def test3(self):
'''create pure python representation of a homogeneous scatterer with
composite kernel. render the c++ computation engine of that kernel.
'''
#shape
from mccomposite.geometry import primitives
shape = primitives.block((1, 1, 1))
#kernel
nprinter = NeutronPrinter()
#composite kernel
composite_kernel = hs.compositeKernel()
composite_kernel.addElement(nprinter)
#scatterer
scatterer = hs.homogeneousScatterer(shape, composite_kernel)
#render the c++ representation
cscatterer = hs.scattererEngine(scatterer)
for i in range(10):
ev = mcni.neutron(r=(0, 0, -5), v=(0, 0, 1))
cscatterer.scatter(ev)
continue
return
def detectorcomponent(name, instrumentxml, coordinate_system, tofparams,
outfilename):
import mccomposite.extensions.Copy
import mccomposite.extensions.HollowCylinder
import mccomponents.detector.optional_extensions.Detector
from instrument.nixml import parse_file
instrument = parse_file(instrumentxml)
import instrument.geometers as ig
instrument.geometer.changeRequestCoordinateSystem(
ig.coordinateSystem(coordinate_system))
from mccomponents.detector.utils import \
getDetectorHierarchyDimensions, assignLocalGeometers
assignLocalGeometers(instrument, coordinate_system=coordinate_system)
detectorSystem = instrument.getDetectorSystem()
detectorSystem.tofparams = tofparams
dims = getDetectorHierarchyDimensions(instrument)
dims = [dim for name, dim in dims]
mca = eventModeMCA(outfilename, dims)
detectorSystem.mca = mca
import mccomponents.homogeneous_scatterer as mh
cds = mh.scattererEngine(detectorSystem,
coordinate_system=coordinate_system)
instrument.geometer = instrument.global_geometer
cds.name = name
return cds
def test1(self):
'detector hierarchy from xml'
from instrument.nixml import parse_file
instrument = parse_file('ARCS.xml')
import instrument.geometers as ig
instrument.geometer.changeRequestCoordinateSystem(
ig.coordinateSystem(coordinate_system))
assignLocalGeometers(instrument, coordinate_system=coordinate_system)
detectorSystem = instrument.getDetectorSystem()
tofparams = 0, 10e-3, 1e-4
detectorSystem.tofparams = tofparams
dims = getDetectorHierarchyDimensions(instrument)
dims = [dim for name, dim in dims]
mca = md.eventModeMCA(outfilename, dims)
detectorSystem.mca = mca
cds = mh.scattererEngine(detectorSystem,
coordinate_system=coordinate_system)
for i in range(nevents):
if i % 1000 == 0: print i
ev = mcni.neutron(r=(0, 0, 0), v=(2000, 1500, 0))
cds.scatter(ev)
continue
instrument.geometer = instrument.global_geometer
return
def test1(self):
'detector hierarchy from xml'
from instrument.nixml import parse_file
instrument = parse_file( 'ARCS.xml' )
import instrument.geometers as ig
instrument.geometer.changeRequestCoordinateSystem(
ig.coordinateSystem( coordinate_system ) )
assignLocalGeometers( instrument, coordinate_system = coordinate_system )
detectorSystem = instrument.getDetectorSystem()
tofparams = 0, 10e-3, 1e-4
detectorSystem.tofparams = tofparams
dims = getDetectorHierarchyDimensions( instrument )
dims = [ dim for name, dim in dims ]
mca = md.eventModeMCA( outfilename, dims )
detectorSystem.mca = mca
cds = mh.scattererEngine( detectorSystem, coordinate_system = coordinate_system )
for i in range(nevents):
if i%1000 == 0: print i
ev = mcni.neutron( r = (0,0,0), v = (1500,0,2000) )
cds.scatter(ev)
continue
instrument.geometer = instrument.global_geometer
return
def samplecomponent(name, sampleassembly_xml):
'''samplecomponent( name, xml ) --> sample simulation component
name: name of the sample
xml: xml file describing the sample assembly
'''
import mccomposite.extensions.HollowCylinder
import os
filename = os.path.realpath(sampleassembly_xml)
dir, filename = os.path.split(os.path.abspath(filename))
save = os.path.abspath(os.curdir)
os.chdir(dir)
from sampleassembly.saxml import parse_file
sa = parse_file(filename)
from sampleassembly_support import sampleassembly2compositescatterer, \
findkernelsfromxmls
scatterercomposite = findkernelsfromxmls(
sampleassembly2compositescatterer(sa))
os.chdir(save)
import mccomponents.homogeneous_scatterer as hs
engine = hs.scattererEngine(scatterercomposite)
engine.name = name
return engine
def test1(self):
'complex. pack, detector, pixel hierarchy'
mca = md.eventModeMCA(
outfilename,
(npacks, ndetsperpack, npixelsperdet,) )
cylinder = operations.subtract( primitives.cylinder( sample2det * 1.1, detlength ),
primitives.cylinder( sample2det * 0.9, detlength ) )
ds = md.detectorSystem( cylinder, tofparams, mca )
pack0 = makepack()
packs = [pack0]
for i in range(1, npacks):
packs.append( mccomposite.scatterercopy( pack0, id = i ) )
continue
for i in range( npacks ):
z = 0 * meter
angle = (i-packindexat0)* 5./180 * N.pi
x = sample2det * math.cos(angle)
y = sample2det * math.sin(angle)
ds.addElement( packs[i], (x,y,z) )
continue
cds = mh.scattererEngine( ds, coordinate_system = "InstrumentScientist" )
for i in range(nevents):
if i%1000 == 0: print i
ev = mcni.neutron( r = (-L1,0,0), v = (vi,0,0) )
cds.scatter(ev)
continue
return
def samplecomponent( name, sampleassembly_xml ):
'''samplecomponent( name, xml ) --> sample simulation component
name: name of the sample
xml: xml file describing the sample assembly
'''
import mccomposite.extensions.HollowCylinder
import os
filename = os.path.realpath( sampleassembly_xml )
dir, filename = os.path.split( os.path.abspath( filename ) )
save = os.path.abspath( os.curdir )
os.chdir( dir )
from sampleassembly.saxml import parse_file
sa = parse_file( filename )
from sampleassembly_support import sampleassembly2compositescatterer, \
findkernelsfromxmls
scatterercomposite = findkernelsfromxmls(
sampleassembly2compositescatterer( sa ) )
os.chdir(save)
import mccomponents.homogeneous_scatterer as hs
engine = hs.scattererEngine( scatterercomposite )
engine.name = name
return engine
def test1a(self):
from sampleassembly.saxml import parse_file
import os
dir, filename = os.path.split(sampleassembly_xml)
save = os.path.abspath(os.curdir)
os.chdir(dir)
sa = parse_file( filename )
from mccomponents.sample.sampleassembly_support \
import sampleassembly2compositescatterer, \
findkernelsfromxmls
scatterercomposite = findkernelsfromxmls(
sampleassembly2compositescatterer( sa ) )
import mccomponents.homogeneous_scatterer as hs
engine = hs.scattererEngine( scatterercomposite )
os.chdir(save)
for i in range(1000):
ev = mcni.neutron( r = (0,0,-5), v = (0,0,3000) )
engine.scatter( ev )
# print ev
continue
return
def test1a(self):
from sampleassembly.saxml import parse_file
import os
dir, filename = os.path.split(sampleassembly_xml)
save = os.path.abspath(os.curdir)
os.chdir(dir)
sa = parse_file(filename)
from mccomponents.sample.sampleassembly_support \
import sampleassembly2compositescatterer, \
findkernelsfromxmls
scatterercomposite = findkernelsfromxmls(
sampleassembly2compositescatterer(sa))
import mccomponents.homogeneous_scatterer as hs
engine = hs.scattererEngine(scatterercomposite)
os.chdir(save)
for i in range(10):
ev = mcni.neutron(r=(0, 0, -5), v=(0, 0, 3000))
engine.scatter(ev)
print ev
continue
return
def test3(self):
'''create pure python representation of a homogeneous scatterer with
composite kernel. render the c++ computation engine of that kernel.
'''
#shape
from mccomposite.geometry import primitives
shape = primitives.block( (1,1,1) )
#kernel
nprinter = NeutronPrinter( )
#composite kernel
composite_kernel = hs.compositeKernel()
composite_kernel.addElement( nprinter )
#scatterer
scatterer = hs.homogeneousScatterer(
shape, composite_kernel)
#render the c++ representation
cscatterer = hs.scattererEngine( scatterer )
for i in range(10):
ev = mcni.neutron( r = (0,0,-5), v = (0,0,1) )
cscatterer.scatter(ev)
continue
return
def makeDispersion():
from mccomponents.sample.phonon import periodicdispersion_fromidf
disp = periodicdispersion_fromidf("phonon-dispersion-fccNi-primitive-reciprocal-unitcell")
from mccomponents.homogeneous_scatterer import kernelEngine, scattererEngine
disp = scattererEngine(disp)
return disp
def test1(self):
'GridSQE'
sqe = createSqe()
gridsqe = ms.gridsqe( sqe )
cgridsqe = mh.scattererEngine( gridsqe )
Q, E = 5.05, 10.5
self.assertAlmostEqual( sqe[ Q,E ][0], sqe_f(Q,E) )
self.assertAlmostEqual( cgridsqe( Q,E ), sqe_f(Q,E) )
return
def test1(self):
'IsotropicKernel'
kernel = ms.isotropickernel( 1., 1. )
ckernel = mh.scattererEngine( kernel )
ev = mcni.neutron( r = (-5,0,0), v = (3000,0,0) )
ckernel.scatter(ev)
print ev
return
def test1(self):
'IsotropicKernel'
kernel = ms.isotropickernel(1., 1.)
ckernel = mh.scattererEngine(kernel)
ev = mcni.neutron(r=(-5, 0, 0), v=(3000, 0, 0))
ckernel.scatter(ev)
print ev
return
def test1(self):
'GridSQE'
sqe = createSqe()
gridsqe = ms.gridsqe(sqe)
cgridsqe = mh.scattererEngine(gridsqe)
Q, E = 5.05, 10.5
self.assertAlmostEqual(sqe[Q, E][0], sqe_f(Q, E))
self.assertAlmostEqual(cgridsqe(Q, E), sqe_f(Q, E))
return
def band(phonon, start, end, npts, cartesian, output, branch, output_npy):
"Given phonon data in IDF format, plot band structure along one direction"
# phonon is the path to a directory with IDF phonon data
# read phonon data
from mccomponents.sample.phonon import periodicdispersion_fromidf as pd
import mcni, numpy as np
disp = pd(phonon)
# and construct the proxy to the c++ data object
import mccomponents.homogeneous_scatterer as mh
cdisp = mh.scattererEngine(disp)
# create Q array
Qs = np.array(start) + (np.array(end) - np.array(start)) * np.arange(
0, 1, 1. / npts)[:, np.newaxis]
# Q will be cartesian
if not cartesian:
# read reciprocal basis vectors from Qgridinfo
import os
reci_basis = recibasis_fromQgridinfo(os.path.join(phonon, 'Qgridinfo'))
Qs = np.dot(Qs, reci_basis)
# compute energies
nbr = disp.dispersion.nBranches
Es = [cdisp.energy(br, mcni.vector3(*Q)) for Q in Qs for br in range(nbr)]
Es = np.array(Es)
Es.shape = -1, nbr
# output
if not output_npy:
output_npy = 'bands-start%s-end%s.npy' % (start, end)
np.save(output_npy, Es)
try:
import matplotlib as mpl
except ImportError:
import warnings
warnings.warn(
"Plotting needs matplotlib. Please install python matplotlib")
return
mpl.use("Agg")
import matplotlib.pyplot as plt
fig = plt.figure()
ax = fig.add_subplot(111)
if branch == -1:
for i in range(nbr):
ax.plot(Es[:, i])
else:
ax.plot(Es[:, branch])
if output:
fig.savefig(output)
else:
plt.show()
return
def test1(self):
'SQEkernel'
sqe = createSqe()
gridsqe = ms.gridsqe( sqe )
sqekernel = ms.sqekernel(
1., 1., 1.,
SQE=gridsqe,
Qrange=(0, 12.), Erange=(-50, 50) )
csqekernel = mh.scattererEngine( sqekernel )
ev = mcni.neutron( r = (-5,0,0), v = (3000,0,0) )
self.assertAlmostEqual( csqekernel.scattering_coefficient(ev), 1 )
self.assertAlmostEqual( csqekernel.absorption_coefficient(ev), 2200./3000. )
return
def band(phonon, start, end, npts, cartesian, output, branch):
"Given phonon data in IDF format, plot band structure along one direction"
# phonon is the path to a directory with IDF phonon data
# read phonon data
from mccomponents.sample.phonon import periodicdispersion_fromidf as pd
import mcni, numpy as np
disp = pd(phonon)
# and construct the proxy to the c++ data object
import mccomponents.homogeneous_scatterer as mh
cdisp = mh.scattererEngine(disp)
# create Q array
Qs = np.array(start) + (np.array(end)-np.array(start)) * np.arange(0, 1, 1./npts)[:, np.newaxis]
# Q will be cartesian
if not cartesian:
# read reciprocal basis vectors from Qgridinfo
import os
reci_basis = recibasis_fromQgridinfo(os.path.join(phonon, 'Qgridinfo'))
Qs = np.dot(Qs, reci_basis)
# compute energies
nbr = disp.dispersion.nBranches
Es = [cdisp.energy(br, mcni.vector3(*Q))
for Q in Qs
for br in range(nbr)]
Es = np.array(Es)
Es.shape = -1, nbr
# output
try:
import matplotlib as mpl
except ImportError:
import warnings
warnings.warn("Plotting needs matplotlib. Please install python matplotlib")
return
mpl.use("Agg")
import matplotlib.pyplot as plt
fig = plt.figure(); ax = fig.add_subplot(111)
if branch == -1:
for i in range(nbr):
ax.plot(Es[:, i])
else:
ax.plot(Es[:, branch])
if output:
fig.savefig(output)
else:
plt.show()
return
def test2(self):
'''create pure python representation of a homogeneous scatterer,
and render the c++ computation engine of that kernel
'''
from mccomposite.geometry import primitives
shape = primitives.block((1, 1, 1))
nprinter = NeutronPrinter()
scatterer = hs.homogeneousScatterer(shape, nprinter)
#render the c++ representation
cscatterer = hs.scattererEngine(scatterer)
for i in range(10):
ev = mcni.neutron(r=(0, 0, -5), v=(0, 0, 1))
cscatterer.scatter(ev)
print ev
continue
return
def test2(self):
'''create pure python representation of a homogeneous scatterer,
and render the c++ computation engine of that kernel
'''
from mccomposite.geometry import primitives
shape = primitives.block( (1,1,1) )
nprinter = NeutronPrinter( )
scatterer = hs.homogeneousScatterer(shape, nprinter)
#render the c++ representation
cscatterer = hs.scattererEngine( scatterer )
for i in range(10):
ev = mcni.neutron( r = (0,0,-5), v = (0,0,1) )
cscatterer.scatter(ev)
print ev
continue
return
def test0(self):
from sampleassembly.saxml import parse_file
sa = parse_file( sampleassembly_xml )
from mccomponents.sample.sampleassembly_support \
import sampleassembly2compositescatterer, \
findkernelsfromxmls
scatterercomposite = findkernelsfromxmls(
sampleassembly2compositescatterer( sa ) )
import mccomponents.homogeneous_scatterer as hs
engine = hs.scattererEngine( scatterercomposite )
for i in range(10):
ev = mcni.neutron( r = (0,0,-5), v = (0,0,3000) )
engine.scatter( ev )
print ev
continue
return
def makeScatterer():
import mccomponents.sample.phonon.xml
from mccomponents.sample.kernelxml import parse_file
scatterer = parse_file('fccNi-plate-scatterer-primitive-reciprocal-unitcell.xml')
kernel = scatterer.kernel()
from sampleassembly.predefined import shapes
plate = shapes.plate(width=0.04, height=0.10, thickness=0.003)
scatterer._shape = plate
from sampleassembly import elements
sample = elements.powdersample('fccNi', shape=plate)
crystal = elements.crystal(unitcell=makeUnitcell())
sample.phase = crystal
kernel.scatterer_origin = sample
from mccomponents.homogeneous_scatterer import scattererEngine
return scattererEngine(scatterer)
def test1a(self):
from sampleassembly.saxml import parse_file
sa = parse_file( sampleassembly_xml )
from mccomponents.sample.sampleassembly_support \
import sampleassembly2compositescatterer, \
findkernelsfromxmls
scatterercomposite = findkernelsfromxmls(
sampleassembly2compositescatterer( sa ) )
import mccomponents.homogeneous_scatterer as hs
engine = hs.scattererEngine( scatterercomposite )
for i in range(10):
ev = mcni.neutron( r = (0,0,-5), v = (0,0,3000) )
engine.scatter( ev )
print ev
continue
return
def makeScatterer():
import mccomponents.sample.phonon.xml
from mccomponents.sample.kernelxml import parse_file
scatterer = parse_file(
'fccNi-plate-scatterer-primitive-reciprocal-unitcell.xml')
kernel = scatterer.kernel()
from sampleassembly.predefined import shapes
plate = shapes.plate(width=0.04, height=0.10, thickness=0.003)
scatterer._shape = plate
from sampleassembly import elements
sample = elements.powdersample('fccNi', shape=plate)
crystal = elements.crystal(unitcell=makeUnitcell())
sample.phase = crystal
kernel.scatterer_origin = sample
from mccomponents.homogeneous_scatterer import scattererEngine
return scattererEngine(scatterer)
def test1(self):
'simple. one detector'
ndets = 1
cylinder = primitives.cylinder( detradius, detlength )
he3tube = md.he3tube(
cylinder, id = 0,
pressure = units.pressure.atm * pressure,
mcweights = (
absorption_weight, scattering_weight, transmission_weight)
)
mca = md.eventModeMCA( 'events.dat', (ndets,npixels,) )
ds = md.detectorSystem( cylinder, tofparams, mca )
m = units.length.meter
for i in range(npixels):
pixel = md.pixel( id = i )
he3tube.addElement(
pixel,
N.array( [0,0,(-0.495+i*0.01)] ) * m,
(0,0,0) )
continue
ds.addElement( he3tube )
cds = mh.scattererEngine( ds, coordinate_system = "InstrumentScientist" )
for i in range(nevents):
if i%1000 == 0 and interactive:
# print i
print '.',
sys.stdout.flush()
ev = mcni.neutron( r = (-L,0,0), v = (vi,0,0) )
cds.scatter(ev)
continue
return
def test1(self):
'complex. pack, detector, pixel hierarchy'
mca = md.eventModeMCA(outfilename, (
npacks,
ndetsperpack,
npixelsperdet,
))
cylinder = operations.subtract(
primitives.cylinder(sample2det * 1.1, detlength),
primitives.cylinder(sample2det * 0.9, detlength))
ds = md.detectorSystem(cylinder, tofparams, mca)
pack0 = makepack()
packs = [pack0]
for i in range(1, npacks):
packs.append(mccomposite.scatterercopy(pack0, id=i))
continue
for i in range(npacks):
z = 0 * meter
angle = (i - packindexat0) * 5. / 180 * N.pi
x = sample2det * math.cos(angle)
y = sample2det * math.sin(angle)
ds.addElement(packs[i], (x, y, z))
continue
cds = mh.scattererEngine(ds, coordinate_system="InstrumentScientist")
for i in range(nevents):
if i % 1000 == 0: print i
ev = mcni.neutron(r=(-L1, 0, 0), v=(vi, 0, 0))
cds.scatter(ev)
continue
return
def slice(crystal, phonon, start, end, npts, cartesian, outhist, eaxis):
"Given phonon data in IDF format, compute slice of SQE data along a specific reciprocal space direction"
# phonon is the path to a directory with IDF phonon data
# read phonon data
from mccomponents.sample.phonon import periodicdispersion_fromidf as pd
import mcni, numpy as np
disp = pd(phonon)
# and construct a proxy to the c++ data object
import mccomponents.homogeneous_scatterer as mh
cdisp = mh.scattererEngine(disp)
# create Q array
start = np.array(start)
end = np.array(end)
step = (end - start) / npts
Qs = start + step * np.arange(0, npts, 1.)[:, np.newaxis]
# Qs: cartesian, hkls: miller indexes
import os
reci_basis = recibasis_fromQgridinfo(os.path.join(phonon, 'Qgridinfo'))
inv_reci_basis = np.linalg.inv(reci_basis)
if cartesian:
hkls = np.dot(Qs, inv_reci_basis)
# these vectors will be used later in method Qtox
start = np.dot(start, inv_reci_basis)
step = np.dot(step, inv_reci_basis)
end = np.dot(end, inv_reci_basis)
else:
hkls = Qs
Qs = np.dot(hkls, reci_basis)
# gather energies and polarizations
nQ = len(Qs)
nbr = disp.dispersion.nBranches
natoms = disp.dispersion.nAtoms
# energies
Es = [cdisp.energy(br, mcni.vector3(*Q)) for Q in Qs for br in range(nbr)]
Es = np.array(Es)
Es.shape = nQ, nbr
# polarizations
pols = [
np.array(cdisp.polarization(br, atom, mcni.vector3(*Q))) for Q in Qs
for br in range(nbr) for atom in range(natoms)
]
pols = np.array(pols)
pols.shape = nQ, nbr, natoms, 3
# get atom positions from crystal structure file
from diffpy.Structure.Parsers import getParser
parser = getParser(os.path.splitext(crystal)[-1][1:])
structure = parser.parseFile(crystal)
atom_positions = [atom.xyz for atom in structure]
# create "events" for later histogramming process to construct slice
events = computeEvents(hkls, Es, pols, atom_positions, reci_basis)
# for x axis of the histogram (along Q)
maxx = np.linalg.norm(end - start)
xaxis = 0, maxx, maxx / npts
# Eaxis = 0, np.max(Es) * 1.1, 1.
Eaxis = eaxis
# functor to convert hkl to "x" value
from distutils.version import LooseVersion
def Qtox(hkl):
if LooseVersion(np.__version__) >= LooseVersion("1.8"):
x = np.linalg.norm(hkl - start, axis=-1)
else:
x = np.array(map(np.linalg.norm, hkl - start))
mask = x == x
return x, mask
# histogramming
h = makeSlice(events, xaxis, Eaxis, Qtox)
# output
import histogram.hdf as hh
hh.dump(h, outhist)
return
def makeDispersion():
from mccomponents.sample.phonon import periodicdispersion_fromidf
disp = periodicdispersion_fromidf('phonon-dispersion-fccNi-primitive-reciprocal-unitcell')
from mccomponents.homogeneous_scatterer import kernelEngine, scattererEngine
disp = scattererEngine(disp)
return disp
def makeDispersion():
from mccomponents.sample.phonon import periodicdispersion_fromidf
disp = periodicdispersion_fromidf(dispersion_dir)
from mccomponents.homogeneous_scatterer import kernelEngine, scattererEngine
disp = scattererEngine(disp)
return disp
def slice(crystal, phonon, start, end, npts, cartesian, outhist, eaxis):
"Given phonon data in IDF format, compute slice of SQE data along a specific reciprocal space direction"
# phonon is the path to a directory with IDF phonon data
# read phonon data
from mccomponents.sample.phonon import periodicdispersion_fromidf as pd
import mcni, numpy as np
disp = pd(phonon)
# and construct a proxy to the c++ data object
import mccomponents.homogeneous_scatterer as mh
cdisp = mh.scattererEngine(disp)
# create Q array
start = np.array(start)
end = np.array(end)
step = (end-start)/npts
Qs = start + step * np.arange(0, npts, 1.)[:, np.newaxis]
# Qs: cartesian, hkls: miller indexes
import os
reci_basis = recibasis_fromQgridinfo(os.path.join(phonon, 'Qgridinfo'))
inv_reci_basis = np.linalg.inv(reci_basis)
if cartesian:
hkls = np.dot(Qs, inv_reci_basis)
# these vectors will be used later in method Qtox
start = np.dot(start, inv_reci_basis)
step = np.dot(step, inv_reci_basis)
end = np.dot(end, inv_reci_basis)
else:
hkls = Qs
Qs = np.dot(hkls, reci_basis)
# gather energies and polarizations
nQ = len(Qs)
nbr = disp.dispersion.nBranches
natoms = disp.dispersion.nAtoms
# energies
Es = [cdisp.energy(br, mcni.vector3(*Q))
for Q in Qs
for br in range(nbr)
]
Es = np.array(Es)
Es.shape = nQ, nbr
# polarizations
pols = [
np.array(cdisp.polarization(br, atom, mcni.vector3(*Q)))
for Q in Qs
for br in range(nbr)
for atom in range(natoms)
]
pols = np.array(pols)
pols.shape = nQ, nbr, natoms, 3
# get atom positions from crystal structure file
from danse.ins.matter.Parsers import getParser
parser = getParser(os.path.splitext(crystal)[-1][1:])
structure = parser.parseFile(crystal)
atom_positions = [atom.xyz for atom in structure]
# create "events" for later histogramming process to construct slice
events = computeEvents(hkls, Es, pols, atom_positions, reci_basis)
# for x axis of the histogram (along Q)
maxx = np.linalg.norm(end-start)
xaxis = 0, maxx, maxx/npts
# Eaxis = 0, np.max(Es) * 1.1, 1.
Eaxis = eaxis
# functor to convert hkl to "x" value
from distutils.version import LooseVersion
def Qtox(hkl):
if LooseVersion(np.__version__) >= LooseVersion("1.8"):
x = np.linalg.norm(hkl-start, axis=-1)
else:
x = np.array(map(np.linalg.norm, hkl-start))
mask = x==x
return x, mask
# histogramming
h = makeSlice(events, xaxis, Eaxis, Qtox)
# output
import histogram.hdf as hh
hh.dump(h, outhist)
return
