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Adrian Quintana edited this page Dec 11, 2017 · 1 revision

Headerinfo

Purpose

This utility extracts or assigns rotation angles and origin offsets from/to the headers of 2D-images. The output document files of this program (-extract option), and of the align2d program have a specific format that allows headerinfo assignment without a selfile. This format is the following:

  • One heading comment line containing information about the column numbers
  • For each image: a comment line with its filename, followed by a document line with its rot, tilt, phi, Xoff & Yoff (& Correlation coefficient, in case of align2d)

An example is shown below:


; Headerinfo columns: rot (1), tilt (2), psi (3), Xoff (4), Yoff (5), Corr (6)
; dbua0000.xmp
   1 6     0.00000    0.00000    0.00000   -0.07325   -1.88320    0.44343
; dbua0001.xmp
   2 6     0.00000    0.00000    0.00000   -0.93609   -1.88635    0.36004

In this type of document files the filename of each image is directly coupled with its corresponding angles and shifts. Therefore, assignment of header information using this type of document files is preferred over using a selfile and a corresponding document file.

Usage


$ headerinfo ...

Parameters

  • `` Extract angles and shifts from the headers of images in selfile, and write output to docfile

OR

  • `` Reset all header information (i.e. set all angles, shifts, weights and mirror flags to zero)

OR

  • `` Assign angles and shifts from a document file to the headers of images.

Where[...] are:

  • `` If the document file was created using the headerinfo , theMLalign2D or the align2d program, the image names are contained in the document file and no selfile is required. If the document file comes from somewhere else (e.g. SPIDER) a corresponding selfile has to be provided. This selfile should have the same number of active images as entries in the docfile, and the order should be the same!
  • `` This flag allows you to verify the assignment process by outputting all assignments to the screen
  • -columns [rot1] [tilt=2] [psi=3] [Xoff=4] [Yoff=5] = This option allows to specify in which column of the document file the respective transformation parameters are
  • -weight [col_w6] = Set ML probability weights, which are read from column numbercol_w. These weights are used in ML optimization
  • -mirror [col_m7] = Set mirror-flipping flags, which are read from column numbercol_m
    • mirror1= upon reading of the images, an reverseX-operation is performed, used inMLalign2D
    • mirror0= no reverseX operation is performed (default)
  • `` Round shifts to integer values (for assign and extract modes)
  • -levels [n0] = Levels of pyramidal reduction. This only applies to the assignment of shifts. If the input docfile has a shift of 8 pixels and the images have pyramidally reduced one level, then the shift written in the header will be 4 pixels. If it has been reduced two levels, then the shift will be 2, and so on

Examples and Notes

Extract geometric information from the headers of images in a selfile:


$ headerinfo -extract -i g0u_precentered.sel -o g0u_precentered.doc

Assign geometric information from a document file created by align2d or headerinfo:


$ headerinfo -assign -i g0u_precentered.doc -verb

Assign geometric information from a different type of document file, and with changing the sign of the origin offsets:


$ headerinfo -assign -i g0u_fromSPIDER.doc -o g0u_fromSPIDER.sel -verb -columns 1 2 3 -4 -5

--Main.AlfredoSolano - 17 Jan 2007

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