This shows you the differences between two versions of the page.
Both sides previous revision Previous revision | Next revision Both sides next revision | ||
pipeline:utilities:sxpipe_resample_micrographs [2018/08/22 11:35] fmerino |
pipeline:utilities:sxpipe_resample_micrographs [2019/04/02 09:17] lusnig |
||
---|---|---|---|
Line 1: | Line 1: | ||
~~NOTOC~~ | ~~NOTOC~~ | ||
- | ===== sxpipe | + | ===== sp_pipe |
Resample Micrographs: | Resample Micrographs: | ||
Line 9: | Line 9: | ||
Usage in command line | Usage in command line | ||
- | | + | |
\\ | \\ | ||
===== Typical usage ===== | ===== Typical usage ===== | ||
- | sxpipe | + | sp_pipe |
There are several modes to run the program: | There are several modes to run the program: | ||
\\ __1. All Micrographs Mode - Process all micrographs in a directory: | \\ __1. All Micrographs Mode - Process all micrographs in a directory: | ||
- | \\ Specify path pattern of input micrographs with a wild card (*).. The path pattern must be enclosed by single quotes (') or double quotes ("). (Note: | + | \\ Specify path pattern of input micrographs with a wild card (*).. The path pattern must be enclosed by single quotes (') or double quotes ("). (Note: |
- | mpirun | + | mpirun |
\\ __2. Selected Micrographs Mode - Process all micrographs in a selection list file:__ | \\ __2. Selected Micrographs Mode - Process all micrographs in a selection list file:__ | ||
\\ In addition input micrographs path pattern, resampling ratio, and output directry, specify a name of micrograph selection list text file using --selection_list option. In this mode, only micrographs in the selection list which matches the file name part of the pattern (ignoring the directory paths) will be processed. If a micrograph name in the selection list does not exists in the directory specified by the micrograph path pattern, processing of the micrograph will be skipped. | \\ In addition input micrographs path pattern, resampling ratio, and output directry, specify a name of micrograph selection list text file using --selection_list option. In this mode, only micrographs in the selection list which matches the file name part of the pattern (ignoring the directory paths) will be processed. If a micrograph name in the selection list does not exists in the directory specified by the micrograph path pattern, processing of the micrograph will be skipped. | ||
- | mpirun | + | mpirun |
\\ __3. Single Micrograph Mode - Process a single micrograph: | \\ __3. Single Micrograph Mode - Process a single micrograph: | ||
\\ In addition input micrographs path pattern, resampling ratio, and output directry, specify a single micrograph name using %%--%%selection_list option. In this mode, only the specified single micrograph will be processed. If this micrograph name does not matches the file name part of the pattern (ignoring the directory paths), the process will exit without processing it. If this micrograph name matches the file name part of the pattern but does not exists in the directory which specified by the micrograph path pattern, again the process will exit without processing it. | \\ In addition input micrographs path pattern, resampling ratio, and output directry, specify a single micrograph name using %%--%%selection_list option. In this mode, only the specified single micrograph will be processed. If this micrograph name does not matches the file name part of the pattern (ignoring the directory paths), the process will exit without processing it. If this micrograph name matches the file name part of the pattern but does not exists in the directory which specified by the micrograph path pattern, again the process will exit without processing it. | ||
- | | + | |
\\ | \\ | ||
===== Input ===== | ===== Input ===== | ||
=== Main Parameters === | === Main Parameters === | ||
- | ; input_micrograph_pattern : Input micrograph path pattern: Specify path pattern of input micrographs with a wild card (*).. The path pattern must be enclosed by single quotes (\') or double quotes (\"). (Note: | + | ; input_micrograph_pattern : Input micrograph path pattern: Specify path pattern of input micrographs with a wild card (*).. The path pattern must be enclosed by single quotes (\') or double quotes (\"). (Note: |
; output_directory : Output directory: The results will be written here. It cannot be an existing one. (default required string) | ; output_directory : Output directory: The results will be written here. It cannot be an existing one. (default required string) | ||
Line 68: | Line 68: | ||
\\ | \\ | ||
==== Files ==== | ==== Files ==== | ||
- | sparx/bin/sxpipe.py | + | sparx/bin/sp_pipe.py |
\\ | \\ | ||
==== See also ==== | ==== See also ==== | ||
- | [[pipeline: | + | [[pipeline: |
\\ | \\ | ||
Line 83: | Line 83: | ||
\\ | \\ | ||
+ |