| --version |
None |
show program's version number and exit |
| --ampcont |
float |
Default=0.05. Amplitude contrast to use for CTF correction phase flipping. |
| --apix |
float |
Default=whatever is on the header of the images. Sampling of the images in angstroms/pixel. |
| --bfactor |
int |
Default=1000. Bfactor ("temperature factor") to use. |
| --cs |
float |
Default=2.7. Cs of the microscope with which the images were collected. |
| --defocus |
float |
Default=None. Target defocus at the tilt axis. If not provided, a "global defocus" value will be estimated automatially. |
| --debug |
None |
Default=False. Shows plots as they are being produced -requires user feedback to proceed. |
| --input |
str |
Default=None. Single 2D image or image stack to calculate CTF for. |
| --path |
str |
Directory to store results in. The default is a numbered series of directories containing the prefix 'tomoctfraw'; for example, sptctf_02 will be the directory by default if 'sptctf_01' already exists. |
| --phaseplate |
None |
Default=False. Supply this if the data were collected with hole-free phase plate. |
| --plots |
None |
Default=False. Turn this option on to generate plots of the background-subtracted 1D power spectrum overlaid with the best CTF fit. Running on a cluster or via ssh remotely might not support plotting. |
| --ppid |
int |
Set the PID of the parent process, used for cross platform PPID |
| --savefft |
None |
Default=False. Saves the average of the ffts of the tiles for an image or its strips. |
| --tilesize |
int |
Tile size to use for strips when --autofit is provided. |
| --tiltangle |
float |
Default=None. Single 2D image or image stack to calculate CTF for. |
| --tltfile |
str |
File containing a list of tilt angles corresponding to the tilt angles of images 0 to n. |
| --verbose, -v |
int |
verbose level [0-9], higner number means higher level of verboseness. |
| --voltage |
int |
Default=300. Voltage of the microscope with which the images where collected. |