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pipeline:window:e2boxer [2018/02/09 16:34] moriya created |
pipeline:window:e2boxer [2019/04/02 09:21] (current) lusnig |
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e2boxer exists in non-MPI version. | e2boxer exists in non-MPI version. | ||
- | \\ __1. First Step__: The command to start e2boxer' | + | \\ __Step 1__: Use this command to start e2boxer' |
e2boxer.py CorrectedSums/ | e2boxer.py CorrectedSums/ | ||
- | \\ __2. Second Step__: After user finished picking, run this command line to export .box files. | + | \\ __Step 2__: After user finished picking, run this command line to export .box files. |
e2boxer.py CorrectedSums/ | e2boxer.py CorrectedSums/ | ||
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===== Input ===== | ===== Input ===== | ||
=== Main Parameters === | === Main Parameters === | ||
- | ; input_micrograph_list : Input micrograph list: Wild cards (e.g. *) can be used to specify a list of micrographs. Not recommended if the number is very large. (default required string) | + | ; input_micrograph_list : Input micrograph list: Wild cards (e.g. *) can be used to specify a list of micrographs. Not recommended if their number is very large. (default required string) |
; %%--%%apix : Pixel size [A]: Angstroms per pixel for all images. (default -1) | ; %%--%%apix : Pixel size [A]: Angstroms per pixel for all images. (default -1) | ||
; %%--%%boxsize : Box size [Pixels]: Box size in pixels. (default -1) | ; %%--%%boxsize : Box size [Pixels]: Box size in pixels. (default -1) | ||
; %%--%%ptclsize : Particle diameter [Pixels]: Longest axis of particle in pixels (diameter, not radius). (default -1) | ; %%--%%ptclsize : Particle diameter [Pixels]: Longest axis of particle in pixels (diameter, not radius). (default -1) | ||
- | ; %%--%%invert : Invert input contrast: | + | ; %%--%%invert : Invert input contrast: |
; %%--%%no_ctf : Disable CTF estimation: Disable CTF estimation. (default False) | ; %%--%%no_ctf : Disable CTF estimation: Disable CTF estimation. (default False) | ||
; %%--%%gui : Interactive GUI mode: Use interactive GUI mode. (default False) | ; %%--%%gui : Interactive GUI mode: Use interactive GUI mode. (default False) | ||
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\\ | \\ | ||
=== Advanced Parameters === | === Advanced Parameters === | ||
- | ; %%--%%allmicrographs : Include all micrographs in a directory: Add all images from micrographs folder. (default False) | ||
; %%--%%unboxedonly : Include only unboxed micrographs: | ; %%--%%unboxedonly : Include only unboxed micrographs: | ||
; %%--%%write_ptcls : Save selected particle: Extract selected particles from micrographs and write to disk. (default False) | ; %%--%%write_ptcls : Save selected particle: Extract selected particles from micrographs and write to disk. (default False) | ||
- | ; %%--%%suffix : Micrograph suffix: Suffix of the micrographs used for particle picking (i.e. suffix=goodali will use micrographs end with _goodali.hdf). It is only useful when --allmicrographs option is True. (default none) | + | |
+ | | ||
; %%--%%voltage : Microscope voltage [kV]: The acceleration voltage of microscope used for imaging. (default -1) | ; %%--%%voltage : Microscope voltage [kV]: The acceleration voltage of microscope used for imaging. (default -1) | ||
; %%--%%cs : Microscope spherical aberration (Cs) [mm]: The spherical aberration (Cs) of microscope used for imaging. (default -1) | ; %%--%%cs : Microscope spherical aberration (Cs) [mm]: The spherical aberration (Cs) of microscope used for imaging. (default -1) | ||
; %%--%%ac : Amplitude contrast [%]: The typical amplitude contrast is in the range of 7% - 14%. The value mainly depends on the thickness of the ice embedding the particles. (default 10.0) | ; %%--%%ac : Amplitude contrast [%]: The typical amplitude contrast is in the range of 7% - 14%. The value mainly depends on the thickness of the ice embedding the particles. (default 10.0) | ||
; %%--%%autopick : Perform automatic particle picking: Provide mode and parameter string (eg - auto_local: | ; %%--%%autopick : Perform automatic particle picking: Provide mode and parameter string (eg - auto_local: | ||
- | ; %%--%%threads : Number of threads: Number of threads to run in parallel on a single computer, when multi-computer parallelism isn't useful. (default 4) | + | ; %%--%%threads : Number of threads: Number of threads to run in parallel on a single computer. (default 4) |
; %%--%%ppid : Parent process PID: Set the PID of the parent process, used for cross platform PPID. (default -1) | ; %%--%%ppid : Parent process PID: Set the PID of the parent process, used for cross platform PPID. (default -1) | ||
; %%--%%verbose : Use verbose mode: Specify verbose level [0-9]. Higner number means higher level of verboseness. (default 0) | ; %%--%%verbose : Use verbose mode: Specify verbose level [0-9]. Higner number means higher level of verboseness. (default 0) | ||
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==== Reference ==== | ==== Reference ==== | ||
+ | |||
+ | \\ | ||
+ | ==== Developer Notes ==== | ||
\\ | \\ | ||
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\\ | \\ | ||
==== See also ==== | ==== See also ==== | ||
+ | [[http:// | ||
\\ | \\ |