EMAN2  Image Header Attribute Naming Conventions

EMAN2 uses a unique name to reference an image header attribute. The following table is the naming conventions.


Attribute Name
DataType
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_x
float
origin location along row (x) in number of pixels
origin_y
float origin location along column (y) in number of pixels
origin_z
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.


Last modified on 10/12/2004, by Liwei Peng (lpeng@bcm.tmc.edu).