| --version |
None |
show program's version number and exit |
| --input |
str |
Comma separated files in .ali, .st .hdf format of the aligned subtiltseries. |
| --inputstem |
str |
Alternative to supplying --input. This is a string common to multiple files to be processed in the CURRENT directory. The common string doesn't need to be at a particular location in the filenames. For example, a series of files "tiltA.hdf, tiltB.hdf, tiltC.hdf" could have either 'hdf', '.hdf', 't,','ti', 'til', 'tilt', etc., as a common string. The key is to choose a string shared ONLY by the files of interest. The files should be multiple subtiltseries in .hdf format; each file should correspond to an individual subtiltseries for a different particle: That is, each file should be a subtiltseries corresponding to an individual subtomogram, as extracted by e2spt_subtilt.py, or as simulated by e2spt_simulation.py |
| --inputdir |
str |
Alternative to --input and --inputstem. Path to a directory containing individual subtiltseries stacks. |
| --path |
str |
Directory to store results in. The default is a numbered series of directories containing the prefix 'sptisr'; for example, sptisr02 will be the directory by default if 'sptisr_01' already exists. |
| --ppid |
int |
Default=1. Set the PID of the parent process, used for cross platform PPID |
| --verbose, -v |
int |
Default 0. Verbose level [0-9], higher number means higher level of verboseness |
| --reconstructor |
str |
Default=fourier:mode=gauss_2. The reconstructor to use to reconstruct the tilt series into a tomogram. Type 'e2help.py reconstructors' at the command line to see all options and parameters available. To specify the interpolation scheme for the fourier reconstructor, specify 'mode'. Options are 'nearest_neighbor', 'gauss_2', 'gauss_3', 'gauss_5'. For example --reconstructor=fourier:mode=gauss_5 |
| --iter |
int |
Number of iterations to run algorithm for. |
| --tltfile |
str |
IMOD-like .tlt file with tilt angles for the aligned tiltseries (or set of subtiltseries). |
| --tiltaxis |
str |
Axis to produce projections about. Default is 'y'; the only other valid option is 'x'. |
| --pad2d |
float |
Default=0.0. Padding factor (e.g., 2.0, to make the box twice as big) to zero-pad the 2d images in the tilt series for reconstruction purposes (the final reconstructed subvolumes will be cropped back to the original size though). |
| --pad3d |
float |
Default=0.0. Padding factor (e.g., 2.0, to make the box twice as big) to zero-pad the volumes for reconstruction purposes (the final reconstructed subvolumes will be cropped back to the original size though). |
| --savevols |
None |
This option will save the reconstructed volumes at each iteration. |
| --outxsize |
int |
Clip the output volume in x to this size. The default size is the nx size of the input images. |
| --outysize |
int |
Clip the output volume in y to this size. The default size is the ny size of the input images. |
| --outzsize |
int |
Clip the output volume in z to this size. The default size is the nx size of the input images. |
| --mask |
str |
Default=None. Masking processor (see e2help.py --verbose=10) applied to the images to aid alignment. Default=None. |
| --preprocess |
str |
Default=None. Any processor (see e2help.py --verbose=10) applied to the images to aid alignment. |
| --lowpass |
str |
Default=None. A lowpass filtering processor (see e2help.py --verbose=10) applied to each volume prior to reprojection generation.. |
| --highpass |
str |
Default=None. A highpass filtering processor (see e2help.py --verbose=10) applied to each volume prior to reprojection generation. |
| --threshold |
str |
Default=None. A threshold processor (see e2help.py --verbose=10) applied to each volume prior to reprojection generation. |
| --saveali |
None |
Default=False. If set, will save the recentered subtiltseries after each iteration. |