def 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
keyword default definitions
-----------------------------------------------------------------------------------------
'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...
"""
# check on fileroot
assert isinstance(fileroot, str)
# keyword argument processing
phaseID = None
sgNum = 225
cellString = 'P'
omeRange = num.r_[-60, 60] # in DEGREES
deltaOme = 0.25 # in DEGREES
minMeas = 24
minCompl = 0.7
minUniqn = 0.5
uncertainty = [0.10, 0.25, .50] # in DEGREES
eulStep = 2 # in DEGREES
nSigmas = 2
minFracG = 0.90
numTrials = 100000
positionFit = True
kwarglen = len(kwargs)
if kwarglen > 0:
argkeys = kwargs.keys()
for i in range(kwarglen):
if argkeys[i] == 'sgNum':
sgNum = kwargs[argkeys[i]]
elif argkeys[i] == 'phaseID':
phaseID = kwargs[argkeys[i]]
elif argkeys[i] == 'cellString':
cellString = kwargs[argkeys[i]]
elif argkeys[i] == 'omeRange':
omeRange = kwargs[argkeys[i]]
elif argkeys[i] == 'deltaOme':
deltaOme = kwargs[argkeys[i]]
elif argkeys[i] == 'minMeas':
minMeas = kwargs[argkeys[i]]
elif argkeys[i] == 'minCompl':
minCompl = kwargs[argkeys[i]]
elif argkeys[i] == 'minUniqn':
minUniqn = kwargs[argkeys[i]]
elif argkeys[i] == 'uncertainty':
uncertainty = kwargs[argkeys[i]]
elif argkeys[i] == 'eulStep':
eulStep = kwargs[argkeys[i]]
elif argkeys[i] == 'nSigmas':
nSigmas = kwargs[argkeys[i]]
elif argkeys[i] == 'minFracG':
minFracG = kwargs[argkeys[i]]
elif argkeys[i] == 'nTrials':
numTrials = kwargs[argkeys[i]]
elif argkeys[i] == 'positionfit':
positionFit = kwargs[argkeys[i]]
else:
raise RuntimeError, "Unrecognized keyword argument '%s'" % (argkeys[i])
# grab some detector geometry parameters for gve file header
mmPerPixel = float(spotsArray.detectorGeom.pixelPitch) # ...these are still hard-coded to be square
nrows_p = spotsArray.detectorGeom.nrows - 1
ncols_p = spotsArray.detectorGeom.ncols - 1
row_p, col_p = spotsArray.detectorGeom.pixelIndicesOfCartesianCoords(spotsArray.detectorGeom.xc,
spotsArray.detectorGeom.yc)
yc_p = ncols_p - col_p
zc_p = nrows_p - row_p
wd_mu = spotsArray.detectorGeom.workDist * 1e3 # in microns (Soeren)
osc_axis = num.dot(fableSampCOB.T, Yl).flatten()
# start grabbing stuff from planeData
planeData = spotsArray.getPlaneData(phaseID=phaseID)
cellp = planeData.latVecOps['dparms']
U0 = planeData.latVecOps['U0']
wlen = planeData.wavelength
dsp = planeData.getPlaneSpacings()
fHKLs = planeData.getSymHKLs()
tThRng = planeData.getTThRanges()
symTag = planeData.getLaueGroup()
tThMin, tThMax = (r2d*tThRng.min(), r2d*tThRng.max()) # single range should be ok since entering hkls
etaMin, etaMax = (0, 360) # not sure when this will ever *NOT* be the case, so setting it
omeMin = spotsArray.getOmegaMins()
omeMax = spotsArray.getOmegaMaxs()
omeRangeString = ''
for iOme in range(len(omeMin)):
if hasattr(omeMin[iOme], 'getVal'):
omeRangeString += 'omegarange %g %g\n' % (omeMin[iOme].getVal('degrees'), omeMax[iOme].getVal('degrees'))
else:
omeRangeString += 'omegarange %g %g\n' % (omeMin[iOme] * r2d, omeMax[iOme] * r2d)
# convert angles
cellp[3:] = r2d*cellp[3:]
# make the theoretical hkls string
gvecHKLString = ''
for i in range(len(dsp)):
for j in range(fHKLs[i].shape[1]):
gvecHKLString += '%1.8f %d %d %d\n' % (1/dsp[i], fHKLs[i][0, j], fHKLs[i][1, j], fHKLs[i][2, j])
# now for the measured data section
# xr yr zr xc yc ds eta omega
gvecString = ''
spotsIter = spotsArray.getIterPhase(phaseID, returnBothCoordTypes=True)
for iSpot, angCOM, xyoCOM in spotsIter:
sR, sC, sOme = xyoCOM # detector coords
sTTh, sEta, sOme = angCOM # angular coords (radians)
sDsp = wlen / 2. / num.sin(0.5*sTTh) # dspacing
# get raw y, z (Fable frame)
yraw = ncols_p - sC
zraw = nrows_p - sR
# convert eta to fable frame
rEta = mapAngle(90. - r2d*sEta, [0, 360], units='degrees')
# make mesaured G vector components in fable frame
mGvec = makeMeasuredScatteringVectors(sTTh, sEta, sOme, convention='fable', frame='sample')
# full Gvec components in fable lab frame (for grainspotter position fit)
gveXYZ = spotsArray.detectorGeom.angToXYO(sTTh, sEta, sOme, outputGve=True)
# no 4*pi
mGvec = mGvec / sDsp
# make contribution
gvecString += '%1.8f %1.8f %1.8f %1.8f %1.8f %1.8f %1.8f %1.8f %d %1.8f %1.8f %1.8f\n' \
% (mGvec[0], mGvec[1], mGvec[2], \
sR, sC, \
1/sDsp, rEta, r2d*sOme, \
iSpot, \
gveXYZ[0, :], gveXYZ[1, :], gveXYZ[2, :])
pass
# write gve file for grainspotter
fid = open(fileroot+'.gve', 'w')
print >> fid, '%1.8f %1.8f %1.8f %1.8f %1.8f %1.8f ' % tuple(cellp) + \
cellString + '\n' + \
'# wavelength = %1.8f\n' % (wlen) + \
'# wedge = 0.000000\n' + \
'# axis = %d %d %d\n' % tuple(osc_axis) + \
'# cell__a %1.4f\n' %(cellp[0]) + \
'# cell__b %1.4f\n' %(cellp[1]) + \
'# cell__c %1.4f\n' %(cellp[2]) + \
'# cell_alpha %1.4f\n' %(cellp[3]) + \
'# cell_beta %1.4f\n' %(cellp[4]) + \
'# cell_gamma %1.4f\n' %(cellp[5]) + \
'# cell_lattice_[P,A,B,C,I,F,R] %s\n' %(cellString) + \
'# chi 0.0\n' + \
'# distance %.4f\n' %(wd_mu) + \
'# fit_tolerance 0.5\n' + \
'# o11 1\n' + \
'# o12 0\n' + \
'# o21 0\n' + \
'# o22 -1\n' + \
'# omegasign %1.1f\n' %(num.sign(deltaOme)) + \
'# t_x 0\n' + \
'# t_y 0\n' + \
'# t_z 0\n' + \
'# tilt_x 0.000000\n' + \
'# tilt_y 0.000000\n' + \
'# tilt_z 0.000000\n' + \
'# y_center %.6f\n' %(yc_p) + \
'# y_size %.6f\n' %(mmPerPixel*1.e3) + \
'# z_center %.6f\n' %(zc_p) + \
'# z_size %.6f\n' %(mmPerPixel*1.e3) + \
'# ds h k l\n' + \
gvecHKLString + \
'# xr yr zr xc yc ds eta omega\n' + \
gvecString
fid.close()
###############################################################
# GrainSpotter ini parameters
#
# fileroot = tempfile.mktemp()
if positionFit:
positionString = 'positionfit'
else:
positionString = '!positionfit'
if numTrials == 0:
randomString = '!random\n'
else:
randomString = 'random %g\n' % (numTrials)
fid = open(fileroot+'_grainSpotter.ini', 'w')
# self.__tempFNameList.append(fileroot)
print >> fid, \
'spacegroup %d\n' % (sgNum) + \
'tthrange %g %g\n' % (tThMin, tThMax) + \
'etarange %g %g\n' % (etaMin, etaMax) + \
'domega %g\n' % (deltaOme) + \
omeRangeString + \
'filespecs %s.gve %s_grainSpotter.log\n' % (fileroot, fileroot) + \
'cuts %d %g %g\n' % (minMeas, minCompl, minUniqn) + \
'eulerstep %g\n' % (eulStep)+ \
'uncertainties %g %g %g\n' % (uncertainty[0], uncertainty[1], uncertainty[2]) + \
'nsigmas %d\n' % (nSigmas) + \
'minfracg %g\n' % (minFracG) + \
randomString + \
positionString + '\n'
fid.close()
return
def fiberSearch(spotsArray, hklList,
iPhase=0,
nsteps=120,
minCompleteness=0.60,
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).
"""
assert hasattr(hklList, '__len__'), "the HKL list must have length, and len(hklList) > 0."
nHKLs = len(hklList)
grainList = []
nGrains = 0
planeData = spotsArray.getPlaneData(iPhase)
csym = planeData.getLaueGroup()
bMat = planeData.latVecOps['B']
if dspTol is None:
dspTol = planeData.strainMag
centroSymRefl = planeData.getCentroSymHKLs()
candidate = Grain(spotsArray, rMat=None,
etaTol=etaTol, omeTol=omeTol)
multiProcMode = xrdbase.haveMultiProc and doMultiProc
#
global foundFlagShared
global multiProcMode_MP
global spotsArray_MP
global candidate_MP
global dspTol_MP
global minCompleteness_MP
global doRefinement_MP
global nStdDev_MP
multiProcMode_MP = multiProcMode
spotsArray_MP = spotsArray
candidate_MP = candidate
dspTol_MP = dspTol
minCompleteness_MP = minCompleteness
doRefinement_MP = doRefinement
nStdDev_MP = nStdDev
"""
set up for shared memory multiprocessing
"""
if multiProcMode:
nCPUs = nCPUs or xrdbase.dfltNCPU
spotsArray.multiprocMode = True
pool = multiprocessing.Pool(nCPUs)
"""
HKL ITERATOR
"""
if isinstance(quitAfter, dict):
n_hkls_to_search = quitAfter['nHKLs']
else:
n_hkls_to_search = nHKLs
if isinstance(quitAfter, int):
quit_after_ngrains = quitAfter
else:
quit_after_ngrains = 0
numTotal = len(spotsArray)
pctClaimed = 0.
time_to_quit = False
tic = time.time()
for iHKL in range(n_hkls_to_search):
print "\n#####################\nProcessing hkl %d of %d\n" % (iHKL+1, nHKLs)
thisHKLID = planeData.getHKLID(hklList[iHKL])
thisRingSpots0 = spotsArray.getHKLSpots(thisHKLID)
thisRingSpots0W = num.where(thisRingSpots0)[0]
unclaimedOfThese = -spotsArray.checkClaims(indices=thisRingSpots0W)
thisRingSpots = copy.deepcopy(thisRingSpots0)
thisRingSpots[thisRingSpots0W] = unclaimedOfThese
if friedelOnly:
# first, find Friedel Pairs
spotsArray.findFriedelPairsHKL(hklList[iHKL],
etaTol=etaTolF,
omeTol=omeTolF)
spotsIteratorI = spotsArray.getIterHKL(hklList[iHKL], unclaimedOnly=True, friedelOnly=True)
# make some stuff for counters
maxSpots = 0.5*(sum(thisRingSpots) - sum(spotsArray.friedelPair[thisRingSpots] == -1))
else:
spotsIteratorI = spotsArray.getIterHKL(hklList[iHKL], unclaimedOnly=True, friedelOnly=False)
maxSpots = sum(thisRingSpots)
"""
SPOT ITERATOR
- this is where we iterate over all 'valid' spots for the current HKL as
subject to the conditions of claims and ID as a friedel pair (when requested)
"""
for iRefl, stuff in enumerate(spotsIteratorI):
unclaimedOfThese = -spotsArray.checkClaims(indices=thisRingSpots0W)
thisRingSpots = copy.deepcopy(thisRingSpots0)
thisRingSpots[thisRingSpots0W] = unclaimedOfThese
if friedelOnly:
iSpot, jSpot, angs_I, angs_J = stuff
Gplus = makeMeasuredScatteringVectors(*angs_I)
Gminus = makeMeasuredScatteringVectors(*angs_J)
Gvec = 0.5*(Gplus - Gminus)
maxSpots = 0.5*(sum(thisRingSpots) - sum(spotsArray.friedelPair[thisRingSpots] == -1))
else:
iSpot, angs_I = stuff
Gvec = makeMeasuredScatteringVectors(*angs_I)
maxSpots = sum(thisRingSpots)
print "\nProcessing reflection %d (spot %d), %d remain unclaimed\n" % (iRefl+1, iSpot, maxSpots)
if multiProcMode and debugMultiproc > 1:
marks = spotsArray._Spots__marks[:]
print 'marks : '+str(marks)
# make the fiber;
qfib = discreteFiber(hklList[iHKL], Gvec,
B=bMat,
ndiv=nsteps,
invert=False,
csym=csym, ssym=None)[0]
# if +/- hkl aren't in the symmetry group, need '-' fiber
if not centroSymRefl[thisHKLID]:
minusHKL = -num.r_[hklList[iHKL]]
qfibM = discreteFiber(minusHKL, Gvec,
B=bMat,
ndiv=nsteps,
invert=False,
csym=csym, ssym=None)[0]
qfib = num.hstack([qfib, qfibM])
pass
# cull out duplicate orientations
qfib = mUtil.uniqueVectors(qfib, tol=1e-4)
numTrials = qfib.shape[1]
"""
THIS IS THE BIGGIE; THE LOOP OVER THE DISCRETE ORIENTATIONS IN THE CURRENT FIBER
"""
if multiProcMode:
foundFlagShared.value = False
qfibList = map(num.array, qfib.T.tolist())
#if debugMultiproc:
# print 'qfibList : '+str(qfibList)
results = num.array(pool.map(testThisQ, qfibList, chunksize=1))
trialGrains = results[num.where(num.array(results, dtype=bool))]
# for trialGrain in trialGrains:
# trialGrain.restore(candidate)
else:
trialGrains = []
for iR in range(numTrials):
foundGrainData = testThisQ(qfib[:, iR])
if foundGrainData is not None:
trialGrains.append(foundGrainData)
break
'end of if multiProcMode'
if len(trialGrains) == 0:
print "No grain found containing spot %d\n" % (iSpot)
# import pdb;pdb.set_trace()
else:
asMaster = multiProcMode
'sort based on completeness'
trialGrainCompletenesses = [tgd['completeness'] for tgd in trialGrains]
order = num.argsort(trialGrainCompletenesses)[-1::-1]
for iTrialGrain in order:
foundGrainData = trialGrains[iTrialGrain]
foundGrain = Grain(spotsArray, grainData=foundGrainData, claimingSpots=False)
'check completeness before accepting, especially important for multiproc'
foundGrain.checkClaims() # updates completeness
if debugMultiproc:
print 'final completeness of candidate is %g' % (foundGrain.completeness)
if foundGrain.completeness >= minCompleteness:
conflicts = foundGrain.claimSpots(asMaster=asMaster)
numConfl = num.sum(conflicts)
if numConfl > 0:
'tried to claim %d spots that are already claimed' % (numConfl)
grainList.append(foundGrain)
nGrains += 1
numUnClaimed = num.sum(-spotsArray.checkClaims())
numClaimed = numTotal - numUnClaimed
pctClaimed = num.float(numClaimed) / numTotal
print "Found %d grains so far, %f%% claimed" % (nGrains,100*pctClaimed)
time_to_quit = (pctClaimed > minPctClaimed) or\
((quit_after_ngrains > 0) and (nGrains >= quit_after_ngrains))
if time_to_quit:
break
'end of iRefl loop'
if time_to_quit:
break
'end of iHKL loop'
rMats = num.empty((len(grainList), 3, 3))
for i in range(len(grainList)):
rMats[i, :, :] = grainList[i].rMat
if outputGrainList:
retval = (rMats, grainList)
else:
retval = rMats
if not preserveClaims:
spotsArray.resetClaims()
toc = time.time()
print 'fiberSearch execution took %g seconds' % (toc-tic)
if multiProcMode:
pool.close()
spotsArray.multiprocMode = False
foundFlagShared.value = False
# global foundFlagShared
# global multiProcMode_MP
# global spotsArray_MP
# global candidate_MP
# global dspTol_MP
# global minCompleteness_MP
# global doRefinement_MP
multiProcMode_MP = None
spotsArray_MP = None
candidate_MP = None
dspTol_MP = None
minCompleteness_MP = None
doRefinement_MP = None
return retval
def fiberSearch(spotsArray,
hklList,
iPhase=0,
nsteps=120,
minCompleteness=0.60,
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).
"""
assert hasattr(
hklList,
'__len__'), "the HKL list must have length, and len(hklList) > 0."
nHKLs = len(hklList)
grainList = []
nGrains = 0
planeData = spotsArray.getPlaneData(iPhase)
csym = planeData.getLaueGroup()
bMat = planeData.latVecOps['B']
if dspTol is None:
dspTol = planeData.strainMag
centroSymRefl = planeData.getCentroSymHKLs()
candidate = Grain(spotsArray, rMat=None, etaTol=etaTol, omeTol=omeTol)
multiProcMode = xrdbase.haveMultiProc and doMultiProc
#
global foundFlagShared
global multiProcMode_MP
global spotsArray_MP
global candidate_MP
global dspTol_MP
global minCompleteness_MP
global doRefinement_MP
global nStdDev_MP
multiProcMode_MP = multiProcMode
spotsArray_MP = spotsArray
candidate_MP = candidate
dspTol_MP = dspTol
minCompleteness_MP = minCompleteness
doRefinement_MP = doRefinement
nStdDev_MP = nStdDev
"""
set up for shared memory multiprocessing
"""
if multiProcMode:
nCPUs = nCPUs or xrdbase.dfltNCPU
spotsArray.multiprocMode = True
pool = multiprocessing.Pool(nCPUs)
"""
HKL ITERATOR
"""
if isinstance(quitAfter, dict):
n_hkls_to_search = quitAfter['nHKLs']
else:
n_hkls_to_search = nHKLs
if isinstance(quitAfter, int):
quit_after_ngrains = quitAfter
else:
quit_after_ngrains = 0
numTotal = len(spotsArray)
pctClaimed = 0.
time_to_quit = False
tic = time.time()
for iHKL in range(n_hkls_to_search):
print "\n#####################\nProcessing hkl %d of %d\n" % (iHKL + 1,
nHKLs)
thisHKLID = planeData.getHKLID(hklList[iHKL])
thisRingSpots0 = spotsArray.getHKLSpots(thisHKLID)
thisRingSpots0W = num.where(thisRingSpots0)[0]
unclaimedOfThese = -spotsArray.checkClaims(indices=thisRingSpots0W)
thisRingSpots = copy.deepcopy(thisRingSpots0)
thisRingSpots[thisRingSpots0W] = unclaimedOfThese
if friedelOnly:
# first, find Friedel Pairs
spotsArray.findFriedelPairsHKL(hklList[iHKL],
etaTol=etaTolF,
omeTol=omeTolF)
spotsIteratorI = spotsArray.getIterHKL(hklList[iHKL],
unclaimedOnly=True,
friedelOnly=True)
# make some stuff for counters
maxSpots = 0.5 * (sum(thisRingSpots) -
sum(spotsArray.friedelPair[thisRingSpots] == -1))
else:
spotsIteratorI = spotsArray.getIterHKL(hklList[iHKL],
unclaimedOnly=True,
friedelOnly=False)
maxSpots = sum(thisRingSpots)
"""
SPOT ITERATOR
- this is where we iterate over all 'valid' spots for the current HKL as
subject to the conditions of claims and ID as a friedel pair (when requested)
"""
for iRefl, stuff in enumerate(spotsIteratorI):
unclaimedOfThese = -spotsArray.checkClaims(indices=thisRingSpots0W)
thisRingSpots = copy.deepcopy(thisRingSpots0)
thisRingSpots[thisRingSpots0W] = unclaimedOfThese
if friedelOnly:
iSpot, jSpot, angs_I, angs_J = stuff
Gplus = makeMeasuredScatteringVectors(*angs_I)
Gminus = makeMeasuredScatteringVectors(*angs_J)
Gvec = 0.5 * (Gplus - Gminus)
maxSpots = 0.5 * (sum(thisRingSpots) - sum(
spotsArray.friedelPair[thisRingSpots] == -1))
else:
iSpot, angs_I = stuff
Gvec = makeMeasuredScatteringVectors(*angs_I)
maxSpots = sum(thisRingSpots)
print "\nProcessing reflection %d (spot %d), %d remain unclaimed\n" % (
iRefl + 1, iSpot, maxSpots)
if multiProcMode and debugMultiproc > 1:
marks = spotsArray._Spots__marks[:]
print 'marks : ' + str(marks)
# make the fiber;
qfib = discreteFiber(hklList[iHKL],
Gvec,
B=bMat,
ndiv=nsteps,
invert=False,
csym=csym,
ssym=None)[0]
# if +/- hkl aren't in the symmetry group, need '-' fiber
if not centroSymRefl[thisHKLID]:
minusHKL = -num.r_[hklList[iHKL]]
qfibM = discreteFiber(minusHKL,
Gvec,
B=bMat,
ndiv=nsteps,
invert=False,
csym=csym,
ssym=None)[0]
qfib = num.hstack([qfib, qfibM])
pass
# cull out duplicate orientations
qfib = mUtil.uniqueVectors(qfib, tol=1e-4)
numTrials = qfib.shape[1]
"""
THIS IS THE BIGGIE; THE LOOP OVER THE DISCRETE ORIENTATIONS IN THE CURRENT FIBER
"""
if multiProcMode:
foundFlagShared.value = False
qfibList = map(num.array, qfib.T.tolist())
#if debugMultiproc:
# print 'qfibList : '+str(qfibList)
results = num.array(pool.map(testThisQ, qfibList, chunksize=1))
trialGrains = results[num.where(num.array(results,
dtype=bool))]
# for trialGrain in trialGrains:
# trialGrain.restore(candidate)
else:
trialGrains = []
for iR in range(numTrials):
foundGrainData = testThisQ(qfib[:, iR])
if foundGrainData is not None:
trialGrains.append(foundGrainData)
break
'end of if multiProcMode'
if len(trialGrains) == 0:
print "No grain found containing spot %d\n" % (iSpot)
# import pdb;pdb.set_trace()
else:
asMaster = multiProcMode
'sort based on completeness'
trialGrainCompletenesses = [
tgd['completeness'] for tgd in trialGrains
]
order = num.argsort(trialGrainCompletenesses)[-1::-1]
for iTrialGrain in order:
foundGrainData = trialGrains[iTrialGrain]
foundGrain = Grain(spotsArray,
grainData=foundGrainData,
claimingSpots=False)
'check completeness before accepting, especially important for multiproc'
foundGrain.checkClaims() # updates completeness
if debugMultiproc:
print 'final completeness of candidate is %g' % (
foundGrain.completeness)
if foundGrain.completeness >= minCompleteness:
conflicts = foundGrain.claimSpots(asMaster=asMaster)
numConfl = num.sum(conflicts)
if numConfl > 0:
'tried to claim %d spots that are already claimed' % (
numConfl)
grainList.append(foundGrain)
nGrains += 1
numUnClaimed = num.sum(-spotsArray.checkClaims())
numClaimed = numTotal - numUnClaimed
pctClaimed = num.float(numClaimed) / numTotal
print "Found %d grains so far, %f%% claimed" % (nGrains, 100 *
pctClaimed)
time_to_quit = (pctClaimed > minPctClaimed) or\
((quit_after_ngrains > 0) and (nGrains >= quit_after_ngrains))
if time_to_quit:
break
'end of iRefl loop'
if time_to_quit:
break
'end of iHKL loop'
rMats = num.empty((len(grainList), 3, 3))
for i in range(len(grainList)):
rMats[i, :, :] = grainList[i].rMat
if outputGrainList:
retval = (rMats, grainList)
else:
retval = rMats
if not preserveClaims:
spotsArray.resetClaims()
toc = time.time()
print 'fiberSearch execution took %g seconds' % (toc - tic)
if multiProcMode:
pool.close()
spotsArray.multiprocMode = False
foundFlagShared.value = False
# global foundFlagShared
# global multiProcMode_MP
# global spotsArray_MP
# global candidate_MP
# global dspTol_MP
# global minCompleteness_MP
# global doRefinement_MP
multiProcMode_MP = None
spotsArray_MP = None
candidate_MP = None
dspTol_MP = None
minCompleteness_MP = None
doRefinement_MP = None
return retval
def 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
keyword default definitions
-----------------------------------------------------------------------------------------
'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...
"""
# check on fileroot
assert isinstance(fileroot, str)
# keyword argument processing
phaseID = None
sgNum = 225
cellString = 'P'
omeRange = num.r_[-60, 60] # in DEGREES
deltaOme = 0.25 # in DEGREES
minMeas = 24
minCompl = 0.7
minUniqn = 0.5
uncertainty = [0.10, 0.25, .50] # in DEGREES
eulStep = 2 # in DEGREES
nSigmas = 2
minFracG = 0.90
numTrials = 100000
positionFit = True
kwarglen = len(kwargs)
if kwarglen > 0:
argkeys = kwargs.keys()
for i in range(kwarglen):
if argkeys[i] == 'sgNum':
sgNum = kwargs[argkeys[i]]
elif argkeys[i] == 'phaseID':
phaseID = kwargs[argkeys[i]]
elif argkeys[i] == 'cellString':
cellString = kwargs[argkeys[i]]
elif argkeys[i] == 'omeRange':
omeRange = kwargs[argkeys[i]]
elif argkeys[i] == 'deltaOme':
deltaOme = kwargs[argkeys[i]]
elif argkeys[i] == 'minMeas':
minMeas = kwargs[argkeys[i]]
elif argkeys[i] == 'minCompl':
minCompl = kwargs[argkeys[i]]
elif argkeys[i] == 'minUniqn':
minUniqn = kwargs[argkeys[i]]
elif argkeys[i] == 'uncertainty':
uncertainty = kwargs[argkeys[i]]
elif argkeys[i] == 'eulStep':
eulStep = kwargs[argkeys[i]]
elif argkeys[i] == 'nSigmas':
nSigmas = kwargs[argkeys[i]]
elif argkeys[i] == 'minFracG':
minFracG = kwargs[argkeys[i]]
elif argkeys[i] == 'nTrials':
numTrials = kwargs[argkeys[i]]
elif argkeys[i] == 'positionfit':
positionFit = kwargs[argkeys[i]]
else:
raise RuntimeError, "Unrecognized keyword argument '%s'" % (
argkeys[i])
# grab some detector geometry parameters for gve file header
mmPerPixel = float(spotsArray.detectorGeom.pixelPitch
) # ...these are still hard-coded to be square
nrows_p = spotsArray.detectorGeom.nrows - 1
ncols_p = spotsArray.detectorGeom.ncols - 1
row_p, col_p = spotsArray.detectorGeom.pixelIndicesOfCartesianCoords(
spotsArray.detectorGeom.xc, spotsArray.detectorGeom.yc)
yc_p = ncols_p - col_p
zc_p = nrows_p - row_p
wd_mu = spotsArray.detectorGeom.workDist * 1e3 # in microns (Soeren)
osc_axis = num.dot(fableSampCOB.T, Yl).flatten()
# start grabbing stuff from planeData
planeData = spotsArray.getPlaneData(phaseID=phaseID)
cellp = planeData.latVecOps['dparms']
U0 = planeData.latVecOps['U0']
wlen = planeData.wavelength
dsp = planeData.getPlaneSpacings()
fHKLs = planeData.getSymHKLs()
tThRng = planeData.getTThRanges()
symTag = planeData.getLaueGroup()
tThMin, tThMax = (r2d * tThRng.min(), r2d * tThRng.max()
) # single range should be ok since entering hkls
etaMin, etaMax = (
0, 360
) # not sure when this will ever *NOT* be the case, so setting it
omeMin = spotsArray.getOmegaMins()
omeMax = spotsArray.getOmegaMaxs()
omeRangeString = ''
for iOme in range(len(omeMin)):
if hasattr(omeMin[iOme], 'getVal'):
omeRangeString += 'omegarange %g %g\n' % (
omeMin[iOme].getVal('degrees'), omeMax[iOme].getVal('degrees'))
else:
omeRangeString += 'omegarange %g %g\n' % (omeMin[iOme] * r2d,
omeMax[iOme] * r2d)
# convert angles
cellp[3:] = r2d * cellp[3:]
# make the theoretical hkls string
gvecHKLString = ''
for i in range(len(dsp)):
for j in range(fHKLs[i].shape[1]):
gvecHKLString += '%1.8f %d %d %d\n' % (
1 / dsp[i], fHKLs[i][0, j], fHKLs[i][1, j], fHKLs[i][2, j])
# now for the measured data section
# xr yr zr xc yc ds eta omega
gvecString = ''
spotsIter = spotsArray.getIterPhase(phaseID, returnBothCoordTypes=True)
for iSpot, angCOM, xyoCOM in spotsIter:
sR, sC, sOme = xyoCOM # detector coords
sTTh, sEta, sOme = angCOM # angular coords (radians)
sDsp = wlen / 2. / num.sin(0.5 * sTTh) # dspacing
# get raw y, z (Fable frame)
yraw = ncols_p - sC
zraw = nrows_p - sR
# convert eta to fable frame
rEta = mapAngle(90. - r2d * sEta, [0, 360], units='degrees')
# make mesaured G vector components in fable frame
mGvec = makeMeasuredScatteringVectors(sTTh,
sEta,
sOme,
convention='fable',
frame='sample')
# full Gvec components in fable lab frame (for grainspotter position fit)
gveXYZ = spotsArray.detectorGeom.angToXYO(sTTh,
sEta,
sOme,
outputGve=True)
# no 4*pi
mGvec = mGvec / sDsp
# make contribution
gvecString += '%1.8f %1.8f %1.8f %1.8f %1.8f %1.8f %1.8f %1.8f %d %1.8f %1.8f %1.8f\n' \
% (mGvec[0], mGvec[1], mGvec[2], \
sR, sC, \
1/sDsp, rEta, r2d*sOme, \
iSpot, \
gveXYZ[0, :], gveXYZ[1, :], gveXYZ[2, :])
pass
# write gve file for grainspotter
fid = open(fileroot + '.gve', 'w')
print >> fid, '%1.8f %1.8f %1.8f %1.8f %1.8f %1.8f ' % tuple(cellp) + \
cellString + '\n' + \
'# wavelength = %1.8f\n' % (wlen) + \
'# wedge = 0.000000\n' + \
'# axis = %d %d %d\n' % tuple(osc_axis) + \
'# cell__a %1.4f\n' %(cellp[0]) + \
'# cell__b %1.4f\n' %(cellp[1]) + \
'# cell__c %1.4f\n' %(cellp[2]) + \
'# cell_alpha %1.4f\n' %(cellp[3]) + \
'# cell_beta %1.4f\n' %(cellp[4]) + \
'# cell_gamma %1.4f\n' %(cellp[5]) + \
'# cell_lattice_[P,A,B,C,I,F,R] %s\n' %(cellString) + \
'# chi 0.0\n' + \
'# distance %.4f\n' %(wd_mu) + \
'# fit_tolerance 0.5\n' + \
'# o11 1\n' + \
'# o12 0\n' + \
'# o21 0\n' + \
'# o22 -1\n' + \
'# omegasign %1.1f\n' %(num.sign(deltaOme)) + \
'# t_x 0\n' + \
'# t_y 0\n' + \
'# t_z 0\n' + \
'# tilt_x 0.000000\n' + \
'# tilt_y 0.000000\n' + \
'# tilt_z 0.000000\n' + \
'# y_center %.6f\n' %(yc_p) + \
'# y_size %.6f\n' %(mmPerPixel*1.e3) + \
'# z_center %.6f\n' %(zc_p) + \
'# z_size %.6f\n' %(mmPerPixel*1.e3) + \
'# ds h k l\n' + \
gvecHKLString + \
'# xr yr zr xc yc ds eta omega\n' + \
gvecString
fid.close()
###############################################################
# GrainSpotter ini parameters
#
# fileroot = tempfile.mktemp()
if positionFit:
positionString = 'positionfit'
else:
positionString = '!positionfit'
if numTrials == 0:
randomString = '!random\n'
else:
randomString = 'random %g\n' % (numTrials)
fid = open(fileroot + '_grainSpotter.ini', 'w')
# self.__tempFNameList.append(fileroot)
print >> fid, \
'spacegroup %d\n' % (sgNum) + \
'tthrange %g %g\n' % (tThMin, tThMax) + \
'etarange %g %g\n' % (etaMin, etaMax) + \
'domega %g\n' % (deltaOme) + \
omeRangeString + \
'filespecs %s.gve %s_grainSpotter.log\n' % (fileroot, fileroot) + \
'cuts %d %g %g\n' % (minMeas, minCompl, minUniqn) + \
'eulerstep %g\n' % (eulStep)+ \
'uncertainties %g %g %g\n' % (uncertainty[0], uncertainty[1], uncertainty[2]) + \
'nsigmas %d\n' % (nSigmas) + \
'minfracg %g\n' % (minFracG) + \
randomString + \
positionString + '\n'
fid.close()
return
def __call__(self, spotsArray, **kwargs):
"""
A word on spacegroup numbers: it appears that grainspotter is using the 'VolA' tag for calls to SgInfo
"""
location = self.__class__.__name__
tic = time.time()
# keyword argument processing
phaseID = None
gVecFName = 'tmpGve'
sgNum = 225
cellString = 'F'
omeRange = num.r_[-60, 60] # in DEGREES
deltaOme = 0.25 # in DEGREES
minMeas = 24
minCompl = 0.7
minUniqn = 0.5
uncertainty = [0.10, 0.25, .50] # in DEGREES
eulStep = 2 # in DEGREES
nSigmas = 2
minFracG = 0.90
numTrials = 100000
positionFit = False
kwarglen = len(kwargs)
if kwarglen > 0:
argkeys = kwargs.keys()
for i in range(kwarglen):
if argkeys[i] == 'sgNum':
sgNum = kwargs[argkeys[i]]
elif argkeys[i] == 'phaseID':
phaseID = kwargs[argkeys[i]]
elif argkeys[i] == 'gVecFName':
gVecFName = kwargs[argkeys[i]]
elif argkeys[i] == 'cellString':
cellString = kwargs[argkeys[i]]
elif argkeys[i] == 'omeRange':
omeRange = kwargs[argkeys[i]]
elif argkeys[i] == 'deltaOme':
deltaOme = kwargs[argkeys[i]]
elif argkeys[i] == 'minMeas':
minMeas = kwargs[argkeys[i]]
elif argkeys[i] == 'minCompl':
minCompl = kwargs[argkeys[i]]
elif argkeys[i] == 'minUniqn':
minUniqn = kwargs[argkeys[i]]
elif argkeys[i] == 'uncertainty':
uncertainty = kwargs[argkeys[i]]
elif argkeys[i] == 'eulStep':
eulStep = kwargs[argkeys[i]]
elif argkeys[i] == 'nSigmas':
nSigmas = kwargs[argkeys[i]]
elif argkeys[i] == 'minFracG':
minFracG = kwargs[argkeys[i]]
elif argkeys[i] == 'nTrials':
numTrials = kwargs[argkeys[i]]
elif argkeys[i] == 'positionfit':
positionFit = kwargs[argkeys[i]]
else:
raise RuntimeError, "Unrecognized keyword argument '%s'" % (argkeys[i])
# cleanup stuff from any previous run
self.cleanup()
planeData = spotsArray.getPlaneData(phaseID=phaseID)
cellp = planeData.latVecOps['dparms']
U0 = planeData.latVecOps['U0']
wlen = planeData.wavelength
dsp = planeData.getPlaneSpacings()
fHKLs = planeData.getSymHKLs()
tThRng = planeData.getTThRanges()
symTag = planeData.getLaueGroup()
tThMin, tThMax = (r2d*tThRng.min(), r2d*tThRng.max()) # single range should be ok since entering hkls
etaMin, etaMax = (0, 360) # not sure when this will ever *NOT* be the case, so setting it
omeMin = spotsArray.getOmegaMins()
omeMax = spotsArray.getOmegaMaxs()
omeRangeString = ''
for iOme in range(len(omeMin)):
omeRangeString += 'omegarange %g %g\n' % (omeMin[iOme] * r2d, omeMax[iOme] * r2d)
# convert angles
cellp[3:] = r2d*cellp[3:]
# make the theoretical hkls string
gvecHKLString = ''
for i in range(len(dsp)):
for j in range(fHKLs[i].shape[1]):
gvecHKLString += '%1.8f %d %d %d\n' % (1/dsp[i], fHKLs[i][0, j], fHKLs[i][1, j], fHKLs[i][2, j])
# now for the measured data section
# xr yr zr xc yc ds eta omega
gvecString = ''
ii = 0
spotsIter = spotsArray.getIterPhase(phaseID, returnBothCoordTypes=True)
for iSpot, angCOM, xyoCOM in spotsIter:
sX, sY, sOme = xyoCOM # detector coords
sTTh, sEta, sOme = angCOM # angular coords (radians)
sDsp = wlen / 2. / num.sin(0.5*sTTh) # dspacing
# convert eta to risoe frame
rEta = mapAngle(90. - r2d*sEta, [0, 360], units='degrees')
# make mesaured G vector components in risoe frame
mGvec = makeMeasuredScatteringVectors(sTTh, sEta, sOme, convention='risoe', frame='sample')
# mQvec = makeMeasuredScatteringVectors(sTTh, sEta, sOme, convention='llnl', frame='lab')
gveXYZ = spotsArray.detectorGeom.angToXYO(sTTh, sEta, sOme, outputGve=True)
mGvec = mGvec / sDsp
# mQvec = 4*num.pi*num.sin(0.5*sTTh)*mQvec/wlen
# make contribution
gvecString += '%1.8f %1.8f %1.8f %1.8f %1.8f %1.8f %1.8f %1.8f %d %1.8f %1.8f %1.8f\n' \
% (mGvec[0], mGvec[1], mGvec[2], \
sX, sY, \
1/sDsp, rEta, r2d*sOme, \
iSpot, \
gveXYZ[0, :], gveXYZ[1, :], gveXYZ[2, :])
# advance counter
ii += 1
# write gve file for grainspotter
f = open(gVecFName+'.gve', 'w')
print >> f, '%1.8f %1.8f %1.8f %1.8f %1.8f %1.8f ' % tuple(cellp) + \
cellString + '\n' + \
'# wavelength = %1.8f\n' % (wlen) + \
'# wedge = 0.000000\n# ds h k l\n' + \
gvecHKLString + \
'# xr yr zr xc yc ds eta omega\n' + \
gvecString
f.close()
###############################################################
# GrainSpotter ini parameters
#
# tempFNameIn = tempfile.mktemp()
if positionFit:
positionString = 'positionfit'
else:
positionString = '!positionfit'
if numTrials == 0:
randomString = '!random\n'
else:
randomString = 'random %g\n' % (numTrials)
tempFNameIn = 'tmpIni'
f = open(tempFNameIn, 'w')
# self.__tempFNameList.append(tempFNameIn)
print >> f, \
'spacegroup %d\n' % (sgNum) + \
'tthrange %g %g\n' % (tThMin, tThMax) + \
'etarange %g %g\n' % (etaMin, etaMax) + \
'domega %g\n' % (deltaOme) + \
omeRangeString + \
'filespecs %s.gve %s.log\n' % (gVecFName, tempFNameIn) + \
'cuts %d %g %g\n' % (minMeas, minCompl, minUniqn) + \
'eulerstep %g\n' % (eulStep)+ \
'uncertainties %g %g %g\n' % (uncertainty[0], uncertainty[1], uncertainty[2]) + \
'nsigmas %d\n' % (nSigmas) + \
'minfracg %g\n' % (minFracG) + \
randomString + \
positionString + '\n'
f.close()
toc = time.time()
print 'in %s, setup took %g' % (location, toc-tic)
tic = time.time()
# tempFNameStdout = tempfile.mktemp()
# self.__tempFNameList.append(tempFNameStdout)
tempFNameStdout = 'tmp.out'
# grainSpotterCmd = '%s %s > %s' % (self.__execName, tempFNameIn, tempFNameStdout)
grainSpotterCmd = '%s %s' % (self.__execName, tempFNameIn)
os.system(grainSpotterCmd)
toc = time.time()
print 'in %s, execution took %g' % (location, toc-tic)
tic = time.time()
# add output files to cleanup list
# self.__tempFNameList += glob.glob(tempFNameIn+'.*')
# collect data from gff file'
gffFile = tempFNameIn+'.gff'
gffData = num.loadtxt(gffFile)
if gffData.ndim == 1:
gffData = gffData.reshape(1, len(gffData))
gffData_U = gffData[:,6:6+9]
# process for output
retval = convertUToRotMat(gffData_U, U0, symTag=symTag)
toc = time.time()
print 'in %s, post-processing took %g' % (location, toc-tic)
tic = time.time()
return retval
