Content

Data

exp=cxif5315:run=147, 198 - dark

exp=cxif5315:run=162 - water sample

exp=cxif5315:run=169 - data sample

Calibration files

Use my local calibration store

[psana]
calib-dir = /reg/neh/home1/dubrovin/LCLS/rel-mengning/calib

Dark files were obtained and deployed using Calibration Management Tool

exp=cxif5315:run=147  dark average, rms, and average difference between runs 147-198:

Image Removed Image Removed Image Removed

References

• 2015-04-08 Quick start, calibration, detector alignment, peak finder, scripts

• 2015-05-04 Angles phi and beta, fraser transformation

• 2015-08-19 Analysis with new peakfinder

• 2015-10-20 Indexing

• 2015-11-06 Geometry re-alignment

• 2015-12-01 Indexing after fraser transformation with β=0

• 2016-02-02 Cross-checks: Lattice and look up table

• 2016-03-25 Masks, Background subtraction

• 2016-04-05 Test of Peak Finders

• 2016-04-25 Test of Peak Finders - V2

• 2016-05-03 Test of Peak Finders - V3

• 2016-04-29 Fit functions and quality

• 2016-04-29 Phi-beta fit results in ARC and EQU

• 2016-05-13 Indexing results

• 2017-02-28 Revision of Analysis

References

• Calibration Management Tool
• Detector alignment tool
• CSPAD Alignment
• Meng's spreadsheet to the runs taken
• Meng's link for the CFEL confluence  that has the data analysis summary
• Meng's amyloid_math1.pdf
  
• Direct mapping of fiber diffraction patterns into reciprocal space, Norbert Stribeck* and Ulrich Nochel (download)
• Preprocessing averaged XFEL data from adenovirus peptide amyloid and derivation of specimen characteristics, David Wojtas and Rick Millane
• Polanyi(1921).Z.Phys.7.pdf
• fiber-diffraction-formalism.pdf - my note
• J.Biol.Chem-2005-v280-N4-2481-Papanikolopoulou.pdf
• Nature-1999-v401-935-Raaij.pdf
• class ImgAlgos.PyAlgos - collection of n-d array processing algorithms
• class Detector.PyDetector - direct access to detector data and calibration n-d arrays
• 2015-10-13-meng-indexing1.pdf , 2015-10-13-meng-lineout_from_169_a.txt- Meng's calculations for indexing
• pyimgalgos (source)
  • FiberIndexing.py (source)
  • FiberAngles.py (source)
  • TDFileContainer.py (source), TDFileContainer (auto-doc)
• Scattering and diffraction

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