| --version |
None |
show program's version number and exit |
| --sep |
int |
The number of classes a particle can contribute towards (default is 1) |
| --align |
str |
specify an aligner to use after classification. Default rotate_translate_tree |
| --aligncmp |
str |
Similarity metric for the aligner |
| --ralign |
str |
specify a refine aligner to use after the coarse alignment |
| --raligncmp |
str |
Similarity metric for the refine aligner |
| --cmp |
str |
Default=auto. The name of a 'cmp' to be used in assessing the aligned images |
| --classmx |
str |
Store results in a classmx_xx.hdf style file |
| --classinfo |
str |
Store results in a classinfo_xx.json style file |
| --classes |
str |
Generate class-averages directly. No bad particle exclusion or iteration. Specify filename. |
| --averager |
str |
Averager to use for class-averages |
| --invartype |
None |
Which type of invariants to generate: (bispec,harmonic) |
| --msamode |
str |
Enable MSA based classification, default=disabled, typically 'pca', see e2msa.py --mode option for full list |
| --nbasisfp |
int |
Only used in MSA mode. Number of MSA basis vectors to use when classifying particles, default=12 |
| --compressbits |
int |
Bits to keep when writing class-averages with compression. 0->lossless floating point. Default 10 (3 significant figures) |
| --threads |
int |
Number of threads to run in parallel on the local computer |
| --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 |