4.10.6 - Setting Solution - JdlSettingSolution

John W. Campbell

4.10.6.1 Introduction

This class stores details of a crystal setting determined from one or more monochromatic oscillation images for use in association with the methods of the JdlSetting3DFT class. An object of the class stores a number of items relating to the initial orientation determined from vectors in a Fourier Transform, a refined setting based on these vectors and a refined setting based on the spot positions on an image.

Class, fields, constructor and methods:

Class Details
Accessible Fields
Constructor
Refinement Method
Listing Methods

4.10.6.2 Class Details

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

4.10.6.3 Accessible Fields

The following accessible fields have been defined:

public int nvect
Number of vectors used from 3DFT search (For a good solution should be 3 but may be 2 as an orientation can be determined from just a pair of cell vectors).
public boolean[] found_vec
Flags indicating which vectors were used from the 3DFT search.
public JdlVec[] peak_vectors
Array of peak positions for the three cell vectors.
public int[] peak_heights
Array of peak heights for the three cell vectors. For a vector not found in the original search the peak height calculated may be less than the used peak threshold value (or even negative).
public JdlCell cell_from_peaks
Cell vectors from peak positions if nvect=3 (otherwise may be null or have zero values)
public int num_checked_vec
Number of cell related vectors for which peak heights were checked; i.e. number of main cell vectors (100, 010, 001) and related cell vectors (011, 101, 110, and 111) (+ a centering vector if appropriate).
public boolean[] checked_vec_found
Array of 'peak found' flags for the 'num_checked_vec' checked cell related vectors; true = found (above threshold), false = not found (not above threshold)
public int[] checked_vec_heights
Array of peak heights for the ncheck checked cell related vectors.
public double[] phi_initial
Missetting angles (phi_x, phi_y, phi_z) from initial solution.
public boolean vecref
Missetting angles refined against peak vectors flag = true yes, = false no.
public double vecref_fmin_before
Missetting angles refinement - fmin before refinement (-1.0 if not set)
public double vecref_fmin_after
Missetting angles refinement - fmin after refinement (-1.0 if not set)
public double[] phi_vecref
Missetting angles (phi_x, phi_y, phi_z) refined against vector peak positions (initially set to phi_initial values).

4.10.6.4 Constructor

4.10.6.4.1 Introduction

A single constructor creates an object with initial values determined for a solution.

Constructor:

Constructor

4.10.6.4.2 Constructor

This constructs a JdlSettingSolution with the initial solution details an missetting angles.

Constructor Definition:
public JdlSettingSolution(int nvect, boolean[] found, JdlVec[] peak_vec, int[] peak_height, JdlCell cell, int nchk, boolean[] chk_found, int[] chk_height, Jdl3x3 umatr, double[] phis)
Parameters List:
nvect
Number of vectors used from 3DFT search (2 or 3)
found
Array of 3 flags indicating which two or three vectors were found from the 3D search (true=found, false = not found)
peak_vec
The three cell vector peak positions.
peak_height
The three cell vector peak heights.
cell
A JdlCell object containing the six cell vectors found from the peak positions in Angstroms and degrees - must be given if nvect=3 but may be zero valued or null otherwise.
nchk
Number of cell related vectors for which peak heights were checked.
chk_found
Array of checked vectors found flags.
chk_height
Array of checked vector heights.
umatr
The 'U' matrix.
phis
Array with the initial missetting angles calculated for the solution.

4.10.6.5 Refinement Method

4.10.6.5.1 Introduction

This section contains a method to refine missetting angles.

Method:

Initial Refinement - refineMissettingAgainstVectors

4.10.6.5.2 Initial Refinement - refineMissettingAgainstVectors

This method refines the solution's missetting angles to give the best angular fit to the measured vectors and to store those values in the object.

Method Definition:
public void refineMissettingAgainstVectors(JdlCell cell, double alam)
Parameters List:
cell
The real cell.
alam
The wavelength in Angstroms.

4.10.6.6 Listing Methods

4.10.6.6.1 Introduction

This section contains methods to list the solution details

Methods:

List Contents - listContents
List Contents - listContents

4.10.6.6.2 List Contents - listContents

This method lists the solution contents (for diagnostic purposes) to varying levels of detail.

Method Definition:
public void listContents(int level)
Parameters List:
level
Listing level (1-3)

4.10.6.6.3 List Contents - listContents

This method lists the solution contents (for diagnostic purposes) to varying levels of detail.

Method Definition:
public void listContents(String str, int level)
Parameters List:
str
A string to identify the solution
level
Listing level (1-3)

⇑ Up 2   ⇑ Up 1   ⇑ Top of this