def genMesh(self,fnOut=None,debug=False):
"""Main mesh generation function.
.. note:: If ``fnOut=None``, will use ``geometry.fnGeo``.
.. note:: If ``fromFile=True``, will generate from .geo file running
gmsh directly on the file. If not, will try to run hard coded FiPy
version for mesh generation via :py:func:`runFiPyMeshGenerator` .
Keyword Args:
fnOut (str): Output filepath for meshfile.
debug (bool): Print debugging messages.
dim (int): Dimension of mesh.
Returns:
fipy.GmshImporter3D: Gmsh mesh object.
"""
if fnOut==None:
fnOut=self.simulation.embryo.geometry.fnGeo.replace(".geo",".msh")
dim=self.simulation.embryo.geometry.getDim()
if self.fromFile:
self.fnMesh=pyfrp_misc_module.fixPath(fnOut)
pyfrp_gmsh_module.runGmsh(self.simulation.embryo.geometry.fnGeo,fnOut=fnOut,debug=debug,volSizeMax=self.volSizePx,dim=dim)
self.importMeshFromFile(self.fnMesh)
else:
self.runFiPyMeshGenerator(self.simulation.embryo.geometry.typ)
return self.mesh
def __init__(self,embryo,typ,fnGeo,center,dim=3):
self.typ=typ
self.embryo=embryo
self.fnGeo=pyfrp_misc_module.fixPath(fnGeo)
self.center=center
self.dim=dim
self.geoFileParameters={}
def setFnMesh(self, fn):
"""Sets the filepath of meshfile.
Imports the new mesh right away using :py:func:`importMeshFromFile`.
"""
self.fnMesh = pyfrp_misc_module.fixPath(fn)
self.importMeshFromFile(self.fnMesh)
return self.fnMesh
def test_readStlFile(): """Test function for readStlFile. Reads in .stl and checks if there are enough vertices read in.""" d=pyfrp_gmsh_IO_module.readStlFile(pyfrp_misc_module.fixPath(pyfrp_misc_module.getMeshfilesDir()+"tests/readStlFile.stl")) assert len(d.vertices) == 5
def setFnGeo(self,fn): """Sets path to .geo file. Args: fn (str): Path to file. Returns: str: Path to file. """ self.fnGeo=pyfrp_misc_module.fixPath(fn) return self.fnGeo
def setFnMesh(self,fn): """Sets the filepath of meshfile. Imports the new mesh right away using :py:func:`importMeshFromFile`. """ self.fnMesh=pyfrp_misc_module.fixPath(fn) self.importMeshFromFile(self.fnMesh) return self.fnMesh
def test_domainSimplifySurfaces():
"""Test domain's simplify surfaces method.
Reads in .stl, tries to the geometry and checks if
it has been simplified properly."""
d=pyfrp_gmsh_IO_module.readStlFile(pyfrp_misc_module.fixPath(pyfrp_misc_module.getMeshfilesDir()+"tests/surfaceFuse.stl"))
d.simplifySurfaces(triangIterations=0,addPoints=False,fixSurfaces=False,debug=False,iterations=3)
sameNormal=d.getAllObjectsWithProp("ruledSurfaces","normal",np.array([0,-1.,0]))
assert len(sameNormal) == 1
def setICimgByFn(self,fn): """Sets image for initial condition interpolation given a filepath. Args: fn (str): Path to file. Returns: numpy.ndarray: New ICimg. """ img=pyfrp_img_module.loadImg(pyfrp_misc_module.fixPath(fn),self.embryo.dataEnc) return self.setICimg(img)
def setICimgByFn(self, fn):
"""Sets image for initial condition interpolation given a filepath.
Args:
fn (str): Path to file.
Returns:
numpy.ndarray: New ICimg.
"""
img = pyfrp_img_module.loadImg(pyfrp_misc_module.fixPath(fn),
self.embryo.dataEnc)
return self.setICimg(img)
def test_domainSimplifySurfaces():
"""Test domain's simplify surfaces method.
Reads in .stl, tries to the geometry and checks if
it has been simplified properly."""
d = pyfrp_gmsh_IO_module.readStlFile(
pyfrp_misc_module.fixPath(pyfrp_misc_module.getMeshfilesDir() +
"tests/surfaceFuse.stl"))
d.simplifySurfaces(triangIterations=0,
addPoints=False,
fixSurfaces=False,
debug=False,
iterations=3)
sameNormal = d.getAllObjectsWithProp("ruledSurfaces", "normal",
np.array([0, -1., 0]))
assert len(sameNormal) == 1
def test_surfaceFuse(): """Test surface fuse function. Reads in .stl, tries to fuse a few surfaces and checks if new surface lineLoop has proper number of vertices.""" d=pyfrp_gmsh_IO_module.readStlFile(pyfrp_misc_module.fixPath(pyfrp_misc_module.getMeshfilesDir()+"tests/surfaceFuse.stl")) sfID=1 toFuseIDs=[2,3,4,5,6,7] # Grab first surface sf1=d.getRuledSurfaceById(sfID)[0] # Try to successively fuse for ID in toFuseIDs: sf1.fuse(d.getRuledSurfaceById(ID)[0],debug=True) assert pyfrp_misc_module.objAttrToList(sf1.lineLoop.getVertices(),'Id') == [1, 2, 4, 5, 6, 7, 8, 9, 3]
def test_surfaceFuse():
"""Test surface fuse function.
Reads in .stl, tries to fuse a few surfaces and checks if new surface
lineLoop has proper number of vertices."""
d = pyfrp_gmsh_IO_module.readStlFile(
pyfrp_misc_module.fixPath(pyfrp_misc_module.getMeshfilesDir() +
"tests/surfaceFuse.stl"))
sfID = 1
toFuseIDs = [2, 3, 4, 5, 6, 7]
# Grab first surface
sf1 = d.getRuledSurfaceById(sfID)[0]
# Try to successively fuse
for ID in toFuseIDs:
sf1.fuse(d.getRuledSurfaceById(ID)[0], debug=True)
assert pyfrp_misc_module.objAttrToList(
sf1.lineLoop.getVertices(), 'Id') == [1, 2, 4, 5, 6, 7, 8, 9, 3]
def genMesh(self, fnOut=None, debug=False):
"""Main mesh generation function.
.. note:: If ``fnOut=None``, will use ``geometry.fnGeo``.
.. note:: If ``fromFile=True``, will generate from .geo file running
gmsh directly on the file. If not, will try to run hard coded FiPy
version for mesh generation via :py:func:`runFiPyMeshGenerator` .
Keyword Args:
fnOut (str): Output filepath for meshfile.
debug (bool): Print debugging messages.
dim (int): Dimension of mesh.
Returns:
fipy.GmshImporter3D: Gmsh mesh object.
"""
if fnOut == None:
fnOut = self.simulation.embryo.geometry.fnGeo.replace(
".geo", ".msh")
dim = self.simulation.embryo.geometry.getDim()
if self.fromFile:
self.fnMesh = pyfrp_misc_module.fixPath(fnOut)
pyfrp_gmsh_module.runGmsh(self.simulation.embryo.geometry.fnGeo,
fnOut=fnOut,
debug=debug,
volSizeMax=self.volSizePx,
dim=dim)
self.importMeshFromFile(self.fnMesh)
else:
self.runFiPyMeshGenerator(self.simulation.embryo.geometry.typ)
return self.mesh
