e2make3dpar

usage: e2make3dpar.py [options]
	Reconstructs 3D volumes using a set of 2D images. Euler angles are extracted from the 2D image headers and symmetry is imposed.
	This is an optimized version with fewer options than e2make3d, but can run in parallel using threads, and has a number of other changes.

	A simple example of usage is:

	e2make3d.py --input=classes.img --sym=c3 --output=recon.mrc --pad=128

	Because there are several default settings, this is more or less equivalent to:

	e2make3d.py --input=classes.img --sym=c3 --output=recon.mrc --pad=128 --keep=1 --recon=fourier --iter=3

	Because the padding is always done using zeroes it is best if your data (or preferably
	the edge pixels of your data) have mean zero. If you are unsure whether your data are
	appropriately normalized you can add the --preprocess flag

	e2make3d.py --input=classes.img --sym=c3 --output=recon.mrc --pad=128 --preprocess=normalize.edgemean

	You can add as many --preprocess arguments as you like, which are applied in
	the order in which they are specified, before padding occurs.

Option	Type	Description
--output	None	Output reconstructed volume file name.
--input	None	The input projections. Project should usually have the xform.projection header attribute, which is used for slice insertion
--input_model	None	If the class-averages have the model_id parameter (produced by e2refinemulti.py), this will use only class-averages with the specified model_id for the reconstruction.
--tlt	str	An imod tlt file containing alignment angles. If specified slices will be inserted using these angles in the IMOD convention
--sym	None	Set the symmetry; if no value is given then the model is assumed to have no symmetry.\nChoices are: i, c, d, tet, icos, or oct.
--fillangle	float	An angular range used for both alt & az over which the projection should be averaged. Generally the angular step used when making projections.
--pad	str	Will zero-pad images to the specifed size (x,y) or (x,x) prior to reconstruction. If not specified or 0 no padding occurs. If a negative value is specified automatic padding is performed.
--padvol	str	Defines the dimensions (x,y,z) or (x,x,x) of the reconstructed volume. If ommitted, implied value based on padded 2D images is used.
--outsize	str	Defines the dimensions (x,y,z) or (x,x,x) of the final volume written to disk, if ommitted, size will be based on unpadded input size
--compressbits	int	Bits to keep when writing volumes with compression. 0->lossless floating point. Default 10 (3 significant figures)
--savenorm	str	If set, will save the normalization volume showing Fourier space filling to the specified file
--keep	float	The fraction of slices to keep, based on quality scores (1.0 = use all slices). See keepsig.
--keepsig	None	If set, keep will be interpreted as a standard deviation coefficient instead of as a percentage.
--keepabs	None	If set, keep will refer to the absolute quality of the class-average, not a local quality relative to other similar sized classes.
--altedgemask	None	If set, assumes tomographic data with a thin specimen, and masks out the +-X edges based on the alt Euler angle.
--no_wt	None	This argument turns automatic weighting off causing all images to be weighted by 1. If this argument is not specified images inserted into the reconstructed volume are weighted by the number of particles that contributed to them (i.e. as in class averages), which is extracted from the image header (as the ptcl_repr attribute).
--sqrt_wt	None	Normally class-averages are weighted into the reconstruction based on the number of particles in the average. This option causes the sqrt of the number of particles to be used instead.
--iterative	None	Uses iterative interpolation in Fourier space instead of single step gridding or interpolation. --mode and --usessnr are ignored with this option.
--itermask	str	Used in iterative mode to define a mask to apply between iterations. The resulting reconstruction won't be masked per-se, but will be biased towards lower densities outside the mask.
--usessnr	None	Makes use of the class_ssnr header data to weight each slice during insertion, instead of the default behavior of just using the number of particles in the average as a global weight.
--mode	str	Fourier reconstruction 'mode' to use. The default should not normally be changed. default='gauss_var'
--noradcor	None	Normally a radial correction will be applied based on the --mode used. This option disables that correction.
--seedmap	str	If specified this volume will be used as a starting point for the reconstruction, filling any missing values in Fourier space. experimental.
--seedweight	float	If seedmap specified, this is how strongly the seedmap will bias existing values. 1 is default, and is equivalent to a one particle weight.
--seedweightmap	str	Specify a full map of weights for the seed. This must be in the same format as the --savenorm output map.
--verbose, -v	int	verbose level [0-9], higher number means higher level of verboseness
--threads	int	Number of threads to run in parallel on a single computer. This is the only parallelism supported by e2make3dpar
--preprocess	str	preprocessor to be applied to the projections prior to 3D insertion. There can be more than one preprocessor and they are applied in the order in which they are specifed. Applied before padding occurs. See e2help.py processors for a complete list of available processors.
--setsf	str	Force the structure factor to match a 'known' curve prior to postprocessing (<filename>, auto or none). default=none
--postprocess	str	postprocessor to be applied to the 3D volume once the reconstruction is completed. There can be more than one postprocessor, and they are applied in the order in which they are specified. See e2help.py processors for a complete list of available processors.
--apix	float	A/pix value for output, overrides automatic values
--useseedasref	None	use seed map as reference to weight the particles.
--parallel	str	Thread/mpi parallelism to use
--ppid	int	Set the PID of the parent process, used for cross platform PPID