def get_structure_graph_scene(
self,
origin=None,
draw_image_atoms=True,
bonded_sites_outside_unit_cell=True,
hide_incomplete_edges=False,
incomplete_edge_length_scale=0.3,
color_edges_by_edge_weight=True,
edge_weight_color_scale="coolwarm",
explicitly_calculate_polyhedra_hull=False,
legend: Optional[Legend] = None,
group_by_symmetry: bool = True,
) -> Scene:
origin = origin or list(
-self.structure.lattice.get_cartesian_coords([0.5, 0.5, 0.5]))
legend = legend or Legend(self.structure)
primitives = defaultdict(list)
sites_to_draw = self._get_sites_to_draw(
draw_image_atoms=draw_image_atoms,
bonded_sites_outside_unit_cell=bonded_sites_outside_unit_cell,
)
color_edges = False
if color_edges_by_edge_weight:
weights = [e[2].get("weight") for e in self.graph.edges(data=True)]
weights = np.array([w for w in weights if w])
if any(weights):
cmap = get_cmap(edge_weight_color_scale)
# try to keep color scheme symmetric around 0
weight_max = max([abs(min(weights)), max(weights)])
weight_min = -weight_max
def get_weight_color(weight):
if not weight:
weight = 0
x = (weight - weight_min) / (weight_max - weight_min)
return "#{:02x}{:02x}{:02x}".format(
*[int(c * 255) for c in cmap(x)[0:3]])
color_edges = True
idx_to_wyckoff = {}
if group_by_symmetry:
sga = SpacegroupAnalyzer(self.structure)
struct_sym = sga.get_symmetrized_structure()
for equiv_idxs, wyckoff in zip(struct_sym.equivalent_indices,
struct_sym.wyckoff_symbols):
for idx in equiv_idxs:
idx_to_wyckoff[idx] = wyckoff
for (idx, jimage) in sites_to_draw:
site = self.structure[idx]
if jimage != (0, 0, 0):
connected_sites = self.get_connected_sites(idx, jimage=jimage)
site = PeriodicSite(
site.species,
np.add(site.frac_coords, jimage),
site.lattice,
properties=site.properties,
)
else:
connected_sites = self.get_connected_sites(idx)
connected_sites = [
cs for cs in connected_sites
if (cs.index, cs.jimage) in sites_to_draw
]
connected_sites_not_drawn = [
cs for cs in connected_sites
if (cs.index, cs.jimage) not in sites_to_draw
]
if color_edges:
connected_sites_colors = [
get_weight_color(cs.weight) for cs in connected_sites
]
connected_sites_not_drawn_colors = [
get_weight_color(cs.weight) for cs in connected_sites_not_drawn
]
else:
connected_sites_colors = None
connected_sites_not_drawn_colors = None
site_scene = site.get_scene(
connected_sites=connected_sites,
connected_sites_not_drawn=connected_sites_not_drawn,
hide_incomplete_edges=hide_incomplete_edges,
incomplete_edge_length_scale=incomplete_edge_length_scale,
connected_sites_colors=connected_sites_colors,
connected_sites_not_drawn_colors=connected_sites_not_drawn_colors,
explicitly_calculate_polyhedra_hull=
explicitly_calculate_polyhedra_hull,
legend=legend,
)
for scene in site_scene.contents:
if group_by_symmetry and scene.name == "atoms" and idx in idx_to_wyckoff:
# will rename to e.g. atoms_N_4e
scene.name = f"atoms_{site_scene.name}_{idx_to_wyckoff[idx]}"
# this is a proof-of-concept to demonstrate hover labels, could create label
# automatically from site properties instead
scene.contents[
0].tooltip = f"{site_scene.name} ({idx_to_wyckoff[idx]})"
primitives[scene.name] += scene.contents
primitives["unit_cell"].append(self.structure.lattice.get_scene())
return Scene(
name="StructureGraph",
origin=origin,
contents=[
Scene(name=k, contents=v, origin=origin)
for k, v in primitives.items()
],
)
def get_structure_graph_scene(
self,
origin=(0, 0, 0),
draw_image_atoms=True,
bonded_sites_outside_unit_cell=True,
hide_incomplete_bonds=False,
explicitly_calculate_polyhedra_hull=False,
) -> Scene:
primitives = defaultdict(list)
sites_to_draw = self._get_sites_to_draw(
draw_image_atoms=draw_image_atoms,
bonded_sites_outside_unit_cell=bonded_sites_outside_unit_cell,
)
for (idx, jimage) in sites_to_draw:
site = self.structure[idx]
if jimage != (0, 0, 0):
connected_sites = self.get_connected_sites(idx, jimage=jimage)
site = PeriodicSite(
site.species,
np.add(site.frac_coords, jimage),
site.lattice,
properties=site.properties,
)
else:
connected_sites = self.get_connected_sites(idx)
true_number_of_connected_sites = len(connected_sites)
connected_sites_being_drawn = [
cs for cs in connected_sites
if (cs.index, cs.jimage) in sites_to_draw
]
number_of_connected_sites_drawn = len(connected_sites_being_drawn)
all_connected_sites_present = (
true_number_of_connected_sites == number_of_connected_sites_drawn)
if hide_incomplete_bonds:
# only draw bonds if the destination site is also being drawn
connected_sites = connected_sites_being_drawn
site_scene = site.get_scene(
connected_sites=connected_sites,
all_connected_sites_present=all_connected_sites_present,
origin=origin,
explicitly_calculate_polyhedra_hull=
explicitly_calculate_polyhedra_hull,
)
for scene in site_scene.contents:
primitives[scene.name] += scene.contents
# we are here ...
# select polyhedra
# split by atom type at center
# see if any intersect, if yes split further
# order sets, with each choice, go to add second set etc if don't intersect
# they intersect if centre atom forms vertex of another atom (caveat: centre atom may not actually be inside polyhedra! not checking for this, add todo)
# def _set_intersects() ->bool:
# def _split_set() ->List: (by type, then..?)
# def _order_sets()... pick 1, ask can add 2? etc
primitives["unit_cell"].append(
self.structure.lattice.get_scene(origin=origin))
return Scene(
name=self.structure.composition.reduced_formula,
contents=[Scene(name=k, contents=v) for k, v in primitives.items()],
)
def get_structure_graph_scene(
self,
origin=(0, 0, 0),
draw_image_atoms=True,
bonded_sites_outside_unit_cell=True,
hide_incomplete_edges=False,
incomplete_edge_length_scale=0.3,
color_edges_by_edge_weight=True,
edge_weight_color_scale="coolwarm",
explicitly_calculate_polyhedra_hull=False,
) -> Scene:
primitives = defaultdict(list)
sites_to_draw = self._get_sites_to_draw(
draw_image_atoms=draw_image_atoms,
bonded_sites_outside_unit_cell=bonded_sites_outside_unit_cell,
)
color_edges = False
if color_edges_by_edge_weight:
weights = [e[2].get("weight") for e in self.graph.edges(data=True)]
weights = np.array([w for w in weights if w])
if any(weights):
cmap = get_cmap(edge_weight_color_scale)
# try to keep color scheme symmetric around 0
weight_max = max([abs(min(weights)), max(weights)])
weight_min = -weight_max
def get_weight_color(weight):
if not weight:
weight = 0
x = (weight - weight_min) / (weight_max - weight_min)
return "#{:02x}{:02x}{:02x}".format(
*[int(c * 255) for c in cmap(x)[0:3]])
color_edges = True
for (idx, jimage) in sites_to_draw:
site = self.structure[idx]
if jimage != (0, 0, 0):
connected_sites = self.get_connected_sites(idx, jimage=jimage)
site = PeriodicSite(
site.species,
np.add(site.frac_coords, jimage),
site.lattice,
properties=site.properties,
)
else:
connected_sites = self.get_connected_sites(idx)
connected_sites = [
cs for cs in connected_sites
if (cs.index, cs.jimage) in sites_to_draw
]
connected_sites_not_drawn = [
cs for cs in connected_sites
if (cs.index, cs.jimage) not in sites_to_draw
]
if color_edges:
connected_sites_colors = [
get_weight_color(cs.weight) for cs in connected_sites
]
connected_sites_not_drawn_colors = [
get_weight_color(cs.weight) for cs in connected_sites_not_drawn
]
else:
connected_sites_colors = None
connected_sites_not_drawn_colors = None
site_scene = site.get_scene(
connected_sites=connected_sites,
connected_sites_not_drawn=connected_sites_not_drawn,
hide_incomplete_edges=hide_incomplete_edges,
incomplete_edge_length_scale=incomplete_edge_length_scale,
connected_sites_colors=connected_sites_colors,
connected_sites_not_drawn_colors=connected_sites_not_drawn_colors,
origin=origin,
explicitly_calculate_polyhedra_hull=
explicitly_calculate_polyhedra_hull,
)
for scene in site_scene.contents:
primitives[scene.name] += scene.contents
# we are here ...
# select polyhedra
# split by atom type at center
# see if any intersect, if yes split further
# order sets, with each choice, go to add second set etc if don't intersect
# they intersect if centre atom forms vertex of another atom (caveat: centre atom may not actually be inside polyhedra! not checking for this, add todo)
# def _set_intersects() ->bool:
# def _split_set() ->List: (by type, then..?)
# def _order_sets()... pick 1, ask can add 2? etc
primitives["unit_cell"].append(
self.structure.lattice.get_scene(origin=origin))
return Scene(
name=self.structure.composition.reduced_formula,
contents=[Scene(name=k, contents=v) for k, v in primitives.items()],
)
def get_structure_graph_scene(
self,
origin=None,
draw_image_atoms=True,
bonded_sites_outside_unit_cell=True,
hide_incomplete_edges=False,
incomplete_edge_length_scale=0.3,
color_edges_by_edge_weight=True,
edge_weight_color_scale="coolwarm",
explicitly_calculate_polyhedra_hull=False,
legend: Optional[Legend] = None,
) -> Scene:
origin = origin or list(
-self.structure.lattice.get_cartesian_coords([0.5, 0.5, 0.5]))
legend = legend or Legend(self.structure)
primitives = defaultdict(list)
sites_to_draw = self._get_sites_to_draw(
draw_image_atoms=draw_image_atoms,
bonded_sites_outside_unit_cell=bonded_sites_outside_unit_cell,
)
color_edges = False
if color_edges_by_edge_weight:
weights = [e[2].get("weight") for e in self.graph.edges(data=True)]
weights = np.array([w for w in weights if w])
if any(weights):
cmap = get_cmap(edge_weight_color_scale)
# try to keep color scheme symmetric around 0
weight_max = max([abs(min(weights)), max(weights)])
weight_min = -weight_max
def get_weight_color(weight):
if not weight:
weight = 0
x = (weight - weight_min) / (weight_max - weight_min)
return "#{:02x}{:02x}{:02x}".format(
*[int(c * 255) for c in cmap(x)[0:3]])
color_edges = True
for (idx, jimage) in sites_to_draw:
site = self.structure[idx]
if jimage != (0, 0, 0):
connected_sites = self.get_connected_sites(idx, jimage=jimage)
site = PeriodicSite(
site.species,
np.add(site.frac_coords, jimage),
site.lattice,
properties=site.properties,
)
else:
connected_sites = self.get_connected_sites(idx)
connected_sites = [
cs for cs in connected_sites
if (cs.index, cs.jimage) in sites_to_draw
]
connected_sites_not_drawn = [
cs for cs in connected_sites
if (cs.index, cs.jimage) not in sites_to_draw
]
if color_edges:
connected_sites_colors = [
get_weight_color(cs.weight) for cs in connected_sites
]
connected_sites_not_drawn_colors = [
get_weight_color(cs.weight) for cs in connected_sites_not_drawn
]
else:
connected_sites_colors = None
connected_sites_not_drawn_colors = None
site_scene = site.get_scene(
connected_sites=connected_sites,
connected_sites_not_drawn=connected_sites_not_drawn,
hide_incomplete_edges=hide_incomplete_edges,
incomplete_edge_length_scale=incomplete_edge_length_scale,
connected_sites_colors=connected_sites_colors,
connected_sites_not_drawn_colors=connected_sites_not_drawn_colors,
explicitly_calculate_polyhedra_hull=
explicitly_calculate_polyhedra_hull,
legend=legend,
)
for scene in site_scene.contents:
primitives[scene.name] += scene.contents
primitives["unit_cell"].append(self.structure.lattice.get_scene())
return Scene(
name=self.structure.composition.reduced_formula,
origin=origin,
contents=[
Scene(name=k, contents=v, origin=origin)
for k, v in primitives.items()
],
)