v3.4.3: Making movies, improving filtering interface, and fixing landscape analysis

[michal-g]

This is a minor release in which we are introducing a new utility for making volume movies using model analysis results, as well as making some fixes and improvements to existing features:

New visualizations

There is a new command cryodrgn_utils make_movies that automatically searches through the output folders created by commands such as cryodrgn analyze and cryodrgn analyze_landscape and produces .mp4 movies of reconstructed volumes using ChimeraX (which must be installed separately). For example, if volumes corresponding to k-means clusters were produced by cryodrgn analyze ... --ksample 50, make_movies will add movie.mp4 under analyze.<epoch>/kmeans50/ with an animation across the fifty k-means volumes:

movie.mp4

See cryodrgn_utils make_movies -h for more details! We have also added some new types of plots (scree plots and grid plots of PCA components) to the landscape analysis Jupyter notebooks.

Improving interactive filtering

Thanks to some help and feedback from the folks at Doppio (see #425, #426) we improved the interface for the interactive particle filtering command cryodrgn filter by adding buttons for choosing to save the selection (or not) rather than requiring an additional query step through the command-line:

Addressing known issues

• incorrect calculation of k-means volumes produced by analyze_landscape (Bug when calculating landscape analysis agglomerative clustering mean volumes #423)
• fixing typos in logging messages (Minor typo in train_vae logger message on AMP #422)
• avoiding printing of FutureWarning messages when using mixed-precision training through torch.cuda.amp:

  cryodrgn/cryodrgn/commands/train_vae.py

  Lines 380 to 386 in 7c07a86

  	if scaler is not None:
  	try:
  	amp_mode = torch.amp.autocast("cuda")
  	except AttributeError:
  	amp_mode = torch.cuda.amp.autocast_mode.autocast()
  	else:
  	amp_mode = contextlib.nullcontext()

• faster evaluation of volumes in GPU for analyze_landscape_full