Enhance image processing and orientation detection in holoptycho#37
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Himanshu Goel (himanshugoel2797) wants to merge 3 commits into
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Enhance image processing and orientation detection in holoptycho#37Himanshu Goel (himanshugoel2797) wants to merge 3 commits into
Himanshu Goel (himanshugoel2797) wants to merge 3 commits into
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- Updated ImagePreprocessorOp to include configurable geometry and normalization parameters for output branches. - Introduced auto-detection of dp_orient in the new detect_orientation.py script. - Modified PtychoApp to support new orientation parameters and normalization settings. - Improved handling of patch flipping in SaveViTResult for better output consistency.
- Added h5py dependency to pixi.toml for HDF5 file handling. - Introduced `dump_scan_h5.py` script to export Tiled scans to HDF5 format, including preprocessing steps and metadata attributes. - Updated `config_from_tiled.py` to auto-detect `panda_upsample` and `vit_normalization`, enhancing scan configuration. - Enhanced argument parsing in `replay_from_tiled.py` to allow configuration of parallel fetch workers for improved performance. - Improved error handling during frame fetching to retry on transient HTTP timeouts. - Adjusted default number of workers for tiled fetches to optimize throughput and prevent connection timeouts.
Garrett Bischof (gwbischof)
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Jun 5, 2026
Move the generic ViT patch-placement algorithms out of holoptycho/mosaic_stitch.py into a new ptychoml.stitch module so they can be shared instead of duplicated. Three placement strategies: - place_patches_fourier_shift / stitch_batch_into: sub-pixel Fourier-shift - stitch_batch_livestitch_into: nearest-integer + touched bounding box - stitch_batch_nearest: plain nearest-integer, edge-clamped Pure numpy + scipy.fft; depends only on fourier_shift from preprocess. Exported via __init__ __all__, covered by tests/test_stitch.py (12 cases: placement, accumulation, counts footprint, livestitch bbox, edge clamping, up-down flip, fourier-vs-nearest parity, per-batch associativity), and documented in README + AGENTS.md. First step of breaking NSLS2/holoptycho#37 into focused PRs: holoptycho will re-export these under their original names (zero behavior change). Co-authored-by: Himanshu Goel <4122621+himanshugoel2797@users.noreply.github.com>
This was referenced Jun 5, 2026
Garrett Bischof (gwbischof)
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Jun 8, 2026
ptychoml renamed PtychoViTInference's 'data_is_shifted' parameter to 'fftshift' (None = auto-detect DC via detect_dc_at_corner). holoptycho main still called PtychoViTInference(data_is_shifted=...), which raises TypeError against the pinned ptychoml (the bump in #38 crossed the rename) — the ViT op would crash on its first batch. Smoke tests missed it: the vit_inference import dies earlier on TILED_BASE_URL, and CI envs skip holoscan entirely. Rename PtychoViTInferenceOp's param data_is_shifted -> fftshift and pass fftshift= to the session; drop data_is_shifted=True in ptycho_holo.py and let it default to None (auto-detect), matching PR #37's end-to-end DC handling that pairs with this PR's preprocess_diffraction(fftshift=fftshift_dp=None). Adds tests/test_vit_session_contract.py to pin the holoptycho<->ptychoml call contract so a future rename fails in CI instead of on the beamline. Co-authored-by: Himanshu Goel <4122621+himanshugoel2797@users.noreply.github.com>
This was referenced Jun 8, 2026
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Very preliminary developments.