ST H - Set values in image/volume Header by name



Allows the user to alter any named position in standard SPIDER image/volume file header.   Example.


ST [Set values in image header]
FI H [File Information - Retrieve file Header values by name]
LI T [List image values - on terminal]



[Enter name of the file whose header will be altered.]

[Enter names of standard SPIDER file header variables you wish to alter. Here: value of PIXSIZ (File header location: 38) and value of: AV (File header location: 9) will be altered.]

.VALUE(S): 99, 33
[Enter values for the standard SPIDER header variables specified above. Here: value of PIXSIZ (File header location: 38) will be set to: 99.0 and the value of: AV (File header location: 9) will be set to: 33. ]


  1. Altering certain positions in a SPIDER header may make the file unreadable in SPIDER!.

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

    Location Name Content
    1NZ Number of slices (planes) in volume (=1 for an image) Previously called: NSLICE. In some legacy 2D images this may be -1
    2NY Number of rows per slice. Previously called: NROW.
    3IREC Total number of records (including header records) in each image of a simple image or stacked image file.
    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.
    12NX Number of pixels (samples) per line. Previously called: NSAM.
    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.
    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.
    31KANGLEFlag that additional rotation angles follow in header. 1 = one additional angle set is present, 2 = two additional angle sets.
    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 Micrograph window number.
    43GLONUM Global image number.
    44-47UNUSED Unassigned.
    48-76 - Used for Xmipp or other local 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





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