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Image Header Attribute Naming Conventions

EMAN2 uses a unique name to reference each image header attribute. The following table lists the conventions:

Table 3.1: Image Attribute Namimg
Attribute Name Data Type Attribute Description
     
apix_x float pixel x size in Å
apix_y float pixel y size in Å
apix_z float pixel z size in Å
nx int image x-direction size in number of pixels
ny int image y-direction size in number of pixels
nz int image z-direction size in number of pixels
origin_row float origin location along row (x) in number of pixels
origin_col float origin location along column (y) in number of pixels
origin_sec float origin location along section (z) in number of pixels
minimum float minimum pixel density value in the image
maximum float maximum pixel density value in the image
mean float mean pixel density value in the image
sigma float sigma pixel density value in the image
square_sum float sum of the squares of each pixel density value in the image
mean_nonzero float mean pixel density value in the image, ignoring pixel whose value =0.
sigma_nonzero float sigma pixel density value in the image, ignoring pixel whose value =0.
kurtosis float kurtosis pixel density value in the image
skewness float skewness pixel density value in the image
orentation_convention string Euler orientation Convention, "EMAN", "MRC", etc
rot_alt float EMAN convention: alt
rot_az float EMAN convention: az
rot_phi float EMAN convention: phi
datatype int pixel data type in the image physical file (e.g., float, int, double, etc). This is an enumeration type.
is_complex int 1 if this image is a complex image. 0 if it is a real image.
is_ri int 1 if this is a complex image and is in real/imaginary format; 0 otherwise.
avgnimg int If the image is the result of averaging, avgnimg is the number of images used in averaging. Otherwise, avgnimg is 0.
label string user-defined label for this image. It is like 'name' in EMAN1.
image_filename string the physical image filename where this image comes from.
image_index int image number in file pointed to by path.
DM3.exposure_number int DM3 image only. exposure number.
DM3.exposure_time double DM3 image only. exposure time in seconds.
DM3.zoom double zoom
DM3.antiblooming int antiblooming
DM3.magnification double Indicated magnification
DM3.frame_type string frame_type
DM3.camera_x int DM3 image only. camera size along x direction in number of pixels.
DM3.camera_y int DM3 image only. camera size along y direction in number of pixels.
DM3.binning_x int DM3 image only. Binning #0
DM3.binning_y int DM3 image only. Binning #1
MRC.nlabels int MRC image only. Number of comment labels in a MRC image.
MRC.labelN string MRC image only. The Nth label, where N is an integer from 1 to 10.
LST.filenum int LIST image only, file number in FileSystem server
LST.reffile string LIST image only, reference file
LST.refn int LIST image only, reference image number
LST.comment string LIST image only, comment
micrograph_id string Micrograph ID.
particle_center_x float x coordinate of particle location in the micrograph
partcle_center_y float y coordinate of particle location in the micrograph
ctf_dimension int CTF dimension, nD, where n is 1, 2, or 3.


next up previous contents index
Next: Testing Framework Up: Developer's Guide Previous: Adding LATEX Packages   Contents   Index
2013-06-11