Script
sim08-make-index-table.py - generates lookup table and a few plots as shown below.
Unit cell
Try to understand crystal symmetry for two unit-cells
Unit cell 1: a=18, b=26, gamma=77
# file name: ./v01-sim-lut-cxifsimu-r0123-2017-04-25T09:52:17.txt
# photon energy = 6003.0000 eV
# wavelength = 2.0654 A
# wave number/Evald radius k = 1/lambda = 0.484172 1/A
# sigma_ql = 0.001453 1/A (approximately = k * <pixel size>/
# sigma_qt = 0.000484 1/A (approximately = k * <pixel size>/<sample-to-detector distance> = k*100um/100mm)
# 3*sigma_ql = 0.004358 1/A
# 3*sigma_qt = 0.001453 1/A
# Triclinic crystal cell parameters:
# a = 18.36 A
# b = 26.65 A
# c = 4.81 A
# alpha = 90.00 deg
# beta = 90.00 deg
# gamma = 77.17 deg
# 3-d space primitive vectors:
# a1 = ( 18.360000, 0.000000, 0.000000)
# a2 = ( 5.917874, 25.984635, 0.000000)
# a3 = ( 0.000000, 0.000000, 4.810000)
# reciprocal space primitive vectors:
# b1 = ( 0.054466, -0.012404, 0.000000)
# b2 = ( 0.000000, 0.038484, 0.000000)
# b3 = ( 0.000000, 0.000000, 0.207900)
![](/download/attachments/221084541/v01-sim-a18.36-b26.65-c4.81-alp90.00-bet90.00-gam77.17-lattice-rotated-beta000-omega000.png?version=1&modificationDate=1493138885000&api=v2)
![](/download/attachments/221084541/v01-sim-a18.36-b26.65-c4.81-alp90.00-bet90.00-gam77.17-lattice-rotated-beta000-omega010.png?version=1&modificationDate=1493138888000&api=v2)
Unit cell 2: a=26, b=18, gamma=77
# file name: ./v01-sim-lut-cxifsimu-r0123-2017-04-25T10:18:21.txt
# photon energy = 6003.0000 eV
# wavelength = 2.0654 A
# wave number/Evald radius k = 1/lambda = 0.484172 1/A
# sigma_ql = 0.001453 1/A (approximately = k * <pixel size>/
# sigma_qt = 0.000484 1/A (approximately = k * <pixel size>/<sample-to-detector distance> = k*100um/100mm)
# 3*sigma_ql = 0.004358 1/A
# 3*sigma_qt = 0.001453 1/A
# Triclinic crystal cell parameters:
# a = 26.65 A
# b = 18.36 A
# c = 4.81 A
# alpha = 90.00 deg
# beta = 90.00 deg
# gamma = 77.17 deg
# 3-d space primitive vectors:
# a1 = ( 26.650000, 0.000000, 0.000000)
# a2 = ( 4.077004, 17.901610, 0.000000)
# a3 = ( 0.000000, 0.000000, 4.810000)
# reciprocal space primitive vectors:
# b1 = ( 0.037523, -0.008546, 0.000000)
# b2 = ( 0.000000, 0.055861, 0.000000)
# b3 = ( 0.000000, 0.000000, 0.207900)
![](/download/attachments/221084541/v01-sim-a26.65-b18.36-c4.81-alp90.00-bet90.00-gam77.17-lattice-rotated-beta000-omega000.png?version=1&modificationDate=1493138891000&api=v2)
![](/download/attachments/221084541/v01-sim-a26.65-b18.36-c4.81-alp90.00-bet90.00-gam77.17-lattice-rotated-beta000-omega010.png?version=1&modificationDate=1493138883000&api=v2)
Presumably maps (qh vs omega) should be the same up to rotations.
Lookup table and maps
Unit cell 1
beta = 0 and 180
![](/download/attachments/221084541/v01-sim-a18.36-b26.65-c4.81-alp90.00-bet90.00-gam77.17-plot-img-prob-omega-vs-qh-for-beta%3A0-0-1.png?version=1&modificationDate=1493138877000&api=v2)
![](/download/attachments/221084541/v01-sim-a18.36-b26.65-c4.81-alp90.00-bet90.00-gam77.17-plot-img-prob-omega-vs-qh-for-beta%3A180-180-1.png?version=1&modificationDate=1493138880000&api=v2)
![](/download/attachments/221084541/v01-sim-a18.36-b26.65-c4.81-alp90.00-bet90.00-gam77.17-plot-his-prob-vs-qh-sym.png?version=1&modificationDate=1493138874000&api=v2)
Unit cell 2
beta = 0 and 180
![](/download/attachments/221084541/v01-sim-a26.65-b18.36-c4.81-alp90.00-bet90.00-gam77.17-plot-img-prob-omega-vs-qh-for-beta%3A0-0-1.png?version=1&modificationDate=1493138869000&api=v2)
![](/download/attachments/221084541/v01-sim-a26.65-b18.36-c4.81-alp90.00-bet90.00-gam77.17-plot-img-prob-omega-vs-qh-for-beta%3A180-180-1.png?version=1&modificationDate=1493138872000&api=v2)
![](/download/attachments/221084541/v01-sim-a26.65-b18.36-c4.81-alp90.00-bet90.00-gam77.17-plot-his-prob-vs-qh-sym.png?version=1&modificationDate=1493138866000&api=v2)
Indexing script
Reconstruct simulated data, plot for hq vs omega
![](/download/attachments/221084541/peaks-idximg-qh-vs-evnum-vs-qh.png?version=1&modificationDate=1493138863000&api=v2)
Comparison of look-up table and reconstructed sample
- All maps are consistent after appropriate rotation
- almost all lattice nodes can be reconstructed (are included in 2-peak events)
Friquency distributions at indexing
![](/download/attachments/221084541/peaks-idx-idx-equ-qh.png?version=1&modificationDate=1493255273000&api=v2)
![](/download/attachments/221084541/peaks-idx-idx-equ-qv.png?version=1&modificationDate=1493255273000&api=v2)
![](/download/attachments/221084541/peaks-idx-idx-npeaks.png?version=1&modificationDate=1493255273000&api=v2)
![](/download/attachments/221084541/peaks-idx-idx-prob.png?version=1&modificationDate=1493255273000&api=v2)
![](/download/attachments/221084541/peaks-idx-idx-beta.png?version=1&modificationDate=1493255272000&api=v2)
![](/download/attachments/221084541/peaks-idx-idx-omega.png?version=1&modificationDate=1493255273000&api=v2)
Reconstructed omega vs simulated
![](/download/attachments/221084541/peaks-idx-omega-rec-vs-sim.png?version=1&modificationDate=1493255273000&api=v2)
![](/download/attachments/221084541/peaks-idx-idx-omega-diff.png?version=1&modificationDate=1493340127000&api=v2)
Reconstructed lattice
- lattice for reconstructed angle omega
- lattice for simulated angle omega
![](/download/attachments/221084541/peaks-idximg-idx-lattce-rec.png?version=1&modificationDate=1493337395000&api=v2)
![](/download/attachments/221084541/peaks-idximg-idx-lattce-sim.png?version=1&modificationDate=1493337395000&api=v2)
l=1 lattice for phi, beta, omega reconstructed for l=0, take the l=1 slice from Fraser's plot and transform it to reciprocal space.
![](/download/attachments/221084541/peaks-idximg-idx-lattce-l1.png?version=1&modificationDate=1493749852000&api=v2)
This is a mess and not clear why...
To do
- lower threshold for peakfinder
- reason for bad phi-beta fits