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eyes:logics:angularreconstitution [2017/06/08 15:55]
vzinch 		eyes:logics:angularreconstitution [2017/06/12 15:29]
vzinch [Concept]
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 ====== AngularReconstitution ====== ====== AngularReconstitution ======
-THIS position should be used for a brief introduction (max 2 sentences!) ​of the logic, stating WHAT and WHY it is doing something. +This logic determines Euler angles ​for a given set of input images based on the common line theorem. This is needed in order to correctly place images (2D projections) in 3D space prior to reconstruction.
 ===== Usage ===== ===== Usage =====
-Here, a general/​generic description ​of HOW the logic is USED should be given. Try to be as general as possible, but also mention prerequisites,​ restrictions,​ advantages, requirements which are specific ​of this logic. Basically everything the user needs to know to successfully use this logic. +The input of this logic - class averages - should be of high quality with enough visible structural features. Choosing more class averages for this logic is not always a good idea, since similar views will result in worse angular assignment. So ideally class averages chosen ​should ​represent all possible distinct views, but without overlapping. If symmetry of the particle is known in advance, it is recommended ​to try running reconstitution both with and without applying symmetry restraints.
- +
-===== Example ==== +
-Here, a very specific example ​should ​be given/​described. In the future, this can be supported by screenshots etc.. For the moment, give an example easy enough for the user to understand, but specific enough to elaborate why a given parameter is a good set for this very situation.+
  
 ===== Modes ===== ===== Modes =====
 ==== Euler ==== ==== Euler ====
-Here, a short introduction ​for the given mode should be placed. Again, state WHAT and WHY this mode us useful in not more than 2 sentences.+This mode is used for de-novo assignment of angles only from the input projections themselves
  
 |< 100% 30% >| |< 100% 30% >|
 ^ Parameters ​                ^ Description ​    ^ ^ Parameters ​                ^ Description ​    ^
-| Some changeable parameter ​ ​| ​Description of this parameter ​| +| Sinograms ​ ​| ​Gives options to read already generated sinograms or to write down sinograms for the images being processed ​| 
-| -> and its sub-parameter ​  | more description | +| Symmetry  ​| Symmetry of the particle (if known) ​|
-| Next main parameter ​       | and more more more | +
-| -> and its sub-parameter ​  | ... descriptions ​|+
  
 |< 100% 30% >| |< 100% 30% >|
 ^ Input   ^ Description ^ ^ Input   ^ Description ^
-| FirstInput ​ ​| ​Input Description 1 | +| In  ​| ​Image or stack of images (a set of class averages)|
-| SecondInput | Input Description 2 | +
-| //​ThirdInput// ​ | Input Description 3: Optional Input in Italic ​|+
  
 |< 100% 30% >| |< 100% 30% >|
 ^ Output ​  ^ Description ^ ^ Output ​  ^ Description ^
-| FirstOutput ​| Output Description | +| Out | The input projections with assigned Euler angles ​|
- +
-|< 100% 30% >| +
-^ New/Changed Header Values ^ Description ^ +
-| headerValue1 | what does it say? how is it changed? | +
-| headerValue2 | what does it say? how is it changed? | +
-| headerValue3 | what does it say? how is it changed? | +
-| headerValue4 | what does it say? how is it changed? ​|+
  
 ==== Anchor set ==== ==== Anchor set ====
-Here, a short introduction for the given mode should be placed. Again, state WHAT and WHY this mode us useful in not more than 2 sentences.+This logic determines ​the angles of stack of projections if the set with known angular relations is available (e.g. 3D model from already performed angular reconstitution) ​
  
 |< 100% 30% >| |< 100% 30% >|
 ^ Parameters ​                ^ Description ​    ^ ^ Parameters ​                ^ Description ​    ^
-| Some changeable parameter ​ ​| ​Description ​of this parameter | +| Symmetry ​ ​| ​Symmetry ​of the particle (if known) ​|
-| -> and its sub-parameter ​  | more description | +
-| Next main parameter ​       | and more more more | +
-| -> and its sub-parameter ​  | ... descriptions ​|+
  
 |< 100% 30% >| |< 100% 30% >|
 ^ Input   ^ Description ^ ^ Input   ^ Description ^
-| FirstInput ​ ​| ​Input Description 1 | +| In  ​| ​Image or stack of images (a set of class averages)| 
-| SecondImput ​| Input Description 2 | +| Anchor set | Projection set with known angular relations (mostly projected 3D-model) ​|
-| ThridImput ​ | Input Description 1 |+
  
 |< 100% 30% >| |< 100% 30% >|
 ^ Output ​  ^ Description ^ ^ Output ​  ^ Description ^
-| FirstOutput ​| Output Description | +| Out | The input projections with assigned Euler angles (no anchor dataset in the output) ​|
- +
-|< 100% 30% >| +
-^ New/Changed Header Values ^ Description ^ +
-| headerValue1 | what does it say? how is it changed? | +
-| headerValue2 | what does it say? how is it changed? | +
-| headerValue3 | what does it say? how is it changed? | +
-| headerValue4 | what does it say? how is it changed? ​|+
  
 ==== Add projection ==== ==== Add projection ====
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 |< 100% 30% >| |< 100% 30% >|
 ^ Parameters ​                ^ Description ​    ^ ^ Parameters ​                ^ Description ​    ^
-| Symmetry ​ | Symmetry of the complex studied ​(if known) |+| Symmetry ​ | Symmetry of the particle ​(if known) |
  
 |< 100% 30% >| |< 100% 30% >|
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 ^ Output ​  ^ Description ^ ^ Output ​  ^ Description ^
 | Out | The input dataset with added input projections with assigned Euler angles | | Out | The input dataset with added input projections with assigned Euler angles |
- 
-|< 100% 30% >| 
-^ New/Changed Header Values ^ Description ^ 
-| headerValue1 | what does it say? how is it changed? | 
-| headerValue2 | what does it say? how is it changed? | 
-| headerValue3 | what does it say? how is it changed? | 
-| headerValue4 | what does it say? how is it changed? | 
  
 ==== Sinograms ==== ==== Sinograms ====
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 |< 100% 30% >| |< 100% 30% >|
 ^ Parameters ​                ^ Description ​    ^ ^ Parameters ​                ^ Description ​    ^
-| Symmetry ​ | Symmetry of the complex studied ​(if known) |+| Symmetry ​ | Symmetry of the particle ​(if known) |
  
 |< 100% 30% >| |< 100% 30% >|
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 ^ Output ​  ^ Description ^ ^ Output ​  ^ Description ^
 | Out | Sinogram | | Out | Sinogram |
 +===== Concept =====
  
-|< 100% 30% >| +This logic is needed as an intermediate step to get from 2D images to a 3D volume. In order to reconstruct the full volume we need to know the relationship between the images (projections) we have - how they are located in 3D relative to each other. ​ 
-^ New/Changed Header Values ^ Description ^ +In case any reference model for the particle ​is available, it can be used as '​anchor set' that would increase the precision of the output.  
-| headerValue1 | what does it say? how is it changed? | +However, when no prior model is available for the particles of interest, determination of [[https://​en.wikipedia.org/​wiki/​Euler_angles|Euler angles]] ​should be done de novo. This logic does it based on [[http://​www.sciencedirect.com/​science/​article/​pii/​0304399187900787|Common line theorem]].
-| headerValue2 | what does it say? how is it changed? | +
-| headerValue3 | what does it say? how is it changed? | +
-| headerValue4 | what does it say? how is it changed? | +
-===== Concept ===== +
-In this paragraph, the "HOW a logic works under the hood" and WHY someone should use it can be elaborated with higher detail. Describes a scenario in an image processing workflow where this logic can be used to solve the resulting problem. Also, wikipages, publications or anything else describing the theory behind an algorithm ​should be linked here, if applicable.+