Xmipp/Spider Format Byte Format Selection Files Document Files Xmipp/Spider Format Byte Format Selection Files Document Files
Xmipp/Spider
FormatThe sipder file is (cols x rows x slices) * 4 + header size bytes long .
note:
- 4 is used because a float number is represented by
4 bytes.
- slices = 1 in case of 2D images.
The image header is a structure that holds important information about the image. Some of the header fields are not used by Xmipp, however, Xmipp preserves the integrity of thet information in order to make them compatible with Spider programs. Xmipp library and progrmas treat the header internally and automatically to avoid direct interaction with this complicate structure. (See imageXmipp and volumenXmipp classes)
Description of the header file: (the fields are defined in C data
types)
Dimension information (Also used by Xmipp)
/* 1*/ float fNslice;
// NUMBER OF SLICES (PLANES) IN VOLUME
// (=1 FOR AN IMAGE)
/* 2 */ float fNrow;
// NUMBER OF ROWS PER SLICE (Rows Y)
Internal information for a complicated calculation of file lenght.
/* 3 */ float fNrec;
// TOTAL NUMBER OF RECORDS .
/* 4 */ float fNlabel;
// AUXILIARY NUMBER TO COMPUTE TOTAL NUMBER OF RECS
File type information (Also used by Xmipp)
/* 5 */ float fIform;
// FILE TYPE SPECIFIER.
// +3 FOR A 3-D FILE
// +1 FOR A 2-D IMAGE
// -1 FOR A 2-D FOURIER TRANSFORM
// -3 FOR A 3-D FOURIER TRANSFORM
// -5 FOR A NEW 2-D FOURIER TRANSFORM
// -7 FOR A NEW 3-D FOURIER TRANSFORM
// +8 FOR A 2-D EIGHT BIT IMAGE FILE
// 11 FOR A 2-D EIGHT BIT COLOR IMAGE FILE
Flag and statistical
information never used by Xmipp (set to 0 except for fAv that is set to
-1)
/* 6 */ float fImami;
// MAXIMUM/MINIMUM FLAG. IS SET AT 0 WHEN THE
// FILE IS CREATED, AND AT 1 WHEN THE MAXIMUM AND
// MINIMUM HAVE BEEN COMPUTED, AND HAVE BEEN STORED
// INTO THIS LABEL RECORD (SEE FOLLOWING WORDS)
/* 7 */ float fFmax;
// MAXIMUM VALUE
/* 8 */ float fFmin;
// MINIMUM VALUE
/* 9 */ float fAv;
// AVERAGE VALUE
/* 10*/ float fSig;
// STANDARD DEVIATION. A VALUE OF -1. INDICATES
// THAT SIG HAS NOT BEEN COMPUTED PREVIOUSLY.
Flag never used by Xmipp
/* 11*/ float fIhist;
// FLAG INDICATING IF THE HISTOGRAM HAS BE
// COMPUTED. NOT USED IN 3D FILES!
Dimesnsion information (Also used by Xmipp)
/* 12*/ float fNcol; // NUMBER OF PIXELS PER LINE (Columns X)
Internal information for a complicated calculation of file lenght.
/* 13*/ float fLabrec; // NUMBER OF LABEL RECORDS IN FILE HEADER
Euler Angles (Also used by Xmipp)
/* 14*/ float fIangle;
// FLAG THAT TILT ANGLES HAVE BEEN FILLED
/* 15*/ float fPhi;
// EULER: ROTATIONAL ANGLE
/* 16*/ float fTheta;
// EULER: TILT ANGLE
/* 17*/ float fPsi;
// EULER: PSI = TILT ANGLE
Aditional translational information (Never used by Xmipp).
/* 18*/ float fXoff;
// X TRANSLATION
/* 19*/ float fYoff;
// Y TRANSLATION
/* 20*/ float fZoff;
// Z TRANSLATION
Scale information (Never used by Xmipp).
/* 21*/ float fScale; // SCALE
Internal information for a complicated calculation of file lenght.
/* 22*/ float fLabbyt;
// TOTAL NUMBER OF BYTES IN LABEL
/* 23*/ float fLenbyt;
// RECORD LENGTH IN BYTES
Empty and unused space
char fNada[24]; // Empty Space (not used)
Flag never used by Xmipp
/* 30*/ float fFlag;
// THAT ANGLES ARE SET. 1 = ONE ADDITIONAL
// ROTATION IS PRESENT, 2 = ADDITIONAL ROTATION
// THAT PRECEEDS THE ROTATION THAT WAS STORED IN 15
Used to contain additional rotation information. Now it's not used (set to 0)
/* 31*/ float fPhi1;
/* 32*/ float fTheta1;
/* 33*/ float fPsi1;
/* 34*/ float fPhi2;
/* 35*/ float fTheta2;
/* 36*/ float fPsi2;
Previously used by Xmipp.
double fGeo_matrix[3][3]; // Geometric
info
float fAngle1;
// angle info
float fr1;
float fr2;
// lift up cosine mask parameters
Used in Xmipp for Radon Transform
float RTflag;
// 1=RT, 2=FFT(RT)
float Astart;
float Aend;
float Ainc;
float Rsigma;
float Tstart;
float Tend;
float Tinc;
Empty and
unused space
char fNada2[584];
Date/Time and title fields (Also used by Xmipp)
/*212-214*/ char szIDat[12]; //
LOGICAL * 1 ARRAY DIMENSIONED 10, CONTAINING
// THE DATE OF CREATION (10 CHARS)
/*215-216*/ char szITim[8];
// LOGICAL * 1 ARRAY DIMENSIONED 8, CONTAINING
// THE TIME OF CREATION (8 CHARS)
/*217-256*/ char szITit[160]; //
LOGICAL * 1 ARRAY DIMENSIONED 160
Byte
FormatAs an example of how information is physically written to disk, imagine a 64x64 image (remember that in Xmipp images the top left corner define the physical origin, see also Matrix2D), the pixels are stored in the following order:
(0,0) (0,1) (0,2) ... (0,63) (1,0) (1,1) ... ... ... ... (63,0) ... (63,63)
where the former coordinates are given as (Y,X).
Selection
FilesHence, each entry in the list is formed by the image name (it might include some path) and the state (ACTIVE=1, or DISCARDED=-1) for this process. Comments can also be included either using ';' or '#' in the first column. The spacing is not relevant at all, and notice that this file is not compatible with the Spider selection files, based on document files using the key as number of the filename. Notice that in Spider selection files you cannot give different image sets (defined by different root names) but in Xmipp you can, as you are giving the full imagename.
# This is a comment
; This is also a comment
prj0001.dem 1
prj0002.dem 1
prj0003.dem 1
prj0004.dem 1
prj0005.dem 1
prj0006.dem -1
prj0007.dem 1
prj0008.dem 1
Test/prj0009.dem 1
Back to the beginning
Document
FilesIn each record you can write in Xmipp as many numerical fields as you like, and the number of fields need not to be the same in all records. However, if you want to keep compatibility with Spider, then the number of fields is restricted to be less than 7, ie, a maximum of 6 (there is a way of extending the record using -999 as key but it has not been implemented in the Xmipp environment).
Between the record key and the data itself goes an integer number which says how many data fields compose this line. If you have 3 data fields, then this number is 3. In Xmipp you can specify as many fields as you like, with some limitation as you only have a single character to specify the number of fields. The trick used is to indicate the number of fields using the ASCII code of the different characters. This way '1' means a single field, '2' two fields, ..., '9' 9 fields, and ':', ';', '<' are respectively 10, 11, 12 fields, and so one. The idea is that the ASCII code ':' is 58 that is 48+10, the ASCII for ';' is 48+11, ...
You can add comments to the document file either with a semicolon (';') in the second column of the line (Spider fashion) or with a semicolon ';' or '#' as the first character of the line, regardless the column it is (Xmipp fashion). Xmipp recognizes both ways of defining comments. Even empty lines (with no characters at all) are also allowed in Xmipp.
Here goes an example of a document file: the first line is the column
number, the second the meaning of the file at that position, later a comment
(typical in Spider) telling you information about the extensions of data
and code (dat in both cases), the name of the file and its creation time.
The following are the different records, in this case there are only 5
records with no correlative keys (notice that the 6th record is commented
out). In all lines the second field is a 2, telling that only the 2 first
numerical fields are relevant in the line. This is a way to manage lines
with a lot of fields in Xmipp mantaining the compatibility with Spider
which only admits 6 numerical fields in the same line.
123456789 123456789 123456789 123456789 123456789
1234565789 123456789 123456789
KEY# REGS/ VALUE
VALUE VALUE
VALUE VALUE
VALUE
LINE
; dat/dat 18-Jul-94 AT
14:29:48 jnk000.dat
1 2 20.000
21.000 21.000
21.000 81.000
81.000
12 2 20.000
56.000 21.000
25.000 21.000
81.000
102 2 20.000
16.000 33.000
21.000 61.000
81.000
8345 2 20.000
21.000 21.000
26.000 21.000
81.000
28345 2 20.000
21.000 21.000
26.000 21.000
81.000
; 6 2 20.000
22.000 21.000
21.000 44.000
81.000as
The spacing between numbers is very important in Spider programs (based in Fortran I/O routines) but not in Xmipp (programmed in C++). To keep compatibility between both systems the exact structure to write a line is
KKKKK N +FFFF.FFFFF +FFFF.FFFFF +FFFF.FFFFF +FFFF.FFFFF...
where K is a Key digit, N is the Number of Fields, and F is a field digit. In Fortran the format string is I5 I16G12.5 and in C++ the following code has been generated
ostream& operator << (ostream&
o, DocLine &DL) {
char aux[30];
string str="";
switch (DL.line_type) {
case (1):
// Print a data line
sprintf(aux,"%5d ",DL.key);
str += aux;
sprintf(aux,"%c ",48+DL.data.size()); str += aux;
for (int i=0; i<DL.data.size(); i++) {
sprintf(aux," % 10.5f",DL.data[i]); str += aux;
}
o << str << endl;
break;
case (2):
// Print a comment
o << DL.text << endl; break;
}
return o;
}
