====== CTFCorrection ======
This logic can estimate ctf parameters from particle power spectra class sums, apply previously calculated ones to images and also lets the user choose the parameters manually. This correction for the phase information modulation during the imaging process is an essential part of getting high resolution structures out of input data.

===== Usage =====
If Ctf parameters are to be estimated, the user needs to provide class sums of classified power spectra due to the higher signal-to-noise ratio as compared to images. Afterwards, the images that make up the class sums can be corrected through the determined parameters, as well as images that contain the ctf information in their header.  

===== Example ====
To push one's dataset to the limits, estimating and applying ctf parameters is needed. So the user would classify the power spectra of the dataset's particles and then estimate the ctf parameters from the resulting classsums. The parameters from this (or from ctf correction of micrographs) can then either be applied directly or, as they're stored as header values, used in successive refinement.

===== Modes/Processes =====

==== Compute CTF parameters ====

In this mode, ctf parameters are calculated from input power spectra class sums through comparison with theoretical power spectra.
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^ Parameters                 ^ Description     ^
| Spherical Abberration  | The spherical abberration of the microscope |
| Max astigmatism  | The spherical abberration of the microscope |
| Max defocus  | Maximum defocus to be considered for the first estimation round |
| Min defocus  | Minimum defocus to be considered for the first estimation round |
| High tension in kV  | Acceleration voltage of the microscope  |
| Pixel size of class sum power spectra | Power spectra's pixel size |

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^ Input   ^ Description ^
| Input Images| Power spectra class sums. Each sum needs to have "classId" in the header |

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^ Output   ^ Description ^
| Classes with ctf info| The input images with ctf information in the header|
| Half-half PS| Half input image, half fitted power spectrum to show validity of the fit|

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^ New/Changed Header Values ^ Description ^
|classId| The class id of the power spectrum|
|defocus| The estimated defocus|
|bFactor| The estimated b-factor|
|bFactorExp| The estimated b-factor exponent|
|astigmMag| The estimated magnitude of the astigmatism|
|astigmDir| The direction of the astigmatism|
|amplitudeContrastRatio| The ratio of amplitude to phase contrast|
|qualityOfPSFit|The cross-correlation coefficient of the power spectrum of the class and the theoretical estimated power spectrum|
|accelerationVoltage|The acceleration voltage used during image acquisition|
|pixelSize| The pixel size of the image|
|sphericalAberration| The spherical aberration of the image|

==== Impose CTF parameters on images ====
In this mode, ctf parameters are applied on input images.They can be provided from the power spectra class sums, out of image headers or through manual input

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^ Parameters                 ^ Description     ^
| Value location: Get from class sums  | Specifies that the power spectra class sums that were used for estimation will be provided as a value source|
| -> Limit based rejection of values | Enables rejection of unrealistic values through comparison with micrograph fit values. For this to work, cropCenterX and cropCenterY need to be in the header |
| -> -> Pixel size of origin micrographs   | The pixel size of the images that micrograph ctf correction was performed on |
| -> -> Sidelength of micrographs | Sidelength of the original micrographs(for now, only square ones are supported|
| Value location: Provided in image headers  | Reads the parameters from the header files |
| -> Group identifier | The header key that specifies which images share the same parameters so that they can be corrected together |
| Value location: Manual user input | Applies parameters that are specified by the user. This is recommended for testing only |
| -> Astigmatism angle in degrees | Astigmatism angle to be applied|
| -> DefocusU | DefocusU to be applied|
| -> DefocusV | DefocusV to be applied|
| -> High tension| DefocusV to be applied|
| -> Spherical abberation(Cs)| Spherical aberation to be applied|

| Apply softfilter mask      | Whether to apply a mask with a soft edge onto the input images |
| Desired size of corrected output images      | The size that the corrected images should have |
| Pixel size in Angstrom    | Pixel size that the images have |


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^ Input   ^ Description ^
| Particles | The images to be corrected |
| Value location: Get from class sums  | 
| -> Half-half PS (or classes with ctf info) | The half-half PS output from previous correction |
| -> Particle power spectra  | Power spectra of the particles |


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^ Output   ^ Description ^
| Corrected images| The images with flipped phases |
| Amplitude masks| Amplitude masks that were used for correction|
| Uncorrected images| Basically the same images as were put into the logic|

===== Concept =====
This method of ctf correction is based on a paper from the stark lab [[http://www.sciencedirect.com/science/article/pii/S1047847703000728|paper from the stark lab ]]