== proc3d ==
'''Misc. 3d image processing'''

''proc3d  <input file>''

''proc3d <input file> <output file> [shrink=<div>] [scale=<factor>] [clip=<x,y,z[,xc,yc,zc]>] [fftclip=<x,y,z>] [rot=<alt,az,phi>] [rotspin=<n1,n2,n3,angle>] [trans=<dx,dy,dz>] [posttrans=<dx,dy,dz>] [center] [acfcen] [apix=<A/pix>] [origin=<x,y,z>] [lp=<filt r>] [hp=<filt r>] [tlp=<filt r>] [unhp=<filt r>] [filefilt=<file>] [rfilt=<type>[,<val1>[,<val2>[,<val3>]]]] [blfilt=<sigma spa,sigma den,iter,localwidth>] [normfilt=<thr,filt>] [axialfilt=<filt r>] [flip] [yflip] [sym=<c?,icos,etc>] [mask=<radius>] [imask=<radius>] [automask=<thr1>,<thr2>] [automask2=<rad>,<thr>,<N>] [maskfile=<file>] [maskfile2=<file>] [maskfile3=<file>] [maskval=<int>] [mask1file=<file>] [maskresample=<ref file>] [maskmerge=<mask file2>] [cut1stquad] [norm] [bin=<thresh>] [bin2] [mult=<constant>] [add=<constant>] [noise=<level>] [signoise=<sig mult>] [setsf=<SF file>] [calcsf=<output>] [icos5fTo3f] [icos3fTo5f] [icos5fTo2f] [icos2fTo5f] [icos5fhalfmap] [tophalf] [icos5fhalf2full] [vtk] [df3] [em] [amira] [amiralabel] [amirashort] [amirabyte] [rawiv] [xplor] [icos] [spider] [spidersingle] [imagic] [mrc8bit] [pif] [hdf] [png] [gwin=<radius>] [edgenorm]''

''proc3d <input 1> <input 2> [apix=<A/pix>] [fsc=<out>] [phase=<out>] [snr=<out>] [rfactor=<out>] [rms=<thresh>] [rdiv=<out>] [rdivf=<out>] [diffmap[=<~binary thr>]] [sum=<output>] [pha1amp2=<out>] [anim=<frames>] [animorph=<frames>,<vecfile>[,<start #>]]''

'''Parameters:'''
|| <input file> ||Get info/stats on this file||
|| <input file> ||Source file||
|| <output file> ||Destination file||
||[shrink=<div>]||Shrinks the image by an integral scaling factor, median filter||
||[scale=<factor>]||Rescales the image, generally used with clip= ||
||[clip=<x,y,z[,xc,yc,zc]>]||Make the output have this size, no scaling||
||[fftclip=<x,y,z>]||Make the output have this size, rescaling by padding FFT||
||[rot=<alt,az,phi>]||Rotate the volume, angles in degrees||
||[rotspin=<n1,n2,n3,angle>]||Rotate the volume around axis (n1,n2,n3) by angle degrees||
||[trans=<dx,dy,dz>]||Translate the volume, before the rotation||
||[posttrans=<dx,dy,dz>]||Translate the volume, after the rotation||
||[center]||Centers volume using center of mass||
||[acfcen]||Centers volume using cross correlation with mirrored model||
||[apix=<A/pix>]||Specify the Angstr/pixel for S scaling||
||[origin=<x,y,z>]||Set the coordinates for the pixel (0,0,0)||
||[lp=<filt r>]||Gaussian lowpass filter, r in angstroms if apix defined, pixels if undef||
||[hp=<filt r>]||Arctan highpass filter||
||[tlp=<filt r>]||Gaussian/artan mix lowpass||
||[unhp=<filt r>]||Undoes the hp= filter||
||[filefilt=<file>]||Applies a filter defined by an x/y text file||
||[rfilt=<type>[,<val1>[,<val2>[,<val3>]]]]||Apply one of a variety of real-space filters||
||[blfilt=<sigma spa,sigma den,iter,localwidth>]||Apply bilateral filtering||
||[normfilt=<thr,filt>]||This filter attempts to perform a 'local normalization' so low density and high density features will be on a more even playing field in an isosurface display. Thr is an isosurface threshold at which all desired features are visible, filt is a normalization size similar to an lp= value||
||[axialfilt=<filt r>]||This filter applies a correction for cases where reconstructions with many 'side' views have produced an asymmetric resolution. Specify the gaussian resolution in the z direction.||
||[flip]||Mirrors the object across the x-y plane||
||[yflip]||Mirrors the object across the x-z plane||
||[sym=<c?,icos,etc>]||Applies the specified symmetry to the map||
||[mask=<radius>]||Applies a circular mask at the given radius ||
||[imask=<radius>]||Applies an inside mask at the given radius||
||[automask=<thr1>,<thr2>]||Tries to mask out only interesting density||
||[automask2=<rad>,<thr>,<N>]||Same goal as automask||
||[maskfile=<file>]||Multiplies the input by the specified file using pixel indices(must be same size)||
||[maskfile2=<file>]||Multiplies the input by the specified file using pixel coordinates instead of pixel indices (can be different size) and use the original cube||
||[maskfile3=<file>]||Multiplies the input by the specified file using pixel coordinates instead of pixel indices (can be different size) and use the smaller cube of the two||
||[maskval=<int>]||Value to be used in a multi-valued masks||
||[mask1file=<file>]||This will take a file containing a set of masks and apply the first mask to the image||
||[maskresample=<ref file>]||Resample the input mask file to use the <ref file> apix, origin and size	||
||[maskmerge=<mask file2>]||Merge the second mask file to the first mask	||
||[cut1stquad]||Cut the first quad frin the map||
||[norm]||Normalizes the output, mean->0 sigma->1||
||[bin=<thresh>]||use the threshold value to turn the 3D map into a binary map||
||[bin2]||Turn any non-zero values into 1 to create a binary map||
||[mult=<constant>]||Scales the densities in the output||
||[add=<constant>]||Adds a constant to the densities||
||[noise=<level>]||Adds flatband noise at specified absolute level||
||[signoise=<sig mult>]||Same, but level in terms of sigma||
||[setsf=<SF file>]||Sets the structure factor based on a 1D x/y text file, must specify apix||
||[calcsf=<output>]||This will calculate a radial structure factor for the current 3D model and write it to the specified output file, must specify apix.||
||[icos5fTo3f]||Rotate the map from icos 5 fold view to 3 fold view||
||[icos3fTo5f]||Rotate the map from icos 3 fold view to 5 fold view||
||[icos5fTo2f]||Rotate the map from icos 5 fold view to 2 fold view||
||[icos2fTo5f]||Rotate the map from icos 2 fold view to 5 fold view||
||[icos5fhalfmap]||The input is the icos 5f top half map generated by the "tophalf" option||
||[tophalf]||The output only keeps the top half map to save some memory||
||[icos5fhalf2full]||Generate full map from the icos5f half map||
||[vtk]||Output should be in VTK format||
||[df3]||Output in df3 format (POVRAY)||
||[em]||Output should be in EM format.||
||[amira]||Output should be in AMIRA format, not MRC||
||[amiralabel]||Output should be in AMIRA labelField format||
||[amirashort]||Output should be in AMIRA short data type format||
||[amirabyte]||Output should be in AMIRA byte data type format||
||[rawiv]||Output should be in RawIV format, not MRC||
||[xplor]||Output should be in XPLOR format, not MRC||
||[icos]||Output should be in ICOS format, not MRC||
||[spider]||Output should be in Spider format, not MRC. Warning, this is a spider stackfile, and Spider may not be able to read stacks of 3D images. spidersingle is a better choice||
||[spidersingle]||Output should be in single-image Spider format, not MRC||
||[imagic]||Output is an IMAGIC file||
||[mrc8bit]||Output an 8 bit MRC image||
||[pif]||Output to a PIF (Purdue Image Format) file||
||[hdf]||Output to a HDF5 (Hierarchical Data Format) file||
||[png]||Output to a PNG (Portable Network Graphics) file||
||[gwin=<radius>]||Apply a Gaussian radial falloff, r is 1/e width||
||[edgenorm]||Normalize the image based on the mean value at the edge of the box||

'''Parameters:'''
|| <input 1> ||Input 1 to compare/process||
|| <input 2> ||Input 2 to compare/process||
||[apix=<A/pix>]||Specify the Angstr/pixel for S scaling||
||[fsc=<out>]||Fourier shell correlation||
||[phase=<out>]||mean phase difference (not residual!)||
||[snr=<out>]||Relative signal to noise ratio between 2 images.||
||[rfactor=<out>]||R factor between inputs||
||[rms=<thresh>]||RMS variation above threshold||
||[rdiv=<out>]||Radial plot of input 1/input 2||
||[rdivf=<out>]||Radial plot of input 1/input 2 in Fourier space||
||[diffmap[=<~binary thr>]]||Generates a difference map in "diffmap.mrc"||
||[sum=<output>]||Adds input files||
||[pha1amp2=<out>]||Makes a new image with the phases from image 1 and the amplitudes from image2||
||[anim=<frames>]||Generates linearly interpolated intermediates between two maps||
||[animorph=<frames>,<vecfile>[,<start #>]]||Generates a linear morphing of one map into another based on a vector file||

'''Usage:'''

''proc3d threed.5a.mrc''

''proc3d threed.1.mrc threed.1a.mrc unhp=1 lp=15''

''proc3d threed.1a.mrc threed.2a.mrc apix=4.67 fsc=corr12.dat''

'''Description'''
This program performs a variety of 3d image processing operations. Like all EMAN programs, it will automatically read any supported file format. It can be invoked in one of 3 ways. The first form simply provides statistical information on a single volume data set.

The second form will copy an input file to and output file after processing it in various ways. Most of the processing is explained in sufficient detail above, but there are a few notes:

 *  The scale operation does NOT resize the volume in voxels. Generally you want to specify both scale and clip.
 *  If apix is not specified, all filters are specified in pixels in Fourier space. If apix is specified, all filters are specified in Angstroms. ie - 'apix=4.5 lp=8' would filter the volume using a Gaussian in fourier space with a 1/e width of 1/8 reciprocal angstroms.
 *  If apix is specified, fsx, phase and rfactor will have their s-axis (1st column) in reciprocal angstroms. Otherwise it will be in Fourier pixels.
 *  The automask options are used to try to eliminate spurious noise outside the model. Automask2 is preferred. To use this, specify 3 numbers. First, the smallest radius from the center of the map that contacts some density of the 'good' part of the map. Second, A threshold density at which all of the undesirable density is disconnected from the desired mass. Finally, a number of 1-voxel 'shells' to include after the correct density has been located (this allows you to use threshold densities higher than the desired isosurface threshold density). The iterative shells will include a 'soft' Gaussian edge after 2 pixels. ie - if you add 8 shells, the density will decay in this region using a 1/2 width of 3 pixels starting at the 3rd pixel. If the number of shells is specified as a negative value, then the mask will have a sharp edge, and any hollow areas inside the mask will be filled in.
 *  To invert the density of a map, use 'mult=-1'.
 *  'phase=' calculates the mean phase difference between two maps, NOT the true phase residual (which is a very messy thing to calculate).
 *  The symmetries supported by 'sym=' are: Cn, Dn and icos. for C and D symmetries, the n-fold axis must be the z axis.
Realfilter options detailed in proc2d docs. 3D - specific filters:

 * 110: Iterative expansion of a binary mask, val1 = number of layers to expand, val2 = number of layers before starting Gaussian decay
 * 111: Iterative expansion of a multilevel mask file (see qsegment). Simultaneoulsy expands all levels and prevents overlap problems.