Page History
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angles -> rotation matrix -> quaternion -> rotation matrix -> angles
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where in and out It was tested that input and output angles and rotation matrix coincide.
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Angles around x,y,z: 0.0 0.0 0.0 quaternion: w, x, y, z: 1.000000 0.000000 0.000000 0.000000 Angles around x,y,z: 30.0 0.0 0.0 quaternion: w, x, y, z: 0.965926 0.258819 0.000000 0.000000 Angles around x,y,z: 60.0 0.0 0.0 quaternion: w, x, y, z: 0.866025 0.500000 0.000000 0.000000 Angles around x,y,z: 90.0 0.0 0.0 quaternion: w, x, y, z: 0.707107 0.707107 0.000000 0.000000 Angles around x,y,z: 120.0 0.0 0.0 quaternion: w, x, y, z: 0.500000 0.866025 0.000000 0.000000 Angles around x,y,z: 150.0 0.0 0.0 quaternion: w, x, y, z: 0.258819 0.965926 0.000000 0.000000 Angles around x,y,z: 0.0 0.0 0.0 quaternion: w, x, y, z: 1.000000 0.000000 0.000000 0.000000 Angles around x,y,z: 0.0 30.0 0.0 quaternion: w, x, y, z: 0.965926 0.000000 0.258819 0.000000 Angles around x,y,z: 0.0 60.0 0.0 quaternion: w, x, y, z: 0.866025 0.000000 0.500000 0.000000 Angles around x,y,z: 0.0 90.0 0.0 quaternion: w, x, y, z: 0.707107 0.000000 0.707107 0.000000 Angles around x,y,z: 0.0 120.0 0.0 quaternion: w, x, y, z: 0.500000 0.000000 0.866025 0.000000 Angles around x,y,z: 0.0 150.0 0.0 quaternion: w, x, y, z: 0.258819 0.000000 0.965926 0.000000 Angles around x,y,z: 0.0 0.0 0.0 quaternion: w, x, y, z: 1.000000 0.000000 0.000000 0.000000 Angles around x,y,z: 0.0 0.0 30.0 quaternion: w, x, y, z: 0.965926 0.000000 0.000000 0.258819 Angles around x,y,z: 0.0 0.0 60.0 quaternion: w, x, y, z: 0.866025 0.000000 0.000000 0.500000 Angles around x,y,z: 0.0 0.0 90.0 quaternion: w, x, y, z: 0.707107 0.000000 0.000000 0.707107 Angles around x,y,z: 0.0 0.0 120.0 quaternion: w, x, y, z: 0.500000 0.000000 0.000000 0.866025 Angles around x,y,z: 0.0 0.0 150.0 quaternion: w, x, y, z: 0.258819 0.000000 0.000000 0.965926 |
Unit cell
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CrystFEL unit cell file version 1.0 lattice_type = triclinic centering = I a = 18.36 A b = 26.65 A c = 4.81 A al = 90.0 deg be = 90.0 deg ga = 102.83 deg |
Detector
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adu_per_eV = 1.0 ; Single panel 0/min_fs = 0 0/max_fs = 1500 0/min_ss = 0 0/max_ss = 1500 0/corner_x = -750.00 0/corner_y = -750.00 0/fs = x 0/ss = y 0/clen = 0.1 ; 10cm 0/res = 9090.99098 ; 110109.92 micron pixel size |
pattern_sim
command to generate simulated events:
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source conda_setup source /reg/g/cfel/crystfel/crystfel-dev/setup-sh cat quaternion_basis_x90.txt | pattern_sim -g sim-det1500x1500.geom -p sim-cell-fiber.cell -o result_x90.h5 --photon-energy=6003 --o result_x90spectrum=tophat --beam-bandwidth=1e-6 --min-size=30 --max-size=30 -n 3 -s 1 --no-noise |
Results
# output file accumulates events... (bug?)
# OR per event with complete control on names etc.
echo "0.587174 0.803196 0.095372 0.031718" | pattern_sim -g sim-det1500x1500.geom -p sim-cell-fiber.cell -o results_x90.h5 --photon-energy=6003 --spectrum=tophat --beam-bandwidth=1e-6 --min-size=30 --max-size=30 -n 1 -s 1 --no-noise --no-fringes |
Results
Rotation angles and associated quaternions
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Angles around x,y,z: 90.0 0.0 0.0 quaternion: w, x, y, z: 0.707107 0.707107 0.000000 0.000000 Angles around x,y,z: 90.0 0.0 30.0 quaternion: w, x, y, z: 0.683013 0.683013 0.183013 0.183013 Angles around x,y,z: 90.0 0.0 600.0 quaternion: w, x, y, z: 0.612372707107 0.612372707107 0.353553000000 0.353553000000 Angles around x,y,z: 90.0 0.0 901.0 quaternion: w, x, y, z: 0.500000707080 0.500000707080 0.500000006171 0.500000006171 Angles around x,y,z: 90.0 0.0 120 2.0 quaternion: w, x, y, z: 0.353553706999 0.353553706999 0.612372012341 0.612372012341 Angles around x,y,z: 90.0 0.0 150 3.0 quaternion: w, x, y, z: 0.183013706864 0.183013706864 0.683013018510 0.683013 |
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018510 Angles around x,y,z: 10890.0 30.50 04.0 quaternion: w, x, y, z: 0.587511706676 0.808640706676 0.017950024678 -0.024706024678 Angles around x,y,z: 10890.0 30.50 305.0 quaternion: w, x, y, z: 0.573887706434 0.776440706434 0.226630030844 0.128195030844 Angles around x,y,z: 10890.0 30.50 606.0 quaternion: w, x, y, z: 0.521153706138 0.691327706138 0.419865037007 0.037007 ... |
Movies generated with default sample size
images for 30um sample size:
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Angles around x,y,z: 272359 Angles around x,y,z: 108.0 3.5 90.0 quaternion: w, x, y, -3.5 0.0 quaternion: w,x,y,z: 0.432903706777 0.559102706777 -0.584487021594 0.397963021594 Angles around x,y,z: 10890.0 -3.5 120 1.0 quaternion: w, x, y, z: 0.315152706562 0.388775706939 -0.709278015425 0.496446027761 Angles around x,y,z: 108 90.0 -3.5 1502.0 quaternion: w, x, y, z: 0.175923706292 0.191953707046 -0.785732009256 0.561098 |
Rotation around omega
Quaternions
Table of quaternions was generated using methods in pyimgalgos/src/Quaternion.py
Self-test for Quaternion
self-test uses a chain of conversions:
angles -> rotation matrix -> quaternion -> rotation matrix -> angles
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where in and out angles and rotation matrix coincide.
Script cxif5315/make-quaternions.py
generates file with a list of quaternions from file with table of angles
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033926 Angles around x,y,z: 90.0 -3.5 3.0 quaternion: w,x,y,z: 0.705970 0.707100 -0.003085 0.040088 Angles around x,y,z: 090.0 0-3.05 04.0 quaternion: w, x, y, z: 10.000000705593 0.000000707100 0.000000003085 0.000000046247 Angles around x,y,z: 3090.0 0-3.05 05.0 quaternion: w, x, y, z: 0.965926705162 0.258819707046 0.000000009256 0.052403 ... |
Movies:
Single images:
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000000 Angles around x,y,z: 6072.0 0-3.05 0.0 quaternion: w, x, y, z: 0.866025808640 0.500000587511 -0.000000024706 0.000000017950 Angles around x,y,z: 9072.0 0-3.05 01.0 quaternion: w, x, y, z: 0.707107808452 0.707107587704 -0.000000019578 0.000000025006 Angles around x,y,z: 120 72.0 0-3.05 02.0 quaternion: w, x, y, z: 0.500000808203 0.866025587853 -0.000000014449 0.000000032060 Angles around x,y,z: 150 72.0 0-3.05 03.0 quaternion: w, x, y, z: 0.258819807893 0.965926587957 -0.000000009318 0.000000039112 Angles around x,y,z: 072.0 0-3.05 04.0 quaternion: w, x, y, z: 10.000000807521 0.000000588015 -0.000000004187 0.000000046160 Angles around x,y,z: 072.0 30-3.05 05.0 quaternion: w, x, y, z: 0.965926807087 0.000000588030 0.258819000944 0.000000 Angles around x,y,z: 0.0 60.0 0.0 quaternion: w, x, y, z: 0.866025 0.000000 0.500000 0.000000 Angles around x,y,z: 0.0 90.0 0.0 quaternion: w, x, y, z: 0.707107 0.000000 0.707107 0.000000 Angles around x,y,z: 0.0 120.0 0.0 quaternion: w, x, y, z: 0.500000 0.000000 0.866025 0.000000 Angles around x,y,z: 0.0 150.0 0.0 quaternion: w, x, y, z: 0.258819 0.000000 0.965926 0.000000 Angles around x,y,z: 0.0 0.0 0.0 quaternion: w, x, y, z: 1.000000 0.000000 0.000000 0.000000 Angles around x,y,z: 0.0 0.0 30.0 quaternion: w, x, y, z: 0.965926 0.000000 0.000000 0.258819 Angles around x,y,z: 0.0 0.0 60.0 quaternion: w, x, y, z: 0.866025 0.000000 0.000000 0.500000 Angles around x,y,z: 0.0 0.0 90.0 quaternion: w, x, y, z: 0.707107 0.000000 0.000000 0.707107 Angles around x,y,z: 0.0 0.0 120.0 quaternion: w, x, y, z: 0.500000 0.000000 0.000000 0.866025 Angles around x,y,z: 0.0 0.0 150.0 quaternion: w, x, y, z: 0.258819 0.000000 0.000000 0.965926 |
Unit cell
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CrystFEL unit cell file version 1.0
lattice_type = triclinic
centering = I
a = 18.36 A
b = 26.65 A
c = 4.81 A
al = 90.0 deg
be = 90.0 deg
ga = 102.83 deg |
Detector
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adu_per_eV = 1.0
; Single panel
0/min_fs = 0
0/max_fs = 1500
0/min_ss = 0
0/max_ss = 1500
0/corner_x = -750.00
0/corner_y = -750.00
0/fs = x
0/ss = y
0/clen = 0.1 ; 10cm
0/res = 9090.9 ; 110 micron pixel size |
pattern_sim
command to generate simulated events:
Code Block |
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cat quaternion_basis_x90.txt | pattern_sim -g det1500x1500.geom -p cell-fiber.cell --photon-energy=6003 -o result_x90 -n 3 -s 1 --no-noise |
Results
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Angles around x,y,z: 90.0 0.0 0.0 quaternion: w, x, y, z: 0.707107 0.707107 0.000000 0.000000
Angles around x,y,z: 90.0 0.0 30.0 quaternion: w, x, y, z: 0.683013 0.683013 0.183013 0.183013
Angles around x,y,z: 90.0 0.0 60.0 quaternion: w, x, y, z: 0.612372 0.612372 0.353553 0.353553
Angles around x,y,z: 90.0 0.0 90.0 quaternion: w, x, y, z: 0.500000 0.500000 0.500000 0.500000
Angles around x,y,z: 90.0 0.0 120.0 quaternion: w, x, y, z: 0.353553 0.353553 0.612372 0.612372
Angles around x,y,z: 90.0 0.0 150.0 quaternion: w, x, y, z: 0.183013 0.183013 0.683013 0.683013 |
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Angles around x,y,z: 108.0 3.5 0.0 quaternion: w, x, y, z: 0.587511 0.808640 0.017950 -0.024706
Angles around x,y,z: 108.0 3.5 30.0 quaternion: w, x, y, z: 0.573887 0.776440 0.226630 0.128195
Angles around x,y,z: 108.0 3.5 60.0 quaternion: w, x, y, z: 0.521153 0.691327 0.419865 0.272359
Angles around x,y,z: 108.0 3.5 90.0 quaternion: w, x, y, z: 0.432903 0.559102 0.584487 0.397963
Angles around x,y,z: 108.0 3.5 120.0 quaternion: w, x, y, z: 0.315152 0.388775 0.709278 0.496446
Angles around x,y,z: 108.0 3.5 150.0 quaternion: w, x, y, z: 0.175923 0.191953 0.785732 0.561098 |
Rotation around omega
Angles around x,y,z: 90.0 0 (0,180,1):
Angles around x,y,z: 90.0 -3.5 (0,180,1):
Summary
- Thomas White did not advice to use
pattern_sim
due to potential bugs. - In stead he suggested to use
diffraction
.
Summary
- Thomas White did not advice to use
pattern_sim
due to potential bugs. - In stead he suggested to use
diffraction
.
...
053205
... |
Movies:
Single images:
Summary
- Thomas White did not advice to use
pattern_sim
due to potential bugs. In stead he suggested to usediffraction
. pattern_sim
has a few problems in different versionssource /reg/g/cfel/crystfel/crystfel-0.6.2/setup-sh # has problems with peak intensity ~25*e6 ADU, not sensitive to adu_per_eV, etc
- --spectrum=tophat --beam-bandwidth=1e-6 - removes photon energy spread
- --min-size=30 --max-size=30 - changes a size of sample and peak size and intensity
- -n NNN - this option generates accumulated image
- ...