This shows you the differences between two versions of the page.
Both sides previous revision Previous revision Next revision | Previous revision | ||
pipeline:window:sxrewindow [2018/08/07 22:03] moriya |
pipeline:window:sxrewindow [2019/04/02 10:32] lusnig [See also] |
||
---|---|---|---|
Line 1: | Line 1: | ||
~~NOTOC~~ | ~~NOTOC~~ | ||
- | ===== sxrewindow | + | ===== sp_rewindow |
Particle Reextraction: | Particle Reextraction: | ||
Line 9: | Line 9: | ||
Usage in command line | Usage in command line | ||
- | | + | |
\\ | \\ | ||
===== Typical usage ===== | ===== Typical usage ===== | ||
- | sxrewindow | + | sp_rewindow |
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 and rebox files with a wild card (*). Use the wild card to indicate the place of variable part of the file names (e.g. serial number, time stamp, and etc). The path pattern must be enclosed by single quotes (') or double quotes ("). (Note: | + | \\ Specify path pattern of input micrographs and rebox files with a wild card (*).. The path pattern must be enclosed by single quotes (') or double quotes ("). (Note: |
- | mpirun | + | mpirun |
\\ You can also ignore per-particle CTF information stored in rebox files and use CTF information stored in the CTER partres.txt instead. | \\ You can also ignore per-particle CTF information stored in rebox files and use CTF information stored in the CTER partres.txt instead. | ||
- | 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 to input micrographs path pattern, rebox files path pattern, and output directry arguments, 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 to input micrographs path pattern, rebox files path pattern, and output directry arguments, 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 to input micrographs path pattern, rebox files path pattern, CTF paramters source, and output directry arguments, 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. Use single processor for this mode. | \\ In addition to input micrographs path pattern, rebox files path pattern, CTF paramters source, and output directry arguments, 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. Use single processor for this mode. | ||
- | | + | |
\\ For negative staining data, use --skip_invert. | \\ For negative staining data, use --skip_invert. | ||
- | mpirun | + | mpirun |
\\ **NOTE:** Please remember to adjust box_size also when setting mic_resample_ratio < 0.1. | \\ **NOTE:** Please remember to adjust box_size also when setting mic_resample_ratio < 0.1. | ||
Line 43: | Line 43: | ||
===== Input ===== | ===== Input ===== | ||
=== Main Parameters === | === Main Parameters === | ||
- | ; input_micrograph_pattern : Input micrograph path pattern: Specify path pattern of input micrographs with a wild card (*). Use the wild card to indicate the place of variable part of the file names (e.g. serial number, time stamp, and etc). 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: |
- | ; input_rebox_pattern : Input rebox path pattern: Specify path pattern of input rebox files with a wild card (*). Use the wild card to indicate the place of variable part of the file names (e.g. serial number, time stamp, and etc). The path pattern must be enclosed by single quotes (') or double quotes ("). (Note: | + | ; input_rebox_pattern : Input rebox path pattern: Specify path pattern of input rebox files 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. This directory will be created automatically and it must not exist previously. (default required string) | + | ; output_directory : Output directory: The results will be written here. It cannot |
; %%--%%selection_list : Micrograph selection file: Specify a name of micrograph selection list text file for Selected Micrographs Mode. The file extension must be ' | ; %%--%%selection_list : Micrograph selection file: Specify a name of micrograph selection list text file for Selected Micrographs Mode. The file extension must be ' | ||
Line 54: | Line 54: | ||
=== Advanced Parameters === | === Advanced Parameters === | ||
; %%--%%mic_resample_ratio : Image size reduction factor (<1): Use a value between 0.0 and 1.0 (excluding 0.0). The new pixel size will be automatically recalculated and stored in CTF paramers when mic_resample_ratio < 1.0 is used. (default 1.0) | ; %%--%%mic_resample_ratio : Image size reduction factor (<1): Use a value between 0.0 and 1.0 (excluding 0.0). The new pixel size will be automatically recalculated and stored in CTF paramers when mic_resample_ratio < 1.0 is used. (default 1.0) | ||
- | ; %%--%%swap_ctf_params : Swap CTF parameters: Swaps CTF parameters by setting the CTF parameters in the specified CTER partres file while ignoring the CTF parameters in the input rebox parameters file. Typically, specify the file produced by sxcter | + | ; %%--%%swap_ctf_params : Swap CTF parameters: Swaps CTF parameters by setting the CTF parameters in the specified CTER partres file while ignoring the CTF parameters in the input rebox parameters file. Typically, specify the file produced by sp_cter |
; %%--%%check_consistency : Check consistency of dataset: Create a text file containing the list of Micrograph ID entries might have inconsitency among the provided dataset. (i.e. mic_consistency_check_info_TIMESTAMP.txt). (default False) | ; %%--%%check_consistency : Check consistency of dataset: Create a text file containing the list of Micrograph ID entries might have inconsitency among the provided dataset. (i.e. mic_consistency_check_info_TIMESTAMP.txt). (default False) | ||
\\ | \\ | ||
===== Output ===== | ===== Output ===== | ||
- | Inside the output directory, the program will write a local BDB stack image for each micrograph. The files are named micrograph name with " | + | Inside the output directory, the program will write a local bdb stack image for each micrograph. The files are named micrograph name with " |
\\ | \\ | ||
Line 87: | Line 87: | ||
\\ | \\ | ||
==== Files ==== | ==== Files ==== | ||
- | sparx/bin/sxrewindow.py | + | sparx/bin/sp_rewindow.py |
\\ | \\ | ||
==== See also ==== | ==== See also ==== | ||
- | [[pipeline: | + | [[pipeline: |
\\ | \\ |