Differences between revisions 3 and 4

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.

--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
--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
--scale	float	Rescales the image by 'n', generally used with clip option.
--sym	string	Symmetry to impose - choices are: c<n>, d<n>, h<n>, tet, oct, icos
--process	string	apply a processor named 'processorname' with all its parameters/values.
--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
--first	int	the first image in the input to process [0 - n-1])
--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
--last	int	the last image in the input to process
--swap	bool	Swap the byte order
--append	bool	Append output image, i.e., do not write inplace.

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

-  ⇤ ← Revision 3 as of 2010-09-14 12:51:12 → 
  Size: 1304
  Editor: SteveLudtke
  Comment:
+   ← Revision 4 as of 2011-03-15 16:08:59 → ⇥
  Size: 3307
  Editor: SteveLudtke
  Comment:
-Deletions are marked like this.
+Additions are marked like this.
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-This program operates on single 3-D image files and EMAN2 BDB databases. While it is possible to put multiple volumes into a single
file akin to 2-D particle stacks, it is not widely supported, so this is not a commonly used capability. It has many command-line options for
+|| ||--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||
|| ||--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||
|| ||--scale||float||Rescales the image by 'n', generally used with clip option.||
|| ||--sym||string||Symmetry to impose - choices are: c<n>, d<n>, h<n>, tet, oct, icos||
|| ||--process||string||apply a processor named 'processorname' with all its parameters/values.||
|| ||--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||
|| ||--first||int||the first image in the input to process [0 - n-1])||
|| ||--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||
|| ||--last||int||the last image in the input to process||
|| ||--swap||bool||Swap the byte order||
|| ||--append||bool||Append output image, i.e., do not write inplace.||


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
-Line 12:
+Line 39:
-operations (for a list, type ''e2help.py processors'').
+operations. For a list, type ''e2help.py processors''.