Maintenance update for FastSurfer (coming from FastSurferCC integration) #757
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… several files - use thread_executor instead of internal own executor object in segstats and brainvolstats - use DO_NOT_SAVE_FILE instead of empty string for defaults in segstats.py - update formatting - fix sphinx warnings (argparse extension) - Remove extra Default statement from device argument - Add Fornix Measure for brainvolstats.py - Add path_or_none arg_type in arg_types.py
…nt component of FastSurfer (also being used by FastSurferCC)
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Pull request overview
This PR performs maintenance updates for FastSurfer as part of the FastSurferCC integration effort, focusing on code organization, type annotations, and improved executor handling.
Key changes:
- Moved LTA utilities from
recon_surfandCerebNetto centralizedFastSurferCNN/utils/lta.pymodule - Standardized thread/process executor usage via
thread_executor()function insegstats.pyandbrainvolstats.py - Enhanced type annotations with
nibabelImage,ShapeType, andAffineMatrix4x4types throughout the codebase
Reviewed changes
Copilot reviewed 29 out of 29 changed files in this pull request and generated 7 comments.
Show a summary per file
| File | Description |
|---|---|
| recon_surf/lta.py | Removed - functionality moved to FastSurferCNN/utils |
| recon_surf/align_seg.py | Updated import to use new lta module location |
| doc/api/recon_surf.rst | Removed lta module from documentation |
| doc/api/FastSurferCNN.utils.rst | Added lta module to utils documentation |
| Tutorial/README.md | Fixed trailing backtick in comment |
| HypVINN/data_loader/dataset.py | Added .cpu() call before .numpy() for tensor conversion |
| FastSurferCNN/utils/run_tools.py | Fixed escaped apostrophe in docstring |
| FastSurferCNN/utils/parser_defaults.py | Removed "Default: auto" text duplication in help string |
| FastSurferCNN/utils/parallel.py | Added shutdown_executors to all exports |
| FastSurferCNN/utils/metrics.py | Fixed escaped apostrophe in docstring |
| FastSurferCNN/utils/lta.py | New module with write_lta and read_lta functions plus LTADict type |
| FastSurferCNN/utils/common.py | Improved line wrapping in error messages |
| FastSurferCNN/utils/brainvolstats.py | Updated to use thread_executor and new type annotations |
| FastSurferCNN/utils/arg_types.py | Added path_or_none function for argument parsing |
| FastSurferCNN/utils/init.py | Added comprehensive type definitions including nibabelImage and ShapeType |
| FastSurferCNN/segstats.py | Replaced ThreadPoolExecutor with thread_executor() and improved formatting |
| FastSurferCNN/run_prediction.py | Updated type annotations to use nibabelImage |
| FastSurferCNN/reduce_to_aseg.py | Updated type annotations with ShapeType and new nibabel types |
| FastSurferCNN/quick_qc.py | Updated to use nibabelImage type |
| FastSurferCNN/models/interpolation_layer.py | Improved code formatting and reduced line lengths |
| FastSurferCNN/data_loader/data_utils.py | Updated return type documentation and nibabelImage usage |
| FastSurferCNN/data_loader/conform.py | Added Union import and updated type annotations |
| CerebNet/utils/lr_scheduler.py | Converted docstrings from Args/Returns to Parameters/Returns format |
| CerebNet/inference.py | Updated to use nibabelImage type and improved docstrings |
| CerebNet/datasets/utils.py | Removed LTADict and read_lta (moved to FastSurferCNN), added type hints |
| CerebNet/datasets/load_data.py | Enhanced docstrings with proper parameter documentation |
| CerebNet/data_loader/loader.py | Added type hints and improved docstring format |
| CerebNet/data_loader/dataset.py | Updated to use nibabelImage type |
| CerebNet/data_loader/augmentation.py | Improved docstring formatting with Notes and References sections |
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Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>
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This PR includes some of the changes that are part of FastSurferCC development, but in FastSurfer directories and also in content not directly part of FastSurferCC. Those changes are