Page History
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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 |
...
Rotation around beta and omega
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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
Code Block | ||||
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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
Code Block | ||||
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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 0.0 090.0 quaternion: w, x, y, z: 0.707107500000 0.707107500000 0.000000500000 0.000000500000 Angles around x,y,z: 90.0 0.0 30120.0 quaternion: w, x, y, z: 0.683013353553 0.683013353553 0.183013612372 0.183013612372 Angles around x,y,z: 90.0 0.0 60150.0 quaternion: w, x, y, z: 0.612372183013 0.612372183013 0.353553683013 0.353553 Angles around x,y,z: 90.0 683013 |
Rotation around beta, phi and omega
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Angles around x,y,z: 72.0.0 -3.5 900.0 quaternion: w, x, y, z: 0.500000808640 0.500000587511 -0.500000024706 0.500000017950 Angles around x,y,z: 9072.0 -3.5 0.0 1201.0 quaternion: w, x, y, z: 0.353553808452 0.353553587704 -0.612372019578 0.612372025006 Angles around x,y,z: 9072.0 0.0-3.5 1502.0 quaternion: w, x, y, z: 0.183013808203 0.183013587853 -0.683013014449 0.683013 |
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Angles around x,y,z: 108032060 Angles around x,y,z: 72.0 -3.5 03.0 quaternion: w, x, y, z: 0.587511807893 0.808640587957 -0.017950009318 -0.024706039112 Angles around x,y,z: 10872.0 -3.5 30 4.0 quaternion: w, x, y, z: 0.573887807521 0.776440588015 -0.226630004187 0.128195046160 Angles around x,y,z: 108 72.0 -3.5 60 5.0 quaternion: w, x, y, z: 0.521153807087 0.691327588030 0.419865000944 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
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
,
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
Code Block | ||||
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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
Code Block | ||||
---|---|---|---|---|
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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
Code Block | ||||
---|---|---|---|---|
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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 |
---|
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
Code Block | ||||
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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 |
Code Block | ||||
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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 |
...
053205 |
Unit cell
Code Block | ||||
---|---|---|---|---|
| ||||
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
Code Block | ||||
---|---|---|---|---|
| ||||
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 = 9098 ; 109.92 micron pixel size |
pattern_sim
command to generate simulated events:
Code Block |
---|
cat quaternion_basis_x90.txt | pattern_sim -g det1500x1500.geom -p cell-fiber.cell -o result_x90 --photon-energy=6003 --spectrum=tophat --beam-bandwidth=1e-6 --min-size=30 --max-size=3 -n 3 -s 1 --no-noise
# 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 det1500x1500.geom -p cell-fiber.cell -o results_x90 --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 around omega
Angles around x,y,z: 90.0 0 (0,180,1):
image generated with defailt sample size
Angles around x,y,z: 90.0 0 -3.5 (0,180,1):
Angles around x,y,z: 90.0 -3.5 (0,180,1):
Angles around x,y,z: 90.0-18 -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
.
...
.0-18 -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
. 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
- ...