A workflow for fluctuation x-ray scattering data analysis

The xFrame's fxs toolkit provides the following capabilities:

Calculating cross-correlation functions from scattering patterns.
Extracting invariants from cross-correlations.
Reconstruction of the electron density based on rotational invarants.
Alignment and Averaging of reconstructions.

No data required

To test the fxs toolkit no data is required, after installation simply follow the getting started guide.

Installation

The fxs toolkit comes bundled as part of xFrame. The additional dependencies needed by fxs can be automatically installed via:

pip install 'xframe[fxs]'

The dependencies are as follows:

essential:
- numpy(BSD-3)
- scipy(BSD-3)
- h5py(BSD-3)
- ruamel.yaml(MIT)
- pysofft(GPL3.0) : 3D rotational alignment
- shtns(CeCILL2.1) : Spherical harmonic Transforms
- pygsl(GPL2.0) : Invariant extraction
- click(BSD-3): Commandline interface
optional:
- pyopencl(MIT/X) : GPU Support
- vtk(BSD-3) : 3D visualization
- matplotlib(BSD compatible) : 2D visualization
- opencv-python(MIT) : 2D visualization
- flt(MIT) : Invariant extraction
- psutil(BSD-3): Hardware info

Note that the python packages pygsl and pyopencl require the libraries gsl and opencl to be installed on your system to function properly.

In order to view the outputed 3d vtk datasets we recomend to install a vtk viewer such as paraview. An example for the usage of paraview can be found here

Setup on Maxwell cluster at Desy

In order to setup xframe on Maxwell you need to follow a few steps (time of writing 9.2023)

Create a conda environment using the commands
```
module load maxwell mamba
. mamba-init
mamba create --name xframe python=3.8
mamba activate xframe
```
You can alternatively call the environment by whatever name you like instead of "xframe"
Install GSL
```
mamba install -c anaconda gsl
```
Install xframe
```
pip install 'xframe[fxs]'
```

This should have done the trick :)
If you are still facing issues feel free to create an issue at github.