def computeFocusedSpectraForRealMonitors(E, m2sout, out):
from mcni.utils.conversion import e2v
v = e2v(E)
from pyre.units.time import second
import histogram.hdf as hh, histogram as H
m1 = hh.load(os.path.join(m2sout, "mon1-tof.h5"), "I(tof)")
L1 = 11.831
t1 = L1 / v # * second
m1p = m1[(t1 * 0.9, t1 * 1.1)]
m1pc = H.histogram("I(tof)", m1p.axes(), data=m1p.I, errors=m1p.E2)
m1pc.setAttribute("title", "Monitor 1 I(tof)")
hh.dump(m1pc, os.path.join(out, "mon1-itof-focused.h5"), "/", "c")
m2 = hh.load(os.path.join(m2sout, "mon2-tof.h5"), "I(tof)")
L2 = 18.5
t2 = L2 / v # * second
m2p = m2[(t2 * 0.9, t2 * 1.1)]
m2pc = H.histogram("I(tof)", m2p.axes(), data=m2p.I, errors=m2p.E2)
m2pc.setAttribute("title", "Monitor 2 I(tof)")
hh.dump(m2pc, os.path.join(out, "mon2-itof-focused.h5"), "/", "c")
return
def loadsimdata(filename):
# load data and apply efficiency
itof = hh.load(filename, 'I(tof)')
eff = hh.load('mon1-eff.h5')
i = itof.I * eff.I
itof.I[:] = i
# clean up
itof[(0.019, None)].I = 0
#
x = itof.tof
y = itof.I
# convert to counts/10 mus
# counts * 10, bins / 10
from smooth import smooth
y = smooth(y, window_len=10, window='flat')
# y = y[:len(x)]
# y *= 10.
indexes = range(5, len(x), 10)
x = x[indexes]
y = y[indexes] * 10
# convert to arcs run #5
# according to ARCS_runinfo.xml of run #5
# beam power 110kW
# total run time is 22590/30 seconds
# the mc simulated was 2MW, 60Hz
y *= 22590 / 30 * 110e3 / (2e6 / 60)
# extra scaling factor, why?
y *= 0.83
return x, y
def testload3(self):
'load a slice of a histogram '
tmpfile = "tmp.h5"
if os.path.exists( tmpfile): os.remove(tmpfile)
cmd = "from histogram.hdf import dump; from histogram import histogram, arange; h = histogram( 'h', [ ('xID', range(10)), ('y', arange(0, 1,0.1)) ] ); from numpy import array; d = array(range(100)); d.shape = 10,10; h[{}] = d, 0; dump(h, %r, '/', 'c') " % tmpfile
os.system( 'python -c %r' % cmd )
if not os.path.exists( tmpfile ): raise "failed to create tmp h5 file of historam"
h1 = load( tmpfile, 'h', xID=(3,6) )
assert h1.shape() == (4,10)
d = h1.data().storage().asNumarray().copy()
d.shape = 40,
print d
self.assertVectorAlmostEqual( d, range(30,70) )
self.assertVectorEqual(
h1.axisFromId(1).binCenters(), (3,4,5,6) )
from numpy import arange
self.assertVectorAlmostEqual(
h1.axisFromId(2).binCenters(), arange(0,1,0.1) )
h2 = load( tmpfile, 'h', xID=(3,6), y=(0.4,0.5) )
assert h2.shape() == (4,2)
d = h2.data().storage().asNumarray().copy()
d.shape = 8,
self.assertVectorAlmostEqual(
d, (34,35,44,45,54,55,64,65) )
self.assertVectorEqual(
h2.axisFromId(1).binCenters(), (3,4,5,6) )
from numpy import arange
self.assertVectorAlmostEqual(
h2.axisFromId(2).binCenters(), (0.4,0.5) )
def test1c1(self):
"singlephonon_sqe2dos: partial update -- keep area"
iqehist = hh.load(os.path.join(datadir, "graphite-Ei_130-iqe.h5"))
initdos = hh.load(os.path.join(datadir, "graphite-Ei_300-dos.h5"))
newdos = sqe2dos.singlephonon_sqe2dos(iqehist,
T=300,
Ecutoff=110.,
elastic_E_cutoff=(-30., 15),
M=12.,
initdos=initdos,
update_weights=[0., 1.])
path = os.path.join(here, 'expected_results', 'test1c1-dos.h5')
# hh.dump(newdos, path)
expected = hh.load(path)
self.assert_(np.allclose(newdos.I, expected.I))
self.assert_(np.allclose(newdos.E, expected.E))
self.assert_(np.allclose(newdos.E2, expected.E2))
# plot
if interactive:
pylab.errorbar(initdos.E, initdos.I, initdos.E2**.5, label='init')
pylab.errorbar(newdos.E, newdos.I, newdos.E2**.5, label='new')
# pylab.errorbar(expected.E, expected.I, expected.E2**.5, label='expected')
pylab.legend()
pylab.show()
return
def testload3(self):
'load a slice of a histogram '
tmpfile = "tmp.h5"
if os.path.exists(tmpfile): os.remove(tmpfile)
cmd = "from histogram.hdf import dump; from histogram import histogram, arange; h = histogram( 'h', [ ('xID', range(10)), ('y', arange(0, 1,0.1)) ] ); from numpy import array; d = array(range(100)); d.shape = 10,10; h[{}] = d, 0;"
cmd += "dump(h, {!r}, '/', 'c') ".format(tmpfile)
os.system('python -c {0!r}'.format(cmd))
if not os.path.exists(tmpfile):
raise "failed to create tmp h5 file of historam"
h1 = load(tmpfile, 'h', xID=(3, 6))
assert h1.shape() == (4, 10)
d = h1.data().storage().asNumarray().copy()
d.shape = 40,
print(d)
self.assertVectorAlmostEqual(d, list(range(30, 70)))
self.assertVectorEqual(h1.axisFromId(1).binCenters(), (3, 4, 5, 6))
from numpy import arange
self.assertVectorAlmostEqual(
h1.axisFromId(2).binCenters(), arange(0, 1, 0.1))
h2 = load(tmpfile, 'h', xID=(3, 6), y=(0.4, 0.5))
assert h2.shape() == (4, 2)
d = h2.data().storage().asNumarray().copy()
d.shape = 8,
self.assertVectorAlmostEqual(d, (34, 35, 44, 45, 54, 55, 64, 65))
self.assertVectorEqual(h2.axisFromId(1).binCenters(), (3, 4, 5, 6))
from numpy import arange
self.assertVectorAlmostEqual(h2.axisFromId(2).binCenters(), (0.4, 0.5))
def loadsimdata(filename):
# load data and apply efficiency
itof = hh.load(filename, 'I(tof)')
eff = hh.load('mon1-eff.h5')
i = itof.I * eff.I
itof.I[:] = i
# clean up
itof[(0.019,None)].I = 0
#
x = itof.tof
y = itof.I
# convert to counts/10 mus
# counts * 10, bins / 10
from smooth import smooth
y = smooth(y, window_len=10, window='flat')
# y = y[:len(x)]
# y *= 10.
indexes = range(5, len(x), 10)
x = x[indexes]
y = y[indexes] * 10
# convert to arcs run #5
# according to ARCS_runinfo.xml of run #5
# beam power 110kW
# total run time is 22590/30 seconds
# the mc simulated was 2MW, 60Hz
y *= 22590/30*110e3/(2e6/60)
# extra scaling factor, why?
y *= 0.83
return x,y
def test1(self):
"multiphonon.getdos"
list(getDOS(os.path.join(datadir, "ARCS_V_annulus.nxs")))
self.assert_(
close_hist(
hh.load('work/final-dos.h5'),
hh.load(
os.path.join(here, 'expected_results',
'getdos-test1-final-dos.h5'))))
return
def main():
iqe1 = hh.load(p1)
iqe2 = hh.load(p2)
sigma_coh, sigma_inc = 1.495, 0.0082
getinel = lambda iqe: iqe[(2.5, 7.), ()].sum('Q')
coh_inel = getinel(iqe1)
incoh_inel = getinel(iqe2)
pl.plot(coh_inel.energy, coh_inel.I / sigma_coh, 'r')
pl.plot(incoh_inel.energy, incoh_inel.I / sigma_inc, 'g')
pl.show()
return
def main():
iqe1 = hh.load(p1)
iqe2 = hh.load(p2)
sigma_coh, sigma_inc = 1.495, 0.0082
getinel = lambda iqe: iqe[(2.5, 7.), ()].sum('Q')
coh_inel = getinel(iqe1)
incoh_inel = getinel(iqe2)
pl.plot(coh_inel.energy, coh_inel.I/sigma_coh, 'r')
pl.plot(incoh_inel.energy, incoh_inel.I/sigma_inc, 'g')
pl.show()
return
def test_sizes(self):
'ndmonitor: w; tests: xwidth, yheight'
outdir = 'out-test_sizes'
histfile = '%s/iw2.h5' % outdir
cmd_fmt = 'mcvine-simulate -components=source,monitor --- \
-overwrite-datafiles=on \
-ncount=1 \
-buffer_size=1 \
-source=Source_simple \
-monitor="NDMonitor(w)" \
-source.xw=0.1 \
-source.yh=0.1 \
-source.radius=0.05 \
-source.dist=1.0 \
-source.dE=10.0 \
-source.E0=60.0 \
-source.gauss=0.0 \
-source.flux=1.0 \
-monitor.wmin=0 \
-monitor.wmax=100 \
-monitor.nw=100 \
-monitor.filename=iw2.h5 \
-monitor.xwidth=%f \
-monitor.yheight=%f \
-geometer.monitor="%s" \
--output-dir=%s'
# Misses monitor
(xw, yh) = (0.1, 0.1)
position = "(0,1,1),(0,0,0)"
cmd = cmd_fmt % (xw, yh, position, outdir)
import os
if os.system(cmd):
raise RuntimeError, "%r failed" % cmd
from histogram.hdf import load
from histogram.hdf.utils import getOnlyEntry
f = histfile
h = load(f, getOnlyEntry(f))
self.assertEqual( h.I.sum() , 0.0)
# Hits monitor
(xw, yh) = (0.1, 0.1)
position = "(0,0,1),(0,0,0)"
outdir = 'out-test_sizes-hits'
histfile = '%s/iw2.h5' % outdir
cmd = cmd_fmt % (xw, yh, position, outdir)
if os.system(cmd):
raise RuntimeError, "%r failed" % cmd
f = histfile
h = load(f, getOnlyEntry(f))
self.assert_( h.I.sum() > 0)
def test_sizes(self):
'ndmonitor: w; tests: xwidth, yheight'
outdir = 'out-test_sizes'
histfile = '%s/iw2.h5' % outdir
cmd_fmt = 'mcvine-simulate -components=source,monitor --- \
-overwrite-datafiles=on \
-ncount=1 \
-buffer_size=1 \
-source=Source_simple \
-monitor="NDMonitor(w)" \
-source.xw=0.1 \
-source.yh=0.1 \
-source.radius=0.05 \
-source.dist=1.0 \
-source.dE=10.0 \
-source.E0=60.0 \
-source.gauss=0.0 \
-source.flux=1.0 \
-monitor.wmin=0 \
-monitor.wmax=100 \
-monitor.nw=100 \
-monitor.filename=iw2.h5 \
-monitor.xwidth=%f \
-monitor.yheight=%f \
-geometer.monitor="%s" \
--output-dir=%s'
# Misses monitor
(xw, yh) = (0.1, 0.1)
position = "(0,1,1),(0,0,0)"
cmd = cmd_fmt % (xw, yh, position, outdir)
import os
if os.system(cmd):
raise RuntimeError, "%r failed" % cmd
from histogram.hdf import load
from histogram.hdf.utils import getOnlyEntry
f = histfile
h = load(f, getOnlyEntry(f))
self.assertEqual(h.I.sum(), 0.0)
# Hits monitor
(xw, yh) = (0.1, 0.1)
position = "(0,0,1),(0,0,0)"
outdir = 'out-test_sizes-hits'
histfile = '%s/iw2.h5' % outdir
cmd = cmd_fmt % (xw, yh, position, outdir)
if os.system(cmd):
raise RuntimeError, "%r failed" % cmd
f = histfile
h = load(f, getOnlyEntry(f))
self.assert_(h.I.sum() > 0)
def test3(self):
"multiphonon.getdos: low T"
list(
getDOS(os.path.join(datadir, "ARCS_V_annulus.nxs"),
T=1.5,
workdir='work-lowT'))
self.assert_(
close_hist(
hh.load('work-lowT/final-dos.h5'),
hh.load(
os.path.join(here, 'expected_results',
'getdos-test3-final-dos.h5'))))
return
def test2(self):
"multiphonon.getdos: MT can"
list(
getDOS(os.path.join(datadir, "ARCS_V_annulus.nxs"),
mt_nxs=os.path.join(datadir, "ARCS_V_annulus.nxs"),
mt_fraction=0.01,
workdir='work-MT'))
self.assert_(
close_hist(
hh.load('work-MT/final-dos.h5'),
hh.load(
os.path.join(here, 'expected_results',
'getdos-test2-final-dos.h5'))))
return
def test1(self):
"multiphonon.ui.batch"
_p = lambda f: os.path.join(self.tmpdir, f)
sample_nxs_list = [_p('1.nxs'), _p('2.nxs')]
mt_nxs_list = [None, None]
batch.process(sample_nxs_list, mt_nxs_list,
os.path.join(here, 'V-params.yaml'))
self.assert_(
np.allclose(
hh.load('work-1.nxs,None/final-dos.h5').I,
hh.load(
os.path.join(here, 'expected_results',
'batch-1-final-dos.h5')).I))
return
def test_rename(self):
"Histogram: rename"
import tempfile
outh5 = tempfile.mktemp()
code = """
from histogram import histogram, arange
h = histogram('h', [('x', arange(10), 'meter')])
h.I = h.x*h.x
h.setAttribute('name', 'abc')
from histogram.hdf import load, dump
dump(h, %r, '/', 'c')
""" % outh5
script = tempfile.mktemp()
open(script, 'w').write(code)
cmd = 'python %s' % script
import os
if os.system(cmd):
raise RuntimeError("%s failed" % cmd)
from histogram.hdf import load
h = load(outh5, 'abc')
os.remove(outh5)
os.remove(script)
return
def test_rename_sliced_histogram_using_rename_method(self):
"Histogram: rename()"
import tempfile
outh5 = tempfile.mktemp()
code = """
from histogram import histogram, arange
h = histogram(
'h',
[('x', arange(10), 'meter'),
('y', arange(15), 'meter'),
]
)
h1 = h[(2,5), ()].sum('x')
h1.rename('abc')
from histogram.hdf import load, dump
dump(h1, %r, '/', 'c')
""" % outh5
script = tempfile.mktemp()
open(script, 'w').write(code)
cmd = 'python %s' % script
import os
if os.system(cmd):
raise RuntimeError, "%s failed" % cmd
from histogram.hdf import load
try:
h = load(outh5, 'abc')
except:
raise RuntimeError, "failed to load histogram from %s" %(
outh5,)
os.remove(outh5)
os.remove(script)
return
def testdump_and_load1c(self):
'dump and load: meta data'
tmpfile = 'test_dump_load_1c.h5'
cmd = '''
from histogram import histogram
x = y = range(10)
h = histogram(
'h',
[ ('tID', x) ],
data = y, errors = y )
h.setAttribute('instrument', 'ARCS')
axis = h.axes()[0]
axis.setAttribute('pi', 3.14)
import histogram.hdf as hh
hh.dump( h, '{0!s}', '/', 'c' )
'''.format(tmpfile)
import os
if os.path.exists(tmpfile):
os.remove(tmpfile)
cmd = 'python -c "{0!s}"'.format(cmd)
if os.system(cmd):
raise "{0!s} failed".format(cmd)
h = load(tmpfile, 'h')
axis = h.axes()[0]
self.assertTrue(axis.isDiscrete())
self.assertEqual(axis.name(), 'tID')
self.assertEqual(h.getAttribute('instrument'), 'ARCS')
data = h.data()
self.assertEqual(axis.attribute('pi'), 3.14)
return
def test1c(self):
"singlephonon_sqe2dos: partial update"
iqehist = hh.load(os.path.join(datadir, "graphite-Ei_130-iqe.h5"))
initdos = hh.load(os.path.join(datadir, "graphite-Ei_300-dos.h5"))
newdos = sqe2dos.singlephonon_sqe2dos(iqehist,
T=300,
Ecutoff=100.,
elastic_E_cutoff=(-30., 15),
M=12.,
initdos=initdos)
# plot
if interactive:
pylab.plot(initdos.E, initdos.I)
pylab.plot(newdos.E, newdos.I)
pylab.show()
return
def test_bregmanSplit():
RF3_read = genfromtxt(os.path.join(data, "RF3_save.txt"))
dos_300 = hh.load(os.path.join(data, 'graphite-Ei_300-DOS.h5'))
DOS_300 = dos_300.I
spacing = dos_300.E[1] - dos_300.E[0]
energytobin = np.int(220 / spacing)
DOS_300[energytobin::] = 0
E_axis_DOS = dos_300.E
E_axis_res = np.arange(-50, 240, 0.1)
left = E_axis_res[E_axis_res < E_axis_DOS[0]]
extended_E_axis_DOS = np.concatenate((left, E_axis_DOS))
extended_g = np.concatenate((np.zeros(left.shape), dos_300.I))
dos_intrp1 = interp1d(extended_E_axis_DOS, extended_g, kind='cubic') # interpolation
interpolated_dos = dos_intrp1(E_axis_res)
E, g = E_axis_res, interpolated_dos
RF_T = np.transpose(RF3_read)
m = convolve_NS(RF_T, RF3_read)
delta = 2. / LA.norm(m, ord=1)
initial_d = np.zeros(g.shape[0])
initial_b = initial_d
mu = 100
lamda = 1
ninnner = 1
nouter = 20
max_cg = 500
R0 = S(g, RF3_read, initial_d, initial_b, mu, lamda, ninnner, nouter, max_cg)
plt.figure()
plt.plot (E_axis_res,R0)
plt.legend()
plt.show()
def run(hfile, p0):
import histogram.hdf as hh
h = hh.load(hfile)
p1, success = fit(h, p0)
print p1
print success
return
def run(hfile, p0):
import histogram.hdf as hh
h = hh.load(hfile)
success, p1, data = fit(h, p0)
print p1
print success
return
def main():
iqe1 = hh.load(p1)
iqe2 = hh.load(p2)
sigma_coh, sigma_inc = 1.495, 0.0082
getel = lambda iqe: iqe[(0.2, None),(-1.2,1.2)].I.sum()
getinel = lambda iqe: iqe[(2.4, 7.1), (None, -1.2)].I.sum() + iqe[(2.4, 7.1), (1.2, None)].I.sum()
coh_el = getel(iqe1) / sigma_coh
coh_inel = getinel(iqe1) / sigma_coh
incoh_el = getel(iqe2) / sigma_inc
incoh_inel = getinel(iqe2) / sigma_inc
print "coherent", coh_el, coh_inel
print "incoherent", incoh_el, incoh_inel
# pl.plot(ie1.energy, ie1.I/sigma_coh, 'r')
# pl.plot(ie2.energy, ie2.I/sigma_inc, 'g')
# pl.show()
return
def testdump_and_load_1d(self):
'dump and load: axis has unit'
tmpfile = 'test_dump_load_hdf5_1d.h5'
cmd = '''
from histogram import histogram
x = y = range(10)
h = histogram(
'h',
[ ('x', x, 'meter') ],
data = y, errors = y )
import histogram.hdf as hh
hh.dump( h, '%s', '/', 'c' )
''' % tmpfile
import os
if os.path.exists(tmpfile):
os.remove( tmpfile )
cmd = 'python -c "%s"' % cmd
if os.system( cmd ):
raise "%s failed" % cmd
h = load( tmpfile, 'h' )
for i in range(10):
self.assertVectorAlmostEqual( h[i], (i,i) )
continue
from histogram._units import tounit
meter = tounit('meter')
self.assertEqual(h.axisFromName('x').unit(), meter)
return
def testdump_and_load1c(self):
'dump and load: meta data'
tmpfile = 'test_dump_load_1c.h5'
cmd = '''
from histogram import histogram
x = y = range(10)
h = histogram(
'h',
[ ('tID', x) ],
data = y, errors = y )
h.setAttribute('instrument', 'ARCS')
axis = h.axes()[0]
axis.setAttribute('pi', 3.14)
import histogram.hdf as hh
hh.dump( h, '%s', '/', 'c' )
''' % tmpfile
import os
if os.path.exists(tmpfile):
os.remove( tmpfile )
cmd = 'python -c "%s"' % cmd
if os.system( cmd ):
raise "%s failed" % cmd
h = load( tmpfile, 'h' )
axis = h.axes()[0]
self.assert_(axis.isDiscrete())
self.assertEqual(axis.name(), 'tID')
self.assertEqual(h.getAttribute('instrument'), 'ARCS')
data = h.data()
self.assertEqual(axis.attribute('pi'), 3.14)
return
def test1(self):
"multiphonon.ms"
mpsqe = hh.load(os.path.join(datadir, "V-S2..5.h5"))
mssqe = ms.sqe(mpsqe, Ei=110.)
if interactive:
H.plot(mssqe, min=0)
return
def testdump_and_load_1d(self):
'dump and load: axis has unit'
tmpfile = 'test_dump_load_hdf5_1d.h5'
cmd = '''
from histogram import histogram
x = y = range(10)
h = histogram(
'h',
[ ('x', x, 'meter') ],
data = y, errors = y )
import histogram.hdf as hh
hh.dump( h, '{0!s}', '/', 'c' )
'''.format(tmpfile)
import os
if os.path.exists(tmpfile):
os.remove(tmpfile)
cmd = 'python -c "{0!s}"'.format(cmd)
if os.system(cmd):
raise "{0!s} failed".format(cmd)
h = load(tmpfile, 'h')
for i in range(10):
self.assertVectorAlmostEqual(h[i], (i, i))
continue
from histogram._units import tounit
meter = tounit('meter')
self.assertEqual(h.axisFromName('x').unit(), meter)
return
def test2(self):
datadir = self.datadir
from mcvine.phonon.powderSQE.IDF import from_data_dir
import mcvine.phonon.powderSQE.IDF as psidf
from mccomponents.sample import phonon as mcphonon
doshist = mcphonon.read_dos.dos_fromidf(os.path.join(datadir, 'DOS')).doshist
disp = psidf.disp_from_datadir(datadir)
IQEhist, mphhist = psidf.from_data_dir(
datadir=datadir,
disp=disp,
N = int(1e6),
Q_bins=np.arange(0, 14, 0.1), E_bins=np.arange(0,90,.5),
doshist=doshist,
T=300., Ei=120., max_det_angle=140.,
include_multiphonon=True,
)
IQEhist = IQEhist + mphhist
hh.dump(IQEhist, 'Si-iqe-test2.h5')
expected = hh.load(os.path.join(here, 'saved_results/Si-all-phonon-Ei_120-T_300-N_1e6.h5'))
max = np.nanmax(expected.I)
reldiff = IQEhist-expected
reldiff.I/=max; reldiff.E2/=max*max
Nbigdiff = (np.abs(reldiff.I)>0.03).sum()
Ngood = (IQEhist.I==IQEhist.I).sum()
Ntotal = IQEhist.size()
self.assertTrue(Ngood*1./Ntotal>.65)
self.assertTrue(Nbigdiff*1./Ngood<.10)
return
def test_rename_sliced_histogram_using_rename_method(self):
"Histogram: rename()"
import tempfile
outh5 = tempfile.mktemp()
code = """
from histogram import histogram, arange
h = histogram(
'h',
[('x', arange(10), 'meter'),
('y', arange(15), 'meter'),
]
)
h1 = h[(2,5), ()].sum('x')
h1.rename('abc')
from histogram.hdf import load, dump
dump(h1, %r, '/', 'c')
""" % outh5
script = tempfile.mktemp()
open(script, 'w').write(code)
cmd = 'python %s' % script
import os
if os.system(cmd):
raise RuntimeError("%s failed" % cmd)
from histogram.hdf import load
try:
h = load(outh5, 'abc')
except:
raise RuntimeError("failed to load histogram from %s" %(
outh5,))
os.remove(outh5)
os.remove(script)
return
def computeAverageEnergy():
from histogram.hdf import load
import os
out = '../mod2sample/out-analyzer'
h = load(os.path.join(out, 'ienergy.h5'), 'ienergy')
e = (h.energy * h.I).sum() / h.I.sum()
return e
def test1(self):
"multiphonon.ms"
mpsqe = hh.load(os.path.join(datadir, "V-S2..5.h5"))
mssqe = ms.sqe(mpsqe, Ei=110.)
if interactive:
H.plot(mssqe, min=0)
return
def crossCheckInputs(self):
inputs = self.inputs
# path = inputs['SQEhist']
path = self.context.excitation_params['SQEhist']
import histogram.hdf as hh
h = hh.load(path)
# Q
Q = h.Q
from pyre.units import parser
parser = parser()
Qmin, Qmax = parser.parse(inputs['Qrange'])
AA = parser.parse('angstrom')
Qmin, Qmax = Qmin * AA, Qmax * AA
if Qmin <= Q[0]:
raise ValueError("Qmin too small. should be larger than %s" % Q[0])
if Qmax >= Q[-1]:
raise ValueError("Qmax too large. should be less than %s" % Q[-1])
# E
E = getattr(h, 'E', None)
if E is None:
E = h.energy
Emin, Emax = parser.parse(inputs['Erange'])
meV = parser.parse('meV')
Emin, Emax = Emin / meV, Emax / meV
if Emin <= E[0]:
raise ValueError("Emin too small. should be larger than %s" % E[0])
if Emax >= E[-1]:
raise ValueError("Emax too large. should be less than %s" % E[-1])
return
def _gethist(path):
from histogram.hdf import load
from histogram.hdf.utils import getOnlyEntry
computation = domaccess.getComputationRecord('arcsbeamconfigurations', id)
dds = director.dds
p = dds.abspath(computation, path)
return load(p, getOnlyEntry(p))
def test_rename(self):
"Histogram: rename"
import tempfile
outh5 = tempfile.mktemp()
code = """
from histogram import histogram, arange
h = histogram('h', [('x', arange(10), 'meter')])
h.I = h.x*h.x
h.setAttribute('name', 'abc')
from histogram.hdf import load, dump
dump(h, %r, '/', 'c')
""" % outh5
script = tempfile.mktemp()
open(script, 'w').write(code)
cmd = 'python %s' % script
import os
if os.system(cmd):
raise RuntimeError, "%s failed" % cmd
from histogram.hdf import load
h = load(outh5, 'abc')
os.remove(outh5)
os.remove(script)
return
def test1(self):
# remove the output directory
if os.path.exists(outputdir):
shutil.rmtree(outputdir)
# build the command to ru
cmd = ['python E_monitor_TestCase_app2.py']
if usempi:
cmd.append('--mpirun.nodes=2')
cmd = ' '.join(cmd)
# run command
if os.system(cmd):
raise RuntimeError, "%s failed" % cmd
# checks
import time
ctime = time.time()
#check output directory exists
self.assert_( os.path.exists( outputdir ) )
# make sure that the final histogram is identical to the
# sum of all the final histograms in different nodes
from histogram.hdf import load
from histogram.hdf.utils import getOnlyEntry
p = os.path.join(outputdir, 'IE.h5')
h = load(p, getOnlyEntry(p))
self.assertEqual(h.I.sum(), 1)
return
def test1a(self):
"singlephonon_sqe2dos: simulated vanadium SQE -> DOS"
S = hh.load(os.path.join(datadir, "V-S1.h5"))
with warnings.catch_warnings(record=True) as ws:
warnings.simplefilter('always')
DOS = sqe2dos.singlephonon_sqe2dos(S,
T=300,
Ecutoff=55.,
elastic_E_cutoff=(0., 0.),
M=50.94)
for w in ws:
assert 'Scaling factor' not in str(w)
E = DOS.E
g = DOS.I
# compare to the original dos data
E1, g1 = loadDOS()
ginterp = np.interp(E1, E, g)
self.assert_(np.allclose(g1, ginterp))
# plot
if interactive:
import pylab
pylab.plot(E1, g1, label="Original DOS")
pylab.plot(E1, ginterp, label="DOS from SQE")
pylab.legend()
pylab.show()
return
def test1(self):
# remove the output directory
if os.path.exists(outputdir):
shutil.rmtree(outputdir)
# build the command to ru
cmd = ['python E_monitor_TestCase_app2.py']
if usempi():
cmd.append('--%s.nodes=2' % launcher)
cmd = ' '.join(cmd)
# run command
if os.system(cmd):
raise RuntimeError, "%s failed" % cmd
# checks
import time
ctime = time.time()
#check output directory exists
self.assert_( os.path.exists( outputdir ) )
# make sure that the final histogram is identical to the
# sum of all the final histograms in different nodes
from histogram.hdf import load
from histogram.hdf.utils import getOnlyEntry
p = os.path.join(outputdir, 'IE.h5')
h = load(p, getOnlyEntry(p))
self.assertEqual(h.I.sum(), 1)
return
def testdump2(self):
'dump two histograms to one hdf'
filename = 'testdump1.h5'
import os
if os.path.exists( filename):
os.remove( filename )
from h5py import File
fs = File( filename, 'w' )
from histogram import histogram, arange
h = histogram('h',
[('x', arange(0,100, 1.) ),
('y', arange(100, 180, 1.) ),],
unit = 'meter',
)
dump( h, None, '/', fs = fs )
h2 = histogram('h2',
[('x', arange(0,100, 1.) ),
('y', arange(100, 180, 1.) ),],
unit = 'meter',
)
dump( h2, None, '/', fs = fs )
#load histogram
h2c = load( filename, '/h2', fs = fs )
print h2c
self.assert_( os.path.exists( filename ))
def plot_dos_iteration(curdir, total_rounds=None):
"""
plot the DOS for each iteration
Parameters
----------
curdir : str
path to the root of the working directory for SQE->DOS calculation
total_rounds : integer
number of iterations
"""
if total_rounds is None:
import glob
dirs = glob.glob(os.path.join(curdir, 'round-*'))
_get_round_no = lambda p: int(os.path.basename(p).lstrip('round-'))
total_rounds = max(map(_get_round_no, dirs)) + 1
# mpl.rcParams['figure.figsize'] = 6,4.5
for round_no in range(total_rounds):
fn = os.path.join(curdir, 'round-' + str(round_no), 'dos.h5')
dos = hh.load(fn)
plt.errorbar(dos.E, dos.I, dos.E2**.5, label=str(round_no))
continue
plt.legend()
return
def computeAverageEnergy():
from histogram.hdf import load
import os
out = '../mod2sample/out-analyzer'
h = load(os.path.join(out, 'ienergy.h5'), 'ienergy')
e = (h.energy * h.I).sum()/h.I.sum()
return e
def test():
Q = 20.
import histogram.hdf as hh
iqe = hh.load('iqe.h5')
run(Q, iqe=iqe)
return
def hist_mcs_sum(outdir, histogramfilename):
"""compute the summed histogram and summed number of mc samples"""
import glob, os
pattern = os.path.join(outdir, '*', histogramfilename)
histfiles = glob.glob(pattern)
pattern = os.path.join(outdir, '*', number_mc_samples_filename)
mcsamplesfiles = glob.glob(pattern)
assert len(histfiles) == len(mcsamplesfiles), "histogram files %s does not match #mcsample files %s" %(len(histfiles), len(mcsamplesfiles))
if not histfiles:
return None, None
# load histograms
from histogram.hdf import load
from histogram.hdf.utils import getOnlyEntry
loadhist = lambda f: load(f, getOnlyEntry(f))
h1 = loadhist(histfiles[0])
# XXX
# due to a bug in h5py, we have to manually make a copy of the histogram
# see http://code.google.com/p/h5py/issues/detail?id=121
import histogram
h1 = histogram.histogram(h1.name(), h1.axes(), h1.I, h1.E2)
# XXX
def _addhistfile(f):
h = loadhist(f)
h1.I += h.I
h1.E2 += h.E2
return
map(_addhistfile, histfiles[1:])
# load number_of_mc_samples
loadmcs = lambda f: float(open(f).read())
mcs = map(loadmcs, mcsamplesfiles)
return h1, sum(mcs)
def testdump2(self):
'dump two histograms to one hdf'
filename = 'testdump1.h5'
import os
if os.path.exists(filename):
os.remove(filename)
from h5py import File
fs = File(filename, 'w')
from histogram import histogram, arange
h = histogram(
'h',
[
('x', arange(0, 100, 1.)),
('y', arange(100, 180, 1.)),
],
unit='meter',
)
dump(h, None, '/', fs=fs)
h2 = histogram(
'h2',
[
('x', arange(0, 100, 1.)),
('y', arange(100, 180, 1.)),
],
unit='meter',
)
dump(h2, None, '/', fs=fs)
#load histogram
h2c = load(filename, '/h2', fs=fs)
print(h2c)
self.assertTrue(os.path.exists(filename))
def test2a(self):
"sqe2dos: V exp"
iqehist = hh.load(os.path.join(datadir, "V-iqe.h5"))
from multiphonon.sqe import interp
newiqe = interp(iqehist, newE=np.arange(-15, 80, 1.))
hh.dump(newiqe, 'V-iqe-interped.h5')
iterdos = sqe2dos.sqe2dos(newiqe,
T=300,
Ecutoff=55.,
elastic_E_cutoff=(-12., 6.7),
M=50.94,
C_ms=.2,
Ei=120.,
workdir='work-V')
with warnings.catch_warnings(record=True) as ws:
warnings.simplefilter('always')
for i, dos in enumerate(iterdos):
# print dos
# plot
if interactive:
# print '*' * 70
pylab.plot(dos.E, dos.I, label='%d' % i)
pass
# check warning
for w in ws:
assert 'Scaling factor' not in str(w)
path = os.path.join(here, 'expected_results',
'sqe2dos-test2a-final-dos.h5')
# hh.dump(dos, path)
expected = hh.load(path)
self.assert_(np.allclose(dos.I, expected.I))
self.assert_(np.allclose(dos.E2, expected.E2))
if interactive:
pylab.figure()
pylab.errorbar(dos.E,
dos.I + dos.I.max() / 5.,
dos.E2**.5,
label='new')
pylab.errorbar(expected.E,
expected.I,
expected.E2**.5,
label='expected')
pylab.legend()
pylab.show()
return
def getTof(beampath):
import json, os
beam_outdir = os.path.join(beampath, 'out')
tof_hist_path = os.path.join(beam_outdir, 'itof.h5')
import histogram.hdf as hh
tofhist = hh.load(tof_hist_path)
tofcenter = (tofhist.tof * tofhist.I).sum() / tofhist.I.sum()
return tofcenter
def test_compare_mcvine():
"""
Tests the acc cpu implementation of a straight guide against mcvine
"""
num_neutrons = 100000
# Run the mcvine instrument first
instr = os.path.join(thisdir, "guide_instrument.py")
mcvine_outdir = 'out.debug-mcvine_guide_cpu_instrument'
if os.path.exists(mcvine_outdir):
shutil.rmtree(mcvine_outdir)
run_script.run1(instr,
mcvine_outdir,
ncount=num_neutrons,
buffer_size=num_neutrons,
guide_factory="mcvine.components.optics.Guide",
overwrite_datafiles=True)
# Run our guide implementation
outdir = 'out.debug-guide_cpu_instrument'
if os.path.exists(outdir):
shutil.rmtree(outdir)
run_script.run1(instr,
outdir,
ncount=num_neutrons,
buffer_size=num_neutrons,
guide_mod="mcvine.acc.components.optics.numpy_guide",
overwrite_datafiles=True)
# Compare output files
mcvine_Ixy = hh.load(os.path.join(mcvine_outdir, "Ixy.h5"))
mcvine_Ixdivx = hh.load(os.path.join(mcvine_outdir, "Ixdivx.h5"))
Ixy = hh.load(os.path.join(outdir, "Ixy.h5"))
Ixdivx = hh.load(os.path.join(outdir, "Ixdivx.h5"))
global interactive
if interactive:
from histogram import plot as plotHist
plotHist(mcvine_Ixy)
plotHist(mcvine_Ixdivx)
plotHist(Ixy)
plotHist(Ixdivx)
assert mcvine_Ixy.shape() == Ixy.shape()
assert mcvine_Ixdivx.shape() == Ixdivx.shape()
assert np.allclose(mcvine_Ixy.data().storage(), Ixy.data().storage())
assert np.allclose(mcvine_Ixdivx.data().storage(), Ixdivx.data().storage())
return
def main():
iqe1 = hh.load(p1)
iqe2 = hh.load(p2)
sigma_coh, sigma_inc = 1.495, 0.0082
getel = lambda iqe: iqe[(0.2, None), (-1.2, 1.2)].I.sum()
getinel = lambda iqe: iqe[(2.4, 7.1), (None, -1.2)].I.sum() + iqe[
(2.4, 7.1), (1.2, None)].I.sum()
coh_el = getel(iqe1) / sigma_coh
coh_inel = getinel(iqe1) / sigma_coh
incoh_el = getel(iqe2) / sigma_inc
incoh_inel = getinel(iqe2) / sigma_inc
print "coherent", coh_el, coh_inel
print "incoherent", incoh_el, incoh_inel
# pl.plot(ie1.energy, ie1.I/sigma_coh, 'r')
# pl.plot(ie2.energy, ie2.I/sigma_inc, 'g')
# pl.show()
return
def testload5(self):
'load with fs specified'
filename = 'tmp.h5'
filename = 'test_dump_load2.h5'
from h5py import File
fs = File(filename)
h = load( filename, '/h', fs = fs )
return
def _gethist(path):
from histogram.hdf import load
from histogram.hdf.utils import getOnlyEntry
computation = domaccess.getComputationRecord(
'arcsbeamconfigurations', id)
dds = director.dds
p = dds.abspath(computation, path)
return load(p, getOnlyEntry(p))
def main():
import sys
Q = eval(sys.argv[1])
iqe = sys.argv[2]
import histogram.hdf as hh
iqe = hh.load(iqe)
p1 = run(Q, iqe=iqe, dQ=0.5)
line = '%s\t%s\n' % (Q, p1[-1])
open('res.dat', 'a').write(line)
return
def test1b(self):
iqehist = hh.load(os.path.join(datadir, "V-iqe.h5"))
from multiphonon.sqe import interp
newiqe = interp(iqehist, newE=np.arange(-50, 50, 1.0))
DOS = sqe2dos.singlephonon_sqe2dos(newiqe, T=300, Ecutoff=65.0, elastic_E_cutoff=(-20.0, 6.7), M=50.94)
# plot
if interactive:
H.plot(DOS)
return
def getDOS(sample_nxs, mt_nxs=None, mt_fraction=0.9,
Emin=-100, Emax=100, dE=1.,
Qmin=0, Qmax=15., dQ=0.1, T=300, Ecutoff=50.,
elastic_E_cutoff=(-20., 7), M=50.94,
C_ms=0.3, Ei=116.446, workdir='work',
iqe_nxs="iqe.nxs", iqe_h5="iqe.h5"):
# prepare paths
if not os.path.exists(workdir):
os.makedirs(workdir)
if not os.path.isabs(iqe_nxs):
iqe_nxs = os.path.abspath(os.path.join(workdir, iqe_nxs))
if not os.path.isabs(iqe_h5):
iqe_h5 = os.path.abspath(os.path.join(workdir, iqe_h5))
# reduce
Eaxis = Emin, Emax, dE
Qaxis = Qmin, Qmax, dQ
raw2iqe(sample_nxs, iqe_nxs, iqe_h5, Eaxis, Qaxis)
iqehist = hh.load(iqe_h5)
if mt_nxs is not None:
_tomtpath = lambda p: os.path.join(
os.path.dirname(p), 'mt-'+os.path.basename(p))
mtiqe_nxs = _tomtpath(iqe_nxs)
mtiqe_h5 = _tomtpath(iqe_h5)
raw2iqe(mt_nxs, mtiqe_nxs, mtiqe_h5, Eaxis, Qaxis)
iqehist -= hh.load(mtiqe_h5) * (mt_fraction, 0)
# to DOS
# interpolate data
from .sqe import interp
# probably don't need this line
newiqe = interp(iqehist, newE = np.arange(Emin, Emax, dE))
# save interpolated data
hh.dump(newiqe, 'iqe-interped.h5')
# create processing engine
from .backward import sqe2dos
print("iterative computation of DOS...")
iterdos = sqe2dos.sqe2dos(
newiqe, T=T, Ecutoff=Ecutoff,
elastic_E_cutoff=elastic_E_cutoff, M=M,
C_ms=C_ms, Ei=Ei, workdir='work')
doslist = list(iterdos)
print("done.")
return doslist
def test3(self):
"plot sqe"
import histogram.hdf as hh, pylab
sqe = hh.load("sqe.h5/S(Q,E)")
self.plotter.plot(sqe)
if interactive:
raw_input("Press ENTER to continue")
pylab.clf()
pylab.close()
return
def test3a(self):
"plot sqe with interpolation"
import histogram.hdf as hh, pylab
sqe = hh.load("sqe.h5/S(Q,E)")
self.plotter.plot(sqe, interpolation="bicubic")
if interactive:
raw_input("Press ENTER to continue")
pylab.clf()
pylab.close()
return
def test_load_slice_and_dump(self):
'load a histogram and dump a slice of it'
tmpfile = 'test_load_slice_and_dump.h5'
if os.path.exists( tmpfile ):
os.remove( tmpfile )
import histogram.hdf as hh
h = hh.load('testload.h5', '/h')
s = h[(10, 30), ()]
hh.dump(s, tmpfile, '/', 'c')
return
def computeFWHM(out):
from histogram.hdf import load
import numpy as np
itof = load(os.path.join(out, 'itof.h5'), 'itof')
max = itof.I.max()
indmax = np.where(itof.I==max)[0][0]
left = itof.I[:indmax]
right = itof.I[indmax:]
leftindex = np.where(left > max/2)[0][0]
rightindex = np.where(right > max/2)[0][-1] + indmax
fwhm = (rightindex-leftindex) * (itof.tof[1]-itof.tof[0])
return fwhm
def read_pixE(self):
from histogram.hdf import load
self.histogram = load(self.path)
phi = self.histogram.phi * deg2rad
nphi = len(phi)
theta = self.histogram.theta * deg2rad
ntheta = len(theta)
import numpy as np
phi = np.tile(phi, ntheta)
theta = np.repeat(theta, nphi)
energy = self.histogram.E
return energy, theta, phi
def test2(self):
iqehist = hh.load(os.path.join(datadir, "V-iqe.h5"))
newsqe = interp(iqehist, newE=np.arange(-50, 50, 1.))
mask = dynamical_range_mask(newsqe, Ei=120)
# plot
if interactive:
import pylab
pylab.imshow(mask.T[::-1])
pylab.clim(0, None)
pylab.colorbar()
pylab.show()
return
def main():
import sys
argv = sys.argv
filenames = argv[1:]
from histogram.hdf import load
hs = [load(f) for f in filenames]
r = compare(hs[0], hs[1])
if r: raise RuntimeError, r
else: print 'same'
return
def test3(self):
'ndmonitor: energy'
cmd = 'mcvine-simulate -components=source,monitor --- -ncount=1e4 -buffer_size=1000 -source=MonochromaticSource -monitor="NDMonitor(energy)" -geometer.monitor="(0,0,1),(0,0,0)" -source.energy=60 -monitor.energymin=0 -monitor.energymax=100 -monitor.nenergy=100 -monitor.filename=ienergy.h5 --output-dir=out-test3'
import os
if os.system(cmd):
raise RuntimeError, "%r failed" % cmd
from histogram.hdf import load
from histogram.hdf.utils import getOnlyEntry
f = 'out-test3/ienergy.h5'
h = load(f, getOnlyEntry(f))
self.assertEqual( h[(58, 62)].sum() , (1., 1.e-4))
return