4.10.5 - Crystal Setting Finder - JdlSetting3DFT

John W. Campbell

4.10.5.1 Introduction

This class provides a class for finding a crystal setting for a known cell from spot positions on small oscillation angle monochromatic rotation images using Fourier transform methods.

Class, constructor and methods:

Class Details
Accessible Fields
Constructor
Setting Method

4.10.5.2 Class Details

Package:
Jdl.JdlPX;
Class name:
JdlSetting3DFT
Class definition:
public class JdlSetting3DFT
Extends:
Object
Implements:
none
Actions:
none

4.10.5.3 Accessible Fields

The following accessible fields have been defined:

static boolean show_debug

4.10.5.4 Constructor

4.10.5.4.1 Introduction

This constructor sets up the parameters required to enable a setting to be found.

Constructor:

Constructor

4.10.5.4.2 Constructor

Create a JdlSetting3DFT object.

Constructor Definition:
public JdlSetting3DFT(JdlSearchImageSpotsList spotlist, JdlCell cell, int latt, Jdl3x3 umat, JdlPositionedDetector posdet, double x_cen, double y_cen, double pixsiz_x, double pixsiz_y, JdlDistortionCorrections distor)
Parameters List:
spotlist
A list of spot positions found from an image search.
cell
The cell parameters.
latt
The lattice type 1-7.
umat
The 'U' matrix
posdet
The positioned detector details.
x_cen
The 'x' centre position of the image in rasters.
y_cen
The 'y' centre position of the image in rasters.
pixsiz_x
The 'x' pixel size in mm.
pixsiz_y
The 'y' pixel size in mm.
distor
A distortions correction object - may be null if not required.

4.10.5.5 Setting Method

4.10.5.5.1 Introduction

This section has a method to determine possible solutions for the setting.

Methods:

Find setting - findCrystalSetting

4.10.5.5.2 Find setting - findCrystalSetting

This method attempts to find solutions for the crystal setting based on the data stored in the object and the additional parameters passed to this method.

Method Definition:
public JdlSettingSolution[] findCrystalSetting(int method, double ang_tol, JdlProgressHandler progress)
Parameters List:
method
Method number 1 or 2. Two possible methods are available for finding peaks in a Fourier transform corresponding to the cell vectors.
Method 1: Rotate a vector in appropriate steps around two angles, one through 90 degress and the other through 360 degrees (As done in MOSFLM program) and look for peaks along those vectors at the cell distances (looking at a grid of 9 points around each such position) and calculating the Fourier transform at these points.
Method 2: Search on an orthogonal grid but only calculate Fourier transform values for points which are within 1.5 grid units of a given cell vector length.
As the required parts of the Fourier transforms a very sparse for both methods, a simple Fourier transform calculation is done (but using integer arithmetic) rather than using a Fast Fourier Transform.
ang_tol
The maximum difference in degrees from an input cell angle to consider as a reasonable match e.g. 2.0 degrees.
progress
Progress handler (may be null if not required)
Method Return:
Returns an array of JdlSettingSolution objects containing details of possible solutions for the setting. If none are found a null is returned.

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