= e2proc3d = Generic 3-D image processing program. The main tasks this program can be used for are: * Convert volumes from one format to another * Perform basic image processing operations such as filters, masks, normalization, etc. * Resize/rescale volumes * Compute FSC curves, structure factors, etc. || ||medianshrink||bool||Downsamples the volume by a factor of n by computing the local median|| || ||meanshrink||bool||Downsamples the volume by a factor of n by computing the local average|| || ||meanshrinkbig||bool||Downsamples the volume by a factor of n without reading the entire volume into RAM. The output file (after shrinking) must fit into RAM. If specified, this must be the ONLY option on the command line. Any other options will be ignored. Output data type will match input data type. Works only on single image files, not stack files.|| || ||meanshrinkbig||bool||Downsamples the volume by a factor of n without reading the entire volume into RAM. The output file (after shrinking) must fit into RAM. If specified, this must be the ONLY option on the command line. Any other options will be ignored. Output data type will match input data type. Works only on single image files, not stack files.|| || ||scale||bool||Rescales the image by 'n', generally used with clip option.|| || ||sym||bool||Symmetry to impose - choices are: c, d, h, tet, oct, icos|| || ||averager||bool||Averager used for --average and --sym options|| || ||clip||bool||Make the output have this size by padding/clipping. 1, 3 or 6 arguments. || || ||fftclip||bool||Make the output have this size, rescaling by padding FFT.|| || ||process||bool||apply a processor named 'processorname' with all its parameters/values.|| || ||apix||bool||A/pixel for S scaling|| || ||origin||bool||Set the coordinates for the pixel (0,0,0) for Chimera. THIS HAS NO IMPACT ON IMAGE PROCESSING !|| || ||mult||bool||Scales the densities by a fixed number in the output|| || ||multfile||bool||Multiplies the volume by another volume of identical size. This can be used to apply masks, etc.|| || ||matchto||bool||Match filtration of input volume to this specified volume.|| || ||outmode||bool||All EMAN2 programs write images with 4-byte floating point values when possible by default. This allows specifying an alternate format when supported (int8, int16, int32, uint8, uint16, uint32). Values are rescaled to fill MIN-MAX range.|| || ||outnorescale||bool||If specified, floating point values will not be rescaled when writing data as integers. Values outside of range are truncated.|| || ||mrc16bit||bool||(deprecated, use --outmode instead) output as 16 bit MRC file|| || ||mrc8bit||bool||(deprecated, use --outmode instead) output as 8 bit MRC file|| || ||add||bool||Adds a constant 'f' to the densities|| || ||addfile||bool||Adds the volume to another volume of identical size|| || ||calcfsc||bool||Calculate a FSC curve between two models. Output is a txt file. This option is the name of the second volume.|| || ||filtertable||bool||Applies a 2 column (S,amp) file as a filter in Fourier space, assumed 0 outside the defined range.|| || ||calcsf||bool||Calculate a radial structure factor. Must specify apix.|| || ||calcradial||bool||Calculate the radial density by shell. Output file becomes a text file. 0 - mean amp, 2 - min, 3 - max, 4 - sigma|| || ||setsf||bool||Set the radial structure factor. Must specify apix.|| || ||tophalf||bool||The output only keeps the top half map|| || ||inputto1||bool||All voxels in the input file are set to 1 after reading. This can be used with mask.* processors to produce a mask file of the correct size.|| || ||icos5fhalfmap||bool||The input is the icos 5f top half map generated by the 'tophalf' option|| || ||outtype||bool||Set output image format, mrc, imagic, hdf, etc|| || ||first||bool||the first image in the input to process [0 - n-1])|| || ||trans||bool||Translate map by dx,dy,dz || || ||resetxf||bool||Reset an existing transform matrix to the identity matrix|| || ||align||bool||Align input map to reference specified with --alignref. As with processors, a sequence of aligners is permitted|| || ||ralignzphi||string||Refine Z alignment within +-10 pixels and phi +-15 degrees (for C symmetries), specify name of alignment reference here not with --alignref|| || ||alignref||bool||Alignment reference volume. May only be specified once.|| || ||alignctod||string||Rotates a map already aligned for C symmetry so the best 2-fold is positioned for specified D symmetry. Does not impose specified symmetry.|| || ||rot||string||Rotate map. Specify az,alt,phi or convention:par=val:par=val:... eg - mrc:psi=22:theta=15:omega=7|| || ||icos5to2||bool||Rotate an icosahedral map from 5-fold on Z (EMAN standard) to 2-fold on Z (MRC standard) orientation|| || ||icos2to5||bool||Rotate an icosahedral map from 2-fold on Z (MRC standard) to 5-fold on Z (EMAN standard) orientation|| || ||last||bool||the last image in the input to process|| || ||swap||bool||Swap the byte order|| || ||average||bool||Computes the average of a stack of 3D volumes|| || ||append||bool||Append output image, i.e., do not write inplace.|| || ||ppid||int||Set the PID of the parent process, used for cross platform PPID|| || ||unstacking||bool||Process a stack of 3D images, then output a a series of numbered single image files|| || ||tomoprep||bool||Produces a special HDF file designed for rapid interactive tomography annotation. This option should be used alone.|| ||-v||verbose||bool||verbose level [0-9], higner number means higher level of verboseness|| || ||step||string||Specify ,. Processes only a subset of the input data. For example, 0,2 would process only the even numbered particles|| This program operates on single 3-D volume files, stacks of 3-D volume files, and EMAN2 BDB databases. It has many command-line options for specific tasks. The generic '--process' option is by far the most powerful, offering access to 180+ different image processing operations. For a list, type ''e2help.py processors''. For specific details on various options, use ''e2proc3d.py --help''. === Examples === convert SPIDER format test.spi to HDF format: {{{ e2proc3d.py test.spi test.hdf }}} extract a volume from a BDB database and convert to HDF format for visualization in Chimera {{{ e2proc3d.py bdb:refine_01#threed_filt_04 volume.hdf }}} apply a 10 A low-pass filter to a volume in-place. {{{ e2proc3d.py bdb:refine_01#threed_filt_04 bdb:refine_01#threed_filt_04 --process=filter.lowpass.gauss:cutoff_freq=0.1 }}}