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 |