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isosurfacesetting.py
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isosurfacesetting.py
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"""
"""
import bpy
import numpy as np
from time import time
class Isosurfacesetting():
"""
Isosurfacesetting object
The Isosurfacesetting object store the isosurface information.
Parameters:
label: str
The label define the batoms object that a Setting belong to.
"""
def __init__(self, label, volume) -> None:
self.label = label
self.name = 'blaseisosurface'
self.draw_volume(volume)
self[1] = [0.002, [1, 1, 0, 0.5]]
def draw_volume(self, volume):
"""
Draw unit cell by edge, however, can not be rendered.
"""
shape = volume.shape
volume = volume.reshape(-1, 1)
npoint = len(volume)
dn = 3 - npoint % 3
verts = np.append(volume, np.zeros((dn, 1)), axis = 0)
verts = verts.reshape(-1, 3)
mesh = bpy.data.meshes.new("mesh_%s_volume"%self.label)
mesh.from_pydata(verts, [], [])
mesh.update()
obj = bpy.data.objects.new("volume_%s"%self.label, mesh)
obj.data = mesh
obj.blasevolume.is_blasevolume = True
obj.blasevolume.shape = shape
obj.blasevolume.npoint = npoint
bpy.data.collections[self.label].children['%s_volume'%self.label].objects.link(obj)
obj.hide_set(True)
@property
def collection(self):
return self.get_collection()
def get_collection(self):
collection = getattr(bpy.data.collections[self.label], self.name)
return collection
@property
def npoint(self):
return self.get_npoint()
def get_npoint(self):
return bpy.data.objects["volume_%s"%self.label].blasevolume.npoint
@npoint.setter
def npoint(self, npoint):
self.set_npoint(npoint)
def set_npoint(self, npoint):
bpy.data.objects["volume_%s"%self.label].blasevolume.npoint = npoint
@property
def mesh(self):
return self.get_mesh()
def get_mesh(self):
mesh = bpy.data.objects["volume_%s"%self.label].data
return mesh
@property
def shape(self):
return self.get_shape()
def get_shape(self):
shape = bpy.data.objects["volume_%s"%self.label].blasevolume.shape
return shape
@property
def volume(self):
return self.get_volume()
def get_volume(self):
n = len(self.mesh.vertices)
volume = np.empty(n*3, dtype=np.float64)
self.mesh.vertices.foreach_get('co', volume)
volume = volume.reshape(-1, 1)
volume = volume[:self.npoint]
volume = volume.reshape(self.shape)
return volume
def __setitem__(self, index, value):
"""
Add isosurface one by one
"""
p = self.find(index)
if p is None:
p = self.collection.add()
p.name = str(index)
if isinstance(value, (int, float)):
value = [value]
p.level = value[0]
if len(value) == 2:
p.color = value[1]
def set_default(self):
"""
"""
for sp, data in self.species.items():
self[sp] = [np.append(data['color'][:3], 0.3), 0.005]
def add_isosurfaces(self, isosurfacepair):
for key in isosurfacepair:
self.set_default(key)
def remove_isosurfaces(self, isosurfacepair):
for key in isosurfacepair:
name = '%s-%s'%(key[0], key[1])
i = self.collection.find(name)
if i != -1:
self.collection.remove(i)
def __repr__(self) -> str:
s = '-'*60 + '\n'
s = 'Center level color \n'
for iso in self.collection:
s += '{0:10s} {1:1.6f} [{2:1.2f} {3:1.2f} {4:1.2f} {5:1.2f}] \n'.format(\
iso.name, iso.level, iso.color[0], iso.color[1], iso.color[2], iso.color[3])
s += '-'*60 + '\n'
return s
def __iter__(self):
item = self.collection
for i in range(len(item)):
yield item[i]
def __len__(self):
return len(self.collection)
def find(self, name):
i = self.collection.find(str(name))
if i == -1:
return None
else:
return self.collection[i]
def build_isosurface(self, cell):
volume = self.volume
isosurface = []
for iso in self.collection:
level = iso.level
color = iso.color
verts, faces = calc_isosurface(volume, cell, level)
isosurface.append((verts, faces, color))
return isosurface
def calc_isosurface(volume, cell, level,
gradient_direction = 'descent',
step_size = 1):
"""
Computes an isosurface from a volume grid.
Parameters:
"""
from blase.tools import get_cell_vertices
from skimage import measure
cell_vertices = get_cell_vertices(cell)
cell_vertices.shape = (2, 2, 2, 3)
cell_origin = cell_vertices[0,0,0]
#
spacing = tuple(1.0/np.array(volume.shape))
mlevel = np.mean(volume)
if not level:
level = mlevel*10
# print('iso level: {0:1.9f}, iso mean: {1:1.9f}'.format(level, mlevel))
scaled_verts, faces, normals, values = measure.marching_cubes(volume, level = level,
spacing=spacing,gradient_direction=gradient_direction ,
allow_degenerate = False, step_size=step_size)
scaled_verts = scaled_verts.dot(cell)
scaled_verts -= cell_origin
faces = list(faces)
return scaled_verts, faces