The old
IMAGIC-5 HEADER FORMAT


  Formats

  The OLD header format (IMAGIC-5)
  The NEW header format (IMAGIC-4D)
  Image file
  Plt file
  Classification (cls) file
  Co-ordinate System
  Euler angles


  The old IMAGIC-5 header file format


NOTE: In the most important header indices the new IMAGIC-4D header format remains compatible with the old IMAGIC-5 format, which is described here.

An IMAGIC file actually exist of two files:
a) a header file with the extension ".hed", which contains information for every image
b) an image file with extension ".img", which contains only raw data (image densities).

The header file contains one (fixed-size) record per image stored. Every header record consists of 256 REAL/float (called DAT1) or INTEGER/int values (called IDAT1) for every image.

The values that must always be set are shown with a blue background.

IDAT1(1) IMN image location number (1,2,3,...)
IDAT1(2) IFOL number of images following (0,1,,...)
only of importance in the first location
IDAT1(3) IERROR error code for this image during IMAGIC run
IDAT1(4) NHFR number of header records per image (=1 always)
IDAT1(5) NMONTH creation month
IDAT1(6) NDAY creation day
IDAT1(7) NYEAR creation year
IDAT1(8) NHOUR creation hour
IDAT1(9) NMINUT creation minute
IDAT1(10) NSEC creation second
IDAT1(11) NPIX2 image size in BYTES as seen from the program
(IDAT1(13)*IDAT1(89))
IDAT1(12) NPIXEL total number of image elements
IDAT1(13) IXLP number of lines per image (for 1D data IYLP1=1)
IDAT1(14) IYLP number of pixels per line
IDAT1(15) TYPE 4 characters determining the image type
REAL : REAL/float
INTG : INTEGER*2/short
PACK : PACK/byte
COMP : 2 REAL / 2 float
RECO : complex format with 0 in imaginary part)
IDAT1(16) IXOLD top left X co-ordinate before CUT-IMAGE (boxing)
IDAT1(17) IYOLD top left Y co-ordinate before CUT-IMAGE (boxing)
DAT1(18) AVDENS average density in image
DAT1(19) SIGMA standard deviation of densities
DAT1(20) VARIAN variance of densities in image
DAT1(21) OLDAVD old average density of this image
DAT1(22) DENSMAX highest density in image
DAT1(23) DENSMIN minimal density in image
IDAT1(24) COMPLEX label indicating that data is always complex
DAT1(25) CXLENGTH cell dimension in Angstr. (x-direction) (MRC(12))
DAT1(26) CYLENGTH cell dimension in Angstr. (y-direction) (MRC(11))
DAT1(27) CZLENGTH cell dimension in Angstr. (z-direction) (MRC(13))
DAT1(28) CALPHA cell angle alpha (MRC(14))
DAT1(29) CBETA cell angle beta (MRC(15))
IDAT1(30)
-
IDAT1(49)
NAME coded NAME/TITLE of the image (80 characters)
DAT1(50) CGAMMA cell angle gamma (MRC(16))
IDAT1(51) MAPC axis corresponding to columns (MRC(17))
(1,2,3 for X,Y,Z)
IDAT1(52) MAPR axis corresponding to rows (MRC(18))
(1,2,3 for X,Y,Z)
IDAT1(53) MAPS axis corresponding to sections (MRC(19))
(1,2,3 for X,Y,Z)
IDAT1(54) ISPG space group (MRC(23))
IDAT1(55) NXSTART number of 1st column in map (def:0) (MRC(6))
(where map starts in columns)
IDAT1(56) NYSTART number of 1st row in map (def:0) (MRC(5))
(where map starts in rows)
IDAT1(57) NZSTART number of 1st section in map (def:0) (MRC(7))
(where map starts in sections)
IDAT1(58) NXINTV number of intervals along X (MRC(9))
IDAT1(59) NYINTV number of intervals along Y (MRC(8))
IDAT1(60) NZINTV number of intervals along Z (MRC(10))
IDAT1(61) IZLP number of 2D planes in 3D data (for 2D: IZLP1=1)
IDAT1(62) I4LP number of 3D volumes in 4D data (for 2D: I4LP1=1)
IDAT1(63) I5LP  
IDAT1(64) I6LP  
DAT1(65) ALPHA Euler angle alpha (3D and Angular Reconst.)
DAT1(66) BETA Euler angle beta (3D and Angular Reconst.)
DAT1(67) GAMMA Euler angle gamma (3D and Angular Reconst.)
IDAT1(68) IMAVERS IMAGIC version used (yyyymmdd)
IDAT1(69) REALTYPE floating point type, machine stamp
16777216 for VAX/VMS
33686018 for OSF,ULTRIX, LINUX, MS Windows
67372036 for SiliconGraphics, SUN, HP, IBM
IDAT1(70)
-
IDAT1(98)
  Variables that control the buffering
during read/write in IMAGIC programs.
PLEASE DO NOT TOUCH !
IDAT1(99) RONLY flag in calling program to open file readonly
(1: readonly)
DAT1(100) ANGLE last rotation angle
DAT1(101) RCP rotational correlation peak
IDAT1(102) IXPEAK shift correlation peak in X direction
IDAT1(103) IYPEAK shift correlation peak in Y direction
DAT1(104) CCC cross correlation peak hight
DAT1(105) ERRAR error in angular reconstitution
if -1.0: the file is a special file (FABOSA)
DAT1(106) ERR3D error in 3D reconstruction (TRUE-THREED)
IDAT1(107) REF (multi-) reference number
DAT1(108) CLASSNO class number in classification
DAT1(109) LOCOLD location number before CUT-IMAGE (boxing)
or copy in ANGULAR and EX-COPY
DAT1(110) OLDAVD old average density
(before NORM-VARIANCE, for example)
DAT1(111) OLDSIGMA old sigma
DAT1(112) XSHIFT last shift in X direction
DAT1(113) YSHIFT last shift in Y direction
DAT1(114) NUMCLS number of class members
DAT1(115) OVQUAL overall class quality
if the image is a class average
DAT1(116) EANGLE equivalent angle
DAT1(117) EXSHIFT equivalent shift in X direction
DAT1(118) EYSHIFT equivalent shift in Y direction
DAT1(119) CMTOTVAR used in MSA/IMAGECOOS
DAT1(120) INFORMAT Gauss norm / real*FT Space information of the data set
IDAT1(121) NUMEIGEN number of eigen values in MSA
IDAT1(122) NIACTIVE number of active images in MSA
DAT1(123) RESOLX Angstrom per pixel/voxel in X direction
if DAT1(105) = -1.0 (FABOSA): mm per pixel
DAT1(124) RESOLY Angstrom per pixel/voxel in Y direction
DAT1(125) RESOLZ Angstrom per pixel/voxel in Z direction
DAT1(126) ALPHA2 Euler angle alpha (from projection matching)
DAT1(127) BETA2 Euler angle beta (from projection matching)
DAT1(128) GAMMA2 Euler angle gamma (from projection matching)
DAT1(126)
-
DAT1(128)
  Special FABOSA variables if DAT1(105) = -1.0
DAT1(129) NMETRIC Metric used in MSA calculations
DAT1(130) ACTMSA a flag indicating whether the "image" is
active or not. Used during MSA calculations
DAT1(131)
-
DAT1(199)
COOSMSA co-ordinates of "image" along factorial axis
number 1 through 69 (maximum possible).
Used during MSA calculations.
DAT1(150) EIGVAL eigenvalues if the "images" represent
eigenimages (eigenvalue #1 into loc#1 etc.)
IDAT1(200)
-
IDAT1(256)
HISTORY coded history of image (228 characters)

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