Mirroring in the Transform3D object
We use the Transform3D class for storing/managing Euler angles and translations. At any time a Transform3D ($$T3D$$) object defines a group of 3 transformations of a rigid body that are applied in a specific order, namely
$$T3D \equiv T_{post} R T_{pre}$$
Where $$T_{pre} is a pre translation, $$R$$ is a rotation and $$T_{post} is a post translation. The Transform3D object stores these transformations internally in a 4x4 matrix, as is commonly the case in computer graphics applications that use homogeneous coordinate systems (i.e. OpenGL). In these approaches the 4x4 transformation matrix $$T3D$$ is constructed in this way
$$T3D = [[R,\mathbf{t}],[\mathbf{0}^T,1]]$$
Where R is a $$3x3$$ rotation matrix and $$\mathbf{t}=(dx,dy,dz)^T$$ is a post translation. In this approach a 3D point $$\mathbf{p}=(x,y,z)^T$$ as represented in homogeneous coordinates as a 4D vector $$\mathbf{p}_{hc}=(x,y,z,1)^T$$ and is multiplied by the matrix $$M$$ to produce the result of applying the transformation
$$ T3D \mathbf{p}_{hc} = ( (R\mathbf{p} + \mathbf{t})^T, 1 )^T $$
In this way the result of applying a Transform3D to a vector is literally a rotation followed by a translation. The Transform3D allows for both pre and post translation and stores the cumulative result internally
$$T3D = T_{post} R T_{pre} = [[I,\mathbf{t}_{post}],[\mathbf{0}^T,1]] [[R,\mathbf{0}],[\mathbf{0}^T,1]] [[I,\mathbf{t}_{pre}],[\mathbf{0}^T,1]] = [[R,R\mathbf{t}_{pre}+\mathbf{t}_{post}],[\mathbf{0}^T,1]]$$
Support for the mirroring operation in Transform3D
See * EMAN2/TransformConventions/Mirroring_Mirroring_in_the_Transform3D_object
Constructing a Transform3D object in Python
In Python you can construct a Transform3D object in a number of ways
1 from EMAN2 import Transform3D
2 t = Transform3D() # t is the identity
3 t = Transfrom3D(EULER_EMAN,25,45,65) # EULER_EMAN rotation convention uses the az, alt, phi
4 t = Transform3D(EULER_SPIDER,24,44,64) # EULER_SPIDER rotation convention uses the phi, theta, psi convention
5 t = Transform3D(25,45,65) # EULER_EMAN convention used by default, arguments are taken as az, alt, phi
6 t = Transform3D(Vec3f(1,2,3),25,45,65,Vec3f(4,5,6)) # Specify a pre trans, followed by EULER_EMAN convention rotations az, alt, phi, followed by the post trans
7 t = Transform3D(25,45,65,Vec3f(4,5,6)) # EULER_EMAN convention rotations az, alt, phi, followed by the post trans
8 t = Transform3D(1,0,0,0,1,0,0,0,1) # Explicitly setting the nine members of the rotation matrix, row wise.
9 s = Transform3D(t) # copy constructor
Setting Transform3D rotations and translation attributes in Python
You can set the pre and post translations, as well as the rotations, directly from Python
1 from EMAN2 import Transform3D
2 t = Transform3D()
3 # setting the rotations
4 t.set_rotation(25,45,65) # EULER_EMAN convention rotations az, alt, phi
5 t.set_rotation(EULER_SPIDER,24,44,64) # EULER_SPIDER rotation convention uses the phi, theta, psi convention
6 t.set_rotation(EULER_EMAN, {"az":25,"alt":45,"phi":65}) # Optional dictionary style approach
7 t.set_rotation(1,0,0,0,1,0,0,0,1) # Explicitly set the nine members of the rotation matrix, row wise.
8 # setting translations
9 t.set_pretrans(1,2,3)# pre translation dx, dy, dz
10 t.set_pretrans(Vec3f(1,2,3)) # also takes Vec3f argument
11 t.set_pretrans([1,2,3]) # also takes tuple argument
12 t.set_posttrans(4,5,6)# post translation dx, dy, dz
13 t.set_posttrans(Vec3f(4,5,6)) # also takes Vec3f argument
14 t.set_posttrans([4,5,6]) # also takes tuple argument
Retrieving transform3D rotations and translation attributes in Python
You can retrieve attributes using similar syntax to that employed for the setter methods