def _transform_schematic(session, transform, center, from_rgba, to_rgba,
length, width, thickness):
axis, rot_center, angle_deg, shift = transform.axis_center_angle_shift()
# Align rot_center at same position along axis as center.
from chimerax.geometry import inner_product
rot_center += inner_product(center - rot_center, axis) * axis
width_axis = center - rot_center
varray, narray, tarray = _axis_square(axis, rot_center, width_axis, length,
width, thickness)
from chimerax.core.models import Model, Surface
s1 = Surface('slab 1', session)
s1.set_geometry(varray, narray, tarray)
s1.color = from_rgba
s2 = Surface('slab 2', session)
from chimerax.geometry import rotation, translation
rot2 = translation(shift * axis) * rotation(
axis, angle_deg, center=rot_center)
varray2 = rot2 * varray
narray2 = rot2.transform_vectors(narray)
s2.set_geometry(varray2, narray2, tarray)
s2.color = to_rgba
m = Model('transform schematic', session)
m.add([s1, s2])
return m
def segment_surface(v, sindex, descrip, color):
from chimerax.core.models import Surface
s = Surface('segment %d %s' % (sindex, descrip), v.session)
va, na, ta = segment_surface_geometry(v, sindex)
s.set_geometry(va, na, ta)
s.color = segment_color(color)
return s
def triangles_model(session,
points,
triangles,
name='vtk polygons',
color=(180, 180, 180, 255)):
from chimerax.core.models import Surface
m = Surface(name, session)
from chimerax import surface
normals = surface.calculate_vertex_normals(points, triangles)
m.set_geometry(points, normals, triangles)
m.color = color
return m
def ellipsoid_surface(axes, lengths, center, color, surface, submodel_name = None,
num_triangles = 1000):
xf = surface.position.inverse()
sa, sc = transform_ellipsoid(axes, center, xf)
varray, narray, tarray = ellipsoid_geometry(sc, sa, lengths, num_triangles = num_triangles)
if submodel_name is None:
s = surface
else:
from chimerax.core.models import Surface
s = Surface(submodel_name, surface.session)
surface.add([s])
s.set_geometry(varray, narray, tarray)
s.color = color
return s
def show_hk_lattice(session,
h,
k,
radius,
orientation='222',
color=(255, 255, 255, 255),
sphere_factor=0,
edge_radius=None,
mesh=False,
replace=True):
varray, tarray, hex_edges = hk_icosahedron_lattice(h, k, radius,
orientation)
interpolate_with_sphere(varray, radius, sphere_factor)
name = 'Icosahedron h = %d, k = %d' % (h, k)
if mesh:
model = sm = _cage_surface(session, name, replace)
sm.set_geometry(varray, None, tarray)
sm.color = color
sm.display_style = sm.Mesh
sm.edge_mask = hex_edges # Hide spokes of hexagons.
if sm.id is None:
session.models.add([sm])
else:
# Make cage from markers.
from chimerax.core.models import Surface
sm = Surface(name, session)
sm.set_geometry(varray, None, tarray)
sm.color = color
sm.display_style = sm.Mesh
sm.edge_mask = hex_edges # Hide spokes of hexagons.
if edge_radius is None:
edge_radius = .01 * radius
mset = _cage_markers(session, name) if replace else None
from chimerax.markers.cmd import markers_from_mesh
model = markers_from_mesh(session, [sm],
color=color,
edge_radius=edge_radius,
markers=mset)
model.name = name
if mset:
mset._prev_markers.delete()
model.hkcage = True
return model
def ellipsoid_mesh(session, name, center, radii, rotation, divisions, color,
opacity):
vertices, edges = lattitude_longtitude_circles(divisions)
# Stretch, rotate and center
vertices *= radii
rotation.transform_points(vertices, in_place=True)
vertices += center
# Create ellipsoid model
from chimerax.core.models import Surface
s = Surface(name, session)
normals = None
s.set_geometry(vertices, normals, edges)
s.color = [int(255 * r) for r in color + [opacity]]
s.display_style = s.Mesh
session.models.add([s])
def mesh_models(session, seg):
surfs = []
from chimerax.core.models import Surface
from chimerax.surface import combine_geometry_vnt
for segment in seg.segments:
if segment.mesh_list is None:
continue
geoms = [mesh_geometry(mesh, seg) for mesh in segment.mesh_list]
if len(geoms) == 0:
continue
va, na, ta = combine_geometry_vnt(geoms)
s = Surface('mesh %d' % segment.id, session)
s.set_geometry(va, na, ta)
# s.display_style = s.Mesh
# s.use_lighting = False
s.color = segment_color(segment.colour)
surfs.append(s)
return surfs
def create_mesh(session, c, transform, rgba, name):
varray, tarray = mesh_geometry(c)
if len(tarray) == 0:
return None
transform.transform_points(varray, in_place=True)
from chimerax.core.models import Surface
s = Surface(name, session)
s.SESSION_SAVE_DRAWING = True
s.clip_cap = True # Cap surface when clipped
from chimerax.surface import calculate_vertex_normals
narray = calculate_vertex_normals(varray, tarray)
s.set_geometry(varray, narray, tarray)
rgba8 = [int(r * 255) for r in rgba]
s.color = rgba8
return s
def calculate_segmentation_surfaces(seg,
where=None,
each=None,
region='all',
step=None,
color=None):
# Warn if number of surfaces is large.
if where is None and each is None:
max_seg_id = _maximum_segment_id(seg)
if max_seg_id > 100:
from chimerax.core.errors import UserError
raise UserError(
'Segmentation %s (#%s) has %d segments (> 100).'
' To create surface for each segment use "each segment" option.'
% (seg.name, seg.id_string, max_seg_id))
# Compute surfaces
conditions = (where if where else []) + ([each] if each else [])
group, attribute_name = _which_segments(seg, conditions)
matrix = seg.matrix(step=step, subregion=region)
from . import segmentation_surfaces
surfs = segmentation_surfaces(matrix, group)
# Transform vertices from index to scene units and compute normals.
geom = []
tf = seg.matrix_indices_to_xyz_transform(step=step, subregion=region)
for region_id, va, ta in surfs:
tf.transform_points(va, in_place=True)
from chimerax.surface import calculate_vertex_normals
na = calculate_vertex_normals(va, ta)
geom.append((region_id, va, na, ta))
# Determine surface coloring.
if color is None:
attr = None if attribute_name == 'segment' else attribute_name
colors = _attribute_colors(seg, attr).attribute_rgba
# Create one or more surface models
from chimerax.core.models import Surface
from chimerax.surface import combine_geometry_xvnt
segsurfs = []
if each is None and len(geom) > 1:
# Combine multiple surfaces into one.
va, na, ta = combine_geometry_xvnt(geom)
name = '%s %d %ss' % (seg.name, len(geom), attribute_name)
s = Surface(name, seg.session)
s.clip_cap = True # Cap surface when clipped
s.set_geometry(va, na, ta)
if color is None:
color_counts = [(colors[region_id], len(sva))
for region_id, sva, sna, sta in geom]
s.vertex_colors = _vertex_colors(len(va), color_counts)
else:
s.color = color
segsurfs.append(s)
else:
# Create multiple surface models
for region_id, va, na, ta in geom:
name = '%s %s %d' % (seg.name, attribute_name, region_id)
s = Surface(name, seg.session)
s.clip_cap = True # Cap surface when clipped
s.set_geometry(va, na, ta)
s.color = colors[region_id] if color is None else color
segsurfs.append(s)
return segsurfs