tomodrgn downsample#

Purpose#

Downsample an image stack or volume by Fourier cropping. Note that where possible, it is preferred to re-extract particles in the appropriate upstream processing software at the desired box size, rather than downsampling here.

Sample usage#

The examples below are adapted from tomodrgn/testing/commandtest*.py, and rely on other outputs from commandtest.py to execute successfully.

# Warp v1 style inputs
tomodrgn \
    downsample \
    data/10076_classE_32_sim.star \
    --source-software cryosrpnt \
    --downsample 16 \
    --batch-size 50 \
    --output output/10076_classE_16_sim.mrcs \
    --write-tiltseries-starfile \
    --lazy

# WarpTools style inputs
tomodrgn \
    downsample \
    data/warptools_test_4-tomos_10-ptcls_box-32_angpix-12_optimisation_set.star \
    --downsample 16 \
    --batch-size 50 \
    --output output/warptools_70S_box-16.mrcs \
    --write-tiltseries-starfile \
    --lazy

Arguments#

usage: downsample [-h]
                  [--source-software {auto,warp,cryosrpnt,nextpyp,cistem,warptools,relion}]
                  --downsample DOWNSAMPLE --output MRCS
                  [--batch-size BATCH_SIZE] [--is-vol] [--chunk CHUNK]
                  [--lazy] [--datadir DATADIR] [--write-tiltseries-starfile]
                  input

Positional Arguments#

input

Input particles or volume (.mrc, .mrcs, .star, or .txt)

Core arguments#

--source-software

Possible choices: auto, warp, cryosrpnt, nextpyp, cistem, warptools, relion

Manually set the software used to extract particles. Default is to auto-detect.

Default: 'auto'

--downsample

New box size in pixels, must be even

--output

Output projection stack (.mrcs)

--batch-size

Batch size for processing images

Default: 5000

--is-vol

Flag if input .mrc is a volume

Default: False

--chunk

Chunksize (in # of images) to split particle stack when loading and saving if full stack + downsampled stack too large for system memory

--lazy

Lazily load each image on the fly if full stack too large for system memory

Default: False

--datadir

Optionally provide path to input .mrcs if loading from a .star file

--write-tiltseries-starfile

If input is a star file, write a downsampled star file

Default: False

Common next steps#

  • Validate that downsampling produced the desired downsampled particles with tomodrgn backproject_voxel or tomodrgn train_nn