Differences between revisions 5 and 8 (spanning 3 versions)

e2proc2d

Generic 2-D image processing program. The main tasks this program can be used for are:

Convert images from one format to another
Perform basic image processing operations such as filters, masks, normalization, etc.
Resize/rescale images
Select subsets of image stacks

Options:

--apix	float	A/pixel for S scaling
--average	bool	Averages all input images (without alignment) and writes a single output image
--calcsf	string	calculate a radial structure factor for the image and write it to the output file, must specify apix. divide into <n> angular bins
--clip	string	Specify the output size in pixels xsize,ysize[,xcenter,ycenter], images can be made larger or smaller.
--exclude	string	Excludes image numbers in EXCLUDE file
--fftavg	string	Incoherent Fourier average of all images and write a single power spectrum image
--process	string	apply a processor named 'processorname' with all its parameters/values.
--mult	float	Multiply image by a constant. mult=-1 to invert contrast.
--first	int	the first image in the input to process [0 - n-1])
--last	int	the last image in the input to process
--list	string	Works only on the image numbers in LIST file
--inplace	bool	Output overwrites input, USE SAME FILENAME, DO NOT 'clip' images.
--interlv	string	Specifies a 2nd input file. Output will be 2 files interleaved.
--meanshrink	int	Reduce an image size by an integral scaling factor using average. Clip is not required.
--medianshrink	int	Reduce an image size by an integral scaling factor, uses median filter. Clip is not required.
--mraprep	bool	this is an experimental option
--mrc16bit	bool	output as 16 bit MRC file
--mrc8bit	bool	output as 8 bit MRC file
--multfile	string	Multiplies the volume by another volume of identical size. This can be used to apply masks, etc.
--norefs	bool	Skip any input images which are marked as references (usually used with classes.*)
--outtype	string	output image format, 'mrc', 'imagic', 'hdf', etc. if specify spidersingle will output single 2D image rather than 2D stack.
--radon	bool	Do Radon transform
--randomize	string	Randomly rotate/translate the image. Specify: da,dxy,flip da is a uniform distribution over +-da degrees, dxy is a uniform distribution on x/y, if flip is 1, random handedness changes will occur
--rotate	float	Rotate clockwise (in degrees)
--rfp	bool	this is an experimental option
--fp	int	This generates rotational/translational 'footprints' for each input particle, the number indicates which algorithm to use (0-6)
--scale	float	Scale by specified scaling factor. Clip must also be specified to change the dimensions of the output map.
--selfcl	int	Output file will be a 180x180 self-common lines map for each image.
--setsfpairs	bool	Applies the radial structure factor of the 1st image to the 2nd, the 3rd to the 4th, etc
--split	int	Splits the input file into a set of n output files
--translate	string	Translate by x,y pixels
--writejunk	bool	Writes the image even if its sigma is 0.
--swap	bool	Swap the byte order
--threed2threed	bool	Process 3D image as a statck of 2D slice, then output as a 3D image
--threed2twod	bool	Process 3D image as a statck of 2D slice, then output as a 2D stack
--twod2threed	bool	Process a stack of 2D images, then output as a 3D image

This program operates on both single 2-D image files, image stacks, EMAN2 BDB databases, and can even treat 3-D volumes as a stack of 2-D images for individual processing. 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 e2proc2d.py --help.

Examples

convert IMAGIC format test.hed to HDF format:

e2proc2d.py test.hed test.hdf

extract a subset of particles from a BDB database and convert to HDF format

e2proc2d.py bdb:particles#stack1 newfile.hdf --first=100 --last=150

apply a 10 A low-pass filter to a stack of particles and write output to a new file.

e2proc2d.py ptcl.hdf ptcl.filt.hdf --process=filter.lowpass.gauss:cutoff_freq=0.1

invert the contrast in a BDB database. Overwrite the original images

e2proc2d.py bdb:particles#set1 bdb:particles#set1 --inplace --mult=-1

-  ⇤ ← Revision 5 as of 2010-05-05 20:02:46 → 
  Size: 693
  Editor: gtang
  Comment:
+   ← Revision 8 as of 2011-03-15 15:59:01 → ⇥
  Size: 4716
  Editor: SteveLudtke
  Comment:
-Deletions are marked like this.
+Additions are marked like this.
 Line 2:
-||<35%><<TableOfContents>> ||
+Generic 2-D image processing program. The main tasks this program can be used for are:

 * Convert images from one format to another
 * Perform basic image processing operations such as filters, masks, normalization, etc.
 * Resize/rescale images
 * Select subsets of image stacks

Options:
|| ||--apix||float||A/pixel for S scaling||
|| ||--average||bool||Averages all input images (without alignment) and writes a single output image||
|| ||--calcsf||string||calculate a radial structure factor for the image and write it to the output file, must specify apix. divide into <n> angular bins||
|| ||--clip||string||Specify the output size in pixels xsize,ysize[,xcenter,ycenter], images can be made larger or smaller.||
|| ||--exclude||string||Excludes image numbers in EXCLUDE file||
|| ||--fftavg||string||Incoherent Fourier average of all images and write a single power spectrum image||
|| ||--process||string||apply a processor named 'processorname' with all its parameters/values.||
|| ||--mult||float||Multiply image by a constant. mult=-1 to invert contrast.||
|| ||--first||int||the first image in the input to process [0 - n-1])||
|| ||--last||int||the last image in the input to process||
|| ||--list||string||Works only on the image numbers in LIST file||
|| ||--inplace||bool||Output overwrites input, USE SAME FILENAME, DO NOT 'clip' images.||
|| ||--interlv||string||Specifies a 2nd input file. Output will be 2 files interleaved.||
|| ||--meanshrink||int||Reduce an image size by an integral scaling factor using average. Clip is not required.||
|| ||--medianshrink||int||Reduce an image size by an integral scaling factor, uses median filter. Clip is not required.||
|| ||--mraprep||bool||this is an experimental option||
|| ||--mrc16bit||bool||output as 16 bit MRC file||
|| ||--mrc8bit||bool||output as 8 bit MRC file||
|| ||--multfile||string||Multiplies the volume by another volume of identical size. This can be used to apply masks, etc.||
|| ||--norefs||bool||Skip any input images which are marked as references (usually used with classes.*)||
|| ||--outtype||string||output image format, 'mrc', 'imagic', 'hdf', etc. if specify spidersingle will output single 2D image rather than 2D stack.||
|| ||--radon||bool||Do Radon transform||
|| ||--randomize||string||Randomly rotate/translate the image. Specify: da,dxy,flip  da is a uniform distribution over +-da degrees, dxy is a uniform distribution on x/y, if flip is 1, random handedness changes will occur||
|| ||--rotate||float||Rotate clockwise (in degrees)||
|| ||--rfp||bool||this is an experimental option||
|| ||--fp||int||This generates rotational/translational 'footprints' for each input particle, the number indicates which algorithm to use (0-6)||
|| ||--scale||float||Scale by specified scaling factor. Clip must also be specified to change the dimensions of the output map.||
|| ||--selfcl||int||Output file will be a 180x180 self-common lines map for each image.||
|| ||--setsfpairs||bool||Applies the radial structure factor of the 1st image to the 2nd, the 3rd to the 4th, etc||
|| ||--split||int||Splits the input file into a set of n output files||
|| ||--translate||string||Translate by x,y pixels||
|| ||--writejunk||bool||Writes the image even if its sigma is 0.||
|| ||--swap||bool||Swap the byte order||
|| ||--threed2threed||bool||Process 3D image as a statck of 2D slice, then output as a 3D image||
|| ||--threed2twod||bool||Process 3D image as a statck of 2D slice, then output as a 2D stack||
|| ||--twod2threed||bool||Process a stack of 2D images, then output as a 3D image||
-Line 5:
+Line 49:
-See [[EMAN2/Programs/e2boxer#tipsandtricks|e3boxer Tips and Tricks]] for more.
+This program operates on both single 2-D image files, image stacks, EMAN2 BDB databases, and can even treat 3-D volumes as a stack
of 2-D images for individual processing. 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''.
-Line 7:
+Line 53:
-== Convert MRC image's storage type ==
By default, the image will be saved as float type, i.e., 4 bytes (16 bit) for each pixel. For MRC format, we can save image as short (2 bytes/16bit) or byte. e2proc2d.py provide options to convert mrc image between these storage types. The following example is for 2D mrc image. You can do similar conversion to 3D mrc image by calling e2proc3d.py.
+For specific details on various options, use ''e2proc2d.py --help''.
-Line 10:
+Line 55:
+=== Examples ===
convert IMAGIC format test.hed to HDF format:
-Line 11:
+Line 58:
-[someone@localhost]$e2proc2d.py --mrc16bit float-image.mrc short-image.mrc
+e2proc2d.py test.hed test.hdf
-Line 13:
+Line 60:
+extract a subset of particles from a BDB database and convert to HDF format
-Line 14:
+Line 63:
-[someone@localhost]$e2proc2d.py --mrc8bit float-image.mrc byte-image.mrc
+e2proc2d.py bdb:particles#stack1 newfile.hdf --first=100 --last=150
-Line 16:
+Line 65:
+apply a 10 A low-pass filter to a stack of particles and write output to a new file. 
{{{
e2proc2d.py ptcl.hdf ptcl.filt.hdf --process=filter.lowpass.gauss:cutoff_freq=0.1
}}}

invert the contrast in a BDB database. Overwrite the original images
{{{
e2proc2d.py bdb:particles#set1 bdb:particles#set1 --inplace --mult=-1
}}}