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 stepscale: If set to any non-zero value, scale will be included in the alignment, and this will be the initial step. Images should be edgenormalized. If the scale goes beyond +-30% alignment will fail. 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 100. 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 0.01. float spin_coeff: The multiplier appied to the spin (if it is too small or too large the simplex will not converge). Default is 10. float stepn0: The initial simplex step size in the first quaternion vecotr component. Default is 1. float stepn1: The initial simplex step size in the second quaternion vecotr component. Default is 1. float stepn2: The initial simplex step size in the third quaternion vecotr component. Default is 1. float stepx: The initial simplex step size in x. Default is 1 float stepy: The initial simplex step size in y. Default is 1 float stepz: The initial simplex step size in z. 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. |
refine_3d_grid | float delta: The angular step size. Default is 1. bool dotrans: Do a translational search. Default is True(1) bool fsrotate: Do rotations in Fourier space float range: The angular range size. Default is 10. 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. 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_symmetry_3d | float sym: The symmetry. Default is icos tranform transform: The transform to move to symmetry axis bool verbose: Turn this on to have useful information printed to standard out. |
3D symmetry aligner |
rotate_trans_flip_scale | emdata flip: float max: Maximum scaling (default: 1.05) int maxshift: Maximum translation in pixels float min: Minimum scaling (default: 0.95) 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 float step: Scaling step (default: 0.01) int useflcf: Use Fast Local Correlation Function rather than CCF for translational alignment |
Performs rotational alignment and follows this with translational and then scaling alignment. |
rotate_trans_flip_scale_iter | emdata flip: float max: Maximum scaling (default: 1.05) int maxiter: Maximum number of iterations int maxshift: Maximum translation in pixels float min: Minimum scaling (default: 0.95) int r1: Inner ring, pixels int r2: Outer ring, pixels float step: Scaling step (default: 0.01) |
Performs rotational alignment and follows this with translational alignment using the iterative method. Does this for each scale and returns the best |
rotate_trans_scale_iter | float max: Maximum scaling (default: 1.05) int maxiter: Maximum number of iterations int maxshift: Maximum translation in pixels float min: Minimum scaling (default: 0.95) int nozero: Zero translation not permitted (useful for CCD images) int r1: Inner ring, pixels int r2: Outer ring, pixels float step: Scaling step (default: 0.01) 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. Does this for each scale and returns the best |
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_3d | 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 bool fsrotate: Do rotations in Fourier space 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 phi0: Lower bound for phi. Default it 0 float phi1: Upper bound for phi. Default it 360 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 |
rotate_translate_3d_grid | float alt0: Lower bound for the altitude direction. Default it 0 float alt1: Upper bound for the altitude direction. Default it 360.0 float az0: Lower bound for the azimuth direction. Default it 0 float az1: Upper bound for the azimuth direction. Default it 180.0 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 phi0: Lower bound for the phi direction. Default it 0 float phi1: Upper bound for the phi direction. Default it 360.0 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 bool verbose: Turn this on to have useful information printed to standard out. |
3D rotational and translational alignment using specified ranges and maximum shifts |
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 |
rotate_translate_flip_resample | int r1: Inner ring, pixels int r2: Outer ring, pixels int tx: Maximum x translation in pixels, Default = 0 int ty: Maximum y translation in pixels, Default = 0 |
Performs rotational alignment, translation align, and flip by resampling to polar coordinates in real space. |
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_resample | int r1: Inner ring, pixels int r2: Outer ring, pixels int tx: Maximum x translation in pixels, Default = 0 int ty: Maximum y translation in pixels, Default = 0 |
Performs rotational alignment and translation align by resampling to polar coordinates in real space. |
rotate_translate_scale | float max: Maximum scaling (default: 1.05) int maxshift: Maximum translation in pixels float min: Minimum scaling (default: 0.95) 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 float step: Scaling step (default: 0.01) int useflcf: Use Fast Local Correlation Function rather than CCF for translational alignment |
Performs rotational alignment and follows this with translational and then scaling alignment. |
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 |
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) |
scale | float max: Maximum scaling (default: 1.05) float min: Minimum scaling (default: 0.95) float step: Scaling step (default: 0.01) |
Performs real space scale alignment |
symalign | string avger: The sort of averager to use, Default=mean 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 float lphi: Lower bound for phi. Default it 0 string sym: The symmetry under which to do the alignment, Default=c1 float uphi: Upper bound for phi. Default it 359.9 |
The image is centered and rotated to the standard orientation for the specified symmetry |
symalignquat | int maxiter: The maximum number of iterations that can be performed by the Simplex minimizer. Default is 100. 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 0.01. float spin_coeff: The multiplier appied to the spin (if it is too small or too large the simplex will not converge). Default is 10. float stepn0: The initial simplex step size in the first quaternion vecotr component. Default is 1. float stepn1: The initial simplex step size in the second quaternion vecotr component. Default is 1. float stepn2: The initial simplex step size in the third quaternion vecotr component. Default is 1. float stepx: The initial simplex step size in x. Default is 1 float stepy: The initial simplex step size in y. Default is 1 float stepz: The initial simplex step size in z. Default is 1. string sym: The symmettry. Default is c1 tranform xform.align3d: The initial guess for to align the particel to sym axis |
Finds the symmetry axis using the simplex algorithm. |
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 |