IMAGIC Formats and Conventions
Image/3D volumeHeader file: IMAGIC4D  IMAGIC5 (OLD header file)
Density file
PLT file
Classification (CLS) file
Coordinate system
Euler angles
IMAGIC Image/3D volume
A single (or a stack of) IMAGIC image/3D volume always consists of two files:
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 (NBLOCKS1) 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 THREEDCUT 
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 32bit real/float number LONG : Each pixel/voxel is represented by a 32bit (signed) integer number INTG : Each pixel/voxel is represented by a 16bit (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 CUTIMAGE 
IDAT1(17)  IYOLD  Top left Y coordinate before CUTIMAGE 
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 ANGRECONST/ANCHORSET (EACH_TO_BEST) 
IDAT1(58)  ACTIVE 
Image/3D volume is active or not (EXLUSIVECOPY 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 SUMALIGNEDIMAGES) 
IDAT1(60)  PGROUP 
Pointgroup 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 PICKPARTICLE or CUTIMAGE/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 (PICKPARTICLES) 
IDAT1(78)  PICKEDGY  Minimal Y distance from edge (PICKPARTICLES) 
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 CUTIMAGE or before copying the output images in ANGREC/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 (classsum) 
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 64bit real/float number
REAL : Each pixel/voxel is represented by a 32bit real/float number
LRGE : Each pixel/voxel is represented by a 64bit (signed) integer number
LONG : Each pixel/voxel is represented by a 32bit (signed) integer number
INTG : Each pixel/voxel is represented by a 16bit (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 coordinates, 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 coordinates file:
1st value: X coordinate, 2nd value: Y coordinate, 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 righthanded system with its (1,1) origin
in the topleft 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:
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:
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 Zaxis. We then rotate along the new Yaxis over the angle BETA. Finally, the rotation GAMMY is a rotation around the new Zaxis. 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 Zaxis ("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 3D orientation are gamma and beta. Alpha is
only the final inplane rotation.
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