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pyimgalgos/src/FiberIndexing.py self-documentation
Script
cxif5315/make-index-table.py
Triclinic crystal cell parameters
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Comparison of the look-up table and data (geometry and lattice parameters are re-tuned)
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Indexing
Script
proc-cxif5315-r0169-peaks-from-file-v2.py - loop over peaks in event and try to associate event peaks with a list of predicted for each crystal orientation. Most probable combination is saved in the file.
File record for event
There are three states for matching peaks in event indexing:
- MATCHED - peak is matched to predicted crystal node,
PEAK-NM - peak in data is not matched with any of predicted nodes,
NODE-NM - predicted crystal node is on Evald sphere, but peak in data is missing.
Event indexing table contains records for all peaks from data and for all predicted nodes from crystal orientation. Each record consists of three parts; status word, peak information, and orientation information. In case if orientation or peak information is missing it is replaced by zeros, like shown in example below.
| Code Block |
|---|
STATE phi-fit beta-fit qh-fit qv-fit dqh[1/A] Exp Run time(sec) time(nsec) fiduc Evnum Reg Seg Row Col Npix Amax Atot rcent ccent rsigma csigma rmin rmax cmin cmax bkgd rms son imrow imcol x[um] y[um] r[um] phi[deg] index beta omega h k l dr[1/A] R(h,k,l) qv[1/A] qh[1/A] P(omega)
NODE-NM -7.98 -12.45 0.000000 0.000000 0.000000 cxif5315 169 1424601179 232228024 105684 85184 N/A 0 0 0 0 0.0 0.0 0.0 0.0 0.00 0.00 0 0 0 0 0.00 0.00 0.00 0 0 0 0 0 0.00 230 180.00 114.50 3 -4 0 0.001658 0.199684 0.000000 0.199336 0.230902
PEAK-NM -7.98 -12.45 0.083921 0.000014 0.000000 cxif5315 169 1424601179 232228024 105684 85184 EQU 1 72 44 31 220.9 1976.6 73.4 42.7 2.49 1.45 70 80 39 46 16.23 19.99 10.23 559 730 17471 2112 17598 6.89 0 0.00 0.00 0 0 0 0.000000 0.000000 0.000000 0.000000 0.000000
MATCHED -7.98 -12.45 0.059485 -0.000022 0.000448 cxif5315 169 1424601179 232228024 105684 85184 EQU 1 119 39 59 1293.5 11106.4 119.0 39.5 1.69 1.50 112 125 36 45 17.81 31.87 40.03 564 683 12306 1551 12403 7.18 230 180.00 114.50 1 -1 0 0.001936 0.060084 0.000000 0.059933 0.135565
MATCHED -7.98 -12.45 -0.166810 -0.000001 0.000288 cxif5315 169 1424601179 232228024 105684 85184 EQU 16 121 101 88 276.3 6888.4 120.0 103.1 2.52 2.93 115 127 98 110 39.18 36.32 6.53 637 247 -35645 -6412 36217 -169.80 230 180.00 114.50 -3 2 0 0.000051 0.167107 0.000000 -0.167098 0.998636 |
This information for all events goes in the file with name like peak-idx-cxif5315-r0169-2015-11-13T17:04:37.txt.
Result presenter
cxif5315/proc-cxif5315-r0169-idx-file.py
reads file obtained in previous section using
| Code Block |
|---|
from pyimgalgos.TDFileContainer import TDFileContainer
from pyimgalgos.TDMatchRecord import TDMatchRecord |
and generates summary tables/images with results as listed below.
Crystal in h,k space
| Code Block |
|---|
k : -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6
h=-4: 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000
h=-3: 0.0000 0.0000 0.0000 0.0000 0.0000 0.0222 0.0618 0.0000 1.0000 0.0075 0.0680 0.0000 0.0000
h=-2: 0.0000 0.0000 0.0156 0.0158 0.0013 0.0000 0.2334 0.6190 0.0272 0.0000 0.0078 0.3472 0.0000
h=-1: 0.0000 0.0070 0.0395 0.0000 0.0023 0.0000 0.1424 0.2158 0.3511 0.0036 0.0273 0.0019 0.0000
h= 0: 0.0000 0.0015 0.0131 0.0135 0.0031 0.0000 0.4409 0.0000 0.0290 0.0600 0.0389 0.0015 0.0000
h= 1: 0.0000 0.0000 0.0319 0.0000 0.3228 0.1522 0.1187 0.0038 0.0000 0.0000 0.0173 0.0089 0.0000
h= 2: 0.0000 0.3036 0.0131 0.0011 0.0043 0.5837 0.2267 0.0000 0.0039 0.0000 0.0000 0.0000 0.0000
h= 3: 0.0000 0.0000 0.0708 0.0049 0.7698 0.0000 0.0699 0.0172 0.0014 0.0035 0.0000 0.0000 0.0000
h= 4: 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 |
References
- Crystal structure, Bravais lattice, Crystal system, Primitive cell, Lattice constant - 3-d lattice
- Reciprocal lattice, Ewald's sphere, Surface diffraction, Miller index - reciprocal space
- PDG-2014
- X-ray crystallography, Bragg's law, Fiber diffraction
- my not on units for q and reciprocal space
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