== e2refine_easy ==
        This is the primary single particle refinement program in EMAN2.1+. It replaces earlier programs such as e2refine.py
and e2refine_evenodd.py. Major features of this program:

 * While a range of command-line options still exist. You should not normally specify more than a few basic requirements. The rest will be auto-selected for you.
 * This program will split your data in half and automatically refine the halves independently to produce a gold standard resolution curve for every step in the refinement.
 * An HTML report file is generated as this program runs (in report/index.html). It is updated on-the-fly and is the best way to monitor the progress of a running job.
 * The gold standard FSC also permits us to automatically filter the structure at each refinement step. The resolution you specify is a target, NOT the filter resolution.
 * Many of the 'advanced' options are hidden in the e2projectmanager.py GUI, because most users should never need to specify them.
 * When continuing a successful refinement, trying to push resolution, etc., using 'startfrom' 

|| ||input||string||The name of the image file containing the particle data||
|| ||model||string||The map to use as a starting point for refinement||
OR
|| ||startfrom||string||Path to an existing refine_xx directory to continue refining from. Alternative to --input and --model.||

Standard Options:
||Short||Name||Type||Description||
|| ||targetres||float||Target resolution in A of this refinement run. Usually works best in at least two steps (low/medium resolution, then final resolution) when starting with a poor starting model. Usually 3-4 iterations is sufficient.||
|| ||speed||int||(1-7) Balances speed vs precision. Larger values sacrifice a bit of potential resolution for significant speed increases. 1 may yield slightly better results but come with a significant performance penalty. default=5||
|| ||sym||bool||Specify symmetry - choices are: c<n>, d<n>, tet, oct, icos.||
|| ||breaksym||bool||If selected, reconstruction will be asymmetric with sym= specifying a known pseudosymmetry, not an imposed symmetry.||
|| ||iter||int||The total number of refinement iterations to perform. Default=auto||
|| ||mass||float||The ~mass of the particle in kilodaltons, used to run normalize.bymass. Due to resolution effects, not always the true mass.||
|| ||apix||float||The angstrom per pixel of the input particles. This argument is required if you specify the --mass argument. If unspecified (set to 0), the convergence plot is generated using either the project apix, or if not an apix of 1.||
|| ||classkeep||float||The fraction of particles to keep in each class, based on the similarity score. (default=0.9 -> 90%%)||
|| ||classautomask||bool||This will apply an automask to the class-average during iterative alignment for better accuracy. The final class averages are unmasked.||
|| ||prethreshold||bool||Applies a threshold to the volume just before generating projections. A sort of aggressive solvent flattening for the reference.||
|| ||m3dkeep||float||The fraction of slices to keep in e2make3d.py. Default=0.8 -> 80%%||
|| ||m3dpostprocess||string||Default=none. An arbitrary post-processor to run after all other automatic processing. Maps are autofiltered, so a low-pass filter should not normally be used here.||
||-P||parallel||string||Run in parallel, specify type:<option>=<value>:<option>=<value>. See http://blake.bcm.edu/emanwiki/EMAN2/Parallel||
|| ||threads||int||Number of threads to run in parallel on a single computer when multi-computer parallelism isn't useful||

Complete Options, including advanced options:
||Short||Name||Type||Description||
|| ||input||string||Image stack containing phase-flipped particles used for alignment||
|| ||inputavg||string||Optional file containing alternate version of the particles to use for reconstruction after alignment||
|| ||model||string||The map to use as a starting point for refinement||
|| ||startfrom||string||Path to an existing refine_xx directory to continue refining from. Alternative to --input and --model.||
|| ||targetres||float||Target resolution in A of this refinement run. Usually works best in at least two steps (low/medium resolution, then final resolution) when starting with a poor starting model. Usually 3-4 iterations is sufficient.||
|| ||speed||int||(1-7) Balances speed vs precision. Larger values sacrifice a bit of potential resolution for significant speed increases. Set to 1 when really pushing resolution. Set to 7 for initial refinements. default=5||
|| ||sym||bool||Specify symmetry - choices are: c<n>, d<n>, tet, oct, icos.||
|| ||breaksym||bool||If selected, reconstruction will be asymmetric with sym= specifying a known pseudosymmetry, not an imposed symmetry.||
|| ||tophat||bool||Instead of imposing a final Wiener filter, use a tophat filter (similar to Relion). Sharper features, but may exaggerate.||
|| ||treeclassify||bool||Classify using a binary tree.||
|| ||m3dold||bool||Use the traditional e2make3d program instead of the new e2make3dpar program||
|| ||iter||int||The total number of refinement iterations to perform. Default=auto||
|| ||mass||float||The ~mass of the particle in kilodaltons, used to run normalize.bymass. Due to resolution effects, not always the true mass.||
|| ||apix||float||The angstrom per pixel of the input particles. Normally set to 0, which will read the value from the header of the input file||
|| ||sep||int||The number of classes each particle can contribute towards (normally 1). Increasing will improve SNR, but produce rotational blurring.||
|| ||classkeep||float||The fraction of particles to keep in each class, based on the similarity score. (default=0.9 -> 90%%)||
|| ||classautomask||bool||This will apply an automask to the class-average during iterative alignment for better accuracy. The final class averages are unmasked.||
|| ||prethreshold||bool||Applies a threshold to the volume just before generating projections. A sort of aggressive solvent flattening for the reference.||
|| ||eulerrefine||bool||Refines Euler angles of class-averages before reconstruction||
|| ||m3dkeep||float||The fraction of slices to keep in e2make3d.py. Default=0.8 -> 80%%||
|| ||m3dpostprocess||string||Default=none. An arbitrary post-processor to run after all other automatic processing. Maps are autofiltered, so a low-pass filter should not normally be used here.||
||-P||parallel||string||Run in parallel, specify type:<option>=<value>:<option>=<value>. See http://blake.bcm.edu/emanwiki/EMAN2/Parallel||
|| ||threads||int||Number of threads to run in parallel on a single computer when multi-computer parallelism isn't useful||
|| ||path||string||The name of a directory where results are placed. Default = create new refine_xx||
||-v||verbose||int||verbose level [0-9], higner number means higher level of verboseness||
|| ||usefilt||string||Specify a particle data file that has been low pass or Wiener filtered. Has a one to one correspondence with your particle data. If specified will be used in projection matching routines, and elsewhere.||
|| ||automaskexpand||int||Default=boxsize/20. Specify number of voxels to expand mask before soft edge. Use this if low density peripheral features are cut off by the mask.||
|| ||automask3d||string||Default=auto. Specify as a processor, eg - mask.auto3d:threshold=1.1:radius=30:nshells=5:nshellsgauss=5.||
|| ||automask3d2||string||Default=none. If specified, this mask will be multiplied by the result of the first mask, eg - using mask.soft to mask out the center of a virus.||
|| ||projector||bool||Default=standard. Projector to use with parameters.||
|| ||orientgen||string||Default=auto. Orientation generator for projections, eg - eman:delta=5.0:inc_mirror=0:perturb=1||
|| ||simalign||string||Default=auto. The name of an 'aligner' to use prior to comparing the images||
|| ||simaligncmp||string||Default=auto. Name of the aligner along with its construction arguments||
|| ||simralign||string||Default=auto. The name and parameters of the second stage aligner which refines the results of the first alignment||
|| ||simraligncmp||string||Default=auto. The name and parameters of the comparitor used by the second stage aligner.||
|| ||simcmp||string||Default=auto. The name of a 'cmp' to be used in comparing the aligned images||
|| ||simmask||string||Default=auto. A file containing a single 0/1 image to apply as a mask before comparison but after alignment||
|| ||shrink||int||Default=auto. Optionally shrink the input particles by an integer amount prior to computing similarity scores. For speed purposes. 0 -> no shrinking||
|| ||shrinks1||int||The level of shrinking to apply in the first stage of the two-stage classification process. Default=0 (autoselect)||
|| ||prefilt||bool||Default=auto. Filter each reference (c) to match the power spectrum of each particle (r) before alignment and comparison. Applies both to classification and class-averaging.||
|| ||cmpdiff||bool||Used only in binary tree classification. Use a mask that focus on the difference of two children.||
|| ||treeincomplete||int||Used only in binary tree classification. Incompleteness of the tree on each level.Default=0||
|| ||classkeepsig||bool||Change the keep ('--keep') criterion from fraction-based to sigma-based.||
|| ||classiter||int||Default=auto. The number of iterations to perform.||
|| ||classalign||string||Default=auto. If doing more than one iteration, this is the name and parameters of the 'aligner' used to align particles to the previous class average.||
|| ||classaligncmp||string||Default=auto. This is the name and parameters of the comparitor used by the fist stage aligner.||
|| ||classralign||string||Default=auto. The second stage aligner which refines the results of the first alignment in class averaging.||
|| ||classraligncmp||string||Default=auto. The comparitor used by the second stage aligner in class averageing.||
|| ||classaverager||string||Default=auto. The averager used to generate the class averages. Default is auto.||
|| ||classcmp||string||Default=auto. The name and parameters of the comparitor used to generate similarity scores, when class averaging.||
|| ||classnormproc||string||Default=auto. Normalization applied during class averaging||
|| ||classrefsf||bool||Use the setsfref option in class averaging. This matches the filtration of the class-averages to the projections for easier comparison. Disabled when ampcorrect=flatten is used.||
|| ||pad||int||Default=auto. To reduce Fourier artifacts, the model is typically padded by ~25 percent - only applies to Fourier reconstruction||
|| ||recon||bool||Default=auto. Reconstructor to use see e2help.py reconstructors -v||
|| ||m3dkeepsig||bool||Default=auto. The standard deviation alternative to the --m3dkeep argument||
|| ||m3dsetsf||string||Default=auto. Name of a file containing a structure factor to apply after refinement||
|| ||m3dpreprocess||string||Default=auto. Normalization processor applied before 3D reconstruction||
|| ||ampcorrect||bool||Will perform amplitude correction via the specified method.  'flatten' requires a target resolution better than 8 angstroms (experimental). 'none' will disable amplitude correction (experimental).||
|| ||classweight||bool||Alter the weight of each class in the reconstruction (experimental).||
|| ||sqrtnorm||bool||If set, the sqrt of the number of particles in each class will be used to weight the direct fourier inversion.||
|| ||lowmem||bool||Default=auto. Make limited use of memory when possible - useful on lower end machines||
|| ||ppid||int||Set the PID of the parent process, used for cross platform PPID||

To run this program, you would normally specify only the following options:
Use these 2 when starting a new "gold standard" refinement from scratch:
  --input=<lst file referencing phase-flipped particles in HDF format>
  --model=<starting map to seed refinement>
Use this, when you have already achieved sufficient resolution to validate the gold-standard, and you are trying to improve resolution/quality:
  --startfrom=<path to existing refine_xx directory to continue from>

Then a subset of these:
  --targetres=<in A>     Resolution to target in Angstroms in this refinement run. Do not be overoptimistic !
                         Generally begin with something conservative like 25, then use --startfrom and reduce
                         to ~12, only after that try for high (3-8 A). Data permitting, of course. Low resolution
                         attempts will run MUCH faster due to more efficient parameters.
  --speed=<1-7>          Default=5. Larger values will run faster, with a coarser angular step. Smaller values will
                         sample the angular step more finely than stric0tly required and increase sep=. A larger value
                         is good for early refinement. A smaller value will push "gold standard" resolution towards its
                         limit.
  --sym=<symmetry>       Symmetry to enforce during refinement (Cn, Dn, icos, oct, cub).
                         Default=c1 (no symmetry)
  --mass=<in kDa>        Putative mass of object in kDa, but as desired volume varies with resolution
                         actual number may vary by as much a ~2x from the true value. The goal is to
                         have a good isosurface in the final map with a threshold of 1.0.
  --parallel=<par spec>  While not strictly required, without this option the refinement will run on a single CPU
                         and you will likely wait a very long time. To use more than one core on a single computer,
                         just say thread:N (eg - thread:4). For other options, like MPI, see:
                         http://blake.bcm.edu/emanwiki/EMAN2/Parallel for details.
  --threads=<ncpu>       For some algorithms, processing in parallel over the network (MPI) works poorly.
                         Running on multiple processors on a single machine may still be worthwhile. If you specify this
                         option, in specific cases it will replace your specified --parallel option. Specify
                         the number of cores that can be used on a single machine. 

Optional:
  --apix=<A/pix>         The value will normally come from the particle data if present. You can override with this.

  --sep=<classes/ptcl>   each particle will be put into N classes. Improves contrast at cost of rotational blur.

  --classkeep=<frac>     fraction of particles to use in final average. Default 90%. Should be >50%

  --m3dkeep=<frac>       fraction of class-averages to use in 3-D map. Default=auto

  --classautomask        applies an automask when aligning particles for improved alignment

  --m3dpostprocess       <name>:<parm>=<value>:...  An arbitrary processor
                         (e2help.py processors -v2) to apply to the 3-D map after each
                         iteration. Default=none

  --path=<path>          Normally the new directory will be named automatically. If you prefer your own convention
                         you can override, but it may cause minor GUI problems if you break the standard naming
                         convention.

'''''Details about the refinement, and parameters which have automatically been selected are discussed in report/index.html'''''