Content-type: text/html Manpage of randomizePhaseAbove

randomizePhaseAbove

Section: User Commands (1)
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NAME

randomizePhaseAbove - randomize fft phase above a specified frequency  

SYNOPSIS

randomizePhaseAbove freq inputFile outputFile
randomizePhaseAbove freq inputFile outputFile flgShuffle  

DESCRIPTION

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.

This program is compute and memory intensive. Pprocessing a 1024x2048x128 volume takes roughly 5 minutes on a 5-10 GHz cpu with at least 5-10 GB of RAM; a 2048x2048x256 volume takes ~20 minutes and requires ~20 GB of RAM. Parallel or gpu processing is not currently available, and running on a system with insufficient memory can cause the program and the system to become unresponsive.

freq
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 above ~0.35.
inputFile
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.
outputFile
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.

 

AUTHOR

John M. Heumann  

SEE ALSO

PEET(1), calcFSC(1), calcUnbiasedFSC(1)


 

Index

NAME
SYNOPSIS
DESCRIPTION
AUTHOR
SEE ALSO

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Time: 21:10:06 GMT, March 20, 2017