feat: GPU acceleration module and scripts#99
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- Delete linumpy/gpu/cuda_env.py entirely - Remove cuda_env imports from gpu/__init__.py - Remove ensure_cuda_env/preload_cuda_libraries from linum_fix_illumination_3d.py and drop the now-obsolete XLA_FLAGS setup (was JAX-specific) - Remove ensure_cuda_env/preload_cuda_libraries from linum_benchmark_gpu.py - Update BaSiCPy docstring to reflect PyTorch backend
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PR #99 — GPU Acceleration (unified CPU/GPU scripts)
Adds the
linumpy/gpu/module (CuPy + JAX primitives) and wires the existing CPU scripts in the repo to pick up an optional GPU path via--use_gpu. Stand-alone*_gpu.pyscript variants are intentionally removed in this PR (replaced by the unified CPU scripts in PR #97).New library module
linumpy/gpu/array_ops.py— cupy/jax array primitives and CPU fallbackscorrections.py— GPU illumination / flat-field correctionscuda_env.py— CUDA environment detection (CUDA version, CuPy availability, JAX plugin status) + device selection; used by every GPU-capable script to negotiate the backendfft_ops.py— GPU FFT (phase-correlation building blocks)image_quality.py— GPU variance / sharpness metricsinterpolation.py— GPU affine/linear resamplingmorphology.py— GPU morphological ops (erode/dilate/tophat)normalization.py— GPU intensity normalization (percentile / rolling-ball) paired withlinumpy/preproc/normalization.pyfrom PR feat: utility modules, preprocessing improvements, galvo correction #97registration.py— GPU phase-correlation + refinement; callable fromlinumpy/stitching/registration.pyScripts
scripts/linum_benchmark_gpu.py— benchmark harness comparing CPU vs GPU on the key hot paths (normalization, registration, resampling)scripts/linum_gpu_info.py— report available CUDA / CuPy / JAX devices and plugin statusRemoved (unified into CPU scripts via
--use_gpu)linum_aip_gpu.py,linum_assess_slice_quality_gpu.py,linum_create_mosaic_grid_3d_gpu.py,linum_estimate_transform_gpu.py,linum_fix_illumination_3d_gpu.py,linum_generate_mosaic_aips_gpu.py,linum_normalize_intensities_per_slice_gpu.py,linum_resample_mosaic_grid_gpu.pyShell helpers
shell_scripts/fix_jax_cuda_plugin.sh— resets a broken JAX CUDA plugin install; autodetects CUDA 12 vs 13 and picks the matchingjax-cuda*-pluginwheelCommits
feat: GPU acceleration module and scripts— initiallinumpy/gpu/dropfeat(gpu): unify CPU/GPU scripts, add normalization module— removes the*_gpu.pyscript variants, addsgpu/normalization.py, hardenscuda_env.pyDependencies
gpu/gpu-cuda12/gpu-cuda13optional extras used here--use_gpuand dispatch intolinumpy/gpu/