EMAN2 Aligner Manual


Last modified on Thu, 09 Dec 2010 13:44:55 CST
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Aligner Name Parameters Description
frm2d int maxshift: Maximum translation in pixels in any direction. If the solution yields a shift beyond this value in any direction, then the refinement is judged a failure and the original alignment is used as the solution.
FRM2D uses two rotational parameters and one translational parameter
refine int maxiter: The maximum number of iterations that can be performed by the Simplex minimizer
int maxshift: Maximum translation in pixels in any direction. If the solution yields a shift beyond this value in any direction, then the refinement is judged a failure and the original alignment is used as the solution.
int mode: Currently unused
float precision: The precision which, if achieved, can stop the iterative refinement before reaching the maximum iterations. Default is 0.04.
float stepaz: The rotational increment used to create the starting simplex. Default is 5
float stepx: The x increment used to create the starting simplex. Default is 1
float stepy: The y increment used to create the starting simplex. Default is 1
tranform xform.align2d: The Transform storing the starting guess. If unspecified the identity matrix is used
Refines a preliminary 2D alignment using a simplex algorithm. Subpixel precision.
refine.3d int maxiter: The maximum number of iterations that can be performed by the Simplex minimizer. Default is 60.
int maxshift: Maximum translation in pixels in any direction. If the solution yields a shift beyond this value in any direction, then the refinement is judged a failure and the original alignment is used as the solution.
float precision: The precision which, if achieved, can stop the iterative refinement before reaching the maximum iterations. Default is 0.04.
float stepalt: The alt increment used to create the starting simplex. Default is 5.
float stepaz: The az increment used to create the starting simplex. Default is 5.
float stepphi: The phi incremenent used to create the starting simplex. Default is 5.
float stepx: The x increment used to create the starting simplex. Default is 1
float stepy: The y increment used to create the starting simplex. Default is 1
float stepz: The z increment used to create the starting simplex. Default is 1.
tranform xform.align3d: The Transform storing the starting guess. If unspecified the identity matrix is used
Refines a preliminary 3D alignment using a simplex algorithm. Subpixel precision.
rotate_flip int imask:
int rfp_mode: Either 0,1 or 2. A temporary flag for testing the rotational foot print
Performs two rotational alignments, one using the original image and one using the hand-flipped image. Decides which alignment is better using a comparitor and returns it
rotate_flip.iterative int r1: Inner ring, pixels
int r2: Outer ring, pixels
Performs two rotational alignments, iterative style, one using the original image and one using the hand-flipped image. Decides which alignment is better using a comparitor and returns it
rotate_precenter Performs rotational alignment and works accurately if the image is precentered
rotate_translate int maxshift: Maximum translation in pixels
int nozero: Zero translation not permitted (useful for CCD images)
int rfp_mode: Either 0,1 or 2. A temporary flag for testing the rotational foot print
int useflcf: Use Fast Local Correlation Function rather than CCF for translational alignment
Performs rotational alignment and follows this with translational alignment.
rotate_translate.iterative int maxiter: Maximum number of iterations
int maxshift: Maximum translation in pixels
int nozero: Zero translation not permitted (useful for CCD images)
int r1: Inner ring, pixels
int r2: Outer ring, pixels
int useflcf: Use Fast Local Correlation Function rather than CCF for translational alignment
Performs rotational alignment and follows this with translational alignment using the iterative method.
rotate_translate_flip emdata flip:
int maxshift: Maximum translation in pixels
int rfp_mode: Either 0,1 or 2. A temporary flag for testing the rotational foot print
int usedot:
int useflcf: Use Fast Local Correlation Function rather than CCF for translational alignment
Does two 'rotate_translate' alignments, one to accommodate for possible handedness change. Decided which alignment is better using a comparitor and returns the aligned image as the solution
rotate_translate_flip.iterative emdata flip:
int maxiter: Maximum number of iterations
int maxshift: Maximum translation in pixels
int r1: Inner ring, pixels
int r2: Outer ring, pixels
Does two 'rotate_translate.iterative' alignments, one to accommodate for possible handedness change. Decided which alignment is better using a comparitor and returns the aligned image as the solution
rotational int rfp_mode: Either 0,1 or 2. A temporary flag for testing the rotational foot print. O is the original eman1 way. 1 is just using calc_ccf without padding. 2 is using calc_mutual_correlation without padding.
Performs rotational alignment,works accurately if the image is precentered, normally called internally in combination with translational and flip alignment
rotational.iterative int r1: Inner ring, pixels
int r2: Outer ring, pixels
Performs rotational alignment using the SPIDER method
rt.3d.grid float dalt: The angle increment in the altitude direction. Default is 10
float daz: The angle increment in the azimuth direction. Default is 10
bool dotrans: Do a translational search. Default is True(1)
float dphi: The angle increment in the phi direction. Default is 10
float lalt: Lower bound for the altitude direction. Default it 0
float laz: Lower bound for the azimuth direction. Default it 0
float lphi: Lower bound for the phi direction. Default it 0
int search: The maximum length of the detectable translational shift - if you supply this parameter you can not supply the maxshiftx, maxshifty or maxshiftz parameters. Each approach is mutually exclusive.
int searchx: The maximum length of the detectable translational shift in the x direction- if you supply this parameter you can not supply the maxshift parameters. Default is 3.
int searchy: The maximum length of the detectable translational shift in the y direction- if you supply this parameter you can not supply the maxshift parameters. Default is 3.
int searchz: The maximum length of the detectable translational shift in the z direction- if you supply this parameter you can not supply the maxshift parameters. Default is 3
float ualt: Upper bound for the altitude direction. Default it 359.9
float uaz: Upper bound for the azimuth direction. Default it 179.9
float uphi: Upper bound for the phi direction. Default it 359.9
bool verbose: Turn this on to have useful information printed to standard out.
3D rotational and translational alignment using specified ranges and maximum shifts
rt.3d.sphere float delta: Angle the separates points on the sphere. This is exclusive of the 'n' paramater. Default is 10
bool dotrans: Do a translational search. Default is True(1)
float dphi: The angle increment in the phi direction. Default is 10
float lphi: Lower bound for phi. Default it 0
int n: An alternative to the delta argument, this is the number of points you want generated on the sphere. Default is OFF
string orientgen: Advanced. The orientation generation strategy. Default is eman
int search: The maximum length of the detectable translational shift - if you supply this parameter you can not supply the maxshiftx, maxshifty or maxshiftz parameters. Each approach is mutually exclusive.
int searchx: The maximum length of the detectable translational shift in the x direction- if you supply this parameter you can not supply the maxshift parameters. Default is 3.
int searchy: The maximum length of the detectable translational shift in the y direction- if you supply this parameter you can not supply the maxshift parameters. Default is 3.
int searchz: The maximum length of the detectable translational shift in the z direction- if you supply this parameter you can not supply the maxshift parameters. Default is 3
string sym: The symmtery to use as the basis of the spherical sampling. Default is c1 (asymmetry).
float uphi: Upper bound for phi. Default it 359.9
bool verbose: Turn this on to have useful information printed to standard out.
3D rotational and translational alignment using spherical sampling. Can reduce the search space if symmetry is supplied
rtf_exhaustive emdata flip:
int maxshift: Maximum translation in pixels
Experimental full 2D alignment with handedness check using semi-exhaustive search (not necessarily better than RTFBest)
rtf_slow_exhaustive float angstep: The angular step (in degrees) to take in the exhaustive search for the solution angle. Typically very small i.e. 3 or smaller.
emdata flip: Optional. This is the flipped version of the images that is being aligned. If specified it will be used for the handedness check, if not a flipped copy of the image will be made
int maxshift: The maximum length of the detectable translational shift
float transtep: The translation step to take when honing the alignment, which occurs after coarse alignment
Experimental full 2D alignment with handedness check using more exhaustive search (not necessarily better than RTFBest)
translational int intonly: Integer pixel translations only
int masked: Treat zero pixels in 'this' as a mask for normalization (default false)
int maxshift: Maximum translation in pixels
int nozero: Zero translation not permitted (useful for CCD images)
int useflcf: Use Fast Local Correlation Function rather than CCF
Translational 2D and 3D alignment by cross-correlation