Cylindra

Major Updates
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- Behavior of `extend_molecules` is completely changed.
- `load_project_for_reanalysis`
- Use global logger widget (27).
- Threading bug fixes.

Dependency
--------------
This version requires following dependencies.
- `magic-class==0.6.14`
- `acryo==0.2.1`
- `impy-array==2.2.1`

New Features
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- Spectra measurement in GUI (17)
- Spline clipper function (18).
- Functions for molecules (21).
- More STA related features (24).
- Batch STA analysis GUI (26).

Changes
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- Apply linear weight ramping during fitting (16).
- Use `acryo>=0.2.0`.
- Remove polarity check and implement new one.
- Split and reorganize the namespace of the main widget (20).
- Use custom points layer for molecules (22)
- Use `polars` in spline properties (23).
- Use `acryo.pipe` as much as possible (25).
- Use `magicclass.logging` (27).

Changes
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- Do not use `List` and `Tuple`.
- Implement flip and confirmation to image processor.
- Implement `DataFrameList` and its widget.
- Use `abstractapi` from magic-class>=0.6.13.

- Fix fatal bug in project model.
- Add IO functions.

New Features
---------------

**GUI**

- Sweeper widget.
- Tomogram simulator widget.
- Project viewer.

**Algorithms**

- Implement rotation to Viterbi alignment.
- Improved cylinder model.
- Add Radon model to describe Radon transformation.
- Use user directory to store global variables.

Bug Fixes
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- Bug fix in spline deletion.

New Features
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- Do not automatically read header in the image loader.
- Show polarity markers in the image.
- Use `CylinderModel` to describe structure. This model includes cylindric shaped molecules generation.
- New C++ function `alleviate` for convolution of molecule positions.

Bug Fixes
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- Spline ID did not match the index, which caused many errors.