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Deletions are marked like this. Additions are marked like this.
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|| ||--process||string||apply a processor named 'processorname' with all its parameters/values.||
|| ||--append||bool||Append output volumes to a stack of volumes (opposite of 'inplace' in e2proc2d.py)||
|| ||--first||int||the first image in the input to process [0 - n-1])||
|| ||--last||int||the last image in the input to process||
|| ||--origin||string|| Set the coordinates for the origin. x,y,z||
|| ||--fftclip||string||Make the output have this size, rescaling by padding FFT. x,y,z||
|| ||--scale||float||Rescales the image by 'n', generally used with clip option.||
|| ||--clip||string||Make the output have this size by padding/clipping. 1, 3 or 6 arguments. x[,y,z[,xc,yc,zc]] ||
|| ||--medianshrink||int||Shrinks the image by integer n using median filter||
|| ||--meanshrink||int||Shrinks the image by integer n using mean filter||
|| ||--sym||string||Symmetry to impose - choices are: c<n>, d<n>, h<n>, tet, oct, icos||
|| ||--apix||float||A/pixel for S scaling||
|| ||--mult||float||Scales the densities by a fixed number in the output||
|| ||--multfile||string||Multiplies the volume by another volume of identical size. This can be used to apply masks, etc.||
|| ||--mrc16bit||bool||output as 16 bit MRC file||
|| ||--mrc8bit||bool||output as 8 bit MRC file||
|| ||--add||float||Adds a constant 'f' to the densities||
|| ||--calcfsc||string||Calculate a FSC curve between two models. Output is a txt file. This option is the name of the second volume.||
|| ||--calcsf||string||Calculate a radial structure factor. Must specify apix.||
|| ||--setsf||string||Set the radial structure factor. Must specify apix.||
|| ||--tophalf||bool||The output only keeps the top half map||
|| ||--icos5fhalfmap||bool||The input is the icos 5f top half map generated by the 'tophalf' option||
|| ||--outtype||string||Set output image format, mrc, imagic, hdf, etc||
|| ||--trans||string||Translate map by dx,dy,dz ||
|| ||--rot||string||Rotate map using EMAN Euler angles z,x,z' or an arbitrary convention. NOTE, at the moment users may only specify az,alt,phi - this is a bug that will be resolved||
|| ||--swap||bool||Swap the byte order||
|| ||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<n>, d<n>, h<n>, 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 <init>,<step>. Processes only a subset of the input data. For example, 0,2 would process only the even numbered particles||

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<n>, d<n>, h<n>, 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 <init>,<step>. 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

EMAN2/Programs/e2proc3d (last edited 2016-10-20 14:20:42 by SteveLudtke)