usage: Usage: e2maskbyclass.py [options] This program will generate a masked stack of particles for each micrograph based on the class-average each particle belongs to. While this will run with any EMAN2.2 generated class-average stack, it is designed to work on averages produced from __ctf_flip_fullres particles. In short: - read a class-average stack - convert each class-average into a 2-D mask - find the original phase-flipped particle for each particle in the class-average - mask each particle on a per-micrograph basis once complete, bispectra can be recomputed based on the masked particles, or the masked particles can be used directly, potentially producing better alignments and averages.
| Option | Type | Description |
|---|---|---|
| --version | None | show program's version number and exit |
| --classes | str | Path to a class-average file (must be EMAN2 HDF averages) |
| --threads | int | Number of alignment threads to run in parallel on a single computer. |
| --nofullresok | None | Overrides the requirement that the class-averages be made from _fullres particle images. |
| --redobispec | None | Recomputes bispectra from masked particles |
| --redoharmonic | None | Recomputes harmonic power from masked particles |
| --gui | None | Permits interactive adjustment of mask parameters |
| --verbose, -v | int | verbose level [0-9], higher number means higher level of verboseness |
| --ppid | int | Set the PID of the parent process, used for cross platform PPID |