def getMesh(handler, meshId):
meshDb = MeshWrapper.get_by_id(int(meshId))
if meshDb == None:
return None
return meshDb.toJSON(reduced=False)
def getMesh(handler, meshId):
meshDb = MeshWrapper.get_by_id(int(meshId))
if meshDb == None:
return None
return meshDb.toJSON(reduced = False)
def updateMesh(handler, jsonMesh, rename = False):
if "undeletable" not in jsonMesh:
jsonMesh["undeletable"] = False
# This basically says to prefer the userId in the input
if 'user_id' in jsonMesh:
userId = jsonMesh['user_id']
else:
userId = handler.user.user_id()
if "id" in jsonMesh:
meshDb = MeshWrapper.get_by_id(jsonMesh["id"])
name = jsonMesh["name"]
else:
# Make sure name isn't taken, or build one that isn't taken
if "name" in jsonMesh:
name = jsonMesh["name"]
usedNames = set([x.name for x in db.Query(MeshWrapper).filter('user_id =', userId).run()])
if name in usedNames:
if rename:
i = 1
name = '{0}_{1}'.format(jsonMesh["name"], i)
while name in usedNames:
i = i + 1
name = '{0}_{1}'.format(jsonMesh["name"], i)
else:
raise Exception("Name is required on new meshes")
meshDb = MeshWrapper()
meshDb.user_id = userId
meshDb.name = name
meshDb.description = jsonMesh["description"]
meshDb.meshFileId = jsonMesh["meshFileId"]
meshDb.subdomains = jsonMesh["subdomains"]
meshDb.uniqueSubdomains = jsonMesh["uniqueSubdomains"]
meshDb.undeletable = jsonMesh["undeletable"]
pymodel = pyurdme.URDMEModel(name = 'test')
meshFileObj = fileserver.FileManager.getFile(handler, meshDb.meshFileId)
pymodel.mesh = pyurdme.URDMEMesh.read_dolfin_mesh(str(meshFileObj["storePath"]))
coordinates = pymodel.mesh.coordinates()
minx = numpy.min(coordinates[:, 0])
maxx = numpy.max(coordinates[:, 0])
miny = numpy.min(coordinates[:, 1])
maxy = numpy.max(coordinates[:, 1])
minz = numpy.min(coordinates[:, 2])
maxz = numpy.max(coordinates[:, 2])
pymodel.add_species(pyurdme.Species('T', 1))
if len(meshDb.subdomains) == 0:
meshDb.subdomains = [1] * len(coordinates)
meshDb.uniqueSubdomains = [1]
pymodel.set_subdomain_vector(numpy.array(meshDb.subdomains))
sd = pymodel.get_subdomain_vector()
vol_accumulator = numpy.zeros(numpy.unique(sd).shape)
for ndx, v in enumerate(pymodel.get_solver_datastructure()['vol']):
vol_accumulator[sd[ndx] - 1] += v
volumes = {}
for s, v in enumerate(vol_accumulator):
volumes[s + 1] = v
meshDb.volumes = volumes
meshDb.boundingBox = [[minx, maxx], [miny, maxy], [minz, maxz]]
return meshDb.put().id()
def setupMeshes(handler):
try:
base = os.path.dirname(os.path.realpath(__file__)) + '/../static/spatial/'
files = [ 'coli_with_membrane_mesh.xml',
'cylinder_mesh.xml',
'unit_cube_with_membrane_mesh.xml',
'unit_sphere_with_membrane_mesh.xml' ]
descriptions = { 'coli_with_membrane_mesh.xml' : 'Simplified E-coli model mesh',
'cylinder_mesh.xml' : 'Cylindrical domain',
'unit_cube_with_membrane_mesh.xml' : 'Cubic domain of edge length 1.0',
'unit_sphere_with_membrane_mesh.xml' : 'Spherical domain with radius 1.0' }
namesToFilenames = { 'E-coli with membrane' : 'coli_with_membrane_mesh.xml',
'Cylinder' : 'cylinder_mesh.xml',
'Unit cube' : 'unit_cube_with_membrane_mesh.xml',
'Unit sphere' : 'unit_sphere_with_membrane_mesh.xml' }
converted = set()
for wrapper in db.GqlQuery("SELECT * FROM MeshWrapper WHERE user_id = :1", handler.user.user_id()).run():
converted.add(wrapper.name)
for name in set(namesToFilenames.keys()) - converted:
fileName = namesToFilenames[name]
meshDb = MeshWrapper()
# To get the subdomains, there is a .txt file stored along with every .xml
baseName, ext = os.path.splitext(fileName)
subdomainsFile = open(os.path.join(base, baseName + '.txt'), 'r')
subdomains = []
for line in subdomainsFile.read().split():
v, s = line.strip().split(',')
v = int(v)
s = int(float(s))
subdomains.append((v, s))
subdomainsFile.close()
subdomains = [y for x, y in sorted(subdomains, key = lambda x : x[0])]
uniqueSubdomains = list(set(subdomains))
meshFile = open(os.path.join(base, fileName), 'r')
meshFileId = fileserver.FileManager.createFile(handler, "meshFiles", fileName, meshFile.read(), 777)
meshFile.close()
meshDb.user_id = handler.user.user_id()
meshDb.name = name
meshDb.description = descriptions[fileName]
meshDb.meshFileId = int(meshFileId)
meshDb.subdomains = subdomains
meshDb.uniqueSubdomains = uniqueSubdomains
meshDb.undeletable = True
pymodel = pyurdme.URDMEModel(name = 'test')
pymodel.mesh = pyurdme.URDMEMesh.read_dolfin_mesh(str(os.path.join(base, fileName)))
coordinates = pymodel.mesh.coordinates()
minx = numpy.min(coordinates[:, 0])
maxx = numpy.max(coordinates[:, 0])
miny = numpy.min(coordinates[:, 1])
maxy = numpy.max(coordinates[:, 1])
minz = numpy.min(coordinates[:, 2])
maxz = numpy.max(coordinates[:, 2])
pymodel.add_species(pyurdme.Species('T', 1))
pymodel.set_subdomain_vector(numpy.array(subdomains))
sd = pymodel.get_subdomain_vector()
vol_accumulator = numpy.zeros(numpy.unique(sd).shape)
for ndx, v in enumerate(pymodel.get_solver_datastructure()['vol']):
vol_accumulator[sd[ndx] - 1] += v
volumes = {}
for s, v in enumerate(vol_accumulator):
volumes[s + 1] = v
meshDb.volumes = volumes
meshDb.boundingBox = [[minx, maxx], [miny, maxy], [minz, maxz]]
meshDb.put()
except:
traceback.print_exc()
print "ERROR: Failed to import example public models"
def deleteMesh(handler, meshId):
meshDb = MeshWrapper.get_by_id(meshId)
meshDb.ghost = True
meshDb.put()
def updateMesh(handler, jsonMesh, rename=False):
if "undeletable" not in jsonMesh:
jsonMesh["undeletable"] = False
# This basically says to prefer the userId in the input
if 'user_id' in jsonMesh:
userId = jsonMesh['user_id']
else:
userId = handler.user.user_id()
if "id" in jsonMesh:
meshDb = MeshWrapper.get_by_id(jsonMesh["id"])
name = jsonMesh["name"]
else:
# Make sure name isn't taken, or build one that isn't taken
if "name" in jsonMesh:
name = jsonMesh["name"]
usedNames = set([
x.name for x in db.Query(MeshWrapper).filter(
'user_id =', userId).run()
])
if name in usedNames:
if rename:
i = 1
name = '{0}_{1}'.format(jsonMesh["name"], i)
while name in usedNames:
i = i + 1
name = '{0}_{1}'.format(jsonMesh["name"], i)
else:
raise Exception("Name is required on new meshes")
meshDb = MeshWrapper()
meshDb.user_id = userId
meshDb.name = name
meshDb.description = jsonMesh["description"]
meshDb.meshFileId = jsonMesh["meshFileId"]
meshDb.subdomains = jsonMesh["subdomains"]
meshDb.uniqueSubdomains = jsonMesh["uniqueSubdomains"]
meshDb.undeletable = jsonMesh["undeletable"]
pymodel = pyurdme.URDMEModel(name='test')
meshFileObj = fileserver.FileManager.getFile(handler,
meshDb.meshFileId)
pymodel.mesh = pyurdme.URDMEMesh.read_dolfin_mesh(
str(meshFileObj["storePath"]))
coordinates = pymodel.mesh.coordinates()
minx = numpy.min(coordinates[:, 0])
maxx = numpy.max(coordinates[:, 0])
miny = numpy.min(coordinates[:, 1])
maxy = numpy.max(coordinates[:, 1])
minz = numpy.min(coordinates[:, 2])
maxz = numpy.max(coordinates[:, 2])
pymodel.add_species(pyurdme.Species('T', 1))
if len(meshDb.subdomains) == 0:
meshDb.subdomains = [1] * len(coordinates)
meshDb.uniqueSubdomains = [1]
pymodel.set_subdomain_vector(numpy.array(meshDb.subdomains))
sd = pymodel.get_subdomain_vector()
vol_accumulator = numpy.zeros(numpy.unique(sd).shape)
for ndx, v in enumerate(pymodel.get_solver_datastructure()['vol']):
vol_accumulator[sd[ndx] - 1] += v
volumes = {}
for s, v in enumerate(vol_accumulator):
volumes[s + 1] = v
meshDb.volumes = volumes
meshDb.boundingBox = [[minx, maxx], [miny, maxy], [minz, maxz]]
return meshDb.put().id()
def setupMeshes(handler):
try:
base = os.path.dirname(
os.path.realpath(__file__)) + '/../static/spatial/'
files = [
'coli_with_membrane_mesh.xml', 'cylinder_mesh.xml',
'unit_cube_with_membrane_mesh.xml',
'unit_sphere_with_membrane_mesh.xml'
]
descriptions = {
'coli_with_membrane_mesh.xml':
'Simplified E-coli model mesh',
'cylinder_mesh.xml':
'Cylindrical domain',
'unit_cube_with_membrane_mesh.xml':
'Cubic domain of edge length 1.0',
'unit_sphere_with_membrane_mesh.xml':
'Spherical domain with radius 1.0'
}
namesToFilenames = {
'E-coli with membrane': 'coli_with_membrane_mesh.xml',
'Cylinder': 'cylinder_mesh.xml',
'Unit cube': 'unit_cube_with_membrane_mesh.xml',
'Unit sphere': 'unit_sphere_with_membrane_mesh.xml'
}
converted = set()
for wrapper in db.GqlQuery(
"SELECT * FROM MeshWrapper WHERE user_id = :1",
handler.user.user_id()).run():
converted.add(wrapper.name)
for name in set(namesToFilenames.keys()) - converted:
fileName = namesToFilenames[name]
meshDb = MeshWrapper()
# To get the subdomains, there is a .txt file stored along with every .xml
baseName, ext = os.path.splitext(fileName)
subdomainsFile = open(os.path.join(base, baseName + '.txt'), 'r')
subdomains = []
for line in subdomainsFile.read().split():
v, s = line.strip().split(',')
v = int(v)
s = int(float(s))
subdomains.append((v, s))
subdomainsFile.close()
subdomains = [y for x, y in sorted(subdomains, key=lambda x: x[0])]
uniqueSubdomains = list(set(subdomains))
meshFile = open(os.path.join(base, fileName), 'r')
meshFileId = fileserver.FileManager.createFile(
handler, "meshFiles", fileName, meshFile.read(), 777)
meshFile.close()
meshDb.user_id = handler.user.user_id()
meshDb.name = name
meshDb.description = descriptions[fileName]
meshDb.meshFileId = int(meshFileId)
meshDb.subdomains = subdomains
meshDb.uniqueSubdomains = uniqueSubdomains
meshDb.undeletable = True
pymodel = pyurdme.URDMEModel(name='test')
pymodel.mesh = pyurdme.URDMEMesh.read_dolfin_mesh(
str(os.path.join(base, fileName)))
coordinates = pymodel.mesh.coordinates()
minx = numpy.min(coordinates[:, 0])
maxx = numpy.max(coordinates[:, 0])
miny = numpy.min(coordinates[:, 1])
maxy = numpy.max(coordinates[:, 1])
minz = numpy.min(coordinates[:, 2])
maxz = numpy.max(coordinates[:, 2])
pymodel.add_species(pyurdme.Species('T', 1))
pymodel.set_subdomain_vector(numpy.array(subdomains))
sd = pymodel.get_subdomain_vector()
vol_accumulator = numpy.zeros(numpy.unique(sd).shape)
for ndx, v in enumerate(pymodel.get_solver_datastructure()['vol']):
vol_accumulator[sd[ndx] - 1] += v
volumes = {}
for s, v in enumerate(vol_accumulator):
volumes[s + 1] = v
meshDb.volumes = volumes
meshDb.boundingBox = [[minx, maxx], [miny, maxy], [minz, maxz]]
meshDb.put()
except:
traceback.print_exc()
print "ERROR: Failed to import example public models"
def deleteMesh(handler, meshId):
meshDb = MeshWrapper.get_by_id(meshId)
meshDb.ghost = True
meshDb.put()
