Data analysis toolbox for in-flight holography experiments, performed at the Free-Electron Laser facilities:
- LCLS (Linac Coherent Light Source) @ SLAC (Stanford Linear Accelerator Center)
- FLASH (Free-Electron Laser Hamburg)
Analysis of scattering patterns of samples and holographic references, illuminated by a single FEL (Free-Electron Laser) pulse [Gorkhover et al., 2018]. Data recorded on pnCCD scattering detectors with clusters as holographic references.
version: 4.0
year: 2021
author: Anatoli Ulmer
email: [email protected]
- pnCCD detector corrections
- holographic reconstruction
- refocusing (manual and automated)
- signal-to-noise estimation
- Wiener devonvolution filter
- graphical interface
Project is created with:
- MATLAB 2020a or later
- Image Processing Toolbox
- Parallel Computing Toolbox
Optionally can be used on Maxwell (Desy) or psana (SLAC) remotely:
To use MATLAB on Maxwell please use FastX2:
- Get FastX2 from within the Desy network.
- Connect to
max-display.desy.dewith your desy credentials using FastX. - (a) Start a XFCE session and start the terminal. OR (b) Start a xterm session.
- Run the desired MATLAB version with
matlab20XXxin the terminal (e.g.matlab2021a).
To use MATLAB on psana please use nomachine:
- Get nomachine
- Login into psnxana - HOWTO
- ssh to a psana machine with available MATLAB licence.
Get list of available licences using:
/reg/common/package/scripts/matlic. Use available machine with:ssh -Y machinename. - Start MATLAB using:
/reg/common/package/matlab/R2016a/bin/matlab.
Run HoloShow.mlapp in MATLAB.
holoShow reads scattering image data files in ASCII format with ending .dat, MATLAB files with ending .mat or HDF5 files with Hummingbird standard structure with ending .cxi or .h5.
INSTRUCTIONS:
1.) Start with executing HoloShow.mlapp and the control window will open together with the hologram window and the reconstruction window.
2.) Pick a file in the pre-chosen file list on the left or load new files with the button above the list. The button below the list will execute first evaluation steps.
3.) In the reconstruction window you see the patterson map consisting of the autocorrelation in the center and cross correlation terms. You can zoom inside this window and with the button 'choose CC' the current view will be set as the new region of interest (ROI). Smaller ROIs will give better results.
4.) The reconstruction usually is defocused in the beginning, because the sample and the reference were not in the same plane. Refocussing can be done manually with the phase slider or automatically with the 'find phase' button. To change the range of the slider you can use the edit field on the right side. With phase here the distance between the particles and the belonging propagation operator is meant.
5.) The focused reconstruction will still have artifacts due to unprecise centering of the hologram and position estimation of the two detector halves. To correct for these artifacts you can use the 'find center' and 'find shifts' buttons.
Now you should have a low resolution reconstruction. Keep in mind that depending on the focal length, information can be shifted between real and imaginary space. After all, what we reconstruct is just the exit wave of the particle. To further refine the reconsruction it is possible to make a deconvolution.
see LICENSE file
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