Tel: +44 (0)1235 56 7675
The purpose of LSQINT is to provide an automatic method for the integration of intensities for fibre diffraction data. The program will handle patterns which are largely crystalline in nature, or patterns which have continuous layerlines, sampling only occurring parallel to the Z axis. More than one lattice can be fitted in a single pattern.
The approach used is to generate profiles and then to fit these profiles to the observed pixel intensities by a robust linear least-squares method or using the maximum entropy algorithm of Skilling and Bryan, Mon. Not. R. astr. Soc. (1984)..Four background subtraction options are available:
FileName: This section enable to select input and output filenames and output option.The path and filename can be entered directly in the text window or selected by using the File Open Dialog Tool, which is opened by clicking the Browse button. If no path is specified, the current directory is searched.For multi-frame BSL image user is able to select start, last and increment and the binary file type if there are more than one binary file exist.
Input Header FileName: Input to LSQINT is provided by the program FTOREC which maps flat area detector data into reciprocal space coordinates, either cartesian or polar.
Standard deviation Input Header FileName: The remapped image is in standard BSL format with the addition of the second header record being used to store extra image information. Optionally, FTOREC produces an image of the standard deviation of pixel values between the four quadrants of the original pattern. If desired, LSQINT can use this image to weight pixel values.
Input Intensity FileName: input intensity file (the format of this file should be similar to the LSQINT output file)to simulate the image file for the intensities.
Output Image Header FileName:A 2-frame BSL file is also output providing a visible indication of the goodness of fit.
Frame1: Data - background
Output Intensity Ascii FileName:an ascii file containing 7 columns. The first three columns contain integers defining h,k,l, the fourth column gives the reciprocal space radius, R of the sampling point and the fifth, the fibre multiplicity of the reflection.
NoFit :force output of equally weighted profiles in the calculated image
SetZero: set negative intensities to zero between least-squares fitting and R-factor calculation
Xplor output: output composite structure factor amplitudes in a format suitable for the version of X-PLOR modified for polycrystalline fibre diffraction. Amplitudes and estimated standard deviations will be calculated according to the method of Sivia & David Acta Cryst. (1995). A50, 703-714 for non-overlapping peaks.
NoCalculate: by default, LSQINT calculates and outputs the calculated image and background. This prevents this behaviour. Background will be in the first frame corresponding to the current image, the total calculated image will be in the second.
BACK - This section enable to select Background subtraction methods can be used successively. GLOBAL background fitting is not allowed with MAXENT intensity fitting.
Global - 8 parameters defining a global background function will be fitted
Circularly symmetric - a background will be formed by radial binning of pixel values, averaging those in the range Lpixel to Hpixel and then fitting a smoothing spline under tension to these values.
Window - Paul Langan's roving window background subtraction method.
Flat plane - local least-squares background fitting and spline fitting.
LIMITS - This section enable to select limits for profile calculation
Layerlines - The first and last layerlines
Radii- The min. and max. radii (image units)
Dlimits - requires two values to follow, the min. and max. d* values
(defaults Dlimits 0.0 Max(d*) Layerlines 0 (Dmax/c*) Radii first pixel last pixel)
Helix - signals use of helical selection rule for Bessel function orders
Mixture - up to five values to follow, corresponding to the c/P(i) where P(i) is the pitch of the i'th component of a multi-component system. The layerline is allowed if any of the c/P(i) = an integer
(default behaviour - no selection rules, all layerlines allowed)
parameter profile parameter refinement
Data type (BRAGG/CONTINUOUS) - Fitting will be performed for Bragg data or for continuous layerline intensity
Cell - 6 cell parameters (a,b,c ,alpha,beta,gamma) for Bragg data, 1(c) for continuous.
Cstar - Defines the initial cell orientation with c* as the axis parallel to the Z axis of the particle (for monoclinic cells, etc). By default, the initial orientation has c parallel to Z. a* always starts in the Z-X plane.
Spacegroup - Space group symbol for Bragg data (default P1)
Missetting - The user to specify the following misetting angles
Add - allow to specify more than one lattice positions and profiles.
Refine - cell and profile refinement
Signals Calculating the standard deviations of pixel values
Signals fitting of intensities by maximum entropy
Run - Signals end of input and causes the final lattice positions and profiles to be calculated.
If the pattern contains a mixture of crystalline sampling and continuous transform, LSQINT, will not deal with a mixture of the two. However LSQINT still can be used to measure the two components (crystalline and continuous) separately - you will have to relate/scale them in some way later on.
LSQINT effectively deals with the Lorentz factor. It also deals with the "normal" polarisation correction. However it does not deal with the extra (very much smaller) horizontal polarisation correction that is required for SR data. This is something that should be taken care of after background subtraction and before the data goes into FTOREC (which does quadrant averaging), since it will depend on sample rotation relative to the orbital plane.
A log file, LSQINT.LOG, is opened when the program is executed. This contains information about the input file, consequences of the input, the parameters for which the profiles are calculated, R-factors and any error messages or warnings. The R-factors which are reported are calculated by the formula,
R'' = sqrt(sum(Po-Pc)**2/sum(Po**2))
where the Po are the observed pixel values minus background and the Pc are the calculated pixel values.
Output is in the form of an ascii file containing 7 columns. The first three columns contain integers defining h,k,l, the fourth column gives the reciprocal space radius, R of the sampling point and the fifth, the fibre multiplicity of the reflection. A non-zero fibre multiplicity is assigned only to the last reflection in the list constituting a multiplet. A reflection is considered to be part of a multiplet with the previous reflection if their positions fall within the same pixel on the input image. The last two columns contain real numbers describing the integrated intensity of the spot and its standard deviation. The standard deviation is calculated directly from the differences between the calculated and observed pixel values over the predicted profile of the peak. A file, DRAGON.OUT, is also created containing a full list of the reflections and their reciprocal space coordinates.
A 2-frame BSL file is also output providing a visible indication of the goodness of fit.
Frame1: Data - background
Diamond Light Source is the UK's national synchrotron science facility, located at the Harwell Science and Innovation Campus in Oxfordshire.
Copyright © 2022 Diamond Light Source
Diamond Light Source Ltd
Harwell Science & Innovation Campus
Diamond Light Source® and the Diamond logo are registered trademarks of Diamond Light Source Ltd
Registered in England and Wales at Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom. Company number: 4375679. VAT number: 287 461 957. Economic Operators Registration and Identification (EORI) number: GB287461957003.