What's Changed

• Write IMOD mod file without IMOD command by @hanjinliu in https://github.com/hanjinliu/cylindra/pull/97
• Fix FutureWarnings by @hanjinliu in https://github.com/hanjinliu/cylindra/pull/98
• Plugin system by @hanjinliu in https://github.com/hanjinliu/cylindra/pull/100
• Fix coverage not correctly calculated by @hanjinliu in https://github.com/hanjinliu/cylindra/pull/101
• Improve coverage by @hanjinliu in https://github.com/hanjinliu/cylindra/pull/102
• Cookiecutter template for creating plugins by @hanjinliu in https://github.com/hanjinliu/cylindra/pull/103
• implement drop_molecules by @hanjinliu in https://github.com/hanjinliu/cylindra/pull/104
• Refactoring and new implementation of landscape/annealing methods by @hanjinliu in https://github.com/hanjinliu/cylindra/pull/106
• Use evaluable string for distance parameters of constrained alignment by @hanjinliu in https://github.com/hanjinliu/cylindra/pull/107
• Find image by relative path by @hanjinliu in https://github.com/hanjinliu/cylindra/pull/109
• fix some CLI by @hanjinliu in https://github.com/hanjinliu/cylindra/pull/110
• Spherical mask creation by @hanjinliu in https://github.com/hanjinliu/cylindra/pull/111
• Fix the behavior of id argument by @hanjinliu in https://github.com/hanjinliu/cylindra/pull/112
• update show_reconstruction by @hanjinliu in https://github.com/hanjinliu/cylindra/pull/113
• Bump actions/download-artifact from 3 to 4.1.7 in /.github/workflows by @dependabot in https://github.com/hanjinliu/cylindra/pull/115
• Update bounding_box design and fix related bugs by @hanjinliu in https://github.com/hanjinliu/cylindra/pull/114
• fix rise angle null values of calculate_lattice_structure by @hanjinliu in https://github.com/hanjinliu/cylindra/pull/117
• Fix molecule positions when scales mismatch between projects by @hanjinliu in https://github.com/hanjinliu/cylindra/pull/119
• Updates for the latest acryo by @hanjinliu in https://github.com/hanjinliu/cylindra/pull/120
• View up-sampled cylindrical power spectrum by @hanjinliu in https://github.com/hanjinliu/cylindra/pull/118
• Add NCC alignment option by @hanjinliu in https://github.com/hanjinliu/cylindra/pull/116
• Add a SplineFitter method to auto-center along spline by @hanjinliu in https://github.com/hanjinliu/cylindra/pull/121
• Fixes for polars=1.7.0 by @hanjinliu in https://github.com/hanjinliu/cylindra/pull/122

New Contributors

• @dependabot made their first contribution in https://github.com/hanjinliu/cylindra/pull/115

Full Changelog: https://github.com/hanjinliu/cylindra/compare/v1.0.0.b4...v1.0.0.b5

This is a small bug-fix release.

What's Changed

• Initialize visibility of project viewer by @hanjinliu in https://github.com/hanjinliu/cylindra/pull/93
• Updates for latest griffe by @hanjinliu in https://github.com/hanjinliu/cylindra/pull/95
• Fix simulated annealer construction with non-regular shape by @hanjinliu in https://github.com/hanjinliu/cylindra/pull/96

Full Changelog: https://github.com/hanjinliu/cylindra/compare/v1.0.0.b3...v1.0.0.b4

What's Changed

• Fix undo operation of align_averaged by @hanjinliu in https://github.com/hanjinliu/cylindra/pull/91
• minor updates for napari=0.5 by @hanjinliu in https://github.com/hanjinliu/cylindra/pull/92

Full Changelog: https://github.com/hanjinliu/cylindra/compare/v1.0.0.b2...v1.0.0.b3

Highlights

• The spectra inspector widget is implemented in #78 #90, as described in the documentation. This widget is useful for manually checking the cylindric power spectra to confirm that the analysis went well.
• The Rust implementation of RMA was optimized in #87 so its performance was greatly improved. The calculation time is nearly the half of the previous versions.

What's Changed

• Widget for validation of CFT by @hanjinliu in https://github.com/hanjinliu/cylindra/pull/78
• fix symbols for orientation by @hanjinliu in https://github.com/hanjinliu/cylindra/pull/79
• Add max_radius arguments by @hanjinliu in https://github.com/hanjinliu/cylindra/pull/80
• Update PyO3 and polars by @hanjinliu in https://github.com/hanjinliu/cylindra/pull/82
• support int8 and int16 by @hanjinliu in https://github.com/hanjinliu/cylindra/pull/84
• Optimize the performance of lazy-loading projects by @hanjinliu in https://github.com/hanjinliu/cylindra/pull/85
• Add bin_size parameter to landscape functions by @hanjinliu in https://github.com/hanjinliu/cylindra/pull/86
• Use Array2 instead of HashMap to speed up RMA by @hanjinliu in https://github.com/hanjinliu/cylindra/pull/87
• Fix random seed problem by @hanjinliu in https://github.com/hanjinliu/cylindra/pull/88
• Fix inspector by @hanjinliu in https://github.com/hanjinliu/cylindra/pull/90

Full Changelog: https://github.com/hanjinliu/cylindra/compare/v1.0.0.b1...v1.0.0.b2

What's Changed

• Open as a napari plugin by @hanjinliu in https://github.com/hanjinliu/cylindra/pull/75
• Improve coverage by @hanjinliu in https://github.com/hanjinliu/cylindra/pull/76
• Simulate projection by @hanjinliu in https://github.com/hanjinliu/cylindra/pull/77

Full Changelog: https://github.com/hanjinliu/cylindra/compare/v1.0.0.b0...v1.0.0.b1

What's Changed

• Update docs by @hanjinliu in https://github.com/hanjinliu/cylindra/pull/59
• Disconnect close/hide button events by @hanjinliu in https://github.com/hanjinliu/cylindra/pull/62
• Update Rust crate versions by @hanjinliu in https://github.com/hanjinliu/cylindra/pull/61
• Use pydantic v2 by @hanjinliu in https://github.com/hanjinliu/cylindra/pull/64
• Better UI/UX by @hanjinliu in https://github.com/hanjinliu/cylindra/pull/66
• Allow reading projects with image path that doesn't exist. by @hanjinliu in https://github.com/hanjinliu/cylindra/pull/67
• Support IO for RELION by @hanjinliu in https://github.com/hanjinliu/cylindra/pull/65
• Read pdb/csv by @hanjinliu in https://github.com/hanjinliu/cylindra/pull/72
• Implement alignment function to extend protofilaments by @hanjinliu in https://github.com/hanjinliu/cylindra/pull/73

Full Changelog: https://github.com/hanjinliu/cylindra/compare/v1.0.0.a9...v1.0.0.b0

This is the version used for the biorxiv preprint.

What's Changed

• Refactor spline properties to the property props by @hanjinliu in https://github.com/hanjinliu/cylindra/pull/54
• Implement regionprops functions by @hanjinliu in https://github.com/hanjinliu/cylindra/pull/55
• Add a global variable to define the sign of rise angle by @hanjinliu in https://github.com/hanjinliu/cylindra/pull/56
• Improve spline fitting by @hanjinliu in https://github.com/hanjinliu/cylindra/pull/58

Full Changelog: https://github.com/hanjinliu/cylindra/compare/v0.13.3...v1.0.0.a9

Changes

• Save script as a runnable file.
• Add update_variable method to global variable widget.
• Fix workflow normalization to allow tab.

New Features

• Implement overwrite_project
• Implement workflow (custom runnable functions) architecture.
• Functions to measure local radii.
• Record monomer mapping offsets after calling align_averaged.
• Implement some specific widgets (CheckBoxes, RandomSeedEdit etc).
• New methods for analysis with project object.
• Improvement of binding potential model. Add angle constraint to annealing model.
• Implement backend low-level API for Viterbi alignment and annealing.

Changed

• fix workflow.
• Refactor config.
• Refactor non-recordable methods to child widgets.
• Do not use projection to determine peaks in local DFT.
• Calculate projection images lazily for performance improvement.
• Use list[T]() since python<3.8 is dropped.
• Record window size of local properties.
• Mask irrelevant requency during infer_polarity.

Bug Fixes

• Project description was not initialized.
• Fix displacement of cylinder model.

Bug Fixes

• Fix save_project when some of the spline properties are missing and add tests for this.
• Fix the output of align_averaged.

Changes

• Keep source spline object in each molecules layer.
• Don't rely on reshaping if possible (#29).
• Refactoring using latest acryo.
• Reimplement all the intensive functions in Rust (#39).
• Implement simulated annealing.
• Renew simulator widget (#41).
• Change the default project structure (#42).
• Refactor impl_preview and setup_function_gui in a separate file.
• Spline linear extrapolation (#44).
• Make the tilt_range parameter tomogram specific, not to reside in the subtomogram analysis widget (#45).
• Make the spline orientation and molecules orientation consistent.
• Add 2D plotting.
• Batchize alignment methods.
• Use ColormapEdit.
• Change spline properties architecture.
• Change global variable architecture.
• More comprehensive tests.
• Implement undo/redo.
• Make spline semi-immutable.

Bug Fixes

• Fix plain clip widget.
• Fix conversion from molecules to IMOD mod file (#31).
• Cylindric monomor mapping had subtle error.
• Fix spline shortening on fitting after clipping.
• Fix recursion error of alleviate().

New Features

• Protofilament-wise extend molecules.
• Update command palette.

Bug Fixes

• Fix polars dtype casting errors.
• Spline-fitter widget was not reproducible (#28).
• Fix open_logger.
• Fix Viterbi alignment.
• Fix seam search without mask images.

Major Updates

• 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

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

Changes

• 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

• 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

• Bug fix in spline deletion.

New Features

• 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

• Spline ID did not match the index, which caused many errors.

Changes

• 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

• 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

• 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