def demo_create_cylinder (dstdir):
# hardcode path for testing purpose
try:
Repository.Delete("cyl")
Repository.Delete("resultCyl")
except:
pass
cyl=Solid.pySolidModel()
ctrL=[0.,0.,15.]
axisL=[0.,0.,1.]
cyl.Cylinder('cyl',2.,30.,ctrL,axisL)
cyl.GetPolyData('resultCyl',0.5)
cyl.GetBoundaryFaces(90)
print ("Creating model: \nFaceID found: " + str(cyl.GetFaceIds()))
cyl.WriteNative(dstdir + "/cylinder.vtp")
from shutil import copyfile
copyfile("cylinder.vtp.facenames2",dstdir + "/cylinder.vtp.facenames")
return dstdir+"/cylinder.vtp"
def demo_create_model (dstdir):
# just copy the model for now
try:
Repository.Delete("cyl")
except:
pass
cyl=Solid.pySolidModel()
cyl.ReadNative("cyl","cylinder.vtp")
from shutil import copyfile
copyfile("cylinder.vtp",dstdir + "/cylinder.vtp")
copyfile("cylinder.vtp.facenames",dstdir + "/cylinder.vtp.facenames")
return dstdir+"/cylinder.vtp"
def demo_create_model(dstdir):
# just copy the model for now
# hardcode path for testing purpose
try:
Repository.Delete("bifurcation")
except:
pass
cyl = Solid.pySolidModel()
cyl.ReadNative("bifurcation", "bifurcation.vtp")
from shutil import copyfile
copyfile("bifurcation.vtp", dstdir + "/bifurcation.vtp")
copyfile("bifurcation.vtp.facenames",
dstdir + "/bifurcation.vtp.facenames")
return dstdir + "/bifurcation.vtp"
def pulsatile_cylinder_create_mesh_TetGen(solidfn, dstdir,
pulsatile_mesh_option):
#
# Mesh the solid
#
print("Creating mesh.")
# create meshsim style script file
fp = open(dstdir + '/cylinder.tgs', 'w+')
fp.write("msinit\n")
fp.write("logon %s \n" % (dstdir + '/cylinder.logfile'))
fp.write("loadModel %s\n" % solidfn)
fp.write("setSolidModel\n")
fp.write("newMesh\n")
fp.write("option surface 1\n")
fp.write("option volume 1\n")
fp.write("option GlobalEdgeSize 0.75\n")
fp.write("wallFaces wall\n")
if pulsatile_mesh_option == 'Boundary Layer Mesh':
fp.write("boundaryLayer 3 0.5 0.7\n")
fp.write("option QualityRatio 1.4\n")
fp.write("option NoBisect 1\n")
fp.write("generateMesh\n")
if pulsatile_mesh_option == 'Boundary Layer Mesh':
fp.write("getBoundaries\n")
fp.write("writeMesh %s vtu 0\n" % (dstdir + '/cylinder.sms'))
fp.write("deleteMesh\n")
fp.write("deleteModel\n")
fp.write("logoff\n")
fp.close()
try:
Repository.Delete("mymesh")
except:
pass
mesh_utils.mesh_readTGS(dstdir + '/cylinder.tgs', 'mymesh')
print("Writing out mesh surfaces.")
os.mkdir(dstdir + '/mesh-complete')
os.mkdir(dstdir + '/mesh-complete/mesh-surfaces')
mesh_utils.mesh_writeCompleteMesh('mymesh', 'cyl', 'cylinder',
dstdir + '/mesh-complete')
def mesh_readTGS(filename, resObjName):
#@author Fanwei Kong based on tetgen.tcl
#@c This function processes a tetgen style meshing
#@c script file.
#@a filename: script filename.
#@a resObj: resulting repository MeshObject.
#@note resObj is not deleted, even if the script file
#@note specifies deleteModel and deleteMesh.
if (int(Repository.Exists(resObjName)) != 0):
raise ValueError("object" + resObjName + "already exists!")
return
solid = "/tmp/mesh_readTGS/solid"
try:
Repository.Delete(solid)
except:
pass
global guiMMvars
guiMMvars['meshGenerateVolumeMesh'] = 0
global guiPDvars
global guiTGvars
geom = Solid.pySolidModel()
resObj = MeshObject.pyMeshObject()
MeshObject.SetKernel(pc.gOptions['meshing_kernel'])
resObj.NewObject(resObjName)
resObj.SetSolidKernel(pc.gOptions['meshing_solid_kernel'])
# lookup for type
types = {}
types[1] = 1
types[2] = 2
types['absolute'] = 1
types['relative'] = 2
types['abs'] = 1
types['rel'] = 2
sides = {}
sides['negative'] = 0
sides['positive'] = 1
sides['both'] = 2
sides[0] = 0
sides[1] = 1
sides[2] = 2
fp = open(filename, 'r')
for line in fp:
# skip comment lines
if (line[0:2] == "\#"):
print("ignoring line: <$line>")
continue
# supported commands
if (line.split()[0] == "logon"):
MeshObject.Logon(line.split()[1])
elif (line.split()[0] == "logoff"):
MeshObject.Logoff
elif (line.split()[0] == "newMesh"):
resObj.NewMesh()
elif (line.split()[0] == "generateMesh"):
resObj.GenerateMesh()
elif (line.split()[0] == "loadModel"):
resObj.LoadModel(line.split()[1])
try:
Repository.Delete(solid)
except:
pass
solidfn = line.split()[1]
geom.ReadNative(solid, solidfn)
#set smasherInputName $solid
if (pc.gOptions['meshing_solid_kernel'] == "PolyData"):
global gPolyDataFaceNames
global gPolyDataFaceNamesInfo
if (os.path.isfile(line.split()[1] + '.facenames')):
with open(line.split()[1] + '.facenames') as f:
exec(f.read())
#import hashlib
#hashlib.md5(open(line.split()[1],'rb').read()).hexdigest()
#if {$mymd5 != $gPolyDataFaceNamesInfo(model_file_md5)} {
# return -code error "ERROR: polydata model ([lrange $line 1 end]) file doesn't match one used to generate facenames ([lindex $line 1].facenames)!"
#}
else:
print("Getting Solid Boundaries...")
gInputReturnVar = 50.0
gInputReturnVar = input(
"Boundary Extraction"
"Enter Boundary Extraction Angle (0-90 degrees):")
guiPDvars['angleForBoundaries'] = gInputReturnVar
geom.GetBoundaryFaces(gInputReturnVar)
allids = geom.GetFaceIds()
numfaces = len(allids)
yesno = input(
"The number of surfaces found was: %i. Is this the correct number of surfaces on your polydata? yes/no"
% numfaces)
if (yesno == "no"):
raise ValueError(
"Try again with a different boundary extraction angle or check the surface of the polydata for deteriorated elements."
)
return
for newid in allids:
gPolyDataFaceNames[newid] = "noname_" + str(newid)
elif (line.split()[0] == "setSolidModel"):
solidPD = "/tmp/solid/pd"
try:
Repository.Delete(solidPD)
except:
pass
#Set the polydatasolid in the mesh object to the current solid model
geom.GetPolyData(solidPD)
resObj.SetVtkPolyData(solidPD)
elif (line.split()[0] == "localSize"):
facename = line.split()[1]
if (facename == ""):
raise ValueError(
"ERROR: Must select a face to add local mesh size on !")
return
faceids = geom.GetFaceIds()
for ids in faceids:
if (gPolyDataFaceNames[ids] == facename):
regionid = ids
resObj.SetMeshOptions("LocalEdgeSize", [float(line.split()[1])])
elif (line.split()[0] == "useCenterlineRadius"):
if (int(guiTGvars['meshWallFirst']) != 1):
raise ValueError(
"ERROR: Must select wall faces for centerline extraction")
return
cappedsolid = "/tmp/solid/cappedpd"
try:
Repository.Delete(cappedsolid)
except:
pass
cappedsolid = PolyDataVMTKGetCenterIds(resObj, "mesh")
polys = PolyDataVMTKCenterlines(cappedsolid, resObj, "mesh")
resObj.SetVtkPolyData(polys[0])
elif (line.split()[0] == "functionBasedMeshing"):
resObj.SetSizeFunctionBasedMesh(float(line.split()[1]),
float(line.split()[2]))
elif (line.split()[0] == "sphereRefinement"):
resObj.SetSphereRefinement(float(line.split()[1]),
float(line.split()[2]),
[float(i) for i in line.split()[3:]])
elif (line.split()[0] == "wallFaces"):
guiTGvars['meshWallFirst'] = 1
resObj.SetMeshOptions("MeshWallFirst", [1])
walls = []
for i in range(1, len(line.split())):
name = line.split()[i]
name_id = return_face_id(geom, name)
walls.append(name_id)
resObj.SetWalls(walls)
elif (line.split()[0] == "boundaryLayer"):
if (guiTGvars['meshWallFirst'] != 1):
raise ValueError(
"ERROR: Must select wall faces for boundary layer")
return
resObj.SetBoundaryLayer(0, 0, 0, int(line.split()[1]),
[float(i) for i in line.split()[2:]])
elif (line.split()[0] == "tolerance"):
resObj.SetTolerance(float(line.split()[1]))
elif (line.split()[0] == "quality"):
resObj.SetQuality(line.split()[1])
elif (line.split()[0] == "writeMesh"):
resObj.WriteMesh(line.split()[1], int(line.split()[-1]))
elif (line.split()[0] == "option"):
if (len(line.split()) == 3):
if (line.split()[1] == "surface"):
resObj.SetMeshOptions("SurfaceMeshFlag",
[int(line.split()[2])])
elif (line.split()[1] == "volume"):
resObj.SetMeshOptions("VolumeMeshFlag",
[int(line.split()[2])])
guiMMvars['meshGenerateVolumeMesh'] = 1
elif (line.split()[1] == "gsize"):
resObj.SetMeshOptions("GlobalEdgeSize",
[float(line.split()[2])])
elif (line.split()[1] == "a"):
resObj.SetMeshOptions("GlobalEdgeSize",
[float(line.split()[2])])
else:
#lappend mylist [lindex $line 2]
resObj.SetMeshOptions(line.split()[1],
[float(line.split()[2])])
else:
for lineval in line.split():
resObj.SetMeshOptions(lineval, [1])
elif (line.split()[0] == "getBoundaries"):
resObj.GetBoundaryFaces(guiPDvars['angleForBoundaries'])
else:
print("ignoring line: " + line)
fp.close()
try:
Repository.Delete(solid)
except:
pass
def mesh_writeCompleteMesh(meshName, solidName, prefix, outdir):
global guiMMvars
global gFilenames
solid = Solid.pySolidModel()
solid.GetModel(solidName)
kernel = solid.GetKernel()
mesh = MeshObject.pyMeshObject()
mesh.GetMesh(meshName)
try:
os.mkdir(outdir + '/mesh-surfaces')
os.mkdir(outdir + '/misc')
except:
pass
ug = "myug"
pd = "mypd"
facepd = "myfacepd"
try:
Repository.Delete(ug)
except:
pass
try:
Repository.Delete(pd)
except:
pass
try:
Repository.Delete(facepd)
except:
pass
if (kernel == "PolyData" and guiMMvars['meshGenerateVolumeMesh'] != 1):
pass
else:
mesh.GetUnstructuredGrid(ug)
ugwriter = vtk.vtkXMLUnstructuredGridWriter()
ugwriter.SetCompressorTypeToZLib()
ugwriter.EncodeAppendedDataOff()
ugwriter.SetInputDataObject(Repository.ExportToVtk(ug))
ugwriter.SetFileName(outdir + '/' + prefix + '.mesh.vtu')
ugwriter.Write()
del ugwriter
mesh.GetPolyData(pd)
pdwriter = vtk.vtkXMLPolyDataWriter()
pdwriter.SetCompressorTypeToZLib()
pdwriter.EncodeAppendedDataOff()
pdwriter.SetInputDataObject(Repository.ExportToVtk(pd))
pdwriter.SetFileName(outdir + '/' + prefix + '.exterior.vtp')
pdwriter.Write()
foundWall = 0
appender = vtk.vtkAppendPolyData()
appender.UserManagedInputsOff()
foundStent = 0
Sappender = vtk.vtkAppendPolyData()
Sappender.UserManagedInputsOff()
name_to_identifier = {}
identifier_to_name = {}
facestr = mesh.GetModelFaceInfo()
facename = ""
for faceinfo in facestr.split(" "):
faceinfo = faceinfo.replace(" ", "")
faceinfo = faceinfo.replace("{", "")
faceinfo = faceinfo.replace("}", "")
i = faceinfo[0]
ident = faceinfo[1]
if (kernel == "Parasolid"):
try:
facename = faceinfo[2]
except:
pass
elif (kernel == "Discrete"):
global gDiscreteModelFaceNames
try:
facename = gDiscreteModelFaceNames[i]
except:
pass
elif (kernel == "PolyData"):
global gPolyDataFaceNames
try:
facename = gPolyDataFaceNames[i]
except:
pass
else:
raise ValueError("ERROR: invalid solid kernel" + kernel)
return
if (facename == ""):
facename = "missing_" + i + "\_" + ident
elif ("noname" in facename.lower()):
print(facename + " is not being written because it has no_name")
else:
name_to_identifier[facename] = ident
identifier_to_name[ident] = facename
try:
Repository.Delete(facepd)
except:
pass
try:
mesh.GetFacePolyData(facepd, int(i))
except:
print("Warning face %s not found, skipping face" % i)
pass
pdwriter.SetInputDataObject(Repository.ExportToVtk(facepd))
pdwriter.SetFileName(outdir + '/mesh-surfaces/' + facename + '.vtp')
pdwriter.Write()
if "wall" in facename:
foundWall = 1
appender.AddInputData(Repository.ExportToVtk(facepd))
if "stent" in facename:
foundStent = 1
appender.AddInputData(Repository.ExportToVtk(facepd))
try:
Repository.Delete(facepd)
except:
pass
if (foundWall):
appender.Update()
cleaner = vtk.vtkCleanPolyData()
cleaner.PointMergingOn()
cleaner.PieceInvariantOff()
cleaner.SetInputDataObject(appender.GetOutput())
cleaner.Update()
pdwriter.SetFileName(outdir + '/walls_combined.vtp')
pdwriter.SetInputDataObject(cleaner.GetOutput())
pdwriter.Write()
del cleaner
del appender
if (foundStent):
Sappender.Update()
Scleaner = vtk.vtkCleanPolyData()
Scleaner.PointMergingOn()
Scleaner.PieceInvariantOff()
Scleaner.SetInputDataObject(Sappender.GetOutput())
Scleaner.Update()
pdwriter.SetFileName(outdir + '/stent_combined.vtp')
pdwriter.SetInputDataObject(Scleaner.GetOutput())
del pdwriter
del Scleaner
del Sappender
#$mesh WriteMetisAdjacency -file $outdir/$prefix.xadj
#mesh_kernel = mesh.GetKernel()
#if (mesh_kernel == "TetGen"):
# gFilenames['tet_mesh_script_file'] = outdir+ "/" + prefix
# guiMMcreateTetGenScriptFile
#elif (mesh_kernel == "MeshSim"):
# gFilenames['mesh_script_file'] = outdir + "/" + prefix
# guiMMcreateMeshSimScriptFile
# mesh.WriteMesh(outdir+'/'+prefix+'.sms')
try:
Repository.Delete(ug)
except:
pass
try:
Repository.Delete(pd)
except:
pass
try:
Repository.Delete(facepd)
except:
pass
def demo_loft_cylinder(dstdir):
Contour.SetContourKernel('Circle')
try:
Repository.Delete('path')
Repository.Delete('ct')
Repository.Delete('ct2')
except:
pass
#generate path
p = Path.pyPath()
p.NewObject('path')
p.AddPoint([0.,0.,0.])
p.AddPoint([0.,0.,30.])
p.CreatePath()
num = p.GetPathPtsNum()
#create two contours
c = Contour.pyContour()
c.NewObject('ct','path',0)
c.SetCtrlPtsByRadius([0.,0.,0.],2)
c.Create()
print ("Contour created: area is: " + str(c.Area()) + "; center is: " +str(c.Center()))
c2 = Contour.pyContour()
c2.NewObject('ct2','path',num-1)
c2.SetCtrlPtsByRadius([0.,0.,30.],2)
c2.Create()
print ("Contour created: area is: " + str(c2.Area()) + "; center is: " +str(c2.Center()))
c.GetPolyData('ctp')
c2.GetPolyData('ct2p')
#processing the contours
numOutPtsAlongLength = 12
numPtsInLinearSampleAlongLength = 240
numLinearPtsAlongLength = 120
dstName='loft'
numOutPtsInSegs = 60
numModes = 20
useFFT = 0
useLinearSampleAlongLength = 1
Geom.SampleLoop('ctp',numOutPtsInSegs,'ctps')
Geom.SampleLoop('ct2p',numOutPtsInSegs,'ct2ps')
Geom.AlignProfile('ctps','ct2ps','ct2psa',0)
srcList = ['ctps','ct2psa']
Geom.LoftSolid(srcList,dstName,numOutPtsInSegs,numOutPtsAlongLength,numLinearPtsAlongLength,numModes,useFFT,useLinearSampleAlongLength)
#cap the cylinder
VMTKUtils.Cap_with_ids(dstName,'cap',0,0)
solid = Solid.pySolidModel()
solid.NewObject('cyl')
solid.SetVtkPolyData('cap')
solid.GetBoundaryFaces(90)
print ("Creating model: \nFaceID found: " + str(solid.GetFaceIds()))
solid.WriteNative(dstdir + "/cylinder.vtp")
Repository.Delete('ctp')
Repository.Delete('ct2p')
Repository.Delete('ct2ps')
Repository.Delete(dstName)
Repository.Delete('cap')
Repository.Delete('path')
from shutil import copyfile
copyfile("cylinder.vtp.facenames2",dstdir + "/cylinder.vtp.facenames")
return dstdir+"/cylinder.vtp"
T = 0.2
Vbar = 135
radius = 2.0
omega = 2.0*math.pi/T
pts = []
for i in range(0,256):
dt = T/255.0
t = float(i)*dt
Vmean = Vbar*(1.0+math.sin(2*math.pi*t/T))
area = math.pi*radius*radius
pts.append([t, -Vmean*area])
terms = Math.FFT(pts, 2,256)
try:
Repository.Delete('outflow')
except:
pass
import os
import stat
os.chmod(fullrundir+'/mesh-complete/mesh-surfaces', 0o777)
Repository.ReadXMLPolyData('outflow',fullrundir+'/mesh-complete/mesh-surfaces/outlet.vtp')
numPts = Geom.NumPts('outflow')
outflowObj = Repository.ExportToVtk('outflow')
outflowScalars = outflowObj.GetPointData().GetScalars()
print ("Reading simulation results: " + resfn)
resReader = vtk.vtkXMLUnstructuredGridReader()
resReader.SetFileName(resfn)
resReader.Update()