Xmipp

File Formats

Metadata Files

In Xmipp metadata information is transferred between programs using metadata files. Metadata files are handled by the metadata class. Metadata files uses the STAR (Self-defining Text Archiving and Retrieval) format. In a nutshell, the STAR format is a plain text format (i.e., human-readable) that defines tag-value pairs with few rules on the composition of the file: XMIPP metadata standard introduces several constrains to ease implementation.

Metadata File Example1: list of Images
# XMIPP_STAR_1 *
##########################################################################
# Comments go here.
##########################################################################

data_ctf
loop_
  _image
   mic001.mrc 
   mic002.mrc

Metadata File Example1: list of Images with CTF information
# XMIPP_STAR_1 *
##########################################################################
# Comments go here.
##########################################################################

data_ctf
loop_
  _image
  _CTF_Sampling_rate
  _CTF_Defocus_U
  _CTF_Defocus_V
  _CTF_Defocus_angle
  _CTF_Voltage
  _CTF_Spherical_aberration
  _CTF_Q0
   mic001.mrc  1.44444444444  20  25  23.8  300  2.2  0.07
   mic002.mrc  1.79487179487  18  12  56.2  200  2  0.10

Xmipp metadata files should satisfy:

  • The only valid data block delimiter is the data_xxx block code
  • Nesting of loops is prohibited
  • Recomendation: File name must end with the extension: ".xmd"
  • Each file must have one or more data blocks.
  • The start of a data block is defined by the keyword "data_" followed by a string for identification (e.g., "data_micrograph").
  • The values are delimited by whitespace (i.e., blanks, tabs, end-of-lines and carriage returns).
  • Tag names always start with an underscore ("_").
  • Each tag name may only be used once within each data block.
  • Data items or values can be numeric, strings of characters or vector.
  • A string is interpreted as a single item when it doesn't contain spaces or when it is enclosed in quotes (single).

Phantom metadata file

Phantom parametric file consist in a file with two MetaDatas. The first MetaData describes global phantom charaterictics (size, background, etc) while the second one is employed to enumerate the different properties of the phantom features.

General Phantom Parameters:

This metadata file describes the general parameters of phantom in block1:

# General Volume Parameters
data_block1
_dimensions3D  'Xdim Ydim Zdim' 
_phantomBGDensity Background_Density
_scale  Scale 

Phantom Feature Parameters:

The phantom consists of some features and these features have some parameters. Second MetaData in the file describes these parameters as below:

# Feature Parameters:
# The feature density (Required)
# The feature center (Required)
data_block2
_featureType 
_featureOperation
_featureDensity
_featureCenter
_featureSpecificVector

fetureType: Used for type of features and can be:

sph(Sphere), blo(Blob), gau(Gaussian), cyl(Cylinder), 
dcy (Double Cylinder),  cub(Cube), ell(Ellipsoid), con(Cone)

featureOperation: The '+' sign means that this feature will be added at those positions of the volume ocuupied by it. '=' instead means that those voxels will be set to the value of the density of this feature (if two features overlap the density of the last one is kept in the overlapping voxels)

featureSpecificVector: Used to store the special parameters of each feature

Sphere, with center at (x0,y0,z0) and radius in pixels [radius]

sph +/- den 'x0 y0 z0' 'radius'

Blob with center at (x0,y0,z0) and radius in pixels [radius], alpha is the tampering factor and order is the order of the Bessel functions (usually 2)

blo +/- den 'x0 y0 z0' 'radius alpha order'

Gaussian with center at (x0,y0,z0) and sigma in pixels [sigma]

gau +/- den 'x0 y0 z0' 'sigma'

Cylinder, initially with base at plane XY and height in Z (-h/2 to h/2) and then it is moved to (x0,y0,z0) (its center) and rotated after (tilt,rot,psi)

cyl +/- den 'x0 y0 z0' 'xradius yradius height rot tilt psi'

double cylinder (two cylinders), initially with base at plane XY and height in Z (-h/2 to h/2), then it is moved to (x0,y0,z0) and rotated after (tilt,rot,psi)

dcy +/- den 'x0 y0 z0' 'radius height separation rot tilt psi'

Cube of size (xdim,ydim,zdim) whose center is moved to (x0,y0,z0) and rotated

cub +/- den 'x0 y0 z0' 'xdim ydim zdim rot tilt psi'

Ellipsoid with 3 radius and then moved and rotated

ell +/- den 'x0 y0 z0' 'xradius yradius zradius rot tilt psi'

Cone, initially with base at plane XY and height in Z (-h/2 to h/2), and then the (0,0,0) point is moved to (x0,y0,z0) and rotated

con +/- den 'x0 y0 z0' 'radius height rot tilt psi'

Here you have an example file with 12 balls in two rings:

# XMIPP_STAR_1 *
# Phantom description file, (generated with phantom help)
data_block1
 _dimensions3D  '65 65 65'
 _phantomBGDensity  0
 _scale  1
data_block2
loop_
 _featureType
 _featureOperation
 _featureDensity
 _featureCenter
 _featureSpecificVector
    sph  +      1      '15          0     -8.5'      '7.5'
    sph  +      1      '7.5       13     -8.5'      '7.5'
    sph  +      1      '7.5      -13     -8.5'      '7.5'
    sph  +      1      '-7.5      13     -8.5'      '7.5'
    sph  +      1      '-7.5     -13     -8.5'      '7.5'
    sph  +      1      '-15         0     -8.5'      '7.5'
    sph  +      1       '15         0      8.5'      '7.5'
    sph  +      1       '7.5      13      8.5'      '7.5'
    sph  +      1       '7.5     -13      8.5'      '7.5'
    sph  +      1       '-7.5     13      8.5'      '7.5'
    sph  +      1       '-7.5    -13      8.5'      '7.5'
    sph  +      1       '-15        0      8.5'      '7.5'

In the following link you can find an example of phantom description file:

http://newxmipp.svn.sourceforge.net/viewvc/newxmipp/trunk/testXmipp/input/phantom_descr.descr

EMX Files

Xmip is committed to support EMX exchange format. Information related with this format will appear here.

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