def read_ply(fname, force_subdivision_mesh=False):
if not have_readply:
print('Warning: readply module not found')
return []
plymesh = readply(fname, vertex_values_per_loop=False)
print('%s: %d vertices, %d faces' %
(fname, plymesh['num_vertices'], plymesh['num_faces']))
#loop_start = plymesh['loop_start']
loop_length = plymesh['loop_length']
mesh_type, minn, maxn = determine_mesh_type(loop_length)
print('Mesh type: %s' % mesh_type)
if force_subdivision_mesh:
print('Forcing subdivision mesh')
vertices = plymesh['vertices']
vertices = vertices.reshape((-1, 3))
indices = plymesh['faces']
if mesh_type.startswith('pure-') and not force_subdivision_mesh:
mesh = ospray.Geometry('mesh')
indices = indices.reshape((-1, minn))
mesh.set_param('index', ospray.data_constructor_vec(indices))
# Get a OSPRAY STATUS: ospray::Mesh ignoring 'index' array with wrong element type (should be vec3ui)
# when passing a pure-quad index array
elif mesh_type == 'mixed-tris-and-quads' and not force_subdivision_mesh:
mesh = ospray.Geometry('mesh')
# Duplicate last index of triangles to get all quads
new_indices = []
first = 0
for n in loop_length:
if n == 3:
new_indices.extend(indices[first:first + 3])
new_indices.append(indices[first + 2])
else:
new_indices.extend(indices[first:first + 4])
first += n
new_indices = numpy.array(new_indices, dtype=numpy.uint32).reshape(
(-1, 4))
mesh.set_param('index', ospray.data_constructor_vec(new_indices))
else:
# Use subdivision surface
mesh = ospray.Geometry('subdivision')
mesh.set_param('index', ospray.data_constructor(indices))
mesh.set_param('face', loop_length)
mesh.set_param('vertex.position', ospray.data_constructor_vec(vertices))
if 'vertex_colors' in plymesh:
print('Have vertex colors')
colors = plymesh['vertex_colors'].reshape((-1, 3))
# RGB -> RGBA
n = colors.shape[0]
alpha = numpy.ones((n, 1), dtype=numpy.float32)
colors = numpy.hstack((colors, alpha))
mesh.set_param('vertex.color', ospray.data_constructor_vec(colors))
mesh.commit()
return [mesh]
def read_pdb(fname, radius=1):
"""Bare-bones pdb reader, ATOM only"""
COLORS = {
'H': (0xff, 0xff, 0xff),
'C': (0x00, 0x00, 0x00),
'N': (0x22, 0x33, 0xff),
'O': (0xff, 0x20, 0x00),
'CL': (0x1f, 0xf0, 0x1f),
'F': (0x1f, 0xf0, 0x1f),
'BR': (0x99, 0x22, 0x00),
'I': (0x66, 0x00, 0xbb),
'HE': (0x00, 0xff, 0xff),
'NE': (0x00, 0xff, 0xff),
'AR': (0x00, 0xff, 0xff),
'XE': (0x00, 0xff, 0xff),
'KR': (0x00, 0xff, 0xff),
'P': (0xff, 0x99, 0x00),
'S': (0xff, 0xe5, 0x22),
'B': (0xff, 0xaa, 0x77),
'TI': (0x99, 0x99, 0x99),
'FE': (0xdd, 0x77, 0x00),
}
with open(fname, 'rt') as f:
positions = []
radii = []
colors = []
N = 0
for line in f:
if not line.startswith('ATOM '):
continue
x = float(line[30:38])
y = float(line[38:46])
z = float(line[46:54])
element = line[76:78].strip()
positions.append((x, y, z))
if element in COLORS:
hexcol = COLORS[element]
else:
hexcol = (0xdd, 0x77, 0xff)
if element != '':
print('No color for element %s' % element)
colors.append((hexcol[0] / 255, hexcol[1] / 255, hexcol[2] / 255))
radii.append(radius)
N += 1
positions = numpy.array(positions, numpy.float32)
radii = numpy.array(radii, numpy.float32)
colors = numpy.array(colors, numpy.float32)
#print(colors.shape, numpy.min(colors), numpy.max(colors))
opacities = numpy.ones(N, 'float32')
colors = numpy.c_[colors, opacities]
positions[:9].tofile('pos9.bin')
colors[:9].tofile('col9.bin')
radii[:9].tofile('radii9.bin')
assert positions.shape[0] == colors.shape[0]
spheres = ospray.Geometry('sphere')
spheres.set_param('sphere.position',
ospray.data_constructor_vec(positions))
spheres.set_param('sphere.radius', ospray.data_constructor(radii))
spheres.commit()
gmodel = ospray.GeometricModel(spheres)
gmodel.set_param('color', ospray.data_constructor_vec(colors))
gmodel.commit()
return gmodel
max_radius = 0.7 / pow(N, 1 / 3)
numpy.random.seed(123456)
positions = numpy.random.rand(N, 3).astype(numpy.float32)
radii = max_radius * numpy.random.rand(N).astype(numpy.float32)
colors = 0.3 + 0.7 * numpy.random.rand(N, 3).astype(numpy.float32)
opacities = numpy.ones(N, 'float32')
colors = numpy.c_[colors, opacities]
assert (numpy.min(colors) >= 0.3)
#colors = numpy.tile(numpy.array([1,0,0,1],'float32'), (N,1))
spheres = ospray.Geometry('sphere')
spheres.set_param('sphere.position',
ospray.data_constructor_vec(positions, True))
spheres.set_param('sphere.radius', ospray.data_constructor(radii, True))
spheres.commit()
gmodel = ospray.GeometricModel(spheres)
# XXX sometimes segfault, plus some spheres are black which should not be possible given
# the colors set
gmodel.set_param('color', ospray.data_constructor_vec(colors))
gmodel.commit()
group = ospray.Group()
group.set_param('geometry', [gmodel])
group.commit()
instance = ospray.Instance(group)
instance.commit()
def read_obj(fname, force_subdivision_mesh=False):
if not have_tinyobjloader:
print('Warning: tinyobjloader module not found')
return []
r = tinyobjloader.ObjReader()
r.ParseFromFile(fname)
attributes = r.GetAttrib()
vertices = numpy.array(attributes.vertices)
vertices = vertices.reshape((-1, 3)).astype('float32')
shapes = r.GetShapes()
print('%s: %d vertices, %d shapes' %
(fname, vertices.shape[0], len(shapes)))
meshes = []
for s in r.GetShapes():
mesh = s.mesh
indices = mesh.numpy_indices() # [ v0, n0, t0, v1, n1, t1, ... ]
vertex_indices = indices[::3]
face_lengths = mesh.numpy_num_face_vertices()
mesh_type, minn, maxn = determine_mesh_type(face_lengths)
print('%s (%s): %d faces' % (s.name, mesh_type, face_lengths.shape[0]))
if mesh_type.startswith('pure-') and not force_subdivision_mesh:
mesh = ospray.Geometry('mesh')
vertex_indices = vertex_indices.reshape(
(-1, minn)).astype('uint32')
mesh.set_param('index',
ospray.data_constructor_vec(vertex_indices))
elif mesh_type == 'mixed-tris-and-quads' and not force_subdivision_mesh:
mesh = ospray.Geometry('mesh')
# Duplicate last index of triangles to get all quads
new_indices = []
first = 0
for n in loop_length:
if n == 3:
new_indices.extend(vertex_indices[first:first + 3])
new_indices.append(vertex_indices[first + 2])
else:
new_indices.extend(vertex_indices[first:first + 4])
first += n
new_indices = numpy.array(new_indices, dtype=numpy.uint32).reshape(
(-1, 4))
mesh.set_param('index', ospray.data_constructor_vec(new_indices))
else:
# Use subdivision surface
mesh = ospray.Geometry('subdivision')
mesh.set_param('index', ospray.data_constructor(vertex_indices))
mesh.set_param('face', face_lengths)
mesh.set_param('vertex.position',
ospray.data_constructor_vec(vertices))
mesh.commit()
meshes.append(mesh)
return meshes
if set_value is not None:
axis, minidx, maxidx, value = set_value
assert axis in [0,1,2]
if axis == 0:
data[minidx:maxidx+1] = value
elif axis == 1:
data[:,minidx:maxidx+1] = value
else:
data[:,:,minidx:maxidx+1] = value
# Keep a reference to the numpy array around, as it will get
# deallocated otherwise
saved_data = data
data = ospray.data_constructor(data, is_shared=True)
volume = ospray.Volume('structuredRegular')
volume.set_param('gridSpacing', tuple(grid_spacing.tolist()))
volume.set_param('data', data)
volume.commit()
# TF
T = 16
if isovalue is not None:
# Fixed color and opacity
tfcolors = numpy.array([[0.8, 0.8, 0.8]], dtype=numpy.float32)
tfopacities = numpy.array([1], dtype=numpy.float32)