IMAGIC Formats and Conventions

IMAGIC image
Header file (IMAGIC-4D) | OLD IMAGIC header file (IMAGIC-5)
Image density file
PLT file
Classification (CLS) file
Co-ordinate system
Euler angles

IMAGIC Image

An IMAGIC image actually consists of two files:
  • a header file with the extension ".hed", which contains information for each image
  • an image file with extension ".img", which contains the image densities.

Note: One never has to specify the extensions ".hed" or ".img". Within IMAGIC the image name is always the one without extension.


IMAGIC header file format

The header file has the extension ".hed" and contains information for each image

The header file contains NBLOCKS (defined in IDAT1(4)) records per image stored. The first header record for each image consists of 256 REAL/float (called DAT1) or INTEGER/int values (called IDAT1). If NBLOCK is > 1 there are additional (NBLOCKS-1) header records (each of length 256 REAL/float), which are used by some IMAGIC commands to store specific data.

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

IDAT1(1) IMN Image location number (1,2,3,...)
IDAT1(2) IFOL Number of all 1D/2D images/sections following (0,1...).
Only of importance in the first location, else set to 0.
Note that the value in IFOL + 1 is the total number of
1D/2D images/2D sections in n the file
IDAT1(3) IERROR Error code for this image during IMAGIC run
IDAT1(4) NBLOCKS Number of header blocks (each block containing
256 REAL/INTEGER values).
For a usual header: NBLOCKS = 1
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 coordinate 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 coded characters determining the image type:
REAL : Each image pixel is represented by a 32-bit real/float number
LONG : Each image pixel is represented by a 32-bit (signed) integer number
INTG : Each image pixel is represented by a 16-bit (signed) integer number
PACK : Each image pixel is represented by one (unsigned) byte number
COMP : Each complex image pixel is represented by two REAL values
IDAT1(16) IXOLD Top left X coordinate before CUT-IMAGE
IDAT1(17) IYOLD Top left Y coordinate before CUT-IMAGE
DAT1(18) AVDENS Average density in image
DAT1(19) SIGMA Sigma of image 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 (Angstrom)
DAT1(26) DEFOCUS2 Defocus value 2 (Angstrom)
DAT1(27) DEFANGLE Defocus angle (degree)
DAT1(28) SINOSTRT
WAVEMAX
Start angle if image is a sinogram
Maximal wave number if image is a spectra
DAT1(29) SINOEND
WAVESTEP
End angle if image is a sinogram
Step size of wave numbers if image is a spectra
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
DAT1(53) EZSHIFT Equivalent shift in Z direction
DAT1(54) EALPHA Equivalent Euler angle alpha (degree)
DAT1(55) EBETA Equivalent Euler angle beta (degree)
DAT1(56) EGAMMA Equivalent Euler angle gamma (degree)
IDAT1(57) REF3DOLD Old 3D membership
before last ANG-RECONST/ANCHORSET (EACH_TO_BEST)
IDAT1(58) ACTIVE Image is active or not (EXLUSIVE-COPY and HEADERS):
ACTIVE > 0 : image is set active
ACTIVE < 0 : image is set inactive
ACTIVE = 0 : not set (treated as being set active)
IDAT1(59) NALISUM Number of images summed
(used in SUM-ALIGNED-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 reconstitution) (degree)
DAT1(66) BETA Euler angle beta (3D and angular reconstitution) (degree)
DAT1(67) GAMMA Euler angle gamma (3D and angular reconstitution) (degree)
IDAT1(68) IMAVERS IMAGIC version, which created the file (yyyymmdd)
IDAT1(69) REALTYPE Floating point type / machine stamp:
16777216: VAX/VMS
33686018: Linux, Unix, Mac OSX, MS Windows, OSF, ULTRIX
67372036: SiliconGraphics, SUN, HP, IBM
IDAT1(70) LOCMICRO Location of the picked particle in the original micrograph
IDAT1(71) IXMICRO Central X coordinate of the picked particle in the original micrograph
IDAT1(72) IYMICRO Central Y coordinate of the picked particle in the original micrograph
IDAT1(73) LOCORIG Location of the picked particle in the "original" file
(usually the file created by PICK-PARTICLE or CUT-IMAGE/APERIODIC)
IDAT1(74) NUMFRAME If file contains a movie or the like: number of frames in each movie
If file does not contain a movie or the like: 0
IDAT1(75) PUPSIZE Typical upper size of particle(s) in the image (in pixels)
IDAT1(76) PLOWSIZE Typical lower size of particle(s) in the image (in pixels)
IDAT1(77) PICKEDGX Minimal X distance from edge (PICK-PARTICLES)
IDAT1(78) PICKEDGY Minimal Y distance from edge (PICK-PARTICLES)
IDAT1(79)
   -
IDAT1(93)
BUFFCTRL Old I/O parameters, which are no more used
IDAT1(94) READIM I/O parameter during IMAGIC run: Image is read in from file or not
(No meaning in a closed file)
IDAT1(95) WRITIM I/O buffering parameter during IMAGIC run: Image is dumped to file or not
(No meaning in a closed file)
IDAT1(96) NUM I/O parameter during IMAGIC run: file number of image file
(No meaning in a closed file)
IDAT1(97) NUMHEAD I/O parameter during IMAGIC run: file number of header file
(No meaning in a closed file)
IDAT1(98) LBUF I/O parameter during IMAGIC run: old READIM/WRITIM parameter
0: buffer whole image -1: read/write line by line
(No meaning in a closed file)
IDAT1(99) READONLY I/O parameter during IMAGIC run: open file action mode
1: open read only 0: open read/write
(No meaning in a closed file)
DAT1(100) ANGLE Last rotation angle (degree)
DAT1(101) VOLTAGE Acceleration voltage (Volt)
DAT1(102) SPHABER Spherical aberration (mm)
DAT1(103) FOCDIST Focal distance of objective (mm)
DAT1(104) CCC Cross correlation peak height
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 or before copying the output images in ANG-REC/NEW
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 (degree)
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 eigenvalues/eigenimages in MSA
IDAT1(122) NIACTIVE Number of active images in MSA calculations
DAT1(123) PIXSIZE Pixel/Voxel size (Angstrom)
If DAT1(105) = -1.0 (FABOSA): mm per pixel
DAT1(124) APERTURE Aperture in the back focal plane of the objective lens (in micrometer)
DAT1(125) CTFQUAL CTF quality
DAT1(126) ALPHA2 Euler angle alpha (from projection matching) (degree)
DAT1(127) BETA2 Euler angle beta (from projection matching) (degree)
DAT1(128) GAMMA2 Euler angle gamma (from projection matching) (degree)
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/was active or not during MSA calculations
DAT1(131)
   -
DAT1(199)
COOSMSA MSA coordinates of the "image" along factorial axes (1 through 69).
If more than 69 eigenimages were used all MSA coordinates are stored
in an additional header block
DAT1(150) EIGVAL Eigenvalue if the "image" represents an eigenimage
IDAT1(200)
-
IDAT1(256)
HISTORY Coded history of image (228 characters)


IMAGIC image density file format

The image density file has the extension ".img" and contains the image densities. This file contains only the raw data.

The raw sata can be stored in the following internal IMAGIC formats (see header index DAT1(15) - TYPE):
   REAL : Each image pixel is represented by a 32-bit real/float number
   LONG : Each image pixel is represented by a 32-bit (signed) integer number
   INTG : Each image pixel is represented by a 16-bit (signed) integer number
   PACK : Each image pixel is represented by one (unsigned) byte number
   COMP : Each complex image pixel is represented by 2 REAL values

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 coordinate system.


IMAGIC PLT file formats

An IMAGIC PLT file (extension: .plt) 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 (extension: .cls) 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.


IMAGIC coordinate system

The IMAGIC coordinate system is defined as follows:

The IMAGIC coordinate 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.

Note 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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