John W. Campbell

Class, constructors and methods:

Class DetailsAccessible Fields

Constructors

Manipulate Spot List

Get Spot Data

Sort Spot List

Spatial Overlaps

Convert Indices

Predict Deconvolution

- Package:
- Jdl.JdlPX;
- Class name:
- JdlPredictedLaueSpotsList
- Class definition:
- public class JdlPredictedLaueSpotsList
- Extends:
- Object
- Implements:
- JdlLaueSpotOutputHandler

- Actions:
- none

Constructors:

Default ConstructorStandard Constructor

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

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

Methods:

Clear list - clearListAdd spot - addSpot

Insert spot - insertSpot

Replace spot - replaceSpot

Delete spot - deleteSpot

Delete spots - deleteImageSpots

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

*Method Definition:*- public void addSpot (JdlPredictedLaueSpot refl)
*Parameters List:*- refl
- The spot to be added.

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

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

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

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

Methods:

Get number of spots - getNumberOfSpotsGet number of spots - getNumberOfImageSpots

Get number of spatial overlaps - getNumberOfSpatialOverlaps

Get spot reference - getSpot

Get spot copy - getSpotCopy

Get sort order - getSortOrder

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

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

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

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

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

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

*Method Return:*- A JdlPredictedLaueSpot object for the spot. 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 and l

= 2, Sorted on nh, nk and nl (nodal indices)

= 3, Sorted on axis 1 coordinate

= 4, Sorted on axis 2 coordinate

= 5, Sorted on 'h'

= 6, Sorted on 'k'

= 7, Sorted on 'l'

= 8, Sorted on 'nh'

= 9, Sorted on 'nk'

= 10, Sorted on 'nl'

= 11, Sorted on lambda - ascending

= 12, Sorted on lambda - descending

= 0, May not be sorted.

Method:

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

= 1, Sort on h, k and l

= 2, Sort on nh, nk and nl (nodal indices)

= 3, Sort on axis 1 coordinate

= 4, Sort on axis 2 coordinate

= 5, Sort on 'h'

= 6, Sort on 'k'

= 7, Sort on 'l'

= 8, Sort on 'nh'

= 9, Sort on 'nk'

= 10, Sort on 'nl'

= 11, Sort on lambda - ascending

= 12, Sort on lambda - descending

Method:

Spatial overlaps - setSpatialOverlapsPredict spot list - predictSpots

Predict spot list - predictSpots

Predict spots set - predictSpotsSet

Predict spots set - predictSpotsSet

*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.

*Method Definition:*- public void predictSpots(JdlDiffractionDataModule ddm, int iset, int irange, int imgnum, 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 (> 0, within the requested rotation range) for which the prediction is to be carried out.
- spat
- If true calculate spatial overlap flags after generating the spot list, if false do not.
- append
- If true, append the spots to any spots already stored. If false clear any stored spots before creating the list.

*Method Definition:*- public void predictSpots(JdlPositionedDetector posdet, JdlPositionedCrystal poscrys, int icrys, int irange, double rotstart, double ang_inc, int imgnum, double rmin, double xmin, double xmax, double ymin, double ymax, 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 >0 (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 for the range in degrees (see also imgnum).
- ang_inc
- The angle increment between images in degrees.
- imgnum
- The number of the image for which the prediction is to be carried out from 1 up within the requested range (The rotation angle used will be rotstart + (imgnum-1)*ang_inc).
- 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 after generating the spot list, if false do not.
- append
- If true, append the spots to any spots already stored. If false clear any stored spots before creating the list.

*Method Definition:*- public void predictSpotsSet(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 predictSpotsSet(JdlPositionedDetector posdet, JdlPositionedCrystal poscrys, int icrys, int irange, double rotstart, double rotend, double anginc, 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.
- anginc
- The angle increment between images 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.

Methods:

Predict deconvolution - deconvPredict*Method Definition:*- public JdlPredictedLaueSpotsList deconvPredict(JdlChebyshevPolynomial curv, double sc_max)
*Parameters List:*- curv
- A wavelength normalisation curve to be used in the deconvolution prediction.
- sc_max
- A maximum scale factor (derived from the wavelength normalisation curve) to be used e.g. 25.0.

*Method Return:*- Returns a new spot list containing the singles and and 'deconvoluted' multiples.

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