Content

Data

exp=cxif5315:run=147, 198 - dark

exp=cxif5315:run=162 - water sample

exp=cxif5315:run=169 - data sample

Detector: CxiDs2.0:Cspad.0

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

Difference of average dark images between runs 147-198 is small, 0.3 ADU, difference rms=0.6 ADU, this proves that CxiDs2.0:Cspad.0 is stable during 50 runs.

Image array averaging

1)  Download configuration file psana-cxif5315-cspad-ds2-NDArrAverage.cfg

2) To get average/rms/max over 10000 events data of run 169 use command:

psana -c psana-cxif5315-cspad-ds2-NDArrAverage.cfg -n 1000 exp=cxif5315:run=169

This command produces files with arrays of size (32x185x388)

• cspad-ndarr-ave-cxif5315-r0169.dat
• cspad-ndarr-rms-cxif5315-r0169.dat
• cspad-ndarr-max-cxif5315-r0169.dat

2) To get average/rms/max over 1000 events (skipping 5000) data for water sample of run 162 use command:

psana -c psana-cxif5315-cspad-ds2-NDArrAverage.cfg -s 5000 -n 1000 exp=cxif5315:run=162

This command produces files with arrays of size (32x185x388)

• cspad-ndarr-ave-cxif5315-r0162.dat
• cspad-ndarr-rms-cxif5315-r0162.dat
• cspad-ndarr-max-cxif5315-r0162.dat

Geometry alignment

In accordance with CSPAD Alignment, use geometry file:

/reg/g/psdm/detector/alignment/cspad/calib-cxi-ds2-2015-01-20/calib/CsPad::CalibV1/CxiDs2.0:Cspad.0/geometry/1-end.data

and array with image from file: cspad-ndarr-ave-cxif5315-r0169.dat

Tuning of geometry can be done with  Detector alignment tool running command:

geo -i cspad-ndarr-ave-cxif5315-r0169.dat -g geo-cxif5315-r0169-swap-tuned.data

Thus obtained geo-cxif5315-r0169-swap-tuned.data gives image, radial, and spectral histograms for averaged array:

Image Removed  Image Removed  Image Removed

or see image array with maximal intensities by the command

geo -i cspad-ndarr-max-cxif5315-r0169.dat -g geo-cxif5315-r0169-swap-tuned.data

looks like: Image Removed  Image Removed  Image Removed,

and similar for water background from run 162: Image Removed

ROI Masks

Using image array in cspad-ndarr-max-cxif5315-r0169.dat and geometry file geo-cxif5315-r0169-swap-tuned.data, one can generate masks using the Mask Editor embedded in Calibration Manager.

Run command calibman, select tab ROI and performing all steps of the mask creation procedure, one can draw ROI on image, create the mask for this image, convert this mask to ndarray, and use this ndarray for data processing. This ndarray can be used later for image reconstruction with the same geometry file.

For data processing of exp=cxif5315:run=169 two masks were produced for arc and equatorial regions:

Image RemovedImage RemovedImage RemovedImage Removed

Image RemovedImage RemovedImage RemovedImage Removed

References

• Calibration Management Tool
• Detector alignment tool
• CSPAD Alignment

• 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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