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 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 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 testOneNumber(self):
out = histogram([1])
self.assertAlmostEqual(out[0,0], 2)
self.assertAlmostEqual(out[0,1], 1)
out = histogram([10])
self.assertAlmostEqual(out[0,0], 16)
self.assertAlmostEqual(out[0,1], 0.125)
def get_hash_mentions(tweets, count=3):
""" returns stats about hashtags and mentions from tweets
tweets: a list of strings
"""
hashtags = strings_startswith(tweets, '#')
mentions = strings_startswith(tweets, '@')
freq_hashtags = sort_dct(histogram(hashtags))
freq_mentions = sort_dct(histogram(mentions))
return freq_hashtags[:count], freq_mentions[:count]
def make_energy_collection(length=600):
collection = dict()
min_E, max_E = -2, 5
bins_per_decade = 10
frac_loss_bins = length / 60
collection['deltaE'] = histogram.histogram(bins=np.logspace(min_E,max_E,(max_E-min_E)*bins_per_decade+1))
collection['frac_loss'] = histogram.histogram_nd(2, bins=np.linspace(0,length,frac_loss_bins+1))
for i in xrange(frac_loss_bins):
collection['bin_'+str(i)+'_dE'] = histogram.histogram(bins=np.array([0]+list(np.logspace(min_E,max_E,(max_E-min_E)*bins_per_decade+1))))
collection['bin_'+str(i)+'_frac_loss'] = histogram.histogram(bins=np.array([0]+list(np.logspace(-7,0,7*bins_per_decade+1))))
return collection
def get_stats(tweets, scr_name, count=2):
""" returns stats about hashtags and user mentions
tweets: a dict of tweet dicts from rest api
"""
hashtags = get_hashtags(tweets)
mentions = get_mentions(tweets)
freq_hashtags = sort_dct(histogram(hashtags))
freq_mentions = sort_dct(histogram(mentions))
freq_mentions = remove_self(freq_mentions, scr_name)
return freq_hashtags[:count], freq_mentions[:count]
def test_pickle_0(self):
a = histogram(category(0, 1, 2),
integer(0, 20, label='ia'),
regular(20, 0.0, 20.0, uoflow=False),
variable(0.0, 1.0, 2.0),
circular(4, label='pa'))
for i in range(len(a.axis(0))):
a.fill(i, 0, 0, 0, 0)
for j in range(len(a.axis(1))):
a.fill(i, j, 0, 0, 0)
for k in range(len(a.axis(2))):
a.fill(i, j, k, 0, 0)
for l in range(len(a.axis(3))):
a.fill(i, j, k, l, 0)
for m in range(len(a.axis(4))):
a.fill(i, j, k, l, m * 0.5 * pi)
io = BytesIO()
pickle.dump(a, io)
io.seek(0)
b = pickle.load(io)
self.assertNotEqual(id(a), id(b))
self.assertEqual(a.dim, b.dim)
self.assertEqual(a.axis(0), b.axis(0))
self.assertEqual(a.axis(1), b.axis(1))
self.assertEqual(a.axis(2), b.axis(2))
self.assertEqual(a.axis(3), b.axis(3))
self.assertEqual(a.axis(4), b.axis(4))
self.assertEqual(a.sum, b.sum)
self.assertEqual(a, b)
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 __init__(self, nAtoms, dimension,
Qaxes, eps_npyarr, E_npyarr,
dos = None):
'''
natoms: number of atoms in the unit cell
dimension:
Qaxes: a tuple of Q axes. Each item is a 2-tuple of (q, n).
q vector is the direction of the Q axis.
n is the number of points along this Q axis.
Example: [ ( (2.2,0,0), 20), ((0,3.1,0), 20), ((0,0,1.4), 20) ] for a 3d dispersion
eps_npyarr: numpy array of poloarization. shape must be (3d case)
nQx, nQy, nQz, nBranches, nAtoms, 3, 2
E_npyarr: numpy array of phonon energy. shape must be (3d case)
nQx, nQy, nQz, nBranches
dos: a 2-tuple of E,Z
'''
base.__init__(self, nAtoms, dimension)
assert len(Qaxes) == dimension
self.Qaxes = Qaxes
self.eps_npyarr = eps_npyarr
self.E_npyarr = E_npyarr
from histogram import histogram
if dos:
e,Z = dos
from .utils import nice_dos
e, Z = nice_dos(e, Z)
self.dos = histogram( 'dos', [ ('energy', e, 'meV') ], data = Z )
pass
return
def test_numpy_conversion_2(self):
a = histogram(integer(0, 2, uoflow=False),
integer(0, 3, uoflow=False),
integer(0, 4, uoflow=False))
r = numpy.zeros((2, 3, 4), dtype=numpy.int8)
for i in range(len(a.axis(0))):
for j in range(len(a.axis(1))):
for k in range(len(a.axis(2))):
for m in range(i+j+k):
a.fill(i, j, k)
r[i,j,k] = i+j+k
d = numpy.zeros((2, 3, 4), dtype=numpy.int8)
for i in range(len(a.axis(0))):
for j in range(len(a.axis(1))):
for k in range(len(a.axis(2))):
d[i,j,k] = a.value(i,j,k)
self.assertTrue(numpy.all(d == r))
c = numpy.array(a) # a copy
v = numpy.asarray(a) # a view
self.assertTrue(numpy.all(c == r))
self.assertTrue(numpy.all(v == r))
def word_generator():
my_file = open("./test2.txt", "r")
lines = my_file.readlines()
my_histogram = histogram(lines)
word = weighted_sample(my_histogram)
return word
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 test_pickle_1(self):
a = histogram(category(0, 1, 2),
integer(0, 3, label='ia'),
regular(4, 0.0, 4.0, uoflow=False),
variable(0.0, 1.0, 2.0))
for i in range(len(a.axis(0))):
a.fill(i, 0, 0, 0, weight=3)
for j in range(len(a.axis(1))):
a.fill(i, j, 0, 0, weight=10)
for k in range(len(a.axis(2))):
a.fill(i, j, k, 0, weight=2)
for l in range(len(a.axis(3))):
a.fill(i, j, k, l, weight=5)
io = BytesIO()
pickle.dump(a, io)
io.seek(0)
b = pickle.load(io)
self.assertNotEqual(id(a), id(b))
self.assertEqual(a.dim, b.dim)
self.assertEqual(a.axis(0), b.axis(0))
self.assertEqual(a.axis(1), b.axis(1))
self.assertEqual(a.axis(2), b.axis(2))
self.assertEqual(a.axis(3), b.axis(3))
self.assertEqual(a.sum, b.sum)
self.assertEqual(a, b)
def test_numpy_conversion_0(self):
a = histogram(integer(0, 3, uoflow=False))
for i in range(10):
a.fill(1)
a.fill(1, count=90)
c = numpy.array(a) # a copy
v = numpy.asarray(a) # a view
for t in (c, v):
self.assertEqual(t.dtype, numpy.uint8)
self.assertTrue(numpy.all(t == numpy.array((0, 100, 0))))
for i in range(20):
a.fill(1)
a.fill(1, count=2 * numpy.ones(40, dtype=numpy.uint32))
# copy does not change, but view does
self.assertTrue(numpy.all(c == numpy.array((0, 100, 0))))
self.assertTrue(numpy.all(v == numpy.array((0, 200, 0))))
a.fill(1, count=100)
c = numpy.array(a)
self.assertEqual(c.dtype, numpy.uint16)
self.assertTrue(numpy.all(c == numpy.array((0, 300, 0))))
# view does not follow underlying switch in word size
self.assertFalse(numpy.all(c == v))
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 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 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()
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 getHistogram(self, scale_factor=1.):
import histogram as H
axes = [('x', self.x_centers, 'm'), ('y', self.y_centers, 'm')]
return H.histogram(
'Iyx', axes,
data=self.out_p*scale_factor,
errors=self.out_p2*scale_factor*scale_factor)
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 histplot(data, ax=None, bins=10, **kwargs):
"""
Histogram plot
Parameters
----------
data : array_like
data
ax : Axes, optional
Axes object. Default is None.
Returns
-------
ax : Axes
The new Axes object
"""
if ax is None:
ax = plt.gca()
counts, bins = histogram(data, bins=bins)
ax.hist(bins[:-1],
bins=bins,
weights=counts,
histtype='bar',
edgecolor=None,
color='steelblue',
alpha=0.9,
**kwargs)
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 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 __init__(self,
nAtoms,
dimension,
Qaxes,
eps_npyarr,
E_npyarr,
dos=None):
'''
natoms: number of atoms in the unit cell
dimension:
Qaxes: a tuple of Q axes. Each item is a 2-tuple of (q, n).
q vector is the direction of the Q axis.
n is the number of points along this Q axis.
Example: [ ( (2.2,0,0), 20), ((0,3.1,0), 20), ((0,0,1.4), 20) ] for a 3d dispersion
eps_npyarr: numpy array of poloarization. shape must be (3d case)
nQx, nQy, nQz, nBranches, nAtoms, 3, 2
E_npyarr: numpy array of phonon energy. shape must be (3d case)
nQx, nQy, nQz, nBranches
dos: a 2-tuple of E,Z
'''
base.__init__(self, nAtoms, dimension)
assert len(Qaxes) == dimension
self.Qaxes = Qaxes
self.eps_npyarr = eps_npyarr
self.E_npyarr = E_npyarr
from histogram import histogram
if dos:
e, Z = dos
from .utils import nice_dos
e, Z = nice_dos(e, Z)
self.dos = histogram('dos', [('energy', e, 'meV')], data=Z)
pass
return
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 compare_6d(n, distrib):
if distrib == 0:
r = np.random.rand(6 * n)
else:
r = 0.3 * np.random.randn(6 * n)
r = r.reshape(n, 6)
best_numpy = float("infinity")
best_boost = float("infinity")
for k in xrange(10):
t = timer()
w, xe = np.histogramdd(r,
bins=(10, 10, 10, 10, 10, 10),
range=((0.0, 1.0), (0.0, 1.0), (0.0, 1.0),
(0.0, 1.0), (0.0, 1.0), (0.0, 1.0)))
t = timer() - t
best_numpy = min(t, best_numpy)
h = histogram(regular_axis(10, 0, 1), regular_axis(10, 0, 1),
regular_axis(10, 0, 1), regular_axis(10, 0, 1),
regular_axis(10, 0, 1), regular_axis(10, 0, 1))
t = timer()
h.fill(r)
t = timer() - t
best_boost = min(t, best_boost)
print "6D"
print "t[numpy] = %.3f" % best_numpy
print "t[boost] = %.3f" % best_boost
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 results_histogram(outcomes):
#storing outcomes and freq in this empty dict
results = {}
for word in outcomes:
results = histogram(outcomes)
return results
def most_frequent(doc, typef='char', to_limit=False):
"""
Sorts the typef in doc in reverse order of frequency.
"""
if typef == 'char':
hist = histogram.histogram(doc)
elif typef == 'word':
hist = word_histogram(doc)
t = []
for x, freq in hist.iteritems():
t.append((freq, x))
t.sort(reverse=True)
result = []
#list of tuples
limit = 0 # to limit only 20 most frequent words
tots = total_freq(t)
for freq, x in t:
#if x!=' ':
# space is not a char
percentage = get_percent_in2points(freq, tots)
result.append((x, freq, percentage))
if typef == 'word' and to_limit == False:
limit += 1
if limit == 20:
break
return result, tots
def testTwoNumbers(self):
out = histogram([1,2])
self.assertEqual(out[0,0], 2)
self.assertEqual(out[0,1], 0.5)
self.assertEqual(out[1,0], 4)
self.assertEqual(out[1,1], 0.25)
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 compare_2d(n, distrib):
if distrib == 0:
r = np.random.rand(n)
else:
r = 0.5 + 0.3 * np.random.randn(n)
r = r.reshape(2, n / 2)
best_numpy = float("infinity")
best_boost = float("infinity")
for k in xrange(50):
t = timer()
w, xe, ye = np.histogram2d(r[0],
r[1],
bins=(100, 100),
range=((0.0, 1.0), (0.0, 1.0)))
t = timer() - t
best_numpy = min(t, best_numpy)
h = histogram(regular(100, 0, 1), regular(100, 0, 1))
t = timer()
h.fill(r[0], r[1])
t = timer() - t
best_boost = min(t, best_boost)
assert (np.all(w == np.array(h)[:-2, :-2]))
print "py:numpy %.3f" % best_numpy
print "py:hd_sd %.3f" % best_boost
def descriptor(imagem, desc, list_of_parameters):
"""
Function to compute feature vector for an image
Parameters
----------
imagem : numpy array
RGB or grayscale image
desc : string
descriptor to compute the features
list_of_parameters : numpy array or list
parameters of each descriptor, can be different sizes depending the descriptor
Returns
-------
features : numpy array
the feature vector computed by the descriptor 'desc'
"""
if desc == 'glcm':
features = glcm.glcm(imagem, [], int(list_of_parameters[1]),
int(list_of_parameters[0]))
elif desc == 'fotf':
features = histogram.histogram(imagem, [])
elif desc == 'lbp':
features = lbp.lbpTexture(imagem, [], 8 * int(list_of_parameters[0]),
int(list_of_parameters[0]))
elif desc == 'hog':
features = hog_rom.HOG(imagem, [], int(list_of_parameters[0]),
int(list_of_parameters[1]))
return features[0]
def coocorrencia(image, d=1, theta=0):
#image=imread(img, as_grey=True)
h = hist.histogram(image.astype('int32'))
Ntonscinza = len(h)
descritoresMC = np.zeros((1, 4)).astype('double')
#greycomatrix(imagem, d, theta, niveis de cinza da imagem)
# g = greycomatrix(image, d, theta, Ntonscinza,normed=True,symmetric=True)
g = greycomatrix(image, [d], [theta], Ntonscinza)
g[0, :] = 0
g[:, 0] = 0
# Para mostrar a matriz de coocorrencia
# print g[:,:,0,0]
# somat = (np.sum(g)).astype('double')
#
# #Matriz de coocorrencia normalizada
# gn = (g/somat).astype('double')
# descritoresMC[0][0] = greycoprops(g, 'ASM')
descritoresMC[0][0] = np.round(greycoprops(g, 'energy'), 2)
descritoresMC[0][1] = np.round(greycoprops(g, 'contrast'), 2)
descritoresMC[0][2] = np.round(greycoprops(g, 'homogeneity'), 2)
# descritoresMC[0][4] = greycoprops(g, 'correlation')
descritoresMC[0][3] = np.round(greycoprops(g, 'dissimilarity'), 2)
#return g[:,:,0,0], gn[:,:,0,0], descritoresMC
return descritoresMC
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 getHistogram(self, scale_factor=1.):
import histogram as H
axes = [('wavelength', self.L_centers, 'angstrom')]
return H.histogram(
'I(wavelength)', axes,
data=self.out_p*scale_factor,
errors=self.out_p2*scale_factor*scale_factor)
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 sample(text):
# converts text to histogram
histo = histogram(text)
# print("histogram: ")
# print(histogram)
# returns number of tokens in histogram
# tokens = 0
# for word in histo:
# tokens += histo[word]
tokens = unique_words(histo)
# print("tokens: ")
# print(tokens)
# cumulative_probability
cum_prob = 0
# random number
ranum = random.uniform(0, 1)
# print("random number: ")
# print(ranum)
# randomly picks one word based on word frequency
for word in histo:
cum_prob += (float(histo[word]) / float(tokens))
# print("cumulative prob: ")
# print(cum_prob)
if cum_prob >= ranum:
return word
def compare_3d(n, distrib):
if distrib == 0:
r = np.random.rand(3 * n)
else:
r = 0.3 * np.random.randn(3 * n)
r = r.reshape(n, 3)
best_numpy = float("infinity")
best_boost = float("infinity")
for k in xrange(10):
t = timer()
w, xe = np.histogramdd(r, bins=(100, 100, 100),
range=((0.0, 1.0),
(0.0, 1.0),
(0.0, 1.0)))
t = timer() - t
best_numpy = min(t, best_numpy)
h = histogram(regular_axis(100, 0, 1),
regular_axis(100, 0, 1),
regular_axis(100, 0, 1))
t = timer()
h.fill(r)
t = timer() - t
best_boost = min(t, best_boost)
print "3D"
print "t[numpy] = %.3f" % best_numpy
print "t[boost] = %.3f" % best_boost
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 test3(self):
'LinearlyInterpolatedDispersion_3D'
import mccomponents.sample.phonon.bindings as bindings
b = bindings.get('BoostPython')
nAtoms = 2
nBranches = 3 * nAtoms
nQx = 10; nQy = 12; nQz = 14
Qaxes = [ ([1,1,0], nQx),
([1,0,1], nQy),
([0,1,1], 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],
fromfunction = lambda qx,qy,qz,br,atom,pol,realimag: qx+qy+qz+br+atom+pol+realimag)
e = H.histogram(
'e', [qx,qy,qz,br],
fromfunction = lambda qx,qy,qz,br: qx+qy+qz+br)
disp = b.linearlyinterpolateddispersion_3d(nAtoms, Qaxes, eps.I, e.I)
Q = b.vector3
# XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
# these tests failed because we are not doing interpolation
# right now since we don't have a good way to do
# it for the polarization vectors.
# right now we just take the value of the closest vertex.
checkDiff = self.assertAlmostEqual
def checkDiff(a, b):
print a,b
checkDiff(disp.energy(0, Q(0,0,0)), 0)
checkDiff(disp.energy(0, Q(1-1e-5,1-1e-5,0)), 1-1e-5)
checkDiff(disp.energy(0, Q(0.5,0.5,0)), 0.5)
checkDiff(disp.energy(0, Q(0.5,0,0.5)), 0.5)
checkDiff(disp.energy(0, Q(0,0.5,0.5)), 0.5)
checkDiff(disp.energy(0, Q(0.5,0.5,1-1e-10)), 1)
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 saveSQE(Q, E, S, name):
h = H.histogram(
name,
[('Q', Q, 'angstrom**-1'),
('E', E, 'meV')],
S)
hh.dump(h, '%s.h5' % (name,))
return
def get_word(histogram):
histo, corp_length = histogram()
index = int(random.random() * corp_length)
summed = 0
for word, freq in histo:
summed += freq
if summed > index:
return word
def test_sampler(hist):
""" tests sampler by running it 10000 times, uncomment line 32 for this"""
test_words = []
for _ in range(10000):
test_words.append(word_sampler(hist))
test_hist = histogram(test_words)
for item in test_hist.keys():
print(f"{item}: {test_hist[item]}")
def histogram_equalization(im, verbose=True):
new_im = np.zeros_like(im)
try:
h, w, ch = im.shape
except ValueError:
h, w = im.shape
ch = 1
hist = histogram(im, verbose=False)[0]
cum_hist = np.cumsum(hist)
for j in range(h):
for i in range(w):
new_im[j, i] = cum_hist[im[j, i]] * 255
if verbose:
fig = plt.figure()
ax11 = fig.add_subplot(2, 3, 1)
ax12 = fig.add_subplot(2, 3, 2)
ax13 = fig.add_subplot(2, 3, 3)
ax21 = fig.add_subplot(2, 3, 4)
ax22 = fig.add_subplot(2, 3, 5)
ax23 = fig.add_subplot(2, 3, 6)
ax11.plot(np.arange(0, 256, 1), hist)
ax11.set_title("Prob Distribuition")
ax12.plot(np.arange(0, 256, 1), cum_hist)
ax12.set_title("Cumalative Prob Distribuition")
ax13.imshow(im, cmap='gray')
ax13.set_title("After")
ax13.axis('off')
new_hist = histogram(new_im, verbose=False)[0]
new_cum_hist = np.cumsum(new_hist)
ax21.plot(np.arange(0, 256, 1), new_hist)
ax21.set_title("New Prob Distribuition")
ax22.plot(np.arange(0, 256, 1), new_cum_hist)
ax22.set_title("New CDF")
ax23.imshow(new_im, cmap='gray')
ax23.set_title("After")
ax23.axis('off')
plt.show()
return new_im
def jsonlisttest():
searchimg = cv2.imread(
'D:/python/histogram_test/searchimage/wahoo_test.jpg',
cv2.IMREAD_COLOR)
findlist_x = histogram.histogram(searchimg)
lst = histogram.matching(searchimg, findlist_x)
return jsonify(lst)
def histogram_matching(im1, im2, verbose=True):
try:
h, w, ch = im1.shape
except ValueError:
h, w = im1.shape
ch = 1
hist1 = histogram(im1, verbose=False)[0]
cum_hist1 = np.cumsum(hist1)
hist2 = histogram(im2, verbose=False)[0]
cum_hist2 = np.cumsum(hist2)
if verbose:
fig = plt.figure()
ax11 = fig.add_subplot(3, 2, 1)
ax12 = fig.add_subplot(3, 2, 2)
ax21 = fig.add_subplot(3, 2, 3)
ax22 = fig.add_subplot(3, 2, 4)
ax31 = fig.add_subplot(3, 2, 5)
ax32 = fig.add_subplot(3, 2, 6)
ax11.plot(np.arange(0, 256, 1), cum_hist1)
ax11.set_title("Original CDF")
ax12.imshow(im1, cmap='gray')
ax12.set_title("Original")
ax12.axis('off')
ax21.plot(np.arange(0, 256, 1), cum_hist2)
ax21.set_title("Desired CDF")
ax22.imshow(im2, cmap='gray')
ax22.set_title("Second Image")
ax22.axis('off')
new_hist = histogram(new_im, verbose=False)[0]
new_cum_hist = np.cumsum(new_hist)
ax31.plot(np.arange(0, 256, 1), new_cum_hist)
ax31.set_title("New CDF")
ax32.imshow(new_im, cmap='gray')
ax32.set_title("New Image")
ax32.axis('off')
plt.show()
return new_im
def test_fill_with_numpy_array_1(self):
ar = lambda *args: numpy.array(args, dtype=float)
a = histogram(integer(0, 3, uoflow=True))
v = ar(-1, 0, 1, 2, 3, 4)
w = ar( 2, 3, 4, 5, 6, 7)
a.fill(v, weight=w)
a.fill((0, 1), weight=(2, 3))
self.assertEqual(a.value(-1), 2)
self.assertEqual(a.value(0), 5)
self.assertEqual(a.value(1), 7)
self.assertEqual(a.value(2), 5)
self.assertEqual(a.variance(-1), 4)
self.assertEqual(a.variance(0), 13)
self.assertEqual(a.variance(1), 25)
self.assertEqual(a.variance(2), 25)
a.fill((1, 2), weight=1)
a.fill(0, weight=(1, 2))
self.assertEqual(a.value(0), 8)
self.assertEqual(a.value(1), 8)
self.assertEqual(a.value(2), 6)
with self.assertRaises(RuntimeError):
a.fill((1, 2), foo=(1, 1))
with self.assertRaises(ValueError):
a.fill((1, 2), weight=(1,))
with self.assertRaises(ValueError):
a.fill((1, 2), weight="ab")
with self.assertRaises(RuntimeError):
a.fill((1, 2), weight=(1, 1), foo=1)
with self.assertRaises(ValueError):
a.fill((1, 2), weight=([1, 1], [2, 2]))
a = histogram(integer(0, 2, uoflow=False),
regular(2, 0, 2, uoflow=False))
a.fill((-1, 0, 1), (-1, 1, 0.1))
self.assertEqual(a.value(0, 0), 0)
self.assertEqual(a.value(0, 1), 1)
self.assertEqual(a.value(1, 0), 1)
self.assertEqual(a.value(1, 1), 0)
a = histogram(integer(0, 3, uoflow=False))
a.fill((0, 0, 1, 2))
a.fill((1, 0, 2, 2))
self.assertEqual(a.value(0), 3)
self.assertEqual(a.value(1), 2)
self.assertEqual(a.value(2), 3)
def __init__(self, name, axes, size=[0.1, 0.1]):
"""
axes: a list of axis
axis: an instance of Axis class, or
(obsolete) a tuple of name, expression, bins, range
name: name of the axis
expression: expression of the axis
bins: number of bins of the axis
ranges: (min, max) tuple for the axis
"""
self.name = name
expressions = self.expressions = []
bins = self.bins = []
ranges = self.ranges = []
haxes = []
self.xwidth = size[0]
self.yheight = size[1]
from histogram import histogram, axis as createAxis
from numpy import histogramdd as hdd, arange
# n='variable name', e='expression', b='number of bins (divisions)', r='range'
for axis in axes:
if isinstance(axis, tuple):
import warnings
warnings.warn(
"It is obsolete to specify an axis using tuple. "
"Please use an Axis instance instead"
)
n, e, b, r = axis
unit = None
else:
n = axis.name
e = axis.expression
b = axis.bins
r = axis.range
unit = axis.unit
# validation
if len(r) != 2:
raise ValueError, "Invalid range: %s. A range has to be a 2-tuple" % (r, )
if r[0] >= r[1]:
raise ValueError, "Invalid range: %s" % (r,)
expressions.append(e)
ranges.append(r)
bins.append(b)
db = (r[1]-r[0])/b
a = createAxis(
n,
boundaries=arange(r[0], r[1]+db/10., db),
unit=unit)
haxes.append(a)
continue
self.histogram = histogram(self.name, haxes)
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 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 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 __init__(self, doshist):
'''doshist: a histogram instance'''
from .utils import nice_dos
E, g = nice_dos(doshist.energy, doshist.I)
import histogram
self.doshist = histogram.histogram(
'dos',
[('energy', E, 'meV')],
g)
return
def test__add__(self):
"histogram: h+b"
h = self._histogram + (1,0)
self.assertVectorEqual( h[0.5, 1], (1,0) )
h = self._histogram + self._histogram2
self.assertVectorEqual( h[1.5,1], (6,6) )
h1 = histogram.histogram( 'h1', [ ['x', range(10)] ] )
h1[()] = 1,1
h2 = histogram.histogram( 'h2', [ ['x', range(10)] ] )
h2[()] = 2,2
h1*=(2.,0)
h2/=(2.,0)
h3 = h1+h2
for x in range(10): self.assertAlmostEqual( h3[x][0], 3 )
return
