class TestCoreShell(unittest.TestCase):
""" Unit tests for calculate_ER (CoreShellModel) """
def setUp(self):
from sas.models.CoreShellModel import CoreShellModel
self.comp = CoreShellModel()
def test(self):
""" Test 1D model for a CoreShell """
self.comp.setParam("radius", 20)
self.comp.setParam("thickness", 20)
self.assertAlmostEqual(self.comp.calculate_ER(), 40)
def setUp(self):
from sas.models.CoreShellModel import CoreShellModel
self.model= CoreShellModel()
self.model.setParam('scale', 1.0)
self.model.setParam('radius', 60.0)
self.model.setParam('thickness', 10.0)
self.model.setParam('core_sld', 1.e-6)
self.model.setParam('shell_sld', 2.e-6)
self.model.setParam('solvent_sld', 3.e-6)
self.model.setParam('background', 0.0)
def setUp(self):
""" Set up zero-SLD-average core-shell model """
from sas.models.CoreShellModel import CoreShellModel
radius = 15
thickness = 5
density = 5
core_vol = 4.0/3.0*math.pi*radius*radius*radius
self.outer_radius = radius+thickness
shell_vol = 4.0/3.0*math.pi*self.outer_radius*self.outer_radius*self.outer_radius - core_vol
self.shell_sld = -1.0*core_vol/shell_vol
self.density = density
# Core-shell
sphere = CoreShellModel()
# Core radius
sphere.setParam('radius', radius)
# Shell thickness
sphere.setParam('thickness', thickness)
sphere.setParam('core_sld', 1.0)
sphere.setParam('shell_sld', self.shell_sld)
sphere.setParam('solvent_sld', 0.0)
sphere.setParam('background', 0.0)
sphere.setParam('scale', 1.0)
self.ana = sphere
canvas = VolumeCanvas.VolumeCanvas()
canvas.setParam('lores_density', self.density)
handle = canvas.add('sphere')
canvas.setParam('%s.radius' % handle, self.outer_radius)
canvas.setParam('%s.contrast' % handle, self.shell_sld)
handle2 = canvas.add('sphere')
canvas.setParam('%s.radius' % handle2, radius)
canvas.setParam('%s.contrast' % handle2, 1.0)
canvas.setParam('scale' , 1.0)
canvas.setParam('background' , 0.0)
self.canvas = canvas
class TestCoreShell(unittest.TestCase):
"""
Testing C++ Cylinder model
"""
def setUp(self):
from sas.models.CoreShellModel import CoreShellModel
self.model= CoreShellModel()
self.model.setParam('scale', 1.0)
self.model.setParam('radius', 60.0)
self.model.setParam('thickness', 10.0)
self.model.setParam('core_sld', 1.e-6)
self.model.setParam('shell_sld', 2.e-6)
self.model.setParam('solvent_sld', 3.e-6)
self.model.setParam('background', 0.0)
def test_simple(self):
"""
Test simple 1D and 2D values
Numbers taken from model that passed validation, before
the update to C++ underlying class.
"""
self.assertAlmostEqual(self.model.run(0.001),
381.27304697150055, 3)
self.assertAlmostEqual(self.model.runXY([0.001,0.001]),
380.93779156218682, 3)
def test_dispersion(self):
"""
Test with dispersion
"""
from sas.models.DisperseModel import DisperseModel
disp = DisperseModel(self.model, ['radius', 'thickness'], [10, 2])
disp.setParam('n_pts', 10)
self.assertAlmostEqual(disp.run(0.001), 407.344127907553, 3)
def test_new_disp(self):
from sas.models.dispersion_models import GaussianDispersion
disp_rm = GaussianDispersion()
self.model.set_dispersion('radius', disp_rm)
self.model.dispersion['radius']['width'] = 0.1666666667
self.model.dispersion['radius']['npts'] = 10
self.model.dispersion['radius']['nsigmas'] = 2
disp_rr = GaussianDispersion()
self.model.set_dispersion('thickness', disp_rr)
self.model.dispersion['thickness']['width'] = 0.2
self.model.dispersion['thickness']['npts'] = 10
self.model.dispersion['thickness']['nsigmas'] = 2
self.assertAlmostEqual(self.model.run(0.001),
1.16747510*407.344127907553, 3)
def __init__(self, radius=15, thickness=5, density = 0.01):
from sas.models.CoreShellModel import CoreShellModel
self.name = 'coreshell'
self.radius = radius
core_vol = 4.0/3.0*math.pi*radius*radius*radius
self.outer_radius = radius+thickness
shell_vol = 4.0/3.0*math.pi*self.outer_radius*self.outer_radius*self.outer_radius - core_vol
self.shell_sld = -1.0*core_vol/shell_vol
self.density = density
# Core-shell
sphere = CoreShellModel()
# Core radius
sphere.setParam('radius', self.radius)
# Shell thickness
sphere.setParam('thickness', thickness)
sphere.setParam('core_sld', 1.0)
sphere.setParam('shell_sld', self.shell_sld)
sphere.setParam('solvent_sld', 0.0)
sphere.setParam('background', 0.0)
sphere.setParam('scale', 1.0)
self.ana = sphere
self.create()
def test_2():
radius = 15.0
thickness = 5.0
core_vol = 4.0/3.0*math.pi*radius*radius*radius
outer_radius = radius+thickness
shell_vol = 4.0/3.0*math.pi*outer_radius*outer_radius*outer_radius - core_vol
shell_sld = -1.0*core_vol/shell_vol
print "Shell SLD", shell_sld
density = .1
vol = 4/3*math.pi*radius*radius*radius
npts = vol*density
canvas = VolumeCanvas.VolumeCanvas()
canvas.setParam('lores_density', density)
handle = canvas.add('sphere')
canvas.setParam('%s.radius' % handle, outer_radius)
canvas.setParam('%s.contrast' % handle, shell_sld)
handle2 = canvas.add('sphere')
canvas.setParam('%s.radius' % handle2, radius)
canvas.setParam('%s.contrast' % handle2, 1.0)
# Core-shell
sphere = CoreShellModel()
# Core radius
sphere.setParam('radius', radius)
# Shell thickness
sphere.setParam('thickness', thickness)
sphere.setParam('core_sld', 1.0)
sphere.setParam('shell_sld', shell_sld)
sphere.setParam('solvent_sld',0.0)
sphere.setParam('background',0.0)
sphere.setParam('scale',1.0)
out = open("lores_test.txt",'w')
out.write("<q> <sim> <ana>\n")
for i in range(65):
q = 0.001 + 0.01*i
# For each volume integral that we change to a sum,
# we must multiply by 1/density = V/N
# Since we want P(r)/V, we will need to multiply
# the sum by 1/(N*density), where N is the number of
# points without overlap. Since we already divide
# by N when calculating I(q), we only need to divide
# by the density here. We divide by N in the
# calculation because it is difficult to estimate it here.
# Put the factor 2 in the simulation two...
sim_1 = canvas.getIq(q)
ana_1 = sphere.run(q)
print "q=%g sim=%g ana=%g ratio=%g" % (q, sim_1, ana_1, sim_1/ana_1)
out.write( "%g %g %g\n" % (q, sim_1, ana_1))
out.close()
def test_7():
from sas.models.CoreShellModel import CoreShellModel
print "Testing core-shell"
radius = 15
thickness = 5
density = 5
core_vol = 4.0/3.0*math.pi*radius*radius*radius
outer_radius = radius+thickness
shell_vol = 4.0/3.0*math.pi*outer_radius*outer_radius*outer_radius - core_vol
shell_sld = -1.0*core_vol/shell_vol
# Core-shell
sphere = CoreShellModel()
# Core radius
sphere.setParam('radius', radius)
# Shell thickness
sphere.setParam('thickness', thickness)
sphere.setParam('core_sld', 1.0)
sphere.setParam('shell_sld', shell_sld)
sphere.setParam('solvent_sld', 0.0)
sphere.setParam('background', 0.0)
sphere.setParam('scale', 1.0)
ana = sphere
canvas = VolumeCanvas.VolumeCanvas()
canvas.setParam('lores_density', density)
handle = canvas.add('sphere')
canvas.setParam('%s.radius' % handle, outer_radius)
canvas.setParam('%s.contrast' % handle, shell_sld)
handle2 = canvas.add('sphere')
canvas.setParam('%s.radius' % handle2, radius)
canvas.setParam('%s.contrast' % handle2, 1.0)
canvas.setParam('scale' , 1.0)
canvas.setParam('background' , 0.0)
""" Testing default core-shell orientation """
qlist = [.0001, 0.002, .01, .1, 1.0, 5.]
for q in qlist:
ana_val = ana.runXY([q, 0.2])
sim_val, err = canvas.getIq2DError(q, 0.2)
print ana_val, sim_val, sim_val/ana_val, err, (sim_val-ana_val)/err
def setUp(self):
from sas.models.CoreShellModel import CoreShellModel
self.comp = CoreShellModel()
def setUp(self):
from sas.models.CoreShellModel import CoreShellModel
radius = 15
thickness = 5
core_vol = 4.0/3.0*math.pi*radius*radius*radius
outer_radius = radius+thickness
shell_vol = 4.0/3.0*math.pi*outer_radius*outer_radius*outer_radius - core_vol
self.shell_sld = -1.0*core_vol/shell_vol
self.canvas = VolumeCanvas.VolumeCanvas()
self.canvas.params['lores_density'] = 0.1
# Core shell model
sphere = CoreShellModel()
# Core radius
sphere.setParam('radius', radius)
# Shell thickness
sphere.setParam('thickness', thickness)
sphere.setParam('core_sld', 1.0)
sphere.setParam('shell_sld', self.shell_sld)
sphere.setParam('solvent_sld', 0.0)
sphere.setParam('background', 0.0)
sphere.setParam('scale', 1.0)
self.sphere = sphere
self.radius = radius
self.outer_radius = outer_radius
class TestCoreShell(unittest.TestCase):
"""
Testing C++ Cylinder model
"""
def setUp(self):
from sas.models.CoreShellModel import CoreShellModel
self.model = CoreShellModel()
self.model.setParam('scale', 1.0)
self.model.setParam('radius', 60.0)
self.model.setParam('thickness', 10.0)
self.model.setParam('core_sld', 1.e-6)
self.model.setParam('shell_sld', 2.e-6)
self.model.setParam('solvent_sld', 3.e-6)
self.model.setParam('background', 0.0)
def test_simple(self):
"""
Test simple 1D and 2D values
Numbers taken from model that passed validation, before
the update to C++ underlying class.
"""
self.assertAlmostEqual(self.model.run(0.001), 381.27304697150055, 3)
self.assertAlmostEqual(self.model.runXY([0.001, 0.001]),
380.93779156218682, 3)
def test_dispersion(self):
"""
Test with dispersion
"""
from sas.models.DisperseModel import DisperseModel
disp = DisperseModel(self.model, ['radius', 'thickness'], [10, 2])
disp.setParam('n_pts', 10)
self.assertAlmostEqual(disp.run(0.001), 407.344127907553, 3)
def test_new_disp(self):
from sas.models.dispersion_models import GaussianDispersion
disp_rm = GaussianDispersion()
self.model.set_dispersion('radius', disp_rm)
self.model.dispersion['radius']['width'] = 0.1666666667
self.model.dispersion['radius']['npts'] = 10
self.model.dispersion['radius']['nsigmas'] = 2
disp_rr = GaussianDispersion()
self.model.set_dispersion('thickness', disp_rr)
self.model.dispersion['thickness']['width'] = 0.2
self.model.dispersion['thickness']['npts'] = 10
self.model.dispersion['thickness']['nsigmas'] = 2
self.assertAlmostEqual(self.model.run(0.001),
1.16747510 * 407.344127907553, 3)
def __init__(self, radius=15, thickness=5, density=0.01):
from sas.models.CoreShellModel import CoreShellModel
self.name = 'coreshell'
self.radius = radius
core_vol = 4.0 / 3.0 * math.pi * radius * radius * radius
self.outer_radius = radius + thickness
shell_vol = 4.0 / 3.0 * math.pi * self.outer_radius * self.outer_radius * self.outer_radius - core_vol
self.shell_sld = -1.0 * core_vol / shell_vol
self.density = density
# Core-shell
sphere = CoreShellModel()
# Core radius
sphere.setParam('radius', self.radius)
# Shell thickness
sphere.setParam('thickness', thickness)
sphere.setParam('core_sld', 1.0)
sphere.setParam('shell_sld', self.shell_sld)
sphere.setParam('solvent_sld', 0.0)
sphere.setParam('background', 0.0)
sphere.setParam('scale', 1.0)
self.ana = sphere
self.create()
def test_2():
radius = 15.0
thickness = 5.0
core_vol = 4.0 / 3.0 * math.pi * radius * radius * radius
outer_radius = radius + thickness
shell_vol = 4.0 / 3.0 * math.pi * outer_radius * outer_radius * outer_radius - core_vol
shell_sld = -1.0 * core_vol / shell_vol
print("Shell SLD", shell_sld)
density = .1
vol = 4 / 3 * math.pi * radius * radius * radius
npts = vol * density
canvas = VolumeCanvas.VolumeCanvas()
canvas.setParam('lores_density', density)
handle = canvas.add('sphere')
canvas.setParam('%s.radius' % handle, outer_radius)
canvas.setParam('%s.contrast' % handle, shell_sld)
handle2 = canvas.add('sphere')
canvas.setParam('%s.radius' % handle2, radius)
canvas.setParam('%s.contrast' % handle2, 1.0)
# Core-shell
sphere = CoreShellModel()
# Core radius
sphere.setParam('radius', radius)
# Shell thickness
sphere.setParam('thickness', thickness)
sphere.setParam('core_sld', 1.0)
sphere.setParam('shell_sld', shell_sld)
sphere.setParam('solvent_sld', 0.0)
sphere.setParam('background', 0.0)
sphere.setParam('scale', 1.0)
out = open("lores_test.txt", 'w')
out.write("<q> <sim> <ana>\n")
for i in range(65):
q = 0.001 + 0.01 * i
# For each volume integral that we change to a sum,
# we must multiply by 1/density = V/N
# Since we want P(r)/V, we will need to multiply
# the sum by 1/(N*density), where N is the number of
# points without overlap. Since we already divide
# by N when calculating I(q), we only need to divide
# by the density here. We divide by N in the
# calculation because it is difficult to estimate it here.
# Put the factor 2 in the simulation two...
sim_1 = canvas.getIq(q)
ana_1 = sphere.run(q)
print("q=%g sim=%g ana=%g ratio=%g" %
(q, sim_1, ana_1, sim_1 / ana_1))
out.write("%g %g %g\n" % (q, sim_1, ana_1))
out.close()
def test_7():
from sas.models.CoreShellModel import CoreShellModel
print("Testing core-shell")
radius = 15
thickness = 5
density = 5
core_vol = 4.0 / 3.0 * math.pi * radius * radius * radius
outer_radius = radius + thickness
shell_vol = 4.0 / 3.0 * math.pi * outer_radius * outer_radius * outer_radius - core_vol
shell_sld = -1.0 * core_vol / shell_vol
# Core-shell
sphere = CoreShellModel()
# Core radius
sphere.setParam('radius', radius)
# Shell thickness
sphere.setParam('thickness', thickness)
sphere.setParam('core_sld', 1.0)
sphere.setParam('shell_sld', shell_sld)
sphere.setParam('solvent_sld', 0.0)
sphere.setParam('background', 0.0)
sphere.setParam('scale', 1.0)
ana = sphere
canvas = VolumeCanvas.VolumeCanvas()
canvas.setParam('lores_density', density)
handle = canvas.add('sphere')
canvas.setParam('%s.radius' % handle, outer_radius)
canvas.setParam('%s.contrast' % handle, shell_sld)
handle2 = canvas.add('sphere')
canvas.setParam('%s.radius' % handle2, radius)
canvas.setParam('%s.contrast' % handle2, 1.0)
canvas.setParam('scale', 1.0)
canvas.setParam('background', 0.0)
""" Testing default core-shell orientation """
qlist = [.0001, 0.002, .01, .1, 1.0, 5.]
for q in qlist:
ana_val = ana.runXY([q, 0.2])
sim_val, err = canvas.getIq2DError(q, 0.2)
print(ana_val, sim_val, sim_val / ana_val, err,
(sim_val - ana_val) / err)
def setUp(self):
from sas.models.CoreShellModel import CoreShellModel
radius = 15
thickness = 5
core_vol = 4.0 / 3.0 * math.pi * radius * radius * radius
outer_radius = radius + thickness
shell_vol = 4.0 / 3.0 * math.pi * outer_radius * outer_radius * outer_radius - core_vol
self.shell_sld = -1.0 * core_vol / shell_vol
self.canvas = VolumeCanvas.VolumeCanvas()
self.canvas.params['lores_density'] = 0.1
# Core shell model
sphere = CoreShellModel()
# Core radius
sphere.setParam('radius', radius)
# Shell thickness
sphere.setParam('thickness', thickness)
sphere.setParam('core_sld', 1.0)
sphere.setParam('shell_sld', self.shell_sld)
sphere.setParam('solvent_sld', 0.0)
sphere.setParam('background', 0.0)
sphere.setParam('scale', 1.0)
self.sphere = sphere
self.radius = radius
self.outer_radius = outer_radius
def setUp(self):
from sas.models.CoreShellModel import CoreShellModel
self.comp = CoreShellModel()
def setUp(self):
""" Set up zero-SLD-average core-shell model """
from sas.models.CoreShellModel import CoreShellModel
radius = 15
thickness = 5
density = 5
core_vol = 4.0/3.0*math.pi*radius*radius*radius
self.outer_radius = radius+thickness
shell_vol = 4.0/3.0*math.pi*self.outer_radius*self.outer_radius*self.outer_radius - core_vol
self.shell_sld = -1.0*core_vol/shell_vol
self.density = density
# Core-shell
sphere = CoreShellModel()
# Core radius
sphere.setParam('radius', radius)
# Shell thickness
sphere.setParam('thickness', thickness)
sphere.setParam('core_sld', 1.0)
sphere.setParam('shell_sld', self.shell_sld)
sphere.setParam('solvent_sld', 0.0)
sphere.setParam('background', 0.0)
sphere.setParam('scale', 1.0)
self.ana = sphere
canvas = VolumeCanvas.VolumeCanvas()
canvas.setParam('lores_density', self.density)
handle = canvas.add('sphere')
canvas.setParam('%s.radius' % handle, self.outer_radius)
canvas.setParam('%s.contrast' % handle, self.shell_sld)
handle2 = canvas.add('sphere')
canvas.setParam('%s.radius' % handle2, radius)
canvas.setParam('%s.contrast' % handle2, 1.0)
canvas.setParam('scale' , 1.0)
canvas.setParam('background' , 0.0)
self.canvas = canvas