Header_assign

header_assign

Purpose

This utility assigns rotation angles, origin offsets (and optionally weights and mirror flags) to the headers of 2D-images.

Usage

$ header_assign ...

Parameters

• `` Input document file containing all angles, translations (and optionally weights & mirror flags) to set to the image headers.
• `` If the document file is ofNewXmipp type (as defined in the documentation of theHeader_extract 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
• `` Force the assignment even if the docfile is of newxmipp-type.
• -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
• -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

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

$ header_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:

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

--Main.SjorsScheres - 24 Apr 2007