Contenttype: text/html
Manpage of multiTiltMask
multiTiltMask
Section: User Commands (1)
Index
Return to Main Contents
NAME
multiTiltMask  generate a Fourier domain mask for multiple tilt axes
SYNOPSIS
multiTiltMask csvFile szMask maskFile
multiTiltMask csvFile szMask maskFile edgeShift
multiTiltMask csvFile szMask maskFile edgeShift flgCos
DESCRIPTION
Generate a Fourier space wedge mask for a tomogram reconstructed from
multiple tiltseries whose tilt axes all pass through the origin.
By default, a binary mask with 0's and 1's indicating missing and valid
data locations, will be generated. If flgCos is nonzero, a floating
point mask will be generated with weights proportional to the cosine of
the tilt angle to compensate for the increased effective thickness
at higher tilts. The resulting mask will be stored in an MRC file with
a name specified by maskFile. multiTiltMask can also be used to
generate masks for single axis tomograms with an arbitrary tilt axis.
NOTE: for dual axis tomograms reconstructed with IMOD, see program
dualAxisMask which will automatically extract the appropriate parameters
from the reconstruction directory and run multiTiltMask with them.
 csvFile

The name of the input csv file specifying the tilt axes orientations and
tilt ranges. Each line in this file corresponds to a tilt series, and must
contain 5 values separated by commas. The first 3 values are Slicer (ZYX)
angles in degrees, listed in the order (X,Y,Z), specifying the rotation to
be applied to Y ([0,1,0]') to define the tilt axis for this series. Similarly,
the last 2 values on each line are the min and max tilts for that series.
 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.
 maskFile

The name of the output MRC file which will containing the binary mask.
 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.
 flgCos

(OPTIONAL, default = 0) In nonzero, generate a floatingpoint mask
with weighting according to the cosine of the tilt angle.
AUTHOR
John Heumann
SEE ALSO
PEET(1), alignSubset(1), averageAll(1), and dualAxisMask(1)
Index
 NAME

 SYNOPSIS

 DESCRIPTION

 AUTHOR

 SEE ALSO

This document was created by
man2html,
using the manual pages.
Time: 18:16:05 GMT, January 11, 2021