Aligner Name | Parameters | Description |
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 stepdelta: The angular increment which represents a good initial step along the sphere, thinking in terms of quaternions. Default is 5. float stepphi: The phi incremenent used to creat the starting simplex. This is the increment applied to the inplane rotation. 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_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_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 |
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 |
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 float dphi: The angle increment in the phi direction. Default is 10. float ralt: The range of angles to sample in the altitude direction. Default is 180. float raz: The range of angles to sample in the azimuth direction. Default is 360. float rphi: The range of angles to sample in the phi direction. Default is 180. 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 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 float dphi: The angle increment in the phi direction. Default is 10. 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 float rphi: The range of angles to sample in the phi direction. Default is 180. 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). 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 |