Header file
Image file
Plt file
Classification (cls) file
Co-ordinate System
Euler angles
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IMAGIC-5 FILE FORMATS
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Formats
Header file Image file Plt file Classification (cls) file Co-ordinate System Euler angles |
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IMAGIC-5 Header file format
An IMAGIC-5 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-5 run |
| IDAT1(4) | NHFR | number of header records per image (=1 always) |
| 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) | NPIX2 |
image size in BYTES as seen from the program (IDAT1(13)*IDAT1(89)) |
| IDAT1(12) | NPIXEL | total number of image elements |
| IDAT1(13) | IXLP | number of lines per image (for 1D data IYLP1=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) | VARIAN | variance of densities in image |
| DAT1(21) | OLDAVD | old average density of this image |
| 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) | CXLENGTH | cell dimension in Angstr. (x-direction) (MRC(12)) |
| DAT1(26) | CYLENGTH | cell dimension in Angstr. (y-direction) (MRC(11)) |
| DAT1(27) | CZLENGTH | cell dimension in Angstr. (z-direction) (MRC(13)) |
| DAT1(28) | CALPHA | cell angle alpha (MRC(14)) |
| DAT1(29) | CBETA | cell angle beta (MRC(15)) |
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IDAT1(30) - IDAT1(49) |
NAME | coded NAME/TITLE of the image (80 characters) |
| DAT1(50) | CGAMMA |
cell angle gamma (MRC(16)) |
| IDAT1(51) | MAPC |
axis corresponding to columns (MRC(17)) (1,2,3 for X,Y,Z) |
| IDAT1(52) | MAPR |
axis corresponding to rows (MRC(18)) (1,2,3 for X,Y,Z) |
| IDAT1(53) | MAPS |
axis corresponding to sections (MRC(19)) (1,2,3 for X,Y,Z) |
| IDAT1(54) | ISPG | space group (MRC(23)) |
| IDAT1(55) | NXSTART |
number of 1st column in map (def:0) (MRC(6)) (where map starts in columns) |
| IDAT1(56) | NYSTART |
number of 1st row in map (def:0) (MRC(5)) (where map starts in rows) |
| IDAT1(57) | NZSTART |
number of 1st section in map (def:0) (MRC(7)) (where map starts in sections) |
| IDAT1(58) | NXINTV | number of intervals along X (MRC(9)) |
| IDAT1(59) | NYINTV | number of intervals along Y (MRC(8)) |
| IDAT1(60) | NZINTV | number of intervals along Z (MRC(10)) |
| IDAT1(61) | IZLP | number of 2D planes in 3D data (for 2D: IZLP1=1) |
| IDAT1(62) | I4LP | number of 3D volumes in 4D data (for 2D: I4LP1=1) |
| 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-5 version used (yyyymmdd) |
| IDAT1(69) | REALTYPE |
floating point type, machine stamp 16777216 for VAX/VMS 33686018 for OSF,ULTRIX, LINUX, MS Windows 67372036 for SiliconGraphics, SUN, HP, IBM |
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IDAT1(70) - IDAT1(98) |
Variables that control the buffering during read/write in IMAGIC-5 programs. PLEASE DO NOT TOUCH ! |
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| IDAT1(99) | RONLY |
flag in calling program to open file readonly (1: readonly) |
| DAT1(100) | ANGLE | last rotation angle |
| DAT1(101) | RCP | rotational correlation peak |
| IDAT1(102) | IXPEAK | shift correlation peak in X direction |
| IDAT1(103) | IYPEAK | shift correlation peak in Y direction |
| 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 (TRUE-THREED) |
| IDAT1(107) | REF | (multi-) reference number |
| DAT1(108) | CLASSNO | class number in classification |
| DAT1(109) | LOCOLD |
location number before CUT-IMAGE (boxing) or copy in ANGULAR and EX-COPY |
| DAT1(110) | OLDAVD |
old average density (before NORM-VARIANCE, for example) |
| DAT1(111) | OLDSIGMA | old sigma |
| DAT1(112) | XSHIFT | last shift in X direction |
| DAT1(113) | YSHIFT | last shift in Y direction |
| DAT1(114) | NUMCLS |
number of class members |
| DAT1(115) | OVQUAL |
overall class quality if the image is a class average |
| DAT1(116) | EANGLE | equivalent angle |
| DAT1(117) | EXSHIFT | equivalent shift in X direction |
| DAT1(118) | EYSHIFT | equivalent shift in Y direction |
| DAT1(119) | CMTOTVAR | used in MSA/IMAGECOOS |
| 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 |
| 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) |
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DAT1(126) - DAT1(128) |
Special 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 |
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DAT1(131) - DAT1(199) |
COOSMSA |
co-ordinates of "image" along factorial axis number 1 through 69 (maximum possible). Used during MSA calculations. |
| DAT1(150) | EIGVAL |
eigenvalues if the "images" represent eigenimages (eigenvalue #1 into loc#1 etc.) |
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IDAT1(200) - IDAT1(256) |
HISTORY |
coded history of image (228 characters)
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IMAGIC-5 image file format
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An IMAGIC-5 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-5 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. |
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| 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-5 co-ordinate system . | |
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IMAGIC-5 PLT file formats
An IMAGIC-5 "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 |
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IMAGIC-5 classification "CLS" File Format
An IMAGIC-5 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). |
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IMAGIC-5 co-ordinate system
The IMAGIC-5 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:
( 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:
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IMAGIC-5 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":
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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