def double_pendulum(theta, length, mass):
gr.clearws()
gr.setviewport(0, 1, 0, 1)
direction = []
position = [(0, 0, 0)]
for i in range(2):
direction.append(
(sin(theta[i]) * length[i] * 2, -cos(theta[i]) * length[i] * 2, 0))
position.append([position[-1][j] + direction[-1][j] for j in range(3)])
gr3.clear()
# draw pivot point
gr3.drawcylindermesh(1, (0, 0.2, 0), (0, 1, 0), (0.4, 0.4, 0.4), 0.4, 0.05)
gr3.drawcylindermesh(1, (0, 0.2, 0), (0, -1, 0), (0.4, 0.4, 0.4), 0.05,
0.2)
gr3.drawspheremesh(1, (0, 0, 0), (0.4, 0.4, 0.4), 0.05)
# draw rods
gr3.drawcylindermesh(2, position, direction, (0.6, 0.6, 0.6) * 2,
(0.05, 0.05), [l * 2 for l in length])
# draw bobs
gr3.drawspheremesh(2, position[1:], (1, 1, 1) * 2, [m * 0.2 for m in mass])
gr3.drawimage(0, 1, 0, 1, 500, 500, gr3.GR3_Drawable.GR3_DRAWABLE_GKS)
gr.updatews()
return
def draw_image(self):
if not self.needs_refresh:
return
self.needs_refresh = False
w, h = (self.w, self.h)
clearws()
setwindow(0, self.w, 0, self.h)
setviewport(0, 1, 0, 1)
setbackgroundcolor(1, 1, 1, 0)
vertices, normals = triangulate(data, \
(1.0/64, 1.0/64, 1.0/128), (-0.5, -0.5, -0.5), self.isolevel)
mesh = createmesh(len(vertices)*3, vertices, normals, \
ones(vertices.shape))
drawmesh(mesh, 1, (0,0,0), (0,0,1), (0,1,0), (1,1,1), (1,1,1))
center = spherical_to_cartesian(-2, pi*self.y/self.h+pi/2, pi*self.x/self.w)
up = spherical_to_cartesian(1, pi*self.y/self.h+pi, pi*self.x/self.w)
cameralookat(center[0], center[1], -0.25+center[2], 0, 0, -0.25, up[0], up[1], up[2])
drawimage(0, self.w, 0, self.h, \
self.w, self.h, GR3_Drawable.GR3_DRAWABLE_GKS)
if self.export:
export("mri.html", 800, 800)
print("Saved current isosurface to mri.html")
self.export = False
clear()
deletemesh(c_int(mesh.value))
def draw_image(self):
w, h = (self.w, self.h)
clearws()
setwindow(0, self.w, 0, self.h)
setviewport(0, 1, 0, 1)
setbackgroundcolor(1, 1, 1, 0)
vertices, normals = triangulate(data, \
(1.0/64, 1.0/64, 1.0/128), (-0.5, -0.5, -0.5), self.isolevel)
mesh = createmesh(len(vertices)*3, vertices, normals, \
ones(vertices.shape))
drawmesh(mesh, 1, (0, 0, 0), (0, 0, 1), (0, 1, 0), (1, 1, 1),
(1, 1, 1))
center = spherical_to_cartesian(-2, pi * self.y / self.h + pi / 2,
pi * self.x / self.w)
up = spherical_to_cartesian(1, pi * self.y / self.h + pi,
pi * self.x / self.w)
cameralookat(center[0], center[1], -0.25 + center[2], 0, 0, -0.25,
up[0], up[1], up[2])
drawimage(0, self.w, 0, self.h, \
self.w, self.h, GR3_Drawable.GR3_DRAWABLE_GKS)
if self.export:
export("mri.html", 800, 800)
print("Saved current isosurface to mri.html")
self.export = False
clear()
deletemesh(c_int(mesh.value))
def draw_image(self):
if not self.needs_refresh:
return
self.needs_refresh = False
gr.clearws()
gr.setwindow(0, self.w, 0, self.h)
gr.setviewport(0, 1, 0, 1)
gr3.setbackgroundcolor(1, 1, 1, 0)
vertices, normals = gr3.triangulate(data,
(1.0 / 64, 1.0 / 64, 1.0 / 128),
(-0.5, -0.5, -0.5), self.isolevel)
mesh = gr3.createmesh(
len(vertices) * 3, vertices, normals, np.ones(vertices.shape))
gr3.drawmesh(mesh, 1, (0, 0, 0), (0, 0, 1), (0, 1, 0), (1, 1, 1),
(1, 1, 1))
center = spherical_to_cartesian(-2,
np.pi * self.y / self.h + np.pi / 2,
np.pi * self.x / self.w)
up = spherical_to_cartesian(1, np.pi * self.y / self.h + np.pi,
np.pi * self.x / self.w)
gr3.cameralookat(center[0], center[1], -0.25 + center[2], 0, 0, -0.25,
up[0], up[1], up[2])
gr3.drawimage(0, self.w, 0, self.h, self.w, self.h,
gr3.GR3_Drawable.GR3_DRAWABLE_GKS)
if self.export:
gr3.export("mri.html", 800, 800)
print("Saved current isosurface to mri.html")
self.export = False
gr3.clear()
gr3.deletemesh(c_int(mesh.value))
def draw(mesh, x=None, y=None, z=None):
gr3.clear()
gr3.drawmesh(mesh, 1, (0,0,0), (0,0,1), (0,1,0), (1,1,1), (1,1,1))
gr3.drawslicemeshes(data, x=x, y=y, z=z)
gr.clearws()
gr3.drawimage(0, 1, 0, 1, 500, 500, gr3.GR3_Drawable.GR3_DRAWABLE_GKS)
gr.updatews()
def draw(mesh, x=None, y=None, z=None):
gr3.clear()
gr3.drawmesh(mesh, 1, (0, 0, 0), (0, 0, 1), (0, 1, 0), (1, 1, 1),
(1, 1, 1))
gr3.drawslicemeshes(data, x=x, y=y, z=z)
gr.clearws()
gr3.drawimage(0, 1, 0, 1, 500, 500, gr3.GR3_Drawable.GR3_DRAWABLE_GKS)
gr.updatews()
def _plot_iso(v):
global _plt
viewport = _plt.kwargs['viewport']
if viewport[3] - viewport[2] < viewport[1] - viewport[0]:
width = viewport[3] - viewport[2]
center_x = 0.5 * (viewport[0] + viewport[1])
x_min = max(center_x - 0.5 * width, viewport[0])
x_max = min(center_x + 0.5 * width, viewport[1])
y_min = viewport[2]
y_max = viewport[3]
else:
height = viewport[1] - viewport[0]
center_y = 0.5 * (viewport[2] + viewport[3])
x_min = viewport[0]
x_max = viewport[1]
y_min = max(center_y - 0.5 * height, viewport[2])
y_max = min(center_y + 0.5 * height, viewport[3])
gr.selntran(0)
usable_vs = v[np.abs(v) != np.inf]
if np.prod(usable_vs.shape) == 0:
return
v_max = usable_vs.max()
v_min = usable_vs.min()
if v_min == v_max:
return
uint16_max = np.iinfo(np.uint16).max
v = (np.clip(v, v_min, v_max) - v_min) / (v_max - v_min) * uint16_max
values = v.astype(np.uint16)
nx, ny, nz = v.shape
isovalue = _plt.kwargs.get('isovalue', 0.5)
rotation = np.radians(_plt.kwargs.get('rotation', 40))
tilt = np.radians(_plt.kwargs.get('tilt', 70))
gr3.clear()
mesh = gr3.createisosurfacemesh(values,
(2 / (nx - 1), 2 / (ny - 1), 2 / (nz - 1)),
(-1., -1., -1.),
int(isovalue * uint16_max))
color = _plt.kwargs.get('color', (0.0, 0.5, 0.8))
gr3.setbackgroundcolor(1, 1, 1, 0)
gr3.drawmesh(mesh, 1, (0, 0, 0), (0, 0, 1), (0, 1, 0), color, (1, 1, 1))
r = 2.5
gr3.cameralookat(r * np.sin(tilt) * np.sin(rotation), r * np.cos(tilt),
r * np.sin(tilt) * np.cos(rotation), 0, 0, 0, 0, 1, 0)
gr3.drawimage(x_min, x_max, y_min, y_max, 500, 500,
gr3.GR3_Drawable.GR3_DRAWABLE_GKS)
gr3.deletemesh(mesh)
gr.selntran(1)
def pendulum(t, theta, omega, acceleration):
gr.clearws()
gr.setviewport(0, 1, 0, 1)
x, y = (sin(theta) * 3.0, -cos(theta) * 3.0)
gr3.clear()
# draw pivot point
gr3.drawspheremesh(1, (0, 0, 0), (0.4, 0.4, 0.4), 0.1)
# draw rod
gr3.drawcylindermesh(1, (0, 0, 0), (x, y, 0), (0.6, 0.6, 0.6), 0.05, 3.0)
# draw sphere
gr3.drawspheremesh(1, (x, y, 0), (1, 1, 1), 0.25)
# show angular velocity
V = 0.3 * omega - sign(omega) * 0.15
gr3.drawcylindermesh(1, (x, y, 0), (cos(theta), sin(theta), 0), (0, 0, 1),
0.05, V)
gr3.drawconemesh(1, (x + cos(theta) * V, y + sin(theta) * V, 0),
(-y, x, 0), (0, 0, 1), 0.1,
sign(omega) * 0.25)
# show angular acceleration
A = 0.3 * acceleration
gr3.drawcylindermesh(1, (x, y, 0), (sin(theta), cos(theta), 0), (1, 0, 0),
0.05, A)
gr3.drawconemesh(1, (x + sin(theta) * A, y + cos(theta) * A, 0),
(x, -y, 0), (1, 0, 0), 0.1, 0.25)
# draw GR3 objects
gr3.drawimage(0, 1, 0.15, 0.85, 500, 350,
gr3.GR3_Drawable.GR3_DRAWABLE_GKS)
gr.settextfontprec(2, gr.TEXT_PRECISION_STRING)
gr.setcharheight(0.024)
gr.settextcolorind(1)
gr.textext(0.05, 0.96, 'Damped Pendulum')
gr.mathtex(0.05, 0.9, '\\omega=\\dot{\\theta}')
gr.mathtex(0.05, 0.83,
'\\dot{\\omega}=-\\gamma\\omega-\\frac{g}{l}sin(\\theta)')
gr.setcharheight(0.020)
gr.textext(0.05, 0.20, 't:%7.2f' % t)
gr.textext(0.05, 0.16, '\\theta:%7.2f' % (theta / pi * 180))
gr.settextcolorind(4)
gr.textext(0.05, 0.12, '\\omega:%7.2f' % omega)
gr.settextcolorind(2)
gr.textext(0.05, 0.08, 'y_{A}:%6.2f' % acceleration)
gr.updatews()
return
def _plot_iso(v):
global _plt
viewport = _plt.kwargs['viewport']
if viewport[3] - viewport[2] < viewport[1] - viewport[0]:
width = viewport[3] - viewport[2]
center_x = 0.5 * (viewport[0] + viewport[1])
x_min = max(center_x - 0.5 * width, viewport[0])
x_max = min(center_x + 0.5 * width, viewport[1])
y_min = viewport[2]
y_max = viewport[3]
else:
height = viewport[1] - viewport[0]
center_y = 0.5 * (viewport[2] + viewport[3])
x_min = viewport[0]
x_max = viewport[1]
y_min = max(center_y - 0.5 * height, viewport[2])
y_max = min(center_y + 0.5 * height, viewport[3])
gr.selntran(0)
usable_vs = v[np.abs(v) != np.inf]
if np.prod(usable_vs.shape) == 0:
return
v_max = usable_vs.max()
v_min = usable_vs.min()
if v_min == v_max:
return
uint16_max = np.iinfo(np.uint16).max
v = (np.clip(v, v_min, v_max) - v_min) / (v_max - v_min) * uint16_max
values = v.astype(np.uint16)
nx, ny, nz = v.shape
isovalue = _plt.kwargs.get('isovalue', 0.5)
rotation = np.radians(_plt.kwargs.get('rotation', 40))
tilt = np.radians(_plt.kwargs.get('tilt', 70))
gr3.clear()
mesh = gr3.createisosurfacemesh(values, (2/(nx-1), 2/(ny-1), 2/(nz-1)),
(-1., -1., -1.),
int(isovalue * uint16_max))
color = _plt.kwargs.get('color', (0.0, 0.5, 0.8))
gr3.setbackgroundcolor(1, 1, 1, 0)
gr3.drawmesh(mesh, 1, (0, 0, 0), (0, 0, 1), (0, 1, 0), color, (1, 1, 1))
r = 2.5
gr3.cameralookat(r*np.sin(tilt)*np.sin(rotation), r*np.cos(tilt), r*np.sin(tilt)*np.cos(rotation), 0, 0, 0, 0, 1, 0)
gr3.drawimage(x_min, x_max, y_min, y_max, 500, 500, gr3.GR3_Drawable.GR3_DRAWABLE_GKS)
gr3.deletemesh(mesh)
gr.selntran(1)
def pendulum(t, theta, omega, acceleration):
gr.clearws()
gr.setviewport(0, 1, 0, 1)
x, y = (sin(theta) * 3.0, -cos(theta) * 3.0)
gr3.clear()
# draw pivot point
gr3.drawspheremesh(1, (0, 0, 0), (0.4, 0.4, 0.4), 0.1)
# draw rod
gr3.drawcylindermesh(1, (0, 0, 0), (x, y, 0), (0.6, 0.6, 0.6), 0.05, 3.0)
# draw sphere
gr3.drawspheremesh(1, (x, y, 0), (1, 1, 1), 0.25)
# show angular velocity
V = 0.3 * omega - sign(omega) * 0.15
gr3.drawcylindermesh(1, (x, y, 0), (cos(theta), sin(theta), 0), (0, 0, 1),
0.05, V)
gr3.drawconemesh(1, (x + cos(theta) * V, y + sin(theta) * V, 0),
(-y, x, 0), (0, 0, 1), 0.1, sign(omega) * 0.25)
# show angular acceleration
A = 0.3 * acceleration
gr3.drawcylindermesh(1, (x, y, 0), (sin(theta), cos(theta), 0), (1, 0, 0),
0.05, A)
gr3.drawconemesh(1, (x + sin(theta) * A, y + cos(theta) * A, 0),
(x, -y, 0), (1, 0, 0), 0.1, 0.25)
# draw GR3 objects
gr3.drawimage(0, 1, 0.15, 0.85, 500, 350, gr3.GR3_Drawable.GR3_DRAWABLE_GKS)
gr.settextfontprec(2, gr.TEXT_PRECISION_STRING)
gr.setcharheight(0.024)
gr.settextcolorind(1)
gr.textext(0.05, 0.96, 'Damped Pendulum')
gr.mathtex(0.05, 0.9, '\\omega=\\dot{\\theta}')
gr.mathtex(0.05, 0.83, '\\dot{\\omega}=-\\gamma\\omega-\\frac{g}{l}sin(\\theta)')
gr.setcharheight(0.020)
gr.textext(0.05, 0.20, 't:%7.2f' % t)
gr.textext(0.05, 0.16, '\\theta:%7.2f' % (theta / pi * 180))
gr.settextcolorind(4)
gr.textext(0.05, 0.12, '\\omega:%7.2f' % omega)
gr.settextcolorind(2)
gr.textext(0.05, 0.08, 'y_{A}:%6.2f' % acceleration)
gr.updatews()
return
def _create_gr3_scene(molecule, show_bonds=True):
"""
Create the GR3 scene from the provided molecule and - if show_bonds is
True (default) - the atomic bonds in the molecule.
"""
gr3.clear()
num_atoms = len(molecule.atomic_numbers)
gr3.drawspheremesh(num_atoms,
molecule.positions,
ATOM_COLORS[molecule.atomic_numbers],
molecule.atomic_radii)
if show_bonds and len(molecule.bonds.index_pairs) > 0:
index_pairs = molecule.bonds.index_pairs
num_bonds = len(molecule.bonds)
bond_positions = molecule.positions[index_pairs[:, 0]]
bond_directions = molecule.positions[index_pairs[:, 1]]-bond_positions
bond_lengths = la.norm(bond_directions, axis=1)
bond_directions /= bond_lengths.reshape(num_bonds, 1)
bond_radii = np.ones(num_bonds, dtype=np.float32)*BOND_RADIUS
bond_colors = np.ones((num_bonds, 3), dtype=np.float32)*0.3
gr3.drawcylindermesh(num_bonds, bond_positions, bond_directions,
bond_colors, bond_radii, bond_lengths)
def _create_gr3_scene(molecule, show_bonds=True):
"""
Create the GR3 scene from the provided molecule and - if show_bonds is
True (default) - the atomic bonds in the molecule.
"""
gr3.clear()
num_atoms = len(molecule.atomic_numbers)
gr3.drawspheremesh(num_atoms,
molecule.positions,
ATOM_COLORS[molecule.atomic_numbers],
molecule.atomic_radii)
if show_bonds and len(molecule.bonds.index_pairs) > 0:
index_pairs = molecule.bonds.index_pairs
num_bonds = len(molecule.bonds)
bond_positions = molecule.positions[index_pairs[:, 0]]
bond_directions = molecule.positions[index_pairs[:, 1]]-bond_positions
bond_lengths = la.norm(bond_directions, axis=1)
bond_directions /= bond_lengths.reshape(num_bonds, 1)
bond_radii = np.ones(num_bonds, dtype=np.float32)*BOND_RADIUS
bond_colors = np.ones((num_bonds, 3), dtype=np.float32)*0.3
gr3.drawcylindermesh(num_bonds, bond_positions, bond_directions,
bond_colors, bond_radii, bond_lengths)
import gr
import gr3
gr.setviewport(0, 1, 0, 1)
for i in range(360):
gr.clearws()
gr3.clear()
gr3.drawmolecule('dna.xyz', bond_delta=2, tilt=45, rotation=i)
gr3.drawimage(0, 1, 0, 1, 500, 500, gr3.GR3_Drawable.GR3_DRAWABLE_GKS)
gr.settextcolorind(0)
gr.settextalign(gr.TEXT_HALIGN_CENTER, gr.TEXT_VALIGN_TOP)
gr.text(0.5, 1, "DNA rendered using gr3.drawmolecule")
gr.updatews()
def _plot_data(**kwargs):
global _plt
_plt.kwargs.update(kwargs)
if not _plt.args:
return
kind = _plt.kwargs.get('kind', 'line')
if _plt.kwargs['clear']:
gr.clearws()
if kind in ('imshow', 'isosurface'):
_set_viewport(kind, _plt.kwargs['subplot'])
elif not _plt.kwargs['ax']:
_set_viewport(kind, _plt.kwargs['subplot'])
_set_window(kind)
if kind == 'polar':
_draw_polar_axes()
else:
_draw_axes(kind)
if 'cmap' in _plt.kwargs:
warnings.warn('The parameter "cmap" has been replaced by "colormap". The value of "cmap" will be ignored.', stacklevel=3)
colormap = _plt.kwargs.get('colormap', gr.COLORMAP_VIRIDIS)
if colormap is not None:
gr.setcolormap(colormap)
gr.uselinespec(" ")
for x, y, z, c, spec in _plt.args:
gr.savestate()
if 'alpha' in _plt.kwargs:
gr.settransparency(_plt.kwargs['alpha'])
if kind == 'line':
mask = gr.uselinespec(spec)
if mask in (0, 1, 3, 4, 5):
gr.polyline(x, y)
if mask & 2:
gr.polymarker(x, y)
elif kind == 'scatter':
gr.setmarkertype(gr.MARKERTYPE_SOLID_CIRCLE)
if z is not None or c is not None:
if c is not None:
c_min = c.min()
c_ptp = c.ptp()
for i in range(len(x)):
if z is not None:
gr.setmarkersize(z[i] / 100.0)
if c is not None:
c_index = 1000 + int(255 * (c[i]-c_min)/c_ptp)
gr.setmarkercolorind(c_index)
gr.polymarker([x[i]], [y[i]])
else:
gr.polymarker(x, y)
elif kind == 'stem':
gr.setlinecolorind(1)
gr.polyline(_plt.kwargs['window'][:2], [0, 0])
gr.setmarkertype(gr.MARKERTYPE_SOLID_CIRCLE)
gr.uselinespec(spec)
for xi, yi in zip(x, y):
gr.polyline([xi, xi], [0, yi])
gr.polymarker(x, y)
elif kind == 'hist':
y_min = _plt.kwargs['window'][2]
for i in range(1, len(y)+1):
gr.setfillcolorind(989)
gr.setfillintstyle(gr.INTSTYLE_SOLID)
gr.fillrect(x[i-1], x[i], y_min, y[i-1])
gr.setfillcolorind(1)
gr.setfillintstyle(gr.INTSTYLE_HOLLOW)
gr.fillrect(x[i-1], x[i], y_min, y[i-1])
elif kind == 'contour':
z_min, z_max = _plt.kwargs['zrange']
gr.setspace(z_min, z_max, 0, 90)
h = [z_min + i/19*(z_max-z_min) for i in range(20)]
if x.shape == y.shape == z.shape:
x, y, z = gr.gridit(x, y, z, 200, 200)
z.shape = np.prod(z.shape)
gr.contour(x, y, h, z, 1000)
_colorbar(0, 20)
elif kind == 'contourf':
z_min, z_max = _plt.kwargs['zrange']
gr.setspace(z_min, z_max, 0, 90)
scale = _plt.kwargs['scale']
gr.setscale(scale)
if x.shape == y.shape == z.shape:
x, y, z = gr.gridit(x, y, z, 200, 200)
z.shape = (200, 200)
gr.surface(x, y, z, gr.OPTION_CELL_ARRAY)
_colorbar()
elif kind == 'hexbin':
nbins = _plt.kwargs.get('nbins', 40)
cntmax = gr.hexbin(x, y, nbins)
if cntmax > 0:
_plt.kwargs['zrange'] = (0, cntmax)
_colorbar()
elif kind == 'heatmap':
x_min, x_max, y_min, y_max = _plt.kwargs['window']
width, height = z.shape
cmap = _colormap()
icmap = np.zeros(256, np.uint32)
for i in range(256):
r, g, b, a = cmap[i]
icmap[i] = (int(r*255) << 0) + (int(g*255) << 8) + (int(b*255) << 16) + (int(a*255) << 24)
z_min, z_max = _plt.kwargs.get('zlim', (np.min(z), np.max(z)))
if z_max < z_min:
z_max, z_min = z_min, z_max
if z_max > z_min:
data = (z - z_min) / (z_max - z_min) * 255
else:
data = np.zeros((width, height))
rgba = np.zeros((width, height), np.uint32)
for x in range(width):
for y in range(height):
rgba[x, y] = icmap[int(data[x, y])]
gr.drawimage(x_min, x_max, y_min, y_max, width, height, rgba)
_colorbar()
elif kind == 'wireframe':
if x.shape == y.shape == z.shape:
x, y, z = gr.gridit(x, y, z, 50, 50)
gr.setfillcolorind(0)
z.shape = np.prod(z.shape)
gr.surface(x, y, z, gr.OPTION_FILLED_MESH)
_draw_axes(kind, 2)
elif kind == 'surface':
if x.shape == y.shape == z.shape:
x, y, z = gr.gridit(x, y, z, 200, 200)
z.shape = np.prod(z.shape)
if _plt.kwargs.get('accelerate', True):
gr3.clear()
gr3.surface(x, y, z, gr.OPTION_COLORED_MESH)
else:
gr.surface(x, y, z, gr.OPTION_COLORED_MESH)
_draw_axes(kind, 2)
_colorbar(0.05)
elif kind == 'plot3':
gr.polyline3d(x, y, z)
_draw_axes(kind, 2)
elif kind == 'scatter3':
gr.polymarker3d(x, y, z)
_draw_axes(kind, 2)
elif kind == 'imshow':
_plot_img(z)
elif kind == 'isosurface':
_plot_iso(z)
elif kind == 'polar':
gr.uselinespec(spec)
_plot_polar(x, y)
elif kind == 'trisurf':
gr.trisurface(x, y, z)
_draw_axes(kind, 2)
_colorbar(0.05)
elif kind == 'tricont':
zmin, zmax = _plt.kwargs['zrange']
levels = np.linspace(zmin, zmax, 20)
gr.tricontour(x, y, z, levels)
gr.restorestate()
if kind in ('line', 'scatter', 'stem') and 'labels' in _plt.kwargs:
_draw_legend()
if _plt.kwargs['update']:
gr.updatews()
if gr.isinline():
return gr.show()
def create_scene(self):
"""
Create GR3 meshes. ``self.results`` contains the mesh data
and in ``self.settings`` is specified which meshes shound be rendered.
"""
c = config.Colors.background
gr3.setbackgroundcolor(c[0], c[1], c[2], 1.0)
gr3.clear()
if self.results is None:
return
show_domains = self.settings.show_domains
show_surface_cavities = self.settings.show_surface_cavities
show_center_cavities = self.settings.show_center_cavities
if show_center_cavities and self.results.center_cavities is not None:
show_surface_cavities = False
elif show_surface_cavities and self.results.surface_cavities is not None:
show_domains = False
self.objectids = [None]
edges = self.results.atoms.volume.edges
num_edges = len(edges)
edge_positions = [edge[0] for edge in edges]
edge_directions = [[edge[1][i]-edge[0][i] for i in range(3)] for edge in edges]
edge_lengths = [sum([c*c for c in edge])**0.5 for edge in edge_directions]
edge_radius = min(edge_lengths)/200
if self.settings.show_bounding_box:
gr3.drawcylindermesh(num_edges, edge_positions, edge_directions,
[config.Colors.bounding_box]*num_edges,
[edge_radius]*num_edges, edge_lengths)
corners = list(set([tuple(edge[0]) for edge in edges] + [tuple(edge[1]) for edge in edges]))
num_corners = len(corners)
gr3.drawspheremesh(num_corners, corners,
[config.Colors.bounding_box]*num_corners,
[edge_radius]*num_corners)
if self.settings.show_atoms and self.results.atoms is not None:
visible_atom_indices = self.settings.visible_atom_indices
if visible_atom_indices is not None:
visible_atom_indices = [comp for comp in visible_atom_indices if 0 <= comp < self.results.atoms.number]
else:
visible_atom_indices = range(self.results.atoms.number)
if len(visible_atom_indices) == 0:
visible_atom_indices = None
if visible_atom_indices is not None:
visible_atom_indices = np.array(visible_atom_indices)
gr3.drawspheremesh(len(visible_atom_indices),
self.results.atoms.positions[visible_atom_indices],
self.results.atoms.colors[visible_atom_indices],
np.ones(len(visible_atom_indices))*config.OpenGL.atom_radius)
if self.settings.show_bonds:
bonds = self.results.atoms.bonds
for start_index, target_indices in enumerate(bonds):
if start_index not in visible_atom_indices:
continue
target_indices = np.array([i for i in target_indices if i in visible_atom_indices])
if len(target_indices) == 0:
continue
start_position = self.results.atoms.positions[start_index]
target_positions = self.results.atoms.positions[target_indices]
directions = target_positions - start_position
bond_lengths = la.norm(directions, axis=1)
directions /= bond_lengths.reshape(len(directions), 1)
gr3.drawcylindermesh(len(target_indices),
target_positions,
-directions,
[config.Colors.bonds] * self.results.atoms.number,
np.ones(bond_lengths.shape)*config.OpenGL.bond_radius,
bond_lengths)
if self.results is None:
return
if show_domains and self.results.domains is not None:
self.draw_cavities(self.results.domains,
config.Colors.domain, 'domain',
self.settings.visible_domain_indices)
if show_surface_cavities and self.results.surface_cavities is not None:
self.draw_cavities(self.results.surface_cavities,
config.Colors.surface_cavity, 'surface cavity',
self.settings.visible_surface_cavity_indices)
if show_center_cavities and self.results.center_cavities is not None:
self.draw_cavities(self.results.center_cavities,
config.Colors.center_cavity, 'center cavity',
self.settings.visible_center_cavity_indices)
def _plot_data(**kwargs):
global _plt
_plt.kwargs.update(kwargs)
if not _plt.args:
return
kind = _plt.kwargs.get('kind', 'line')
if _plt.kwargs['clear']:
gr.clearws()
if kind in ('imshow', 'isosurface'):
_set_viewport(kind, _plt.kwargs['subplot'])
elif not _plt.kwargs['ax']:
_set_viewport(kind, _plt.kwargs['subplot'])
_set_window(kind)
if kind == 'polar':
_draw_polar_axes()
else:
_draw_axes(kind)
gr.setcolormap(_plt.kwargs.get('colormap', gr.COLORMAP_COOLWARM))
gr.uselinespec(" ")
for x, y, z, c, spec in _plt.args:
gr.savestate()
if 'alpha' in _plt.kwargs:
gr.settransparency(_plt.kwargs['alpha'])
if kind == 'line':
mask = gr.uselinespec(spec)
if mask in (0, 1, 3, 4, 5):
gr.polyline(x, y)
if mask & 2:
gr.polymarker(x, y)
elif kind == 'scatter':
gr.setmarkertype(gr.MARKERTYPE_SOLID_CIRCLE)
if z is not None or c is not None:
if c is not None:
c_min = c.min()
c_ptp = c.ptp()
for i in range(len(x)):
if z is not None:
gr.setmarkersize(z[i] / 100.0)
if c is not None:
c_index = 1000 + int(255 * (c[i]-c_min)/c_ptp)
gr.setmarkercolorind(c_index)
gr.polymarker([x[i]], [y[i]])
else:
gr.polymarker(x, y)
elif kind == 'stem':
gr.setlinecolorind(1)
gr.polyline(_plt.kwargs['window'][:2], [0, 0])
gr.setmarkertype(gr.MARKERTYPE_SOLID_CIRCLE)
gr.uselinespec(spec)
for xi, yi in zip(x, y):
gr.polyline([xi, xi], [0, yi])
gr.polymarker(x, y)
elif kind == 'hist':
y_min = _plt.kwargs['window'][2]
for i in range(1, len(y)+1):
gr.setfillcolorind(989)
gr.setfillintstyle(gr.INTSTYLE_SOLID)
gr.fillrect(x[i-1], x[i], y_min, y[i-1])
gr.setfillcolorind(1)
gr.setfillintstyle(gr.INTSTYLE_HOLLOW)
gr.fillrect(x[i-1], x[i], y_min, y[i-1])
elif kind == 'contour':
z_min, z_max = _plt.kwargs['zrange']
gr.setspace(z_min, z_max, 0, 90)
h = [z_min + i/19*(z_max-z_min) for i in range(20)]
if x.shape == y.shape == z.shape:
x, y, z = gr.gridit(x, y, z, 200, 200)
z.shape = np.prod(z.shape)
gr.contour(x, y, h, z, 1000)
_colorbar(0, 20)
elif kind == 'contourf':
z_min, z_max = _plt.kwargs['zrange']
gr.setspace(z_min, z_max, 0, 90)
if x.shape == y.shape == z.shape:
x, y, z = gr.gridit(x, y, z, 200, 200)
z.shape = (200, 200)
if _plt.kwargs['scale'] & gr.OPTION_Z_LOG != 0:
z = np.log(z)
gr.surface(x, y, z, gr.OPTION_CELL_ARRAY)
_colorbar()
elif kind == 'hexbin':
nbins = _plt.kwargs.get('nbins', 40)
cntmax = gr.hexbin(x, y, nbins)
if cntmax > 0:
_plt.kwargs['zrange'] = (0, cntmax)
_colorbar()
elif kind == 'heatmap':
x_min, x_max, y_min, y_max = _plt.kwargs['window']
width, height = z.shape
cmap = _colormap()
icmap = np.zeros(256, np.uint32)
for i in range(256):
r, g, b, a = cmap[i]
icmap[i] = (int(r*255) << 0) + (int(g*255) << 8) + (int(b*255) << 16) + (int(a*255) << 24)
z_range = np.ptp(z)
if z_range > 0:
data = (z - np.min(z)) / z_range * 255
else:
data = np.zeros((width, height))
rgba = np.zeros((width, height), np.uint32)
for x in range(width):
for y in range(height):
rgba[x, y] = icmap[int(data[x, y])]
gr.drawimage(x_min, x_max, y_min, y_max, width, height, rgba)
_colorbar()
elif kind == 'wireframe':
if x.shape == y.shape == z.shape:
x, y, z = gr.gridit(x, y, z, 50, 50)
gr.setfillcolorind(0)
z.shape = np.prod(z.shape)
gr.surface(x, y, z, gr.OPTION_FILLED_MESH)
_draw_axes(kind, 2)
elif kind == 'surface':
if x.shape == y.shape == z.shape:
x, y, z = gr.gridit(x, y, z, 200, 200)
z.shape = np.prod(z.shape)
if _plt.kwargs.get('accelerate', True):
gr3.clear()
gr3.surface(x, y, z, gr.OPTION_COLORED_MESH)
else:
gr.surface(x, y, z, gr.OPTION_COLORED_MESH)
_draw_axes(kind, 2)
_colorbar(0.05)
elif kind == 'plot3':
gr.polyline3d(x, y, z)
_draw_axes(kind, 2)
elif kind == 'scatter3':
gr.polymarker3d(x, y, z)
_draw_axes(kind, 2)
elif kind == 'imshow':
_plot_img(z)
elif kind == 'isosurface':
_plot_iso(z)
elif kind == 'polar':
gr.uselinespec(spec)
_plot_polar(x, y)
elif kind == 'trisurf':
gr.trisurface(x, y, z)
_draw_axes(kind, 2)
_colorbar(0.05)
gr.restorestate()
if kind in ('line', 'scatter', 'stem') and 'labels' in _plt.kwargs:
_draw_legend()
if _plt.kwargs['update']:
gr.updatews()
if gr.isinline():
return gr.show()