IMAGIC Formats and Conventions

Image/3D volume
Header file: IMAGIC-4D | IMAGIC-5 (OLD header file)
Density file
PLT file
Classification (CLS) file
Co-ordinate system
Euler angles

IMAGIC Image/3D volume

A single (or a stack of) IMAGIC image/3D volume always consists of two files:
  • a header file with the extension ".hed" which contains information for each image/section
  • a density/image file with extension ".img" which contains the image/3D volume densities.

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

Note: A 3D volume is stored as a stack of 2D sections each with its own header and image. the relevant 3D header values are only stored in the header of its first section.


IMAGIC header file format

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

The header file contains NBLOCKS (defined in IDAT1(4)) records per image/section stored. The first header record for each image/section 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 Overall number of image/section in file (location) (1,2,3,...)
IDAT1(2) IFOL Number of all 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 images/sections in the file.
IDAT1(3) IERROR Error code during an IMAGIC run
(No meaning in a closed file)
IDAT1(4) NBLOCKS Number of header blocks (each block containing
256 REAL/INTEGER values).
For a usual header: NBLOCKS = 1
IDAT1(5) CMONTH Creation month
IDAT1(6) CDAY Creation day
IDAT1(7) CYEAR Creation year
IDAT1(8) CHOUR Creation hour
IDAT1(9) CMINUT Creation minute
IDAT1(10) CSEC Creation second
IDAT1(11) RSIZE Image/section 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/section (for 1D data IXLP=1)
IDAT1(14) IYLP Number of pixels per line
IDAT1(15) TYPE 4 coded characters determining the data type/format:
REAL : Each pixel/voxel is represented by a 32-bit real/float number
LONG : Each pixel/voxel is represented by a 32-bit (signed) integer number
INTG : Each pixel/voxel is represented by a 16-bit (signed) integer number
PACK : Each pixel/voxel is represented by one (unsigned) byte number
COMP : Each complex pixel/voxel 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/section
DAT1(19) SIGMA Sigma of image/section densities
DAT1(20) USER1 At user's own disposal
DAT1(21) USER2 At user's own disposal
DAT1(22) DENSMAX Highest density in image/section
DAT1(23) DENSMIN Minimal density in image/section
IDAT1(24) COMPLEX Label indicating that densities are 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 represents a sinogram
Maximal wave number if image represents a spectrum
DAT1(29) SINOEND
WAVESTEP
End angle if image represents a sinogram
Step size of wave numbers if image represents a spectrum
IDAT1(30)
    -
IDAT1(49)
NAME Coded NAME/TITLE (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/3D volume is active or not (EXLUSIVE-COPY and HEADERS):
ACTIVE > 0 : image/3D volume is set active
ACTIVE < 0 : image/3D volume 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) NFRAME 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) STATS2D 2D statistics is set (1) or not (0)
IDAT1(80) STATS3D 3D statistics is set (1) or not (0)
DAT1(81) MAX3D Maximal density in 3D volume
DAT1(82) MIN3D Minimal density in 3D volume
DAT1(83) AVDENS3D Average density in 3D volume
DAT1(84) SIGMA3D Sigma of densities in 3D volume
DAT1(85) DISPMAX Maximum scaling value in DISPLAY
DAT1(86) DISPMIN Minimum scaling value in DISPLAY
IDAT1(87) STATSMOV Movie frames statistics is set (1) or not (0)
DAT1(88) MAXMOV Maximal density in related movie sum
DAT1(89) MINMOV Minimal density in related movie sum
DAT1(90) AVDMOV Average density in related movie sum
DAT1(91) SIGMOV Sigma of densities in related movie sum
DAT1(92) ZOOM Last zoom factor
DAT1(93) EZOOM Equivalent zoom factor
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 if input was MSA eigeniltered
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) NCLS Number of members if the input represents a class average (class-sum)
DAT1(115) OVQUAL Overall quality if input represents a class average
Added variance if input represents a class member
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) NEIGEN Number of eigenvalues/eigenvectors in MSA calculations
IDAT1(122) NIACTIVE Number of active images/3D volumes 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 if the image/3D volume was active or not during MSA calculations
DAT1(131)
   -
DAT1(199)
COOSMSA MSA coordinates of the image/3D volume along factorial axes (1 through 69).
If more than 69 eigenvectors were used all MSA coordinates are stored in an additional header block.
DAT1(150) EIGVAL Eigenvalue if the image/3D volume represents an eigenvector
IDAT1(200)
-
IDAT1(256)
HISTORY Coded history of image/3D volume (228 characters)


IMAGIC density/image file format

The density/image file has the extension ".img" and contains the image/section 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):
   DBLE : Each pixel/voxel is represented by a 64-bit real/float number
   REAL : Each pixel/voxel is represented by a 32-bit real/float number
   LRGE : Each pixel/voxel is represented by a 64-bit (signed) integer number
   LONG : Each pixel/voxel is represented by a 32-bit (signed) integer number
   INTG : Each pixel/voxel is represented by a 16-bit (signed) integer number
   PACK : Each pixel/voxel is represented by one (unsigned) byte number
   COMP : Each complex pixel/voxel 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/section. The length of the lines is NY and the number of lines is NX:


The centre of an image/section, for almost all operations, 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:


The centre, for almost all operations, is given by:

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


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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