Difference: CemSparxNotes (1 vs. 9)

Revision 931 Jul 2015 - Main.BillRice

META TOPICPARENT	name="CemITApplications"

Contents

Install

download and install EMAN2 daily release

in EMAN2/eman2.cshrc, Pythonpath needs to be corrected from default:

   setenv PYTHONPATH ${EMAN2DIR}/python/Python-2.7.1-ucs4/lib/python2.7/:${EMAN2DIR}/lib:${EMAN2DIR}/bin:${PYTHONPATH}

Setup

make sure PYTHONPATH is clear (setenv PYTHONPATH)
source EMAN2/eman2.cshrc
to run python program that imports sparx or eman2, need to use THEIR version
- EMAN2/Python/bin/python

Use

most instructions are on the sparx wiki

conversion of stacks

/cryoem/script/prep_sxali.xsh will convert a stack to hdf5 format and add all params:

#!/bin/tcsh
# little script to convert a stack to hdf format and get all params ready for sparx alignment

e2proc2d.py $1 $1:r.hdf
sxheader.py $1:r.hdf --params="active" --one
sxheader.py $1:r.hdf --params="xform.align2d" --zero

echo made new stack $1:r.hdf, all images active and 2d alignment params zeroed

command line

to run in interactive mode, run command "sparx"
- this uses ipython, loads all eman2 and sparx libs, graphics are available

making scripts

for python scripts, need to run the python which came with eman2 and import the proper libs

put the following at start of scripts:

#! ${EMAN2DIR}/python/Python-2.6.5-ucs4/bin/python

from EMAN2 import *
from sparx import *
# add any other needed libs

some little tools when running interactively

load an image, view it , get some info, and write new image to file:

data=EMData()  #create an object to hold the image
data.read_image("recon_1-20.hdf",0)  #reads the first image from the stack recon_1-20.hdf
display(data)  # view the image using e2display
data.get_attr("minimum") # print min value of image
data.get_attr("maximum") # max
data.get_attr("mean")  #mean value of image
data.get_attr("sigma")  # std dev
data.get_attr("nx") # x-size of image -- use ny nz for other dims
data2 = data * 5 #make new image with 5X intensities of original
data2.write_image("out.hdf",0)  # write image data to file, hdf5 format

stack info

nimages = EMUtil.get_image_count("recon_1-20.hdf")

make a mask

mask = model_circle(r,nx,ny)  # makes a model image of size nx by ny with filled circle (density 1) of radius r

normalize an image: goal is to mask out particle, then get mean and std deviation of corners of box. Norm_image = (Image-BKG_mean)/(BKG_sd)
this way background has mean 0 and sd 1

data=EMData()  #create an object to hold the image
data.read_image("raw.hdf",0)  #reads the first image from the stack
nx = data.get_attr("nx")
ny=nx # image should be square of course
r=nx/2 # this will mask only the corners of the image
mask=model_circle(r,nx,ny)
square=model_blank(nx,ny,bckg=1)
inv_mask = square-mask  # can do math on images!
back_1d = Util.compress_image_mask(data,inv_mask)  # converts all image data under the mask to a 1D image -- for getting the stats of the corner data
mean = back_1d.get_attr("mean")
sd = back_1d.get_attr("sigma")
norm = (data - mean) / sd  # can also do scalar math on images!
norm.write_image("normalised.hdf",0)

a script to do this on an entire stack, rather than one file, is in /cryem/script/normalise_stack.py

get all attribues from an image:
```
all_alltrib=data.get_attr_dict()
```

Added:

>
>

Notes stolen from sparx site for convenience

REFER TO ORIGINAL WEBSITE FOR UP TO DATE DOCS
EMAN2 supports many image formats, including all major EM file formats (SPIDER, IMAGIC, MRC, ...). However, it is recommended to use '''hdf''' file format whenever possible as only this format supports attributes set in file header with sufficient flexibility.

We have recently added '''bdb''' file format to our programs. The reading and writing of this file format is much faster than '''hdf''' file format. The '''bdb''' files are stored in a directory called EMAN2DB, there are usually two files for an image stack, one is for the image information, the other is for the header information. However, we don't deal with these two files directly, instead, we use "bdb:filename" outside the EMAN2DB directory to represent the image stack.

- '''Notice''': It is dangerous to move the EMAN2DB directory, especially between different machines. Hence, if you do need to move the '''bdb''' file, it is recommended that you first convert it to the '''hdf''' file using ''sxcpy.py'' command:

. ''sxcpy.py bdb:filename filename.hdf''

After moving the '''hdf''' file to the desired location, you can use ''sxcpy.py'' command again to convert it back to '''bdb''' file format

. ''sxcpy.py filename.hdf bdb:filename''

READ IMAGE

To read a single image from a one-image file:

  . a = EMData()
  . a.read_image("name.hdf")   
  . a.read_image("bdb:name")
 . or
  . a = [[get_image]]("name.hdf") 
  . a = [[get_image]]("bdb:name")

To read a single image from a stack file:

  . a = EMData()
  . i=12
  . a.read_image("name.hdf" , i) 
  . a.read_image("bdb:name", i)

'''Note''': image numbers are from 0 to ''n''-1, where ''n'' is the total number of images in the stack file.

To read all images from a stack file:

  . a = EMData.read_images("name.hdf") 
  . a = EMData.read_images("bdb:name")

To obtain the number of images in the stack file

  
. stack = "data.hdf"  
  . stack = "bdb:data"
  . n = EMUtil.get_image_count(stack)

'''Note''': it is not possible to obtain other characteristics (image size, image format, ...) without reading one file into the memory.

To read header information of an image

 . ima = EMData()
 . ima.read_image(stack, 0, True)

Set ALLOWTOPICVIEW =

-- BillRice - 17 Feb 2011

Added:

>
>

Revision 821 Dec 2011 - Main.DavidStokes

META TOPICPARENT	name="CemITApplications"

Contents

Install

Install

download and install EMAN2 daily release

in EMAN2/eman2.cshrc, Pythonpath needs to be corrected from default:

   setenv PYTHONPATH ${EMAN2DIR}/python/Python-2.7.1-ucs4/lib/python2.7/:${EMAN2DIR}/lib:${EMAN2DIR}/bin:${PYTHONPATH}

Added:

>
>

Setup

make sure PYTHONPATH is clear (setenv PYTHONPATH)
source EMAN2/eman2.cshrc
to run python program that imports sparx or eman2, need to use THEIR version
- EMAN2/Python/bin/python

Use

most instructions are on the sparx wiki

conversion of stacks

/cryoem/script/prep_sxali.xsh will convert a stack to hdf5 format and add all params:

#!/bin/tcsh
# little script to convert a stack to hdf format and get all params ready for sparx alignment

e2proc2d.py $1 $1:r.hdf
sxheader.py $1:r.hdf --params="active" --one
sxheader.py $1:r.hdf --params="xform.align2d" --zero

echo made new stack $1:r.hdf, all images active and 2d alignment params zeroed

command line

to run in interactive mode, run command "sparx"
- this uses ipython, loads all eman2 and sparx libs, graphics are available

making scripts

for python scripts, need to run the python which came with eman2 and import the proper libs

put the following at start of scripts:

#! ${EMAN2DIR}/python/Python-2.6.5-ucs4/bin/python

from EMAN2 import *
from sparx import *
# add any other needed libs

some little tools when running interactively

load an image, view it , get some info, and write new image to file:

data=EMData()  #create an object to hold the image
data.read_image("recon_1-20.hdf",0)  #reads the first image from the stack recon_1-20.hdf
display(data)  # view the image using e2display
data.get_attr("minimum") # print min value of image
data.get_attr("maximum") # max
data.get_attr("mean")  #mean value of image
data.get_attr("sigma")  # std dev
data.get_attr("nx") # x-size of image -- use ny nz for other dims
data2 = data * 5 #make new image with 5X intensities of original
data2.write_image("out.hdf",0)  # write image data to file, hdf5 format

stack info

nimages = EMUtil.get_image_count("recon_1-20.hdf")

make a mask

mask = model_circle(r,nx,ny)  # makes a model image of size nx by ny with filled circle (density 1) of radius r

normalize an image: goal is to mask out particle, then get mean and std deviation of corners of box. Norm_image = (Image-BKG_mean)/(BKG_sd)
this way background has mean 0 and sd 1

data=EMData()  #create an object to hold the image
data.read_image("raw.hdf",0)  #reads the first image from the stack
nx = data.get_attr("nx")
ny=nx # image should be square of course
r=nx/2 # this will mask only the corners of the image
mask=model_circle(r,nx,ny)
square=model_blank(nx,ny,bckg=1)
inv_mask = square-mask  # can do math on images!
back_1d = Util.compress_image_mask(data,inv_mask)  # converts all image data under the mask to a 1D image -- for getting the stats of the corner data
mean = back_1d.get_attr("mean")
sd = back_1d.get_attr("sigma")
norm = (data - mean) / sd  # can also do scalar math on images!
norm.write_image("normalised.hdf",0)

a script to do this on an entire stack, rather than one file, is in /cryem/script/normalise_stack.py

get all attribues from an image:
```
all_alltrib=data.get_attr_dict()
```

Set ALLOWTOPICVIEW =

-- BillRice - 17 Feb 2011

Revision 717 Feb 2011 - Main.BillRice

   META TOPICPARENT   name="CemITApplications" 

Contents
 
 Install
  Use 
 
 
  conversion of stacks
 
   command line
   making scripts 
  some little tools when running interactively
 
 
 


 Install 
 
  download and install EMAN2 daily release
  in EMAN2/eman2.cshrc, Pythonpath needs to be corrected from default:    setenv PYTHONPATH ${EMAN2DIR}/python/Python-2.7.1-ucs4/lib/python2.7/:${EMAN2DIR}/lib:${EMAN2DIR}/bin:${PYTHONPATH}

 

 Use 
 
 most instructions are on the sparx wiki
 
 conversion of stacks 
 
 /cryoem/script/prep_sxali.xsh will convert a stack to hdf5 format and add all params: #!/bin/tcsh
# little script to convert a stack to hdf format and get all params ready for sparx alignment

e2proc2d.py $1 $1:r.hdf
sxheader.py $1:r.hdf --params="active" --one
sxheader.py $1:r.hdf --params="xform.align2d" --zero

echo made new stack $1:r.hdf, all images active and 2d alignment params zeroed

 

 command line 
 
 to run in interactive mode, run command "sparx" 
 this uses ipython, loads all eman2 and sparx libs, graphics are available
 
 
 making scripts 
 
 for python scripts, need to run the python which came with eman2 and import the proper libs
  put the following at start of scripts: #! ${EMAN2DIR}/python/Python-2.6.5-ucs4/bin/python

from EMAN2 import *
from sparx import *
# add any other needed libs

 

 some little tools when running interactively 
 
 load an image, view it , get some info, and write new image to file: data=EMData()  #create an object to hold the image
data.read_image("recon_1-20.hdf",0)  #reads the first image from the stack recon_1-20.hdf
display(data)  # view the image using e2display
data.get_attr("minimum") # print min value of image
data.get_attr("maximum") # max
data.get_attr("mean")  #mean value of image
data.get_attr("sigma")  # std dev
data.get_attr("nx") # x-size of image -- use ny nz for other dims
data2 = data * 5 #make new image with 5X intensities of original
data2.write_image("out.hdf",0)  # write image data to file, hdf5 format

 
 

 stack info nimages = EMUtil.get_image_count("recon_1-20.hdf")

 
 

 make a mask mask = model_circle(r,nx,ny)  # makes a model image of size nx by ny with filled circle (density 1) of radius r

 
 

 normalize an image: goal is to mask out particle, then get mean and std deviation of corners of box. Norm_image = (Image-BKG_mean)/(BKG_sd)
  this way background has mean 0 and sd 1
 
data=EMData()  #create an object to hold the image
data.read_image("raw.hdf",0)  #reads the first image from the stack
nx = data.get_attr("nx")
ny=nx # image should be square of course
r=nx/2 # this will mask only the corners of the image
mask=model_circle(r,nx,ny)
square=model_blank(nx,ny,bckg=1)
inv_mask = square-mask  # can do math on images!
back_1d = Util.compress_image_mask(data,inv_mask)  # converts all image data under the mask to a 1D image -- for getting the stats of the corner data
mean = back_1d.get_attr("mean")
sd = back_1d.get_attr("sigma")
norm = (data - mean) / sd  # can also do scalar math on images!
norm.write_image("normalised.hdf",0)
 
 
 a script to do this on an entire stack, rather than one file, is in /cryem/script/normalise_stack.py
-  META TOPICPARENT
+ name="CemITApplications"
-<
<
->
>
+ get all attribues from an image:
->
>
+all_alltrib=data.get_attr_dict()
  Set ALLOWTOPICVIEW = 
 

-- BillRice - 17 Feb 2011

Revision 617 Feb 2011 - Main.BillRice

   META TOPICPARENT   name="CemITApplications" 

Contents
 
 Install
  Use 
 
 
  conversion of stacks
 
   command line
   making scripts 
  some little tools when running interactively
 
 
 


 Install 
 
  download and install EMAN2 daily release
  in EMAN2/eman2.cshrc, Pythonpath needs to be corrected from default:    setenv PYTHONPATH ${EMAN2DIR}/python/Python-2.7.1-ucs4/lib/python2.7/:${EMAN2DIR}/lib:${EMAN2DIR}/bin:${PYTHONPATH}

 

 Use 
 
 most instructions are on the sparx wiki
 
 conversion of stacks 
 
 /cryoem/script/prep_sxali.xsh will convert a stack to hdf5 format and add all params: #!/bin/tcsh
# little script to convert a stack to hdf format and get all params ready for sparx alignment

e2proc2d.py $1 $1:r.hdf
sxheader.py $1:r.hdf --params="active" --one
sxheader.py $1:r.hdf --params="xform.align2d" --zero

echo made new stack $1:r.hdf, all images active and 2d alignment params zeroed

 

 command line 
 
 to run in interactive mode, run command "sparx" 
 this uses ipython, loads all eman2 and sparx libs, graphics are available
 
 
 making scripts 
 
 for python scripts, need to run the python which came with eman2 and import the proper libs
  put the following at start of scripts: #! ${EMAN2DIR}/python/Python-2.6.5-ucs4/bin/python

from EMAN2 import *
from sparx import *
# add any other needed libs

 

 some little tools when running interactively
-  META TOPICPARENT
+ name="CemITApplications"
-<
<
+ load an image, view it and get some info:
->
>
+ load an image, view it , get some info, and write new image to file:
 data=EMData()  #create an object to hold the image
data.read_image("recon_1-20.hdf",0)  #reads the first image from the stack recon_1-20.hdf
display(data)  # view the image using e2display
data.get_attr("minimum") # print min value of image
data.get_attr("maximum") # max
data.get_attr("mean")  #mean value of image
data.get_attr("sigma")  # std dev
data.get_attr("nx") # x-size of image -- use ny nz for other dims
-<
<
+data.write_image("out.hdf",0)  # write image data to file, hdf5 format
->
>
+data2 = data * 5 #make new image with 5X intensities of original
->
>
+data2.write_image("out.hdf",0)  # write image data to file, hdf5 format
  stack info nimages = EMUtil.get_image_count("recon_1-20.hdf")

 
 

 make a mask mask = model_circle(r,nx,ny)  # makes a model image of size nx by ny with filled circle (density 1) of radius r

 
 

 normalize an image: goal is to mask out particle, then get mean and std deviation of corners of box. Norm_image = (Image-BKG_mean)/(BKG_sd)
  this way background has mean 0 and sd 1
 
data=EMData()  #create an object to hold the image
data.read_image("raw.hdf",0)  #reads the first image from the stack
nx = data.get_attr("nx")
ny=nx # image should be square of course
r=nx/2 # this will mask only the corners of the image
mask=model_circle(r,nx,ny)
square=model_blank(nx,ny,bckg=1)
inv_mask = square-mask  # can do math on images!
back_1d = Util.compress_image_mask(data,inv_mask)  # converts all image data under the mask to a 1D image -- for getting the stats of the corner data
mean = back_1d.get_attr("mean")
sd = back_1d.get_attr("sigma")
norm = (data - mean) / sd  # can also do scalar math on images!
norm.write_image("normalised.hdf",0)
 
 
 a script to do this on an entire stack, rather than one file, is in /cryem/script/normalise_stack.py
 


 

 Set ALLOWTOPICVIEW = 
 

-- BillRice - 17 Feb 2011

Revision 517 Feb 2011 - Main.BillRice

META TOPICPARENT	name="CemITApplications"

Contents

Install

download and install EMAN2 daily release

in EMAN2/eman2.cshrc, Pythonpath needs to be corrected from default:

   setenv PYTHONPATH ${EMAN2DIR}/python/Python-2.7.1-ucs4/lib/python2.7/:${EMAN2DIR}/lib:${EMAN2DIR}/bin:${PYTHONPATH}

Use

most instructions are on the sparx wiki

conversion of stacks

/cryoem/script/prep_sxali.xsh will convert a stack to hdf5 format and add all params:

#!/bin/tcsh
# little script to convert a stack to hdf format and get all params ready for sparx alignment

e2proc2d.py $1 $1:r.hdf
sxheader.py $1:r.hdf --params="active" --one
sxheader.py $1:r.hdf --params="xform.align2d" --zero

echo made new stack $1:r.hdf, all images active and 2d alignment params zeroed

command line

to run in interactive mode, run command "sparx"
- this uses ipython, loads all eman2 and sparx libs, graphics are available

making scripts

for python scripts, need to run the python which came with eman2 and import the proper libs

put the following at start of scripts:

#! ${EMAN2DIR}/python/Python-2.6.5-ucs4/bin/python

from EMAN2 import *
from sparx import *
# add any other needed libs

some little tools when running interactively

load an image, view it and get some info:

data=EMData()  #create an object to hold the image
data.read_image("recon_1-20.hdf",0)  #reads the first image from the stack recon_1-20.hdf
display(data)  # view the image using e2display
data.get_attr("minimum") # print min value of image
data.get_attr("maximum") # max
data.get_attr("mean")  #mean value of image
data.get_attr("sigma")  # std dev
data.get_attr("nx") # x-size of image -- use ny nz for other dims

Added:

>
>

data.write_image("out.hdf",0) # write image data to file, hdf5 format

stack info

nimages = EMUtil.get_image_count("recon_1-20.hdf")

make a mask

mask = model_circle(r,nx,ny)  # makes a model image of size nx by ny with filled circle (density 1) of radius r

normalize an image: goal is to mask out particle, then get mean and std deviation of corners of box. Norm_image = (Image-BKG_mean)/(BKG_sd)
this way background has mean 0 and sd 1

data=EMData()  #create an object to hold the image
data.read_image("raw.hdf",0)  #reads the first image from the stack
nx = data.get_attr("nx")
ny=nx # image should be square of course

Changed:

<
<

r=nx # this will mask only the corners of the image

>
>

r=nx/2 # this will mask only the corners of the image

mask=model_circle(r,nx,ny) square=model_blank(nx,ny,bckg=1) inv_mask = square-mask # can do math on images!

Changed:

<
<

back_1d = compress_image_mask(data,inv_mask) # converts all image data under the mask to a 1D image -- for getting the stats of the corner data

>
>

back_1d = Util.compress_image_mask(data,inv_mask) # converts all image data under the mask to a 1D image -- for getting the stats of the corner data

mean = back_1d.get_attr("mean") sd = back_1d.get_attr("sigma") norm = (data - mean) / sd # can also do scalar math on images! norm.write_image("normalised.hdf",0)

a script to do this on an entire stack, rather than one file, is in /cryem/script/normalise_stack.py

Set ALLOWTOPICVIEW =

-- BillRice - 17 Feb 2011

Revision 417 Feb 2011 - Main.BillRice

META TOPICPARENT	name="CemITApplications"

Contents

Install

download and install EMAN2 daily release

in EMAN2/eman2.cshrc, Pythonpath needs to be corrected from default:

   setenv PYTHONPATH ${EMAN2DIR}/python/Python-2.7.1-ucs4/lib/python2.7/:${EMAN2DIR}/lib:${EMAN2DIR}/bin:${PYTHONPATH}

Use

most instructions are on the sparx wiki

conversion of stacks

/cryoem/script/prep_sxali.xsh will convert a stack to hdf5 format and add all params:

#!/bin/tcsh
# little script to convert a stack to hdf format and get all params ready for sparx alignment

e2proc2d.py $1 $1:r.hdf
sxheader.py $1:r.hdf --params="active" --one
sxheader.py $1:r.hdf --params="xform.align2d" --zero

echo made new stack $1:r.hdf, all images active and 2d alignment params zeroed

command line

to run in interactive mode, run command "sparx"
- this uses ipython, loads all eman2 and sparx libs, graphics are available

Added:

>
>

making scripts

for python scripts, need to run the python which came with eman2 and import the proper libs

put the following at start of scripts:

#! ${EMAN2DIR}/python/Python-2.6.5-ucs4/bin/python

from EMAN2 import *
from sparx import *
# add any other needed libs

some little tools when running interactively

load an image, view it and get some info:

data=EMData()  #create an object to hold the image
data.read_image("recon_1-20.hdf",0)  #reads the first image from the stack recon_1-20.hdf
display(data)  # view the image using e2display
data.get_attr("minimum") # print min value of image
data.get_attr("maximum") # max
data.get_attr("mean")  #mean value of image
data.get_attr("sigma")  # std dev
data.get_attr("nx") # x-size of image -- use ny nz for other dims

stack info

nimages = EMUtil.get_image_count("recon_1-20.hdf")

make a mask

mask = model_circle(r,nx,ny)  # makes a model image of size nx by ny with filled circle (density 1) of radius r

normalize an image: goal is to mask out particle, then get mean and std deviation of corners of box. Norm_image = (Image-BKG_mean)/(BKG_sd)
this way background has mean 0 and sd 1

data=EMData()  #create an object to hold the image
data.read_image("raw.hdf",0)  #reads the first image from the stack
nx = data.get_attr("nx")
ny=nx # image should be square of course
r=nx # this will mask only the corners of the image
mask=model_circle(r,nx,ny)
square=model_blank(nx,ny,bckg=1)
inv_mask = square-mask  # can do math on images!
back_1d = compress_image_mask(data,inv_mask)  # converts all image data under the mask to a 1D image -- for getting the stats of the corner data
mean = back_1d.get_attr("mean")
sd = back_1d.get_attr("sigma")
norm = (data - mean) / sd  # can also do scalar math on images!
norm.write_image("normalised.hdf",0)

a script to do this on an entire stack, rather than one file, is in /cryem/script/normalise_stack.py

Set ALLOWTOPICVIEW =

-- BillRice - 17 Feb 2011

Revision 317 Feb 2011 - Main.BillRice

META TOPICPARENT	name="CemITApplications"

Contents

Install

Install

download and install EMAN2 daily release

Changed:

<
<

in EMAN2/eman2.cshrc, Pythonpath should be set to

   ${EMAN@DIR}/python/Python-2.7.1-ucs4/lib/python2.7/:${EMAN2DIR}/lib:${EMAN2DIR}/bin:${PYTHONPATH}

>
>

in EMAN2/eman2.cshrc, Pythonpath needs to be corrected from default:

   setenv PYTHONPATH ${EMAN2DIR}/python/Python-2.7.1-ucs4/lib/python2.7/:${EMAN2DIR}/lib:${EMAN2DIR}/bin:${PYTHONPATH}

Use

most instructions are on the sparx wiki

conversion of stacks

/cryoem/script/prep_sxali.xsh will convert a stack to hdf5 format and add all params:

#!/bin/tcsh
# little script to convert a stack to hdf format and get all params ready for sparx alignment

e2proc2d.py $1 $1:r.hdf
sxheader.py $1:r.hdf --params="active" --one
sxheader.py $1:r.hdf --params="xform.align2d" --zero

echo made new stack $1:r.hdf, all images active and 2d alignment params zeroed

command line

to run in interactive mode, run command "sparx"
- this uses ipython, loads all eman2 and sparx libs, graphics are available
for python scripts, need to run the python which came with eman2 and import the proper libs

put the following at start of scripts:

#! ${EMAN2DIR}/python/Python-2.6.5-ucs4/bin/python

from EMAN2 import *
from sparx import *
# add any other needed libs

some little tools when running interactively

load an image, view it and get some info:

data=EMData()  #create an object to hold the image
data.read_image("recon_1-20.hdf",0)  #reads the first image from the stack recon_1-20.hdf
display(data)  # view the image using e2display
data.get_attr("minimum") # print min value of image
data.get_attr("maximum") # max
data.get_attr("mean")  #mean value of image
data.get_attr("sigma")  # std dev
data.get_attr("nx") # x-size of image -- use ny nz for other dims

stack info

nimages = EMUtil.get_image_count("recon_1-20.hdf")

make a mask

mask = model_circle(r,nx,ny)  # makes a model image of size nx by ny with filled circle (density 1) of radius r

normalize an image: goal is to mask out particle, then get mean and std deviation of corners of box. Norm_image = (Image-BKG_mean)/(BKG_sd)
this way background has mean 0 and sd 1

data=EMData()  #create an object to hold the image
data.read_image("raw.hdf",0)  #reads the first image from the stack
nx = data.get_attr("nx")
ny=nx # image should be square of course
r=nx # this will mask only the corners of the image
mask=model_circle(r,nx,ny)
square=model_blank(nx,ny,bckg=1)
inv_mask = square-mask  # can do math on images!
back_1d = compress_image_mask(data,inv_mask)  # converts all image data under the mask to a 1D image -- for getting the stats of the corner data
mean = back_1d.get_attr("mean")
sd = back_1d.get_attr("sigma")
norm = (data - mean) / sd  # can also do scalar math on images!
norm.write_image("normalised.hdf",0)

Added:

>
>

a script to do this on an entire stack, rather than one file, is in /cryem/script/normalise_stack.py

Set ALLOWTOPICVIEW =

-- BillRice - 17 Feb 2011

Revision 217 Feb 2011 - Main.BillRice

   META TOPICPARENT   name="CemITApplications" 

Contents
 
 Install
  Use 
 
 
  conversion of stacks
 
   command line 
  some little tools when running interactively
 
 
 


 Install 
 
  download and install EMAN2 daily release
  in EMAN2/eman2.cshrc, Pythonpath should be set to    ${EMAN@DIR}/python/Python-2.7.1-ucs4/lib/python2.7/:${EMAN2DIR}/lib:${EMAN2DIR}/bin:${PYTHONPATH}

 

 Use 
 
 most instructions are on the sparx wiki
 
 conversion of stacks 
 
 /cryoem/script/prep_sxali.xsh will convert a stack to hdf5 format and add all params: #!/bin/tcsh
# little script to convert a stack to hdf format and get all params ready for sparx alignment

e2proc2d.py $1 $1:r.hdf
sxheader.py $1:r.hdf --params="active" --one
sxheader.py $1:r.hdf --params="xform.align2d" --zero

echo made new stack $1:r.hdf, all images active and 2d alignment params zeroed

 

 command line 
 
 to run in interactive mode, run command "sparx" 
 this uses ipython, loads all eman2 and sparx libs, graphics are available
 
  for python scripts, need to run the python which came with eman2 and import the proper libs
  put the following at start of scripts: #! ${EMAN2DIR}/python/Python-2.6.5-ucs4/bin/python

from EMAN2 import *
from sparx import *
# add any other needed libs

 

 some little tools when running interactively 
 
 load an image, view it and get some info: data=EMData()  #create an object to hold the image
data.read_image("recon_1-20.hdf",0)  #reads the first image from the stack recon_1-20.hdf
display(data)  # view the image using e2display
data.get_attr("minimum") # print min value of image
data.get_attr("maximum") # max
data.get_attr("mean")  #mean value of image
data.get_attr("sigma")  # std dev
data.get_attr("nx") # x-size of image -- use ny nz for other dims

 
 

 stack info nimages = EMUtil.get_image_count("recon_1-20.hdf")

 
 

 make a mask mask = model_circle(r,nx,ny)  # makes a model image of size nx by ny with filled circle (density 1) of radius r

 
 

 normalize an image: goal is to mask out particle, then get mean and std deviation of corners of box. Norm_image = (Image-BKG_mean)/(BKG_sd)
  this way background has mean 0 and sd 1
 
data=EMData()  #create an object to hold the image
-  META TOPICPARENT
+ name="CemITApplications"
-<
<
+data.read_image("recon_1-20.hdf",0)  #reads the first image from the stack recon_1-20.hdf
->
>
+data.read_image("raw.hdf",0)  #reads the first image from the stack
->
>
+nx = data.get_attr("nx")
ny=nx # image should be square of course
r=nx # this will mask only the corners of the image
 mask=model_circle(r,nx,ny)
square=model_blank(nx,ny,bckg=1)
-<
<
+inv_mask = square-mask
->
>
+inv_mask = square-mask  # can do math on images!
 back_1d = compress_image_mask(data,inv_mask)  # converts all image data under the mask to a 1D image -- for getting the stats of the corner data
mean = back_1d.get_attr("mean")
sd = back_1d.get_attr("sigma")
-<
<
+norm = (data - mean) / sd
->
>
+norm = (data - mean) / sd  # can also do scalar math on images!
 norm.write_image("normalised.hdf",0)
 


 

 Set ALLOWTOPICVIEW = 
 

-- BillRice - 17 Feb 2011

Revision 117 Feb 2011 - Main.BillRice

META TOPICPARENT	name="CemITApplications"

Contents

Install

download and install EMAN2 daily release

in EMAN2/eman2.cshrc, Pythonpath should be set to

   ${EMAN@DIR}/python/Python-2.7.1-ucs4/lib/python2.7/:${EMAN2DIR}/lib:${EMAN2DIR}/bin:${PYTHONPATH}

Use

most instructions are on the sparx wiki

conversion of stacks

/cryoem/script/prep_sxali.xsh will convert a stack to hdf5 format and add all params:

#!/bin/tcsh
# little script to convert a stack to hdf format and get all params ready for sparx alignment

e2proc2d.py $1 $1:r.hdf
sxheader.py $1:r.hdf --params="active" --one
sxheader.py $1:r.hdf --params="xform.align2d" --zero

echo made new stack $1:r.hdf, all images active and 2d alignment params zeroed

command line

to run in interactive mode, run command "sparx"
- this uses ipython, loads all eman2 and sparx libs, graphics are available
for python scripts, need to run the python which came with eman2 and import the proper libs

put the following at start of scripts:

#! ${EMAN2DIR}/python/Python-2.6.5-ucs4/bin/python

from EMAN2 import *
from sparx import *
# add any other needed libs

some little tools when running interactively

load an image, view it and get some info:

data=EMData()  #create an object to hold the image
data.read_image("recon_1-20.hdf",0)  #reads the first image from the stack recon_1-20.hdf
display(data)  # view the image using e2display
data.get_attr("minimum") # print min value of image
data.get_attr("maximum") # max
data.get_attr("mean")  #mean value of image
data.get_attr("sigma")  # std dev
data.get_attr("nx") # x-size of image -- use ny nz for other dims

stack info

nimages = EMUtil.get_image_count("recon_1-20.hdf")

make a mask

mask = model_circle(r,nx,ny)  # makes a model image of size nx by ny with filled circle (density 1) of radius r

normalize an image: goal is to mask out particle, then get mean and std deviation of corners of box. Norm_image = (Image-BKG_mean)/(BKG_sd)
this way background has mean 0 and sd 1

data=EMData()  #create an object to hold the image
data.read_image("recon_1-20.hdf",0)  #reads the first image from the stack recon_1-20.hdf
mask=model_circle(r,nx,ny)
square=model_blank(nx,ny,bckg=1)
inv_mask = square-mask
back_1d = compress_image_mask(data,inv_mask)  # converts all image data under the mask to a 1D image -- for getting the stats of the corner data
mean = back_1d.get_attr("mean")
sd = back_1d.get_attr("sigma")
norm = (data - mean) / sd
norm.write_image("normalised.hdf",0)

Set ALLOWTOPICVIEW =

-- BillRice - 17 Feb 2011

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