def import_obj(mdlobj, obj_mat, reg_mat, add_to_model_objects=True):
""" Create a new Blender mesh object.
Currently, this is used by both the swig and pyparsing based importers. In
addition to creating a new mesh object, a red material is applied to all
surface regions and a gray material is applied to the rest of the mesh.
"""
meshes = bpy.data.meshes
objs = bpy.data.objects
scn = bpy.context.scene
scn_objs = scn.objects
objname = mdlobj.name
print(objname, len(mdlobj.vertices), len(mdlobj.faces))
obj = objs.get(objname)
# Overwrite existing object if it has the same name as the object we are
# trying to import
if obj:
scn.objects.unlink(obj)
objs.remove(obj)
mesh = meshes.new(objname)
mesh.from_pydata(mdlobj.vertices, [], mdlobj.faces)
mesh.materials.append(obj_mat)
mesh.materials.append(reg_mat)
obj = objs.new(objname, mesh)
scn_objs.link(obj)
# Object needs to be active to add a region to it because of how
# init_region (called by add_region_by_name) works.
scn.objects.active = obj
all_regions = []
for reg_name, regions in mdlobj.regions.items():
obj.mcell.regions.add_region_by_name(bpy.context, reg_name)
reg = obj.mcell.regions.region_list[reg_name]
reg.set_region_faces(obj.data, regions.faces)
all_regions.extend(regions.faces)
# Get list of face indices
face_list = [0] * len(mesh.polygons)
mesh.polygons.foreach_get('index', face_list)
# Create list of 1s and 0s. 1 if corresponding face index is in a region,
# 0 otherwise.
all_regions_set = set(all_regions)
material_list = [1 if f in all_regions_set else 0 for f in face_list]
# Faces that belong to a region are colored red
mesh.polygons.foreach_set("material_index", material_list)
if add_to_model_objects:
preserve_selection_use_operator(bpy.ops.mcell.model_objects_add, obj)
mesh.validate(verbose=True)
mesh.update()
def import_obj(mdlobj, obj_mat, reg_mat, add_to_model_objects=True):
""" Create a new Blender mesh object.
Currently, this is used by both the swig and pyparsing based importers. In
addition to creating a new mesh object, a red material is applied to all
surface regions and a gray material is applied to the rest of the mesh.
"""
meshes = bpy.data.meshes
objs = bpy.data.objects
scn = bpy.context.scene
scn_objs = scn.objects
objname = mdlobj.name
print(objname, len(mdlobj.vertices), len(mdlobj.faces))
obj = objs.get(objname)
# Overwrite existing object if it has the same name as the object we are
# trying to import
if obj:
scn.objects.unlink(obj)
objs.remove(obj)
mesh = meshes.new(objname)
mesh.from_pydata(mdlobj.vertices, [], mdlobj.faces)
mesh.materials.append(obj_mat)
mesh.materials.append(reg_mat)
obj = objs.new(objname, mesh)
scn_objs.link(obj)
# Object needs to be active to add a region to it because of how
# init_region (called by add_region_by_name) works.
scn.objects.active = obj
all_regions = []
for reg_name, regions in mdlobj.regions.items():
obj.mcell.regions.add_region_by_name(bpy.context, reg_name)
reg = obj.mcell.regions.region_list[reg_name]
reg.set_region_faces(obj.data, regions.faces)
all_regions.extend(regions.faces)
# Get list of face indices
face_list = [0] * len(mesh.polygons)
mesh.polygons.foreach_get('index', face_list)
# Create list of 1s and 0s. 1 if corresponding face index is in a region,
# 0 otherwise.
all_regions_set = set(all_regions)
material_list = [1 if f in all_regions_set else 0 for f in face_list]
# Faces that belong to a region are colored red
mesh.polygons.foreach_set("material_index", material_list)
if add_to_model_objects:
preserve_selection_use_operator(bpy.ops.mcell.model_objects_add, obj)
mesh.validate(verbose=True)
mesh.update()
def sbml2blender(inputFilePath,addObjects):
print("loading .xml file... " + inputFilePath)
#extrapolate object data from SBML file
csgObjects = readSBMLFileCSGObject(inputFilePath)
paramObject = readSBMLFileParametricObject(inputFilePath)
print("length of objects: " + str(len(csgObjects)))
#generates sphere or bounding box in Blender
#track average endosome size
sum_size = 0.0 #sum of volumes
n_size = 0.0 #number of endosomes
#track average endosome surface area
sum_surf = 0.0
n_surf = 0.0
csgObjectNames = []
domainTypes = []
name = []
size = []
location = []
rotation = []
domain = []
ind = 0
for csgobject in csgObjects:
if( csgobject[1] == 'SOLID_SPHERE' or csgobject[1] == 'sphere'):
name.append(csgobject[0])
size.append([float(csgobject[2]), float(csgobject[3]), float(csgobject[4])])
location.append([float(csgobject[8]), float(csgobject[9]), float(csgobject[10])])
rotation.append([float(csgobject[5]), float(csgobject[6]), float(csgobject[7])])
domain.append(csgobject[11])
if domain[ind] not in domainTypes:
domainTypes.append(domain[ind])
csgObjectNames.append(domain[ind])
sum_size += (4.0/3.0)*(3.14)*(size[ind][0])*(size[ind][1])*(size[ind][2])
n_size += 1
sum_surf += surface_area_sphere(size[ind][0],size[ind][1],size[ind][2])
n_surf += 1
ind = ind + 1
for domainType in domainTypes:
ind = 0
print(domainType)
for csgObjectName in csgObjectNames:
print(csgObjectName)
if domain[ind]==domainType:
print("match")
obj = generateSphere(domainType+str(ind),size[ind],location[ind],rotation[ind])
ind = ind + 1
bpy.ops.object.select_pattern(pattern=domainType+'*')
bpy.ops.object.join()
obj.name = domainType
bpy.ops.object.mode_set(mode='EDIT')
bpy.ops.mesh.faces_shade_smooth()
bpy.ops.object.mode_set(mode='OBJECT')
if addObjects:
preserve_selection_use_operator(bpy.ops.mcell.model_objects_add, obj)
bpy.ops.object.select_all(action='DESELECT')
namingPatterns = domainTypes
print(namingPatterns)
'''
#bpy.ops.object.join()
print("Here are the domains: ")
print(csgObjectNames)
#extract groups of strings with a lvenshtein distance less than 4
csgObjectNames.sort()
namingPatterns = []
# while len(csgObjectNames) > 0:
for domainType in domainTypes:
print(domainType)
#namingPatterns.append([x for x in csgObjectNames if domainType==x])
#csgObjectNames = [x for x in csgObjectNames if domainType==x]
#extract common prefix for groups of strings
namingPatterns = domainTypes
print(namingPatterns)
#namingPatterns = [common_prefix(x) for x in namingPatterns]
#group objects by pattern - now domainType
print(namingPatterns)
for namingPattern in namingPatterns:
#for domainType in domainTypes:
print("Current domain: ")
print(namingPattern)
bpy.ops.object.select_name(name=format(namingPattern), extend=False)
#bpy.ops.object.select_pattern(pattern='{0}*'.format(namingPattern), extend=False)
#bpy.ops.object.select_pattern(pattern="devin2", extend=False)
#bpy.ops.object.select_pattern(pattern="ivan1", extend=False)
bpy.ops.object.join()
obj = bpy.data.objects[bpy.context.active_object.name]
#obj.name = namingPattern
obj.name = namingPattern
bpy.ops.object.mode_set(mode='EDIT')
bpy.ops.mesh.faces_shade_smooth()
bpy.ops.object.mode_set(mode='OBJECT')
if addObjects:
preserve_selection_use_operator(bpy.ops.mcell.model_objects_add, obj)
#for name in csgObjectNames:
#bpy.ops.object.select_by_type(type='MESH', extend=False)
#bpy.ops.object.join()
'''
csgObjectNames = []
for csgobject in csgObjects:
if( csgobject[1] == 'SOLID_CUBE' or csgobject[1] == 'cube'):
name = csgobject[0]
location = [float(csgobject[2]), float(csgobject[3]), float(csgobject[4])]
size = [float(csgobject[2]), float(csgobject[3]), float(csgobject[4])]
location = [float(csgobject[8]), float(csgobject[9]), float(csgobject[10])]
obj = generateCube(name,size,location)
csgObjectNames.append(name)
# if addObjects:
# preserve_selection_use_operator(bpy.ops.mcell.model_objects_add, obj)
#extract groups of strings with a lvenshtein distance less than 4
csgObjectNames.sort()
namingPatterns = []
while len(csgObjectNames) > 0:
namingPatterns.append([x for x in csgObjectNames if levenshtein(csgObjectNames[0],x) <= 4])
csgObjectNames = [x for x in csgObjectNames if levenshtein(csgObjectNames[0],x) > 4]
#extract common prefix for groups of strings
namingPatterns = [common_prefix(x) for x in namingPatterns]
#group objects by pattern
for namingPattern in namingPatterns:
bpy.ops.object.select_pattern(pattern='{0}*'.format(namingPattern), extend=False)
bpy.ops.object.join()
obj = bpy.data.objects[bpy.context.active_object.name]
obj.name = namingPattern
if addObjects:
preserve_selection_use_operator(bpy.ops.mcell.model_objects_add, obj)
# print("The average endosome size is: " + str((sum_size/(n_size*1.0))))
# print("The average endosome surface area is " + str((sum_surf/(n_surf*1.0))))
for csgobject in paramObject:
obj = generateMesh(csgobject)
if addObjects:
preserve_selection_use_operator(bpy.ops.mcell.model_objects_add, obj)