Sericossypha

Fixes an installation bug in 2.0.19.

Sericossypha

• improved test suite and added GitHub Actions runner
• numerous minor fixes and code quality improvements

As usual, see the NEWS file for full details.

Mitrospingus

• added initial implementation of a Makeflow (https://github.com/cooperative-computing-lab/cctools) backend as an alternative to our in-house server-executor backend
• updated Pyro4 to Pyro5

Mitrospingidae

• adds Singularity support
• improved execution logging
• fix a type mismatch in the default minctracc command template

Rhodinocichlidae

• user-editable shell command templates with Jinja2 (see README.md for usage)
• fix a bug where files could be created in incorrect subdirectory (but in correct row of generated .csv files)

Thraupidae

A few highlights (see NEWS file as usual):

• enabling MAGeT as part of MBM pipeline automatically segments the nonlinear average as well as individual subjects.
• --use-robust-averaging flag in nonlinear model building pipelines (uses mincbigaverage's "--robust" flag).
• more MAGeT-based masking options:
  • --mask-dilation=$n flag dilates atlas masks by n voxels.
  • --hard-mask applies atlas masks to subjects via mincmath (not enabled by default).
  • --hard-mask-dilation dilates masks by $n voxels before applying them to images (not additive with --mask-dilation).
• various bugfixes and internal improvements.

Cardinalidae

• fix a file naming bug when minctracc is used for average building
• fixes to reduce memory/vmem usage with upstream Numpy/OpenBLAS wheels
• rotational_minctracc.py now uses both source and target masks if present
• bug fixes to output CSV file generation
• improved help documentation for --restart and --smart-restart
• create fewer intermediate resamplings
• minimum Python version is now correctly specified as 3.6 due to use of format strings
• typing module is removed as a dependency since it's present in 3.6 and incompatible with 3.8
• various other small bugfixes and internals changes

Malaconotidae

• in the two-level pipeline, the inputs specified via --csv-file are now by default relative
  to the csv file rather than the current working directory; this matches the behaviour of MBM.py.
  To get the opposite behaviour, MBM and twolevel now support a new flag, --csv-paths-relative-to-wd
• switched from xfmavg to xfmavg_scipy.py; this adds a dependency on minc2-simple (see INSTALL)
• fixed a bug causing installation failure with Python > 3.6.4
• fixed crashes at startup in certain flag combinations
• pipeline correctly handles undefined PYDPIPER_CONFIG_FILE environment variable
• various other minor changes

Threskiornithidae

Many internal changes for supporting upcoming TissueVision code and several quality of life improvements for the user. Here are some highlights but go look at NEWS!

• improvements to output CSVs for MBM and twolevel model pipelines: use analysis.csv for most cases
• additional outputs to analysis.csv: masks, segmentations
• --resolution flag works correctly (i.e., not ignored)
• --time-to-seppuku flag changed to --max-idle-time
• --smart-restart flag added to allow manually modifying files and have Pydpiper automatically recompute all succeeding stages
• a warning is signalled if PYDPIPER_CONFIG_FILE doesn't point to a readable file

Laniidae

Many internal and user-visible changes; see NEWS for details; some highlights:

• support for antsRegistration (currently with a fixed set of parameters)
• better output CSVs for MBM.py (c/o Nick)
• a new longitudinal registration topology
• internal modularization to support more registrations
  • new topologies for MBM.py/two-level/chain via the --registration-strategy flag
  • some internal work on ITK/NIfTI-based tools (Elastix, Demons, DRAMMS)
    but not supported yet by main pipelines - to be continued.
• several additional configuration options (all optional!) for execution control;
  disable MBM common space registration by default on behalf of non-MICe users