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Address mesh IO #212
This commit is contained in:
Rowan Cockett
@@ -0,0 +1,416 @@
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import numpy as np, os
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from SimPEG import Utils
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class TensorMeshIO(object):
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@classmethod
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def readUBC(TensorMesh, 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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"""
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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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tensMsh = TensorMesh([h1,h2,h3],x0)
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return tensMsh
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@classmethod
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def readVTK(TensorMesh, 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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tensMsh = TensorMesh([hx,hy,hz],x0)
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# Grap the models
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models = {}
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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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models[modelName] = modArr
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# Return the data
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return tensMsh, models
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def writeVTK(mesh, fileName, models=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 models, 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, VTK_VERSION
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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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if models is not None:
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for item in models.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(models.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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if float(VTK_VERSION.split('.')[0]) >=6:
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vtrWriteFilter.SetInputData(vtkObj)
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else:
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vtuWriteFilter.SetInput(vtuObj)
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vtrWriteFilter.SetFileName(fileName)
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vtrWriteFilter.Update()
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def readModelUBC(mesh, fileName):
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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 = Utils.mkvc(model)
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return model
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def writeModelUBC(mesh, fileName, 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 = Utils.mkvc(modelMatT[::-1,:,:])
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np.savetxt(fileName, modelMatTR.ravel())
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def writeUBC(mesh, fileName, models=None):
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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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if models is None: return
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assert type(models) is dict, 'models must be a dict'
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for key in models:
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assert type(key) is str, 'The dict key is a file name'
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mesh.writeModelUBC(key, models[key])
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class TreeMeshIO(object):
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def writeUBC(mesh, fileName, models=None):
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"""
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Write UBC ocTree mesh and model files from a simpeg ocTree mesh and model.
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:param str fileName: File to write to
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:param simpeg.Mesh.TreeMesh mesh: The mesh
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:param dictionary models: The models in a dictionary, where the keys is the name of the of the model file
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"""
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# Calculate information to write in the file.
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# Number of cells in the underlying mesh
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nCunderMesh = np.array([h.size for h in mesh.h],dtype=np.int64)
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# The top-south-west most corner of the mesh
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tswCorn = mesh.x0 + np.array([0,0,np.sum(mesh.h[2])])
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# Smallest cell size
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smallCell = np.array([h.min() for h in mesh.h])
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# Number of cells
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nrCells = mesh.nC
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## Extract iformation about the cells.
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# cell pointers
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cellPointers = np.array([c._pointer for c in mesh])
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# cell with
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cellW = np.array([ mesh._levelWidth(i) for i in cellPointers[:,-1] ])
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# Need to shift the pointers to work with UBC indexing
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# UBC Octree indexes always the top-left-close (top-south-west) corner first and orders the cells in z(top-down),x,y vs x,y,z(bottom-up).
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# Shift index up by 1
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ubcCellPt = cellPointers[:,0:-1].copy() + np.array([1.,1.,1.])
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# Need reindex the z index to be from the top-left-close corner and to be from the global top.
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ubcCellPt[:,2] = ( nCunderMesh[-1] + 2) - (ubcCellPt[:,2] + cellW)
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# Reorder the ubcCellPt
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ubcReorder = np.argsort(ubcCellPt.view(','.join(3*['float'])),axis=0,order=['f2','f1','f0'])[:,0]
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# Make a array with the pointers and the withs, that are order in the ubc ordering
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indArr = np.concatenate((ubcCellPt[ubcReorder,:],cellW[ubcReorder].reshape((-1,1)) ),axis=1)
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## Write the UBC octree mesh file
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with open(fileName,'w') as mshOut:
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mshOut.write('{:.0f} {:.0f} {:.0f}\n'.format(nCunderMesh[0],nCunderMesh[1],nCunderMesh[2]))
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mshOut.write('{:.4f} {:.4f} {:.4f}\n'.format(tswCorn[0],tswCorn[1],tswCorn[2]))
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mshOut.write('{:.3f} {:.3f} {:.3f}\n'.format(smallCell[0],smallCell[1],smallCell[2]))
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mshOut.write('{:.0f} \n'.format(nrCells))
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np.savetxt(mshOut,indArr,fmt='%i')
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## Print the models
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# Assign the model('s) to the object
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if models is not None:
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# indUBCvector = np.argsort(cX0[np.argsort(np.concatenate((cX0[:,0:2],cX0[:,2:3].max() - cX0[:,2:3]),axis=1).view(','.join(3*['float'])),axis=0,order=('f2','f1','f0'))[:,0]].view(','.join(3*['float'])),axis=0,order=('f2','f1','f0'))[:,0]
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for item in models.iteritems():
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# Save the data
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np.savetxt(item[0],item[1][ubcReorder],fmt='%3.5e')
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@classmethod
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def readUBC(TreeMesh, meshFile):
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"""
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Read UBC 3D OcTree mesh and/or modelFiles
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Input:
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:param str meshFile: path to the UBC GIF OcTree mesh file to read
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Output:
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:return SimPEG.Mesh.TreeMesh mesh: The octree mesh
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:return list of ndarray's: models as a list of numpy array's
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"""
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## Read the file lines
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fileLines = np.genfromtxt(meshFile,dtype=str,delimiter='\n')
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# Extract the data
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nCunderMesh = np.array(fileLines[0].split(),dtype=float)
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# I think this is the case?
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if np.unique(nCunderMesh).size >1:
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raise Exception('SimPEG TreeMeshes have the same number of cell in all directions')
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tswCorn = np.array(fileLines[1].split(),dtype=float)
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smallCell = np.array(fileLines[2].split(),dtype=float)
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nrCells = np.array(fileLines[3].split(),dtype=float)
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# Read the index array
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indArr = np.genfromtxt(fileLines[4::],dtype=np.int)
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## Calculate simpeg parameters
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h1,h2,h3 = [np.ones(nr)*sz for nr,sz in zip(nCunderMesh,smallCell)]
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x0 = tswCorn - np.array([0,0,np.sum(h3)])
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# Need to convert the index array to a points list that complies with SimPEG TreeMesh.
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# Shift to start at 0
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simpegCellPt = indArr[:,0:-1].copy()
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simpegCellPt[:,2] = ( nCunderMesh[-1] + 2) - (simpegCellPt[:,2] + indArr[:,3])
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# Need reindex the z index to be from the bottom-left-close corner and to be from the global bottom.
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simpegCellPt = simpegCellPt - np.array([1.,1.,1.])
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# Calculate the cell level
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simpegLevel = np.log2(np.min(nCunderMesh)) - np.log2(indArr[:,3])
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# Make a pointer matrix
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simpegPointers = np.concatenate((simpegCellPt,simpegLevel.reshape((-1,1))),axis=1)
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## Make the tree mesh
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mesh = TreeMesh([h1,h2,h3],x0)
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mesh._cells = set([mesh._index(p) for p in simpegPointers.tolist()])
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# Figure out the reordering
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mesh._simpegReorderUBC = np.argsort(np.array([mesh._index(i) for i in simpegPointers.tolist()]))
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# mesh._simpegReorderUBC = np.argsort((np.array([[1,1,1,-1]])*simpegPointers).view(','.join(4*['float'])),axis=0,order=['f3','f2','f1','f0'])[:,0]
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return mesh
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def readModelUBC(mesh, fileName):
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"""
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Read UBC OcTree model and get vector
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Input:
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:param fileName, path to the UBC GIF model file to read
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Output:
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:return numpy array, OcTree model
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"""
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if type(fileName) is list:
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out = {}
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for f in fileName:
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out[f] = mesh.readModelUBC(f)
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return out
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assert hasattr(mesh, '_simpegReorderUBC'), 'The file must have been loaded from a UBC format.'
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assert mesh.dim == 3
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modList = []
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modArr = np.loadtxt(fileName)
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if len(modArr.shape) == 1:
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modList.append(modArr[mesh._simpegReorderUBC])
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else:
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modList.append(modArr[mesh._simpegReorderUBC,:])
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return modList
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def writeVTK(mesh, fileName, models=None):
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"""
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Function to write a VTU file from a SimPEG TreeMesh and model.
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"""
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import vtk
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from vtk import vtkXMLUnstructuredGridWriter as Writer, VTK_VERSION
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from vtk.util.numpy_support import numpy_to_vtk, numpy_to_vtkIdTypeArray
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if str(type(mesh)).split()[-1][1:-2] not in 'SimPEG.Mesh.TreeMesh.TreeMesh':
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raise IOError('mesh is not a SimPEG TreeMesh.')
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# Make the data parts for the vtu object
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# Points
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mesh.number()
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ptsMat = mesh._gridN + mesh.x0
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vtkPts = vtk.vtkPoints()
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vtkPts.SetData(numpy_to_vtk(ptsMat,deep=True))
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# Cells
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cellConn = np.array([c.nodes for c in mesh],dtype=np.int64)
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cellsMat = np.concatenate((np.ones((cellConn.shape[0],1),dtype=np.int64)*cellConn.shape[1],cellConn),axis=1).ravel()
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cellsArr = vtk.vtkCellArray()
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cellsArr.SetNumberOfCells(cellConn.shape[0])
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cellsArr.SetCells(cellConn.shape[0],numpy_to_vtkIdTypeArray(cellsMat,deep=True))
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# Make the object
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vtuObj = vtk.vtkUnstructuredGrid()
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vtuObj.SetPoints(vtkPts)
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vtuObj.SetCells(vtk.VTK_VOXEL,cellsArr)
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# Add the level of refinement as a cell array
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cellSides = np.array([np.array(vtuObj.GetCell(i).GetBounds()).reshape((3,2)).dot(np.array([-1, 1])) for i in np.arange(vtuObj.GetNumberOfCells())])
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uniqueLevel, indLevel = np.unique(np.prod(cellSides,axis=1),return_inverse=True)
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refineLevelArr = numpy_to_vtk(indLevel.max() - indLevel,deep=1)
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refineLevelArr.SetName('octreeLevel')
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vtuObj.GetCellData().AddArray(refineLevelArr)
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# Assign the model('s) to the object
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if models is not None:
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for item in models.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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vtuObj.GetCellData().AddArray(vtkDoubleArr)
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||||
# Make the writer
|
||||
vtuWriteFilter = Writer()
|
||||
if float(VTK_VERSION.split('.')[0]) >=6:
|
||||
vtuWriteFilter.SetInputData(vtuObj)
|
||||
else:
|
||||
vtuWriteFilter.SetInput(vtuObj)
|
||||
vtuWriteFilter.SetFileName(fileName)
|
||||
# Write the file
|
||||
vtuWriteFilter.Update()
|
||||
|
||||
+559
-558
File diff suppressed because it is too large
Load Diff
@@ -100,11 +100,12 @@ except Exception, e:
|
||||
|
||||
from InnerProducts import InnerProducts
|
||||
from TensorMesh import TensorMesh, BaseTensorMesh
|
||||
from MeshIO import TreeMeshIO
|
||||
import time
|
||||
|
||||
MAX_BITS = 20
|
||||
|
||||
class TreeMesh(BaseTensorMesh, InnerProducts):
|
||||
class TreeMesh(BaseTensorMesh, InnerProducts, TreeMeshIO):
|
||||
|
||||
_meshType = 'TREE'
|
||||
|
||||
|
||||
@@ -102,408 +102,6 @@ def closestPoints(mesh, pts, gridLoc='CC'):
|
||||
|
||||
return nodeInds
|
||||
|
||||
def readUBCTensorMesh(fileName):
|
||||
"""
|
||||
Read UBC GIF 3DTensor mesh and generate 3D Tensor mesh in simpegTD
|
||||
|
||||
Input:
|
||||
:param fileName, path to the UBC GIF mesh file
|
||||
|
||||
Output:
|
||||
:param SimPEG TensorMesh object
|
||||
:return
|
||||
"""
|
||||
|
||||
# Interal function to read cell size lines for the UBC mesh files.
|
||||
def readCellLine(line):
|
||||
for seg in line.split():
|
||||
if '*' in seg:
|
||||
st = seg
|
||||
sp = seg.split('*')
|
||||
re = np.array(sp[0],dtype=int)*(' ' + sp[1])
|
||||
line = line.replace(st,re.strip())
|
||||
return np.array(line.split(),dtype=float)
|
||||
|
||||
# Read the file as line strings, remove lines with comment = !
|
||||
msh = np.genfromtxt(fileName,delimiter='\n',dtype=np.str,comments='!')
|
||||
|
||||
# Fist line is the size of the model
|
||||
sizeM = np.array(msh[0].split(),dtype=float)
|
||||
# Second line is the South-West-Top corner coordinates.
|
||||
x0 = np.array(msh[1].split(),dtype=float)
|
||||
# Read the cell sizes
|
||||
h1 = readCellLine(msh[2])
|
||||
h2 = readCellLine(msh[3])
|
||||
h3temp = readCellLine(msh[4])
|
||||
h3 = h3temp[::-1] # Invert the indexing of the vector to start from the bottom.
|
||||
# Adjust the reference point to the bottom south west corner
|
||||
x0[2] = x0[2] - np.sum(h3)
|
||||
# Make the mesh
|
||||
from SimPEG import Mesh
|
||||
tensMsh = Mesh.TensorMesh([h1,h2,h3],x0)
|
||||
return tensMsh
|
||||
|
||||
def readUBCTensorModel(fileName, mesh):
|
||||
"""
|
||||
Read UBC 3DTensor mesh model and generate 3D Tensor mesh model in simpeg
|
||||
|
||||
Input:
|
||||
:param fileName, path to the UBC GIF mesh file to read
|
||||
:param mesh, TensorMesh object, mesh that coresponds to the model
|
||||
|
||||
Output:
|
||||
:return numpy array, model with TensorMesh ordered
|
||||
"""
|
||||
f = open(fileName, 'r')
|
||||
model = np.array(map(float, f.readlines()))
|
||||
f.close()
|
||||
model = np.reshape(model, (mesh.nCz, mesh.nCx, mesh.nCy), order = 'F')
|
||||
model = model[::-1,:,:]
|
||||
model = np.transpose(model, (1, 2, 0))
|
||||
model = mkvc(model)
|
||||
|
||||
return model
|
||||
|
||||
def writeUBCTensorMesh(fileName, mesh):
|
||||
"""
|
||||
Writes a SimPEG TensorMesh to a UBC-GIF format mesh file.
|
||||
|
||||
:param str fileName: File to write to
|
||||
:param simpeg.Mesh.TensorMesh mesh: The mesh
|
||||
|
||||
"""
|
||||
assert mesh.dim == 3
|
||||
s = ''
|
||||
s += '%i %i %i\n' %tuple(mesh.vnC)
|
||||
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.
|
||||
origin.dtype = float
|
||||
|
||||
s += '%.2f %.2f %.2f\n' %tuple(origin)
|
||||
s += ('%.2f '*mesh.nCx+'\n')%tuple(mesh.hx)
|
||||
s += ('%.2f '*mesh.nCy+'\n')%tuple(mesh.hy)
|
||||
s += ('%.2f '*mesh.nCz+'\n')%tuple(mesh.hz[::-1])
|
||||
f = open(fileName, 'w')
|
||||
f.write(s)
|
||||
f.close()
|
||||
|
||||
def writeUBCTensorModel(fileName, mesh, model):
|
||||
"""
|
||||
Writes a model associated with a SimPEG TensorMesh
|
||||
to a UBC-GIF format model file.
|
||||
|
||||
:param str fileName: File to write to
|
||||
:param simpeg.Mesh.TensorMesh mesh: The mesh
|
||||
:param numpy.ndarray model: The model
|
||||
"""
|
||||
|
||||
# Reshape model to a matrix
|
||||
modelMat = mesh.r(model,'CC','CC','M')
|
||||
# Transpose the axes
|
||||
modelMatT = modelMat.transpose((2,0,1))
|
||||
# Flip z to positive down
|
||||
modelMatTR = mkvc(modelMatT[::-1,:,:])
|
||||
|
||||
np.savetxt(fileName, modelMatTR.ravel())
|
||||
|
||||
def writeUBCocTreeFiles(fileName,mesh,modelDict=None):
|
||||
'''
|
||||
Write UBC ocTree mesh and model files from a simpeg ocTree mesh and model.
|
||||
|
||||
:param str fileName: File to write to
|
||||
:param simpeg.Mesh.TreeMesh mesh: The mesh
|
||||
:param dictionary modelDict: The models in a dictionary, where the keys is the name of the of the model file
|
||||
|
||||
'''
|
||||
|
||||
# Calculate information to write in the file.
|
||||
# Number of cells in the underlying mesh
|
||||
nCunderMesh = np.array([h.size for h in mesh.h],dtype=np.int64)
|
||||
# The top-south-west most corner of the mesh
|
||||
tswCorn = mesh.x0 + np.array([0,0,np.sum(mesh.h[2])])
|
||||
# Smallest cell size
|
||||
smallCell = np.array([h.min() for h in mesh.h])
|
||||
# Number of cells
|
||||
nrCells = mesh.nC
|
||||
|
||||
## Extract iformation about the cells.
|
||||
# cell pointers
|
||||
cellPointers = np.array([c._pointer for c in mesh])
|
||||
# cell with
|
||||
cellW = np.array([ mesh._levelWidth(i) for i in cellPointers[:,-1] ])
|
||||
# Need to shift the pointers to work with UBC indexing
|
||||
# UBC Octree indexes always the top-left-close (top-south-west) corner first and orders the cells in z(top-down),x,y vs x,y,z(bottom-up).
|
||||
# Shift index up by 1
|
||||
ubcCellPt = cellPointers[:,0:-1].copy() + np.array([1.,1.,1.])
|
||||
# Need reindex the z index to be from the top-left-close corner and to be from the global top.
|
||||
ubcCellPt[:,2] = ( nCunderMesh[-1] + 2) - (ubcCellPt[:,2] + cellW)
|
||||
|
||||
# Reorder the ubcCellPt
|
||||
ubcReorder = np.argsort(ubcCellPt.view(','.join(3*['float'])),axis=0,order=['f2','f1','f0'])[:,0]
|
||||
# Make a array with the pointers and the withs, that are order in the ubc ordering
|
||||
indArr = np.concatenate((ubcCellPt[ubcReorder,:],cellW[ubcReorder].reshape((-1,1)) ),axis=1)
|
||||
|
||||
## Write the UBC octree mesh file
|
||||
with open(fileName,'w') as mshOut:
|
||||
mshOut.write('{:.0f} {:.0f} {:.0f}\n'.format(nCunderMesh[0],nCunderMesh[1],nCunderMesh[2]))
|
||||
mshOut.write('{:.4f} {:.4f} {:.4f}\n'.format(tswCorn[0],tswCorn[1],tswCorn[2]))
|
||||
mshOut.write('{:.3f} {:.3f} {:.3f}\n'.format(smallCell[0],smallCell[1],smallCell[2]))
|
||||
mshOut.write('{:.0f} \n'.format(nrCells))
|
||||
np.savetxt(mshOut,indArr,fmt='%i')
|
||||
|
||||
## Print the models
|
||||
# Assign the model('s) to the object
|
||||
if modelDict is not None:
|
||||
# indUBCvector = np.argsort(cX0[np.argsort(np.concatenate((cX0[:,0:2],cX0[:,2:3].max() - cX0[:,2:3]),axis=1).view(','.join(3*['float'])),axis=0,order=('f2','f1','f0'))[:,0]].view(','.join(3*['float'])),axis=0,order=('f2','f1','f0'))[:,0]
|
||||
for item in modelDict.iteritems():
|
||||
# Save the data
|
||||
np.savetxt(item[0],item[1][ubcReorder],fmt='%3.5e')
|
||||
|
||||
def readUBCocTreeFiles(meshFile,modelFiles=None):
|
||||
"""
|
||||
Read UBC 3D OcTree mesh and/or modelFiles
|
||||
|
||||
Input:
|
||||
:param str meshFile: path to the UBC GIF OcTree mesh file to read
|
||||
:param list of str modelFiles: list of paths modelFiles
|
||||
|
||||
Output:
|
||||
:return SimPEG.Mesh.TreeMesh mesh: The octree mesh
|
||||
:return list of ndarray's: models as a list of numpy array's
|
||||
"""
|
||||
|
||||
## Read the file lines
|
||||
fileLines = np.genfromtxt(meshFile,dtype=str,delimiter='\n')
|
||||
# Extract the data
|
||||
nCunderMesh = np.array(fileLines[0].split(),dtype=float)
|
||||
# I think this is the case?
|
||||
if np.unique(nCunderMesh).size >1:
|
||||
raise Exception('SimPEG TreeMeshes have the same number of cell in all directions')
|
||||
tswCorn = np.array(fileLines[1].split(),dtype=float)
|
||||
smallCell = np.array(fileLines[2].split(),dtype=float)
|
||||
nrCells = np.array(fileLines[3].split(),dtype=float)
|
||||
# Read the index array
|
||||
indArr = np.genfromtxt(fileLines[4::],dtype=np.int)
|
||||
|
||||
## Calculate simpeg parameters
|
||||
h1,h2,h3 = [np.ones(nr)*sz for nr,sz in zip(nCunderMesh,smallCell)]
|
||||
x0 = tswCorn - np.array([0,0,np.sum(h3)])
|
||||
# Need to convert the index array to a points list that complies with SimPEG TreeMesh.
|
||||
# Shift to start at 0
|
||||
simpegCellPt = indArr[:,0:-1].copy()
|
||||
simpegCellPt[:,2] = ( nCunderMesh[-1] + 2) - (simpegCellPt[:,2] + indArr[:,3])
|
||||
# Need reindex the z index to be from the bottom-left-close corner and to be from the global bottom.
|
||||
simpegCellPt = simpegCellPt - np.array([1.,1.,1.])
|
||||
|
||||
# Calculate the cell level
|
||||
simpegLevel = np.log2(np.min(nCunderMesh)) - np.log2(indArr[:,3])
|
||||
# Make a pointer matrix
|
||||
simpegPointers = np.concatenate((simpegCellPt,simpegLevel.reshape((-1,1))),axis=1)
|
||||
|
||||
## Make the tree mesh
|
||||
from SimPEG.Mesh import TreeMesh
|
||||
mesh = TreeMesh([h1,h2,h3],x0)
|
||||
mesh._cells = set([mesh._index(p) for p in simpegPointers.tolist()])
|
||||
|
||||
# Figure out the reordering
|
||||
simpegReorder = np.argsort(np.array([mesh._index(i) for i in simpegPointers.tolist()]))
|
||||
# simpegReorder = np.argsort((np.array([[1,1,1,-1]])*simpegPointers).view(','.join(4*['float'])),axis=0,order=['f3','f2','f1','f0'])[:,0]
|
||||
|
||||
if modelFiles is None:
|
||||
return mesh
|
||||
else:
|
||||
modList = []
|
||||
for modFile in modelFiles:
|
||||
modArr = np.loadtxt(modFile)
|
||||
if len(modArr.shape) == 1:
|
||||
modList.append(modArr[simpegReorder])
|
||||
else:
|
||||
modList.append(modArr[simpegReorder,:])
|
||||
return mesh, modList
|
||||
|
||||
def readVTRFile(fileName):
|
||||
"""
|
||||
Read VTK Rectilinear (vtr xml file) and return SimPEG Tensor mesh and model
|
||||
|
||||
Input:
|
||||
:param vtrFileName, path to the vtr model file to write to
|
||||
|
||||
Output:
|
||||
:return SimPEG TensorMesh object
|
||||
:return SimPEG model dictionary
|
||||
|
||||
"""
|
||||
# Import
|
||||
from vtk import vtkXMLRectilinearGridReader as vtrFileReader
|
||||
from vtk.util.numpy_support import vtk_to_numpy
|
||||
|
||||
# Read the file
|
||||
vtrReader = vtrFileReader()
|
||||
vtrReader.SetFileName(fileName)
|
||||
vtrReader.Update()
|
||||
vtrGrid = vtrReader.GetOutput()
|
||||
# Sort information
|
||||
hx = np.abs(np.diff(vtk_to_numpy(vtrGrid.GetXCoordinates())))
|
||||
xR = vtk_to_numpy(vtrGrid.GetXCoordinates())[0]
|
||||
hy = np.abs(np.diff(vtk_to_numpy(vtrGrid.GetYCoordinates())))
|
||||
yR = vtk_to_numpy(vtrGrid.GetYCoordinates())[0]
|
||||
zD = np.diff(vtk_to_numpy(vtrGrid.GetZCoordinates()))
|
||||
# Check the direction of hz
|
||||
if np.all(zD < 0):
|
||||
hz = np.abs(zD[::-1])
|
||||
zR = vtk_to_numpy(vtrGrid.GetZCoordinates())[-1]
|
||||
else:
|
||||
hz = np.abs(zD)
|
||||
zR = vtk_to_numpy(vtrGrid.GetZCoordinates())[0]
|
||||
x0 = np.array([xR,yR,zR])
|
||||
|
||||
# Make the SimPEG object
|
||||
from SimPEG import Mesh
|
||||
tensMsh = Mesh.TensorMesh([hx,hy,hz],x0)
|
||||
|
||||
# Grap the models
|
||||
modelDict = {}
|
||||
for i in np.arange(vtrGrid.GetCellData().GetNumberOfArrays()):
|
||||
modelName = vtrGrid.GetCellData().GetArrayName(i)
|
||||
if np.all(zD < 0):
|
||||
modFlip = vtk_to_numpy(vtrGrid.GetCellData().GetArray(i))
|
||||
tM = tensMsh.r(modFlip,'CC','CC','M')
|
||||
modArr = tensMsh.r(tM[:,:,::-1],'CC','CC','V')
|
||||
else:
|
||||
modArr = vtk_to_numpy(vtrGrid.GetCellData().GetArray(i))
|
||||
modelDict[modelName] = modArr
|
||||
|
||||
# Return the data
|
||||
return tensMsh, modelDict
|
||||
|
||||
def writeVTRFile(fileName,mesh,model=None):
|
||||
"""
|
||||
Makes and saves a VTK rectilinear file (vtr) for a simpeg Tensor mesh and model.
|
||||
|
||||
Input:
|
||||
:param str, path to the output vtk file
|
||||
:param mesh, SimPEG TensorMesh object - mesh to be transfer to VTK
|
||||
:param model, dictionary of numpy.array - Name('s) and array('s). Match number of cells
|
||||
|
||||
"""
|
||||
# Import
|
||||
from vtk import vtkRectilinearGrid as rectGrid, vtkXMLRectilinearGridWriter as rectWriter
|
||||
from vtk.util.numpy_support import numpy_to_vtk
|
||||
|
||||
# Deal with dimensionalities
|
||||
if mesh.dim >= 1:
|
||||
vX = mesh.vectorNx
|
||||
xD = mesh.nNx
|
||||
yD,zD = 1,1
|
||||
vY, vZ = np.array([0,0])
|
||||
if mesh.dim >= 2:
|
||||
vY = mesh.vectorNy
|
||||
yD = mesh.nNy
|
||||
if mesh.dim == 3:
|
||||
vZ = mesh.vectorNz
|
||||
zD = mesh.nNz
|
||||
# Use rectilinear VTK grid.
|
||||
# Assign the spatial information.
|
||||
vtkObj = rectGrid()
|
||||
vtkObj.SetDimensions(xD,yD,zD)
|
||||
vtkObj.SetXCoordinates(numpy_to_vtk(vX,deep=1))
|
||||
vtkObj.SetYCoordinates(numpy_to_vtk(vY,deep=1))
|
||||
vtkObj.SetZCoordinates(numpy_to_vtk(vZ,deep=1))
|
||||
|
||||
# Assign the model('s) to the object
|
||||
if model is not None:
|
||||
for item in model.iteritems():
|
||||
# Convert numpy array
|
||||
vtkDoubleArr = numpy_to_vtk(item[1],deep=1)
|
||||
vtkDoubleArr.SetName(item[0])
|
||||
vtkObj.GetCellData().AddArray(vtkDoubleArr)
|
||||
# Set the active scalar
|
||||
vtkObj.GetCellData().SetActiveScalars(model.keys()[0])
|
||||
vtkObj.Update()
|
||||
|
||||
|
||||
# Check the extension of the fileName
|
||||
ext = os.path.splitext(fileName)[1]
|
||||
if ext is '':
|
||||
fileName = fileName + '.vtr'
|
||||
elif ext not in '.vtr':
|
||||
raise IOError('{:s} is an incorrect extension, has to be .vtr')
|
||||
# Write the file.
|
||||
vtrWriteFilter = rectWriter()
|
||||
if float(VTK_VERSION.split('.')[0]) >=6:
|
||||
vtrWriteFilter.SetInputData(vtkObj)
|
||||
else:
|
||||
vtuWriteFilter.SetInput(vtuObj)
|
||||
vtrWriteFilter.SetFileName(fileName)
|
||||
vtrWriteFilter.Update()
|
||||
|
||||
def writeVTUFile(fileName,ocTreeMesh,modelDict=None):
|
||||
'''
|
||||
Function to write a VTU file from a SimPEG TreeMesh and model.
|
||||
'''
|
||||
from vtk import vtkXMLUnstructuredGridWriter as Writer, VTK_VERSION
|
||||
from vtk.util.numpy_support import numpy_to_vtk
|
||||
|
||||
# Make the object
|
||||
vtuObj = simpegOcTree2vtuObj(ocTreeMesh,modelDict)
|
||||
|
||||
# Make the writer
|
||||
vtuWriteFilter = Writer()
|
||||
if float(VTK_VERSION.split('.')[0]) >=6:
|
||||
vtuWriteFilter.SetInputData(vtuObj)
|
||||
else:
|
||||
vtuWriteFilter.SetInput(vtuObj)
|
||||
vtuWriteFilter.SetFileName(fileName)
|
||||
# Write the file
|
||||
vtuWriteFilter.Update()
|
||||
|
||||
def simpegOcTree2vtuObj(simpegOcTreeMesh,modelDict=None):
|
||||
'''
|
||||
Convert simpeg OcTree mesh and model to a VTK vtu object.
|
||||
|
||||
'''
|
||||
import vtk
|
||||
from vtk.util.numpy_support import numpy_to_vtk, numpy_to_vtkIdTypeArray
|
||||
|
||||
if str(type(simpegOcTreeMesh)).split()[-1][1:-2] not in 'SimPEG.Mesh.TreeMesh.TreeMesh':
|
||||
raise IOError('simpegOcTreeMesh is not a SimPEG TreeMesh.')
|
||||
|
||||
# Make the data parts for the vtu object
|
||||
# Points
|
||||
try:
|
||||
ptsMat = simpegOcTreeMesh._gridN + simpegOcTreeMesh.x0
|
||||
except:
|
||||
simpegOcTreeMesh.number()
|
||||
ptsMat = simpegOcTreeMesh._gridN + simpegOcTreeMesh.x0
|
||||
vtkPts = vtk.vtkPoints()
|
||||
vtkPts.SetData(numpy_to_vtk(ptsMat,deep=True))
|
||||
# Cells
|
||||
cellConn = np.array([c.nodes for c in simpegOcTreeMesh],dtype=np.int64)
|
||||
|
||||
cellsMat = np.concatenate((np.ones((cellConn.shape[0],1),dtype=np.int64)*cellConn.shape[1],cellConn),axis=1).ravel()
|
||||
cellsArr = vtk.vtkCellArray()
|
||||
cellsArr.SetNumberOfCells(cellConn.shape[0])
|
||||
cellsArr.SetCells(cellConn.shape[0],numpy_to_vtkIdTypeArray(cellsMat,deep=True))
|
||||
|
||||
# Make the object
|
||||
vtuObj = vtk.vtkUnstructuredGrid()
|
||||
vtuObj.SetPoints(vtkPts)
|
||||
vtuObj.SetCells(vtk.VTK_VOXEL,cellsArr)
|
||||
# Add the level of refinement as a cell array
|
||||
cellSides = np.array([np.array(vtuObj.GetCell(i).GetBounds()).reshape((3,2)).dot(np.array([-1, 1])) for i in np.arange(vtuObj.GetNumberOfCells())])
|
||||
uniqueLevel, indLevel = np.unique(np.prod(cellSides,axis=1),return_inverse=True)
|
||||
refineLevelArr = numpy_to_vtk(indLevel.max() - indLevel,deep=1)
|
||||
refineLevelArr.SetName('octreeLevel')
|
||||
vtuObj.GetCellData().AddArray(refineLevelArr)
|
||||
# Assign the model('s) to the object
|
||||
if modelDict is not None:
|
||||
for item in modelDict.iteritems():
|
||||
# Convert numpy array
|
||||
vtkDoubleArr = numpy_to_vtk(item[1],deep=1)
|
||||
vtkDoubleArr.SetName(item[0])
|
||||
vtuObj.GetCellData().AddArray(vtkDoubleArr)
|
||||
|
||||
return vtuObj
|
||||
|
||||
def ExtractCoreMesh(xyzlim, mesh, meshType='tensor'):
|
||||
"""
|
||||
Extracts Core Mesh from Global mesh
|
||||
|
||||
@@ -4,11 +4,65 @@ import SimPEG as simpeg
|
||||
from SimPEG.Mesh import TensorMesh, TreeMesh
|
||||
|
||||
|
||||
class TestOcTreeIO(unittest.TestCase):
|
||||
class TestTensorMeshIO(unittest.TestCase):
|
||||
|
||||
def setUp(self):
|
||||
h = np.ones(16)
|
||||
mesh = simpeg.Mesh.TreeMesh([h,2*h,3*h])
|
||||
mesh = TensorMesh([h,2*h,3*h])
|
||||
self.mesh = mesh
|
||||
|
||||
def test_UBCfiles(self):
|
||||
|
||||
mesh = self.mesh
|
||||
# Make a vector
|
||||
vec = np.arange(mesh.nC)
|
||||
# Write and read
|
||||
mesh.writeUBC('temp.msh', {'arange.txt':vec})
|
||||
meshUBC = TensorMesh.readUBC('temp.msh')
|
||||
vecUBC = meshUBC.readModelUBC('arange.txt')
|
||||
|
||||
# The mesh
|
||||
assert mesh.__str__() == meshUBC.__str__()
|
||||
assert np.sum(mesh.gridCC - meshUBC.gridCC) == 0
|
||||
assert np.sum(vec - vecUBC) == 0
|
||||
assert np.all(np.array(mesh.h) - np.array(meshUBC.h) == 0)
|
||||
|
||||
|
||||
vecUBC = mesh.readModelUBC('arange.txt')
|
||||
assert np.sum(vec - vecUBC) == 0
|
||||
|
||||
mesh.writeModelUBC('arange2.txt', vec + 1)
|
||||
vec2UBC = mesh.readModelUBC('arange2.txt')
|
||||
assert np.sum(vec + 1 - vec2UBC) == 0
|
||||
|
||||
print 'IO of UBC tensor mesh files is working'
|
||||
os.remove('temp.msh')
|
||||
os.remove('arange.txt')
|
||||
os.remove('arange2.txt')
|
||||
|
||||
def test_VTKfiles(self):
|
||||
mesh = self.mesh
|
||||
vec = np.arange(mesh.nC)
|
||||
|
||||
mesh.writeVTK('temp.vtr', {'arange.txt':vec})
|
||||
meshVTR, models = TensorMesh.readVTK('temp.vtr')
|
||||
|
||||
assert mesh.__str__() == meshVTR.__str__()
|
||||
assert np.all(np.array(mesh.h) - np.array(meshVTR.h) == 0)
|
||||
|
||||
assert 'arange.txt' in models
|
||||
vecVTK = models['arange.txt']
|
||||
assert np.sum(vec - vecVTK) == 0
|
||||
|
||||
print 'IO of VTR tensor mesh files is working'
|
||||
os.remove('temp.vtr')
|
||||
|
||||
|
||||
class TestOcTreeMeshIO(unittest.TestCase):
|
||||
|
||||
def setUp(self):
|
||||
h = np.ones(16)
|
||||
mesh = TreeMesh([h,2*h,3*h])
|
||||
mesh.refine(3)
|
||||
mesh._refineCell([0,0,0,3])
|
||||
mesh._refineCell([0,2,0,3])
|
||||
@@ -19,9 +73,10 @@ class TestOcTreeIO(unittest.TestCase):
|
||||
mesh = self.mesh
|
||||
# Make a vector
|
||||
vec = np.arange(mesh.nC)
|
||||
# Write aand read
|
||||
simpeg.Utils.meshutils.writeUBCocTreeFiles('temp.msh',mesh,{'arange.txt':vec})
|
||||
meshUBC, vecUBC = simpeg.Utils.meshutils.readUBCocTreeFiles('temp.msh',['arange.txt'])
|
||||
# Write and read
|
||||
mesh.writeUBC('temp.msh', {'arange.txt':vec})
|
||||
meshUBC = TreeMesh.readUBC('temp.msh')
|
||||
vecUBC = meshUBC.readModelUBC('arange.txt')
|
||||
|
||||
# The mesh
|
||||
assert mesh.__str__() == meshUBC.__str__()
|
||||
@@ -35,7 +90,7 @@ class TestOcTreeIO(unittest.TestCase):
|
||||
def test_VTUfiles(self):
|
||||
mesh = self.mesh
|
||||
vec = np.arange(mesh.nC)
|
||||
simpeg.Utils.meshutils.writeVTUFile('temp.vtu',mesh,{'arange':vec})
|
||||
mesh.writeVTK('temp.vtu',{'arange':vec})
|
||||
print 'Writing of VTU files is working'
|
||||
os.remove('temp.vtu')
|
||||
|
||||
|
||||
Reference in New Issue
Block a user