Differences between revisions 8 and 9

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
	averager	string	If --average is specified, this is the averager to use (e2help.py averager). Default=mean
	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
	calccont	bool	Compute the low resolution azimuthal contrast of each image and put it in the header as eval_contrast_lowres. Larger values imply more 'interesting' images.
	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.
	add	float	Adds a constant 'f' to the densities
	addfile	string	Adds the volume to another volume of identical size
	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
	select	string	Works only on the images in named selection set from bdb:select
	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.
	extractboxes	bool	Extracts box locations from the image header to produce a set of .box files for only the particles in the .lst files
	meanshrink	float	Reduce an image size by an integral (1.5 also allowed) scaling factor using average. eg - 2 will reduce image size to 1/2. Clip is not required.
	medianshrink	int	Reduce an image size by an integral scaling factor, uses median filter. eg - 2 will reduce image size to 1/2. Clip is not required.
	fouriershrink	float	Reduce an image size by an arbitrary scaling factor by clipping in Fourier space. eg - 2 will reduce image size to 1/2.
	mraprep	bool	this is an experimental option
	outmode	string	All EMAN2 programs write images with 4-byte floating point values when possible by default. This allows specifying an alternate format when supported (float, 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
	fixintscaling	string	When writing to an 8 or 16 bit integer format the data must be scaled. 'noscale' will assume the pixel values are already correct, 'sane' will pick a good range, a number will set the range to mean+=sigma*number
	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
	rotavg	bool	Compute the 1-D rotational average of each image as a final step before writing the output
	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.
	anisotropic	string	Anisotropic scaling, stretches on one axis and compresses the orthogonal axis. Specify amount,angle. See e2evalrefine
	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
	headertransform	int	This will take the xform.align2d header value from each particle, and apply it. Pass 0 to perform the transform or 1 to perform the inverse.
-v	verbose	int	verbose level [0-9], higner number means higher level of verboseness
-v	verbose	int	verbose level [0-9], higner number means higher level of verboseness
	writejunk	bool	Writes the image even if its sigma is 0.
	swap	bool	Swap the byte order
	threed2threed	bool	Process 3D image as a stack of 2D slices, then output as a 3D image
	threed2twod	bool	Process 3D image as a stack of 2D slices, then output as a 2D stack
	twod2threed	bool	Process a stack of 2D images, then output as a 3D image.
	unstacking	bool	Process a stack of 2D images, then output a a series of numbered single image files
	ppid	int	Set the PID of the parent process, used for cross platform PPID
	step	string	Specify <init>,<step>. Processes only a subset of the input data. For example, 0,2 would process only the even numbered particles
-P	parallel	string	Run in parallel, specify type:n=<proc>:option:option

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 8 as of 2011-03-15 15:59:01 → 
  Size: 4716
  Editor: SteveLudtke
  Comment:
+   ← Revision 9 as of 2016-10-20 14:05:27 → ⇥
  Size: 7336
  Editor: SteveLudtke
  Comment:
-Deletions are marked like this.
+Additions are marked like this.
 Line 11:
-|| ||--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||
+|| ||apix||float||A/pixel for S scaling||
|| ||average||bool||Averages all input images (without alignment) and writes a single output image||
|| ||averager||string||If --average is specified, this is the averager to use (e2help.py averager). Default=mean||
|| ||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||
|| ||calccont||bool||Compute the low resolution azimuthal contrast of each image and put it in the header as eval_contrast_lowres. Larger values imply more 'interesting' images.||
|| ||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.||
|| ||add||float||Adds a constant 'f' to the densities||
|| ||addfile||string||Adds the volume to another volume of identical size||
|| ||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||
|| ||select||string||Works only on the images in named selection set from bdb:select||
|| ||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.||
|| ||extractboxes||bool||Extracts box locations from the image header to produce a set of .box files for only the particles in the .lst files||
|| ||meanshrink||float||Reduce an image size by an integral (1.5 also allowed) scaling factor using average. eg - 2 will reduce image size to 1/2. Clip is not required.||
|| ||medianshrink||int||Reduce an image size by an integral scaling factor, uses median filter. eg - 2 will reduce image size to 1/2. Clip is not required.||
|| ||fouriershrink||float||Reduce an image size by an arbitrary scaling factor by clipping in Fourier space. eg - 2 will reduce image size to 1/2.||
|| ||mraprep||bool||this is an experimental option||
|| ||outmode||string||All EMAN2 programs write images with 4-byte floating point values when possible by default. This allows specifying an alternate format when supported (float, 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||
|| ||fixintscaling||string||When writing to an 8 or 16 bit integer format the data must be scaled. 'noscale' will assume the pixel values are already correct, 'sane' will pick a good range, a number will set the range to mean+=sigma*number||
|| ||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||
|| ||rotavg||bool||Compute the 1-D rotational average of each image as a final step before writing the output||
|| ||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.||
|| ||anisotropic||string||Anisotropic scaling, stretches on one axis and compresses the orthogonal axis. Specify amount,angle. See e2evalrefine||
|| ||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||
|| ||headertransform||int||This will take the xform.align2d header value from each particle, and apply it. Pass 0 to perform the transform or 1 to perform the inverse.||
||-v||verbose||int||verbose level [0-9], higner number means higher level of verboseness||
||-v||verbose||int||verbose level [0-9], higner number means higher level of verboseness||
|| ||writejunk||bool||Writes the image even if its sigma is 0.||
|| ||swap||bool||Swap the byte order||
|| ||threed2threed||bool||Process 3D image as a stack of 2D slices, then output as a 3D image||
|| ||threed2twod||bool||Process 3D image as a stack of 2D slices, then output as a 2D stack||
|| ||twod2threed||bool||Process a stack of 2D images, then output as a 3D image.||
|| ||unstacking||bool||Process a stack of 2D images, then output a a series of numbered single image files||
|| ||ppid||int||Set the PID of the parent process, used for cross platform PPID||
|| ||step||string||Specify <init>,<step>. Processes only a subset of the input data. For example, 0,2 would process only the even numbered particles||
||-P||parallel||string||Run in parallel, specify type:n=<proc>:option:option||