Xmipp

xmipp_angular_continuous_assign (v3.0)

Usage

Make a continuous angular assignment This program assigns Euler angles to experimental projections by minimizing the difference between the given experimental image and the central slice of a reference volume in Fourier space. All interpolations are based on a B-spline model of the images and the volume. The translations are also optimized. Since an iterative optimization is performed, it must be initialized with some rough estimate of the angles. The output of xmipp_angular_predict can be used as initialization without any transformation. The method is fully described at http://www.ncbi.nlm.nih.gov/pubmed/15885434

Parameters

-i, --input <input_file>
Metadata with initial alignment
--mode <mode=overwrite>
Metadata writing mode.
where <mode> can be:
  • overwrite Replace the content of the file with the Metadata
  • append Write the Metadata as a new block, removing the old one
-o, --output <output_file=>
Metadata with output alignment
--ref <volume>
Reference volume
--gaussian_Fourier <s=0.5>
Weighting sigma in Fourier space Small values of this parameter concentrate the optimization on low frequencies. This value should be below 1.
--gaussian_Real <s=0.5>
Weighting sigma in Real space Small values of this parameter concentrate the optimization in the image center. This value should be below 1.
--zerofreq_weight <s=0.>
Zero-frequency weight
--max_iter <max=60>
Maximum number of iterations Convergence might be reached before this number of iterations
--max_shift <s=-1>
Maximum shift allowed Use this option to limit the maximum shift that the optimization process can find. If the minimum is found beyond this limit (note it is an absolute limit on the shift and it is not relative to the initial shift), then the solution given by the initial guess is kept since the optimized one looks suspicious.
--max_angular_change <a=-1>
Maximum angular change allowed Use this option to limit the maximum angular change with respect to the initial solution that the optimization algorithm can find. If the solution found is beyond this limit, then the initial solution is returned instead of the optimized one since this latter looks suspicious.

Examples and notes

A typical use is:
xmipp_angular_continuous_assign -i anglesFromDiscreteAssignment.doc --ref reference.vol -o assigned_angles.xmd

User's comments

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