ST - Set values in image header

(09/27/06)

PURPOSE

Allows the user to:
1. Put image tilt angles into header.
2. Alter any specified buffer position in the file header.
3. Clear the statistical values in header of a file.
4. Put maximum and minimum into header if known a priori.

SEE ALSO

ST H [Set values in image/volume Header by name]
FI X [File Information - Retrieve file header value(s) by location]
LI T [List image values - on terminal]

USAGE

.OPERATION: ST

.INPUT FILE: PIC001
[Enter the name of the file to be manipulated.]

.(A)NGLES, (B)UF, (P)COPY, (C)LEAR, OR (F)IX:
[Option A : Angles. Put new angles into header.

Option B : Buffer. Put new values into specified locations in the header. (Can be any location)

Option P : Copy Header Angles. Copies header angles from the input file to header of the output file. Output file must already exist. It is not created. Input file remains unchanged.

Option C : Clear. Unsets the flag indicating that the MAX and MIN have been stored in the header.

Option F : Fix. Puts MINIMUM, MAXIMUM, AVERAGE & S.D. statistical values into header, if known a priori.

For "A" SPIDER will ask:

.ANGLE SET 1, 2,OR 3: 1
[There are three sets of angles that can be stored in the file header. Normally set: 1 should be used. For details of the other two sets see manual chapter for operation "VO CEUL" (combine Euler rotations)]

.ENTER PHI AND THETA: 30.0,60.0

.ENTER PSI: 90.0

For "B" SPIDER will ask:

.ENTER NUMBER(S) OF HEADER LOCATION TO BE CHANGED: 17

.ENTER NEW VALUE FOR EACH HEADER LOCATION CHANGED: 75.0

For "P" SPIDER will ask:

.OUTPUT FILE: PIC002
[Enter the name of the output file.]

For "F" SPIDER will ask:

.ENTER IMAGE MAXIMUM: 5.0

.ENTER IMAGE MINIMUM: 0.0

.AVERAGE AND STANDARD DEVIATION AVAILABLE (Y/N)': Y
[These values are now required otherwise they may be inconsistent with the min. and max.]

.ENTER AVERAGE, STANDARD DEVIATION: 2.0, 1.0

NOTES

  1. If a file is write-protected, the file cannot be overwritten by any operation. Any attempt to overwrite the file will result in an error message.

  2. Option 'C' is useful to force SPIDER to correct inaccurate MIN & MAX information.

  3. Option 'B' is usually used to correct damaged file headers.

  4. Some locations from the file header that can be set:

    Location Name Content
    1NSLICE Number of slices (planes) in volume (=1 for an image) In some legacy 2D images this may be -1)
    2NROW Number of rows per slice.
    3IREC Total number of records (including header records) in each image of a simple image or stacked image file.
    4UNUSEDUnassigned
    5IFORM File type specifier.
    1 R 2D image.
    3 R 3D volume.
    -11 FO 2D Fourier, mixed radix odd
    -12 FE 2D Fourier, mixed radix even
    -21 FO 3D Fourier, mixed radix odd
    -22 FE 3D Fourier, mixed radix even
    6IMAMIMaximum/minimum flag = 0 when the file is created, and = 1 when the maximum, minimum, average, and standard deviation have been computed and stored into this header record (see following locations).
    7FMAX Maximum data value.
    8FMIN Minimum data value.
    9AV Average data value.
    10SIG Standard deviation of data. A value of -1.0 or 0.0 indicates that SIG has not been computed.
    11UNUSED Obsolete, no longer used.
    12NSAM Number of pixels (samples) per line.
    13LABREC Number of records in file header (label).
    14IANGLE Flag that following three tilt angles are present.
    15PHI Tilt angle: phi (See note #2 below).
    16THETA Tilt angle: theta.
    17GAMMA Tilt angle: gamma (also called psi).
    18XOFF X translation.
    19YOFF Y translation.
    20ZOFF Z translation.
    21SCALE Scale factor.
    22LABBYT Total number of bytes in header.
    23LENBYT Record length in bytes.
    24ISTACK/
    MAXINDX    		Position has a value of 0 in simple 2D or 3D (non-stack) files. In an "image stack" there is one overall stack header followed by a stack of images, in which each image has its own image header. A value of >0 in this position in the overall stack header indicates a stack of images. A value of <0 in this position in the overall stack header indicates an indexed stack of images and gives the maximum image number (MAXINDX) allowed in the index.
    25UNUSEDUnused now. Prior to release 9.0, a '-1' at this location in an overall stack indicated a valid stack and in the stacked images, a value of 1 indicated that this image was in use (existed).
    26MAXIMPosition is only used in the overall header for a stacked image file. There, this position contains the number of the highest image currently used in the stack. This number is updated, if necessary, when an image is added or deleted from the stack.
    27IMGNUMPosition is only used in a stacked image header. There, this position contains the number of the current image or zero if this image is unused.
    28LASTINDXPosition is only used in overall header of indexed stacks. There, this position is the highest index location currently in use.
    29UNUSEDUnassigned
    30UNUSEDUnassigned
    31KANGLEFlag that additional rotation angles follow in header. 1 = one additional angle set is present, 2 = two additional angle sets. These rotation angles preceed any rotation stored in positions: 15..18.
    32PHI1 Angle.
    33THETA1 Angle.
    34PSI1 Angle.
    35PHI2 Angle.
    36THETA2 Angle.
    37PSI2 Angle.
    38PIXSIZ Pixel size (Angstroms).
    39EV Electron voltage used.
    40PROJ Project number.
    41MIC Micrograph number.
    42NUM Image number.
    43-49UNUSED Unassigned.
    50-76 - Used for Xmipp transforms.
    77-100- Unassigned.
    101 PSI3 Projection angle: Psi (From 'PJ 3Q').
    102 THETA3 Projection angle: Theta (From 'PJ 3Q').
    103 PHI3 Projection angle: Phi (From 'PJ 3Q').
    104 LANGLE If = 1 then projection angles: PSI3, THETA3 & PHI3 are present in header.
    105-211 - Unassigned
    212-214CDAT11 Character creation date e.g. 27-MAY-1999
    215-216CTIM8 Character creation time e.g. 09:43:19
    217-256 CTIT160 Character title

SUBROUTINES

UTIL1, SETVAL, SETLAB

CALLER

UTIL1
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