usage: prog [options] <image> <image2>.... The even newer version of e2boxer. Complete rewrite..
| Option | Type | Description |
|---|---|---|
| --version | None | show program's version number and exit |
| --allmicrographs | None | Add all images from micrographs folder |
| --unboxedonly | None | Only include image files without existing box locations |
| --boxsize, -B | int | Box size in pixels |
| --ptclsize, -P | int | Longest axis of particle in pixels (diameter, not radius) |
| --compressbits | int | Bits to keep when writing images with compression. 0->lossless floating point. Default 6 |
| --write_dbbox | None | Export EMAN1 .box files |
| --write_ptcls | None | Extract selected particles from micrographs and write to disk |
| --invert | None | If specified, inverts input contrast. Particles MUST be white on a darker background. |
| --no_ctf | None | Disable CTF determination |
| --suffix | str | Suffix of the micrographs used for particle picking (i.e. suffix=goodali will use micrographs end with __goodali.hdf). It is only useful when [allmicrographs] is True. |
| --apix | float | Angstroms per pixel for all images |
| --voltage | float | Microscope voltage in KV |
| --cs | float | Microscope Cs (spherical aberation) |
| --ac | float | Amplitude contrast (percentage, default=10) |
| --autopick | str | Perform automatic particle picking. Provide mode and parameter string, eg - auto_local:threshold=5.5 |
| --gui | None | Interactive GUI mode |
| --threads | int | Number of threads to run in parallel on a single computer when multi-computer parallelism isn't useful |
| --ppid | int | Set the PID of the parent process, used for cross platform PPID |
| --device | str | For Convnet training only. Pick a device to use. chose from cpu, gpu, or gpuX (X=0,1,...) when multiple gpus are available. default is cpu |
| --verbose, -v | int | verbose level [0-9], higher number means higher level of verboseness |
For more information go to emanwiki/EMAN2/Programs/e2boxer.