4.8.7 - Predicted Laue Spot - JdlPredictedLaueSpot

John W. Campbell

4.8.7.1 Introduction

This class stores details of a predicted Laue spot (indices, detector position, wavelength, multiplicity and other parameters calculated during a prediction). Most of the item values are accessible via public fields as well as via methods though a few are restricted to package access. The class implements the interfaces Cloneable and Comparable so that spots may be copied and spot lists sorted on indices or detector positions. If a 'quick' prediction was done, not all values will be set.

Class, fields, constructors and methods:

Class Details
Accessible Fields
Constructors
Set Parameters
Get Parameters
Sort Order

4.8.7.2 Class Details

Package:
Jdl.JdlPX;
Class name:
JdlPredictedLaueSpot
Class definition:
public class JdlPredictedLaueSpot
Extends:
Object
Implements:
Cloneable

Comparable
Comparator<JdlPredictedLaueSpot>
Actions:
none

4.8.7.3 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 NHKL
Flag to sort on nodal h, k and l indices (together).
public final static int AXIS1_COORDINATE
Flag to sort on local axis 1 coordinate.
public final static int AXIS2_COORDINATE
Flag to sort on local axis 2 coordinate.
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.
public final static int NH
Flag to sort on nodal 'h' index.
public final static int NK
Flag to sort on nodal 'k' index.
public final static int NL
Flag to sort on nodal 'l' index.
public final static int LAMBDA_ASC
Flag to sort on lambda ascending;
public final static int LAMBDA_DESC
Flag to sort on lambda descending;
static int sort_option
public short h
'h' index.
public short k
'k' index.
public short l
'l' index.
public short nh
Nodal 'h' index.
public short nk
Nodal 'k' index.
public short nl
Nodal 'l' index.
public short ksym
Symmetry no. 0=not defined (0 if measured/predicted indices stored) or set to the symmetry operator number if indices have been converted to the unique set)
public double lambda
Wavelength (For minimum recorded harmonic for a multiple).
public short mult
Multiplicity (1 for a single) (-mult for a reflection deconvoluted from a multiple of multiplicity 'mult').
public short minharm
Minimum harmonic present for a multiple.
public short maxharm
Maximum harmonic present for a multiple.
public short incharm
Harmonic increment for a multiple (set to 1 for a single or for a reflection deconvoluted from a multiple ). This allows for systematic absences.
public float ax1_coord
Axis 1 (e.g. x) detector coordinate (in mm).
public float ax2_coord
Axis 2 (e.g. y) detector coordinate (in mm).
public short crystal_number
Crystal number > 0 (0 if not set).
public int image_number
Image number (or identifier e.g. packed range & image no.) > 0 (0 if not set).
public double dmin_thr2
(Dmin threshold)**2. For a multiple this is the value for the minimum harmonic present.
float[] xr
Reciprocal lattice coordinates.
byte spatial_overlap
Spatial overlap flag:
= 1, Overlapped
= 0, Not overlapped
= -1, Not set

4.8.7.4 Constructors

4.8.7.4.1 Introduction

Constructors are available to construct a JdlPredictedSpot object with default (mostly unset) values or given a set of the main values required from a prediction. Where values are given, double and float versions are available.

Constructors:

Empty Constructor
Double Parameters Constructor. This sets all parameters except the

4.8.7.4.2 Empty Constructor

This constructs an empty object.

Constructor Definition:
public JdlPredictedLaueSpot()
Parameters List:
none

4.8.7.4.3 Double Parameters Constructor. This sets all parameters except the

spatial overlap flag. Measured (rather than unique) indices are input and the summetry number/flag is set to 0.

Constructor Definition:
public JdlPredictedLaueSpot(int h, int k, int l, int nh, int nk, int nl, double lambda, int mult, int minharm, int maxharm, int incharm, double ax1_coord, double ax2_coord, int crys_num, int img_num, double dmin_thr2, double[] xr)
Parameters List:
h
The 'h' index (for minimum harmonic present).
k
The 'k' index (for minimum harmonic present).
l
The 'l' index (for minimum harmonic present).
nh
The nodal 'h' index.
nk
The nodal 'k' index.
nl
The nodal 'l' index.
lambda
The wavelength (for minimum harmonic present).
mult
Multiplicity (1 for a single) (-mult for a reflection deconvoluted from a multiple of multiplicity 'mult').
minharm
Minimum harmonic for a multiple.
maxharm
Maximum harmonic for a multiple.
incharm
Harmonic increment for a multiple (give 1 for a single or for a reflection deconvoluted from a multiple).
ax1_coord
Axis 1 (e.g. x) detector coordinate (in mm).
ax2_coord
Axis 2 (e.g. y) detector coordinate (in mm).
crys_num
The crystal number > (give 0 for unset).
img_num
The image number >0 (give 0 for unset).
dmin_thr2
(Dmin threshold)**2 (for minimum harmonic present).
xr
Three element array containing reciprocal lattice coordinates.

4.8.7.5 Set Parameters

4.8.7.5.1 Introduction

This section has methods to set specific parameters or groups of parameters.

Methods:

Set indices - setIndices
Set indices - setIndices
Set nodal indices - setNodalIndices
Set nodal indices - setNodalIndices
Reset indices and symmetry - resetIndices
Set wavelength - setLambda
Set multiplicity - setMultiplicity
Set coordinates - setCoordinates
Set crystal number - setCrystalNumber
Set image number - setImageNumber
Set dmin squared threshold - setDminThr2
Set reciprocal lattice coordinates - setRLCoordinates
Set spatial overlap - setSpatialOverlap

4.8.7.5.2 Set indices - setIndices

This method sets the values of the spot indices given the three individual values.

Method Definition:
public void setIndices (int h, int k, int l)
Parameters List:
h
The 'h' index (for minimum harmonic present).
k
The 'k' index (for minimum harmonic present).
l
The 'l' index (for minimum harmonic present).

4.8.7.5.3 Set indices - setIndices

This method sets the values of the spot indices held in an integer array.

Method Definition:
public void setIndices (int[] hkl)
Parameters List:
hkl
A three element array containing the spot indices (for minimum harmonic present).

4.8.7.5.4 Set nodal indices - setNodalIndices

This method sets the values of the nodal indices given the three individual values.

Method Definition:
public void setNodalIndices (int nh, int nk, int nl)
Parameters List:
nh
The nodal 'h' index.
nk
The nodal 'k' index.
nl
The nodal 'l' index.

4.8.7.5.5 Set nodal indices - setNodalIndices

This method sets the values of the nodal indices held in an integer array.

Method Definition:
public void setNodalIndices (int[] nhkl)
Parameters List:
nhkl
A three element array containing the spot indices.

4.8.7.5.6 Reset indices and symmetry - resetIndices

This method is used to re-input the indices and nodal indices and the symmetry flag.

Method Definition:
public void resetIndices (int h, int k, int l, int nh, int nk, int nl, int ksym)
Parameters List:
h
The 'h' index (for minimum harmonic present).
k
The 'k' index (for minimum harmonic present).
l
The 'l' index (for minimum harmonic present).
nh
The nodal 'h' index.
nk
The nodal 'k' index.
nl
The nodal 'l' index.
ksym
Symmetry flag. This must be set to 0 if measured indices are given or to the number of the symmetry operator (which converts between the measured and unique indices) if unique indices are given.

4.8.7.5.7 Set wavelength - setLambda

This method sets the wavelength (for minimum harmonic present).

Method Definition:
public void setLambda(double lambda)
Parameters List:
lambda
The wavelength (for minimum harmonic present).

4.8.7.5.8 Set multiplicity - setMultiplicity

This method sets the multiplicity details.

Method Definition:
public void setMultiplicity(int mult, int minharm, int maxharm, int incharm)
Parameters List:
mult
Multiplicity (1 for a single) (-mult for a reflection deconvoluted from a multiple of multiplicity 'mult').
minharm
Minimum harmonic for a multiple.
maxharm
Maximum harmonic for a multiple.
incharm
Harmonic increment for a multiple (give 1 for a single or a reflection deconvoluted from a multiple).

4.8.7.5.9 Set coordinates - setCoordinates

This method sets the predicted spot coordinates on the detector.

Method Definition:
public void setCoordinates (double ax1_coord, double ax2_coord)
Parameters List:
ax1_coord
Axis 1 (e.g. x) detector coordinate (in mm).
ax2_coord
Axis 2 (e.g. y) detector coordinate (in mm).

4.8.7.5.10 Set crystal number - setCrystalNumber

This method sets the crystal number.

Method Definition:
public void setCrystalNumber (int icrys)
Parameters List:
icrys
The crystal number (>0, 0 = unset).

4.8.7.5.11 Set image number - setImageNumber

This method sets the image number.

Method Definition:
public void setImageNumber (int imgnum)
Parameters List:
imgnum
The image number (>0, 0 = unset).

4.8.7.5.12 Set dmin squared threshold - setDminThr2

This method sets the (dmin threshold)** value (for minimum harmonic present).

Method Definition:
public void setDminThr2(double dmin_thr2)
Parameters List:
dmin_thr2
The (dmin threshold)** value.

4.8.7.5.13 Set reciprocal lattice coordinates - setRLCoordinates

This method sets the values of the reciprocal lattice coordinates for the spot (for minimum harmonic present).

Method Definition:
public void setRLCoordinates (double[] xr)
Parameters List:
xr
Array holding the reciprocal lattice x, y, z coordinates for the spot.

4.8.7.5.14 Set spatial overlap - setSpatialOverlap

This method sets the value of the spatial overlap flag.

Method Definition:
public void setSpatialOverlap (int spov)
Parameters List:
spov
Spatial overlap flag:
= 1, Overlapped
= 0, Not overlapped
= -1, Not set

4.8.7.6 Get Parameters

4.8.7.6.1 Introduction

This section has methods to get the values of the stored parameters. The parameters are described in more detail, where appropriate, in the field definitions and in the descriptions of the methods which set the values.

Methods:

Get index h - getH
Get index k - getK
Get index l - getL
Get indices - getHKL
Get indices - getSelectedHKL
Get nodal index h - getNodalH
Get nodal index k - getNodalK
Get nodal index l - getNodalL
Get nodal indices - getNodalHKL
Get wavelength - getLambda
Get multiplicity - getMultiplicity
Get minimum harmonic - getMinimumHarmonic
Get maximum harmonic - getMaximumHarmonic
Get harmonic increment - getHarmonicIncrement
Get coordinates - getCoordinates
Get crystal number - getCrystalNumber
Get image number - getImageNumber
Get dmin squared threshold - getDminThr2
Get reciprocal lattice coordinates - getRLCoordinates
Get spatial overlap - getSpatialOverlap

4.8.7.6.2 Get index h - getH

Returns the value of the 'h' index.

Method Definition:
public int getH()
Parameters List:
none
Method Return:
The 'h' index.

4.8.7.6.3 Get index k - getK

Returns the value of the 'k' index.

Method Definition:
public int getK()
Parameters List:
none
Method Return:
The 'k' index.

4.8.7.6.4 Get index l - getL

Returns the value of the 'l' index.

Method Definition:
public int getL()
Parameters List:
none
Method Return:
The 'l' index.

4.8.7.6.5 Get indices - getHKL

Return the spot indices in an array.

Method Definition:
public void getHKL (int[] hkl)
Parameters List:
hkl
Integer array in which to return the indices.

4.8.7.6.6 Get indices - getSelectedHKL

Return the spot indices for various options in an array.

Method Definition:
public void getSelectedHKL (int[] hkl, int opt)
Parameters List:
hkl
Integer array in which to return the indices.
opt
Index version required esp. for multiples:
= 0, Return the indices for the minimum harmonic present
= 1, Return the indices for the maximum harmonic present
= 2, Return the nodal indices

4.8.7.6.7 Get nodal index h - getNodalH

Returns the value of the nodal 'h' index.

Method Definition:
public int getNodalH()
Parameters List:
none
Method Return:
The 'nh' index.

4.8.7.6.8 Get nodal index k - getNodalK

Returns the value of the nodal 'k' index.

Method Definition:
public int getNodalK()
Parameters List:
none
Method Return:
The 'nk' index.

4.8.7.6.9 Get nodal index l - getNodalL

Returns the value of the nodal 'l' index.

Method Definition:
public int getNodalL()
Parameters List:
none
Method Return:
The 'nl' index.

4.8.7.6.10 Get nodal indices - getNodalHKL

Return the nodal indices in an array.

Method Definition:
public void getNodalHKL (int[] nhkl)
Parameters List:
nhkl
Integer array in which to return the indices.

4.8.7.6.11 Get wavelength - getLambda

This method returns the wavelength.

Method Definition:
public double getLambda()
Parameters List:
none
Method Return:
The wavelength.

4.8.7.6.12 Get multiplicity - getMultiplicity

This method returns the multiplicity for the spot.

Method Definition:
public int getMultiplicity()
Parameters List:
none
Method Return:
The multiplicity (1 for a single) (-mult for a reflection deconvoluted from a multiple of multiplicity 'mult').

4.8.7.6.13 Get minimum harmonic - getMinimumHarmonic

This method returns the minimum harmonic for a multiple spot.

Method Definition:
public int getMinimumHarmonic()
Parameters List:
none
Method Return:
The minimum harmonic number.

4.8.7.6.14 Get maximum harmonic - getMaximumHarmonic

This method returns the maximum harmonic for a multiple spot.

Method Definition:
public int getMaximumHarmonic()
Parameters List:
none
Method Return:
The minimum harmonic number.

4.8.7.6.15 Get harmonic increment - getHarmonicIncrement

This method returns the harmonic increment for a multiple spot.

Method Definition:
public int getHarmonicIncrement()
Parameters List:
none
Method Return:
The harmonic increment.

4.8.7.6.16 Get coordinates - getCoordinates

Return the detector coordinates

Method Definition:
public JdlXY getCoordinates()
Parameters List:
none
Method Return:
The detector coordinates in mm.

4.8.7.6.17 Get crystal number - getCrystalNumber

Returns the crystal number.

Method Definition:
public int getCrystalNumber()
Parameters List:
none
Method Return:
The crystal number.

4.8.7.6.18 Get image number - getImageNumber

Returns the image number.

Method Definition:
public int getImageNumber()
Parameters List:
none
Method Return:
The image number.

4.8.7.6.19 Get dmin squared threshold - getDminThr2

This method returns the (dmin threshold)** value (for minimum harmonic present).

Method Definition:
public double getDminThr2()
Parameters List:
none
Method Return:
dmin_thr2 The (dmin threshold)** value.

4.8.7.6.20 Get reciprocal lattice coordinates - getRLCoordinates

Returns the predicted reciprocal lattice coordinates.

Method Definition:
public void getRLCoordinates(double[] xr)
Parameters List:
xr
3 element array in which to return the reciprocal lattice coordinates.

4.8.7.6.21 Get spatial overlap - getSpatialOverlap

Returns the value of the spatial overlap flag if set.

Method Definition:
public int getSpatialOverlap()
Parameters List:
none
Method Return:
The spatial overlap flag

4.8.7.7 Sort Order

4.8.7.7.1 Introduction

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

Methods:

Set sort order - setSortOption
Get sort order - getSortOption

4.8.7.7.2 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 nodal h, k and l
= 3, Sort on axis 1 coordinate
= 4, Sort on axis 2 coordinate
= 5, Sort on 'h'
= 6, Sort on 'k'
= 7, Sort on 'l'

4.8.7.7.3 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 spot list has actually been sorted.

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

⇑ Up 2   ⇑ Up 1   ⇑ Top of this