6 +- .../src/aimsdata/fibers/trackvisbundlereader.cc | 8 +- .../src/aimsdata/fibers/trackvisbundlereader.h | 7 +- aimsdata/src/aimsdata/io/argheader.cc | 32 ++-- aimsdata/src/aimsdata/io/fileFormat_bucket.cc | 11 ++ aimsdata/src/aimsdata/io/finder.cc | 6 +- aimsdata/src/aimsdata/io/finder.h | 4 +- .../transformation/transformationgraph3d.cc | 18 +++ aimsdata/src/aimstrx/CMakeLists.txt | 30 ++++ aimsdata/src/aimstrx/fibers/trxbundlereader.cc | 161 +++++++++++++++++++ aimsdata/src/aimstrx/fibers/trxbundlereader.h | 31 ++++ aimsdata/src/aimstrx/plugin/trxplugin.cc | 89 +++++++++++ aimsdata/src/aimstrx/plugin/trxplugin.h | 22 +++ project_info.cmake | 2 +- pyaims/python/soma/aims/__init__.py | 35 ++++- pyaims/python/soma/aims/io_ext.py | 106 ++++++++++++- pyaims/python/soma/aims/spmnormalizationreader.py | 12 +- pyaims/python/soma/aims/tests/test_pyaims.py | 156 +++++++++++++++++- pyaims/src/sip/aims.sip | 10 ++ pyaims/src/sip/generatedtypes.py | 2 + pyaims/src/sip/rcobject.sip | 22 +++ pyaims/src/sip/typessub.py | 3 + 29 files changed, 885 insertions(+), 130 deletions(-) create mode 100644 aimsdata/src/aimstrx/CMakeLists.txt create mode 100644 aimsdata/src/aimstrx/fibers/trxbundlereader.cc create mode 100644 aimsdata/src/aimstrx/fibers/trxbundlereader.h create mode 100644 aimsdata/src/aimstrx/plugin/trxplugin.cc create mode 100644 aimsdata/src/aimstrx/plugin/trxplugin.h Updating git repository /home_local/a-sac-ns-brainvisa/bbi-daily/soma-env-0.0/src/aims-gpl $ git fetch --tags --prune origin '+refs/heads/*:refs/remotes/origin/*' Depuis https://github.com/brainvisa/aims-gpl c3ee90f..f21dccc master -> origin/master $ git update-ref --no-deref refs/bv_head refs/remotes/origin/master $ git -c remote.origin.skipDefaultUpdate remote update $ git merge --ff-only refs/bv_head Mise à jour c3ee90f..f21dccc Fast-forward project_info.cmake | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) Updating git repository /home_local/a-sac-ns-brainvisa/bbi-daily/soma-env-0.0/src/anatomist-free $ git fetch --tags --prune origin '+refs/heads/*:refs/remotes/origin/*' Depuis https://github.com/brainvisa/anatomist-free fd95dce9..b2f3c582 master -> origin/master b79c388c..9f7fe715 soma-env-6.0 -> origin/soma-env-6.0 $ git update-ref --no-deref refs/bv_head refs/remotes/origin/master $ git -c remote.origin.skipDefaultUpdate remote update $ git merge --ff-only refs/bv_head Mise à jour fd95dce9..b2f3c582 Fast-forward project_info.cmake | 2 +- sphinxman/changelog.md | 8 ++++++++ src/lib/object/actions.cc | 2 +- src/lib/sparsematrix/connectivitymatrix.cc | 13 +++++++++++-- 4 files changed, 21 insertions(+), 4 deletions(-) Updating git repository /home_local/a-sac-ns-brainvisa/bbi-daily/soma-env-0.0/src/anatomist-gpl $ git fetch --tags --prune origin '+refs/heads/*:refs/remotes/origin/*' Depuis https://github.com/brainvisa/anatomist-gpl 067c495..f98a01b master -> origin/master $ git update-ref --no-deref refs/bv_head refs/remotes/origin/master $ git -c remote.origin.skipDefaultUpdate remote update $ git merge --ff-only refs/bv_head Mise à jour 067c495..f98a01b Fast-forward project_info.cmake | 2 +- pyanatomist/python/anatomist/base.py | 2 +- pyanatomist/python/anatomist/cpp/simplecontrols.py | 6 +++--- pyanatomist/python/anatomist/direct/api.py | 2 ++ pyanatomist/src/sip/glComponent.sip | 2 +- pyanatomist/src/sip/palette.sip | 9 ++++++--- 6 files changed, 14 insertions(+), 9 deletions(-) Updating git repository /home_local/a-sac-ns-brainvisa/bbi-daily/soma-env-0.0/src/axon $ git fetch --tags --prune origin '+refs/heads/*:refs/remotes/origin/*' Depuis https://github.com/brainvisa/axon f0811b8c..98d37787 master -> origin/master $ git update-ref --no-deref refs/bv_head refs/remotes/origin/master $ git -c remote.origin.skipDefaultUpdate remote update $ git merge --ff-only refs/bv_head Mise à jour f0811b8c..98d37787 Fast-forward .../data management/processes/database_qc_table.py | 27 +++++++++++++++++++--- foms/shared-brainvisa-1.0.json | 2 +- python/brainvisa/info.py | 2 +- sphinxdoc/user_doc/changelog.md | 8 +++++++ 4 files changed, 34 insertions(+), 5 deletions(-) Updating git repository /home_local/a-sac-ns-brainvisa/bbi-daily/soma-env-0.0/src/bioprocessing $ git fetch --tags --prune origin '+refs/heads/*:refs/remotes/origin/*' Depuis https://bioproj.cea.fr/git/bioprocessing 88928c8..cb8a653 master -> origin/master $ git update-ref --no-deref refs/bv_head refs/remotes/origin/master $ git -c remote.origin.skipDefaultUpdate remote update $ git merge --ff-only refs/bv_head Mise à jour 88928c8..cb8a653 Fast-forward .../gff/SliceSerieLandmarksGenerateParallel.py | 205 ++++++++++++++++++++ .../gff/SliceSerieLandmarksRegistrationParallel.py | 116 ++++++----- .../VolumeApplyPropagativeRegistrationParallel.py | 214 +++++++++++++++++++++ .../projects/gff/VolumeLandmarksGenerate.py | 139 +++++++++++++ .../toolbox/microscopy/BoundingBoxCziGeneration.py | 154 ++++++++++----- project_info.cmake | 2 +- python/bioprocessing/__init__.py | 5 +- python/bioprocessing/landmarks.py | 94 +++++++++ python/soma/aims/multires.py | 1 - 9 files changed, 822 insertions(+), 108 deletions(-) create mode 100644 brainvisa/toolboxes/bioprocessing/processes/research/projects/gff/SliceSerieLandmarksGenerateParallel.py create mode 100644 brainvisa/toolboxes/bioprocessing/processes/research/projects/gff/VolumeApplyPropagativeRegistrationParallel.py create mode 100644 brainvisa/toolboxes/bioprocessing/processes/research/projects/gff/VolumeLandmarksGenerate.py create mode 100644 python/bioprocessing/landmarks.py Updating git repository /home_local/a-sac-ns-brainvisa/bbi-daily/soma-env-0.0/src/brainrat-gpl $ git fetch --tags --prune origin '+refs/heads/*:refs/remotes/origin/*' Depuis https://bioproj.cea.fr/git/brainrat-gpl cd02b40..a38f070 master -> origin/master $ git update-ref --no-deref refs/bv_head refs/remotes/origin/master $ git -c remote.origin.skipDefaultUpdate remote update $ git merge --ff-only refs/bv_head Mise à jour cd02b40..a38f070 Fast-forward python/brainrat/info.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) Updating git repository /home_local/a-sac-ns-brainvisa/bbi-daily/soma-env-0.0/src/brainrat-private $ git fetch --tags --prune origin '+refs/heads/*:refs/remotes/origin/*' Depuis https://bioproj.cea.fr/git/brainrat-private f552333..aaecedf master -> origin/master $ git update-ref --no-deref refs/bv_head refs/remotes/origin/master $ git -c remote.origin.skipDefaultUpdate remote update $ git merge --ff-only refs/bv_head Mise à jour f552333..aaecedf Fast-forward project_info.cmake | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) Updating git repository /home_local/a-sac-ns-brainvisa/bbi-daily/soma-env-0.0/src/brainvisa-cmake $ git fetch --tags --prune origin '+refs/heads/*:refs/remotes/origin/*' $ git update-ref --no-deref refs/bv_head refs/remotes/origin/master $ git -c remote.origin.skipDefaultUpdate remote update $ git merge --ff-only refs/bv_head Déjà à jour. $ pre-commit install pre-commit installed at .git/hooks/pre-commit Updating git repository /home_local/a-sac-ns-brainvisa/bbi-daily/soma-env-0.0/src/brainvisa-cmake $ git fetch --tags --prune origin '+refs/heads/*:refs/remotes/origin/*' $ git update-ref --no-deref refs/bv_head refs/remotes/origin/master $ git -c remote.origin.skipDefaultUpdate remote update $ git merge --ff-only refs/bv_head Déjà à jour. $ pre-commit install pre-commit installed at .git/hooks/pre-commit Updating git repository /home_local/a-sac-ns-brainvisa/bbi-daily/soma-env-0.0/src/brainvisa-share $ git fetch --tags --prune origin '+refs/heads/*:refs/remotes/origin/*' Depuis https://github.com/brainvisa/brainvisa-share bbff818..d810004 master -> origin/master $ git update-ref --no-deref refs/bv_head refs/remotes/origin/master $ git -c remote.origin.skipDefaultUpdate remote update $ git merge --ff-only refs/bv_head Mise à jour bbff818..d810004 Fast-forward ...morphologist_normative_brain_volumes_stats.json | 93332 +++++++++++++++++++ ...ologist_normative_brain_volumes_stats.json.minf | 1 + project_info.cmake | 2 +- 3 files changed, 93334 insertions(+), 1 deletion(-) create mode 100644 normative_tables/morphologist/ukb_hcp_abcd_openbhb26-strat/morphologist_normative_brain_volumes_stats.json create mode 100644 normative_tables/morphologist/ukb_hcp_abcd_openbhb26-strat/morphologist_normative_brain_volumes_stats.json.minf Updating git repository /home_local/a-sac-ns-brainvisa/bbi-daily/soma-env-0.0/src/brainvisa-spm $ git fetch --tags --prune origin '+refs/heads/*:refs/remotes/origin/*' Depuis https://github.com/brainvisa/brainvisa-spm d2087b5..50f4b51 master -> origin/master $ git update-ref --no-deref refs/bv_head refs/remotes/origin/master $ git -c remote.origin.skipDefaultUpdate remote update $ git merge --ff-only refs/bv_head Mise à jour d2087b5..50f4b51 Fast-forward info.py | 2 +- python/soma/spm/spm_launcher.py | 3 +-- 2 files changed, 2 insertions(+), 3 deletions(-) Updating git repository /home_local/a-sac-ns-brainvisa/bbi-daily/soma-env-0.0/src/brainvisa_freesurfer $ git fetch --tags --prune origin '+refs/heads/*:refs/remotes/origin/*' Depuis https://github.com/brainvisa/brainvisa_freesurfer 1574c5b..b4a9fda master -> origin/master $ git update-ref --no-deref refs/bv_head refs/remotes/origin/master $ git -c remote.origin.skipDefaultUpdate remote update $ git merge --ff-only refs/bv_head Mise à jour 1574c5b..b4a9fda Fast-forward .../Import_FROM_FreeSurfer_TO_Morpho.procdoc | 27 +- .../processes/morphologist_from_freesurfer.py | 55 +++ project_info.cmake | 2 +- python/brainvisa/freesurfer/__init__.py | 0 python/brainvisa/freesurfer/capsul/__init__.py | 0 .../capsul/import_freesurfer_to_morpho.py | 363 +++++++++++++++ .../capsul/morphologist_from_freesurfer.py | 507 +++++++++++++++++++++ 7 files changed, 935 insertions(+), 19 deletions(-) create mode 100644 brainvisa/toolboxes/freesurfer/processes/morphologist_from_freesurfer.py create mode 100644 python/brainvisa/freesurfer/__init__.py create mode 100644 python/brainvisa/freesurfer/capsul/__init__.py create mode 100644 python/brainvisa/freesurfer/capsul/import_freesurfer_to_morpho.py create mode 100644 python/brainvisa/freesurfer/capsul/morphologist_from_freesurfer.py Updating git repository /home_local/a-sac-ns-brainvisa/bbi-daily/soma-env-0.0/src/capsul $ git fetch --tags --prune origin '+refs/heads/*:refs/remotes/origin/*' Depuis https://github.com/populse/capsul 079a7d42..2ae22371 gh-pages -> origin/gh-pages 90a2a2db..88aa7fab master -> origin/master $ git update-ref --no-deref refs/bv_head refs/remotes/origin/master $ git -c remote.origin.skipDefaultUpdate remote update $ git merge --ff-only refs/bv_head Mise à jour 90a2a2db..88aa7fab Fast-forward capsul/attributes/fom_index.py | 86 +++++++++++++++++++++++++++++++++++++++ capsul/info.py | 2 +- capsul/pipeline/pipeline_tools.py | 20 +++++++-- capsul/process/runprocess.py | 23 +++++++++-- capsul/qt_apps/main_window.py | 6 +-- 5 files changed, 126 insertions(+), 11 deletions(-) create mode 100644 capsul/attributes/fom_index.py $ pre-commit install pre-commit installed at .git/hooks/pre-commit Updating git repository /home_local/a-sac-ns-brainvisa/bbi-daily/soma-env-0.0/src/constellation-gpl $ git fetch --tags --prune origin '+refs/heads/*:refs/remotes/origin/*' Depuis https://github.com/brainvisa/constellation-gpl 110934b..4b11ec2 master -> origin/master $ git update-ref --no-deref refs/bv_head refs/remotes/origin/master $ git -c remote.origin.skipDefaultUpdate remote update $ git merge --ff-only refs/bv_head Mise à jour 110934b..4b11ec2 Fast-forward project_info.cmake | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) Updating git repository /home_local/a-sac-ns-brainvisa/bbi-daily/soma-env-0.0/src/constellation-nonfree $ git fetch --tags --prune origin '+refs/heads/*:refs/remotes/origin/*' Depuis https://github.com/brainvisa/constellation-nonfree 77484c7..2cb7705 master -> origin/master $ git update-ref --no-deref refs/bv_head refs/remotes/origin/master $ git -c remote.origin.skipDefaultUpdate remote update $ git merge --ff-only refs/bv_head Mise à jour 77484c7..2cb7705 Fast-forward python/constel/info.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) Updating git repository /home_local/a-sac-ns-brainvisa/bbi-daily/soma-env-0.0/src/cortical_surface-gpl $ git fetch --tags --prune origin '+refs/heads/*:refs/remotes/origin/*' Depuis https://github.com/brainvisa/cortical_surface-gpl 50af02f..571abe4 master -> origin/master $ git update-ref --no-deref refs/bv_head refs/remotes/origin/master $ git -c remote.origin.skipDefaultUpdate remote update $ git merge --ff-only refs/bv_head Mise à jour 50af02f..571abe4 Fast-forward .../brainvisa-3.2.0/cortical_surface.py | 4 +- .../processes/anatomy/ParameterizeSulcus2015.py | 1124 ++++++++++---------- .../AnatomistShowTextureExtremaAsSpheres.py | 6 +- project_info.cmake | 2 +- 4 files changed, 582 insertions(+), 554 deletions(-) Updating git repository /home_local/a-sac-ns-brainvisa/bbi-daily/soma-env-0.0/src/cortical_surface-nonfree $ git fetch --tags --prune origin '+refs/heads/*:refs/remotes/origin/*' Depuis https://github.com/brainvisa/cortical_surface-nonfree f607afc..9b0400d master -> origin/master $ git update-ref --no-deref refs/bv_head refs/remotes/origin/master $ git -c remote.origin.skipDefaultUpdate remote update $ git merge --ff-only refs/bv_head Mise à jour f607afc..9b0400d Fast-forward project_info.cmake | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) Updating git repository /home_local/a-sac-ns-brainvisa/bbi-daily/soma-env-0.0/src/disco $ git fetch --tags --prune origin '+refs/heads/*:refs/remotes/origin/*' Depuis https://bioproj.cea.fr/git/brainvisa-disco 3d2a8d0..0d1f8b3 master -> origin/master $ git update-ref --no-deref refs/bv_head refs/remotes/origin/master $ git -c remote.origin.skipDefaultUpdate remote update $ git merge --ff-only refs/bv_head Mise à jour 3d2a8d0..0d1f8b3 Fast-forward bin/disco_apply_transform_to_icbm.py | 6 ++++++ project_info.cmake | 2 +- 2 files changed, 7 insertions(+), 1 deletion(-) $ pre-commit install pre-commit installed at .git/hooks/pre-commit Updating git repository /home_local/a-sac-ns-brainvisa/bbi-daily/soma-env-0.0/src/highres-cortex $ git fetch --tags --prune origin '+refs/heads/*:refs/remotes/origin/*' Depuis https://github.com/neurospin/highres-cortex 1bb4c84..efaab07 master -> origin/master $ git update-ref --no-deref refs/bv_head refs/remotes/origin/master $ git -c remote.origin.skipDefaultUpdate remote update $ git merge --ff-only refs/bv_head Mise à jour 1bb4c84..efaab07 Fast-forward project_info.cmake | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) $ pre-commit install pre-commit installed at .git/hooks/pre-commit Updating git repository /home_local/a-sac-ns-brainvisa/bbi-daily/soma-env-0.0/src/morpho-deepsulci $ git fetch --tags --prune origin '+refs/heads/*:refs/remotes/origin/*' Depuis https://github.com/brainvisa/morpho-deepsulci eff9fb8..1ccf0e8 master -> origin/master $ git update-ref --no-deref refs/bv_head refs/remotes/origin/master $ git -c remote.origin.skipDefaultUpdate remote update $ git merge --ff-only refs/bv_head Mise à jour eff9fb8..1ccf0e8 Fast-forward project_info.cmake | 2 +- share/foms/morpho-deepsulci-bids-1.0.json | 8 +++++++- 2 files changed, 8 insertions(+), 2 deletions(-) Updating git repository /home_local/a-sac-ns-brainvisa/bbi-daily/soma-env-0.0/src/morphologist-baby $ git fetch --tags --prune origin '+refs/heads/*:refs/remotes/origin/*' Depuis https://bioproj.cea.fr/git/brainvisa-t1mri/morphologist-baby 5dcfbd3..facd37e master -> origin/master $ git update-ref --no-deref refs/bv_head refs/remotes/origin/master $ git -c remote.origin.skipDefaultUpdate remote update $ git merge --ff-only refs/bv_head Mise à jour 5dcfbd3..facd37e Fast-forward project_info.cmake | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) Updating git repository /home_local/a-sac-ns-brainvisa/bbi-daily/soma-env-0.0/src/morphologist-gpl $ git fetch --tags --prune origin '+refs/heads/*:refs/remotes/origin/*' Depuis https://github.com/brainvisa/morphologist-gpl 63d25b17..bcaddf2c master -> origin/master $ git update-ref --no-deref refs/bv_head refs/remotes/origin/master $ git -c remote.origin.skipDefaultUpdate remote update $ git merge --ff-only refs/bv_head Mise à jour 63d25b17..bcaddf2c Fast-forward .../morphologist/hierarchies/shared/anatomy.py | 12 + .../processes/foetus/imprints_skeleton.py | 22 ++ .../processes/morphometry/morpho_report.procdoc | 19 +- .../normative_brainvolumes_stats_mult.procdoc | 15 +- .../registration/replace_normalization.py | 7 + .../components/corticalfoldsgraph.py | 5 +- changelog.md | 1 + project_info.cmake | 2 +- .../morphologist/morphometry/global_sulc_morpho.py | 217 ++++++++----- python/morphologist/capsul/axon/sulcigraph.py | 2 + .../capsul/foetus/imprints_skeleton.py | 62 ++++ .../morphologist/capsul/qc/ana_morpho_viewers.py | 90 +++++- python/morphologist/capsul/qc/database_qc_table.py | 351 +++++++++++++++++---- python/morphologist/capsul/qc/find_viewer.py | 2 +- python/morphologist/capsul/qc/index_db.py | 49 +++ .../capsul/qc/morphologist_qc_table.py | 107 +++++++ .../morphologist/capsul/replace_normalization.py | 185 +++++++++++ .../capsul/sulci_manip/graph_pointcloud_label.py | 2 - .../talairachtransformationfromnormalization.py | 1 - python/morphologist/sulci_foetus/__init__.py | 0 .../sulci_foetus/imprints_to_immortals.py | 205 ++++++++++++ share/foms/morphologist-auto-1.0.json | 103 +++++- share/foms/morphologist-bids-2.0.json | 246 +++++++++++---- share/foms/morphologist-bids-auto-1.0.json | 300 ++++++++++++++---- sphinx/user_doc/changelog.md | 25 ++ sphinx/user_doc/conf.py | 12 +- sphinx/user_doc/images/bv_qc.jpg | Bin 0 -> 127045 bytes sphinx/user_doc/images/bv_qc_table.jpg | Bin 0 -> 400670 bytes sphinx/user_doc/images/bv_qc_viewer.jpg | Bin 0 -> 364541 bytes sphinx/user_doc/images/morpho_report.jpg | Bin 0 -> 264923 bytes sphinx/user_doc/index.rst | 15 + sphinx/user_doc/morphologist-cli.rst | 18 ++ sphinx/user_doc/morphologist-qc.rst | 128 ++++++++ 33 files changed, 1918 insertions(+), 285 deletions(-) create mode 100644 brainvisa/toolboxes/morphologist/processes/foetus/imprints_skeleton.py create mode 100644 brainvisa/toolboxes/morphologist/processes/registration/replace_normalization.py create mode 120000 changelog.md create mode 100644 python/morphologist/capsul/foetus/imprints_skeleton.py create mode 100644 python/morphologist/capsul/qc/index_db.py create mode 100644 python/morphologist/capsul/qc/morphologist_qc_table.py create mode 100644 python/morphologist/capsul/replace_normalization.py create mode 100644 python/morphologist/sulci_foetus/__init__.py create mode 100644 python/morphologist/sulci_foetus/imprints_to_immortals.py create mode 100644 sphinx/user_doc/images/bv_qc.jpg create mode 100644 sphinx/user_doc/images/bv_qc_table.jpg create mode 100644 sphinx/user_doc/images/bv_qc_viewer.jpg create mode 100644 sphinx/user_doc/images/morpho_report.jpg create mode 100644 sphinx/user_doc/morphologist-cli.rst create mode 100644 sphinx/user_doc/morphologist-qc.rst Updating git repository /home_local/a-sac-ns-brainvisa/bbi-daily/soma-env-0.0/src/morphologist-nonfree $ git fetch --tags --prune origin '+refs/heads/*:refs/remotes/origin/*' Depuis https://github.com/brainvisa/morphologist-nonfree 5a9929b..220389f master -> origin/master $ git update-ref --no-deref refs/bv_head refs/remotes/origin/master $ git -c remote.origin.skipDefaultUpdate remote update $ git merge --ff-only refs/bv_head Mise à jour 5a9929b..220389f Fast-forward project_info.cmake | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) Updating git repository /home_local/a-sac-ns-brainvisa/bbi-daily/soma-env-0.0/src/morphologist-ui $ git fetch --tags --prune origin '+refs/heads/*:refs/remotes/origin/*' Depuis https://github.com/brainvisa/morphologist febe7af..a83f257 master -> origin/master $ git update-ref --no-deref refs/bv_head refs/remotes/origin/master $ git -c remote.origin.skipDefaultUpdate remote update $ git merge --ff-only refs/bv_head Mise à jour febe7af..a83f257 Fast-forward bin/morphologist | 14 +++---- morphologist/core/analysis.py | 47 +++++++++++------------ morphologist/core/backends/pyanatomist_backend.py | 8 ++-- morphologist/core/gui/__init__.py | 5 +-- morphologist/core/gui/qt_backend.py | 6 +-- morphologist/core/gui/resources_qt5.py | 2 +- morphologist/core/gui/runner_widget.py | 20 +++++----- morphologist/core/gui/subjects_widget.py | 8 +--- morphologist/core/runner.py | 42 +++++++++++++------- morphologist/core/study.py | 3 ++ morphologist/gui/main_window.py | 35 +++++++++-------- morphologist/info.py | 2 +- 12 files changed, 97 insertions(+), 95 deletions(-) Updating git repository /home_local/a-sac-ns-brainvisa/bbi-daily/soma-env-0.0/src/nuclear_imaging-gpl $ git fetch --tags --prune origin '+refs/heads/*:refs/remotes/origin/*' Depuis https://github.com/cati-neuroimaging/nuclear_imaging-gpl + af41ee47...97d411fc cat12_deformation -> origin/cat12_deformation (mise à jour forcée) 61e637b2..a5d73e10 master -> origin/master + afa5d156...f1fb6b31 synthseg -> origin/synthseg (mise à jour forcée) $ git update-ref --no-deref refs/bv_head refs/remotes/origin/master $ git -c remote.origin.skipDefaultUpdate remote update $ git merge --ff-only refs/bv_head Mise à jour 61e637b2..a5d73e10 Fast-forward .../toolboxes/nuclearimaging/processes/voxelByVoxelAnalysis_spm12.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) Updating git repository /home_local/a-sac-ns-brainvisa/bbi-daily/soma-env-0.0/src/nuclear_imaging-nonfree $ git fetch --tags --prune origin '+refs/heads/*:refs/remotes/origin/*' $ git update-ref --no-deref refs/bv_head refs/remotes/origin/master $ git -c remote.origin.skipDefaultUpdate remote update $ git merge --ff-only refs/bv_head Déjà à jour. Updating git repository /home_local/a-sac-ns-brainvisa/bbi-daily/soma-env-0.0/src/populse-db $ git fetch --tags --prune origin '+refs/heads/*:refs/remotes/origin/*' Depuis https://github.com/populse/populse_db 71493a2..e715e45 master -> origin/master $ git update-ref --no-deref refs/bv_head refs/remotes/origin/master $ git -c remote.origin.skipDefaultUpdate remote update $ git merge --ff-only refs/bv_head Mise à jour 71493a2..e715e45 Fast-forward docs/source/populse_db.rst | 8 -------- pyproject.toml | 2 +- 2 files changed, 1 insertion(+), 9 deletions(-) $ pre-commit install pre-commit installed at .git/hooks/pre-commit Updating git repository /home_local/a-sac-ns-brainvisa/bbi-daily/soma-env-0.0/src/primatologist-gpl $ git fetch --tags --prune origin '+refs/heads/*:refs/remotes/origin/*' Depuis https://bioproj.cea.fr/git/primatologist-gpl fe19b9a..fdd4bc1 master -> origin/master $ git update-ref --no-deref refs/bv_head refs/remotes/origin/master $ git -c remote.origin.skipDefaultUpdate remote update $ git merge --ff-only refs/bv_head Mise à jour fe19b9a..fdd4bc1 Fast-forward .../processes/analysis/HierarchicalRoiAnalysis.py | 12 ++++++++++++ python/primatologist/atlas.py | 4 ++-- python/primatologist/info.py | 2 +- 3 files changed, 15 insertions(+), 3 deletions(-) Updating git repository /home_local/a-sac-ns-brainvisa/bbi-daily/soma-env-0.0/src/soma-base $ git fetch --tags --prune origin '+refs/heads/*:refs/remotes/origin/*' Depuis https://github.com/populse/soma-base 0b79e21..a94a09d master -> origin/master c25c154..ffc288d qt6 -> origin/qt6 $ git update-ref --no-deref refs/bv_head refs/remotes/origin/master $ git -c remote.origin.skipDefaultUpdate remote update $ git merge --ff-only refs/bv_head Mise à jour 0b79e21..a94a09d Fast-forward python/soma/__init__.py | 1 - python/soma/activate_virtualenv.py | 5 +- python/soma/api.py | 10 ++- python/soma/application.py | 9 ++- python/soma/archive.py | 5 +- python/soma/bufferandfile.py | 6 +- python/soma/config.py | 3 +- python/soma/controller/controller.py | 16 ++++- python/soma/crypt.py | 11 ++- python/soma/debug.py | 4 -- python/soma/factory.py | 20 ++---- python/soma/fom.py | 132 ++++++++++++++++------------------- python/soma/functiontools.py | 3 - python/soma/global_naming.py | 7 +- python/soma/html.py | 21 +++--- python/soma/importer.py | 14 ++-- python/soma/info.py | 10 +-- python/soma/logging.py | 3 - python/soma/mpfork.py | 27 ++++--- python/soma/mpfork2.py | 26 +++---- python/soma/notification.py | 82 ++++++++++------------ python/soma/path.py | 25 +++---- python/soma/qimage2ndarray.py | 6 +- python/soma/qt_gui/qt_backend.py | 10 +-- python/soma/safemkdir.py | 5 +- python/soma/serialization.py | 14 ++-- python/soma/singleton.py | 5 +- python/soma/somatime.py | 3 - python/soma/sorted_dictionary.py | 41 ++++------- python/soma/sqlite_tools.py | 8 +-- python/soma/stringtools.py | 4 +- python/soma/subprocess.py | 57 ++------------- python/soma/thread_calls.py | 6 +- python/soma/topological_sort.py | 23 +++--- python/soma/translation.py | 2 - python/soma/undefined.py | 4 -- python/soma/uuid.py | 21 +++--- 37 files changed, 248 insertions(+), 401 deletions(-) $ pre-commit install pre-commit installed at .git/hooks/pre-commit Updating git repository /home_local/a-sac-ns-brainvisa/bbi-daily/soma-env-0.0/src/soma-io $ git fetch --tags --prune origin '+refs/heads/*:refs/remotes/origin/*' Depuis https://github.com/brainvisa/soma-io 774569d..5157c30 master -> origin/master 1f2bc09..8266663 qt6 -> origin/qt6 e28809d..f9a90e6 soma-env-6.0 -> origin/soma-env-6.0 $ git update-ref --no-deref refs/bv_head refs/remotes/origin/master $ git -c remote.origin.skipDefaultUpdate remote update $ git merge --ff-only refs/bv_head Mise à jour 774569d..5157c30 Fast-forward project_info.cmake | 2 +- soma-env/soma-env-recipe.yaml | 10 +- src/libcartobase/CMakeLists.txt | 4 +- src/libcartobase/smart/test_rcobject.cc | 48 +++++++ src/libcartobase/smart/test_rcobject.h | 27 ++++ .../transformation/affinetransformation3d_base.cc | 19 ++- src/somatiff/checker/tiffformatchecker.cc | 149 ++++++++++++++++++--- 7 files changed, 230 insertions(+), 29 deletions(-) create mode 100644 src/libcartobase/smart/test_rcobject.cc create mode 100644 src/libcartobase/smart/test_rcobject.h Updating git repository /home_local/a-sac-ns-brainvisa/bbi-daily/soma-env-0.0/src/soma-workflow $ git fetch --tags --prune origin '+refs/heads/*:refs/remotes/origin/*' Depuis https://github.com/populse/soma-workflow 8387c05..36fa60e gh-pages -> origin/gh-pages b7daa5a..49c26c9 master -> origin/master $ git update-ref --no-deref refs/bv_head refs/remotes/origin/master $ git -c remote.origin.skipDefaultUpdate remote update $ git merge --ff-only refs/bv_head Mise à jour b7daa5a..49c26c9 Fast-forward python/soma_workflow/info.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) $ pre-commit install pre-commit installed at .git/hooks/pre-commit Updating git repository /home_local/a-sac-ns-brainvisa/bbi-daily/soma-env-0.0/src/sulci-nonfree $ git fetch --tags --prune origin '+refs/heads/*:refs/remotes/origin/*' Depuis https://github.com/brainvisa/sulci-nonfree 0dfd46d..96ef603 master -> origin/master $ git update-ref --no-deref refs/bv_head refs/remotes/origin/master $ git -c remote.origin.skipDefaultUpdate remote update $ git merge --ff-only refs/bv_head Mise à jour 0dfd46d..96ef603 Fast-forward project_info.cmake | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) Summary of Git repositories in /home_local/a-sac-ns-brainvisa/bbi-daily/soma-env-0.0/src ======================================================================================== ┌───── * uncommitted working tree changes │┌──── + uncommitted index changes ││┌─── $ stash present │││┌── % untracked files ││││ ┌ HEAD ││││ │ ┌ update status ││││ │ │ ┌ bv_maker upstream state ││││ │ │ │ ┌ Git upstream state ││││ │ │ │ │┌ Directory master (9e78763c) ✓ U= aims-free master (f21dccc) ✓ U= aims-gpl master (b2f3c582) ✓ U= anatomist-free master (f98a01b) ✓ U= anatomist-gpl master (98d37787) ✓ U= axon master (cb8a653) ✓ U= bioprocessing master (a38f070) ✓ U= brainrat-gpl master (aaecedf) ✓ U= brainrat-private master (850b6f3) ✓ U= brainvisa-cmake master (850b6f3) ✓ U= brainvisa-cmake master (d810004) ✓ U= brainvisa-share master (50f4b51) ✓ U= brainvisa-spm master (b4a9fda) ✓ U= brainvisa_freesurfer master (88aa7fab) ✓ U= capsul master (4b11ec2) ✓ U= constellation-gpl master (2cb7705) ✓ U= constellation-nonfree master (571abe4) ✓ U= cortical_surface-gpl master (9b0400d) ✓ U= cortical_surface-nonfree master (0d1f8b3) ✓ U= disco master (efaab07) ✓ U= highres-cortex master (1ccf0e8) ✓ U= morpho-deepsulci master (facd37e) ✓ U= morphologist-baby master (bcaddf2c) ✓ U= morphologist-gpl master (220389f) ✓ U= morphologist-nonfree master (a83f257) ✓ U= morphologist-ui master (a5d73e10) ✓ U= nuclear_imaging-gpl master (ee5e900) ✓ U= nuclear_imaging-nonfree master (e715e45) ✓ U= populse-db master (fdd4bc1) ✓ U= primatologist-gpl master (a94a09d) ✓ U= soma-base master (5157c30) ✓ U= soma-io master (49c26c9) ✓ U= soma-workflow master (96ef603) ✓ U= sulci-nonfree bv_maker summary: OK step sources: /home_local/a-sac-ns-brainvisa/bbi-daily/soma-env-0.0/src, started: 2026/09/24 04:12, stopped: 2026/09/24 04:12 All went good. Finished: SUCCESS