John W. Campbell

Class, constructors and methods:

Class DetailsAccessible Fields

Constructors

Manipulate Reflection List

Get Reflection Data

Sort Reflection List

Spatial Overlaps

Predict Reflections

Convert Indices

- Package:
- Jdl.JdlPX;
- Class name:
- JdlPredictedReflectionsList
- Class definition:
- public class JdlPredictedReflectionsList
- Extends:
- Object
- Implements:
- JdlRotReflOutputHandler

- Actions:
- none

Constructors:

Default ConstructorStandard Constructor

*Constructor Definition:*- public JdlPredictedReflectionsList()
*Parameters List:*- none

*Constructor Definition:*- public JdlPredictedReflectionsList (int nr, int inc)
*Parameters List:*- nr
- The initial capacity required (number of reflections).
- inc
- The increment in number of reflections required each time the list needs to be expanded.

Methods:

Clear list - clearListAdd reflection - addReflection

Insert reflection - insertReflection

Replace reflection - replaceReflection

Delete reflection - deleteReflection

Delete reflections - deleteImageReflections

Put hkl - putHKL

*Method Definition:*- public void clearList()
*Parameters List:*- none

*Method Definition:*- public void addReflection (JdlPredictedReflection refl)
*Parameters List:*- refl
- The reflection to be added.

*Method Definition:*- public void insertReflection (JdlPredictedReflection refl, int iref)
*Parameters List:*- refl
- The reflection to be inserted.
- iref
- The position within the list where the reflection is to be inserted (reflection positions numbered from 1 upwards).

*Method Definition:*- public void replaceReflection (JdlPredictedReflection refl, int iref)
*Parameters List:*- refl
- The reflection to replace a current reflection.
- iref
- The position within the list where the reflection is to be replaced (reflection positions numbered from 1 upwards).

*Method Definition:*- public void deleteReflection (int iref)
*Parameters List:*- iref
- The position within the list of the reflection to be deleted (reflection positions numbered from 1 upwards).

*Method Definition:*- public void deleteImageReflections (int imgnum)
*Parameters List:*- imgnum
- The image number of the image for which the reflections are to be deleted.

*Method Definition:*- public void putHKL (int iref, int h, int k, int l, int ksym)
*Parameters List:*- iref
- The position within the list of the reflection for which the indices are to be reset (reflection positions numbered from 1 upwards).
- h
- The new 'h' index.
- k
- The new 'k' index.
- l
- The new 'l' index.
- ksym
- The symmetry operator number used to generate the indices or 0 to unset this item (see JdlPredictedReflection class for further details).

Methods:

Get number of reflections - getNumberOfReflectionsGet number of reflections - getNumberOfImageReflections

Get number of spatial overlaps - getNumberOfSpatialOverlaps

Get reflection reference - getReflection

Get reflection copy - getReflectionCopy

Get sort order - getSortOrder

*Method Definition:*- public int getNumberOfReflections()
*Parameters List:*- none
*Method Return:*- The number of reflections in the list.

*Method Definition:*- public int getNumberOfImageReflections(int icrys, int imgnum)
*Parameters List:*- icrys
- The selected crystal number.
- imgnum
- The selected image number.

*Method Return:*- The number of reflections in the list for the requested crystal and image.

*Method Definition:*- public int getNumberOfSpatialOverlaps(int icrys, int imgnum)
*Parameters List:*- icrys
- The selected crystal number (-1 = all crystal numbers).
- imgnum
- The selected image number (-1 = all image numbers).

*Method Return:*- The number of reflections in the list for the requested crystal and image.

*Method Definition:*- public JdlPredictedReflection getReflection (int iref)
*Parameters List:*- iref
- The position in the list of the reflection to be returned (from 1 upwards).

*Method Return:*- The JdlPredictedReflection object for the reflection (reference to stored object - not a copy/clone).

*Method Definition:*- public JdlPredictedReflection getReflectionCopy (int iref)
*Parameters List:*- The
- position in the list of the reflection to be returned (from 1 upwards).

*Method Return:*- A JdlPredictedReflection object for the reflection. This is a clone (copy) of the stored object.

*Method Definition:*- public int getSortOrder()
*Parameters List:*- none
*Method Return:*-
The sort order:

= 1, Sorted on h, k, l

= 2, Sorted on local axis 1 coordinate

= 3, Sorted on local axis 2 coordinate

= 4, Sorted on h

= 5, Sorted on k

= 6, Sorted on l

= 0, May not be sorted.

Method:

Sort reflection list - sortReflectionList*Method Definition:*- public void sortReflectionList (int srt_opt)
*Parameters List:*- sort_opt
- Sort order option:

= 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'

Method:

Spatial overlaps - setSpatialOverlaps*Method Definition:*- public int setSpatialOverlaps (int icrys, int img_id, double spotd)
*Parameters List:*- icrys
- The selected crystal number.
- img_id
- The selected image number or identifier as stored when the spot list was predicted.
- spotd
- The spot diameter for the image im mm.

*Method Return:*- The number of spatially overlapped spots found for the image.

Methods:

Predict reflection list - predictReflectionsPredict reflection list - predictReflections

Predict reflection set - predictReflectionSet

Predict reflection set - predictReflectionSet

*Method Definition:*- public void predictReflections(JdlDiffractionDataModule ddm, int iset, int irange, int imgnum, boolean quick, boolean recorded, boolean spat, boolean append)
*Parameters List:*- ddm
- The JdlDiffractionDataModule object containing the detector and crystal data.
- iset
- The set number within the Diffraction Data Module.
- irange
- The rotation range number.
- imgnum
- The number of the image from 1 up (within the requested rotation range) for which the prediction is to be carried out.
- quick
- If set to true a quick prediction will be carried out with fewer details being calculated for each reflection. If false the full detailed prediction will be performed (see the parameters of the JdlRotReflOutputHandler outputPredictedReflection(..) method for details of the items which are calculated.
- recorded
- If true, store only reflections flagged as being recorded. If false include predicted but non-recorded reflections.
- spat
- If true calculate spatial overlap flags after generating the reflection list, if false do not.
- append
- If true, append the reflections to any reflections already stored. If false clear any stored reflections before creating the list.

*Method Definition:*- public void predictReflections(JdlPositionedDetector posdet, JdlPositionedCrystal poscrys, int icrys, int irange, double rotstart, double oscang, int imgnum, double rmin, double xmin, double xmax, double ymin, double ymax, boolean quick, boolean recorded, boolean spat, boolean append)
*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.
- icrys
- The crystal number (The image may be identified by the crystal number and image number).
- irange
- A rotation range number for which 'rotstart' is the start angle.
- rotstart
- The start rotation angle in degrees (see also imgnum).
- oscang
- The oscillation angle in degrees.
- imgnum
- The number of the image for which the prediction is to be carried out from 1 up (The rotation range used will be from rotstart + (imgnum-1)*oscang to rotstart + imgnum*oscang).
- rmin
- Minimum radius for prediction in mm.
- xmin
- Minimum 'x' limit for prediction in mm (ignored if xmin = xmax)
- xmax
- Maximum 'x' limit for prediction in mm (ignored if xmax = xmin)
- ymin
- Minimum 'y' limit for prediction in mm (ignored if ymin = ymax)
- ymax
- Maximum 'y' limit for prediction in mm (ignored if ymax = ymin)
- quick
- If set to true a quick prediction will be carried out with fewer details being calculated for each reflection. If false the full detailed prediction will be performed (see the parameters of the JdlRotReflOutputHandler outputPredictedReflection(..) method for details of the items which are calculated.
- recorded
- If true, store only reflections flagged as being recorded. If false include predicted but non-recorded reflections.
- spat
- If true calculate spatial overlap flags after generating the reflection list, if false do not.
- append
- If true, append the reflections to any reflections already stored. If false clear any stored reflections before creating the list.

*Method Definition:*- public void predictReflectionSet(JdlDiffractionDataModule ddm, int iset, int irange, int setting_opt, boolean spat, JdlProgressHandler progress)
*Parameters List:*- ddm
- The JdlDiffractionDataModule object containing the detector and crystal data.
- iset
- The set number within the Diffraction Data Module.
- irange
- The rotation range number.
- setting_opt
- This determines the exact setting parameters used for
each image prediction:

= 0, Use the setting parameters defined for the first image of the complete dataset

= 1, Use the setting parameters defined for the first image of the specified range

= 2, Use the setting parameters defined for each individual image

Note that, in most cases, it is likely that the setting parameters for all images of the set will in fact be identical. - spat
- If true calculate spatial overlap flags after generating the reflection list, if false do not.
- progress
- Progress handler (may be null if not required).

*Method Definition:*- public void predictReflectionSet(JdlPositionedDetector posdet, JdlPositionedCrystal poscrys, int icrys, int irange, double rotstart, double rotend, double oscang, double rmin, double xmin, double xmax, double ymin, double ymax, boolean spat, JdlProgressHandler progress)
*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.
- icrys
- The crystal number (The image may be identified by the crystal number and image identifier).
- irange
- a range number > 0 to be associated with the given rotation range.
- rotstart
- The start rotation angle in degrees.
- rotend
- The end rotation angle in degrees.
- oscang
- The oscillation angle in degrees.
- rmin
- Minimum radius for prediction in mm.
- xmin
- Minimum 'x' limit for prediction in mm (ignored if xmin = xmax)
- xmax
- Maximum 'x' limit for prediction in mm (ignored if xmax = xmin)
- ymin
- Minimum 'y' limit for prediction in mm (ignored if ymin = ymax)
- ymax
- Maximum 'y' limit for prediction in mm (ignored if ymax = ymin)
- spat
- If true calculate spatial overlap flags for each image, if false do not.
- progress
- Progress handler (may be null if not required).

Methods:

Convert to unique - indicesToUniqueConvert to measured - indicesToMeasured

*Method Definition:*- public boolean indicesToUnique (JdlSymmetry symm)
*Parameters List:*- symm
- The symmetry (must be complete).

*Method Return:*- Returns true ik Ok, false if symmetry not complete.

*Method Definition:*- public boolean indicesToMeasured (JdlSymmetry symm)
*Parameters List:*- symm
- The symmetry (must be complete).

*Method Return:*- Returns true ik Ok, false if symmetry not complete.

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