IMAGIC Formats and Conventions
Image/3D volumeHeader 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:
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. |
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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 |
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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) | RE | (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) |
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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 |
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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 |
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IDAT1(200) - IDAT1(256) |
HISTORY |
Coded history of image/3D volume (228 characters)
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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:
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 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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