def setUp(self):
""" Set up cylinder model """
radius = 5
length = 40
density = 20
# Analytical model
self.ana = CylinderModel()
self.ana.setParam('scale', 1.0)
self.ana.setParam('background', 0.0)
self.ana.setParam('sld', 1.0)
self.ana.setParam('sld_solvent', 0.0)
self.ana.setParam('radius', radius)
self.ana.setParam('length', length)
# Simulation model
self.model = VolumeCanvas.VolumeCanvas()
cyl = VolumeCanvas.CylinderDescriptor()
self.handle = self.model.addObject(cyl)
self.model.setParam('lores_density', density)
self.model.setParam('scale', 1.0)
self.model.setParam('background', 0.0)
self.model.setParam('%s.contrast' % self.handle, 1.0)
self.model.setParam('%s.radius' % self.handle, radius)
self.model.setParam('%s.length' % self.handle, length)
def setUp(self):
""" Set up cylinder model """
radius = 5
length = 40
density = 20
# Analytical model
self.ana = CylinderModel()
self.ana.setParam('scale', 1.0)
self.ana.setParam('background', 0.0)
self.ana.setParam('sld', 1.0)
self.ana.setParam('sld_solvent', 0.0)
self.ana.setParam('radius', radius)
self.ana.setParam('length', length)
self.ana.setParam('theta', math.pi / 2.0)
self.ana.setParam('phi', math.pi / 2.0)
# Simulation model
self.model = VolumeCanvas.VolumeCanvas()
self.handle = self.model.add('cylinder')
self.model.setParam('lores_density', density)
self.model.setParam('scale', 1.0)
self.model.setParam('background', 0.0)
self.model.setParam('%s.radius' % self.handle, radius)
self.model.setParam('%s.length' % self.handle, length)
self.model.setParam('%s.contrast' % self.handle, 1.0)
self.model.setParam('%s.orientation' % self.handle, [0, 0, 0])
def setUp(self):
""" Set up ellipsoid """
radius_a = 60
radius_b = 10
density = 30
self.ana = EllipsoidModel()
self.ana.setParam('scale', 1.0)
self.ana.setParam('background', 0.0)
self.ana.setParam('sld', 1.0)
self.ana.setParam('sld_solvent', 0.0)
self.ana.setParam('radius_polar', radius_a)
self.ana.setParam('radius_equatorial', radius_b)
# Default orientation is there=1.57, phi=0
# Radius_a is along the x direction
canvas = VolumeCanvas.VolumeCanvas()
self.handle = canvas.add('ellipsoid')
canvas.setParam('lores_density', density)
canvas.setParam('scale', 1.0)
canvas.setParam('background', 0.0)
canvas.setParam('%s.radius_x' % self.handle, radius_a)
canvas.setParam('%s.radius_y' % self.handle, radius_b)
canvas.setParam('%s.radius_z' % self.handle, radius_b)
canvas.setParam('%s.contrast' % self.handle, 1.0)
self.canvas = canvas
def setUp(self):
""" Set up ellipsoid """
radius_a = 10
radius_b = 15
density = 5
self.ana = EllipsoidModel()
self.ana.setParam('scale', 1.0)
self.ana.setParam('background', 0.0)
self.ana.setParam('sld', 1.0)
self.ana.setParam('sld_solvent', 1.0)
self.ana.setParam('radius_polar', radius_a)
self.ana.setParam('radius_equatorial', radius_b)
canvas = VolumeCanvas.VolumeCanvas()
self.handle = canvas.add('ellipsoid')
canvas.setParam('lores_density', density)
canvas.setParam('scale', 1.0)
canvas.setParam('background', 0.0)
canvas.setParam('%s.radius_x' % self.handle, radius_a)
canvas.setParam('%s.radius_y' % self.handle, radius_b)
canvas.setParam('%s.radius_z' % self.handle, radius_b)
canvas.setParam('%s.contrast' % self.handle, 1.0)
self.canvas = canvas
self.ana.setParam('theta', 1.57)
self.ana.setParam('phi', 0)
self.canvas.setParam('%s.orientation' % self.handle, [0, 0, 0])
def setUp(self):
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()
sphere.setParam('scale', 1.0)
sphere.setParam('background', 0.0)
sphere.setParam('sld_core', 1.0)
sphere.setParam('sld_shell', self.shell_sld)
sphere.setParam('sld_solvent', 0.0)
# Core radius
sphere.setParam('radius', radius)
# Shell thickness
sphere.setParam('thickness', thickness)
self.sphere = sphere
self.radius = radius
self.outer_radius = outer_radius
def get_panels(self, parent):
"""
Create and return a list of panel objects
"""
self.parent = parent
# 3D viewer
self.plotPanel = SimCanvas.SimPanel(self.parent,
-1,
style=wx.RAISED_BORDER)
# Central simulation panel
self.paramPanel = ShapeParameters.ShapeParameterPanel(
self.parent,
q_min=self.q_min,
q_max=self.q_max,
q_npts=self.q_npts,
pt_density=DEFAULT_PT_DENSITY,
style=wx.RAISED_BORDER)
# Simulation
self.volCanvas = VolumeCanvas.VolumeCanvas()
self.volCanvas.setParam('lores_density', DEFAULT_PT_DENSITY)
self.adapter = ShapeAdapter.ShapeVisitor()
self._data_1D = None
self.calc_thread_1D = None
self.speedCheck = False
self.speed = 3.0e-7
# Q-values for plotting simulated I(Q)
step = (self.q_max - self.q_min) / (self.q_npts - 1)
self.x = np.arange(self.q_min, self.q_max + step * 0.01, step)
# Set the list of panels that are part of the simulation perspective
self.perspective = []
self.perspective.append(self.plotPanel.window_name)
self.perspective.append(self.paramPanel.window_name)
# Bind state events
self.parent.Bind(ShapeParameters.EVT_ADD_SHAPE, self._onAddShape)
self.parent.Bind(ShapeParameters.EVT_DEL_SHAPE, self._onDelShape)
self.parent.Bind(ShapeParameters.EVT_Q_RANGE, self._on_q_range_changed)
self.parent.Bind(ShapeParameters.EVT_PT_DENSITY,
self._on_pt_density_changed)
return [self.plotPanel, self.paramPanel]
def setUp(self):
""" Set up zero-SLD-average core-shell model """
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()
sphere.setParam('scale', 1.0)
sphere.setParam('background', 0.0)
# Core radius
sphere.setParam('radius', radius)
# Shell thickness
sphere.setParam('thickness', thickness)
sphere.setParam('sld_core', 1.0)
sphere.setParam('sld_shell', self.shell_sld)
sphere.setParam('sld_solvent', 0.0)
self.ana = sphere
canvas = VolumeCanvas.VolumeCanvas()
canvas.setParam('lores_density', self.density)
canvas.setParam('scale', 1.0)
canvas.setParam('background', 0.0)
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)
self.canvas = canvas
def setUp(self):
"""
Set up canvas
"""
self.model = VolumeCanvas.VolumeCanvas()
handle = self.model.add('sphere')
radius = 10
density = .1
ana = SphereModel()
ana.setParam('scale', 1.0)
ana.setParam('background', 0.0)
ana.setParam('sld', 1.0)
ana.setParam('sld_solvent', 0.0)
ana.setParam('radius', radius)
self.ana = ana
self.model.setParam('lores_density', density)
self.model.setParam('scale', 1.0)
self.model.setParam('background', 0.0)
self.model.setParam('%s.contrast' % handle, 1.0)
self.model.setParam('%s.radius' % handle, radius)
def setUp(self):
self.canvas = VolumeCanvas.VolumeCanvas()
def setUp(self):
self.model = VolumeCanvas.VolumeCanvas()
self.model.add('cylinder', 'cyl')
self.model.add('sphere', 'sph')
self.model.add('ellipsoid', 'elli')
self.model.add('singlehelix', 'shelix')
def setUp(self):
self.canvas = VolumeCanvas.VolumeCanvas()
self.canvas.params['lores_density'] = 0.05