axis = np.array([ 0.66931818,-0.98578066,0.73593251]) rMat1 = xf.makeBinaryRotMat(axis) rMat2 = xfcapi.makeBinaryRotMat(axis) print "makeBinaryRotMat results match: ",np.linalg.norm(rMat1-rMat2)/np.linalg.norm(rMat1) < epsf bHat = np.array([0.0,0.0,-1.0]) eta = np.array([1.0,0.0,0.0]) rMat1 = xf.makeEtaFrameRotMat(bHat,eta) rMat2 = xfcapi.makeEtaFrameRotMat(bHat,eta) print "makeEtaFrameRotMat results match: ",np.linalg.norm(rMat1-rMat2)/np.linalg.norm(rMat1) < epsf angles = np.array([random.uniform(-np.pi,np.pi),random.uniform(-np.pi,np.pi),random.uniform(-np.pi,np.pi)]) aMin = np.array([random.uniform(-np.pi,np.pi),random.uniform(-np.pi,np.pi)]) aMax = np.array([random.uniform(-np.pi,np.pi),random.uniform(-np.pi,np.pi)]) va1 = xf.validateAngleRanges(angles,aMin,aMax) va2 = xfcapi.validateAngleRanges(angles,aMin,aMax) print angles print aMin,aMax print va1,va2 print "validateAngleRanges results match: ",np.array_equiv(va1,va2) angle = np.array([0.1]) axis = np.array([[ 0.47792,-0.703887,0.525486]]) axis /= np.linalg.norm(axis) vecs = np.array([[ 1.0, 2.0, 3.0]]) rVec1 = xf.rotate_vecs_about_axis(angle,axis.T,vecs.T) rVec2 = xfcapi.rotate_vecs_about_axis(angle,axis,vecs) print "rotate_vecs_about_axis results match: ",np.linalg.norm(rVec1.T-rVec2)/np.linalg.norm(rVec1) < epsf
def paintGridThis(quat):
"""
"""
# pull local vars from globals set in paintGrid
global symHKLs_MP, wavelength_MP
global omeMin_MP, omeMax_MP, omeTol_MP
global etaMin_MP, etaMax_MP, etaTol_MP
global omeIndices_MP, etaIndices_MP
global omeEdges_MP, etaEdges_MP
global hklList_MP, hklIDs_MP
global etaOmeMaps_MP
global bMat_MP
global threshold_MP
symHKLs = symHKLs_MP
wavelength = wavelength_MP
hklIDs = hklIDs_MP
hklList = hklList_MP
omeMin = omeMin_MP
omeMax = omeMax_MP
omeTol = omeTol_MP
omeIndices = omeIndices_MP
omeEdges = omeEdges_MP
etaMin = etaMin_MP
etaMax = etaMax_MP
etaTol = etaTol_MP
etaIndices = etaIndices_MP
etaEdges = etaEdges_MP
etaOmeMaps = etaOmeMaps_MP
bMat = bMat_MP
threshold = threshold_MP
# need this for proper index generation
omegas = [omeEdges[0] + (i+0.5)*(omeEdges[1] - omeEdges[0]) for i in range(len(omeEdges) - 1)]
etas = [etaEdges[0] + (i+0.5)*(etaEdges[1] - etaEdges[0]) for i in range(len(etaEdges) - 1)]
delOmeSign = num.sign(omegas[1] - omegas[0])
del_ome = abs(omegas[1] - omegas[0])
del_eta = abs(etas[1] - etas[0])
dpix_ome = round(omeTol / del_ome)
dpix_eta = round(etaTol / del_eta)
debug = False
if debug:
print "using ome, eta dilitations of (%d, %d) pixels" % (dpix_ome, dpix_eta)
nHKLs = len(hklIDs)
rMat = rotMatOfQuat(quat)
nPredRefl = 0
nMeasRefl = 0
reflInfoList = []
dummySpotInfo = num.nan * num.ones(3)
hklCounterP = 0 # running count of excpected (predicted) HKLs
hklCounterM = 0 # running count of "hit" HKLs
for iHKL in range(nHKLs):
# select and C-ify symmetric HKLs
these_hkls = num.array(symHKLs[hklIDs[iHKL]].T, dtype=float, order='C')
# oscillation angle arrays
oangs = xfcapi.oscillAnglesOfHKLs(these_hkls, 0., rMat, bMat, wavelength)
angList = num.vstack(oangs)
if not num.all(num.isnan(angList)):
angList[:, 1] = xf.mapAngle(angList[:, 1])
angList[:, 2] = xf.mapAngle(angList[:, 2])
if omeMin is None:
omeMin = [-num.pi, ]
omeMax = [ num.pi, ]
if etaMin is None:
etaMin = [-num.pi, ]
etaMax = [ num.pi, ]
angMask = num.logical_and(
xf.validateAngleRanges(angList[:, 1], etaMin, etaMax),
xf.validateAngleRanges(angList[:, 2], omeMin, omeMax))
allAngs_m = angList[angMask, :]
# not output # # duplicate HKLs
# not output # allHKLs_m = num.vstack([these_hkls, these_hkls])[angMask, :]
culledTTh = allAngs_m[:, 0]
culledEta = allAngs_m[:, 1]
culledOme = allAngs_m[:, 2]
# not output # culledHKLs = allHKLs_m.T
nThisPredRefl = len(culledTTh)
hklCounterP += nThisPredRefl
for iTTh in range(nThisPredRefl):
culledEtaIdx = num.where(etaEdges - culledEta[iTTh] > 0)[0]
if len(culledEtaIdx) > 0:
culledEtaIdx = culledEtaIdx[0] - 1
if culledEtaIdx < 0:
culledEtaIdx = None
else:
culledEtaIdx = None
culledOmeIdx = num.where(omeEdges - culledOme[iTTh] > 0)[0]
if len(culledOmeIdx) > 0:
if delOmeSign > 0:
culledOmeIdx = culledOmeIdx[0] - 1
else:
culledOmeIdx = culledOmeIdx[-1]
if culledOmeIdx < 0:
culledOmeIdx = None
else:
culledOmeIdx = None
if culledEtaIdx is not None and culledOmeIdx is not None:
if dpix_ome > 0 or dpix_eta > 0:
i_dil, j_dil = num.meshgrid(num.arange(-dpix_ome, dpix_ome + 1),
num.arange(-dpix_eta, dpix_eta + 1))
i_sup = omeIndices[culledOmeIdx] + num.array([i_dil.flatten()], dtype=int)
j_sup = etaIndices[culledEtaIdx] + num.array([j_dil.flatten()], dtype=int)
# catch shit that falls off detector...
# ...maybe make this fancy enough to wrap at 2pi?
i_max, j_max = etaOmeMaps[iHKL].shape
idx_mask = num.logical_and(num.logical_and(i_sup >= 0, i_sup < i_max),
num.logical_and(j_sup >= 0, j_sup < j_max))
pixelVal = etaOmeMaps[iHKL][i_sup[idx_mask], j_sup[idx_mask]]
else:
pixelVal = etaOmeMaps[iHKL][omeIndices[culledOmeIdx], etaIndices[culledEtaIdx] ]
isHit = num.any(pixelVal >= threshold[iHKL])
if isHit:
hklCounterM += 1
pass
pass
# disabled # if debug:
# disabled # print "hkl %d -->\t%d\t%d\t%d\t" % (iHKL, culledHKLs[0, iTTh], culledHKLs[1, iTTh], culledHKLs[2, iTTh]) + \
# disabled # "isHit=%d\tpixel value: %g\n" % (isHit, pixelVal) + \
# disabled # "eta index: %d,%d\tetaP: %g\n" % (culledEtaIdx, etaIndices[culledEtaIdx], r2d*culledEta[iTTh]) + \
# disabled # "ome index: %d,%d\tomeP: %g\n" % (culledOmeIdx, omeIndices[culledOmeIdx], r2d*culledOme[iTTh])
# disabled # pass
pass # close conditional on valid reflections
pass # close loop on signed reflections
pass # close loop on HKL
if hklCounterP == 0:
retval = 0.
else:
retval = float(hklCounterM) / float(hklCounterP)
return retval
def paintGridThis(quat):
"""
"""
# pull local vars from globals set in paintGrid
global symHKLs_MP, wavelength_MP
global omeMin_MP, omeMax_MP, omeTol_MP, omePeriod_MP
global etaMin_MP, etaMax_MP, etaTol_MP
global omeIndices_MP, etaIndices_MP
global omeEdges_MP, etaEdges_MP
global hklList_MP, hklIDs_MP
global etaOmeMaps_MP
global bMat_MP
global threshold_MP
symHKLs = symHKLs_MP
wavelength = wavelength_MP
hklIDs = hklIDs_MP
hklList = hklList_MP
omeMin = omeMin_MP
omeMax = omeMax_MP
omeTol = omeTol_MP
omePeriod = omePeriod_MP
omeIndices = omeIndices_MP
omeEdges = omeEdges_MP
etaMin = etaMin_MP
etaMax = etaMax_MP
etaTol = etaTol_MP
etaIndices = etaIndices_MP
etaEdges = etaEdges_MP
etaOmeMaps = etaOmeMaps_MP
bMat = bMat_MP
threshold = threshold_MP
# need this for proper index generation
omegas = [
omeEdges[0] + (i + 0.5) * (omeEdges[1] - omeEdges[0])
for i in range(len(omeEdges) - 1)
]
etas = [
etaEdges[0] + (i + 0.5) * (etaEdges[1] - etaEdges[0])
for i in range(len(etaEdges) - 1)
]
delOmeSign = num.sign(omegas[1] - omegas[0])
del_ome = abs(omegas[1] - omegas[0])
del_eta = abs(etas[1] - etas[0])
dpix_ome = round(omeTol / del_ome)
dpix_eta = round(etaTol / del_eta)
debug = False
if debug:
print "using ome, eta dilitations of (%d, %d) pixels" % (dpix_ome,
dpix_eta)
nHKLs = len(hklIDs)
rMat = rotMatOfQuat(quat)
nPredRefl = 0
nMeasRefl = 0
reflInfoList = []
dummySpotInfo = num.nan * num.ones(3)
hklCounterP = 0 # running count of excpected (predicted) HKLs
hklCounterM = 0 # running count of "hit" HKLs
for iHKL in range(nHKLs):
# select and C-ify symmetric HKLs
these_hkls = num.array(symHKLs[hklIDs[iHKL]].T, dtype=float, order='C')
# oscillation angle arrays
oangs = xfcapi.oscillAnglesOfHKLs(these_hkls, 0., rMat, bMat,
wavelength)
angList = num.vstack(oangs)
if not num.all(num.isnan(angList)):
idx = -num.isnan(angList[:, 0])
angList = angList[idx, :]
angList[:, 1] = xf.mapAngle(angList[:, 1])
angList[:, 2] = xf.mapAngle(angList[:, 2], omePeriod)
if omeMin is None:
omeMin = [
-num.pi,
]
omeMax = [
num.pi,
]
if etaMin is None:
etaMin = [
-num.pi,
]
etaMax = [
num.pi,
]
angMask = num.logical_and(
xf.validateAngleRanges(angList[:, 1], etaMin, etaMax),
xf.validateAngleRanges(angList[:, 2], omeMin, omeMax))
allAngs_m = angList[angMask, :]
# not output # # duplicate HKLs
# not output # allHKLs_m = num.vstack([these_hkls, these_hkls])[angMask, :]
culledTTh = allAngs_m[:, 0]
culledEta = allAngs_m[:, 1]
culledOme = allAngs_m[:, 2]
# not output # culledHKLs = allHKLs_m.T
nThisPredRefl = len(culledTTh)
hklCounterP += nThisPredRefl
for iTTh in range(nThisPredRefl):
culledEtaIdx = num.where(etaEdges - culledEta[iTTh] > 0)[0]
if len(culledEtaIdx) > 0:
culledEtaIdx = culledEtaIdx[0] - 1
if culledEtaIdx < 0:
culledEtaIdx = None
else:
culledEtaIdx = None
culledOmeIdx = num.where(omeEdges - culledOme[iTTh] > 0)[0]
if len(culledOmeIdx) > 0:
if delOmeSign > 0:
culledOmeIdx = culledOmeIdx[0] - 1
else:
culledOmeIdx = culledOmeIdx[-1]
if culledOmeIdx < 0:
culledOmeIdx = None
else:
culledOmeIdx = None
if culledEtaIdx is not None and culledOmeIdx is not None:
if dpix_ome > 0 or dpix_eta > 0:
i_dil, j_dil = num.meshgrid(
num.arange(-dpix_ome, dpix_ome + 1),
num.arange(-dpix_eta, dpix_eta + 1))
i_sup = omeIndices[culledOmeIdx] + num.array(
[i_dil.flatten()], dtype=int)
j_sup = etaIndices[culledEtaIdx] + num.array(
[j_dil.flatten()], dtype=int)
# catch shit that falls off detector...
# ...maybe make this fancy enough to wrap at 2pi?
i_max, j_max = etaOmeMaps[iHKL].shape
idx_mask = num.logical_and(
num.logical_and(i_sup >= 0, i_sup < i_max),
num.logical_and(j_sup >= 0, j_sup < j_max))
pixelVal = etaOmeMaps[iHKL][i_sup[idx_mask],
j_sup[idx_mask]]
else:
pixelVal = etaOmeMaps[iHKL][omeIndices[culledOmeIdx],
etaIndices[culledEtaIdx]]
isHit = num.any(pixelVal >= threshold[iHKL])
if isHit:
hklCounterM += 1
pass
pass
# disabled # if debug:
# disabled # print "hkl %d -->\t%d\t%d\t%d\t" % (iHKL, culledHKLs[0, iTTh], culledHKLs[1, iTTh], culledHKLs[2, iTTh]) + \
# disabled # "isHit=%d\tpixel value: %g\n" % (isHit, pixelVal) + \
# disabled # "eta index: %d,%d\tetaP: %g\n" % (culledEtaIdx, etaIndices[culledEtaIdx], r2d*culledEta[iTTh]) + \
# disabled # "ome index: %d,%d\tomeP: %g\n" % (culledOmeIdx, omeIndices[culledOmeIdx], r2d*culledOme[iTTh])
# disabled # pass
pass # close conditional on valid reflections
pass # close loop on signed reflections
pass # close loop on HKL
if hklCounterP == 0:
retval = 0.
else:
retval = float(hklCounterM) / float(hklCounterP)
return retval
bHat = np.array([0.0, 0.0, -1.0])
eta = np.array([1.0, 0.0, 0.0])
rMat1 = xf.makeEtaFrameRotMat(bHat, eta)
rMat2 = xfcapi.makeEtaFrameRotMat(bHat, eta)
print "makeEtaFrameRotMat results match: ", np.linalg.norm(
rMat1 - rMat2) / np.linalg.norm(rMat1) < epsf
angles = np.array([
random.uniform(-np.pi, np.pi),
random.uniform(-np.pi, np.pi),
random.uniform(-np.pi, np.pi)
])
aMin = np.array([random.uniform(-np.pi, np.pi), random.uniform(-np.pi, np.pi)])
aMax = np.array([random.uniform(-np.pi, np.pi), random.uniform(-np.pi, np.pi)])
va1 = xf.validateAngleRanges(angles, aMin, aMax)
va2 = xfcapi.validateAngleRanges(angles, aMin, aMax)
print angles
print aMin, aMax
print va1, va2
print "validateAngleRanges results match: ", np.array_equiv(va1, va2)
angle = np.array([0.1])
axis = np.array([[0.47792, -0.703887, 0.525486]])
axis /= np.linalg.norm(axis)
vecs = np.array([[1.0, 2.0, 3.0]])
rVec1 = xf.rotate_vecs_about_axis(angle, axis.T, vecs.T)
rVec2 = xfcapi.rotate_vecs_about_axis(angle, axis, vecs)
print "rotate_vecs_about_axis results match: ", np.linalg.norm(
rVec1.T - rVec2) / np.linalg.norm(rVec1) < epsf
def paintGridThis(quat):
"""
"""
# Unpack common parameters into locals
symHKLs = paramMP['symHKLs']
symHKLs_ix = paramMP['symHKLs_ix']
wavelength = paramMP['wavelength']
hklList = paramMP['hklList']
omeMin = paramMP['omeMin']
omeMax = paramMP['omeMax']
omeTol = paramMP['omeTol']
omePeriod = paramMP['omePeriod']
omeIndices = paramMP['omeIndices']
omeEdges = paramMP['omeEdges']
etaMin = paramMP['etaMin']
etaMax = paramMP['etaMax']
etaTol = paramMP['etaTol']
etaIndices = paramMP['etaIndices']
etaEdges = paramMP['etaEdges']
etaOmeMaps = paramMP['etaOmeMaps']
bMat = paramMP['bMat']
threshold = paramMP['threshold']
# need this for proper index generation
delOmeSign = num.sign(omeEdges[1] - omeEdges[0])
del_ome = abs(omeEdges[1] - omeEdges[0])
del_eta = abs(etaEdges[1] - etaEdges[0])
dpix_ome = round(omeTol / del_ome)
dpix_eta = round(etaTol / del_eta)
debug = False
if debug:
print "using ome, eta dilitations of (%d, %d) pixels" \
% (dpix_ome, dpix_eta)
nHKLs = len(symHKLs_ix) - 1
rMat = rotMatOfQuat(quat)
nPredRefl = 0
nMeasRefl = 0
reflInfoList = []
dummySpotInfo = num.nan * num.ones(3)
# Compute the oscillation angles of all the symHKLs at once
oangs_pair = xfcapi.oscillAnglesOfHKLs(
symHKLs, 0., rMat, bMat, wavelength)
# Interleave the two produced oang solutions to simplify later processing
oangs = num.empty((len(symHKLs)*2, 3), dtype=oangs_pair[0].dtype)
oangs[0::2] = oangs_pair[0]
oangs[1::2] = oangs_pair[1]
# Map all of the angles at once
oangs[:, 1] = xf.mapAngle(oangs[:, 1])
oangs[:, 2] = xf.mapAngle(oangs[:, 2], omePeriod)
# Create a mask of the good ones
oangMask = num.logical_and(
~num.isnan(oangs[:, 0]),
num.logical_and(
xf.validateAngleRanges(oangs[:, 1], etaMin, etaMax),
xf.validateAngleRanges(oangs[:, 2], omeMin, omeMax)))
hklCounterP = 0 # running count of excpected (predicted) HKLs
hklCounterM = 0 # running count of "hit" HKLs
for iHKL in range(nHKLs):
start, stop = symHKLs_ix[iHKL:iHKL+2]
start, stop = (2*start, 2*stop)
angList = oangs[start:stop]
angMask = oangMask[start:stop]
allAngs_m = angList[angMask, :]
if len(allAngs_m) > 0:
# not output # # duplicate HKLs
# not output # allHKLs_m = num.vstack(
# [these_hkls, these_hkls]
# )[angMask, :]
culledTTh = allAngs_m[:, 0]
culledEta = allAngs_m[:, 1]
culledOme = allAngs_m[:, 2]
# not output # culledHKLs = allHKLs_m.T
nThisPredRefl = len(culledTTh)
hklCounterP += nThisPredRefl
for iTTh in range(nThisPredRefl):
culledEtaIdx = num.where(etaEdges - culledEta[iTTh] > 0)[0]
if len(culledEtaIdx) > 0:
culledEtaIdx = culledEtaIdx[0] - 1
if culledEtaIdx < 0:
culledEtaIdx = None
else:
culledEtaIdx = None
culledOmeIdx = num.where(omeEdges - culledOme[iTTh] > 0)[0]
if len(culledOmeIdx) > 0:
if delOmeSign > 0:
culledOmeIdx = culledOmeIdx[0] - 1
else:
culledOmeIdx = culledOmeIdx[-1]
if culledOmeIdx < 0:
culledOmeIdx = None
else:
culledOmeIdx = None
if culledEtaIdx is not None and culledOmeIdx is not None:
if dpix_ome > 0 or dpix_eta > 0:
i_dil, j_dil = _meshgrid2d(
num.arange(-dpix_ome, dpix_ome + 1),
num.arange(-dpix_eta, dpix_eta + 1)
)
i_sup = omeIndices[culledOmeIdx] + num.array(
[i_dil.flatten()], dtype=int
)
j_sup = etaIndices[culledEtaIdx] + num.array(
[j_dil.flatten()], dtype=int
)
# catch shit that falls off detector...
# ...maybe make this fancy enough to wrap at 2pi?
i_max, j_max = etaOmeMaps[iHKL].shape
idx_mask = num.logical_and(
num.logical_and(i_sup >= 0, i_sup < i_max),
num.logical_and(j_sup >= 0, j_sup < j_max)
)
pixelVal = etaOmeMaps[iHKL][
i_sup[idx_mask], j_sup[idx_mask]
]
else:
pixelVal = etaOmeMaps[iHKL][
omeIndices[culledOmeIdx], etaIndices[culledEtaIdx]
]
isHit = num.any(pixelVal >= threshold[iHKL])
if isHit:
hklCounterM += 1
# if debug:
# print "hkl %d -->\t%d\t%d\t%d\t" % (
# iHKL, culledHKLs[0, iTTh], culledHKLs[1, iTTh],
# culledHKLs[2, iTTh]
# ) \
# + "isHit=%d\tpixel value: %g\n" % (isHit, pixelVal) \
# + "eta index: %d,%d\tetaP: %g\n" % (
# culledEtaIdx, etaIndices[culledEtaIdx],
# r2d*culledEta[iTTh]
# ) \
# + "ome index: %d,%d\tomeP: %g\n" % (
# culledOmeIdx, omeIndices[culledOmeIdx],
# r2d*culledOme[iTTh]
# )
#
# close conditional on valid reflections
# close loop on signed reflections
# close loop on HKL
if hklCounterP == 0:
retval = 0.
else:
retval = float(hklCounterM) / float(hklCounterP)
return retval
