Add optional smoothing Fix #212#310
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Pull request overview
Adds an optional --smooth FWHM parameter across rbc metrics, rbc functional, and rbc all so that smoothing is no longer always performed; raw + z-scored raw derivatives are always produced, and smoothed variants are emitted only when requested.
Changes:
- Replace required/default smoothing (
fwhm=6.0) with optionalsmooth: float | Nonethroughout CLI args, orchestration, and workflows. - Update metrics workflow outputs to always include raw + z-scored raw maps, and optionally include smoothed + z-scored smoothed maps.
- Extend export + test coverage for conditional smoothed outputs and correct BIDS
desc-label construction.
Reviewed changes
Copilot reviewed 16 out of 16 changed files in this pull request and generated 5 comments.
Show a summary per file
| File | Description |
|---|---|
| tests/unit/orchestration/test_functional.py | Updates orchestration test to use smooth instead of fwhm. |
| tests/unit/cli/test_metrics.py | Updates metrics CLI tests for --smooth default/validation and parser wiring. |
| tests/unit/cli/test_functional.py | Adds smooth to functional CLI namespace fixture. |
| tests/unit/cli/test_all.py | Updates all CLI tests for --smooth default/validation and parser wiring. |
| tests/unit/bids/test_exports.py | Updates export fixtures/count assertions; adds tests for conditional smoothed exports and desc labels. |
| tests/full_pipeline/test_metrics.py | Adjusts pipeline test to tolerate optional (None) outputs. |
| src/rbc/workflows/metrics.py | Makes smoothing optional; always computes z-scored raw maps; adds optional smoothed + z-scored smoothed outputs. |
| src/rbc/workflows/functional.py | Adds optional smoothing path for cleaned BOLD export. |
| src/rbc/orchestration/metrics.py | Threads smooth through orchestration and passes it into exports. |
| src/rbc/orchestration/functional.py | Threads smooth through functional orchestration and exports. |
| src/rbc/orchestration/all.py | Threads smooth through the combined pipeline for metrics exporting. |
| src/rbc/cli/metrics.py | Renames --fwhm to --smooth, makes it optional, and updates validation/args. |
| src/rbc/cli/functional.py | Adds optional --smooth to functional CLI and passes through to orchestration. |
| src/rbc/cli/all.py | Renames --fwhm to --smooth, makes it optional, and updates validation/args. |
| src/rbc/bids/metrics.py | Exports raw + z-scored raw always; conditionally exports smoothed variants when smooth is set. |
| src/rbc/bids/functional.py | Conditionally exports smoothed cleaned BOLD when requested. |
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Adds
--smooth FWHMflag torbc metrics,rbc functional,rbc all,rbc longitudinal metrics,rbc longitudinal functional, andrbc longitudinal allto control smoothing of derivative outputs and cleaned BOLD.Changes:
desc-zstd) are always produced. When--smooth FWHMis set, the following are additionally exported:desc-sm{fwhm}) and z-scored smoothed (desc-sm{fwhm}Zstd)desc-sm{fwhm}preproc), export-only, applied post-regression and bandpass filteringrbc.core.metrics.smoothingtorbc.core.common3dBlurToFWHMthat it correctly handles both 3D derivative maps and 4D BOLD timeseries