4.7.5 - Re-flag Reflection - JdlReflectionReflag

John W. Campbell

4.7.5.1 Introduction

This class is used, for example, in conjunction with the 'interactive' rotation prediction simulations JdlPXSimulations object. It enables the recalculation of a predicted rotation reflection flag for reduced values of the following parameters:
The oscillation angle (rotimg_end-rotimg_start)
The mosaicity (eta)
The horizontal beam divergence (divh)
The vertical beam divergence (divv)
The correlated dispersion term (delcor)
The dispersion (delamb)

Class, constructors and methods:

Class Details
Accessible Fields
Constructors

4.7.5.2 Class Details

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

4.7.5.3 Accessible Fields

No fields with public, package or protected access defined.

4.7.5.4 Constructors

4.7.5.4.1 Introduction

Constructors are available to construct a JdlReflectionReflag object with either a specific list of parameters or with objects containing these values.

Constructors:

Standard Constructor
Constructor 2
Constructor 3
Set current oscillation angle - setCurrentOscillationAngle
Set current mosaicity - setCurrentMosaicity
Set current horizontal divergence - setCurrentHorizontalDivergence
Set current vertical divergence - setCurrentVerticalDivergence
Set current correlated dispersion - setCurrentCorrelatedDispersion
Set current dispersion - setCurrentDispersion
Get current oscillation angle - getCurrentOscillationAngle
Get current mosaicity - getCurrentMosaicity
Get current horizontal divergence - getCurrentHorizontalDivergence
Get current vertical divergence - getCurrentVerticalDivergence
Get current correlated dispersion - getCurrentCorrelatedDispersion
Get current dispersion - getCurrentDispersion
Get full oscillation angle - getFullOscillationAngle
Get full mosaicity - getFullMosaicity
Get full horizontal divergence - getFullHorizontalDivergence
Get full vertical divergence - getFullVerticalDivergence
Get full correlated dispersion - getFullCorrelatedDispersion
Get full dispersion - getFullDispersion
Reset reflection details - resetReflection

4.7.5.4.2 Standard Constructor

This constructs the object with explicitly defined parameters. These must be the same as those used when the 'over-predicted' reflection list, whose reflections are to be re-flagged, was created. The over-prediction factor is specified as one of the parameters and current values for the variable items are taken as the values used in the prediction divided by the over-prediction factor.

Constructor Definition:
public JdlReflectionReflag(double rotimg_start, double rotimg_end, double eta, int isyn, int iax_h, int iax_v, double divh, double divv, double delcor, double delamb, double[] scax, int nwmax, double multfac)
Parameters List:
rotimg_start
The start angle for the rotation range in degrees.
rotimg_end
The end angle for the rotation range in degrees. The over-predicted oscillation angle is assumed to be rotimg_end - rotimg_start.
eta
Mosaicity (full width, degrees).
isyn
Source type flag =0 lab source, =1 synchrotron.
iax_h
No. of horizontal axis in laborarory system (1=x, 2=y, 3=z).
iax_v
No. of vertical axis in laborarory system (1=x, 2=y, 3=z).
divh
Horizontal beam divergence (full width, degrees).
divv
Vertical beam divergence (full width, degrees).
delcor
Correlated dispersion term (only used for synchrotron) (fullwidth, degrees).
delamb
Dispersion (delta(lambda)/lambda).
scax[3]
Scan axis direction vector wrt laboratory axes.
nwmax
Maximum no. of images over which a spot may be spread.
multfac
The over-prediction factor.

4.7.5.4.3 Constructor 2

Construct a JdlReflectionReflag object from JdlPositionedDetector and JdlPositionedCrystal objects. These objects must contain the parameter values of eta, divh, divv, delcor and delamb used in the over-prediction and the range required rotimg_start to rotimg_end must also be for the over-prediction.

Constructor Definition:
public JdlReflectionReflag(JdlPositionedDetector posdet, JdlPositionedCrystal poscrys, double rotimg_start, double rotimg_end, double multfac)
Parameters List:
posdet
A JdlPositionedDetector object containing details of the positioned detector, gonioneter and X-ray source.
poscrys
A JdlPositionedCrystal containing details of the crystal cell, symmetry and setting.
rotimg_start
The start angle for the rotation range in degrees.
rotimg_end
The end angle for the rotation range in degrees. The over-predicted oscillation angle is assumed to be rotimg_end - rotimg_start.
multfac
The over-prediction factor.

4.7.5.4.4 Constructor 3

Construct a JdlReflectionReflag object from a JdlDiffractionDataModule object.

Constructor Definition:
public JdlReflectionReflag( JdlDiffractionDataModule ddm, int iset, int img, int irange, int imgnum, boolean scaled, double multfac)
Parameters List:
ddm
The JdlDiffractionDataModule object containing the detector and crystal data used in the prediction. NOTE: In this case, in contrast to that for the other constructors, the JdlDiffractionDataModule object may contain the prediction values for the prediction before scaling up for the over-prediction (see 'scaled' parameter).
iset
The set number within the Diffraction Data Module.
img
The (reference) image number - normally 1.
irange
The rotation range number.
imgnum
The number of the image (within the requested rotation range) for which the prediction was carried out.
scaled
If true, it is assumed that the DDM data contains the relevant parameters (eta, divh, divv, delcor and delamb and the oscillation angle) already scaled up by 'multfac'. If false, then it is assumed that the DDM data contains the relevant parameters (eta, divh, divv, delcor and delamb and the oscillation angle) with values prior to scaling up by multfac for the over-prediction.
multfac
The over-prediction factor.

4.7.5.4.5 Set current oscillation angle - setCurrentOscillationAngle

This method sets a new value for the current oscillation angle used by the resetReflection(..) method. This must not exceed the value used in the over-prediction.

Method Definition:
public void setCurrentOscillationAngle(double osc)
Parameters List:
osc
The oscillation angle in degrees.

4.7.5.4.6 Set current mosaicity - setCurrentMosaicity

This method sets a new value for the current mosaicity used by the resetReflection(..) method. This must not exceed the value used in the over-prediction.

Method Definition:
public void setCurrentMosaicity(double eta)
Parameters List:
eta
Mosaicity (full width, degrees).

4.7.5.4.7 Set current horizontal divergence - setCurrentHorizontalDivergence

This method sets a new value for the current horizontal divergence used by the resetReflection(..) method. This must not exceed the value used in the over-prediction.

Method Definition:
public void setCurrentHorizontalDivergence(double divh)
Parameters List:
divh
Horizontal beam divergence (full width, degrees).

4.7.5.4.8 Set current vertical divergence - setCurrentVerticalDivergence

This method sets a new value for the current vertical divergence used by the resetReflection(..) method. This must not exceed the value used in the over-prediction.

Method Definition:
public void setCurrentVerticalDivergence(double divv)
Parameters List:
divv
Vertical beam divergence (full width, degrees).

4.7.5.4.9 Set current correlated dispersion - setCurrentCorrelatedDispersion

This method sets a new value for the current correlated dispersion term used by the resetReflection(..) method. This must not exceed the value used in the over-prediction.

Method Definition:
public void setCurrentCorrelatedDispersion(double delcor)
Parameters List:
delcor
Correlated dispersion term (only used for synchrotron) (fullwidth, degrees).

4.7.5.4.10 Set current dispersion - setCurrentDispersion

This method sets a new value for the current dispersion used by the resetReflection(..) method. This must not exceed the value used in the over-prediction.

Method Definition:
public void setCurrentDispersion(double delamb)
Parameters List:
delamb
Dispersion (delta(lambda)/lambda).

4.7.5.4.11 Get current oscillation angle - getCurrentOscillationAngle

This method returns the value for the current oscillation angle used by the resetReflection(..) method.

Method Definition:
public double getCurrentOscillationAngle()
Parameters List:
none

4.7.5.4.12 Get current mosaicity - getCurrentMosaicity

This method returns the value for the current mosaicity used by the resetReflection(..) method.

Method Definition:
public double getCurrentMosaicity()
Parameters List:
none

4.7.5.4.13 Get current horizontal divergence - getCurrentHorizontalDivergence

This method returns the value for the current horizontal divergence used by the resetReflection(..) method.

Method Definition:
public double getCurrentHorizontalDivergence()
Parameters List:
none

4.7.5.4.14 Get current vertical divergence - getCurrentVerticalDivergence

This method returns the value for the current vertical divergence used by the resetReflection(..) method.

Method Definition:
public double getCurrentVerticalDivergence()
Parameters List:
none

4.7.5.4.15 Get current correlated dispersion - getCurrentCorrelatedDispersion

This method returns the value for the current correlated dispersion term used by the resetReflection(..) method.

Method Definition:
public double getCurrentCorrelatedDispersion()
Parameters List:
none

4.7.5.4.16 Get current dispersion - getCurrentDispersion

This method returns the value for the current dispersion used by the resetReflection(..) method.

Method Definition:
public double getCurrentDispersion()
Parameters List:
none

4.7.5.4.17 Get full oscillation angle - getFullOscillationAngle

This method returns the value for the full oscillation angle used in the prediction.

Method Definition:
public double getFullOscillationAngle()
Parameters List:
none

4.7.5.4.18 Get full mosaicity - getFullMosaicity

This method returns the value for the full mosaicity used in the prediction.

Method Definition:
public double getFullMosaicity()
Parameters List:
none

4.7.5.4.19 Get full horizontal divergence - getFullHorizontalDivergence

This method returns the value for the full horizontal divergence used in the prediction.

Method Definition:
public double getFullHorizontalDivergence()
Parameters List:
none

4.7.5.4.20 Get full vertical divergence - getFullVerticalDivergence

This method returns the value for the full vertical divergence used in the prediction.

Method Definition:
public double getFullVerticalDivergence()
Parameters List:
none

4.7.5.4.21 Get full correlated dispersion - getFullCorrelatedDispersion

This method returns the value for the full correlated dispersion term used in the prediction.

Method Definition:
public double getFullCorrelatedDispersion()
Parameters List:
none

4.7.5.4.22 Get full dispersion - getFullDispersion

This method returns the value for the full dispersion used in the prediction.

Method Definition:
public double getFullDispersion()
Parameters List:
none

4.7.5.4.23 Reset reflection details - resetReflection

This method recalculates the parameters which depend on the variable items and returns an updated JdlPredictedReflection object with these updated parameters.

Method Definition:
public JdlPredictedReflection resetReflection(JdlPredictedReflection refl)
Parameters List:
refl
The reflection as predicted originally.
Method Return:
The reflection with details updated to reflect the changes in the variable items.

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