Module: xrd.indexer

1 Class

class hexrd.xrd.indexer.GrainSpotter

Interface to grain spotter, which must be in the user’s path

__init__()

9 Functions

hexrd.xrd.indexer.convertUToRotMat(Urows, U0, symTag='Oh', display=False)

Takes GrainSpotter gff ouput in rows

U11 U12 U13 U21 U22 U23 U13 U23 U33

and takes it into the hexrd/APS frame of reference

Urows comes from grainspotter’s gff output U0 comes from xrd.crystallography.latticeVectors.U0

convertRotMatToFableU(rMats, U0=array([[ 1., 0., 0.],

[ 0., 1., 0.],

[ 0., 0., 1.]]), symTag='Oh', display=False)

Makes GrainSpotter gff ouput

U11 U12 U13 U21 U22 U23 U13 U23 U33

and takes it into the hexrd/APS frame of reference

Urows comes from grainspotter’s gff output U0 comes from xrd.crystallography.latticeVectors.U0

hexrd.xrd.indexer.testThisQ(thisQ)

NOTES: (*) doFit is not done here – in multiprocessing, that would end

up happening on a remote process and then different processes would have different data, unless spotsArray were made to be fancier

(*) kludge stuff so that this function is outside of fiberSearch

hexrd.xrd.indexer.fiberSearch(spotsArray, hklList, iPhase=0, nsteps=120, minCompleteness=0.6, minPctClaimed=0.95, preserveClaims=False, friedelOnly=True, dspTol=None, etaTol=0.025, omeTol=0.025, etaTolF=0.00225, omeTolF=0.00875, nStdDev=2, quitAfter=None, doRefinement=True, debug=True, doMultiProc=True, nCPUs=None, outputGrainList=False)

This indexer finds grains by performing 1-d searches along the fibers under the valid spots associated with each reflection order specified in hklList. The set of spots used to generate the candidate orientations may be restricted to Friedel pairs only.

hklList must have length > 0; Dach hkl entry in hklList must be a tuple, not a list

the output is a concatenated list of orientation matrices ((n, 3, 3) numpy.ndarray).

hexrd.xrd.indexer.pgRefine(x, etaOmeMaps, omegaRange, threshold)

hexrd.xrd.indexer.paintGrid(quats, etaOmeMaps, threshold=None, bMat=None, omegaRange=None, etaRange=None, omeTol=0.017453292519943295, etaTol=0.017453292519943295, omePeriod=(-3.141592653589793, 3.141592653589793), doMultiProc=False, nCPUs=None, debug=False)

do a direct search of omega-eta maps to paint each orientation in quats with a completeness

bMat is in CRYSTAL frame

etaOmeMaps is instance of xrd.xrdutil.CollapseOmeEta

omegaRange=([-num.pi/3., num.pi/3.],) for example

*) lifted mainly from grain.py

*) self.etaGrid, self.omeGrid = num.meshgrid(self.etaEdges, self.omeEdges)

this means that ETA VARIES FASTEST!

...make a new function that gets called by grain to do the g-vec angle computation?

hexrd.xrd.indexer.paintGridThis(quat)

hexrd.xrd.indexer.writeGVE(spotsArray, fileroot, **kwargs)

write Fable gve file from Spots object

fileroot is the root string used to write the gve and ini files

Outputs:

No return value, but writes the following files:

<fileroot>.gve <fileroot>_grainSpotter.ini (points to –> <fileroot>_grainSpotter.log)

Keyword arguments:

Mainly for GrainSpotter .ini file, but some are needed for gve files

‘sgNum’: <225> ‘phaseID’: <None> ‘cellString’: <F> ‘omeRange’: <-60, 60, 120, 240> the oscillation range(s)

**currently pulls from spots

‘deltaOme’: <0.25, 0.25> the oscillation delta(s)

**currently pulls from spots

‘minMeas’: <24> ‘minCompl’: <0.7> ‘minUniqn’: <0.5> ‘uncertainty’: <[0.10, 0.25, .50]> the min [tTh, eta, ome] uncertainties

in degrees

‘eulStep’: <2> ‘nSigmas’: <2> ‘minFracG’: <0.90> ‘nTrials’: <100000> ‘positionfit’: <True>

Notes:

*) The omeRange is currently pulled from the spotsArray input; the kwarg

has no effect as of now. Will change this to ‘override’ the spots info if the user, say, wants to pare down the range.

*) There is no etaRange argument yet, but presumably GrainSpotter knows

how to deal with this. Pending feature...