Manpage of randomizePhaseAbove
Section: User Commands (1)
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randomizePhaseAbove - randomize fft phase above a specified frequency
randomizePhaseAbove freq inputFile outputFile
randomizePhaseAbove freq inputFile outputFile flgShuffle
Given a MRC file containing a real 3D volume, compute its discrete
Fourier transform, randomize the phases of terms above a specified
radial frequency, and save the resulting real output volume. (Note: 1D
and 2D "volumes" are now also allowed, but have not been well tested).
Phase randomization can be used to identify unrealistic resolution
estimates from Fourier Shell Correlations (FSCs) as a result of
overfitting noise or of masking. See Chen et al (2013),
Ultramicroscopy: 24-35 for more details.
EXPERIMENTAL: Phase randomization can also be used in addition to or
in place of low-pass filtering to avoid overfitting during alignment.
See the randomizePhaseAbove setting on the PEET man page for details.
This program is compute and memory intensive. Processing a 2048x2048x256
volume requires ~5 minutes on an 8-core, 3.3 GHz system with at least 32 GB
of ram. GPU processing is not currently available, and running on a system
with insufficient memory can cause the program and the system to become
Radial cutoff frequency expressed as a fraction of the sampling
frequency. Must be between 0 and 0.5 * sqrt( 3 ) = ~0.866. The Nyquist
frequency corresponds to 0.5, so it would be unusual to need values
The input MRC file, which must contain a real volume. Internally,
this volume will always be procssed as single-precision floating
point, regardless of the original storage mode.
Where to save the output MRC file. Any previously existing file in
this location will be silently overwritten. The output volume will
always be saved as single precsion floating point, independent of
the mode of the input volume.
John M. Heumann
PEET(1), calcFSC(1), calcUnbiasedFSC(1)
- SEE ALSO
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Time: 18:16:05 GMT, January 11, 2021