Deleted local 'visulize' folder

This commit is contained in:
Gudni UBC-Talva
2013-11-25 17:44:26 -08:00
parent 6b15d373f8
commit b29cc6e08d
5 changed files with 115 additions and 502 deletions
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import vtk
#import mpl
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from vtkTools import vtkTools
from vtkView import vtkView
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import numpy as np, vtk, vtk.util.numpy_support as npsup, pdb
from SimPEG.utils import mkvc
class vtkTools(object):
"""
Class that interacts with VTK visulization toolkit.
"""
def __init__(self):
""" Initializes the VTK vtkTools.
"""
pass
@staticmethod
def makeCellVTKObject(mesh,model):
"""
Make and return a cell based VTK object for a simpeg mesh and model.
Input:
: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
Output:
:rtype: vtkRecilinearGrid object
:return: vtkObj
"""
# 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.
# Asaign the spatial information.
vtkObj = vtk.vtkRectilinearGrid()
vtkObj.SetDimensions(xD,yD,zD)
vtkObj.SetXCoordinates(npsup.numpy_to_vtk(vX,deep=1))
vtkObj.SetYCoordinates(npsup.numpy_to_vtk(vY,deep=1))
vtkObj.SetZCoordinates(npsup.numpy_to_vtk(vZ,deep=1))
# Assign the model('s) to the object
for item in model.iteritems():
# Convert numpy array
vtkDoubleArr = npsup.numpy_to_vtk(item[1],deep=1)
vtkDoubleArr.SetName(item[0])
vtkObj.GetCellData().AddArray(vtkDoubleArr)
vtkObj.GetCellData().SetActiveScalars(model.keys()[0])
return vtkObj
@staticmethod
def makeFaceVTKObject(mesh,model):
"""
Make and return a face based VTK object for a simpeg mesh and model.
Input:
:param mesh, SimPEG TensorMesh object - mesh to be transfer to VTK
:param model, dictionary of numpy.array - Name('s) and array('s).
Property array must be order hstack(Fx,Fy,Fz)
Output:
:rtype: vtkUnstructuredGrid object
:return: vtkObj
"""
## Convert simpeg mesh to VTK properties
# Convert mesh nodes to vtkPoints
vtkPts = vtk.vtkPoints()
vtkPts.SetData(npsup.numpy_to_vtk(mesh.gridN,deep=1))
# Define the face "cells"
# Using VTK_QUAD cell for faces (see VTK file format)
nodeMat = mesh.r(np.arange(mesh.nN,dtype='int64'),'N','N','M')
def faceR(mat,length):
return mat.T.reshape((length,1))
# First direction
nTFx = np.prod(mesh.nFx)
FxCellBlock = np.hstack([ 4*np.ones((nTFx,1),dtype='int64'),faceR(nodeMat[:,:-1,:-1],nTFx),faceR(nodeMat[:,1: ,:-1],nTFx),faceR(nodeMat[:,1: ,1: ],nTFx),faceR(nodeMat[:,:-1,1: ],nTFx)] )
FyCellBlock = np.array([],dtype='int64')
FzCellBlock = np.array([],dtype='int64')
# Second direction
if mesh.dim >= 2:
nTFy = np.prod(mesh.nFy)
FyCellBlock = np.hstack([ 4*np.ones((nTFy,1),dtype='int64'),faceR(nodeMat[:-1,:,:-1],nTFy),faceR(nodeMat[1: ,:,:-1],nTFy),faceR(nodeMat[1: ,:,1: ],nTFy),faceR(nodeMat[:-1,:,1: ],nTFy)] )
# Third direction
if mesh.dim == 3:
nTFz = np.prod(mesh.nFz)
FzCellBlock = np.hstack([ 4*np.ones((nTFz,1),dtype='int64'),faceR(nodeMat[:-1,:-1,:],nTFz),faceR(nodeMat[1: ,:-1,:],nTFz),faceR(nodeMat[1: ,1: ,:],nTFz),faceR(nodeMat[:-1,1: ,:],nTFz)] )
# Cells -cell array
FCellArr = vtk.vtkCellArray()
FCellArr.SetNumberOfCells(np.sum(mesh.nF))
FCellArr.SetCells(np.sum(mesh.nF)*5,npsup.numpy_to_vtkIdTypeArray(np.vstack([FxCellBlock,FyCellBlock,FzCellBlock]),deep=1))
# Cell type
FCellType = npsup.numpy_to_vtk(vtk.VTK_QUAD*np.ones(np.sum(mesh.nF),dtype='uint8'),deep=1)
# Cell location
FCellLoc = npsup.numpy_to_vtkIdTypeArray(np.arange(0,np.sum(mesh.nF)*5,5,dtype='int64'),deep=1)
## Make the object
vtkObj = vtk.vtkUnstructuredGrid()
# Set the objects properties
vtkObj.SetPoints(vtkPts)
vtkObj.SetCells(FCellType,FCellLoc,FCellArr)
# Assign the model('s) to the object
for item in model.iteritems():
# Convert numpy array
vtkDoubleArr = npsup.numpy_to_vtk(item[1],deep=1)
vtkDoubleArr.SetName(item[0])
vtkObj.GetCellData().AddArray(vtkDoubleArr)
vtkObj.GetCellData().SetActiveScalars(model.keys()[0])
vtkObj.Update()
return vtkObj
@staticmethod
def makeEdgeVTKObject(mesh,model):
"""
Make and return a edge based VTK object for a simpeg mesh and model.
Input:
:param mesh, SimPEG TensorMesh object - mesh to be transfer to VTK
:param model, dictionary of numpy.array - Name('s) and array('s).
Property array must be order hstack(Ex,Ey,Ez)
Output:
:rtype: vtkUnstructuredGrid object
:return: vtkObj
"""
## Convert simpeg mesh to VTK properties
# Convert mesh nodes to vtkPoints
vtkPts = vtk.vtkPoints()
vtkPts.SetData(npsup.numpy_to_vtk(mesh.gridN,deep=1))
# Define the face "cells"
# Using VTK_QUAD cell for faces (see VTK file format)
nodeMat = mesh.r(np.arange(mesh.nN,dtype='int64'),'N','N','M')
def edgeR(mat,length):
return mat.T.reshape((length,1))
# First direction
nTEx = np.prod(mesh.nEx)
ExCellBlock = np.hstack([ 2*np.ones((nTEx,1),dtype='int64'),edgeR(nodeMat[:-1,:,:],nTEx),edgeR(nodeMat[1:,:,:],nTEx)])
# Second direction
if mesh.dim >= 2:
nTEy = np.prod(mesh.nEy)
EyCellBlock = np.hstack([ 2*np.ones((nTEy,1),dtype='int64'),edgeR(nodeMat[:,:-1,:],nTEy),edgeR(nodeMat[:,1:,:],nTEy)])
# Third direction
if mesh.dim == 3:
nTEz = np.prod(mesh.nEz)
EzCellBlock = np.hstack([ 2*np.ones((nTEz,1),dtype='int64'),edgeR(nodeMat[:,:,:-1],nTEz),edgeR(nodeMat[:,:,1:],nTEz)])
# Cells -cell array
ECellArr = vtk.vtkCellArray()
ECellArr.SetNumberOfCells(np.sum(mesh.nE))
ECellArr.SetCells(np.sum(mesh.nE)*3,npsup.numpy_to_vtkIdTypeArray(np.vstack([ExCellBlock,EyCellBlock,EzCellBlock]),deep=1))
# Cell type
ECellType = npsup.numpy_to_vtk(vtk.VTK_LINE*np.ones(np.sum(mesh.nE),dtype='uint8'),deep=1)
# Cell location
ECellLoc = npsup.numpy_to_vtkIdTypeArray(np.arange(0,np.sum(mesh.nE)*3,3,dtype='int64'),deep=1)
## Make the object
vtkObj = vtk.vtkUnstructuredGrid()
# Set the objects properties
vtkObj.SetPoints(vtkPts)
vtkObj.SetCells(ECellType,ECellLoc,ECellArr)
# Assign the model('s) to the object
for item in model.iteritems():
# Convert numpy array
vtkDoubleArr = npsup.numpy_to_vtk(item[1],deep=1)
vtkDoubleArr.SetName(item[0])
vtkObj.GetCellData().AddArray(vtkDoubleArr)
vtkObj.GetCellData().SetActiveScalars(model.keys()[0])
return vtkObj
@staticmethod
def makeRenderWindow(ren):
renwin = vtk.vtkRenderWindow()
renwin.AddRenderer(ren)
iren = vtk.vtkRenderWindowInteractor()
iren.SetRenderWindow(renwin)
return iren, renwin
@staticmethod
def closeRenderWindow(iren):
renwin = iren.GetRenderWindow()
renwin.Finalize()
iren.TerminateApp()
del iren, renwin
@staticmethod
def makeVTKActor(vtkObj):
""" Makes a vtk mapper and Actor"""
mapper = vtk.vtkDataSetMapper()
mapper.SetInput(vtkObj)
actor = vtk.vtkActor()
actor.SetMapper(mapper)
actor.GetProperty().SetColor(0,0,0)
actor.GetProperty().SetRepresentationToWireframe()
return actor
@staticmethod
def makeVTKLODActor(vtkObj,clipper):
"""Make LOD vtk Actor"""
selectMapper = vtk.vtkDataSetMapper()
selectMapper.SetInputConnection(clipper.GetOutputPort())
selectMapper.SetScalarVisibility(1)
selectMapper.SetColorModeToMapScalars()
selectMapper.SetScalarModeToUseCellData()
selectMapper.SetScalarRange(clipper.GetInputDataObject(0,0).GetCellData().GetArray(0).GetRange())
selectActor = vtk.vtkLODActor()
selectActor.SetMapper(selectMapper)
selectActor.GetProperty().SetEdgeColor(1,0.5,0)
selectActor.GetProperty().SetEdgeVisibility(0)
selectActor.VisibilityOn()
selectActor.SetScale(1.01, 1.01, 1.01)
return selectActor
@staticmethod
def setScalar2View(vtkObj,scalarName):
""" Sets the sclar to view """
useArr = vtkObj.GetCellData().GetArray(scalarName)
if useArr == None:
raise IOError('Nerty array {:s} in the vtkObject'.format(scalarName))
vtkObj.GetCellData().SetActiveScalars(scalarName)
@staticmethod
def makeRectiVTKVOIThres(vtkObj):
"""Make volume of interest and threshold for rectilinear grid."""
cellCore = vtk.vtkExtractRectilinearGrid()
cellCore.SetInput(vtkObj)
cellCore.SetVOI(vtkObj.GetExtent())
cellThres = vtk.vtkThreshold()
cellThres.AllScalarsOn()
cellThres.SetInputConnection(cellCore.GetOutputPort())
cellThres.ThresholdByUpper(-1)
cellThres.Update()
return cellThres.GetOutput(), cellCore.GetOutput()
@staticmethod
def makePlaneClipper(vtkObj):
"""Makes a plane and clipper """
plane = vtk.vtkPlane()
clipper = vtk.vtkClipDataSet()
clipper.SetInputConnection(vtkObj.GetProducerPort())
clipper.SetClipFunction(plane)
clipper.InsideOutOff()
return clipper, plane
@staticmethod
def makePlaneWidget(vtkObj,iren,plane,actor):
"""Make an interactive planeWidget"""
# Callback function
def movePlane(obj, events):
obj.GetPlane(intPlane)
intActor.VisibilityOn()
# Associate the line widget with the interactor
planeWidget = vtk.vtkImplicitPlaneWidget()
planeWidget.SetInteractor(iren)
planeWidget.SetPlaceFactor(1.25)
planeWidget.SetInput(vtkObj)
planeWidget.PlaceWidget()
#planeWidget.AddObserver("InteractionEvent", movePlane)
planeWidget.SetScaleEnabled(0)
planeWidget.SetEnabled(1)
planeWidget.SetOutlineTranslation(0)
planeWidget.GetPlaneProperty().SetOpacity(0.1)
return planeWidget
@staticmethod
def startRenderWindow(iren):
""" Start a vtk rendering window"""
iren.Initialize()
renwin = iren.GetRenderWindow()
renwin.Render()
iren.Start()
# Simple write/read VTK xml model functions.
@staticmethod
def writeVTPFile(fileName,vtkPolyObject):
'''Function to write vtk polydata file (vtp).'''
polyWriter = vtk.vtkXMLPolyDataWriter()
polyWriter.SetInput(vtkPolyObject)
polyWriter.SetFileName(fileName)
polyWriter.Update()
@staticmethod
def writeVTUFile(fileName,vtkUnstructuredGrid):
'''Function to write vtk unstructured grid (vtu).'''
Writer = vtk.vtkXMLUnstructuredGridWriter()
Writer.SetInput(vtkUnstructuredGrid)
Writer.SetFileName(fileName)
Writer.Update()
@staticmethod
def writeVTRFile(fileName,vtkRectilinearGrid):
'''Function to write vtk rectilinear grid (vtr).'''
Writer = vtk.vtkXMLRectilinearGridWriter()
Writer.SetInput(vtkRectilinearGrid)
Writer.SetFileName(fileName)
Writer.Update()
@staticmethod
def writeVTSFile(fileName,vtkStructuredGrid):
'''Function to write vtk structured grid (vts).'''
Writer = vtk.vtkXMLStructuredGridWriter()
Writer.SetInput(vtkStructuredGrid)
Writer.SetFileName(fileName)
Writer.Update()
@staticmethod
def readVTSFile(fileName):
'''Function to read vtk structured grid (vts) and return a grid object.'''
Reader = vtk.vtkXMLStructuredGridReader()
Reader.SetFileName(fileName)
Reader.Update()
return Reader.GetOutput()
@staticmethod
def readVTUFile(fileName):
'''Function to read vtk structured grid (vtu) and return a grid object.'''
Reader = vtk.vtkXMLUnstructuredGridReader()
Reader.SetFileName(fileName)
Reader.Update()
return Reader.GetOutput()
@staticmethod
def readVTRFile(fileName):
'''Function to read vtk structured grid (vtr) and return a grid object.'''
Reader = vtk.vtkXMLRectilinearGridReader()
Reader.SetFileName(fileName)
Reader.Update()
return Reader.GetOutput()
@staticmethod
def readVTPFile(fileName):
'''Function to read vtk structured grid (vtp) and return a grid object.'''
Reader = vtk.vtkXMLPolyDataReader()
Reader.SetFileName(fileName)
Reader.Update()
return Reader.GetOutput()
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import numpy as np, vtk
import SimPEG as simpeg
#import SimPEG.visulize.vtk.vtkTools as vtkSP # Always get an error for this import
class vtkView(object):
"""
Class for storing and view of SimPEG models in VTK (visulization toolkit).
Inputs:
:param mesh, SimPEG mesh.
:param propdict, dictionary of property models.
Can have these dictionary names:
'cell' - cell model; 'face' - face model; 'edge' - edge model
The dictionary properties are given as dictionaries with:
{'NameOfThePropertyModel': np.array of the properties}.
The property array has to be ordered in compliance with SimPEG standards.
::
Example of usages.
ToDo
"""
def __init__(self,mesh,propdict):
"""
"""
self.name = 'VTK figure of SimPEG model'
self.extent = [0,mesh.nCx-1,0,mesh.nCy-1,0,mesh.nCz-1]
self.limits = [0, 10000]
self._mesh = mesh
# Set vtk object containers
self._cell = None
self._faces = None
self._edges = None
self._readPropertyDictionary(propdict)
# Setup hidden properties
self._ren = None
self._iren = None
self._renwin = None
self._core = None
self._viewobj = None
self._plane = None
self._clipper = None
self._widget = None
self._actor = None
self._lut = None
def _readPropertyDictionary(self,propdict):
"""
Reads the property and assigns to the object
"""
import SimPEG.visulize.vtk.vtkTools as vtkSP
# Test the property dictionary
if len(propdict) > 3:
raise(Exception,'Too many input items in the property dictionary')
for propitem in propdict.iteritems():
if propitem[0] in ['cell','face','edge']:
if propitem[0] == 'cell':
self._cell = vtkSP.makeCellVTKObject(self._mesh,propitem[1])
if propitem[0] == 'face':
self._face = vtkSP.makeFaceVTKObject(self._mesh,propitem[1])
if propitem[0] == 'edge':
self._edge = vtkSP.makeEdgeVTKObject(self._mesh,propitem[1])
else:
raise(Exception,'{:s} is not allowed as a dictonary key. Can be \'cell\',\'face\',\'edge\'.'.format(propitem[0]))
def Show(self,imageType='cell'):
"""
Open the VTK figure window and show the mesh.
Inputs:
param: str imageType: type of image {'cell','face','edge'}
"""
#vtkSP = simpeg.visulize.vtk.vtkTools
import SimPEG.visulize.vtk.vtkTools as vtkSP
# Make a renderer
self._ren = vtk.vtkRenderer()
# Make renderwindow. Returns the interactor.
self._iren, self._renwin = vtkSP.makeRenderWindow(self._ren)
# Sort out the actor
if imageType == 'cell':
self._vtkobj, self._core = vtkSP.makeRectiVTKVOIThres(self._cell)
elif imageType == 'face':
self._vtkobj, self._core = vtkSP.makeRectiVTKVOIThres(self._face)
elif imageType == 'edge':
self._vtkobj, self._core = vtkSP.makeRectiVTKVOIThres(self._edge)
else:
raise Exception("{:s} is not a vailid imageType. Has to be 'cell':'face':'edge'".format(imageType))
global intPlane, intActor
self._clipper, intPlane = vtkSP.makePlaneClipper(self._vtkobj)
intActor = vtkSP.makeVTKLODActor(self._vtkobj,self._clipper)
self._widget = vtkSP.makePlaneWidget(self._vtkobj,self._iren,self._clipper.GetClipFunction(),self._actor)
# Callback function
self._plane = intPlane
self._actor = intActor
def movePlane(obj, events):
global intPlane, intActor
obj.GetPlane(intPlane)
intActor.VisibilityOn()
self._widget.AddObserver("InteractionEvent",movePlane)
lut = vtk.vtkLookupTable()
lut.SetNumberOfColors(256)
lut.SetHueRange(0,0.66667)
lut.Build()
self._lut = lut
self._actor.GetMapper().SetLookupTable(lut)
# Set renderer options
self._ren.SetBackground(.5,.5,.5)
self._ren.AddActor(self._actor)
# Start the render Window
vtkSP.startRenderWindow(self._iren)
# Close the window when exited
vtkSP.closeRenderWindow(self._iren)
del self._iren, self._renwin
@@ -0,0 +1,115 @@
{
"metadata": {
<<<<<<< HEAD
"name": "3D rendering with vtkTools"
=======
"name": ""
>>>>>>> develop
},
"nbformat": 3,
"nbformat_minor": 0,
"worksheets": [
{
"cells": [
{
"cell_type": "code",
"collapsed": false,
<<<<<<< HEAD
"input": "import numpy as np, vtk\nimport SimPEG as simpeg",
"language": "python",
"metadata": {},
"outputs": [],
"prompt_number": 1
=======
"input": [
"import numpy as np, vtk\n",
"import SimPEG as simpeg"
],
"language": "python",
"metadata": {},
"outputs": [],
"prompt_number": 5
>>>>>>> develop
},
{
"cell_type": "code",
"collapsed": false,
<<<<<<< HEAD
"input": "#Make a mesh and model\nx0 = np.zeros(3)\nh1 = np.ones(20)*5\nh2 = np.ones(10)*10\nh3 = np.ones(5)*20\n\nmesh = simpeg.mesh.TensorMesh([h1,h2,h3],x0)\n",
"language": "python",
"metadata": {},
"outputs": [],
"prompt_number": 2
=======
"input": [
"#Make a mesh and model\n",
"x0 = np.zeros(3)\n",
"h1 = np.ones(20)*50\n",
"h2 = np.ones(10)*100\n",
"h3 = np.ones(5)*200\n",
"\n",
"mesh = simpeg.mesh.TensorMesh([h1,h2,h3],x0)\n"
],
"language": "python",
"metadata": {},
"outputs": [],
"prompt_number": 6
>>>>>>> develop
},
{
"cell_type": "code",
"collapsed": false,
<<<<<<< HEAD
"input": "# Make a models that correspond to the cells, faces and edges.\nmodels = {'cell':{'Test':np.arange(0,mesh.nC),'AllOnce':np.ones(mesh.nC)},'face':{'Test':np.arange(0,np.sum(mesh.nF)),'AllOnce':np.ones(np.sum(mesh.nF))},'edge':{'Test':np.arange(0,np.sum(mesh.nE)),'AllOnce':np.ones(np.sum(mesh.nE))}}\n# Make the vtk viewer object.\nvtkViewer = simpeg.visulize.vtk.vtkView(mesh,models) \n ",
"language": "python",
"metadata": {},
"outputs": [],
"prompt_number": 3
=======
"input": [
"# Make a models that correspond to the cells, faces and edges.\n",
"models = {'cell':{'Test':np.arange(0,mesh.nC),'AllOnce':np.ones(mesh.nC)},'face':{'Test':np.arange(0,np.sum(mesh.nF)),'AllOnce':np.ones(np.sum(mesh.nF))},'edge':{'Test':np.arange(0,np.sum(mesh.nE)),'AllOnce':np.ones(np.sum(mesh.nE))}}\n",
"# Make the vtk viewer object.\n",
"vtkViewer = simpeg.visualize.vtk.vtkView(mesh,models) \n",
" "
],
"language": "python",
"metadata": {},
"outputs": [],
"prompt_number": 7
>>>>>>> develop
},
{
"cell_type": "code",
"collapsed": false,
<<<<<<< HEAD
"input": "# Show the image \nvtkViewer.Show(imageType='cell')\n",
"language": "python",
"metadata": {},
"outputs": [],
"prompt_number": 4
},
{
"cell_type": "code",
"collapsed": false,
"input": "",
"language": "python",
"metadata": {},
"outputs": [],
"prompt_number": 4
=======
"input": [
"# Show the image \n",
"vtkViewer.Show()\n"
],
"language": "python",
"metadata": {},
"outputs": [],
"prompt_number": "*"
>>>>>>> develop
}
],
"metadata": {}
}
]
}