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applyBinaryMask

Section: User Commands (1)
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NAME

applyBinaryMask - mask a real 3D volume in real or Fourier space

SYNOPSIS

applyBinaryMask maskFilename inFilename outFilename
applyBinaryMask maskFilename inFilename outFilename flgFFT
applyBinaryMask maskFilename inFilename outFilename flgFFT flgRescale

DESCRIPTION

applyBinaryMask forms the voxel-by-voxel product the supplied mask with either the input volume or its FFT and writes the resulting real/object space result to the output file. This is useful for verifying mask alignments, for example, and for assessing the impact of a missing tomographic data (e.g. the "missing wedge") on a test volume.

maskFilename: is the path to the MRC file containing the binary mask volume. Non-zero entries in the volume will be treated as ones.
inFilename: is the path to the file containing the volume to be masked as an MRC image. The input and mask volumes must be the same dimensions.
outFilename: is the path to which the resulting output will be written. Contents of any pre-existing file at this location will be lost.
flgFFT = [0 | 1]: By default, the mask is applied directly to the input volume. To apply the mask to the FFT of the volume and then take the inverse FFT, set flgFFT to 1. In the Fourier domain, the center of the mask is taken to be at 0 frequency.
flgRescale = [0 | 1]: By default, applyBinary mask scales the output volume to have the same min and max voxel values as the input. To suppress re-scaling, set flgRescale to 0.

AUTHOR

John Heumann