def 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
"""
numU, testDim = Urows.shape
assert testDim == 9, "Your input must have 9 columns; yours has %d" % (testDim)
qin = quatOfRotMat(Urows.reshape(numU, 3, 3))
qout = num.dot( quatProductMatrix( quatOfRotMat(fableSampCOB), mult='left' ), \
num.dot( quatProductMatrix( quatOfRotMat(U0.T), mult='right'), \
qin ).squeeze() ).squeeze()
if qout.ndim == 1:
qout = toFundamentalRegion(qout.reshape(4, 1), crysSym=symTag, sampSym=None)
else:
qout = toFundamentalRegion(qout, crysSym=symTag, sampSym=None)
if display:
print "quaternions in (Fable convention):"
print qin.T
print "quaternions out (hexrd convention, symmetrically reduced)"
print qout.T
pass
Uout = rotMatOfQuat(qout)
return Uout
def convertRotMatToFableU(rMats, U0=num.eye(3), 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
"""
numU = num.shape(num.atleast_3d(rMats))[0]
qin = quatOfRotMat(num.atleast_3d(rMats))
qout = num.dot( quatProductMatrix( quatOfRotMat(fableSampCOB.T), mult='left' ), \
num.dot( quatProductMatrix( quatOfRotMat(U0), mult='right'), \
qin ).squeeze() ).squeeze()
if qout.ndim == 1:
qout = toFundamentalRegion(qout.reshape(4, 1), crysSym=symTag, sampSym=None)
else:
qout = toFundamentalRegion(qout, crysSym=symTag, sampSym=None)
if display:
print "quaternions in (hexrd convention):"
print qin.T
print "quaternions out (Fable convention, symmetrically reduced)"
print qout.T
pass
Uout = rotMatOfQuat(qout)
return Uout
def convertRotMatToFableU(rMats, U0=num.eye(3), 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
"""
numU = num.shape(num.atleast_3d(rMats))[0]
qin = quatOfRotMat(num.atleast_3d(rMats))
qout = num.dot( quatProductMatrix( quatOfRotMat(fableSampCOB.T), mult='left' ), \
num.dot( quatProductMatrix( quatOfRotMat(U0), mult='right'), \
qin ).squeeze() ).squeeze()
if qout.ndim == 1:
qout = toFundamentalRegion(qout.reshape(4, 1),
crysSym=symTag,
sampSym=None)
else:
qout = toFundamentalRegion(qout, crysSym=symTag, sampSym=None)
if display:
print "quaternions in (hexrd convention):"
print qin.T
print "quaternions out (Fable convention, symmetrically reduced)"
print qout.T
pass
Uout = rotMatOfQuat(qout)
return Uout
def 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
"""
numU, testDim = Urows.shape
assert testDim == 9, "Your input must have 9 columns; yours has %d" % (
testDim)
qin = quatOfRotMat(Urows.reshape(numU, 3, 3))
qout = num.dot( quatProductMatrix( quatOfRotMat(fableSampCOB), mult='left' ), \
num.dot( quatProductMatrix( quatOfRotMat(U0.T), mult='right'), \
qin ).squeeze() ).squeeze()
if qout.ndim == 1:
qout = toFundamentalRegion(qout.reshape(4, 1),
crysSym=symTag,
sampSym=None)
else:
qout = toFundamentalRegion(qout, crysSym=symTag, sampSym=None)
if display:
print "quaternions in (Fable convention):"
print qin.T
print "quaternions out (hexrd convention, symmetrically reduced)"
print qout.T
pass
Uout = rotMatOfQuat(qout)
return Uout
def 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
"""
global multiProcMode_MP
global spotsArray_MP
global candidate_MP
global dspTol_MP
global minCompleteness_MP
global doRefinement_MP
global nStdDev_MP
# assign locals
multiProcMode = multiProcMode_MP
spotsArray = spotsArray_MP
candidate = candidate_MP
dspTol = dspTol_MP
minCompleteness = minCompleteness_MP
doRefinement = doRefinement_MP
nStdDev = nStdDev_MP
nSigmas = 2 # ... make this a settable option?
if multiProcMode:
global foundFlagShared
foundGrainData = None
#print "testing %d of %d"% (iR+1, numTrials)
thisRMat = rotMatOfQuat(thisQ)
ppfx = ''
if multiProcMode:
proc = multiprocessing.current_process()
ppfx = str(proc.name)+' : '
if multiProcMode and foundFlagShared.value:
"""
map causes this function to be applied to all trial orientations,
but skip evaluations after an acceptable grain has been found
"""
if debugMultiproc > 1:
print ppfx+'skipping on '+str(thisQ)
return foundGrainData
else:
if debugMultiproc > 1:
print ppfx+'working on '+str(thisQ)
pass
candidate.findMatches(rMat=thisRMat,
strainMag=dspTol,
claimingSpots=False,
testClaims=True,
updateSelf=True)
if debugMultiproc > 1:
print ppfx+' for '+str(thisQ)+' got completeness : '+str(candidate.completeness)
if candidate.completeness >= minCompleteness:
## attempt to filter out 'junk' spots here by performing full
## refinement before claiming
fineEtaTol = candidate.etaTol
fineOmeTol = candidate.omeTol
if doRefinement:
if multiProcMode and foundFlagShared.value:
'some other process beat this one to it'
return foundGrainData
print ppfx+"testing candidate q = [%1.2e, %1.2e, %1.2e, %1.2e]" %tuple(thisQ)
# not needed # candidate.fitPrecession(display=False)
## first fit
candidate.fit(display=False)
## auto-tolerace based on statistics of current matches
validRefls = candidate.grainSpots['iRefl'] > 0
fineEtaTol = nStdDev * num.std(candidate.grainSpots['diffAngles'][validRefls, 1])
fineOmeTol = nStdDev * num.std(candidate.grainSpots['diffAngles'][validRefls, 2])
## next fits with finer tolerances
for iLoop in range(3):
candidate.findMatches(etaTol=fineEtaTol,
omeTol=fineOmeTol,
claimingSpots=False,
testClaims=True,
updateSelf=True)
# not needed # candidate.fitPrecession(display=False)
candidate.fit(display=False)
if candidate.completeness < minCompleteness:
print ppfx+"candidate failed"
return foundGrainData
if multiProcMode and foundFlagShared.value:
'some other process beat this one to it'
return foundGrainData
# not needed # candidate.fitPrecession(display=False)
# not needed? # candidate.fit(display=False)
# not needed? # candidate.findMatches(etaTol=fineEtaTol,
# not needed? # omeTol=fineOmeTol,
# not needed? # claimingSpots=False,
# not needed? # testClaims=True,
# not needed? # updateSelf=True)
else:
## at least do precession correction
candidate.fitPrecession(display=False)
candidate.findMatches(rMat=thisRMat,
strainMag=dspTol,
claimingSpots=False,
testClaims=True,
updateSelf=True)
fineEtaTol = candidate.etaTol
fineOmeTol = candidate.omeTol
if candidate.completeness < minCompleteness:
print ppfx+"candidate failed"
return foundGrainData
if multiProcMode and foundFlagShared.value:
'some other process beat this one to it'
return foundGrainData
if multiProcMode:
foundFlagShared.value = True
# # newGrain uses current candidate.rMat
# # do not do claims here -- those handled outside of this call
# foundGrain = candidate.newGrain(
# spotsArray, claimingSpots=False,
# omeTol=fineOmeTol,
# etaTol=fineEtaTol)
# if multiProcMode:
# foundGrain.strip()
cInfo = quatOfRotMat(candidate.rMat).flatten().tolist()
cInfo.append(candidate.completeness)
print ppfx+"Grain found at q = [%1.2e, %1.2e, %1.2e, %1.2e] with completeness %g" \
% tuple(cInfo)
foundGrainData = candidate.getGrainData()
'tolerances not actually set in candidate, so set them manually'
foundGrainData['omeTol'] = fineOmeTol
foundGrainData['etaTol'] = fineEtaTol
return foundGrainData
def 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
"""
global multiProcMode_MP
global spotsArray_MP
global candidate_MP
global dspTol_MP
global minCompleteness_MP
global doRefinement_MP
global nStdDev_MP
# assign locals
multiProcMode = multiProcMode_MP
spotsArray = spotsArray_MP
candidate = candidate_MP
dspTol = dspTol_MP
minCompleteness = minCompleteness_MP
doRefinement = doRefinement_MP
nStdDev = nStdDev_MP
nSigmas = 2 # ... make this a settable option?
if multiProcMode:
global foundFlagShared
foundGrainData = None
#print "testing %d of %d"% (iR+1, numTrials)
thisRMat = rotMatOfQuat(thisQ)
ppfx = ''
if multiProcMode:
proc = multiprocessing.current_process()
ppfx = str(proc.name) + ' : '
if multiProcMode and foundFlagShared.value:
"""
map causes this function to be applied to all trial orientations,
but skip evaluations after an acceptable grain has been found
"""
if debugMultiproc > 1:
print ppfx + 'skipping on ' + str(thisQ)
return foundGrainData
else:
if debugMultiproc > 1:
print ppfx + 'working on ' + str(thisQ)
pass
candidate.findMatches(rMat=thisRMat,
strainMag=dspTol,
claimingSpots=False,
testClaims=True,
updateSelf=True)
if debugMultiproc > 1:
print ppfx + ' for ' + str(thisQ) + ' got completeness : ' + str(
candidate.completeness)
if candidate.completeness >= minCompleteness:
## attempt to filter out 'junk' spots here by performing full
## refinement before claiming
fineEtaTol = candidate.etaTol
fineOmeTol = candidate.omeTol
if doRefinement:
if multiProcMode and foundFlagShared.value:
'some other process beat this one to it'
return foundGrainData
print ppfx + "testing candidate q = [%1.2e, %1.2e, %1.2e, %1.2e]" % tuple(
thisQ)
# not needed # candidate.fitPrecession(display=False)
## first fit
candidate.fit(display=False)
## auto-tolerace based on statistics of current matches
validRefls = candidate.grainSpots['iRefl'] > 0
fineEtaTol = nStdDev * num.std(
candidate.grainSpots['diffAngles'][validRefls, 1])
fineOmeTol = nStdDev * num.std(
candidate.grainSpots['diffAngles'][validRefls, 2])
## next fits with finer tolerances
for iLoop in range(3):
candidate.findMatches(etaTol=fineEtaTol,
omeTol=fineOmeTol,
claimingSpots=False,
testClaims=True,
updateSelf=True)
# not needed # candidate.fitPrecession(display=False)
candidate.fit(display=False)
if candidate.completeness < minCompleteness:
print ppfx + "candidate failed"
return foundGrainData
if multiProcMode and foundFlagShared.value:
'some other process beat this one to it'
return foundGrainData
# not needed # candidate.fitPrecession(display=False)
# not needed? # candidate.fit(display=False)
# not needed? # candidate.findMatches(etaTol=fineEtaTol,
# not needed? # omeTol=fineOmeTol,
# not needed? # claimingSpots=False,
# not needed? # testClaims=True,
# not needed? # updateSelf=True)
else:
## at least do precession correction
candidate.fitPrecession(display=False)
candidate.findMatches(rMat=thisRMat,
strainMag=dspTol,
claimingSpots=False,
testClaims=True,
updateSelf=True)
fineEtaTol = candidate.etaTol
fineOmeTol = candidate.omeTol
if candidate.completeness < minCompleteness:
print ppfx + "candidate failed"
return foundGrainData
if multiProcMode and foundFlagShared.value:
'some other process beat this one to it'
return foundGrainData
if multiProcMode:
foundFlagShared.value = True
# # newGrain uses current candidate.rMat
# # do not do claims here -- those handled outside of this call
# foundGrain = candidate.newGrain(
# spotsArray, claimingSpots=False,
# omeTol=fineOmeTol,
# etaTol=fineEtaTol)
# if multiProcMode:
# foundGrain.strip()
cInfo = quatOfRotMat(candidate.rMat).flatten().tolist()
cInfo.append(candidate.completeness)
print ppfx+"Grain found at q = [%1.2e, %1.2e, %1.2e, %1.2e] with completeness %g" \
% tuple(cInfo)
foundGrainData = candidate.getGrainData()
'tolerances not actually set in candidate, so set them manually'
foundGrainData['omeTol'] = fineOmeTol
foundGrainData['etaTol'] = fineEtaTol
return foundGrainData