John W. Campbell
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
- Package:
- Jdl.JdlPX;
- Class name:
- JdlUniqueReflection
- Class definition:
- public class JdlUniqueReflection
- Extends:
- Object
- Implements:
- Comparable
Comparator<JdlUniqueReflection>
- 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 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).
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
This constructs an empty object.
- Constructor Definition:
- public JdlUniqueReflection()
- Parameters List:
- none
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.
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
This method clears all the reflection measurement counts.
- Method Definition:
- public void clearCounts()
- Parameters List:
- none
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)
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
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
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
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
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'
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.
This section has a single method to list the contents of the object
primarily for diagnostic purposes.
Method:
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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