v1.4.0

New features

• Added lk.HiddenMarkovModel for classifying data traces exhibiting transitions between discrete states. For more information, see the tutorials section on Population Dynamics.
• Added option to crop beads out of a kymograph using Kymo.crop_beads().
• Added API to determine bead edges in a kymograph using Kymo.estimate_bead_edges().
• Added emission_path() and plot_path() methods to lk.GaussianMixtureModel
• Added option to File to pass a custom mapping from Photon count detector to RGB colors colors. This is useful to reconstruct images on systems with non-standard imaging modules.
• Added option to customize the filter width of the Gaussian filter that is applied prior to spot detection in lk.track_greedy(). Increasing this value results in fewer false detections at the cost of resolution. Note that the current default is set to half a pixel to preserve the old behavior.
• Added option to determine the viscosity and density of water with NaCl dissolved in it using lk.viscosity_of_water() and lk.density_of_water().
• Added ImageStack.close() to force close file handles. Note that this prohibits further access to images from the ImageStack it is called on, but also any ImageStack derived from it (i.e. through ImageStack.define_tether() or ImageStack.crop_by_pixels()).
• Added option to filter kymograph spot detections where there are no detections in adjacent frames using adjacency_filter=True in lk.track_greedy().
• Add option to include_dead_time to ImageStack.plot_correlated() for Scan and ImageStack. This parameter defaults to True.

Bug fixes

• Fixed a bug where the time indicator was off by one frame in ImageStack.plot_correlated() and ImageStack.export_video().
• Fixed a bug where the time between frames was incorrectly not excluded when calling ImageStack.frame_timestamp_ranges() with include_dead_time=False. Note that Scan and Kymo are not affected.
• Fixed a bug where ImageStack.plot_correlated() was not excluding the dead time between frames.
• Fixed a bug where color adjustments on a single channel ImageStack would not be applied unless a channel was provided as argument. This bug was introduced in v1.3.0.
• Changed the DateTime tag on TIFFs exported with Pylake from Scan and Kymo objects. Before the change, the start and end of the scanning period in nanoseconds was stored. After the change, we store the starting timestamp of the frame, followed by the starting timestamp of the next frame to be consistent with data exported from Bluelake. The scanning time is stored in the field Exposure time (ms) on the Description tag.
• Fixed tests to be compatible with pytest>=8.0.0.
• Ensure in returns True for a valid data path (e.g. "Force HF/Force 1x" in file should return True).

Improvements

• ImageStack now closes any file handles it has open upon garbage collection.

Deprecations

• Deprecated GaussianMixtureModel.from_channel(). The class constructor now accepts Slice instances directly.
• Deprecated GaussianMixtureModel.label(). Use GaussianMixtureModel.state_path() instead. Note, the returned instance is type Slice rather than np.ndarray. The data can be accessed via model.state_path(channel_slice).data.
• Deprecated GaussianMixtureModel.exit_flag Use GaussianMixtureModel.fit_info() instead. Note, the returned instance is a GmmFitInfo dataclass with attributes matching the keys of the dict returned from exit_flag (along with bic and aic; see next point).
• Deprecated GaussianMixtureModel.bic and GaussianMixtureModel.aic properties. These values can now be accessed via the bic and aic properties of GaussianMixtureModel.fit_info.

Breaking changes (alpha functionality)

• trace_kwargs and label_kwargs are now keyword-only arguments for GaussianMixtureModel.plot().

Other changes

• Bump tifffile dependency to >=2022.7.28.