| --version |
None |
show program's version number and exit |
| --anglesindxinfilename |
int |
Default=None. The filename of the images will be split at any occurence of the following delimiters: '_', '-', '+', '[' , ']' , ',' , ' ' (the two last ones are a comma and a blank space). Provide the index (position) of the angle in the split filename. For example, if the filename of an image is "my_specimen-oct-10-2015_-50_deg-from_k2 camera.mrc", it will be split into ['my','specimen','oct','10','2015','','50','deg','from','k2','camera','mrc']. The angle '-50', is at position 6 (starting from 0). Therefore, you would provide --anglesindxinfilename=6, assuming all images to be stacked/processed are similarly named. No worries about the minus sign disappearing. The program will look at whether there's a minus sign immediately preceeding the position where the angle info is. |
| --apix |
float |
True apix of images to be written on final stack. |
| --bidirectional |
None |
This will assume the first image is at 0 degrees and will stack images from --lowerend through 0, and then will stack the rest from 0+tiltstep throgh --upperend. If --negativetiltseries is supplied, images will be stacked from --upperend through 0, then from 0-tiltstep through --lowerend. |
| --clip |
str |
Resize the 2-D images in the tilt series. If one number is provided, then x and y dimensions will be made the same. To specify both dimensions, supply two numbers, --clip=x,y. Clipping will be about the center of the image. |
| --exclude |
str |
Comma separated list of numbers corresponding to images to exclude. --unstack or --restack must be supplied. You can also exclude by ranges. For example: Recall that the FIRST image INDEX is 0. --exclude=1,5-7,10,12,15-19 will exclude images 1,5,6,7,10,12,15,16,17,18,19 |
| --highesttilt |
float |
Highest tilt angle. If not supplied, it will be assumed to be 1* --tiltrange. |
| --include |
str |
Comma separated list of numbers corresponding to images to include (all others will be excluded). --unstack or --restack must be supplied. Recall that the FIRST image INDEX is 0. --include=1,5-7,10,12,15-19 will include images 1,5,6,7,10,12,15,16,17,18,19 |
| --invert |
None |
"This will multiply the pixel values by -1. |
| --lowesttilt |
float |
Lowest tilt angle. If not supplied, it will be assumed to be -1* --tiltrange. |
| --mirroraxis |
str |
Options are x or y, and the mirrored copy of the 2-D images will be generated before being put into the tilt series. |
| --negativetiltseries |
None |
This indicates that the tilt series goes from -tiltrange to +tiltrange, or 0 to -tiltrange, then +tiltstep to +tiltrange if --bidirectional is specified. |
| --normalizeimod |
None |
Default=False. This will apply 'newstack -float 2' to the input stack. Requires IMOD. Does not apply to --unstack or --restack. |
| --outmode |
str |
All EMAN2 programs write images with 4-byte floating point values when possible by default. This allows specifying an alternate format when supported: float, int8, int16, int32, uint8, uint16, uint32. Values are rescaled to fill MIN-MAX range. |
| --path |
str |
Directory to store results in. The default is a numbered series of directories containing the prefix 'sptstacker'; for example, sptstacker_02 will be the directory by default if 'sptstacker_01' already exists. |
| --ppid |
int |
Set the PID of the parent process, used for cross platform PPID |
| --restack |
str |
.hdf, or 3D .st, .mrc, .ali, or .mrcs stack file to restack. This option can be used with --include or --exclude to unstack only specific images. Recall that the FIRST image INDEX is 0 (but unstacked image will be numbered from 1). --exclude=1,5-7,10,12,15-19 will exclude images 1,5,6,7,10,12,15,16,17,18,19 |
| --replacestring |
str |
default=None. Comma separated strings to replace in the input filenames with an underscore. For example, if --stem2stack=data, and this triggers the program to find images named 'data[1].mrc', 'data[2].mrc', etc., supplying --replacestring=[,] will first change the filename of the images to 'data_1_.mrc, data_2_.mrc, etc. |
| --shrink |
float |
Default=0.0 (not used). Shrinking factor to do Fourier cropping of the images in a titlseries; can be a fractional number (for example, 1.5) |
| --stackregardless |
None |
"Stack images found with the common string provided through --stem2stack, even if the number of images does not match the predicted number of tilt angles. |
| --stem2stack |
str |
String common to all the files to put into an .st stack, which is in .MRC format; for example, --stem2stack=.hdf will process all .hdf files in the current directory. If not specified, all valid EM imagefiles in the current directory will be put into an .st stack. |
| --tltfile |
str |
".tlt file IF unstacking an aligned tilt series with --unstack=<stackfile> or restacking a tiltseries with --restack=<stackfile> |
| --tiltrange |
float |
If provided, this will make --lowesttilt=-1*tiltrange and --highesttilt=tiltrange. If the range is asymmetric, supply --lowesttilt and --highesttilt directly. |
| --tiltstep |
float |
Step between tilts. Required if using --stem2stack. |
| --unstack |
str |
.hdf, or 3D .st, .mrc, .ali, or .mrcs stack file to unstack. This option can be used with --include or --exclude to unstack only specific images. Recall that the FIRST image INDEX is 0 (but unstacked image will be numbered from 1). --exclude=1,5-7,10,12,15-19 will exclude images 1,5,6,7,10,12,15,16,17,18,19 |
| --verbose, -v |
int |
verbose level [0-9], higher number means higher level of verboseness. |