John W. Campbell
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
- Package:
- Jdl.JdlPX;
- Class name:
- JdlRefineOrientation
- Class definition:
- public class JdlRefineOrientation
- Extends:
- Object
- Implements:
- JdlLeastSquaresRefineable
- Actions:
- none
No fields with public, package or protected access defined.
A single constructor is used to create a JdlRefineOrientation object prior
to calling one of the refinement methods.
Constructor:
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.
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
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.
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.
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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