Cylindra

Changes
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- Simplify seam search outputs.
- Add `cutoff` argument to seam search for much better results.
- Dynamic doc generation.
- Delete napari.yaml and add console entry point.

Bug Fixes
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- Minor bug fix in layer feature evaluation.
- Fix silent index error on spline change.
- Bug fix in reading global properties from csv.
- Bug fix in reset_choices in volume menu of sub viewer.

Improvements
-----------------
- Use rotated auto correlation to improve reference free rough alignment.
- Consider bin size in local- and global-CFT.

Others
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- Use latest `magic-class`
- Use `FieldGroup` to refactor widgets.
- Use docstrings for tooltip creation.
- Bug fix in confirmation.
- Use new type annotations.
- Use `thread_worker.to_callback` to refactor large part of codes.
- Use latest `impy-array`
- Use slicer as much as possible.
- Add `napari.yaml`

Highlights
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- Use `acryo` for subtomogram averaging. Accordingly, many simplification and improvements in structural reconstruction.
- Experimental polarity check functions.
- Viterbi alignment of distance-constrained and distance-and-angle-constrained method (implemented in C++).
- Missing wedge compensation.
- Curvature-oriented approximation of 3D spline. Accordingly, global variable is changed to fit this.

New Features
----------------
- Use relative path in project file if possible.
- Add binning option in local/global-CFT.
- Use Yen's thresholding to determine proper iso-surface threshold to show reconstruction.
- Write time spent on each long-running algorithm in log.
- Support `"nearest"` interpolation.
- Add method in GUI to concatenate molecule layers.

Changes
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- Change in default arguments (interpolation of subtomogram alignment: 1 → 3; alignment method: PCC → ZNCC).

Seems very stable now.

New Features
---------------
- Molecules rendering.
- Both PCC and ZNCC are working.
- Use `magic-class`'s `thread_worker` instead of `napari` built-in. Concomitantly, remove `nbatch` arguments.
- Add previews to some methods.
- Multi-template alignment worked.
- `align_averaged` tries many rotation angles than before.
- Add `translate_random` to `Molecules`.
- Improved convolution of molecule intervals.

Designs
--------
- Capitalization using `set_design` to follow Python naming rules.
- Alignment is largely refactored.
- Port features to `Molecules`.
- Merge feature control and feature viewer into a single widget.

Bug Fixes
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- Fix min/max of skew angle. Verified using TMV images.

- Add image processor and image previewer.
- Use ZNCC instead of PCC for spline fitting and refinement.
- Fix `layers.events.removing`.

GUI is largely improved.

- Subtomogram averaging
- Molecule feature visualization
- Project management
- More comprehensive tests