4.8.3 - Predicted Reflection - JdlPredictedReflection

John W. Campbell

4.8.3.1 Introduction

Class, fields, constructors and methods:

4.8.3.2 Class Details

Package:

Jdl.JdlPX;

Class name:

JdlPredictedReflection

Class definition:

public class JdlPredictedReflection

Extends:

Object

Implements:

Cloneable
Comparable
Comparator<JdlPredictedReflection>

Actions:

none

4.8.3.3 Accessible Fields

public final static int HKL

Flag to sort on 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.

static int sort_option

public short h

'h' index.

public short k

'k' index.

public short l

'l' index.

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 recorded_status

Recorded reflection flag:
= 0, Not recorded
= 1, Fully recorded
= 2, Good partial (<= nwmax images)
= 3, Too-wide partial (> nwmax images)
= 4, Within cusp but part visible
= 100, Quick prediction - predicted but not categorised

public float phi

Phi value when reciprocal lattice point is on the Ewald sphere (in degrees).

public float phi_width

Reflection width (in degrees) - will not be set for a quick prediction.

public float lorentz_factor

Lorentz factor - will not be set for a quick prediction.

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 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)

float rotimg_start

Start angle for oscillation range being used

float[] xrlpe

Coordinates of reciprocal lattice point on Ewald sphere.

short nimg

No. of images over which spot spread:
= 1, Full spot - or quick prediction
= 0, Too wide (>nwmax images)
= - 1, Not set

short ifirst

First image for spot as an offset from the current image (set to 0 for a quick prediction). If nimg==-1 this will not be set.

byte inr_flag

Reflection not recorded flag:
= 0, Recorded (or a quick prediction)
= 1, On rotation axis
= 2, Within cusp
= 3, Outside extended resolution limit
= 4, Not-recorded but still in list
= -1, Not set

byte spatial_overlap

Spatial overlap flag:
= 1, Overlapped
= 0, Not overlapped
= -1, Not set

4.8.3.4 Constructors

4.8.3.4.1 Introduction

Constructors:

4.8.3.4.2 Empty Constructor

Constructor Definition:

public JdlPredictedReflection()

Parameters List:

none

4.8.3.4.3 Double Parameters Constructor

Constructor Definition:

public JdlPredictedReflection(int h, int k, int l, double ax1_coord, double ax2_coord, int rec_status, double phi, double phiw, double lorfac)

Parameters List:

h

The 'h' index.

k

The 'k' index.

l

The 'l' index.

ax1_coord

Axis 1 (e.g. x) detector coordinate (in mm).

ax2_coord

Axis 2 (e.g. y) detector coordinate (in mm).

rec_status

Recorded reflection flag:
= 0, Not recorded
= 1, Fully recorded
= 2, Good partial (<= nwmax images)
= 3, Too-wide partial (> nwmax images)
= 4, Within cusp but part visible
= 100, Quick prediction - predicted but not categorised

phi

Phi value when reciprocal lattice point is on the Ewald sphere (in degrees).

phiw

Reflection width (in degrees) - not set for a quick prediction.

lorfac

Lorentz factor.

4.8.3.4.4 Float Parameters Constructor

Constructor Definition:

public JdlPredictedReflection(short h, short k, short l, float ax1_coord, float ax2_coord, short rec_status, float phi, float phiw, float lorfac)

Parameters List:

h

The 'h' index.

k

The 'k' index.

l

The 'l' index.

ax1_coord

Axis 1 (e.g. x) detector coordinate (in mm).

ax2_coord

Axis 2 (e.g. y) detector coordinate (in mm).

rec_status

Recorded reflection flag:
= 0, Not recorded
= 1, Fully recorded
= 2, Good partial (<= nwmax images)
= 3, Too-wide partial (> nwmax images)
= 4, Within cusp but part visible
= 100, Quick prediction - predicted but not categorised

phi

Phi value when reciprocal lattice point is on the Ewald sphere (in degrees).

phiw

Reflection width (in degrees) - not set for a quick prediction.

lorfac

Lorentz factor.

4.8.3.5 Set Parameters

4.8.3.5.1 Introduction

Methods:

4.8.3.5.2 Set indices - setIndices

Method Definition:

public void setIndices (int h, int k, int l)

Parameters List:

h

The 'h' index.

k

The 'k' index.

l

The 'l' index.

4.8.3.5.3 Set indices - setIndices

Method Definition:

public void setIndices (int[] hkl)

Parameters List:

hkl

A three element array containing the reflection indices.

4.8.3.5.4 Set coordinates - setCoordinates

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).

4.8.3.5.5 Set recorded status - setRecordedStatus

Method Definition:

public void setRecordedStatus(int rec_status)

Parameters List:

rec_status

Recorded reflection flag:
= 0, Not recorded
= 1, Fully recorded
= 2, Good partial (<= nwmax images)
= 3, Too-wide partial (> nwmax images)
= 4, Within cusp but part visible
= 100, Quick prediction - predicted but not categorised

4.8.3.5.6 Set phi - setPhi

Method Definition:

public void setPhi (double phi, double phi_width)

Parameters List:

phi

Phi value when reciprocal lattice point is on the Ewald sphere (in degrees).

phi_width

Reflection width (in degrees) - not set for a quick prediction.

4.8.3.5.7 Set Lorenz factor - setLorentzFactor

Method Definition:

public void setLorentzFactor (double lorfac)

Parameters List:

lorfac

Lorentz factor.

4.8.3.5.8 Set crystal number - setCrystalNumber

Method Definition:

public void setCrystalNumber (int icrys)

Parameters List:

icrys

The crystal number (>0, 0 = not set).

4.8.3.5.9 Set image number - setImageNumber

Method Definition:

public void setImageNumber (int imgnum)

Parameters List:

imgnum

The image number (>0, 0 = not set).

4.8.3.5.10 Set symmetry number - setSymmetryFlag

Method Definition:

public void setSymmetryFlag (int ksym)

Parameters List:

ksym

The number of the symmetry operator (0=not defined (usually 0 if measured/predicted indices stored)) or set to symmetry the symmetry operator number if indices have been converted to the unique set).

4.8.3.5.11 Set rotation image start - setRotationImageStart

Method Definition:

public void setRotationImageStart (double rotimg_start)

Parameters List:

rotimg_start

Start angle for oscillation range.

4.8.3.5.12 Set reciprocal lattice coordinates - setRLCoordinates

Method Definition:

public void setRLCoordinates (double[] xr)

Parameters List:

xr

Array holding the reciprocal lattice x, y, z coordinates for the reflection.

4.8.3.5.13 Set non-recorded flag - setNotRecordedFlag

Method Definition:

public void setNotRecordedFlag (int inr_flag)

Parameters List:

inr_flag

Status flag for non-recorded reflections:
= 0, Recorded (or a quick prediction)
= 1, On rotation axis
= 2, Within cusp
= 3, Outside extended resolution limit
= 4, Not-recorded but still in list
= -1, Not set

4.8.3.5.14 Set number of images - setNumberOfImages

Method Definition:

public void setNumberOfImages (int nimg, int ifirst)

Parameters List:

nimg

No. of images over which spot spread:
= 1, Full spot - or quick prediction
= 0, Too wide (>nwmax images)
= - 1, Not set

ifirst

First image for spot as an offset from the current image (set to 0 for a quick prediction).

4.8.3.5.15 Set spatial overlap - setSpatialOverlap

Method Definition:

public void setSpatialOverlap (int spov)

Parameters List:

spov

Spatial overlap flag:
= 1, Overlapped
= 0, Not overlapped
= -1, Not set

4.8.3.6 Get Parameters

4.8.3.6.1 Introduction

Methods:

4.8.3.6.2 Get index h - getH

Method Definition:

public int getH()

Parameters List:

none

Method Return:

The 'h' index.

4.8.3.6.3 Get index k - getK

Method Definition:

public int getK()

Parameters List:

none

Method Return:

The 'k' index.

4.8.3.6.4 Get index l - getL

Method Definition:

public int getL()

Parameters List:

none

Method Return:

The 'l' index.

4.8.3.6.5 Get indices - getHKL

Method Definition:

public void getHKL (int[] hkl)

Parameters List:

hkl

Integer array in which to return the indices.

4.8.3.6.6 Get coordinates - getCoordinates

Method Definition:

public JdlXY getCoordinates()

Parameters List:

none

Method Return:

The detector coordinates in mm.

4.8.3.6.7 Get recorded status - getRecordedStatus

Method Definition:

public int getRecordedStatus ()

Parameters List:

none

Method Return:

The recorded status flag.

4.8.3.6.8 Get phi - getPhi

Method Definition:

public double getPhi()

Parameters List:

none

Method Return:

The phi value.

4.8.3.6.9 Get phi width - getPhiWidth

Method Definition:

public double getPhiWidth()

Parameters List:

none

Method Return:

The phi width value.

4.8.3.6.10 Get Lorentz factor - getLorentzFactor

Method Definition:

public double getLorentzFactor()

Parameters List:

none

Method Return:

The Lorentz factor.

4.8.3.6.11 Get crystal number - getCrystalNumber

Method Definition:

public int getCrystalNumber ()

Parameters List:

none

Method Return:

The crystal number.

4.8.3.6.12 Get image number - getImageNumber

Method Definition:

public int getImageNumber ()

Parameters List:

none

Method Return:

The image number.

4.8.3.6.13 Get symmetry number - getSymmetryFlag

Method Definition:

public int getSymmetryFlag ()

Parameters List:

none

Method Return:

The symmetry operator number.

4.8.3.6.14 Get rotation image start - getRotationImageStart

Method Definition:

public double getRotationImageStart ()

Parameters List:

none

Method Return:

Start angle for oscillation range.

4.8.3.6.15 Get reciprocal lattice coordinates - getRLCoordinates

Method Definition:

public void getRLCoordinates(double[] xr)

Parameters List:

xr

3 element array in which to return the reciprocal lattice coordinates.

4.8.3.6.16 Get non-recorded flag - getNotRecordedFlag

Method Definition:

public int getNotRecordedFlag ()

Parameters List:

none

Method Return:

The non-recorded status flag.

4.8.3.6.17 Get number of images - getNumberOfImages

Method Definition:

public int getNumberOfImages ()

Parameters List:

none

Method Return:

The number of images.

4.8.3.6.18 Get first image offset - getFirstImageOffset

Method Definition:

public int getFirstImageOffset()

Parameters List:

none

Method Return:

The image offset.

4.8.3.6.19 Get spatial overlap - getSpatialOverlap

Method Definition:

public int getSpatialOverlap()

Parameters List:

none

Method Return:

The spatial overlap flag

4.8.3.7 Sort Order

4.8.3.7.1 Introduction

Methods:

4.8.3.7.2 Set sort order - setSortOption

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'

4.8.3.7.3 Get sort order - getSortOption

Method Definition:

public static int getSortOption()

Parameters List:

none

Method Return:

The sort order flag.