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 geometry_node_surfaces(primitives, place, color, materials, colors,
session):
from collada import polylist, triangleset
splist = []
for p in primitives:
if isinstance(p, polylist.Polylist):
p = p.triangleset()
if not isinstance(p, triangleset.TriangleSet):
continue # Skip line sets.
t = p.vertex_index # N by 3 array of vertex indices for triangles
t = t.copy() # array from pycollada is not contiguous.
v = p.vertex # M by 3 array of floats for vertex positions
ni = p.normal_index # N by 3 array of normal indices for triangles
n = p.normal # M by 3 array of floats for vertex normals
# Collada allows different normals on the same vertex in different triangles,
# but Hydra only allows one normal per vertex.
if n is None:
vn = None
else:
from numpy import empty
vn = empty(v.shape, n.dtype)
vn[t.ravel(), :] = n[ni.ravel(), :]
vcolors = vertex_colors(p, t, len(v), colors)
c = material_color(materials.get(p.material), color)
name = '%d' % (len(splist) + 1)
from chimerax.core.models import Surface
sp = Surface(name, session)
sp.set_geometry(v, vn, t)
sp.color_list = [c]
sp.position_list = [place]
if not vcolors is None:
sp.vertex_colors = vcolors
sp.clip_cap = True
splist.append(sp)
return splist
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