4.9.2 - Refine orientation - JdlRefineOrientation

John W. Campbell

4.9.2.1 Introduction

This class enables a crystal orientation and related parameters to be refined using a set of observed reflection positions on a diffraction image.

Class, fields, constructors and methods:

Class Details
Accessible Fields
Constructors
Methods

4.9.2.2 Class Details

Package:
Jdl.JdlPX;
Class name:
JdlRefineOrientation
Class definition:
public class JdlRefineOrientation
Extends:
Object
Implements:
JdlLeastSquaresRefineable
Actions:
none

4.9.2.3 Accessible Fields

No fields with public, package or protected access defined.

4.9.2.4 Constructors

4.9.2.4.1 Introduction

A single constructor is used to create a JdlRefineOrientation object prior to calling one of the refinement methods.

Constructor:

Constructor

4.9.2.4.2 Constructor

This constructs a JdlRefineOrientation object with a Vector of observed reflections and detector related parameters.

Constructor Definition:
public JdlRefineOrientation (Vector<JdlObservedReflection> refobs, JdlPositionedDetector pdet, double pixsiz_x, double pixsiz_y, double[][] umat)
Parameters List:
refobs
A vector with the list of observed reflections to be used in the refinement.
pdet
The positioned detector
pixsiz_x
The pixel dimension in mm along the first local image axis.
pixsiz_x
The pixel dimension in mm along the second local image axis.
umat
The setting 'U' matrix.

4.9.2.5 Methods

4.9.2.5.1 Introduction

This section contains methods to refine selected parameters or to refine the PhiZ parameter on its own.

Methods:

Refine parameters - refineParameters
Refine PhiZ - refinePhiZ
Set scaling factors - setScalingFactors

4.9.2.5.2 Refine parameters - refineParameters

This method refines the selected parameters. Note that the PhiZ parameter needs to be refined separately using the refinePhiZ(..) method.

Method Definition:
public JdlRefinedOrientationParameters refineParameters(double[] phis, double x_cen, double y_cen, double ctod, double[] cellc, int isys, double phirot, double oscang, boolean refine_phixy, boolean refine_cen, boolean refine_ctod, boolean[] refine_cell)
Parameters List:
phis
The starting values for the missetting angles.
x_cen
The centre position along the 1'st local image axis in rasters.
y_cen
The centre position along the 2'nd local image axis in rasters.
ctod
The crystal to detector distance in mm.
cellc
The cell parameters in contracted form - see contractCell method in JdlCrystalCalculations class.
isys
The crystal system number 1-7 (Tri, Mon, Ort, Tet, Hex, Rho, Cub)
phirot
Setting of spindle axis in degrees at start of oscillation range.
oscang
Oscillation angle in degrees.
refine_phixy
If true, refine PhiX and PhiY; if false, do not.
refine_cen
If true, refine x_cen and y_cen; if false, do not.
refine_ctod
If true, refine ctod; if false, do not.
refine_cell
Flags for each of the cell parameters in the contracted cell. If true, refine that cell parameter; if false, do not.
Method Return:
Returns the refined parameters and other details in a JdlRefinedOrientationParameters object.

4.9.2.5.3 Refine PhiZ - refinePhiZ

This method refines the PhiZ parameter which needs to be refined separately from the other parameters..

Method Definition:
public JdlRefinedOrientationParameters refinePhiZ(double[] phis, double x_cen, double y_cen, double ctod, double[] cellc, int isys, double phirot, double oscang)
Parameters List:
phis
The starting values for the missetting angles.
x_cen
The centre position along the 1'st local image axis in rasters.
y_cen
The centre position along the 2'nd local image axis in rasters.
ctod
The crystal to detector distance in mm.
cellc
The cell parameters in contracted form - see contractCell method in JdlCrystalCalculations class.
isys
The crystal system number 1-7 (Tri, Mon, Ort, Tet, Hex, Rho, Cub)
phirot
Setting of spindle axis in degrees at start of oscillation range.
oscang
Oscillation angle in degrees.
Method Return:
Returns the refined parameters and other details in a JdlRefinedOrientationParameters object.

4.9.2.5.4 Set scaling factors - setScalingFactors

This method enables different refinement scaling factors to be set for the various classes of parameter to be refined. By default all the scaling factors are set to 1.0.

Method Definition:
public void setScalingFactors (double scal_phis, double scal_cen, double scal_ctod, double scal_clen, double scal_cang)
Parameters List:
scal_phis
Scaling factor for Phi angles (PhiX, PHiY - not used for PhiZ which needs refined on its own)
scal_cen
Scaling factor for centre position refinement.
scal_ctod
Scaling factor for crystal to detector distance.
scal_clen
Scaling factor for cell lengths.
scal_cang
Scaling factor for cell angles.

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