Cppxfel Initial Orientation Matrix Refinement

Initial orientation matrix refinement covers the first stage of the dedicated C++ code in cppxfel and uses an input file which is called integrate.txt by default. This should have been generated during the previous stage.

The contents of integrate.txt

One can look at the contents of integrate.txt by executing:

cat integrate.txt

This shows an input script along the following lines:

ORIENTATION_MATRIX_LIST matrices.dat
NEW_MATRIX_LIST orientations.dat

SPACE_GROUP 197
UNIT_CELL 105.917757854 105.917757854 105.917757854 90.0 90.0 90.0
FIX_UNIT_CELL ON

MM_PER_PIXEL 0.11
BEAM_CENTRE 881.755 881.5075
DETECTOR_DISTANCE 91.0018
INTEGRATION_WAVELENGTH 1.45738121124 

PANEL_LIST panels.txt
METROLOGY_SEARCH_SIZE 1

SHOEBOX_FOREGROUND_RADIUS 1
SHOEBOX_NEITHER_RADIUS 2
SHOEBOX_BACKGROUND_RADIUS 3

INTENSITY_THRESHOLD 12
ABSOLUTE_INTENSITY OFF
REFINE_ORIENTATIONS ON

VERBOSITY_LEVEL 1

COMMANDS

INTEGRATE

The matrix information from indexing is passed through using the generated file

matrices.dat

under the keyword ORIENTATION_MATRIX_LIST which was produced in the previous stage. One can see the contents of matrices.dat:

head -20 matrices.dat

image shot-s00-20130316165156302
wavelength 1.45690748941
distance 91.0018
centre 881.755 881.5075
unitcell 0.00945122403519 0.0 0.0 -5.78701450245e-19 0.00945122403519 0.0 -5.78701450245e-19 -1.51989185671e-18 0.00945122403519 
rotation 0.209524357745 -0.976621953811 0.0480531252429 -0.360236467579 -0.122785692599 -0.924745024923 0.909026529282 0.176446119331 -0.377541436183 
image shot-s01-20130316165035212
wavelength 1.45496194705
distance 91.0018
centre 881.755 881.5075
unitcell 0.00944171966033 0.0 0.0 7.80781215281e-18 0.00944171966033 0.0 3.61484632923e-18 2.67460240614e-18 0.00944171966033 
rotation -0.351867835054 0.0121912864248 0.935970298241 -0.852741351745 -0.416546104403 -0.315153184867 0.386032658825 -0.909032846184 0.156965190022 
image shot-s00-20130316165041011
wavelength 1.45643207192
distance 91.0018
centre 881.755 881.5075
unitcell 0.00943218298265 0.0 0.0 1.51682978341e-18 0.00943218298265 0.0 3.61119512738e-18 5.77535560549e-19 0.00943218298265 
rotation -0.21213292526 0.320476950034 0.92319778299 -0.956128815937 -0.263369266933 -0.128274380022 0.202032941263 -0.909907222596 0.362286539789 
image shot-s00-20130316165215513
wavelength 1.45673961831
distance 91.0018

The image tag has the name of the image file minus the extension. The values for the detector distance, beam centre and wavelength are over-ridden by the values in the integrate.txt file if they are present, but the over-riding values can be removed if the values vary from one image to another. The orientation matrix is constructed from the unit cell matrix and the rotation matrix listed.

Executing integrate.txt

This integration input file can be executed through cppxfel using the following command:

cppxfel.run -i integrate.txt

Wavelength histograms

The output tracks individual images which execute on different threads as their orientation matrices are refined. An example of a wavelength histogram created is shown below. These wavelength histograms were first described in Ginn et al, Nat Comms 2015.

Wavelength histogram for shot-s00-20130316165134721.img
1.41322	.
1.41759	
1.42196	
1.42633	.
1.4307	.
1.43508	..
1.43945	
1.44382	..
1.44819	.....
1.45256	.........
1.45693	..................
1.4613	......................................................................
1.46567	...............................................
1.47004	.....
1.47441	.......
1.47878	...
1.48315	.
1.48752	.
1.4919	..
1.49627	

These integration peaks should be as long and narrow as possible, depending on the extent of over-prediction as determined by the parameter OVER_PRED_BANDWIDTH.

Final integration summary table

The initial orientation matrix refinement commands finish with a summary table detailing the main results for each crystal and each image.