Describe the bug
Installing using the spec file doesn't include healpy in the environment. This gives the following error:
(opusdsd-0.3.2b) jkrieger@elnath ~/scipion3/software/em/opusdsd-0.3.2b (main) $ python -m cryodrgn.commands.preprocess -h
Traceback (most recent call last):
File "/home/jkrieger/miniconda3/envs/opusdsd-0.3.2b/lib/python3.9/runpy.py", line 197, in _run_module_as_main
return _run_code(code, main_globals, None,
File "/home/jkrieger/miniconda3/envs/opusdsd-0.3.2b/lib/python3.9/runpy.py", line 87, in _run_code
exec(code, run_globals)
File "/data/jkrieger/scipion3/software/em/opusdsd-0.3.2b/cryodrgn/commands/preprocess.py", line 12, in <module>
from cryodrgn import utils
File "/data/jkrieger/scipion3/software/em/opusdsd-0.3.2b/cryodrgn/utils.py", line 12, in <module>
import healpy as hp
ModuleNotFoundError: No module named 'healpy'
To Reproduce
git clone -b main https://github.com/alncat/opusDSD opusdsd-0.3.2b && cd opusdsd-0.3.2b; eval "$(/home/jkrieger/miniconda3/bin/conda shell.bash hook)"&& conda create -y --name opusdsd-0.3.2b --file spec-file && conda activate opusdsd-0.3.2b
python -m cryodrgn.commands.preprocess -h
Expected behavior
I would have expected the preprocess script to run in some way and give me help about how to use it. This happens fine when using environment.yml instead:
git clone -b main https://github.com/alncat/opusDSD opusdsd-0.3.2b && cd opusdsd-0.3.2b; eval "$(/home/jkrieger/miniconda3/bin/conda shell.bash hook)"&& conda env create -y --name opusdsd-0.3.2b --file environment.yml && conda activate opusdsd-0.3.2b
python -m cryodrgn.commands.preprocess -h
usage: preprocess.py [-h] -o MRCS [--relion31] [--datadir DATADIR] [--ind PKL] [-D D] [--uninvert-data] [--window-r WINDOW_R] [--no-window] [--no-keep-real] [-b B] [--chunk CHUNK]
[--no-lazy] [--max-threads MAX_THREADS]
mrcs
Preprocess a dataset for more streamlined cryoDRGN training
positional arguments:
mrcs Input particles or volume (.mrc, .mrcs, .star, or .txt)
optional arguments:
-h, --help show this help message and exit
-o MRCS Output .mrcs
--relion31 Flag for relion3.1 star format
--datadir DATADIR Optionally provide path to input .mrcs if loading from a .star or .cs file
Image preprocessing settings:
--ind PKL Filter particle stack by these indices
-D D New box size in pixels (if downsampling), must be even
--uninvert-data Do not invert data sign
--window-r WINDOW_R Circular windowing mask inner radius (default: 0.85)
--no-window Turn off real space windowing of dataset
--no-keep-real Turn off real space windowing of dataset
Extra arguments for volume generation:
-b B Batch size for processing images (default: 5000)
--chunk CHUNK Chunksize (in # of images) to split particle stack when saving
--no-lazy Load whole dataset (faster than loading in batches)
--max-threads MAX_THREADS
Maximum number of CPU cores for parallelization (default: 16)
Additional context
I can't think of anything else that's relevant.
Describe the bug
Installing using the spec file doesn't include healpy in the environment. This gives the following error:
To Reproduce
Expected behavior
I would have expected the preprocess script to run in some way and give me help about how to use it. This happens fine when using environment.yml instead:
Additional context
I can't think of anything else that's relevant.