vtkpy folder added

vtk_py/BiV.geo

@@ -0,0 +1,54 @@
+Geometry.HideCompounds = 1;
+
+Mesh.CharacteristicLengthFactor = <<Meshsize>> ;// Fine
+
+Mesh.Algorithm    = 6; // (1=MeshAdapt, 2=Automatic, 5=Delaunay, 6=Frontal, 7=bamg, 8=delquad) (Default=2)
+Mesh.RecombineAll = 0;
+
+Mesh.RemeshAlgorithm = 1; // (0=no split, 1=automatic, 2=automatic only with metis) (Default=0)
+
+Mesh.RemeshParametrization = 7; // (0=harmonic_circle, 1=conformal_spectral, 2=rbf, 3=harmonic_plane, 4=convex_circle, 5=convex_plane, 6=harmonic square, 7=conformal_fe) (Default=4)
+
+Mesh.Algorithm3D    = 4; // (1=Delaunay, 4=Frontal, 5=Frontal Delaunay, 6=Frontal Hex, 7=MMG3D, 9=R-tree) (Default=1)
+Mesh.Recombine3DAll = 0;
+
+Mesh.Optimize = 1;
+Mesh.OptimizeNetgen = 1;
+
+Mesh.Smoothing = 0;
+
+Merge <<LVfilename>>;
+Merge <<RVfilename>>;
+Merge <<Epifilename>>;
+
+CreateTopology;
+
+ll[] = Line "*";
+L_LV_base = newl; Compound Line(L_LV_base) = ll[2];
+L_RV_base = newl; Compound Line(L_RV_base) = ll[0];
+L_epi_base = newl; Compound Line(L_epi_base) = ll[1];
+// Physical Line("EPI_BASE") = {L_epi_base};
+//Physical Line(0) = {L_epi_base};
+
+ss[] = Surface "*";
+S_LV = news; Compound Surface(S_LV) = ss[0];
+S_RV = news; Compound Surface(S_RV) = ss[1];
+S_epi = news; Compound Surface(S_epi) = ss[2];
+// Physical Surface("LV") = {S_LV};
+// Physical Surface("RV") = {S_RV};
+// Physical Surface("epi") = {S_epi};
+//Physical Surface(3) = {S_epi};
+//Physical Surface(1) = {S_RV};
+//Physical Surface(2) = {S_LV};
+
+
+LL_base = newll; Line Loop(LL_base) = {L_LV_base, L_RV_base, L_epi_base};
+S_base = news; Plane Surface(S_base) = {LL_base};
+// Physical Surface("BASE") = {S_base};
+//Physical Surface(4) = {S_base};
+
+SL_wall = newsl; Surface Loop(SL_wall) = {S_LV, S_RV, S_epi, S_base};
+V_wall = newv; Volume(V_wall) = {SL_wall};
+//Physical Volume("WALL") = {V_wall};
+Physical Volume(0) = {V_wall};
+

vtk_py/CreateVertexFromPoint.py

@@ -0,0 +1,19 @@
+########################################################################
+
+import sys
+import vtk
+
+########################################################################
+
+def CreateVertexFromPoint(ugrid):
+
+	vertices = vtk.vtkCellArray()
+	for p in range(ugrid.GetNumberOfPoints()):
+		vert = vtk.vtkVertex()
+		vert.GetPointIds().SetId(0, p)
+		vertices.InsertNextCell(vert)
+
+	ugrid.SetCells(1, vertices)
+
+
+

vtk_py/LV.geo

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+Geometry.HideCompounds = 1;
+
+Mesh.CharacteristicLengthFactor = <<mesh_d>>;  // Coarse
+
+Mesh.Algorithm    = 6; // (1=MeshAdapt, 2=Automatic, 5=Delaunay, 6=Frontal, 7=bamg, 8=delquad) (Default=2)
+Mesh.RecombineAll = 0;
+
+Mesh.RemeshAlgorithm = 1; // (0=no split, 1=automatic, 2=automatic only with metis) (Default=0)
+
+Mesh.RemeshParametrization = 7; // (0=harmonic_circle, 1=conformal_spectral, 2=rbf, 3=harmonic_plane, 4=convex_circle, 5=convex_plane, 6=harmonic square, 7=conformal_fe) (Default=4)
+
+Mesh.Algorithm3D    = 4; // (1=Delaunay, 4=Frontal, 5=Frontal Delaunay, 6=Frontal Hex, 7=MMG3D, 9=R-tree) (Default=1)
+Mesh.Recombine3DAll = 0;
+
+Mesh.Optimize = 1;
+Mesh.OptimizeNetgen = 1;
+
+Mesh.Smoothing = 0;
+
+Merge "<<Endofilename>>";
+Merge "<<Epifilename>>";
+
+CreateTopology;
+
+ll[] = Line "*";
+L_LV_base = newl; Compound Line(L_LV_base) = ll[1];
+L_epi_base = newl; Compound Line(L_epi_base) = ll[0];
+//Physical Line("EPI_BASE") = {L_epi_base};
+
+ss[] = Surface "*";
+S_LV = news; Compound Surface(S_LV) = ss[0];
+S_epi = news; Compound Surface(S_epi) = ss[1];
+Physical Surface("LV") = {S_LV};
+Physical Surface("epi") = {S_epi};
+
+LL_base = newll; Line Loop(LL_base) = {L_LV_base, L_epi_base};
+S_base = news; Plane Surface(S_base) = {LL_base};
+Physical Surface("BASE") = {S_base};
+
+SL_wall = newsl; Surface Loop(SL_wall) = {S_LV, S_epi, S_base};
+V_wall = newv; Volume(V_wall) = {SL_wall};
+Physical Volume("WALL") = {V_wall};
+
+
+//
+//// P1 = newp; Point(P1) = {36., 74., 70.};
+//// Field[1] = Attractor;
+//// Field[1].NodesList = {P1};
+//// Field[2] = Threshold;
+//// Field[2].IField = 1;
+//// Field[2].LcMin = 100.;
+//// Field[2].LcMax = 100.;
+//// Field[2].DistMin = 0.;
+//// Field[2].DistMax = 10.;
+//// Background Field = 2;
+//
+//// Field[1] = Box;
+//// Field[1].VIn = 5.;
+//// Field[1].VOut = 5.;
+//// Field[1].XMin = 30.; 
+//// Field[1].XMax = 40.;
+//// Field[1].YMin = 70.;
+//// Field[1].YMax = 80.;
+//// Field[1].ZMin = 69.;
+//// Field[1].ZMax = 71.;
+//// Background Field = 1;
+
+
+
+
+
+
+
+

vtk_py/LV_original.geo

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+Geometry.HideCompounds = 1;
+
+Mesh.CharacteristicLengthFactor = <<mesh_d>>;  // Coarse
+
+Mesh.Algorithm    = 6; // (1=MeshAdapt, 2=Automatic, 5=Delaunay, 6=Frontal, 7=bamg, 8=delquad) (Default=2)
+Mesh.RecombineAll = 0;
+
+Mesh.RemeshAlgorithm = 1; // (0=no split, 1=automatic, 2=automatic only with metis) (Default=0)
+
+Mesh.RemeshParametrization = 7; // (0=harmonic_circle, 1=conformal_spectral, 2=rbf, 3=harmonic_plane, 4=convex_circle, 5=convex_plane, 6=harmonic square, 7=conformal_fe) (Default=4)
+
+Mesh.Algorithm3D    = 4; // (1=Delaunay, 4=Frontal, 5=Frontal Delaunay, 6=Frontal Hex, 7=MMG3D, 9=R-tree) (Default=1)
+Mesh.Recombine3DAll = 0;
+
+Mesh.Optimize = 1;
+Mesh.OptimizeNetgen = 1;
+
+Mesh.Smoothing = 0;
+
+Merge "<<Endofilename>>";
+Merge "<<Epifilename>>";
+
+CreateTopology;
+
+ll[] = Line "*";
+L_LV_base = newl; Compound Line(L_LV_base) = ll[1];
+L_epi_base = newl; Compound Line(L_epi_base) = ll[0];
+//Physical Line("EPI_BASE") = {L_epi_base};
+
+ss[] = Surface "*";
+S_LV = news; Compound Surface(S_LV) = ss[0];
+S_epi = news; Compound Surface(S_epi) = ss[1];
+Physical Surface("LV") = {S_LV};
+Physical Surface("epi") = {S_epi};
+
+LL_base = newll; Line Loop(LL_base) = {L_LV_base, L_epi_base};
+S_base = news; Plane Surface(S_base) = {LL_base};
+Physical Surface("BASE") = {S_base};
+
+SL_wall = newsl; Surface Loop(SL_wall) = {S_LV, S_epi, S_base};
+V_wall = newv; Volume(V_wall) = {SL_wall};
+Physical Volume("WALL") = {V_wall};
+
+
+//
+//// P1 = newp; Point(P1) = {36., 74., 70.};
+//// Field[1] = Attractor;
+//// Field[1].NodesList = {P1};
+//// Field[2] = Threshold;
+//// Field[2].IField = 1;
+//// Field[2].LcMin = 100.;
+//// Field[2].LcMax = 100.;
+//// Field[2].DistMin = 0.;
+//// Field[2].DistMax = 10.;
+//// Background Field = 2;
+//
+//// Field[1] = Box;
+//// Field[1].VIn = 5.;
+//// Field[1].VOut = 5.;
+//// Field[1].XMin = 30.; 
+//// Field[1].XMax = 40.;
+//// Field[1].YMin = 70.;
+//// Field[1].YMax = 80.;
+//// Field[1].ZMin = 69.;
+//// Field[1].ZMax = 71.;
+//// Background Field = 1;
+
+
+
+
+
+
+
+

vtk_py/Set4ChamberDirection.py

@@ -0,0 +1,62 @@
+########################################################################
+import argparse
+import numpy as np
+from dolfin import *
+import math
+########################################################################
+
+
+def Set4ChamberDirection(mesh, outfilename, apexC, apexR, basalC, basalN, outdirectory="./"):
+
+
+	def BCbase(x, on_boundary):
+		basalNorm = np.linalg.norm(basalN)
+		basalNN = 1.0/basalNorm*np.array(basalN)
+
+		return (x[0] - basalC[0])*basalNN[0] + (x[1] - basalC[1])*basalNN[1]  < DOLFIN_EPS  and  on_boundary
+
+	def BCapex(x, on_boundary):
+		return (x[0] - apexC[0])**2 + (x[1] - apexC[1])**2 < apexR[0]**2  and  on_boundary
+
+
+	V = FunctionSpace(mesh, 'Lagrange', 1)
+        u0 = Constant(1.0)
+	u1 = Constant(0.0)
+
+	bc =[DirichletBC(V, u1, BCapex), DirichletBC(V, u0, BCbase)] 
+
+	# Define variational problem
+	u = TrialFunction(V)
+	v = TestFunction(V)
+	f = Constant(0)
+	a = inner(nabla_grad(u), nabla_grad(v))*dx
+	L = f*v*dx
+
+	# Compute solution
+	u = Function(V)
+	solve(a == L, u, bc)
+	u_a = u.vector().array()
+
+	# Compute gradient
+	V_g = VectorFunctionSpace(mesh, 'Lagrange', 1)
+	v = TestFunction(V_g)
+	w = TrialFunction(V_g)
+
+	a = inner(w, v)*dx
+	L = inner(grad(u), v)*dx
+	grad_u = Function(V_g)
+	solve(a == L, grad_u)
+	#normalize_grad_u = project(grad_u/sqrt(dot(grad_u, grad_u)), V_g)
+	grad_u.rename('matdir', 'matdir')
+
+	#plot(normalize_grad_u, interactive=True)
+	pvdoutfile = outdirectory+outfilename+"_matdir.pvd"
+	file15 = File(pvdoutfile)
+	file15 << grad_u
+
+	#plot(normalize_grad_u, interactive=True)
+	pvdoutfile2 = outdirectory+outfilename+"_dirsoln.pvd"
+	file16 = File(pvdoutfile2)
+	file16 << u 
+
+