def simulateGrain(self,
rMat=numpy.eye(3),
vMat=numpy.r_[1., 1., 1., 0., 0., 0.],
planeData=None,
detector=None,
omegaRanges=[OMEGA_PERIOD],
output=None):
"""
Simulate a grain with choice of active material
"""
if planeData is None:
planeData = self.activeMaterial.planeData
if detector is None:
detector = self.detector
dummySpots = SPT.Spots(planeData, None, detector, omegaRanges)
sg = G.Grain(dummySpots, rMat=rMat, vMat=vMat)
if output is not None:
if isinstance(output, file):
fid = output
elif isinstance(output, str):
fid = open(output, 'w')
else:
raise RuntimeError("output must be a file object or string")
sg.findMatches(filename=fid)
return sg
def makeRandGrains(numGrains, omegaMM, detectorGeom):
spotsDummy = Spots(planeData, None, detectorGeom, omegaMM)
if numGrains == 1:
rMats = num.atleast_3d(num.eye(3)).T
else:
quats = num.atleast_2d(ors.Quat.getRandQuat(n=numGrains)).T
rMats = ors.quatToMat(quats)
gList = []
for rMat in rMats:
g = grain.Grain(spotsDummy, rMat=rMat)
gList.append(g)
return gList
def refine_grains(self,
minCompl,
nSubIter=3,
doFit=False,
etaTol=valunits.valWUnit('etaTol', 'angle', 1.0,
'degrees'),
omeTol=valunits.valWUnit('etaTol', 'angle', 1.0,
'degrees'),
fineDspTol=5.0e-3,
fineEtaTol=valunits.valWUnit('etaTol', 'angle', 0.5,
'degrees'),
fineOmeTol=valunits.valWUnit('etaTol', 'angle', 0.5,
'degrees')):
"""
refine a grain list
"""
# refine grains formally using a multi-pass refinement
nGrains = self.rMats.shape[0]
grainList = []
for iG in range(nGrains):
#indexer.progress_bar(float(iG) / nGrains)
grain = G.Grain(self.spots_for_indexing,
rMat=self.rMats[iG, :, :],
etaTol=etaTol,
omeTol=omeTol,
claimingSpots=False)
if grain.completeness > minCompl:
for i in range(nSubIter):
grain.fit()
s1, s2, s3 = grain.findMatches(etaTol=etaTol,
omeTol=omeTol,
strainMag=fineDspTol,
updateSelf=True,
claimingSpots=False,
doFit=doFit,
testClaims=True)
if grain.completeness > minCompl:
grainList.append(grain)
pass
pass
pass
self.grainList = grainList
self._fitRMats = numpy.array(
[self.grainList[i].rMat for i in range(len(grainList))])
return
def makeRandGrains(numGrains, omegaMM, detectorGeom):
spotsDummy = Spots(planeData, None, detectorGeom, omegaMM)
if numGrains == 1:
import orientations as ors
r = ors.RotInv(3.08805198 - num.pi, 0., 1., 0.).toMatrix()
# r = num.eye(3)
rMats = num.atleast_3d(r).T
else:
quats = num.atleast_2d(ors.Quat.getRandQuat(n=numGrains)).T
rMats = ors.quatToMat(quats)
gList = []
for rMat in rMats:
g = grain.Grain(spotsDummy, rMat=rMat)
gList.append(g)
return gList
hklListForIndex,
iPhase=planeData.phaseID,
nsteps=720,
minCompleteness=0.70,
minPctClaimed=0.75,
friedelOnly=False,
dspTol=None,
etaTol=etaTol,
omeTol=omeTol,
debug=True,
doMultiProc=opts.doMultiProc,
doRefinement=False)
print 'found %d grains' % (rMat.shape[0])
# etaTol = valunits.valWUnit("etaTol","ANGLE",0.0625,"degrees")
# omeTol = valunits.valWUnit("omeTol","ANGLE",0.2500,"degrees")
firstGrain = grain.Grain(spotsForFit,
rMat=rMat[0, :, :],
etaTol=etaTol,
omeTol=omeTol)
firstGrain.fit()
reflInfo, fPairs, completeness = firstGrain.findMatches(
updateSelf=True)
print 'after fit, completeness is %g' % (completeness)
######################################################################
# add more tests here as see fit
# return