def make_membranes(scale, loc=(0,0,0)):
geom.box(loc, scale, name='Membrane')
modifiers.subsurf(4)
modifiers.solidify(0, 0.04)
# Seperate Inner and Outer membrane
bpy.ops.mesh.separate(type='LOOSE')
# Rename
bpy.data.objects['Membrane'].name = 'Inner-Membrane'
bpy.data.objects['Membrane.001'].name = 'Outer-Membrane'
# Materialize Outer-Membrane
setMaterial(bpy.data.objects['Outer-Membrane'], makeMaterial('Membrane.Outer', (0,1,0), (1,1,1), 1))
def make_cristae(name='Cristae',
loc=(0, 0, 0),
scale=(0.1, 1, 1),
loop_cut_scale_val=2.4):
# Initial box
cristae = geom.box(loc=loc, scale=(0.1, 1, 1), name=name)
# Loop cut on front face 2x horizontally and vertically
face = getPolygonByNormal(cristae, Vector((1, 0, 0)))
edit.loop_cut(getEdgeForFaceAtIndex(cristae, face, 0).index, 2)
bpy.ops.transform.resize(value=(1, cristae_disc_loop_cut_scale_val, 1))
edit.loop_cut(getEdgeForFaceAtIndex(cristae, face, 1).index, 2)
bpy.ops.transform.resize(value=(1, 1, cristae_disc_loop_cut_scale_val))
# Subdivision surface 4x
modifiers.subsurf(4)
# Set base material
setMaterial(cristae, makeMaterial('Cristae.Base', (1, 1, 1), (1, 1, 1), 1))
selectVerticesAndAssignMaterial(
cristae, 'Cristae.Pinch', {'y': {
'lt': -0.89
}}, makeMaterial('Cristae.Pinch', (1, 0, 0), (1, 1, 1), 1))
selectVerticesAndAssignMaterial(
cristae, 'Cristae.Wall', {'y': {
'gte': -0.91
}}, makeMaterial('Cristae.Wall', (0, 0, 1), (1, 1, 1), 1))
setMode('OBJECT')
def make_cristae(name='Cristae', loc=(0,0,0), scale=(0.1, 1, 1), side='right', loop_cut_scale_val=2.4, subsurf_level=2):
# Initial box
cristae = geom.box(loc=loc, scale=scale, name=name)
# Loop cut on front face 2x horizontally and vertically
face = getPolygonByNormal(cristae, Vector((1, 0, 0)))
edit.loop_cut(getEdgeForFaceAtIndex(cristae, face, 0).index, 2)
bpy.ops.transform.resize(value=(1, loop_cut_scale_val, 1))
edit.loop_cut(getEdgeForFaceAtIndex(cristae, face, 1).index, 2)
bpy.ops.transform.resize(value=(1, 1, loop_cut_scale_val))
# Subdivision surface
modifiers.subsurf(subsurf_level)
# Set base material
setMaterial(cristae, makeMaterial('Membrane.Inner.Base', (1,1,1), (1,1,1), 1))
# TODO figure out what these numbers should be procedurally
# was 0.89, 0.91 with 4x subdiv.
pinchThreshold = 0.90
wallThreshold = 0.95
if side == 'right':
selectVerticesAndAssignMaterial(cristae, 'Membrane.Inner.Pinch', {'y': {'lt': -pinchThreshold}}, makeMaterial('Membrane.Inner.Pinch', (1,0,0), (1,1,1), 1))
selectVerticesAndAssignMaterial(cristae, 'Membrane.Inner.Wall', {'y': {'gte': -wallThreshold}}, makeMaterial('Membrane.Inner.Wall', (0,0,1), (1,1,1), 1))
elif side == 'left':
selectVerticesAndAssignMaterial(cristae, 'Membrane.Inner.Pinch', {'y': {'gte': pinchThreshold}}, makeMaterial('Membrane.Inner.Pinch', (1,0,0), (1,1,1), 1))
selectVerticesAndAssignMaterial(cristae, 'Membrane.Inner.Wall', {'y': {'lt': wallThreshold}}, makeMaterial('Membrane.Inner.Wall', (0,0,1), (1,1,1), 1))
setMode('OBJECT')
def make_membranes(scale, loc=(0, 0, 0)):
geom.box(loc, scale, name='Membrane')
modifiers.subsurf(4)
modifiers.solidify(0, 0.04)
# Seperate Inner and Outer membrane
bpy.ops.mesh.separate(type='LOOSE')
# Rename
bpy.data.objects['Membrane'].name = 'Inner-Membrane'
bpy.data.objects['Membrane.001'].name = 'Outer-Membrane'
# Materialize Outer-Membrane
setMaterial(bpy.data.objects['Outer-Membrane'],
makeMaterial('Membrane.Outer', (0, 1, 0), (1, 1, 1), 1))
def make_cristae(name='Cristae',
loc=(0, 0, 0),
scale=(0.1, 1, 1),
side='right',
loop_cut_scale_val=2.4,
subsurf_level=2):
# Initial box
cristae = geom.box(loc=loc, scale=scale, name=name)
# Loop cut on front face 2x horizontally and vertically
face = getPolygonByNormal(cristae, Vector((1, 0, 0)))
edit.loop_cut(getEdgeForFaceAtIndex(cristae, face, 0).index, 2)
bpy.ops.transform.resize(value=(1, loop_cut_scale_val, 1))
edit.loop_cut(getEdgeForFaceAtIndex(cristae, face, 1).index, 2)
bpy.ops.transform.resize(value=(1, 1, loop_cut_scale_val))
# Subdivision surface
modifiers.subsurf(subsurf_level)
# Set base material
setMaterial(cristae,
makeMaterial('Membrane.Inner.Base', (1, 1, 1), (1, 1, 1), 1))
# TODO figure out what these numbers should be procedurally
# was 0.89, 0.91 with 4x subdiv.
pinchThreshold = 0.90
wallThreshold = 0.95
if side == 'right':
selectVerticesAndAssignMaterial(
cristae, 'Membrane.Inner.Pinch', {'y': {
'lt': -pinchThreshold
}}, makeMaterial('Membrane.Inner.Pinch', (1, 0, 0), (1, 1, 1), 1))
selectVerticesAndAssignMaterial(
cristae, 'Membrane.Inner.Wall', {'y': {
'gte': -wallThreshold
}}, makeMaterial('Membrane.Inner.Wall', (0, 0, 1), (1, 1, 1), 1))
elif side == 'left':
selectVerticesAndAssignMaterial(
cristae, 'Membrane.Inner.Pinch', {'y': {
'gte': pinchThreshold
}}, makeMaterial('Membrane.Inner.Pinch', (1, 0, 0), (1, 1, 1), 1))
selectVerticesAndAssignMaterial(
cristae, 'Membrane.Inner.Wall', {'y': {
'lt': wallThreshold
}}, makeMaterial('Membrane.Inner.Wall', (0, 0, 1), (1, 1, 1), 1))
setMode('OBJECT')
def make_cristae(name='Cristae', loc=(0,0,0), scale=(0.1, 1, 1), loop_cut_scale_val=2.4):
# Initial box
cristae = geom.box(loc=loc, scale=(0.1, 1, 1), name=name)
# Loop cut on front face 2x horizontally and vertically
face = getPolygonByNormal(cristae, Vector((1, 0, 0)))
edit.loop_cut(getEdgeForFaceAtIndex(cristae, face, 0).index, 2)
bpy.ops.transform.resize(value=(1, cristae_disc_loop_cut_scale_val, 1))
edit.loop_cut(getEdgeForFaceAtIndex(cristae, face, 1).index, 2)
bpy.ops.transform.resize(value=(1, 1, cristae_disc_loop_cut_scale_val))
# Subdivision surface 4x
modifiers.subsurf(4)
# Set base material
setMaterial(cristae, makeMaterial('Cristae.Base', (1,1,1), (1,1,1), 1))
selectVerticesAndAssignMaterial(cristae, 'Cristae.Pinch', {'y': {'lt': -0.89}}, makeMaterial('Cristae.Pinch', (1,0,0), (1,1,1), 1))
selectVerticesAndAssignMaterial(cristae, 'Cristae.Wall', {'y': {'gte': -0.91}}, makeMaterial('Cristae.Wall', (0,0,1), (1,1,1), 1))
setMode('OBJECT')
def make_mitochondria(length=3, width=1, num_rows=30, padding_factor=0.2, do_laplace=False, skip_material_cleaning=True, export=False):
# Settings
# TODO paramaterize
mito_length = 0.8*length
row_width = mito_length / num_rows
# cristae_width = row_width*(1 - 2*padding_factor)
cristae_width = 12.67 * 0.002
cristae_disc_subsurf_level = 2
# cristae_disc_loop_cut_scale_val = 2.4
inner_membrane_subsurf_level = 2
laplace_smooth_factor = 15
make_membranes(scale=(length, width, 1))
unselect_all()
innerMembane = bpy.data.objects['Inner-Membrane']
vertices = sorted(select_some(innerMembane, center=0.0, threshold=0.01), key=itemgetter('x'))
j_spaces = []
start = 0 - mito_length
# for i in range(0, 2):
for i in range(0, num_rows+1):
x = start + 2*row_width*i
y = -2
for v in vertices:
if v['x'] >= x:
j_spaces.append(2*v['y'])
y = v['y'] + width
break
dist = random.random() * 0.5
j_1 = j_spaces[i] * (random.random()*dist + 0.25)
y -= j_1
j_2 = (j_spaces[i]-j_1) * (random.random()*(dist) + 0.25)
y2 = y - j_2 - width*2
spacage = j_2 / j_spaces[i]
if x >= start + (start+2*mito_length)*0.05 and x <= (start+2*mito_length)*0.95:
make_cristae(name='Cristae.' + numToStr(i*2), loc=(x, y, 0), scale=(cristae_width, 1, 1), subsurf_level=cristae_disc_subsurf_level)
make_cristae(name='Cristae.' + numToStr(i*2 + 1), loc=(x, y2, 0), scale=(cristae_width, 1, 1), side='left', subsurf_level=cristae_disc_subsurf_level)
# Select all cristaes
# for i in range(0, num_rows+1):
# bpy.data.objects['Cristae.' + numToStr(i*2)].select = True
# bpy.data.objects['Cristae.' + numToStr(i*2 + 1)].select = True
for obj in bpy.data.objects:
if 'Cristae' in obj.name:
obj.select = True
# Join Cristaes
bpy.ops.object.join()
# bpy.data.objects['Cristae.' + numToStr(num_rows*2 + 1)].name = 'Cristae.All'
# bpy.data.objects['Cristae.All'].select = True
modifiers.boolean(bpy.data.objects['Inner-Membrane'], 'UNION')
# TODO fix cristae's ending up outside
# bpy.ops.mesh.separate(type='LOOSE')
# unselect_all()
#
# for obj in bpy.data.objects:
# if 'Cristae' in obj.name and obj.name != 'Cristae.All.001':
# obj.select = True
# # bpy.data.objects['Cristae.All'].select = True
# # bpy.data.objects['Cristae.All.002'].select = True
# bpy.ops.object.delete()
# Remove top half of outer membrane
unselect_all()
bpy.context.scene.objects.active = bpy.data.objects['Outer-Membrane']
bpy.data.objects['Outer-Membrane'].select = True
remove_top_outer()
# Remove old inner membrane
setMode('OBJECT')
unselect_all()
bpy.data.objects['Inner-Membrane'].select = True
bpy.ops.object.delete()
# Rename
# bpy.data.objects['Cristae.All.001'].name = 'Inner-Membrane'
# bpy.data.objects['Cristae.All'].name = 'Inner-Membrane'
# Should be only one Cristae\.d+
for obj in bpy.data.objects:
if 'Cristae' in obj.name:
obj.name = 'Inner-Membrane'
bpy.data.objects['Inner-Membrane'].select = True
bpy.context.scene.objects.active = bpy.data.objects['Inner-Membrane']
modifiers.subsurf(inner_membrane_subsurf_level)
modifiers.corrective_smooth(1, 5, True)
if (do_laplace):
modifiers.laplacian_smooth(laplace_smooth_factor)
# === bisect ===
setMode('EDIT')
bpy.ops.mesh.select_all(action='SELECT')
bpy.ops.mesh.bisect(plane_co=(0,0,0), plane_no=(0,0,1), xstart=10, xend=545, ystart=572, yend=572)
mesh = bmesh.from_edit_mesh(bpy.context.object.data)
zs = []
for v in mesh.verts:
v2 = bpy.context.object.matrix_world * v.co
if v.select == True:
v.select = False
zs.append(v2.z)
mz = max(zs)
for v in mesh.verts:
v2 = bpy.context.object.matrix_world * v.co
if v2.z > mz:
v.select = True
bpy.ops.mesh.delete(type='VERT')
setMode('OBJECT')
unselect_all()
reset_box = geom.box(loc=(5,5,5), name='Reset-Box')
# === Solidifiy outer membrane ===
bpy.data.objects['Outer-Membrane'].select = True
#bpy.ops.object.duplicate_move()
unselect_all()
bpy.data.objects['Outer-Membrane'].select = True
bpy.context.scene.objects.active = bpy.data.objects['Outer-Membrane']
modifiers.solidify(0, 4 * 0.002, True)
#unselect_all()
#bpy.data.objects['Outer-Membrane.001'].select = True
#bpy.context.scene.objects.active = bpy.data.objects['Outer-Membrane.001']
#modifiers.solidify(0, 4 * 0.002, False, True)
# Make and join to reset box then fix up
unselect_all()
bpy.data.objects['Inner-Membrane'].select = True
bpy.data.objects['Reset-Box'].select = True
bpy.context.scene.objects.active = bpy.data.objects['Reset-Box']
bpy.ops.object.join()
setMode('EDIT')
bpy.ops.mesh.separate(type='LOOSE')
setMode('OBJECT')
unselect_all()
bpy.data.objects['Reset-Box.001'].select = True
bpy.ops.object.delete()
bpy.data.objects['Reset-Box'].name = 'Inner-Membrane'
# Solidify Inner-Membrane
unselect_all()
bpy.data.objects['Inner-Membrane'].select = True
modifiers.solidify(0, 4 * 0.002)
# Clean up materials
if not skip_material_cleaning:
remove_unused_materials(bpy.data.objects['Inner-Membrane'])
unselect_all()
bpy.data.objects['Inner-Membrane'].select = True
bpy.data.objects['Outer-Membrane'].select = True
bpy.ops.object.join()
bpy.data.objects['Inner-Membrane'].name = 'Mitochondria'
unselect_all()
bpy.data.objects['Mitochondria'].select = True
bpy.ops.object.shade_smooth()
unselect_all()
bpy.data.objects['Mitochondria'].select = True
if export:
bpy.ops.export_scene.obj(
filepath='/Users/jmazz/Desktop/mitochondria.obj',
check_existing=False,
axis_forward='-Z',
axis_up='Y',
use_selection=True,
use_uvs=False,
use_materials=False,
group_by_material=True
)
def make_mitochondria(length=3,
width=1,
num_rows=30,
padding_factor=0.2,
do_laplace=False,
skip_material_cleaning=True,
export=False):
# Settings
# TODO paramaterize
mito_length = 0.8 * length
row_width = mito_length / num_rows
# cristae_width = row_width*(1 - 2*padding_factor)
cristae_width = 12.67 * 0.002
cristae_disc_subsurf_level = 2
# cristae_disc_loop_cut_scale_val = 2.4
inner_membrane_subsurf_level = 2
laplace_smooth_factor = 15
make_membranes(scale=(length, width, 1))
unselect_all()
innerMembane = bpy.data.objects['Inner-Membrane']
vertices = sorted(select_some(innerMembane, center=0.0, threshold=0.01),
key=itemgetter('x'))
j_spaces = []
start = 0 - mito_length
# for i in range(0, 2):
for i in range(0, num_rows + 1):
x = start + 2 * row_width * i
y = -2
for v in vertices:
if v['x'] >= x:
j_spaces.append(2 * v['y'])
y = v['y'] + width
break
dist = random.random() * 0.5
j_1 = j_spaces[i] * (random.random() * dist + 0.25)
y -= j_1
j_2 = (j_spaces[i] - j_1) * (random.random() * (dist) + 0.25)
y2 = y - j_2 - width * 2
spacage = j_2 / j_spaces[i]
if x >= start + (start + 2 * mito_length) * 0.05 and x <= (
start + 2 * mito_length) * 0.95:
make_cristae(name='Cristae.' + numToStr(i * 2),
loc=(x, y, 0),
scale=(cristae_width, 1, 1),
subsurf_level=cristae_disc_subsurf_level)
make_cristae(name='Cristae.' + numToStr(i * 2 + 1),
loc=(x, y2, 0),
scale=(cristae_width, 1, 1),
side='left',
subsurf_level=cristae_disc_subsurf_level)
# Select all cristaes
# for i in range(0, num_rows+1):
# bpy.data.objects['Cristae.' + numToStr(i*2)].select = True
# bpy.data.objects['Cristae.' + numToStr(i*2 + 1)].select = True
for obj in bpy.data.objects:
if 'Cristae' in obj.name:
obj.select = True
# Join Cristaes
bpy.ops.object.join()
# bpy.data.objects['Cristae.' + numToStr(num_rows*2 + 1)].name = 'Cristae.All'
# bpy.data.objects['Cristae.All'].select = True
modifiers.boolean(bpy.data.objects['Inner-Membrane'], 'UNION')
# TODO fix cristae's ending up outside
# bpy.ops.mesh.separate(type='LOOSE')
# unselect_all()
#
# for obj in bpy.data.objects:
# if 'Cristae' in obj.name and obj.name != 'Cristae.All.001':
# obj.select = True
# # bpy.data.objects['Cristae.All'].select = True
# # bpy.data.objects['Cristae.All.002'].select = True
# bpy.ops.object.delete()
# Remove top half of outer membrane
unselect_all()
bpy.context.scene.objects.active = bpy.data.objects['Outer-Membrane']
bpy.data.objects['Outer-Membrane'].select = True
remove_top_outer()
# Remove old inner membrane
setMode('OBJECT')
unselect_all()
bpy.data.objects['Inner-Membrane'].select = True
bpy.ops.object.delete()
# Rename
# bpy.data.objects['Cristae.All.001'].name = 'Inner-Membrane'
# bpy.data.objects['Cristae.All'].name = 'Inner-Membrane'
# Should be only one Cristae\.d+
for obj in bpy.data.objects:
if 'Cristae' in obj.name:
obj.name = 'Inner-Membrane'
bpy.data.objects['Inner-Membrane'].select = True
bpy.context.scene.objects.active = bpy.data.objects['Inner-Membrane']
modifiers.subsurf(inner_membrane_subsurf_level)
modifiers.corrective_smooth(1, 5, True)
if (do_laplace):
modifiers.laplacian_smooth(laplace_smooth_factor)
# === bisect ===
setMode('EDIT')
bpy.ops.mesh.select_all(action='SELECT')
bpy.ops.mesh.bisect(plane_co=(0, 0, 0),
plane_no=(0, 0, 1),
xstart=10,
xend=545,
ystart=572,
yend=572)
mesh = bmesh.from_edit_mesh(bpy.context.object.data)
zs = []
for v in mesh.verts:
v2 = bpy.context.object.matrix_world * v.co
if v.select == True:
v.select = False
zs.append(v2.z)
mz = max(zs)
for v in mesh.verts:
v2 = bpy.context.object.matrix_world * v.co
if v2.z > mz:
v.select = True
bpy.ops.mesh.delete(type='VERT')
setMode('OBJECT')
unselect_all()
reset_box = geom.box(loc=(5, 5, 5), name='Reset-Box')
# === Solidifiy outer membrane ===
bpy.data.objects['Outer-Membrane'].select = True
#bpy.ops.object.duplicate_move()
unselect_all()
bpy.data.objects['Outer-Membrane'].select = True
bpy.context.scene.objects.active = bpy.data.objects['Outer-Membrane']
modifiers.solidify(0, 4 * 0.002, True)
#unselect_all()
#bpy.data.objects['Outer-Membrane.001'].select = True
#bpy.context.scene.objects.active = bpy.data.objects['Outer-Membrane.001']
#modifiers.solidify(0, 4 * 0.002, False, True)
# Make and join to reset box then fix up
unselect_all()
bpy.data.objects['Inner-Membrane'].select = True
bpy.data.objects['Reset-Box'].select = True
bpy.context.scene.objects.active = bpy.data.objects['Reset-Box']
bpy.ops.object.join()
setMode('EDIT')
bpy.ops.mesh.separate(type='LOOSE')
setMode('OBJECT')
unselect_all()
bpy.data.objects['Reset-Box.001'].select = True
bpy.ops.object.delete()
bpy.data.objects['Reset-Box'].name = 'Inner-Membrane'
# Solidify Inner-Membrane
unselect_all()
bpy.data.objects['Inner-Membrane'].select = True
modifiers.solidify(0, 4 * 0.002)
# Clean up materials
if not skip_material_cleaning:
remove_unused_materials(bpy.data.objects['Inner-Membrane'])
unselect_all()
bpy.data.objects['Inner-Membrane'].select = True
bpy.data.objects['Outer-Membrane'].select = True
bpy.ops.object.join()
bpy.data.objects['Inner-Membrane'].name = 'Mitochondria'
unselect_all()
bpy.data.objects['Mitochondria'].select = True
bpy.ops.object.shade_smooth()
unselect_all()
bpy.data.objects['Mitochondria'].select = True
if export:
bpy.ops.export_scene.obj(
filepath='/Users/jmazz/Desktop/mitochondria.obj',
check_existing=False,
axis_forward='-Z',
axis_up='Y',
use_selection=True,
use_uvs=False,
use_materials=False,
group_by_material=True)