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Content
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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
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[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:
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:
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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:
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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
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Apparently, this geometry file had wrong indexes associated with quads (cable swap) that gives misaligned 2x1s in quads. This problem should be fixed in the file
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Tuning of geometry can be done with Detector alignment tool running command:
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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:
or see image array with maximal intensities by the command
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geo -i cspad-ndarr-max-cxif5315-r0169.dat -g geo-cxif5315-r0169-swap-tuned.data |
looks like: ,
and similar for water background from run 162:
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
etc.
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
...