====== Random conical tilt (RCT) ======
Calculates Random conical Tilt volumes from a set of tilted raw images by the aid of a stack of the classified untilted counter parts. This is an experimental method to Determine the Euler angles
===== Usage =====
To run this logic two stacks of the same size, on of the tilted and one of the untilted images have to be prepared. It is necessary that the images in both stacks are in the same order. The tilted images should be at least normalised. The untilted images need to refined on a 2D level to give good class averages. in general Class averages should contain about 100 particles.   

===== Parameter and I/Os =====

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^ Parameters                 ^ Description     ^
| Class Number  | from which class shout the RCT be calculated? If -1 is given the RCT is calculated for every class. |
| tilted inplane Rotation | inplane rotation of the tilt axis, **none** not recommended will yield in unuseable results, **simple** the same inplane rotation is assumed for every image, **complex** in plane rotation is given as IO, assuming that the in plane rotation is not the same for every micrograph.  |
| -> tilted angle rotation  | in plane rotation of tilt axis in degree. Can be determined by the picker |
| mode  | Mode of reconstruction **exact** back projection, **fourier** Fourier reconstruction, **sirt** Sirt algorithm. For details see [[eyes:logics:reconstruction|]] |
| Normalize 3D | Should the resulting 3D Volumes be normalized? |
| Reproject 3D | Shall there be Backprojections of the input images? |
|Symmetry | Is there a point group symmetry known for the molecule? |
| experimental tilt angle | angle of goniometer rotation. Can be also determined in the picker | 
|tilted with angle| FIXME|

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^ Input   ^ Description ^
| tilted  | normalized and maybe filtered otherwise untreated stack of tilted images |
| untilted | output of a [[eyes:logics:classification]] logic of the untilted images |
| //tilt angles// | stack of images containing the tilt angles in the header, as written by the picker |

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^ Output   ^ Description ^
| 3ds | Stack of reconstructed 3D volumes one stack for each 2D class |


===== Concept =====
Random conical tilt as described in [[http://www.sciencedirect.com/science/article/pii/S0969212610001577?via%3Dihub]]