John W. Campbell
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
- Package:
- Jdl.JdlPX;
- Class name:
- JdlPredictedLaueSpot
- Class definition:
- public class JdlPredictedLaueSpot
- Extends:
- Object
- Implements:
- Cloneable
Comparable
Comparator<JdlPredictedLaueSpot>
- Actions:
- none
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
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
This constructs an empty object.
- Constructor Definition:
- public JdlPredictedLaueSpot()
- Parameters List:
- none
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.
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
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).
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).
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.
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.
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.
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).
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).
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).
This method sets the crystal number.
- Method Definition:
- public void setCrystalNumber (int icrys)
- Parameters List:
- icrys
- The crystal number (>0, 0 = unset).
This method sets the image number.
- Method Definition:
- public void setImageNumber (int imgnum)
- Parameters List:
- imgnum
- The image number (>0, 0 = unset).
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.
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.
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
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
Returns the value of the 'h' index.
- Method Definition:
- public int getH()
- Parameters List:
- none
- Method Return:
-
The 'h' index.
Returns the value of the 'k' index.
- Method Definition:
- public int getK()
- Parameters List:
- none
- Method Return:
-
The 'k' index.
Returns the value of the 'l' index.
- Method Definition:
- public int getL()
- Parameters List:
- none
- Method Return:
-
The 'l' index.
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.
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
Returns the value of the nodal 'h' index.
- Method Definition:
- public int getNodalH()
- Parameters List:
- none
- Method Return:
-
The 'nh' index.
Returns the value of the nodal 'k' index.
- Method Definition:
- public int getNodalK()
- Parameters List:
- none
- Method Return:
-
The 'nk' index.
Returns the value of the nodal 'l' index.
- Method Definition:
- public int getNodalL()
- Parameters List:
- none
- Method Return:
-
The 'nl' index.
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.
This method returns the wavelength.
- Method Definition:
- public double getLambda()
- Parameters List:
- none
- Method Return:
-
The wavelength.
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').
This method returns the minimum harmonic for a multiple spot.
- Method Definition:
- public int getMinimumHarmonic()
- Parameters List:
- none
- Method Return:
-
The minimum harmonic number.
This method returns the maximum harmonic for a multiple spot.
- Method Definition:
- public int getMaximumHarmonic()
- Parameters List:
- none
- Method Return:
-
The minimum harmonic number.
This method returns the harmonic increment for a multiple spot.
- Method Definition:
- public int getHarmonicIncrement()
- Parameters List:
- none
- Method Return:
-
The harmonic increment.
Return the detector coordinates
- Method Definition:
- public JdlXY getCoordinates()
- Parameters List:
- none
- Method Return:
-
The detector coordinates in mm.
Returns the crystal number.
- Method Definition:
- public int getCrystalNumber()
- Parameters List:
- none
- Method Return:
-
The crystal number.
Returns the image number.
- Method Definition:
- public int getImageNumber()
- Parameters List:
- none
- Method Return:
-
The image number.
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.
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.
Returns the value of the spatial overlap flag if set.
- Method Definition:
- public int getSpatialOverlap()
- Parameters List:
- none
- Method Return:
-
The spatial overlap flag
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
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'
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.
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