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Adrian Quintana edited this page Dec 11, 2017 · 1 revision

angular_discrete_assign

Purpose

This program assigns Euler angles to experimental projections by matching with ideal projections. This matching is done via a DWT correlation. For every experimental projection, differentpsis (in-plane rotations) and shifts are tried (by exhaustive search). For each possible combination of these two variables, the best correlating ideal projection is sought using a fast multirresolution algorithm.

The output of this program is a document file with the predicted angles for each experimental image. The format of this file is


; Predicted_Rot Predicted_Tilt Predicted_Psi Predicted_ShiftX Predicted_ShiftY Corr

This file may be input to xmipp_angular_distance or xmipp_docfile_histogram to compute statistics about the angular assignment step.

Usage


$ angular_discrete_assign -i [selfile in] ...

Parameters

  • `` Set of files and initial shifts. Although the file is a full alignment docfile for compatibility with other alignment programs, only the shifts are taken in consideration in global searches; in local searches, all parameters in the initial docfile are considered.
  • ``. A gallery of reference projections, it must have been produced byCreateProjectionLibrary
  • `` Do not produce on screen information
  • `` Document file with the predicted angles of the experimental projections. Note that these angles and shifts are not written in the experimental image headers.
  • `` Symmetry file if the particle is symmetric. The description of this file may be found at xmipp_symmetrize
  • -max_proj_change [ang-1] = Ideal projections are not considered if their projection direction is further than this maximum change. If the change is -1, then this option is disabled
  • -max_psi_change [ang-1] =
  • -max_shift_change [r0] = Maximum psi (in-plane rotation) and shift explored
  • -psi_step [ang5] =
  • -proj_step [ang5] =
  • -shift_step [r1] = Step size inpsi (in-plane rotation), rotational and tilting angle (only used when projecting the reference images from a reference volume) and shift when they are explored
  • -keep [th50= This parameter controls how many images pass from one subband to the next
  • -smin [s1] =
  • -smax [s-1] = Scales to consider. Scale 0 is the finest,log2(Xdim) is the highest. If the highest is not given, then the coarsest possible is used
  • -pick [mth1] = After exploring all the subbands, one decision must be taken about the best matching reference projection.Mth0= takes the absolute correlation maximum.Mth1= takes the correlation maximum of the most populated group
  • `` Do a 5D search instead of 3D+2D.

For debugging:

  • `` Show debugging information of the rot-tilt process
  • `` Show debugging information of the psi-shift process
  • `` Show debugging information about the final decision for selecting the angles

Examples and notes

A typical use of this program for a complete search assignment is


$ angular_discrete_assign -i experimental.sel -ref reference.sel -oang assigned_angles.txt -max_shift_change 2

A typical use of this program for a refinement search assignment (subsearch) is


$ angular_discrete_assign -i experimental.sel -ref reference.sel -oang assigned_angles.txt -max_shift_change 2 \
-max_psi_change 30 -max_proj_change 30

--Main.AlfredoSolano - 29 Jan 2007

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