lumicks/pylake: v1.3.0

New features

• Added option to export ImageStack and Scan stacks to movies correlated with channel data. Simply pass a Slice to the channel_slice parameter of Scan.export_video() or ImageStack.export_video().
• Added more options for plotting color channels for images:
  • Shortcuts "r", "g", and "b" can now be used for plotting single color channels in addition to "red", "green", and "blue".
  • Two-channel visualizations can be plotted using "rg", "gb", or "rb".
• Added option to filter tracks by duration in seconds using lk.filter_tracks(tracks, minimum_duration=duration_in_seconds).
• Added option to align plots vertically by passing vertical=True to Scan.plot_correlated and ImageStack.plot_correlated().
• Added duration property to KymoTrack which returns the duration (in seconds) that the track was observed.
• Added KymoTrackGroup.filter() to filter tracks in-place. tracks.filter(minimum_duration=2) is equivalent to tracks = lk.filter_tracks(tracks, minimum_duration=2).

Bug fixes

• Fixed a bug in Scan.plot() in which the default aspect ratio was calculated such that pixels always appeared square. For scans with non-square pixel sizes, this would result in distortion of the image.
• Fixed a bug in Slice.downsampled_like that would fail to raise an error due to a lack of overlap between the low frequency and high frequency channel when the high frequency channel starts within the last sample of the low frequency channel.
• Fixed lk.download_from_doi() to align with new Zenodo REST API.
• Don't store animation writer in a temporary variable as this results in a matplotlib error when attempting to export a movie on jupyter notebook.

Improvements

• Kymographs consisting of a single scan line now return a valid line_time_seconds. This allows certain downstream functionality, such as Kymo.plot().
• Issue a more descriptive error when attempting to compute a diffusion constant of a track with no points.
• Pylake can now handle kymographs that were erroneously stored in the Scan field. Kymographs with a pre-specified number of lines to record were incorrectly being marked on the timeline and exported as Scan instead of Kymograph in versions of Bluelake prior to 2.5.0.