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Add model-based detect_denoise modes - #208

Draft
henryhng wants to merge 14 commits into
electronmicroscopy:mainfrom
henryhng:denoise-model-v2
Draft

Add model-based detect_denoise modes#208
henryhng wants to merge 14 commits into
electronmicroscopy:mainfrom
henryhng:denoise-model-v2

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@henryhng

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Summary

Model-based detection denoise modes for ShowDiffraction.

Verification

  • Checks run: PYTHONPATH=src pytest -q (13 passed in the denoise test module; parametrized model tests skip when scikit-image/denova are absent)
  • User workflow exercised: raw vs anscombe vs denova_tv12 side-by-side Auto pipeline in JupyterLab
  • Data: public (Fe3O4 tutorial SAED, pyxem twinned nanowire from Zenodo 15490547)
  • Backend and hardware: CPU (devcontainer); denova CUDA/MPS path unverified here
  • Load/render/interaction timing: n/a (no frontend changes)
  • Evidence artifacts or screenshots: https://henryhg.com/research/denoise-model

Core checklist (every PR)

  • The change includes focused tests for Python state/export behavior and
    frontend build coverage where possible; start with PYTHONPATH=src:. pytest -q
    and npm run build, or run scripts/widget_local_signoff.sh.
  • Before committing, inspect git status --short and git diff --stat;
    do not commit generated HTML, docs builds, screenshots, local notebooks,
    private data, or machine-specific notes.
  • Committed notebooks carry NO baked widget state (metadata.widgets) and
    pass scripts/check_notebook_sizes.py. (No notebook changes in this PR's increment.)
  • Only the sections below that this PR touches are kept; the rest are
    deleted from this description.

This PR workflow follows the packaging standards for reproducible scientific
software described in scikit-package:
S. Lee, C. Myers, A. Yang, T. Zhang, Y. Xiao, and S. J. L. Billinge,
Digital Discovery (2026), DOI
10.1039/d6dd00121a.

@henryhng
henryhng marked this pull request as draft August 10, 2026 23:59
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