mirror of
https://github.com/wassname/simpeg.git
synced 2026-09-09 11:34:26 +08:00
Merge branch 'dev' into em/dev
This commit is contained in:
Lindsey Heagy
@@ -26,7 +26,14 @@ def SolverWrapD(fun, factorize=True, checkAccuracy=True, accuracyTol=1e-6):
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def __init__(self, A, **kwargs):
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self.A = A.tocsc()
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self.checkAccuracy = kwargs.get("checkAccuracy", checkAccuracy)
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if kwargs.has_key("checkAccuracy"): del kwargs["checkAccuracy"]
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self.accuracyTol = kwargs.get("accuracyTol", accuracyTol)
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if kwargs.has_key("accuracyTol"): del kwargs["accuracyTol"]
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self.kwargs = kwargs
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if factorize:
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self.solver = fun(self.A, **kwargs)
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@@ -57,8 +64,8 @@ def SolverWrapD(fun, factorize=True, checkAccuracy=True, accuracyTol=1e-6):
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else:
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X[:,i] = fun(self.A, b[:,i], **self.kwargs)
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if checkAccuracy:
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_checkAccuracy(self.A, b, X, accuracyTol)
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if self.checkAccuracy:
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_checkAccuracy(self.A, b, X, self.accuracyTol)
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return X
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def clean(self):
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@@ -81,6 +88,12 @@ def SolverWrapI(fun, checkAccuracy=True, accuracyTol=1e-5):
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def __init__(self, A, **kwargs):
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self.A = A
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self.checkAccuracy = kwargs.get("checkAccuracy", checkAccuracy)
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if kwargs.has_key("checkAccuracy"): del kwargs["checkAccuracy"]
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self.accuracyTol = kwargs.get("accuracyTol", accuracyTol)
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if kwargs.has_key("accuracyTol"): del kwargs["accuracyTol"]
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self.kwargs = kwargs
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def __mul__(self, b):
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@@ -108,8 +121,8 @@ def SolverWrapI(fun, checkAccuracy=True, accuracyTol=1e-5):
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else:
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X[:,i] = out
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if checkAccuracy:
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_checkAccuracy(self.A, b, X, accuracyTol)
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if self.checkAccuracy:
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_checkAccuracy(self.A, b, X, self.accuracyTol)
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return X
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def clean(self):
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@@ -1,6 +1,6 @@
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from matutils import *
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from codeutils import *
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from meshutils import exampleLrmGrid, meshTensor, closestPoints, readUBCTensorMesh, writeUBCTensorMesh, writeUBCTensorModel, readVTRFile, writeVTRFile
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from meshutils import *
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from curvutils import volTetra, faceInfo, indexCube
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from interputils import interpmat
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from CounterUtils import *
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@@ -17,7 +17,7 @@ def memProfileWrapper(towrap, *funNames):
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For example::
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foo_mem = memProfile(foo,'my_func')
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foo_mem = memProfileWrapper(foo,['my_func'])
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fooi = foo_mem()
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for i in range(5):
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fooi.my_func()
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@@ -102,223 +102,6 @@ def closestPoints(mesh, pts, gridLoc='CC'):
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return nodeInds
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def readUBCTensorMesh(fileName):
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"""
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Read UBC GIF 3DTensor mesh and generate 3D Tensor mesh in simpegTD
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Input:
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:param fileName, path to the UBC GIF mesh file
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Output:
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:param SimPEG TensorMesh object
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:return
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"""
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# Interal function to read cell size lines for the UBC mesh files.
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def readCellLine(line):
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for seg in line.split():
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if '*' in seg:
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st = seg
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sp = seg.split('*')
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re = np.array(sp[0],dtype=int)*(' ' + sp[1])
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line = line.replace(st,re.strip())
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return np.array(line.split(),dtype=float)
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# Read the file as line strings, remove lines with comment = !
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msh = np.genfromtxt(fileName,delimiter='\n',dtype=np.str,comments='!')
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# Fist line is the size of the model
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sizeM = np.array(msh[0].split(),dtype=float)
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# Second line is the South-West-Top corner coordinates.
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x0 = np.array(msh[1].split(),dtype=float)
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# Read the cell sizes
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h1 = readCellLine(msh[2])
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h2 = readCellLine(msh[3])
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h3temp = readCellLine(msh[4])
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h3 = h3temp[::-1] # Invert the indexing of the vector to start from the bottom.
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# Adjust the reference point to the bottom south west corner
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x0[2] = x0[2] - np.sum(h3)
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# Make the mesh
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from SimPEG import Mesh
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tensMsh = Mesh.TensorMesh([h1,h2,h3],x0)
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return tensMsh
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def readUBCTensorModel(fileName, mesh):
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"""
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Read UBC 3DTensor mesh model and generate 3D Tensor mesh model in simpeg
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Input:
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:param fileName, path to the UBC GIF mesh file to read
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:param mesh, TensorMesh object, mesh that coresponds to the model
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Output:
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:return numpy array, model with TensorMesh ordered
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"""
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f = open(fileName, 'r')
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model = np.array(map(float, f.readlines()))
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f.close()
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model = np.reshape(model, (mesh.nCz, mesh.nCx, mesh.nCy), order = 'F')
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model = model[::-1,:,:]
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model = np.transpose(model, (1, 2, 0))
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model = mkvc(model)
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return model
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def writeUBCTensorMesh(fileName, mesh):
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"""
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Writes a SimPEG TensorMesh to a UBC-GIF format mesh file.
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:param str fileName: File to write to
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:param simpeg.Mesh.TensorMesh mesh: The mesh
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"""
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assert mesh.dim == 3
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s = ''
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s += '%i %i %i\n' %tuple(mesh.vnC)
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origin = mesh.x0 + np.array([0,0,mesh.hz.sum()]) # Have to it in the same operation or use mesh.x0.copy(), otherwise the mesh.x0 is updated.
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origin.dtype = float
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s += '%.2f %.2f %.2f\n' %tuple(origin)
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s += ('%.2f '*mesh.nCx+'\n')%tuple(mesh.hx)
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s += ('%.2f '*mesh.nCy+'\n')%tuple(mesh.hy)
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s += ('%.2f '*mesh.nCz+'\n')%tuple(mesh.hz[::-1])
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f = open(fileName, 'w')
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f.write(s)
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f.close()
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def writeUBCTensorModel(fileName, mesh, model):
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"""
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Writes a model associated with a SimPEG TensorMesh
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to a UBC-GIF format model file.
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:param str fileName: File to write to
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:param simpeg.Mesh.TensorMesh mesh: The mesh
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:param numpy.ndarray model: The model
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"""
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# Reshape model to a matrix
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modelMat = mesh.r(model,'CC','CC','M')
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# Transpose the axes
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modelMatT = modelMat.transpose((2,0,1))
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# Flip z to positive down
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modelMatTR = mkvc(modelMatT[::-1,:,:])
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np.savetxt(fileName, modelMatTR.ravel())
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def readVTRFile(fileName):
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"""
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Read VTK Rectilinear (vtr xml file) and return SimPEG Tensor mesh and model
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Input:
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:param vtrFileName, path to the vtr model file to write to
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Output:
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:return SimPEG TensorMesh object
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:return SimPEG model dictionary
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"""
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# Import
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from vtk import vtkXMLRectilinearGridReader as vtrFileReader
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from vtk.util.numpy_support import vtk_to_numpy
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# Read the file
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vtrReader = vtrFileReader()
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vtrReader.SetFileName(fileName)
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vtrReader.Update()
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vtrGrid = vtrReader.GetOutput()
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# Sort information
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hx = np.abs(np.diff(vtk_to_numpy(vtrGrid.GetXCoordinates())))
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xR = vtk_to_numpy(vtrGrid.GetXCoordinates())[0]
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hy = np.abs(np.diff(vtk_to_numpy(vtrGrid.GetYCoordinates())))
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yR = vtk_to_numpy(vtrGrid.GetYCoordinates())[0]
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zD = np.diff(vtk_to_numpy(vtrGrid.GetZCoordinates()))
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# Check the direction of hz
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if np.all(zD < 0):
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hz = np.abs(zD[::-1])
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zR = vtk_to_numpy(vtrGrid.GetZCoordinates())[-1]
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else:
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hz = np.abs(zD)
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zR = vtk_to_numpy(vtrGrid.GetZCoordinates())[0]
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x0 = np.array([xR,yR,zR])
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# Make the SimPEG object
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from SimPEG import Mesh
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tensMsh = Mesh.TensorMesh([hx,hy,hz],x0)
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# Grap the models
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modelDict = {}
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for i in np.arange(vtrGrid.GetCellData().GetNumberOfArrays()):
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modelName = vtrGrid.GetCellData().GetArrayName(i)
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if np.all(zD < 0):
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modFlip = vtk_to_numpy(vtrGrid.GetCellData().GetArray(i))
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tM = tensMsh.r(modFlip,'CC','CC','M')
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modArr = tensMsh.r(tM[:,:,::-1],'CC','CC','V')
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else:
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modArr = vtk_to_numpy(vtrGrid.GetCellData().GetArray(i))
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modelDict[modelName] = modArr
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# Return the data
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return tensMsh, modelDict
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def writeVTRFile(fileName,mesh,model=None):
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"""
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Makes and saves a VTK rectilinear file (vtr) for a simpeg Tensor mesh and model.
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Input:
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:param str, path to the output vtk file
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:param mesh, SimPEG TensorMesh object - mesh to be transfer to VTK
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:param model, dictionary of numpy.array - Name('s) and array('s). Match number of cells
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"""
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# Import
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from vtk import vtkRectilinearGrid as rectGrid, vtkXMLRectilinearGridWriter as rectWriter
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from vtk.util.numpy_support import numpy_to_vtk
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# Deal with dimensionalities
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if mesh.dim >= 1:
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vX = mesh.vectorNx
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xD = mesh.nNx
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yD,zD = 1,1
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vY, vZ = np.array([0,0])
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if mesh.dim >= 2:
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vY = mesh.vectorNy
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yD = mesh.nNy
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if mesh.dim == 3:
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vZ = mesh.vectorNz
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zD = mesh.nNz
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# Use rectilinear VTK grid.
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# Assign the spatial information.
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vtkObj = rectGrid()
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vtkObj.SetDimensions(xD,yD,zD)
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vtkObj.SetXCoordinates(numpy_to_vtk(vX,deep=1))
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vtkObj.SetYCoordinates(numpy_to_vtk(vY,deep=1))
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vtkObj.SetZCoordinates(numpy_to_vtk(vZ,deep=1))
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# Assign the model('s) to the object
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for item in model.iteritems():
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# Convert numpy array
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vtkDoubleArr = numpy_to_vtk(item[1],deep=1)
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vtkDoubleArr.SetName(item[0])
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vtkObj.GetCellData().AddArray(vtkDoubleArr)
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# Set the active scalar
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vtkObj.GetCellData().SetActiveScalars(model.keys()[0])
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vtkObj.Update()
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# Check the extension of the fileName
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ext = os.path.splitext(fileName)[1]
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if ext is '':
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fileName = fileName + '.vtr'
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elif ext not in '.vtr':
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raise IOError('{:s} is an incorrect extension, has to be .vtr')
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# Write the file.
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vtrWriteFilter = rectWriter()
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vtrWriteFilter.SetInput(vtkObj)
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vtrWriteFilter.SetFileName(fileName)
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vtrWriteFilter.Update()
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def ExtractCoreMesh(xyzlim, mesh, meshType='tensor'):
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"""
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Extracts Core Mesh from Global mesh
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