def get_histogram(monitor):
from mcstas2.utils.carray import bpptr2npyarr
core = monitor.core()
nx = core.nx
ny = core.ny
n = nx * ny
shape = nx, ny
# xmin = core.x_min; xmax = core.x_max
# ymin = core.y_min; ymax = core.y_max
xmin = attr(core, "xmin", "x_min")
xmax = attr(core, "xmax", "x_max")
ymin = attr(core, "ymin", "y_min")
ymax = attr(core, "ymax", "y_max")
dx = (xmax - xmin) / nx
dy = (ymax - ymin) / ny
Iarr = bpptr2npyarr(core.getPSD_p_00(), 'double', n).copy()
E2arr = bpptr2npyarr(core.getPSD_p2_00(), 'double', n).copy()
Iarr.shape = E2arr.shape = shape
from histogram import histogram, axis, arange
xaxis = axis('x', arange(xmin, xmax, dx))
yaxis = axis('y', arange(ymin, ymax, dy))
h = histogram('I(x,y)', [xaxis, yaxis], data=Iarr, errors=E2arr)
return h
def get_histogram( monitor ):
from mcstas2.utils.carray import bpptr2npyarr
core = monitor.core()
xmin = 0; xmax = 1
ymin = 0; ymax = 1
dx = 0.1
dy = 0.1
# xmin = core.xmin; xmax = core.xmax
# ymin = core.ymin; ymax = core.ymax
# dx = xmax - xmin
# dy = ymax - ymin
# OUTPUT PARAMETERS (DEFS, Vars)
#Iarr = bpptr2npyarr( core.getDEFS( ), 'double', n ).copy() #?
#E2arr = bpptr2npyarr( core.getPSD_p2_00( ), 'double', n ).copy()
#Iarr.shape = E2arr.shape = shape
from histogram import histogram, axis, arange
xaxis = axis( 'x', arange( xmin, xmax, dx ) )
yaxis = axis( 'y', arange( ymin, ymax, dy ) )
h = histogram( 'I(x,y)', [xaxis,yaxis], data = [2,yaxis], errors=[2,yaxis]) #Iarr) #, errors = E2arr )
return h
def get_histogram(monitor):
from mcstas2.utils.carray import bpptr2npyarr
core = monitor.core()
xmin = 0
xmax = 1
ymin = 0
ymax = 1
dx = 0.1
dy = 0.1
# xmin = core.xmin; xmax = core.xmax
# ymin = core.ymin; ymax = core.ymax
# dx = xmax - xmin
# dy = ymax - ymin
# OUTPUT PARAMETERS (DEFS, Vars)
#Iarr = bpptr2npyarr( core.getDEFS( ), 'double', n ).copy() #?
#E2arr = bpptr2npyarr( core.getPSD_p2_00( ), 'double', n ).copy()
#Iarr.shape = E2arr.shape = shape
from histogram import histogram, axis, arange
xaxis = axis('x', arange(xmin, xmax, dx))
yaxis = axis('y', arange(ymin, ymax, dy))
h = histogram('I(x,y)', [xaxis, yaxis], data=[2, yaxis],
errors=[2, yaxis]) #Iarr) #, errors = E2arr )
return h
def process(path):
basename = os.path.basename(path)
from nslice.Run import Run
run = Run(path)
print "instrument=%s, Ei=%s, psi=%s" % (
run.instrument, run.Ei, run.psi)
from nslice.XtalOrientation import XtalOrientation
a = b = 8.87; c = 5.2
from math import pi
twopi = 2*pi
ra,rb,rc = [twopi/a, 0,0], [0,twopi/b,0], [0,0,twopi/c]
u,v = [1,0,0], [0,1,0]
xtal_ori = XtalOrientation(ra,rb,rc, u,v, run.psi)
h,k,l,E = run.compute_hklE(xtal_ori)
I, error = run.read_data()
h.shape = k.shape = l.shape = E.shape = I.shape = error.shape = -1
hklEIE = np.vstack((h,k,l,E,I,error))
from nslice.slice import slice_hE
H, edges = slice_hE(
hklEIE,
k=[0.95,1.05], l=[-1,1],
h=(-1, 6, 0.02), E=(-5, 10, 0.1),
)
import histogram, histogram.hdf as hh
axes = [
histogram.axis('h', boundaries=edges[0]),
histogram.axis('E', unit='meV', boundaries=edges[1]),
]
h = histogram.histogram('I(h,E)', axes=axes, data=H)
hh.dump(h, 'I_hE.h5')
return
def events2Idpt( events, instrument, tofparams ):
from mccomponents.detector.utils import \
getDetectorHierarchyDimensions
dims = getDetectorHierarchyDimensions( instrument )
# 1st attempt to create axes
from histogram import histogram, axis, arange
axes = [ axis('%sID' % name.lower(), range(n)) for name, n in dims ]
# the first level of detectors (tubes, packs, or others) need
# special attention. ids of that level could be not continuous.
detectorSystem = instrument.getDetectorSystem()
assert len(detectorSystem.elements()) == dims[0][1]
ids = [ element.id() for element in detectorSystem.elements() ]
axes[0] = axis( axes[0].name(), ids )
detaxes = axes
#tof axis
tmin, tmax, tstep = tofparams
tofaxis = axis( 'tof', boundaries = arange( tmin, tmax+tstep/10., tstep ), unit = 'second' )
#all axes
axes = detaxes + [tofaxis]
#histogram
hist = histogram( 'Idpt', axes )
#get the numpy array which will accept events
npixels = hist.size()/tofaxis.size()
Ipixtof = hist.data().storage().asNumarray()
Ipixtof.shape = npixels, -1
events2Ipixtof( events, Ipixtof )
return hist
def computeVolume(self, paths=None, **kwds):
H = None
sa = None
edges = None
for path in paths or self.paths:
print path
edges1, H1, sa1 = self.computeVolumeForOneRun(path, **kwds)
if H is None:
edges, H, sa = edges1, H1, sa1
else:
H += H1
sa += sa1
continue
import histogram
axes = [
histogram.axis(kwds['x'], boundaries=edges[0]),
histogram.axis(kwds['y'], boundaries=edges[1]),
histogram.axis(kwds['z'], boundaries=edges[2]),
]
return histogram.histogram(
'I(%(x)s,%(y)s,%(z)s)' % kwds,
axes=axes,
data=H / sa,
)
def makeSlice(events, xaxis, Eaxis, Qtox):
"""convert input events into a histogram (slice)
Qtox:
convert Q to x. also return a mask. since some Q points should be
discarded
"""
import numpy as np
data = np.array(list(events))
# convert Q to x
Q = data[:, :3]
x, mask = Qtox(Q)
E = data[mask, 3]
sample = np.vstack((x, E)).T
#
xbins = np.arange(*xaxis)
Ebins = np.arange(*Eaxis)
bins = xbins, Ebins
weights = data[mask, -1]
I, edges = np.histogramdd(sample, bins=bins, weights=weights)
import histogram as H, histogram.hdf as hh
axes = [
H.axis('x', boundaries=edges[0]),
H.axis('E', boundaries=edges[1]),
]
return H.histogram('IxE', axes=axes, data=I)
def get_histogram( monitor ):
from mcstas2.utils.carray import bpptr2npyarr
core = monitor.core()
nx = core.nxchan; ny =core.nychan; nb = core.nbchan
n = nx * ny * nb
shape = nx, ny, nb
xmin = -core.xwidth/2; xmax = core.xwidth/2
ymin = -core.yheight/2; ymax = core.yheight/2
dx = (xmax - xmin)/nx
dy = (ymax - ymin)/ny
if core.bmax!=0:
bmax=core.bmax
bmin=core.bmin
db=(bmax-bmin)/nb
else :
db = core.deltab
bmin=0;
bmax=nb*db+bmin
Iarr = bpptr2npyarr( core.getTOF_p_00( ), 'double', n ).copy()
E2arr = bpptr2npyarr( core.getTOF_p2_00( ), 'double', n ).copy()
Iarr.shape = E2arr.shape = shape
from histogram import histogram, axis, arange
xaxis = axis( 'x', boundaries=arange( xmin, xmax+dx/10, dx ) )
yaxis = axis( 'y', boundaries=arange( ymin, ymax+dy/10, dy ) )
baxis = axis( 'b', boundaries=arange( bmin, bmax+db/10, db ) )
h = histogram(
'I(x,y,b)', [xaxis,yaxis,baxis],
data = Iarr, errors = E2arr )
return h
def load_mcvine_psf_qE(self, adjust_energy_center=False):
path = self.sim_path
qaxis = self.qaxis; Eaxis = self.Eaxis
dEs = np.load(os.path.join(path, 'dEs.npy'))
dqs = np.load(os.path.join(path, 'dxs.npy'))
probs = np.load(os.path.join(path, 'probs.npy'))
hist, qedges, Eedges = np.histogram2d(dqs, dEs, bins=(np.arange(*qaxis), np.arange(*Eaxis)), weights=probs)
# remove outliers
median = np.median(hist[hist>0])
normal = hist[hist<median*100]; normal_max = np.max(normal)
hist[hist>median*100] = normal_max
# adjust energy center
if adjust_energy_center:
hist_E = hist.sum(axis=0)
Ebincenters = (Eedges[1:] + Eedges[:-1])/2
Ecenter = (Ebincenters*hist_E).sum()/hist_E.sum()
Eedges -= Ecenter
# res(q, E) histogram
qaxis = H.axis('q', boundaries=qedges)
Eaxis = H.axis('E', boundaries=Eedges)
self.mcvine_psf_qE = reshist = H.histogram('res', (qaxis, Eaxis), data=hist)
self.qEgrids = np.meshgrid(reshist.q, reshist.E)
# res(E) histogram
self.mcvine_psf_E = reshist.sum('q')
# res(q) histogram
Emin = Eedges[0]; Emax = Eedges[-1]; middle = (Emin+Emax)/2; Erange = Emax-Emin
self.mcvine_psf_q = reshist[(), (middle-Erange/20, middle+Erange/20)].sum('E')
return
def sqehist(E, g, **kwds):
"a simple wrapper of method sqe to return a histogram"
Q,E,S = sqe(E,g, **kwds)
import histogram as H
Qaxis = H.axis('Q', Q, '1./angstrom')
Eaxis = H.axis('E', E, 'meV')
return H.histogram("SP SQE", [Qaxis, Eaxis], S)
def makeSlice(events, xaxis, Eaxis, Qtox):
"""convert input events into a histogram (slice)
Qtox:
convert Q to x. also return a mask. since some Q points should be
discarded
"""
import numpy as np
data = np.array(list(events))
# convert Q to x
Q = data[:, :3]
x,mask = Qtox(Q)
E = data[mask, 3]
sample = np.vstack((x, E)).T
#
xbins = np.arange(*xaxis)
Ebins = np.arange(*Eaxis)
bins = xbins, Ebins
weights = data[mask, -1]
I, edges = np.histogramdd(sample, bins=bins, weights=weights)
import histogram as H, histogram.hdf as hh
axes = [
H.axis('x', boundaries=edges[0]),
H.axis('E', boundaries=edges[1]),
]
return H.histogram('IxE', axes=axes, data = I)
def get_histogram(monitor):
from mcstas2.utils.carray import bpptr2npyarr
core = monitor.core()
nx = core.nx
ny = core.ny
assert nx == int(nx)
nx = int(nx)
assert ny == int(ny)
ny = int(ny)
n = nx * ny
shape = nx, ny
Iarr = bpptr2npyarr(core.getPSD_p_00(), 'double', n).copy()
E2arr = bpptr2npyarr(core.getPSD_p2_00(), 'double', n).copy()
Iarr.shape = E2arr.shape = shape
from histogram import histogram, axis, arange
dx = 360. / nx
xaxis = axis('x', arange(0, 360, dx), unit='deg')
dy = 180. / ny
yaxis = axis('y', arange(-90, 90, dy), unit='deg')
h = histogram('I(x,y)', [xaxis, yaxis], data=Iarr, errors=E2arr)
return h
def get_histogram( monitor ):
from mcstas2.utils.carray import bpptr2npyarr
core = monitor.core()
nx = core.nx; ny =core.ny
n = nx * ny
shape = nx, ny
# xmin = core.x_min; xmax = core.x_max
# ymin = core.y_min; ymax = core.y_max
xmin = attr(core, "xmin", "x_min");
xmax = attr(core, "xmax", "x_max");
ymin = attr(core, "ymin", "y_min");
ymax = attr(core, "ymax", "y_max");
dx = (xmax - xmin)/nx
dy = (ymax - ymin)/ny
Iarr = bpptr2npyarr( core.getPSD_p_00( ), 'double', n ).copy()
E2arr = bpptr2npyarr( core.getPSD_p2_00( ), 'double', n ).copy()
Iarr.shape = E2arr.shape = shape
from histogram import histogram, axis, arange
xaxis = axis( 'x', arange( xmin, xmax, dx ) )
yaxis = axis( 'y', arange( ymin, ymax, dy ) )
h = histogram( 'I(x,y)', [xaxis,yaxis], data = Iarr, errors = E2arr )
return h
def test_values2indexes(self):
"Histogram: values2indexes"
from histogram import histogram, axis, arange
x = axis( 'x', arange(1., 10., 1.) )
y = axis( 'y', arange(-1., 1., 0.1) )
h = histogram('h', (x,y) )
self.assertVectorEqual( h.values2indexes( (2, 0.2) ), (1,12) )
return
def test_values2indexes(self):
"Histogram: values2indexes"
from histogram import histogram, axis, arange
x = axis( 'x', arange(1., 10., 1.) )
y = axis( 'y', arange(-1., 1., 0.1) )
h = histogram('h', (x,y) )
self.assertVectorEqual( h.values2indexes( (2, 0.2) ), (1,12) )
return
def test_axisFromId(self):
"Histogram: axisFromId"
from histogram import histogram, axis, arange
x = axis( 'x', arange(1., 10., 1.) )
y = axis( 'y', arange(-1., 1., 0.1) )
h = histogram('h', (x,y) )
self.assertEqual( h.axisFromId(1), x )
self.assertEqual( h.axisFromId(2), y )
return
def test__idiv__2(self):
"histogram: h/=h1"
h = self._histogram.copy()
h2 = self._histogram2
h /= h2
self.assertVectorAlmostEqual( h[1.5,1], (1,2.0/3) )
h = self._histogram.copy()
h2 = createHistogram( noerror = True )
h /= h2
self.assertVectorAlmostEqual( h[1.5,1], (1,1./3) )
from histogram import histogram, axis, arange, datasetFromFunction
x = axis('x', arange(1, 2, .2 ) )
y = axis('y', arange(0, 3, .5 ) )
def fa(x,y): return x*y + x
ha = histogram('a', [x,y], datasetFromFunction( fa, (x,y) ) )
for xi in x.binCenters():
for yi in y.binCenters():
self.assertAlmostEqual( fa(xi,yi), ha[xi,yi][0] )
def fb(x,y): return x
hb = histogram('b', [x,y], datasetFromFunction( fb, (x,y) ) )
hc = ha/hb
for xi in x.binCenters():
for yi in y.binCenters():
self.assertAlmostEqual( yi+1, hc[xi,yi][0] )
def fberr(x,y): return 0*x
hb = histogram('b', [x,y], datasetFromFunction( fb, (x,y) ),
datasetFromFunction( fberr, (x,y) ) )
hc = ha/hb
for xi in x.binCenters():
for yi in y.binCenters():
self.assertAlmostEqual( yi+1, hc[xi,yi][0] )
#involve units
h1 = histogram(
'h1',
[ ('x', [1,2,3]),
],
unit = 'meter',
data = [1,2,3],
errors = [1,2,3],
)
h2 = histogram(
'h2',
[ ('x', [1,2,3]),
],
data = [1,1,1],
errors = [1,1,1],
unit = 'second',
)
h3 = h1/h2
self.assertVectorAlmostEqual( h3.I, (1,2,3) )
self.assertVectorAlmostEqual( h3.E2, (2,6,12) )
return
def test__idiv__2(self):
"histogram: h/=h1"
h = self._histogram.copy()
h2 = self._histogram2
h /= h2
self.assertVectorAlmostEqual( h[1.5,1], (1,2.0/3) )
h = self._histogram.copy()
h2 = createHistogram( noerror = True )
h /= h2
self.assertVectorAlmostEqual( h[1.5,1], (1,1./3) )
from histogram import histogram, axis, arange, datasetFromFunction
x = axis('x', arange(1, 2, .2 ) )
y = axis('y', arange(0, 3, .5 ) )
def fa(x,y): return x*y + x
ha = histogram('a', [x,y], datasetFromFunction( fa, (x,y) ) )
for xi in x.binCenters():
for yi in y.binCenters():
self.assertAlmostEqual( fa(xi,yi), ha[xi,yi][0] )
def fb(x,y): return x
hb = histogram('b', [x,y], datasetFromFunction( fb, (x,y) ) )
hc = ha/hb
for xi in x.binCenters():
for yi in y.binCenters():
self.assertAlmostEqual( yi+1, hc[xi,yi][0] )
def fberr(x,y): return 0*x
hb = histogram('b', [x,y], datasetFromFunction( fb, (x,y) ),
datasetFromFunction( fberr, (x,y) ) )
hc = ha/hb
for xi in x.binCenters():
for yi in y.binCenters():
self.assertAlmostEqual( yi+1, hc[xi,yi][0] )
#involve units
h1 = histogram(
'h1',
[ ('x', [1,2,3]),
],
unit = 'meter',
data = [1,2,3],
errors = [1,2,3],
)
h2 = histogram(
'h2',
[ ('x', [1,2,3]),
],
data = [1,1,1],
errors = [1,1,1],
unit = 'second',
)
h3 = h1/h2
self.assertVectorAlmostEqual( h3.I, (1,2,3) )
self.assertVectorAlmostEqual( h3.E2, (2,6,12) )
return
def test0(self):
import histogram as H
qaxis = H.axis('Q', boundaries=H.arange(0, 13.0, 0.1))
eaxis = H.axis('energy', boundaries=H.arange(-50, 50, 1.0))
sqe = H.histogram('sqe', [qaxis, eaxis],
fromfunction=lambda q, e: q * q + e * e)
from mccomponents.sample.idf import writeSQE
writeSQE(sqe, datapath)
return
def test_axisFromId(self):
"Histogram: axisFromId"
from histogram import histogram, axis, arange
x = axis( 'x', arange(1., 10., 1.) )
y = axis( 'y', arange(-1., 1., 0.1) )
h = histogram('h', (x,y) )
self.assertEqual( h.axisFromId(1), x )
self.assertEqual( h.axisFromId(2), y )
return
def setParameters(
self,
Q_params, E_params, ARCSxml, Ei, emission_time):
keys = [
'detector-system-dimensions',
'moderator-sample distance',
'pixelID-position mapping binary file',
'detector axes',
'solidangles',
]
infos = self._readInstrumentInfo(ARCSxml, keys=keys)
npacks, ndetsperpack, npixelsperdet = infos[
'detector-system-dimensions']
mod2sample = infos['moderator-sample distance']
pixelPositionsFilename = infos[
'pixelID-position mapping binary file']
self._debug.log( "pixel-positions-filename=%s" % pixelPositionsFilename)
self._debug.log( 'E_params (unit: meV) = %s' % (E_params, ) )
self._debug.log( 'Q_params (unit: angstrom^-1) = %s' % (Q_params, ) )
self._debug.log( 'mod2sample distance = %s' % mod2sample )
self._debug.log( 'Incident energy (unit: meV) = %s' % (Ei, ) )
self._debug.log( 'emission_time (unit: microsecond) = %s' % (emission_time, ) )
E_begin, E_end, E_step = E_params # meV
Q_begin, Q_end, Q_step = Q_params # angstrom^-1
Q_axis = histogram.axis('Q', boundaries = histogram.arange(
Q_begin, Q_end, Q_step) )
E_axis = histogram.axis('energy', boundaries = histogram.arange(
E_begin, E_end, E_step) )
h = histogram.histogram(
'I(Q,E)',
[
Q_axis,
E_axis,
],
data_type = 'int',
)
pixelPositions = arcseventdata.readpixelpositions(
pixelPositionsFilename, npacks, ndetsperpack, npixelsperdet )
# remember a few things so that we can do normalization
mpiRank = self.mpiRank
if mpiRank == 0:
pixelSolidAngles = infos['solidangles'].I
self._remember( Ei, pixelPositions, pixelSolidAngles )
self.out_histogram = h
self.pixelPositions = pixelPositions
self.Ei = Ei
self.mod2sample = mod2sample
self.emission_time = emission_time
return
def read(directory,
omega2_idf_file='Omega2',
qgridinfo_file='Qgridinfo',
weightedq_file='WeightedQ',
nD=3):
''' read omega2 data file in idf format
nD is the dimension of the qgrid.
it is assumed that the qgrid is regular, and is defined in qgridinfo_file
The qgridinfo_file is a python file that defines vars bi, {i=1..nD} and ni, {i=1..nD}
'''
import os
from idf.Omega2 import read
info, omega2 = read(os.path.join(directory, omega2_idf_file))
qgridinfo = _retrieveQgridinfo(directory,
qgridinfo_file,
weightedq_file,
nD=nD)
#
nQ, nbXnD = omega2.shape
#
import operator
nis = [qgridinfo['n' + str(i)] for i in range(1, nD + 1)]
assert nQ == reduce(operator.__mul__, nis),\
"Q points mismatch: nQ=%s, {ni}=%s" % (nQ, nis)
# number of basis
nb = nbXnD / nD
#
import histogram as H
# Q axes
Qaxes = []
for i in range(nD):
ni = qgridinfo['n' + str(i + 1)]
bi = qgridinfo['b' + str(i + 1)]
Qiaxis = H.axis('Q' + str(i + 1),
H.arange(0, 1 + 1e-10, 1. / (ni - 1)),
'1./angstrom',
attributes={'b': bi})
Qaxes.append(Qiaxis)
continue
# basis
basisaxis = H.axis('basisID', range(nb))
# dimension
Daxis = H.axis('dimensionID', range(nD))
#
axes = Qaxes + [basisaxis, Daxis]
#
omega2.shape = [axis.size() for axis in axes]
h = H.histogram('Omega2', axes, data=omega2)
return h
def test():
from histogram import histogram, axis, arange, plot
xaxis = axis('x', arange(5), unit='meter')
yaxis = axis('y', arange(7), unit='cm')
axes = [xaxis, yaxis]
h = histogram("intensity", axes, fromfunction=lambda x, y: x**2 + y**2)
print(h)
plot(h)
help(h)
slice = h[3, ()]
def test():
from histogram import histogram, axis, arange, plot
xaxis = axis('x', arange(5), unit='meter')
yaxis = axis('y', arange(7), unit='cm')
axes = [xaxis, yaxis]
h = histogram( "intensity", axes, fromfunction=lambda x,y: x**2+y**2)
print h
plot(h)
help(h)
slice = h[3, ()]
def testReplaceAxis(self):
'Hisogram: replaceAxis'
from histogram import histogram, axis, arange
a = axis('a', arange(1,10,1.0))
b = axis('b', arange(1,100,10.))
h = histogram( 'h', [a] )
self.assert_(a is h.axisFromName('a'))
h.replaceAxis(name='a', axis=b)
self.assert_(b is h.axisFromName('a'))
return
def createSqe():
import histogram as H
qaxis = H.axis( 'Q', boundaries = H.arange(0, 13.0, 0.1) )
eaxis = H.axis( 'energy', boundaries = H.arange(-50, 50, 1.0) )
sqe = H.histogram(
'sqe',
[ qaxis, eaxis ],
fromfunction = sqe_f
)
return sqe
def testReplaceAxis(self):
'Hisogram: replaceAxis'
from histogram import histogram, axis, arange
a = axis('a', arange(1,10,1.0))
b = axis('b', arange(1,100,10.))
h = histogram( 'h', [a] )
self.assertTrue(a is h.axisFromName('a'))
h.replaceAxis(name='a', axis=b)
self.assertTrue(b is h.axisFromName('a'))
return
def createSqe():
import histogram as H
qaxis = H.axis( 'Q', boundaries = H.arange(0, 13.0, 0.1) )
eaxis = H.axis( 'energy', boundaries = H.arange(-50, 50, 1.0) )
sqe = H.histogram(
'sqe',
[ qaxis, eaxis ],
fromfunction = sqe_f
)
return sqe
def test0(self):
import histogram as H
qaxis = H.axis( 'Q', boundaries = H.arange(0, 13.0, 0.1) )
eaxis = H.axis( 'energy', boundaries = H.arange(-50, 50, 1.0) )
sqe = H.histogram(
'sqe',
[ qaxis, eaxis ],
fromfunction = lambda q,e: q*q+e*e )
from mccomponents.sample.idf import writeSQE
writeSQE( sqe, datapath )
return
def interp(iqehist, newE):
"""compute a new IQE histogram using the new energy array
* iqehist: input IQE histogram
* newE: new energy centers array
"""
from scipy import interpolate
mask = iqehist.I != iqehist.I
# find energy boundaries of dynamic range for each Q
def get_boundary_indexes(a):
nz = np.nonzero(a)[0]
if nz.size:
return nz[0], nz[-1]
else:
return 0, 0
boundary_indexes = [get_boundary_indexes(row) for row in np.logical_not(mask)]
try:
E = iqehist.energy
except:
E = iqehist.E
Eranges = [(E[ind1], E[ind2]) for ind1, ind2 in boundary_indexes]
#
iqehist.I[mask] = 0
iqehist.E2[mask] = 0
Q = iqehist.Q
f = interpolate.interp2d(E, Q, iqehist.I, kind="linear")
E2f = interpolate.interp2d(E, Q, iqehist.E2, kind="linear")
dE = E[1] - E[0]
Emin = E[0] // dE * dE
Emax = E[-1] // dE * dE
# Enew = np.arange(Emin, Emax+dE/2, dE)
newS = f(newE, Q)
newS_E2 = E2f(newE, Q)
# create new histogram
Eaxis = H.axis("E", newE, unit="meV")
Qaxis = H.axis("Q", Q, unit="1./angstrom")
newHist = H.histogram("IQE", [Qaxis, Eaxis], data=newS, errors=newS_E2)
#
for Erange, q in zip(Eranges, Q):
Emin, Emax = Erange
if Emin > newE[0]:
Emin = min(Emin, newE[-1])
newHist[q, (None, Emin)].I[:] = np.nan
newHist[q, (None, Emin)].E2[:] = np.nan
if Emax < newE[-1]:
Emax = max(Emax, newE[0])
newHist[q, (Emax, None)].I[:] = np.nan
newHist[q, (Emax, None)].E2[:] = np.nan
continue
return newHist
def getSqeHistogramFromMantidWS(reduced, outfile, qaxis=None, eaxis=None):
from mantid import simpleapi as msa
# if eaxis is not specified, use the data in reduced workspace
if eaxis is None:
Edim = reduced.getXDimension()
emin = Edim.getMinimum()
emax = Edim.getMaximum()
de = Edim.getX(1) - Edim.getX(0)
eaxis = emin, de, emax
qmin, dq, qmax = qaxis
nq = int(round((qmax - qmin) / dq))
emin, de, emax = eaxis
ne = int(round((emax - emin) / de))
md = msa.ConvertToMD(
InputWorkspace=reduced,
QDimensions='|Q|',
dEAnalysisMode='Direct',
MinValues="%s,%s" % (qmin, emin),
MaxValues="%s,%s" % (qmax, emax),
)
binned = msa.BinMD(
InputWorkspace=md,
AxisAligned=1,
AlignedDim0="|Q|,%s,%s,%s" % (qmin, qmax, nq),
AlignedDim1="DeltaE,%s,%s,%s" % (emin, emax, ne),
)
# convert to histogram
import histogram as H, histogram.hdf as hh
data = binned.getSignalArray().copy()
err2 = binned.getErrorSquaredArray().copy()
nev = binned.getNumEventsArray()
data /= nev
err2 /= (nev * nev)
import numpy as np
qaxis = H.axis('Q',
boundaries=np.arange(qmin, qmax + dq / 2., dq),
unit='1./angstrom')
eaxis = H.axis('E',
boundaries=np.arange(emin, emax + de / 2., de),
unit='meV')
hist = H.histogram('IQE', (qaxis, eaxis), data=data, errors=err2)
if outfile.endswith('.nxs'):
import warnings
warnings.warn(
"reduce function no longer writes iqe.nxs nexus file. it only writes iqe.h5 histogram file"
)
outfile = outfile[:-4] + '.h5'
hh.dump(hist, outfile)
return
def read(directory,
omega2_idf_file='Omega2', qgridinfo_file='Qgridinfo', weightedq_file='WeightedQ',
nD=3):
''' read omega2 data file in idf format
nD is the dimension of the qgrid.
it is assumed that the qgrid is regular, and is defined in qgridinfo_file
The qgridinfo_file is a python file that defines vars bi, {i=1..nD} and ni, {i=1..nD}
'''
import os
from idf.Omega2 import read
info, omega2 = read(os.path.join(directory,omega2_idf_file))
qgridinfo = _retrieveQgridinfo(directory, qgridinfo_file, weightedq_file, nD=nD)
#
nQ, nbXnD = omega2.shape
#
import operator
nis = [qgridinfo['n'+str(i)] for i in range(1, nD+1)]
assert nQ == reduce(operator.__mul__, nis),\
"Q points mismatch: nQ=%s, {ni}=%s" % (nQ, nis)
# number of basis
nb = nbXnD / nD
#
import histogram as H
# Q axes
Qaxes = []
for i in range(nD):
ni = qgridinfo['n'+str(i+1)]
bi = qgridinfo['b'+str(i+1)]
Qiaxis = H.axis('Q'+str(i+1), H.arange(0, 1+1e-10, 1./(ni-1)), '1./angstrom',
attributes = {'b': bi} )
Qaxes.append(Qiaxis)
continue
# basis
basisaxis = H.axis('basisID', range(nb))
# dimension
Daxis = H.axis('dimensionID', range(nD))
#
axes = Qaxes+[basisaxis, Daxis]
#
omega2.shape = [axis.size() for axis in axes]
h = H.histogram('Omega2', axes, data = omega2)
return h
def resample( hist1, size ):
import histogram as H
assert hist1.dimension() == 1
assert hist1.shape()[0] > display_size*10
xaxis = hist1.axes()[0]
xbb = xaxis.binBoundaries().asNumarray()
front, back = xbb[0], xbb[-1]
step = (back-front)/size
newxbb = H.arange( front, back+step/2, step)
newxaxis = H.axis( xaxis.name(), boundaries = newxbb, unit = xaxis.unit() )
newhist = H.histogram(
hist1.name(),
[ newxaxis ] )
newxc = newxaxis.binCenters()
for x in newxc[1:-1] :
newhist[ x ] = hist1[ (x-step/2, x+step/2) ].sum()
continue
newhist[ newxc[0] ]= hist1[ (newxbb[0], newxc[0] + step/2) ].sum()
newhist[ newxc[-1] ]= hist1[ (newxc[-1]-step/2, newxbb[-1]-step*1.e-10) ].sum()
return newhist
def test_combined_1(self):
'Axis: slice and changeUnit'
taxis= axis('t', range(10), unit='second' )
from histogram.SlicingInfo import SlicingInfo
slice = taxis[ SlicingInfo( (3,9) ) ]
self.assertRaises( RuntimeError, slice.changeUnit, 'millisecond' )
return
def resample(hist1, size):
import histogram as H
assert hist1.dimension() == 1
assert hist1.shape()[0] > display_size * 10
xaxis = hist1.axes()[0]
xbb = xaxis.binBoundaries().asNumarray()
front, back = xbb[0], xbb[-1]
step = 1. * (back - front) / size
newxbb = H.arange(front, back + step / 2., step)
newxaxis = H.axis(xaxis.name(), boundaries=newxbb, unit=xaxis.unit())
newhist = H.histogram(hist1.name(), [newxaxis])
newxc = newxaxis.binCenters()
for x in newxc[1:-1]:
newhist[x] = hist1[(x - step / 2., x + step / 2.)].sum()
continue
newhist[newxc[0]] = hist1[(newxbb[0], newxc[0] + step / 2.)].sum()
newhist[newxc[-1]] = hist1[(newxc[-1] - step / 2.,
newxbb[-1] - step * 1.e-10)].sum()
return newhist
def setParameters(
self,
ARCSxml, d_params,
emission_time):
info.log( 'd_params (unit: AA) = %s' % (d_params, ) )
info.log( 'emission_time (unit: microsecond) = %s' % (emission_time, ) )
infos = self._readInstrumentInfo(ARCSxml)
npacks, ndetsperpack, npixelsperdet = infos[
'detector-system-dimensions']
mod2sample = infos['moderator-sample distance']
pixelPositionsFilename = infos[
'pixelID-position mapping binary file']
d_begin, d_end, d_step = d_params # angstrom
d_axis = histogram.axis('d spacing', boundaries = histogram.arange(
d_begin, d_end, d_step) )
detaxes = infos['detector axes']
h = histogram.histogram(
'I(pdpd)',
detaxes + [d_axis],
data_type = 'int',
)
info.log( "reading pixelID->position map..." )
pixelPositions = arcseventdata.readpixelpositions(
pixelPositionsFilename, npacks, ndetsperpack, npixelsperdet)
self.out_histogram = h
self.pixelPositions = pixelPositions
self.mod2sample = mod2sample
self.emission_time = emission_time
return
def slice2hist(ifile, ofile):
import histogram as H, histogram.hdf as hh
from mantid import simpleapi as msa
def eliminateUnitDimension(shape):
for d in shape:
if d>1: yield d
return
ws = msa.Load(ifile)
I = ws.getSignalArray()
I.shape = tuple(eliminateUnitDimension(I.shape))
E2 = ws.getErrorSquaredArray()
E2.shape = I.shape
axes = []
for i in range(ws.getNumDims()):
dim = ws.getDimension(i)
if dim.getNBins() > 1:
axis = H.axis(
dim.getName(),
unit="1",
centers = [dim.getX(ind) for ind in range(dim.getNBins())]
)
axes.append(axis)
continue
h = H.histogram("slice", axes, data=I, errors=E2)
hh.dump(h, ofile)
return
def getpixelinfo_mergedpixels(ARCSxml, pixelresolution):
npixels = 128
assert npixels%pixelresolution==0
from arcseventdata.combinepixels import combinepixels, geometricInfo, geometricInfo_MergedPixels
from histogram import axis
pixelaxis = axis('pixelID', range(0, 128, pixelresolution))
info.log('merging pixels')
phi_p, psi_p, dist_p, sa_p, dphi_p, dpsi_p = combinepixels(ARCSxml, pixelaxis, pixelresolution)
positions, radii, heights = geometricInfo(ARCSxml)
positions, radii, heights = geometricInfo_MergedPixels(positions, radii, heights, pixelresolution)
widths = radii*2
phis = phi_p.I
psis = psi_p.I
dists = dist_p.I
sas = sa_p.I
# 06/30/2009: was told that the last two columns are angles
da1 = widths/dists
da2 = sas/da1
dists.shape = phis.shape = psis.shape = widths.shape = heights.shape = -1,
da1.shape = da2.shape = -1,
#return dists, phis, psis, widths, heights
return dists, phis, psis, da1, da2
def test_combined_1(self):
'Axis: slice and changeUnit'
taxis = axis('t', list(range(10)), unit='second')
from histogram.SlicingInfo import SlicingInfo
slice = taxis[SlicingInfo((3, 9))]
self.assertRaises(RuntimeError, slice.changeUnit, 'millisecond')
return
def e2Id(
events, n, pixelpositions,
dspacing_params = None,
Idspacing = None,
preNeXus_tofUnit = 1.e-7, mod2sample = 13.5):
'''e2Id(events, n, pixelpositions, Idspacing = None,
dspacing_params = None,
npacks = 115, ndetsperpack = 8, npixelsperdet = 128,
preNeXus_tofUnit = 1.e-7, mod2sample = 13.5) --> integrate events to I(d spacing) histogram
Either Idspacing or dspacing_params must be given
Idspacing:
histogram I(d spacing). If this is None, a histogram will be created
using dspacing_params.
dspacing_params:
begin, end, and step of dspacing. unit: angstrom
If Idspacing is given, this is ignored.
events:
neutron events
n:
number of neutron events to process
pixelpositions:
array of pixel positions
preNeXus_tofUnit:
unit of event.tof in the pre-Nexus data format. unit: second
mod2sample:
moderator-sample distance. unit: meter
return:
the I(d spacing) histogram
'''
if Idspacing is None:
if dspacing_params is None:
raise ValueError, "Must provide either the (min, max, step) of d axis or the I(d) histogram"
dspacing_begin, dspacing_end, dspacing_step = dspacing_params # angstrom
import histogram
daxis = histogram.axis(
'd',
boundaries = histogram.arange(dspacing_begin, dspacing_end, dspacing_step),
unit = 'angstrom',
)
Idspacing = histogram.histogram(
'I(d spacing)',
[daxis],
data_type = 'int',
)
pass
events2Idspacing(
events, n, Idspacing, pixelpositions,
tofUnit = preNeXus_tofUnit, mod2sample = mod2sample)
return Idspacing
def setParameters(
self,
ARCSxml, tof_params, pack_params = (1,115), pixel_step = 1 ):
infos = self._readInstrumentInfo(ARCSxml)
npacks, ndetsperpack, npixelsperdet = infos[
'detector-system-dimensions']
mod2sample = infos['moderator-sample distance']
pixelPositionsFilename = infos[
'pixelID-position mapping binary file']
info.log( 'tof_params (unit: microsecond) = %s' % (tof_params, ) )
import numpy
tof_begin, tof_end, tof_step = numpy.array(tof_params)*1.e-6 #convert from microseconds to seconds
tof_axis = histogram.axis(
'tof',
boundaries = histogram.arange(tof_begin, tof_end, tof_step),
unit = 'second' )
detaxes = infos['detector axes']
#pixel axis need to be changed if pixel resolution is not 1
if pixel_step != 1:
pixelAxis = detaxes[2]
npixelspertube = pixelAxis.size()
pixelAxis = histogram.axis(
'pixelID',
boundaries = range(0, npixelspertube+1, pixel_step),
)
detaxes[2] = pixelAxis
#pack axis
startpack, endpack = pack_params
packaxis = histogram.axis(
'detectorpackID',
range( startpack, endpack+1 ) )
detaxes[0] = packaxis
h = histogram.histogram(
'I(pdpt)',
detaxes + [tof_axis],
data_type = 'int',
)
self.out_histogram = h
return
def computeSlice(self, paths=None, **kwds):
H = None; sa = None; edges = None
for path in paths or self.paths:
print path
edges1, H1, sa1 = self.computeSliceForOneRun(path, **kwds)
if H is None:
edges, H, sa = edges1, H1, sa1
else:
H += H1; sa += sa1
continue
import histogram
axes = [
histogram.axis(kwds['x'], boundaries=edges[0]),
histogram.axis(kwds['y'], boundaries=edges[1]),
]
return histogram.histogram('I(%(x)s,%(y)s)'%kwds, axes=axes, data=H/sa)
def makeDispersion():
nAtoms = 2
nBranches = 3 * nAtoms
nQx = 10; nQy = 12; nQz = 14
Qaxes = [ ([1,0,0], nQx),
([0,1,0], nQy),
([0,0,1], nQz),
]
import histogram as H
qx = H.axis('qx', H.arange(0, 1+1e-10, 1./(nQx-1)))
qy = H.axis('qy', H.arange(0, 1+1e-10, 1./(nQy-1)))
qz = H.axis('qz', H.arange(0, 1+1e-10, 1./(nQz-1)))
br = H.axis('branchId', range(nBranches))
atoms = H.axis('atomId', range(nAtoms))
pols = H.axis('polId', range(3))
realimags = H.axis('realimagId', range(2))
eps = H.histogram('eps', [qx,qy,qz,br,atoms,pols,realimags])
eps.I[:] = 1
e = H.histogram('e', [qx,qy,qz,br],
fromfunction = lambda qx,qy,qz,br: (qx*qx+qy*qy+qz*qz)/3.*50,
)
disp = b.linearlyinterpolateddispersion_3d(nAtoms, Qaxes, eps.I, e.I)
disp = b.periodicdispersion(disp, ((1,0,0), (0,1,0), (0,0,1)))
return disp
def makeDispersion():
nAtoms = 2
nBranches = 3 * nAtoms
nQx = 10
nQy = 12
nQz = 14
Qaxes = [
([1, 0, 0], nQx),
([0, 1, 0], nQy),
([0, 0, 1], nQz),
]
import histogram as H
qx = H.axis('qx', H.arange(0, 1 + 1e-10, 1. / (nQx - 1)))
qy = H.axis('qy', H.arange(0, 1 + 1e-10, 1. / (nQy - 1)))
qz = H.axis('qz', H.arange(0, 1 + 1e-10, 1. / (nQz - 1)))
br = H.axis('branchId', range(nBranches))
atoms = H.axis('atomId', range(nAtoms))
pols = H.axis('polId', range(3))
realimags = H.axis('realimagId', range(2))
eps = H.histogram('eps', [qx, qy, qz, br, atoms, pols, realimags])
eps.I[:] = 1
e = H.histogram(
'e',
[qx, qy, qz, br],
fromfunction=lambda qx, qy, qz, br:
(qx * qx + qy * qy + qz * qz) / 3. * 50,
)
disp = b.linearlyinterpolateddispersion_3d(nAtoms, Qaxes, eps.I, e.I)
disp = b.periodicdispersion(disp, ((1, 0, 0), (0, 1, 0), (0, 0, 1)))
return disp
def run(scan=None, poolsize=None, output=None, **volume_opts):
scan = load_mod(scan)['scan']
def worker(work_q, H, sa):
while not work_q.empty():
f = work_q.get()
print f
one(f, H, sa, scan, volume_opts)
continue
return
shape, edges = scan.volumeOutputDims(**volume_opts)
size = shape[0] * shape[1] * shape[2]
from multiprocessing import Process, Queue, Array
shared_H = Array('d', size)
shared_sa = Array('d', size)
work_q = Queue()
for path in scan.paths:
work_q.put(path)
processes = []
for w in xrange(poolsize):
p = Process(target=worker, args=(work_q, shared_H, shared_sa))
p.start()
processes.append(p)
continue
for p in processes:
p.join()
import histogram
axes = [
histogram.axis(volume_opts['x'], boundaries=edges[0]),
histogram.axis(volume_opts['y'], boundaries=edges[1]),
histogram.axis(volume_opts['z'], boundaries=edges[2]),
]
H = mparr2nparr(shared_H)
sa = mparr2nparr(shared_sa)
H.shape = sa.shape = shape
h = histogram.histogram('I(%(x)s,%(y)s,%(z)s)' % volume_opts,
axes=axes,
data=H / sa)
import histogram.hdf as hh
hh.dump(h, output)
return
def test_getattribute(self):
'Histogram: __getattribute__'
from histogram import histogram, axis, arange
x = axis( 'x', arange(1., 10., 1.) )
y = axis( 'y', arange(-1., 1., 0.1) )
h = histogram('h', (x,y) )
self.assertVectorEqual( h.x, x.binCenters() )
self.assertVectorEqual( h.y, y.binCenters() )
t1 = h.I; t2 = h.data().storage().asNumarray()
t1.shape = t2.shape = -1,
self.assertVectorEqual( t1, t2 )
t1 = h.E2; t2 = h.errors().storage().asNumarray()
t1.shape = t2.shape = -1,
self.assertVectorEqual( t1, t2 )
return
def test_getattribute(self):
'Histogram: __getattribute__'
from histogram import histogram, axis, arange
x = axis( 'x', arange(1., 10., 1.) )
y = axis( 'y', arange(-1., 1., 0.1) )
h = histogram('h', (x,y) )
self.assertVectorEqual( h.x, x.binCenters() )
self.assertVectorEqual( h.y, y.binCenters() )
t1 = h.I; t2 = h.data().storage().asNumarray()
t1.shape = t2.shape = -1,
self.assertVectorEqual( t1, t2 )
t1 = h.E2; t2 = h.errors().storage().asNumarray()
t1.shape = t2.shape = -1,
self.assertVectorEqual( t1, t2 )
return
def test_changeUnit(self):
'Axis: changeUnit'
taxis = axis('t', list(range(3)), unit='second')
taxis.changeUnit('millisecond')
self.assertVectorAlmostEqual(taxis.binBoundaries().asNumarray(),
[-500, 500, 1500, 2500])
self.assertVectorAlmostEqual(taxis.binCenters(), [0, 1000, 2000])
self.assertEqual(taxis.cellIndexFromValue(0), 0)
return
def run(scan=None, poolsize=None, output=None, **volume_opts):
scan = load_mod(scan)['scan']
def worker(work_q, H, sa):
while not work_q.empty():
f = work_q.get()
print f
one(f, H, sa, scan, volume_opts)
continue
return
shape, edges = scan.volumeOutputDims(**volume_opts)
size = shape[0] * shape[1] * shape[2]
from multiprocessing import Process, Queue, Array
shared_H = Array('d', size)
shared_sa = Array('d', size)
work_q = Queue()
for path in scan.paths: work_q.put(path)
processes = []
for w in xrange(poolsize):
p = Process(target=worker, args=(work_q, shared_H, shared_sa))
p.start()
processes.append(p)
continue
for p in processes:
p.join()
import histogram
axes = [
histogram.axis(volume_opts['x'], boundaries=edges[0]),
histogram.axis(volume_opts['y'], boundaries=edges[1]),
histogram.axis(volume_opts['z'], boundaries=edges[2]),
]
H = mparr2nparr(shared_H)
sa = mparr2nparr(shared_sa)
H.shape = sa.shape = shape
h = histogram.histogram(
'I(%(x)s,%(y)s,%(z)s)'%volume_opts, axes=axes, data=H/sa)
import histogram.hdf as hh
hh.dump(h, output)
return
def test_changeUnit(self):
'Axis: changeUnit'
taxis= axis('t', range(3), unit='second' )
taxis.changeUnit( 'millisecond' )
self.assertVectorAlmostEqual( taxis.binBoundaries().asNumarray(),
[-500, 500, 1500, 2500] )
self.assertVectorAlmostEqual( taxis.binCenters(),
[0, 1000, 2000] )
self.assertEqual( taxis.cellIndexFromValue( 0 ), 0 )
return
def get_histogram( monitor ):
from mcstas2.utils.carray import bpptr2npyarr
core = monitor.core()
n = core.nchan
Iarr = bpptr2npyarr( core.getTOF_p( ), 'double', n ).copy()
E2arr = bpptr2npyarr( core.getTOF_p2( ), 'double', n ).copy()
from histogram import histogram, axis, arange
dt = (core.tmax-core.tmin)/core.nchan
taxis = axis( 'tof', arange( core.tmin+dt/2., core.tmax+dt/2-0.1*dt, dt ), unit = 's' )
h = histogram( 'I(tof)', [taxis], data = Iarr, errors = E2arr )
return h
def process(path):
basename, ext = os.path.splitext(os.path.basename(path))
from nslice.Run import Run
run = Run(path)
print "instrument=%s, Ei=%s, psi=%s" % (run.instrument, run.Ei, run.psi)
from nslice.XtalOrientation import XtalOrientation
a = b = 8.87
c = 5.2
from math import pi
twopi = 2 * pi
ra, rb, rc = [twopi / a, 0, 0], [0, twopi / b, 0], [0, 0, twopi / c]
u, v = [1, 0, 0], [0, 1, 0]
xtal_ori = XtalOrientation(ra, rb, rc, u, v, run.psi)
h, k, l, E = run.compute_hklE(xtal_ori)
I, error = run.read_data()
h.shape = k.shape = l.shape = E.shape = I.shape = error.shape = -1
hklEIE = np.vstack((h, k, l, E, I, error))
from nslice.slice import slice
H, edges = slice(
hklEIE,
x='h',
y='k',
u='l',
v='E',
E=[-2, 2],
l=[-5, 5],
h=(-5, 5, 0.02),
k=(-5, 5, 0.02),
)
import histogram, histogram.hdf as hh
axes = [
histogram.axis('h', boundaries=edges[0]),
histogram.axis('k', boundaries=edges[1]),
]
h = histogram.histogram('I(h,k)', axes=axes, data=H)
hh.dump(h, '%s-I_hk.h5' % basename)
return
def sqehist(E, g, **kwds):
"""a simple wrapper of method sqe to return a histogram
Please see method sqe for details of all keyword parameters
Parameters
----------
E:numpy array of floats
energies in meV
g:numpy array of floats
density of states at the specified energies
"""
Q, E, S = sqe(E, g, **kwds)
import histogram as H
Qaxis = H.axis('Q', Q, '1./angstrom')
Eaxis = H.axis('E', E, 'meV')
return H.histogram("SP SQE", [Qaxis, Eaxis], S)
def get_histogram(monitor):
from mcstas2.utils.carray import bpptr2npyarr
core = monitor.core()
nQ = core.nQ
nE = core.nE
n = nQ * nE
shape = nQ, nE
Iarr = bpptr2npyarr(core.getIQE_p(), 'double', n).copy()
E2arr = bpptr2npyarr(core.getIQE_p2(), 'double', n).copy()
Iarr.shape = E2arr.shape = shape
from histogram import histogram, axis, arange
dE = (core.Emax - core.Emin) / nE
Eaxis = axis('energy', arange(core.Emin, core.Emax, dE), unit='meV')
dQ = (core.Qmax - core.Qmin) / nQ
Qaxis = axis('Q', arange(core.Qmin, core.Qmax, dQ), unit='angstrom**-1')
h = histogram('I(Q,E)', [Qaxis, Eaxis], data=Iarr, errors=E2arr)
return h
def get_histogram(monitor):
from mcstas2.utils.carray import bpptr2npyarr
core = monitor.core()
n = core.nchan
Iarr = bpptr2npyarr(core.getE_p(), 'double', n).copy()
E2arr = bpptr2npyarr(core.getE_p2(), 'double', n).copy()
from histogram import histogram, axis, arange
dE = (core.Emax - core.Emin) / core.nchan
Eaxis = axis('energy',
arange(core.Emin + dE / 2, core.Emax, dE),
unit='meV')
h = histogram('I(E)', [Eaxis], data=Iarr, errors=E2arr)
return h
def get_histogram(monitor):
from mcstas2.utils.carray import bpptr2npyarr
core = monitor.core()
n = core.nchan
Iarr = bpptr2npyarr(core.getL_p(), 'double', n).copy()
E2arr = bpptr2npyarr(core.getL_p2(), 'double', n).copy()
from histogram import histogram, axis, arange
dL = (core.Lmax - core.Lmin) / core.nchan
Laxis = axis('wavelength',
arange(core.Lmin + dL / 2, core.Lmax + dL / 2, dL),
unit='angstrom')
h = histogram('I(L)', [Laxis], data=Iarr, errors=E2arr)
return h
def get_histogram(monitor):
from mcstas2.utils.carray import bpptr2npyarr
core = monitor.core()
n = core.nchan
Iarr = bpptr2npyarr(core.getTOF_p(), 'double', n).copy()
E2arr = bpptr2npyarr(core.getTOF_p2(), 'double', n).copy()
from histogram import histogram, axis, arange
dt = (core.tmax - core.tmin) / core.nchan
taxis = axis('tof',
arange(core.tmin + dt / 2., core.tmax + dt / 2 - 0.1 * dt,
dt),
unit='s')
h = histogram('I(tof)', [taxis], data=Iarr, errors=E2arr)
return h
def readSQE( datapath, Q = 'Q', E = 'E', Sqe = 'Sqe' ):
'read idf Q,E,Sqe and construct a S(Q,E) histogram'
qpath = os.path.join( datapath, Q )
import Q
q = Q.read( qpath)[1]
q.shape = q.size,
epath = os.path.join( datapath, E )
import E
e = E.read( epath)[1]
e.shape = e.size,
sqepath = os.path.join( datapath, Sqe )
import Sqe
s = Sqe.read( sqepath)[1]
import histogram as H
qaxis = H.axis( 'Q', boundaries = q )
eaxis = H.axis( 'energy', boundaries = e )
return H.histogram(
'S(Q,E)',
[qaxis, eaxis],
data = s )
def test1(self):
"multiphonon.forward.dos2sqe"
from dos import loadDOS
E, g = loadDOS()
Eaxis = H.axis('E', unit='meV', centers=E)
doshist = H.histogram('DOS', [Eaxis], g)
dE = E[1] - E[0]
iqe = hh.load(os.path.join(datadir, 'V-iqe.h5'))
from multiphonon.sqe import interp
newiqe = interp(iqe, newE=np.arange(iqe.energy[0], 80., dE))
hh.dump(newiqe, 'V-iqe-interped.h5')
from multiphonon.forward import dos2sqe
sqe = dos2sqe(doshist, 0.01, newiqe, 300, 50.94, 120.)
return