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= e2proc3d.py = = 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.

|| ||--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||


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
}}}

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.

--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

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)