e2spt_boxer_old

usage: 
	
	e2spt_boxer.py <tomogram> <options>.

	This program has two modalities: 

	1) bring up a Graphical User Inteface (GUI) to interactively find features in a tomogram, allowing to find multiple types of features kept as separate sets and to save metadata in the new EMAN2 tomogram framework (2017).
	For this, you would a command similar to:
		
		e2spt_boxer.py tomo.rec --inmemory.
	
	2) extract particles from a tomogram using a coordinates file WITHOUT opening the GUI. This is useful when re-exctracting particles from a tomogram, when extracting only a subset of particles, when extracting particles on a remote machine without needing the -X server, when extracting particles multiple times from tomograms reconstructed using diferent algorithms, parameters, or filters, or when the sampling size of the coordinates file does not match the sampling size of the raw tomogram. 
	In this case, you woukld run a command similar to:
	
		e2spt_boxer.py tomo_raw.rec --coords coords_bin4.txt --cshrink 4 --output ptcls_sirt12.hdf --path sptboxer_sirt12 --normproc normalize.edgemean --invert --boxsize 256 --bruteaverage

Option	Type	Description
--version	None	show program's version number and exit
--coords	str	Default=None. Used to extract particles without the GUI. Provide a coordinates file that contains the center coordinates of the subvolumes you want to extract from the command line (without bringing up the GUI).
--output	str	Default=None. Used to extract particles without the GUI. Requires --coords. If not specified, the suffix '_ptlcs' will be attached to the name of the input tomogram. Otherwise, specify here the name of the stack file where to write the extracted subvolumes.
--inmemory	None	Default=False. If on, this option will read the entire tomogram into memory. Much faster than reading 'from disk', but you must have enough RAM!
--invert	None	Default=False. If on, this option means you want the contrast to me inverted while boxing, AND for the extracted sub-volumes.\nRemember that EMAN2 MUST work with "white" protein. You can very easily figure out what the original color\nof the protein is in your data by looking at the gold fiducials or the edge of the carbon hole in your tomogram.\nIf they look black you MUST specify this option
--apix	float	apix
--bruteaverage	None	Default=False. If specified, this will generate an "as is" average of all the subvolumes (no alignment performed). This can be useful to see if, on average, particles correspond to the desired specimen and are reasonably centered.
--boxsize, -B	int	Default=0. Used to extract particles without the GUI. Requires --coords. Box size in pixels
--cshrink	int	Default=1 (not used; no scaling of --coords). Used to extract particles without the GUI. Requires --coords. Specifies the factor by which to multiply the coordinates in --coords, so that they can be at the same scale as the RAW tomogram (or whatever tomogram you intend for the particles to be extracted from).\nFor example, provide --cshrink=2 if the coordinates were determined in a binned-by-2 (shrunk-by-2) tomogram,\nbut you want to extract the subvolumes from a tomogram without binning/shrinking (which should be 2x larger).
--subset	int	Default=0 (not used). Used to extract particles without the GUI. Requires --coords. Specify how many subvolumes from --coords you want to extract; e.g, if you specify 10, the first 10 particles will be extracted.\n0 means "box them all" because it makes no sense to box none.
--normproc	str	Default=normalize. Used to extract particles without the GUI. Requires --coords. Normalization processor applied to particles before extraction. Use --normproc=normalize.edgemean if the particles have a clear solvent background (i.e., they're not part of a larger complex or embeded in a membrane.
--path	str	Default=none (not used). Used to extract particles without the GUI. Requires --coords. Name of directory to save data to.
--verbose, -v	int	verbose level [0-9], higner number means higher level of verboseness
--ppid	int	Set the PID of the parent process, used for cross platform PPID