Size: 2561
Comment:
|
Size: 2340
Comment:
|
Deletions are marked like this. | Additions are marked like this. |
Line 10: | Line 10: |
Creating just rotations: | def get_params2D(ima, xform = "xform.align2d"): """ retrieve 2D alignment parameters from the header alpha tx ty mirror scale """ t = ima.get_attr(xform) d = t.get_params("2D") return d["alpha"],d["tx"],d["ty"],d["mirror"],d["scale"] |
Line 12: | Line 19: |
. RA=Transform3D(0,0,25); # Default is the ZXZ convention . RA=Transform3D(EULER_SPIDER,0,0,25); # This is the typical ZYZ convention . RA=Transform3D(m11,m12,m13,m21,m22,m23,m31,m32,m33) # create the transformation by entering . components Creating more complicated transformations using set : |
def set_params2D(ima, p, xform = "xform.align2d"): """ set 2D alignment parameters in the header alpha tx ty mirror scale """ t = Transform({"type":"2D","alpha":p[0],"tx":p[1],"ty":p[2],"mirror":p[3],"scale":p[4]}) ima.set_attr(xform, t) |
Line 18: | Line 27: |
def get_params3D(ima, xform = "xform.align3d"): """ retrieve 3D alignment parameters from the header phi theta psi tx ty tz mirror scale """ t = ima.get_attr(xform) d = t.get_params("spider") return d["phi"],d["theta"],d["psi"],d["tx"],d["ty"],d["tz"],d["mirror"],d["scale"] |
|
Line 19: | Line 36: |
. RA = Transform3D(); # this creates the 3D identity matrix . RA.set_rotation(0,0,25); # creates a matrix that will rotate 2D images by 25 degrees . RA.set_posttrans(Vec3f(1,0,0)); # the matrix will now also shift 1 pixel in the x-direction . RA.set_scale(1); # Occaisionally one will wish to rescale. . |
def set_params3D(ima, p, xform = "xform.align3d"): """ set 3D alignment parameters in the header phi theta psi tx ty tz mirror scale """ t = Transform({"type":"spider","phi":p[0],"theta":p[1],"psi":p[2],"tx":p[3],"ty":p[4],"tz":p[5],"mirror":p[6],"scale":p[7]}) ima.set_attr(xform, t) |
Line 25: | Line 44: |
The following code will multiple (combine) two sets of Eulerian angles: | def get_params_proj(ima, xform = "xform.projection"): """ retrieve projection alignment parameters from the header phi theta psi s2x s2y """ t = ima.get_attr(xform) d = t.get_params("spider") return d["phi"],d["theta"],d["psi"],-d["tx"],-d["ty"] |
Line 27: | Line 53: |
. a=even_angles(2.,symmetry='d4',method="P",phiEqpsi = "Zero") . R2 = Transform3D(EULER_SPIDER,90.,0.,0.) . for i in xrange(len(a)): . R1 = Transform3D(EULER_SPIDER,a[i][0],a[i][1],a[i][2]) . R3=R1*R2 . compeuler = R3.get_rotation(EULER_SPIDER) . compphi = compeuler["phi"] ; compphi = (compphi +360.0)%360.0 . comptheta = compeuler["theta"]; comptheta = (comptheta+360.0)%360.0 . comppsi = compeuler["psi"]; comppsi = (comppsi +360.0)%360.0 . print a[i] . print compphi,comptheta,comppsi |
def set_params_proj(ima, p, xform = "xform.projection"): """ set projection alignment parameters in the header phi theta psi s2x s2y """ t = Transform({"type":"spider","phi":p[0],"theta":p[1],"psi":p[2]}) t.set_trans(Vec2f(-p[3], -p[4])) ima.set_attr(xform, t) |
Line 44: | Line 65: |
. b) There is also a set_rotation via a dictionary object, which we will explain at length soon. . c) The first two lines of the second block of commands, could have been written as the second line of the first block of commands. This command sets RA to a rotation that rotates a 2D image by 25 degrees around the Z-axis. . d) There are corresponding "get" calls to extract the information from the transformation matrices. SPARX has some of its own, that are wrappers for these get calls. More later. |
|
Line 52: | Line 71: |
P. R. Baldwin | P.A. Penczek |
Name
Transform Class
Usage
Examples
Here are some examples of creating a Transform3D object. Much more here: [http://blake.bcm.edu/emanwiki/Eman2TransformInPython].
All angles are in degrees
def get_params2D(ima, xform = "xform.align2d"):
- """
- retrieve 2D alignment parameters from the header alpha tx ty mirror scale
def set_params2D(ima, p, xform = "xform.align2d"):
- """
- set 2D alignment parameters in the header alpha tx ty mirror scale
def get_params3D(ima, xform = "xform.align3d"):
- """
- retrieve 3D alignment parameters from the header phi theta psi tx ty tz mirror scale
def set_params3D(ima, p, xform = "xform.align3d"):
- """
- set 3D alignment parameters in the header phi theta psi tx ty tz mirror scale
def get_params_proj(ima, xform = "xform.projection"):
- """
- retrieve projection alignment parameters from the header phi theta psi s2x s2y
def set_params_proj(ima, p, xform = "xform.projection"):
- """
- set projection alignment parameters in the header phi theta psi s2x s2y
Notes:
- a) We could have used EMAN, IMAGIC, SPIN, QUATERNION, SGIROT, MRC, XYZ, MATRIX instead of the SPIDER of EULER_SPIDER above.
Description
Purpose: to apply rotation/shift/scaling operations for 2D or 3D images via a variety of methods.
Author
P.A. Penczek
Maintainer
P. R. Baldwin
Keywords
- category 1
- FUNDAMENTALS
Files
libEM
See also
Maturity
Infancy