Prepare napari-curvealign for merge and fix ROI mode-switch desync#39

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Phil-Dua wants to merge 109 commits intomainfrom

napari-curvealign

Commits on Sep 29, 2025

Add CurveAlign Python API: complete implementation with organized types, pluggable visualization, and framework integration

Phil-Dua
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hinerm
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Update README to document CurveAlign Python API integration and usage in tme-quant

Phil-Dua
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hinerm
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Add setup notes and clean up moved Python API: remove broken virtual environment, add installation instructions

Phil-Dua
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hinerm
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gitignore: add Python API ignores in tme-quant; streamline Curvelets_API ignores; copy CurveAlign API docs into tme-quant/doc/curvealign

Phil-Dua
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hinerm
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docs(curvealign): add API_OUTLINE.md (MATLAB mapping) alongside Python API docs

Phil-Dua
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hinerm
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Refactor CurveAlign Python API to granular architecture

Phil-Dua
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hinerm
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Clean up old monolithic files after granular refactoring

Phil-Dua
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hinerm
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Test and align granular CurveAlign API: fix imports, update CI workflow

Phil-Dua
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hinerm
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Remove redundant test_new_architecture.py - superseded by comprehensive test_granular_api.py

Phil-Dua
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hinerm
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Update .gitignore: add .test_env, enhance Python ignores, add output artifacts

Phil-Dua
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hinerm
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Integrate CT-FIRE: parallel granular API, unified interface

Phil-Dua
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hinerm
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Organize tests: move to proper API directories, fix imports, update CI

Phil-Dua
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hinerm
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CI: install pytest-cov to satisfy coverage addopts; run subpackage tests

Phil-Dua
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hinerm
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Fix CI tests: validate mode, alias std_angle, add map_std_window, expose compute_features

Phil-Dua
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hinerm
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CI: add total_curvelets alias in stats for legacy tests

Phil-Dua
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hinerm
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Refactor to src/test layout: src/curvealign & src/ctfire; move tests; drop path hacks; simplify CI
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Clean up structure: rename packages to src/curvealign_py & src/ctfire_py; move tests to tests/; integrate pyproject.toml; update imports
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Final cleanup: remove old curvealign_py/ and pycurvelets/; update napari plugin to use new curvealign_py API
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Fix import typos: curvealign_py_py -> curvealign_py; update .gitignore
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Remove obsolete tests: pycurvelets-based test_new_curv.py, test_relative_angles.py, napari_curvealign_test.py
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Update README.md and simple_usage.py: highlight modern Python API, comprehensive examples.
Phil-Dua
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Consolidate virtual environments: remove .api_env .test_env, use single .venv
Phil-Dua
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Commits on Oct 1, 2025

Commits on Oct 20, 2025

Commits on Nov 5, 2025

Add Napari plugin with segmentation, ROI Manager, and multi-environment support
Phil-Dua
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Commits on Nov 10, 2025

Commits on Nov 12, 2025

Commits on Nov 19, 2025

Enhance napari plugin to match MATLAB CurveAlign functionality
Phil-Dua
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Commits on Nov 27, 2025

Enhance ROI manager annotations with segmentation-driven workflow.
Phil-Dua
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Commits on Dec 3, 2025

Extend CurveAlign napari ROI manager with MATLAB-parity features: add measurement dialog with histogram/export, tabular ROI list, refined detection options, CT-FIRE/curvelets overlay hook, and view…
Phil-Dua
committed

Commits on Jan 14, 2026

Improve napari segmentation scoping and grouping; ensure segmentation runs on the selected image (image list or labels-parent), tag labels with parent, per-image mask cache, mask-source note for RO…
Phil-Dua
committed

Commits on Jan 15, 2026

Add batch pipeline and post-processing plots; refactor segmentation reuse; align ROI analysis defaults with MATLAB (keep/scale/group/dist); stabilize FDCT with padding/retry and strict curvelops re…
Phil-Dua
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Commits on Jan 26, 2026

Commits on Jan 28, 2026

Commits on Feb 2, 2026

Commits on Feb 3, 2026

Commits on Feb 9, 2026

Commits on Feb 16, 2026

Replace StarDist with cellcast for nuclei segmentation

Phil-Dua
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cursoragent
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Commits on Feb 19, 2026

Commits on Feb 23, 2026

Restart napari-curvealign: migrate to pycurvelets API

Phil-Dua
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cursoragent
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Commits on Feb 24, 2026

Commits on Feb 25, 2026