v0.5.0

What's Changed

Adds:

• GEFF import / export.
• A model now supports custom time properties (reference_time_property) instead of relying on the frame property. reference_time_property needs to be set at the model level. It is used by default when computing time-related properties, but can be case-by-case overwritten by any time property if needed.
• A model now has an internal time property timepoint.
• If not given, the time-step of the data is automatically computed at the model creation if there is graph data to infer from. After model creation, it can be set with Model.set_time_step().
• Property.type is now a Flag instead of a Literal to support multi-type properties, e.g. lineage_ID (type: Node | Lineage).
• Model metadata is now a Dataclass (ModelMetadata).
• New Model.has_cycle_data() method to check if a model has cycle data.
• Functions for standard properties creation are now into pycellin.graph.properties subpackage.
• A lot of small refactoring.
• Improve test coverage to ~45% (but still way to go).

Renames:

• Feature.data_type into Feature.dtype
• cell_length property into rod_length, and cell_width property into rod_width
• Feature.name into Feature.identifier and add a new Feature.name
• Model.metadata into Model.model_metadata
• Globally replace the word feature by property and feat by prop

Fixes:

• Model._categorize_props()

Next version:

• v0.5.1 ⇒ user documentation + API documentation

Full Changelog: v0.4.2...v0.5.0

v0.4.2

What's Changed

Adds:

• Trackmate XML loader can now read Mastodon XMLs

Fixes:

• Rare instances where ImageData tag was not read properly in TrackMate loader

Full Changelog: v0.4.1...v0.4.2

v0.4.1

What's Changed

Adds:

• Cycle features can be propagated to cell lineages with model.propagate_cycle_features()

Improves:

• model.update() now accepts a list of feature names to restrict which features to recompute
• TrackMate exporter now returns the exported model, with all its modifications
• Refactor _prepare_model_for_export()
• Rewrites feature removal and adds unit testing

Fixes:

• Cycle features were not computed properly during update
• Cycle features were not exported properly when exporting to TrackMate XML
• Incorrect data_type for cells cycle feature

Full Changelog: v0.4.0...v0.4.1

v0.4.0

What's Changed

Adds:

• Can load/export from/to trackpy tracking format
• CTC loader now extracts cell segmentation if label images are given
• Add cycle_duration as mandatory cycle feature
• More unit testing (but still far from a respectable coverage)

Fixes:

• More robust TrackMate exporter
• More robust computation for DivisionTime and DivisionRate (supports gaps and 0 value for DivisionTime)

Full Changelog: v0.3.6b...v0.4.0

v0.3.6b

First test release

Full Changelog: https://github.com/Image-Analysis-Hub/pycellin/commits/v0.3.6b