Convert
usage: convert [-h] [-o OUTPUT] [--from {auto,coord,csv,star,box}]
[--to {auto,coord,csv,star,json,box}] [--suffix SUFFIX]
[-t THRESHOLD] [-s DOWN_SCALE] [-x UP_SCALE]
[--voltage VOLTAGE] [--detector-pixel-size DETECTOR_PIXEL_SIZE]
[--magnification MAGNIFICATION]
[--amplitude-contrast AMPLITUDE_CONTRAST] [--invert-y]
[--imagedir IMAGEDIR] [--image-ext IMAGE_EXT]
[--boxsize BOXSIZE] [-v VERBOSE]
files [files ...]
Positional Arguments
- files
path to input particle file(s). when multiple input files are given, they are concatentated into a single output file.
Named Arguments
- -o, --output
path to output particle file (default: stdout)
- --from
Possible choices: auto, coord, csv, star, box
file format of the INPUT file (default: detect format automatically based on file extension)
Default: “auto”
- --to
Possible choices: auto, coord, csv, star, json, box
file format of the OUTPUT file. NOTE: when converting to JSON or BOX formats, OUTPUT must specify the destination directory. (default: detect format automatically based on file extension)
Default: “auto”
- --suffix
suffix to append to file names when writing to directory (default: none)
Default: “”
- -t, --threshold
threshold the particles by score (optional)
Default: -inf
- -s, --down-scale
DOWN-scale coordinates by this factor. new coordinates will be coord_new = (x/s)*coord_cur. (default: 1)
Default: 1
- -x, --up-scale
UP-scale coordinates by this factor. new coordinates will be coord_new = (x/s)*coord_cur. (default: 1)
Default: 1
- --voltage
voltage metadata (optional)
Default: -1
- --detector-pixel-size
detector pixel size metadata (optional)
Default: -1
- --magnification
magnification metadata (optional)
Default: -1
- --amplitude-contrast
amplitude contrast metadata (optional)
Default: -1
- --invert-y
invert (mirror) the y-axis particle coordinates. requires also specifying –imagedir.
Default: False
- --imagedir
directory of images. only required to invert the y-axis - sometimes necessary for particles picked on .tiff images
- --image-ext
image file extension. required for converting to STAR and BOX formats and to find images when –invert-y is set. (default=.mrc)
Default: “.mrc”
- --boxsize
size of particle boxes. required for converting to BOX format.
Default: 0
- -v, --verbose
verbosity of information printed (default: 0)
Default: 0