This is an old revision of the document!
FourierProcesses
THIS position should be used for a brief introduction (max 2 sentences!) of the logic, stating WHAT and WHY it is doing something.
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.
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/Processes
Bispectrum
Calculates a Bispectrum for the two input image stacks, which is defined as the third order cumulant-generating function:
B(f1,f2) = F*(f1+f2).F(f1).F(f2)
where f1 and f2 are the input images , F is an images' Fourier Transform and F* its conjugate.
For every pair of images, a bispectrum is generated. While both inputs can have different sizes, the amount of generated bispectra is equal to the maximum number of unambigous image pairs that can be formed, which is the size of the smaller of the two stacks.
Also, both images need to have the same dimensions (and dimensionality).
Center corrected power spectrum
Use this module to generate power spectra of single particles used as input data during CTF correction. Note: For K2 Particles, turn off the highpass filter for power spectra.
| Parameters | Description |
|---|---|
| Output size | Width and height size of the power spectra. The new size is achieved by cropping (this changes the pixel size of the power spectra!) [in pixel] |
| Highpass value | Gaussian highpass filter value used directly on the input data. [0…1] |
| Apply softmask | If checked, applies a circular soft mask to the input images. |
| Apply highpass filter | If checked, applies a highpass filter to the computed power spectra. |
| Low freq cutoff | If Apply highpass filter to power spectra is checked, this value defines the Gaussian highpass value used to filter the computed power spectra. [0…1] |
| Constant value to add | This value is added to each pixel of the power spectrum. [a floating point number] |
| Logarithmic power spectrum | If checked, calculates the pixel values of the power spectrum on a logarithmic scale. |
| Filtering type | Select, whether a cosine- or Gaussian-shaped transition curve should be used for filtering. |
Bispectrum
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.