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===== e2boxer =====
Particle Coordinates (NEW): Generate files containing particle coordinates for all input micrographs by picking particles manual and/or automatically.

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===== Usage =====

Usage in command line

  e2boxer.py  input_micrograph_list  --apix=PIXEL_SIZE  --boxsize=BOX_SIZE  --ptclsize=PARTICLE_DIAMETER  --invert  --no_ctf  --gui  --write_dbbox  --allmicrographs  --unboxedonly  --write_ptcls  --suffix=SUFFIX  --voltage=VOLTAGE  --cs=CS  --ac=AMP_CONTRAST  --autopick=MODE  --threads=THREADS  --ppid=PPID  --verbose=LEVEL

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===== Typical usage =====

e2boxer exists in non-MPI version.

\\ __Step 1__: Use this command to start e2boxer's GUI with a list of micrographs using the right settings.
  e2boxer.py CorrectedSums/corrsum_dose_filtered/*.mrc --apix=1.14 --boxsize=352 --invert --no_ctf --gui

\\ __Step 2__: After user finished picking, run this command line to export .box files.
  e2boxer.py CorrectedSums/corrsum_dose_filtered/*.mrc --apix=1.14 --boxsize=352 --invert --no_ctf --write_dbbox

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===== Input =====
=== Main Parameters ===
  ; 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)
  ; %%--%%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)
  ; %%--%%invert : Invert input contrast: Preferably, particles should be brigt on a dark background. (default False)
  ; %%--%%no_ctf : Disable CTF estimation: Disable CTF estimation. (default False)
  ; %%--%%gui : Interactive GUI mode: Use interactive GUI mode. (default False)
  ; %%--%%write_dbbox : Export EMAN1 box files: Export EMAN1 box files (.box extension). (default False)

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=== Advanced Parameters ===
  ; %%--%%unboxedonly : Include only unboxed micrographs: Only include image files without existing box locations. (default False)
  ; %%--%%write_ptcls : Save selected particle: Extract selected particles from micrographs and write to disk. (default False)
  ; %%--%%allmicrographs : Include all micrographs in a directory: Add all images from micrographs folder. (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): %%--%%allmicrographs==True
  ; %%--%%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)
  ; %%--%%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:threshold=5.5). (default none)
  ; %%--%%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)
  ; %%--%%verbose : Use verbose mode: Specify verbose level [0-9]. Higner number means higher level of verboseness. (default 0)

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===== Output =====

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===== Description =====

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==== Method ====

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==== Reference ====

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==== Developer Notes ====

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==== Author / Maintainer ====
EMAN2 Group

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==== Keywords ====
Category 1:: APPLICATIONS

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==== Files ====
programs/e2boxer.py

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==== See also ====
[[http://blake.bcm.edu/emanwiki/EMAN2/Programs/convnet_pickparticle|Particle Picking with Convolution Neural Network]]

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==== Maturity ====
Beta:: Under development

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==== Bugs ====