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dualAxisMask

Section: User Commands (1)
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NAME

dualAxisMask - generate a Fourier domain mask for a dual axis tomogram  

SYNOPSIS

dualAxisMask szMask dirname basename edgeShift  

DESCRIPTION

Generate a binary mask with 0's and 1's indicating missing and valid data locations, respectively, in Fourier space for a tomogram reconstructed from two approximately orthogonal tilt series using IMOD. The resulting binary mask will be stored as an MRC file containing unsigned bytes and named <basename>_DualAxisMask.mrc. dualAxisMask will extract the necessary parameters from the original IMOD reconstruction directory in <basename> and then run multiTiltMask to generate the mask file.

For each axis, the minimum and maximum tilt angle will be extracted from the corresponding tilt file, <basename>{a|b}.tlt, and clockwise sample rotation from the minimum to the maximum tilt angle assumed. Rotation from maximum to minimum tilt passing through 90 degrees is not currently supported.

szMask
The desired size of the 3D mask in voxels. This should be a single, even integer, since the resulting mask with always be cubical.
dirname
The path to the IMOD directory in which the original dual axis reconstruction was done.
basename
The basename used for the IMOD reconstruction. For example, if the original projection stacks were store in BBa.st and BBb.st, the basename would be "BB".
edgeShift
(OPTIONAL, default = 0) The number of voxels to shift the mask boundary perpendicular to the bounding planes to ensure that all useful frequency information is included.
 

AUTHOR

John Heumann  

SEE ALSO

PEET(1), alignSubset(1), averageAll(1), and multiTiltMask(1)


 

Index

NAME
SYNOPSIS
DESCRIPTION
AUTHOR
SEE ALSO

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Time: 21:10:05 GMT, March 20, 2017