--flip option causes error in analyze_landscape_full

[cbeck22]

Hi!

I'm running cryoDRGN v3.3.3, and I'm trying to use the analyze_landscape_full command. I'm running it in the results directory containing the weights and z .pkl files.

The command results in the following error if used with the --flip option:

cryodrgn analyze_landscape_full . 99 --flip > landscape_full.log
Traceback (most recent call last):
  File "/programs/x86_64-linux//cryodrgn/3.3.3/cryodrgn/bin/cryodrgn", line 8, in <module>
    sys.exit(main_commands())
  File "/programs/x86_64-linux/cryodrgn/3.3.3/miniconda/lib/python3.9/site-packages/cryodrgn/command_line.py", line 68, in main_commands
    _get_commands(
  File "/programs/x86_64-linux/cryodrgn/3.3.3/miniconda/lib/python3.9/site-packages/cryodrgn/command_line.py", line 63, in _get_commands
    args.func(args)
  File "/programs/x86_64-linux/cryodrgn/3.3.3/miniconda/lib/python3.9/site-packages/cryodrgn/commands/analyze_landscape_full.py", line 339, in main
    z, embeddings = generate_and_map_volumes(
  File "/programs/x86_64-linux/cryodrgn/3.3.3/miniconda/lib/python3.9/site-packages/cryodrgn/commands/analyze_landscape_full.py", line 231, in generate_and_map_volumes
    vol = vol[::-1]
ValueError: step must be greater than zero

However, the command runs properly when the --flip option is not used. Is this a bug? The --flip option worked successfully for the regular analyze_landscape command.

Best,
cbeck

[michal-g]

Hey, this is indeed a bug on our side — we had been assuming that PyTorch tensor objects support negative slices in the same manner as numpy arrays (e.g. vol[::-1]) but this is not the case, nor is it expected to be the case for the foreseeable future, as outlined here: pytorch/pytorch#59786

I've updated the vol = vol[::-1] line in analyze_landscape_full to be vol = vol.flip([0]) as in the code used by analyze_landscape for the same operation, which allows the command to run to completion with --flip. This fix will be part of the v3.4.2 release and has been made available in the meantime through our beta release channel:

pip install -i https://test.pypi.org/simple/ --extra-index-url https://pypi.org/simple/ 'cryodrgn<=3.4.2' --pre

Let us know if you find any other problems with the landscape analyses tools!

-Mike