feat(n4): GPU-accelerated N4 bias field correction#109
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FIrgolitsch wants to merge 1 commit intochain-mergedfrom
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feat(n4): GPU-accelerated N4 bias field correction#109FIrgolitsch wants to merge 1 commit intochain-mergedfrom
FIrgolitsch wants to merge 1 commit intochain-mergedfrom
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Add N4 bias-field correction with CPU/GPU backends, replacing the
previous z-intensity normalization approach.
Library:
- linumpy/intensity/bias_field.py: high-level API for N4 correction
- linumpy/intensity/normalization.py: extended to support N4 backend
- linumpy/gpu/{bias_field,bspline,n4}.py: GPU kernels (CuPy)
- Removes linumpy/gpu/normalization.py (superseded)
Scripts:
- scripts/linum_correct_bias_field.py: replaces linum_normalize_z_intensity
- scripts/diagnostics/linum_benchmark_n4_gpu.py: CPU vs GPU performance
- scripts/diagnostics/linum_n4_gpu_visual_compare.py: visual comparison
Tests:
- linumpy/tests/test_bias_field*.py
- linumpy/tests/test_gpu_{bspline,n4}.py
- linumpy/tests/test_n4_gpu_{equivalency,perf}.py
- Extended test_intensity_normalization.py
Workflow integration:
- workflows/reconst_3d/soct_3d_reconst.nf: add correct_bias_field process
- workflows/reconst_3d/nextflow.config: N4 parameters
Build:
- pyproject.toml: swap entry-point linum_normalize_z_intensity ->
linum_correct_bias_field, add scipy-stubs/networkx-stubs dev deps,
add lint exemptions for linumpy/gpu/* and N4 diagnostic scripts
Docs:
- docs/N4_GPU.md: GPU acceleration guide
- docs/n4_gpu_benchmark.json + image: performance data
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Adds N4 bias-field correction with CPU/GPU backends, replacing the previous z-intensity normalization.
Stacked PR. Base will be retargeted to
mainonce the chain (#95, #97, #98, #99, #100, #101, #108, #106, #107, #87) merges.Library
linumpy/intensity/bias_field.py\u2014 high-level APIlinumpy/intensity/normalization.py\u2014 extended for N4 backendlinumpy/gpu/{bias_field,bspline,n4}.py\u2014 GPU kernels (CuPy)linumpy/gpu/normalization.py(superseded)Scripts
scripts/linum_correct_bias_field.py\u2014 replaceslinum_normalize_z_intensityscripts/diagnostics/linum_benchmark_n4_gpu.pyscripts/diagnostics/linum_n4_gpu_visual_compare.pyTests
linumpy/tests/test_bias_field*.py,test_gpu_{bspline,n4}.pylinumpy/tests/test_n4_gpu_{equivalency,perf}.pytest_intensity_normalization.pyWorkflow integration
workflows/reconst_3d/soct_3d_reconst.nf: addscorrect_bias_fieldprocessworkflows/reconst_3d/nextflow.config: N4 parametersBuild
pyproject.toml: entry-point swap (linum_normalize_z_intensity\u2192linum_correct_bias_field),scipy-stubs/networkx-stubsdev deps, lint exemptions forlinumpy/gpu/*and N4 diagnostic scripts