Write PeakShape

[Owen Arnold]

These algorithms should be writing out peak shape information:

IntegrateMD IntegrateEllipsoids IntegratePeaksHybrid

Drawing of these types in the PeaksViewer will require a redesign of parts of the peaks viewer and is the subject of a later ticket.

[Owen Arnold]

changes in 10878 will allow this to happen.

[Owen Arnold]

refs #10904. IntegratePeaksMD algorithms done.

IntegratePeaksMD v1 and v2 write out integrated peak info in the form of PeakShape

PeakShapeSpherical adapted to write out background outer radius and background inner radius as well as the peak radius. Factories also updated for this, unit tests added to and updated for this.

I got a little worried that someone may change the integer values agaist the enum entries of SpecialCoordinateSystem. So I put in place a unit test to sanity check those.

Changeset: 4427109cf115e1a82aa734433567825260d8c5d2

[Owen Arnold]

refs #10904. Ellipsoid shape.

Changeset: 2387ce56192b68b8e817acc2f7867c9bc706e9bf

[Owen Arnold]

refs #10904. Factory for elliptical peak shapes

Changeset: 78da6586affaaeb716be0bf5a600a8faa90aaead

[Owen Arnold]

refs #10904. Hook new factory into loader.

Changeset: 8d327c5fb2c546e06cdb04f9f45b3666f20a999a

[Owen Arnold]

refs #10904. Write from IntegrateEllipsoids.

Changeset: 3d558b329cc794b4b193e860851f62f88234b6e8

[Owen Arnold]

This is being verified as ​pull request #179.

[Owen Arnold]

refs #10904. Mv PeakShape an fix warnings.

Changeset: 0dd26e09dce1a86ae91341ae120499db6bd7b61c

[Owen Arnold]

refs #10904. Fix remaining warning.

Changeset: 43d4e257400c3dd46d1e2f081a192d06158d7593

[Owen Arnold]

refs #10904. Expose PeakShape to python.

Changeset: bf2702633f1a18ab35ab234fd0378f52aa2767f8

[Owen Arnold]

refs #10904 SpecialCoords API->Kernel

Since we have put PeakShape in Geometry, SpecialCoordinateSystem must be moved to the Kernel package out of API.

Changeset: 561214347d175ee881aadba4e8796c51f8c359e5

[Owen Arnold]

refs #10904. Python tests for PeakShape.

Also fix GCC and Windows warnings

Changeset: 8996ec68fc0f83d080026fbe978c8519d819b551

[Owen Arnold]

refs #10904. Resolve conflict with master.

Changeset: f910af2cda11091a56dd9cd69fd3621e9c4bcb9a

[Owen Arnold]

Tester:

What's been done as part of this ticket has been well covered by unit tests. In addition, there are some new things that can be done in python (see below)

Setup steps

# Basic parameters  for  Triphylite Crystal
#Name of the workspaces to create
ws_name = "TOPAZ_3132"
filename = ws_name +"_event.nxs"
ws = LoadEventNexus(Filename=filename,FilterByTofMin=3000, FilterByTofMax=16000)

# -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
# Part 1. Basic Reduction

# Spherical Absorption and Lorentz Corrections
ws = AnvredCorrection(InputWorkspace=ws, LinearScatteringCoef=0.451, LinearAbsorptionCoef=0.993, Radius=0.14)

# Convert to Q space
LabQ = ConvertToDiffractionMDWorkspace(InputWorkspace=ws, LorentzCorrection='0',
        OutputDimensions='Q (lab frame)', SplitInto=2, SplitThreshold=150)

# Find peaks
PeaksLattice = FindPeaksMD(InputWorkspace=LabQ,MaxPeaks=100)

# 3d integration to centroid peaks
PeaksLattice = CentroidPeaksMD(InputWorkspace=LabQ,
    PeakRadius=0.12, PeaksWorkspace=PeaksLattice)

# Find the UB matrix using the peaks and known lattice parameters
FindUBUsingLatticeParameters(PeaksWorkspace=PeaksLattice, a=10.3522, b=6.0768, c=4.7276,
                alpha=90, beta=90, gamma=90, NumInitial=20, Tolerance=0.12)

# And index to HKL
IndexPeaks(PeaksWorkspace=PeaksLattice, Tolerance=0.12)

Then run

PeaksLatticeFFT = IntegratePeaksMD(InputWorkspace=LabQ, PeakRadius=0.12,
    BackgroundOuterRadius=0.18,BackgroundInnerRadius=0.15,
    PeaksWorkspace=PeaksLatticeFFT)

# The new bit:
shape = PeaksLatticeFFT.getPeak(0).getPeakShape()
print shape.toJSON()

And you should get this:

{
   "algorithm_name" : "IntegratePeaksMD",
   "algorithm_version" : 2,
   "background_inner_radius" : 0.150,
   "background_outer_radius" : 0.180,
   "frame" : 1,
   "radius" : 0.120,
   "shape" : "spherical"
}

Then run

PeaksLatticeFFT = IntegrateEllipsoids(InputWorkspace=ws, PeaksWorkspace=PeaksLatticeFFT) 
    
# The new bit
shape = PeaksLatticeFFT.getPeak(0).getPeakShape()
print shape.toJSON()

And you should get this:

{
   "algorithm_name" : "IntegrateEllipsoids",
   "algorithm_version" : -1,
   "background_inner_radius0" : 0.1569320366997004,
   "background_inner_radius1" : 0.1904709902029069,
   "background_inner_radius2" : 0.2009385702055810,
   "background_outer_radius0" : 0.1977219764573250,
   "background_outer_radius1" : 0.2399784099709861,
   "background_outer_radius2" : 0.2531667343589144,
   "direction0" : "-0.397112 0.592816 0.700622",
   "direction1" : "-0.674626 -0.706126 0.215095",
   "direction2" : "-0.622239 0.387241 -0.68034",
   "frame" : 1,
   "radius0" : 0.1569320366997004,
   "radius1" : 0.1904709902029069,
   "radius2" : 0.2009385702055810,
   "shape" : "ellipsoid"
}

[Owen Arnold]

refs #10904. Fix windows build.

Changeset: a22ac8e3d0f6fead27e7209c2dc4f6232d24c62f

[Owen Arnold]

Jenkins retest this please

[Owen Arnold]

Jenkins retest this please

[Owen Arnold]

refs #10904. Fix bad include.

Changeset: 53d30cb05751da73fef600a749f5a88086e31c2d

[Martyn Gigg]

Jenkins, retest this please

[Martyn Gigg]

The builds have got themselves into some odd state with this pull request. I suggest closing it without merging and opening a fresh one.

[Owen Arnold]

This is being verified as ​pull request #196.

[Owen Arnold]

refs #10904. Scope resolution for enum

Changeset: df4c56ab348ef6b5abd194d30c0ef4f2347327a9

[Martyn Gigg]

The script from the ticket works as expected and so do all of the methods on the new PeakShape class. I can see that most of the changes are due to the move of the SpecialCoordinateSystem.

[Martyn Gigg]

Merge pull request #196 from mantidproject/feature/10904_apply_peak_shape

Full changeset: ​35142efce2f65370653d5b5d210ba1a6dedd7147

[Stuart Campbell]

This ticket has been transferred to github issue ​11743