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multiTiltMask

Section: User Commands (1)
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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 tilt-series 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 non-zero, 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 (Z-Y-X) 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 non-zero, generate a floating-point 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

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Time: 18:16:05 GMT, January 11, 2021