4.8.10 - Unique Reflection - JdlUniqueReflection

John W. Campbell

4.8.10.1 Introduction

This class stores details of a unique reflection with a series of items to hold counts of measurements associated with that reflection so that unique data coverage may be analysed. The item descriptions are given for rotation images with the equivalent meanings used for Laue images given in square brackets. For the Laue measurements, the items double, triple and multiple>3 indicate individual reflections which have been deconvoluted from such harmonics.

Class, fields, constructors and methods:

Class Details
Accessible Fields
Constructors
Handle Counts
Compare Reflection
Sort Order
List Contents

4.8.10.2 Class Details

Package:
Jdl.JdlPX;
Class name:
JdlUniqueReflection
Class definition:
public class JdlUniqueReflection
Extends:
Object
Implements:
Comparable
Comparator<JdlUniqueReflection>
Actions:
none

4.8.10.3 Accessible Fields

The following accessible fields have been defined:

public final static int HKL
Flag to sort on h, k and l indices (together).
public final static int H
Flag to sort on h index.
public final static int K
Flag to sort on k index.
public final static int L
Flag to sort on l index.
static int sort_option
public short h
'h' index.
public short k
'k' index.
public short l
'l' index.
public float[] xrl
Coordinates of reciprocal lattice point.
public short xpix
Pixel 'x' position on display (reserved for JdlShowUnique object use).
public short ypix
Pixel 'y' position on display (reserved for JdlShowUnique object use).
public short n_full_p
Count number of full [single] reflection measurements +h+k+l.
public short n_full_m
Count number of full [single] reflection measurements -h-k-l.
public short n_part2_p
Count number of 2 image partial reflection [double] measurements +h+k+l.
public short n_part2_m
Count number of 2 image partial reflection [double] measurements -h-k-l.
public short n_part3_p
Count number of 3 image partial reflection [triple] measurements +h+k+l.
public short n_part3_m
Count number of 3 image partial reflection [triple] measurements -h-k-l.
public short n_partn_p
Count no. of partial reflection measurements (more than 3 images but less than a requested maximum no. of images) [multiple > 3] +h+k+l.
public short n_partn_m
Count no. of partial reflection measurements (more than 3 images but less than a requested maximum no. of images) [multiple > 3] -h-k-l.
public short n_unk_p
Count number of unknown (e.g from merged MTZ file) reflection measurements +h+k+l.
public short n_unk_m
Count number of unknown (e.g from merged MTZ file) reflection measurements -h-k-l.
public short n_unk_u
Count number of unknown (e.g from merged MTZ file) reflection measurements of unknown sign.
public short n_full_sp_p
Count number of full [single] reflection measurements +h+k+l (for spatial overlaps).
public short n_full_sp_m
Count number of full [single] reflection measurements -h-k-l (for spatial overlaps).
public short n_part2_sp_p
Count number of 2 image partial reflection measurements [double] +h+k+l (for spatial overlaps).
public short n_part2_sp_m
Count number of 2 image partial reflection measurements [double] -h-k-l (for spatial overlaps).
public short n_part3_sp_p
Count number of 3 image partial reflection measurements [triple] +h+k+l (for spatial overlaps).
public short n_part3_sp_m
Count number of 3 image partial reflection measurements [triple] -h-k-l (for spatial overlaps).
public short n_partn_sp_p
Count no. of partial reflection measurements (more than 3 images but less than a requested maximum no. of images) [multiple > 3] +h+k+l (for spatial overlaps).
public short n_partn_sp_m
Count no. of partial reflection measurements (more than 3 images but less than a requested maximum no. of images) [multiple > 3] -h-k-l (for spatial overlaps).

4.8.10.4 Constructors

4.8.10.4.1 Introduction

Constructors are available to construct a JdlUniqueReflection object with default (unset) values or given a set of the main values required from a prediction.

Constructors:

Empty Constructor
Standard Constructor

4.8.10.4.2 Empty Constructor

This constructs an empty object.

Constructor Definition:
public JdlUniqueReflection()
Parameters List:
none

4.8.10.4.3 Standard Constructor

This constructs a the object with indices and reciprocal lattice coordinates and with zeroed counts.

Constructor Definition:
public JdlUniqueReflection(int h, int k, int l, double xr, double yr, double zr)
Parameters List:
h
The 'h' index.
k
The 'k' index.
l
The 'l' index.
xr
Reciprocal lattice 'x' coordinate.
yr
Reciprocal lattice 'y' coordinate.
zr
Reciprocal lattice 'z' coordinate.

4.8.10.5 Handle Counts

4.8.10.5.1 Introduction

This section has methods to clear all the counts and to increment counts based on some reflection flags.

Methods:

Clear counts - clearCounts
Increment counts - incrementCounts

4.8.10.5.2 Clear counts - clearCounts

This method clears all the reflection measurement counts.

Method Definition:
public void clearCounts()
Parameters List:
none

4.8.10.5.3 Increment counts - incrementCounts

This method increments the appropriate counts based on the given reflection measurement flags.

Method Definition:
public void incrementCounts(int ipart, int isign, int ispat)
Parameters List:
ipart
Full/partial [single/multiple] flag:
= 1, full [single]
= 2, partial over 2 images [from double]
= 3, partial over 3 images [from triple]
> 3, partial over >3 images probably up to a user defined maximum [from a multiple > 3]
= 0, unknown (e.g. from merged MTZ file)
isign
Reflection sign:
= +1, for +h+k+l class
= -1, for -h-k-l class
= 0, unknown (only allowed if ipart=0)
ispat
Spatial overlap flag:
= 0, Not spatially overlapped
= 1, Spatially overlapped spot
(ignored for 'unknown' full/partial class of reflections)

4.8.10.6 Compare Reflection

4.8.10.6.1 Introduction

This section has a method to compare the reflection the reflection indices with a given set of indices.

Method:

Compare indices - compareIndices
Compare indices - compareIndices

4.8.10.6.2 Compare indices - compareIndices

This method compares the reflection indices with a given set of indices in order h, k, l.

Method Definition:
public int compareIndices(short h, short k, short l)
Parameters List:
h
The 'h' index for comparison.
k
The 'k' index for comparison.
l
The 'l' index for comparison.
Method Return:
Return:
= -1, The indices are lower than those of the unique reflection
= 0, The indices are the same
= 1, The idices are greater than those of the unique reflection

4.8.10.6.3 Compare indices - compareIndices

This method compares the reflection indices with a given set of indices in order h, k, l.

Method Definition:
public int compareIndices(int h, int k, int l)
Parameters List:
h
The 'h' index for comparison.
k
The 'k' index for comparison.
l
The 'l' index for comparison.
Method Return:
Return:
= -1, The indices are lower than those of the unique reflection
= 0, The indices are the same
= 1, The idices are greater than those of the unique reflection

4.8.10.7 Sort Order

4.8.10.7.1 Introduction

This section has methods to set and return the value of the flag which will determine the sort order of a reflection list if it is sorted.

Methods:

Set sort order - setSortOption
Get sort order - getSortOption

4.8.10.7.2 Set sort order - setSortOption

This method sets the required sort order flag.

Method Definition:
public static void setSortOption (int srt_opt)
Parameters List:
srt_opt
Flag to set the sort order:
= 1, Sort on h, k and l
= 2, Sort on axis 1 coordinate
= 3, Sort on axis 2 coordinate
= 4, Sort on 'h'
= 5, Sort on 'k'
= 6, Sort on 'l'

4.8.10.7.3 Get sort order - getSortOption

This method returns the current value of the sort order flag. Note that it does not indicate, for example, that a reflection list has actually been sorted.

Method Definition:
public static int getSortOption()
Parameters List:
none
Method Return:
The sort order flag.

4.8.10.8 List Contents

4.8.10.8.1 Introduction

This section has a single method to list the contents of the object primarily for diagnostic purposes.

Method:

List contents - listContents

4.8.10.8.2 List contents - listContents

This method lists selected contents of the object.

Method Definition:
public void listContents(int iopt)
Parameters List:
iopt
List option:
= 1, List h, k, l and counts for non-overlapped and unknown reflections
= 2, List h, k, l and counts for overlapped reflections
= 3, List h, k, l and pixel positions and reciprocal lattice coordinates

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