IMAGIC
FILE FORMATS



  Formats

  Header file (IMAGIC-4D)
  Old IMAGIC-5 header file
  Image file
  Plt file
  Classification (cls) file
  Co-ordinate System
  Euler angles


  IMAGIC Header file format (IMAGIC-4D)


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) ADDHEAD always 1 at the moment
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) RSIZE image size in BYTES as seen from the program
IDAT1(12) IZOLD top left Z co-ordinate before THREED-CUT
IDAT1(13) IXLP number of lines per image (for 1D data IXLP=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) USER1 at user's own disposal
DAT1(21) USER2 at user's own disposal
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) DEFOCUS1 defocus value 1
DAT1(26) DEFOCUS2 defocus value 2
DAT1(27) DEFANGLE defocus angle
DAT1(28) SINOSTRT start angle if image is a sinogram
DAT1(29) SINOEND end angle if image is a sinogram
IDAT1(30)
    -
IDAT1(49)
NAME coded NAME/TITLE of the image (80 characters)
DAT1(50) CCC3D 3D simularity criteria
IDAT1(51) REF3D 3D membership
IDAT1(52) MIDENT micrograph identification number
IDAT1(53) EZSHIFT equivalent shift in Z direction
DAT1(54) EALPHA equivalent Euler angle alpha
DAT1(55) EBETA equivalent Euler angle beta
DAT1(56) EGAMMA equivalent Euler angle gamma
IDAT1(57) FREE currently not used
IDAT1(58) FREE currently not used
IDAT1(59) NALISUM number of images summed
(used in SUM-ALI-IMAGES)
IDAT1(60) PGROUP point-group symmetry in international notation
(622, for example)
IDAT1(61) IZLP number of 2D planes in 3D data
(for 1D/2D: IZLP1=1)
IDAT1(62) I4LP number of "objects" in file:
1D (IXLP=1): number of 1D spectra
2D (IZLP=1): number of 2D images
3D (IZLP>1): number of 3D volumes
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, which created the file (yyyymmdd)
IDAT1(69) REALTYPE floating point type / machine stamp
16777216: VAX/VMS
33686018: OSF,ULTRIX,LINUX,MS Windows
67372036: SiliconGraphics,SUN,HP,IBM
IDAT1(70)
   -
IDAT1(99)
BUFFCTRL variables that control the buffering during read/write in IMAGIC programs.
PLEASE DO NOT TOUCH !
DAT1(100) ANGLE last rotation angle
DAT1(101) VOLTAGE acceleration voltage (kv)
DAT1(102) SPABERR spherical aberration (mm)
DAT1(103) PCOHER partial coherence
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
IDAT1(107) REF (multi-) reference number
DAT1(108) CLASSNO class number in MSA classification
DAT1(109) LOCOLD location number before CUT-IMAGE (boxing)
or before copy in ANG-RECONST or EX-COPY
DAT1(110) REPQUAL representation quality
Used in MSA-RUN and MSA (eigen) filtering
DAT1(111) ZSHIFT last shift in Z direction
DAT1(112) XSHIFT last shift in X direction
DAT1(113) YSHIFT last shift in Y direction
DAT1(114) NUMCLS number of members in the class specified in CLASSNO, if this image represents a class average (class-sum image)
DAT1(115) OVQUAL overall quality of the class in CLASSNO
DAT1(116) EANGLE equivalent angle
DAT1(117) EXSHIFT equivalent shift in X direction
DAT1(118) EYSHIFT equivalent shift in Y direction
DAT1(119) CMTOTVAR total variance in data matrix relative to centre of mass (MSA calculations)
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 calculations
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)
  specific 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 axes
(1 through 69). Used during MSA calculations
DAT1(150) EIGVAL eigenvalue if the "images" represents an
eigenimage
IDAT1(200)
-
IDAT1(256)
HISTORY coded history of image (228 characters)


  IMAGIC image file format


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 image file contains only the raw data. Depending on the internal IMAGIC format used, which can be REAL, INTG, PACK or COMP, the data is stored as REAL/float, INTEGER/int, INTEGER*1/byte or 2x REAL/float, respectively.


The first pixel stored is the upper left one. The data is stored line by line, section by section, volume by volume. Please also refer to the definition of the IMAGIC co-ordinate system .


  IMAGIC PLT file formats


An IMAGIC "plt" file is an ASCII format text file to store co-ordinates, euler angles, data...

It can contain maximal five values per line which have to be seperated by blanks (or a comma).


Plt plot (graphics) file:

1st value: value along horizontal axis, 2nd value: value along vertical axis, 3rd value: number of curve. The first three lines for every curve can specify the title and the descriptions of the two axis.

Plt co-ordinates file:

1st value: X co-ordinate, 2nd value: Y co-ordinate, 3rd value: location number

Plt Euler angle file:

1st value: alpha, 2nd value: beta, 3rd value: gamma

Plt location number file:

(Only) one location number per line


  IMAGIC classification "CLS" File Format


An IMAGIC classification ("cls") file is a data file an ASCII format, which contains the members belonging to the classes of an MSA classification.

The information is stored class by class. For every class the following values are stored:

a) 1st line: class number, number of class members, overall class quality
b) next lines: location numbers of the class members (16 values per line)

The class members are sorted by overall quality.

All values are seperated by blank(s).


  IMAGIC co-ordinate system


The IMAGIC co-odination system is defined as follows:

The IMAGIC co-ordinate system is a right-handed system with its (1,1) origin in the top-left corner of the image. The length of the lines is NY and the number of lines is NX:

The centre of the image, for almost all operations on the image, is given by:

( IXMID , IYMID ) = ( NX/2 + 1 , NY/2 + 1 ).

This point is also the default centre of rotational symmetric masks and the like.


In three dimensions:



  IMAGIC Euler angles


In IMAGIC the Euler angles alpha, beta, gamma are defined as three subsequent rotations. The first rotation angle ALPHA describes a rotation around the Z-axis. We then rotate along the new Y-axis over the angle BETA. Finally, the rotation GAMMY is a rotation around the new Z-axis. All rotations are counter clockwise.

PNote that these are Euler angles as seen from the object.

Normally a user does not think in this way but tries to imagine how the particle would look like "in his hands":

a) look at the particle along the Z-axis ("north pole")
b) rotate the particle clockwise by GAMMA
c) rotate the particle into the plane clockwise by BETA
d) rotate the particle clockwise by ALPHA

PLEASE NOTE:
The important angles to define a 3-D orientation are gamma and beta. Alpha is only the final in-plane rotation.



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