Differences between revisions 8 and 11 (spanning 3 versions)
 ⇤ ← Revision 8 as of 2008-03-18 18:57:12 → Size: 2980 Editor: penczek Comment: ← Revision 11 as of 2008-03-18 19:32:34 → ⇥ Size: 5702 Editor: penczek Comment: Deletions are marked like this. Additions are marked like this. Line 19: Line 19: {{{`((x'),(y'),(z'))=[[cos psi cos theta cos phi - sin psi sin phi,cos psi cos theta sin phi + sin psi cos phi, -cos psi sin theta],[-sin psi cos theta cos phi - cos psi sin phi,-sin psi cos theta sin phi + cos psi cos phi,sin psi cos theta cos],[sin theta cos phi,sin theta sin phi,cos theta]]((x),(y),(z))`}}} {{{`((x'),(y'),(z'))=[[cos psi cos theta cos phi - sin psi sin phi, cos psi cos theta sin phi + sin psi cos phi, -cos psi sin theta],[-sin psi cos theta cos phi - cos psi sin phi, -sin psi cos theta sin phi + cos psi cos phi, sin psi sin theta],[sin theta cos phi, sin theta sin phi, cos theta]]((x),(y),(z))`}}} Line 21: Line 21: This is called a ''ZYZ'' convention since the matrices appear in the order from right to left as clockwise rotations around ''z'', ''y'', and ''z'', respectively. By “clockwise rotation around ''z''", we mean that, when viewed along the positive axis, the rotation of the object looks clockwise. Recall that it is the matrix at the rightmost end that is applied first. So one might write a 3DEM rotation as  {{{`(phi, theta, psi)`}}}, where {{{`phi`}}} is applied first, {{{`theta`}}} second and {{{`psi`}}} lastly. This is called a ''ZYZ'' convention since the matrices appear in the order from right to left as clockwise rotations around ''z'', ''y'', and ''z'', respectively. By “clockwise rotation around ''z''", we mean that, when viewed along the positive axis, the rotation of the object looks clockwise. Recall that it is the matrix at the rightmost end that is applied first. So one might write a 3DEM rotation as {{{`(phi, theta, psi)`}}}, where {{{`phi`}}} is applied first, {{{`theta`}}} second and {{{`psi`}}} lastly. Line 24: Line 24: = Euler angles and projection directions =The operation of linear {{{`3D -> 2D`}}} projection ('''''ray transform''''') is given by two steps: 1. Rotate the 3D structure by three Eulerian angles, 2. Add (integrate) densities along lines parallel to the new {{{`z'`}}} axis.Thus, in this case projection of a 3D object results in a 2D image.Based on definition of Euler angles above, it is easy to see that first two Eulerian angles {{{`(phi, theta)`}}} define '''''projection direction''''', while {{{`psi`}}} defines rotation of projection in-plane of projection. Thus, as far as projections are concerned {{{`psi`}}} is a trivial angle, as its change does not change the 'information content' of the projection.'''''Projection direction''''' given by {{{`(phi, theta)`}}} can be thought of as a unitary vector (vector of length one) pointing from the origin of the system of coordinates to the surface of a unitary ball. A set of such points visualizes distribution of projection directions when 3D reconstruction is considered (See [http://blake.bcm.edu/emanwiki/EMAN2/Symmetry].)The range of possible Eulerian angles for an asymmetric structure is {{{`0<=phi<=360, 0<=theta<=180, 0<=psi<=360)`}}}. However, for each projection whose direction is {{{`(phi, theta, psi)`}}} there exists a projection that is related to it by an ''in-plane mirror operation along x-axis'' and whose direction is {{{`(180+phi, 180-theta, -psi)`}}}. Note the projection direction of the mirrored projection is alos in the same range of Eulerian angles as all angles are given modulo 360 degrees (i.e., if say {{{`phi > 360`}}}, then {{{`phi = phi - 360`}}}, also if {{{`phi < 0`}}}, then {{{`phi = phi + 360`}}}.By default SPARX will not generate mirrored versions of reference projections in exhaustive searches in 3D projection alignment procedures. Whether given projection data has to be mirrored is determined computationally internal to SPARX operations (see: Penczek, P., Radermacher, R. and Frank, J.: Three-dimensional reconstruction of single particles embedded in ice. Ultramicroscopy 40:33-53, 1992. and also Joyeux, L. and Penczek, P.A.: Efficiency of 2D alignment methods. Ultramicroscopy 92:33-46, 2002.)For more details see: . Vainshtein, B.K., Penczek, P.A.: Three-dimensional reconstruction, in U. Shmueli (Ed.), International Tables for Crystallography 3 edn., vol. B Reciprocal Space, 2008 in press.= Point-group symmetries =There are five possible point-group symmetries, i.e., symmetries in which one point in 3-D remains unmoved. In SPARX, they are defined by a [:symmetry:] symbol: 1. 'cn' -  2. 'dn' -  3. 'oct' -  4. 'tet' -  5. 'icos' - Also see:

# Euler angles

Internally, SPARX shares with EMAN2 basic functionality of rotations/shifts/change of scale of multidimensional objects as provided by the [:transformClass:] Transform Class.

In practice it means that one can use the following conventions of Euler angles: SPIDER, EMAN, IMAGIC, SPIN, QUATERNION, SGIROT, MRC, XYZ, and MATRIX. However, SPARX system relies on SPIDER convention, which means that whenever user is prompted to provide Euler angles or when the system prints values of Euler angles, they are always in SPIDER convention. Also, much of the code uses internally Euler angles in SPIDER convention.

The explanation of various conventions and details of implementation are given in:

• Baldwin, P.R., Penczek, P.A.: The transform class in SPARX and EMAN2. J. Struct. Biol., 157, pp.250-261, 2007.

In what follows we focus on SPIDER convention. Traditionally in EM the direction of propagation of the electron beam is thought to coincide with z axis, which in addition uniquely specifies xy as the plane in which the data is collected. Thus, it is convenient to express the rotations with respect to the z axis. By using a ZYZ convention (rotation around the z axis, followed by a rotation around y, and another around z), one benefits from the fact that the description bears a simple relation to the description of a point on a sphere; that is to say, we can think of the decomposition as the description of a point on the sphere (the first two Eulerian angles YZ) and a final in-plane rotation (the final Z-Eulerian angle). We denote three respective Euler angles as phi `(phi)`, theta `(theta)`, psi `(psi)` and the corresponding rotation in matrix notation as a product of three matrices:

`R_Z(psi) R_Y(theta) R_Z(phi)=`

`((x'),(y'),(z'))=[[cos psi,sin psi, 0],[-sin psi,cos psi,0],[0,0,1]] [[cos theta,0,-sin theta],[0,1,0],[sin theta,0,cos theta]] [[cos phi,sin phi, 0],[-sin phi,cos phi,0],[0,0,1]]((x),(y),(z))`

or as one `3x3` rotation matrix:

`((x'),(y'),(z'))=[[cos psi cos theta cos phi - sin psi sin phi, cos psi cos theta sin phi + sin psi cos phi, -cos psi sin theta],[-sin psi cos theta cos phi - cos psi sin phi, -sin psi cos theta sin phi + cos psi cos phi, sin psi sin theta],[sin theta cos phi, sin theta sin phi, cos theta]]((x),(y),(z))`

This is called a ZYZ convention since the matrices appear in the order from right to left as clockwise rotations around z, y, and z, respectively. By “clockwise rotation around z", we mean that, when viewed along the positive axis, the rotation of the object looks clockwise. Recall that it is the matrix at the rightmost end that is applied first. So one might write a 3DEM rotation as `(phi, theta, psi)`, where `phi` is applied first, `theta` second and `psi` lastly.

# Euler angles and projection directions

The operation of linear `3D -> 2D` projection (ray transform) is given by two steps:

1. Rotate the 3D structure by three Eulerian angles,
2. Add (integrate) densities along lines parallel to the new `z'` axis.

Thus, in this case projection of a 3D object results in a 2D image.

Based on definition of Euler angles above, it is easy to see that first two Eulerian angles `(phi, theta)` define projection direction, while `psi` defines rotation of projection in-plane of projection. Thus, as far as projections are concerned `psi` is a trivial angle, as its change does not change the 'information content' of the projection.

Projection direction given by `(phi, theta)` can be thought of as a unitary vector (vector of length one) pointing from the origin of the system of coordinates to the surface of a unitary ball. A set of such points visualizes distribution of projection directions when 3D reconstruction is considered (See [http://blake.bcm.edu/emanwiki/EMAN2/Symmetry].)

The range of possible Eulerian angles for an asymmetric structure is `0<=phi<=360, 0<=theta<=180, 0<=psi<=360)`. However, for each projection whose direction is `(phi, theta, psi)` there exists a projection that is related to it by an in-plane mirror operation along x-axis and whose direction is `(180+phi, 180-theta, -psi)`. Note the projection direction of the mirrored projection is alos in the same range of Eulerian angles as all angles are given modulo 360 degrees (i.e., if say `phi > 360`, then `phi = phi - 360`, also if `phi < 0`, then `phi = phi + 360`.

By default SPARX will not generate mirrored versions of reference projections in exhaustive searches in 3D projection alignment procedures. Whether given projection data has to be mirrored is determined computationally internal to SPARX operations (see: Penczek, P., Radermacher, R. and Frank, J.: Three-dimensional reconstruction of single particles embedded in ice. Ultramicroscopy 40:33-53, 1992. and also Joyeux, L. and Penczek, P.A.: Efficiency of 2D alignment methods. Ultramicroscopy 92:33-46, 2002.)

For more details see:

• Vainshtein, B.K., Penczek, P.A.: Three-dimensional reconstruction, in U. Shmueli (Ed.), International Tables for Crystallography 3 edn., vol. B Reciprocal Space, 2008 in press.

# Point-group symmetries

There are five possible point-group symmetries, i.e., symmetries in which one point in 3-D remains unmoved. In SPARX, they are defined by a [:symmetry:] symbol:

1. 'cn' -
2. 'dn' -
3. 'oct' -
4. 'tet' -
5. 'icos' -

Also see: [http://blake.bcm.edu/emanwiki/EMAN2/Symmetry]

Euler_angles (last edited 2018-01-27 19:21:04 by penczek)