def setUp(self): self.cell = vtkStructuredGrid() pts = vtkPoints() pts.SetDataTypeToDouble() pts.InsertNextPoint(-1.0, -1.0, -1.0) pts.InsertNextPoint( 1.0, -1.0, -1.0) pts.InsertNextPoint( 1.0, 1.0, -1.0) pts.InsertNextPoint(-1.0, 1.0, -1.0) pts.InsertNextPoint(-1.0, -1.0, 1.0) pts.InsertNextPoint( 1.0, -1.0, 1.0) pts.InsertNextPoint( 1.0, 1.0, 1.0) pts.InsertNextPoint(-1.0, 1.0, 1.0) self.cell.SetDimensions(2,2,2) self.cell.SetPoints(pts) scalar = vtkDoubleArray() scalar.SetName('scalar') scalar.SetNumberOfTuples(8) scalar.SetValue(0, 0.0) scalar.SetValue(1, 0.0) scalar.SetValue(2, 0.0) scalar.SetValue(3, 0.0) scalar.SetValue(4, 1.0) scalar.SetValue(5, 1.0) scalar.SetValue(6, 1.0) scalar.SetValue(7, 1.0) self.cell.GetPointData().SetScalars(scalar)
def setUp(self): self.cell = vtkUnstructuredGrid() pts = vtkPoints() pts.SetDataTypeToDouble() pts.InsertNextPoint(-1.0, -1.0, -1.0) pts.InsertNextPoint( 1.0, -1.0, -1.0) pts.InsertNextPoint( 1.0, 1.0, -1.0) pts.InsertNextPoint(-1.0, 1.0, -1.0) pts.InsertNextPoint(-1.0, -1.0, 1.0) pts.InsertNextPoint( 1.0, -1.0, 1.0) pts.InsertNextPoint( 1.0, 1.0, 1.0) pts.InsertNextPoint(-1.0, 1.0, 1.0) self.cell.SetPoints(pts) self.cell.Allocate(1,1) ids = vtkIdList() for i in range(8): ids.InsertId(i,i) self.cell.InsertNextCell(vtk_const.VTK_HEXAHEDRON, ids) scalar = vtkDoubleArray() scalar.SetName('scalar') scalar.SetNumberOfTuples(8) scalar.SetValue(0, 0.0) scalar.SetValue(1, 0.0) scalar.SetValue(2, 0.0) scalar.SetValue(3, 0.0) scalar.SetValue(4, 1.0) scalar.SetValue(5, 1.0) scalar.SetValue(6, 1.0) scalar.SetValue(7, 1.0) self.cell.GetPointData().SetScalars(scalar)
def SetPoints(self, pts): """Given a VTKArray instance, sets the points of the dataset.""" from vtk.vtkCommonCore import vtkPoints pts = numpyTovtkDataArray(pts) p = vtkPoints() p.SetData(pts) self.VTKObject.SetPoints(p)
def processPartition(idx, iterator): import os os.environ["PMI_PORT"] = pmi_port os.environ["PMI_ID"] = str(idx) os.environ["PV_ALLOW_BATCH_INTERACTION"] = "1" os.environ["DISPLAY"] = ":0" import paraview paraview.options.batch = True from vtk.vtkPVVTKExtensionsCore import vtkDistributedTrivialProducer from vtk.vtkCommonCore import vtkIntArray, vtkPoints from vtk.vtkCommonDataModel import vtkPolyData, vtkPointData, vtkCellArray pointData = vtkIntArray() pointData.SetName('scalar') pointData.Allocate(maxIndex) partData = vtkIntArray() partData.SetName('pid') partData.Allocate(maxIndex) points = vtkPoints() points.Allocate(maxIndex) for row in iterator: coord = idxToCoord(row[0]) points.InsertNextPoint(coord[0], coord[1], coord[2]) pointData.InsertNextTuple1(row[1]) partData.InsertNextTuple1(idx) cells = vtkCellArray() cells.Allocate(points.GetNumberOfPoints() + 1) cells.InsertNextCell(points.GetNumberOfPoints()) for i in range(points.GetNumberOfPoints()): cells.InsertCellPoint(i) dataset = vtkPolyData() dataset.SetPoints(points) dataset.SetVerts(cells) dataset.GetPointData().AddArray(pointData) dataset.GetPointData().SetScalars(partData) vtkDistributedTrivialProducer.SetGlobalOutput('Spark', dataset) from vtk.vtkPVClientServerCoreCore import vtkProcessModule from paraview import simple from paraview.web import wamp as pv_wamp from paraview.web import protocols as pv_protocols from vtk.web import server pm = vtkProcessModule.GetProcessModule() class Options(object): debug = False nosignalhandlers = True host = 'localhost' port = 9753 timeout = 300 content = '/data/sebastien/SparkMPI/runtime/visualizer/dist' forceFlush = False sslKey = '' sslCert = '' ws = 'ws' lp = 'lp' hp = 'hp' nows = False nobws = False nolp = False fsEndpoints = '' uploadPath = None testScriptPath = '' baselineImgDir = '' useBrowser = 'nobrowser' tmpDirectory = '.' testImgFile = '' class _VisualizerServer(pv_wamp.PVServerProtocol): dataDir = '/data' groupRegex = "[0-9]+\\.[0-9]+\\.|[0-9]+\\." excludeRegex = "^\\.|~$|^\\$" allReaders = True viewportScale = 1.0 viewportMaxWidth = 2560 viewportMaxHeight = 1440 def initialize(self): # Bring used components self.registerVtkWebProtocol( pv_protocols.ParaViewWebFileListing( _VisualizerServer.dataDir, "Home", _VisualizerServer.excludeRegex, _VisualizerServer.groupRegex)) self.registerVtkWebProtocol( pv_protocols.ParaViewWebProxyManager( baseDir=_VisualizerServer.dataDir, allowUnconfiguredReaders=_VisualizerServer.allReaders)) self.registerVtkWebProtocol(pv_protocols.ParaViewWebColorManager()) self.registerVtkWebProtocol(pv_protocols.ParaViewWebMouseHandler()) self.registerVtkWebProtocol( pv_protocols.ParaViewWebViewPort( _VisualizerServer.viewportScale, _VisualizerServer.viewportMaxWidth, _VisualizerServer.viewportMaxHeight)) self.registerVtkWebProtocol( pv_protocols.ParaViewWebViewPortImageDelivery()) self.registerVtkWebProtocol( pv_protocols.ParaViewWebViewPortGeometryDelivery()) self.registerVtkWebProtocol(pv_protocols.ParaViewWebTimeHandler()) self.registerVtkWebProtocol( pv_protocols.ParaViewWebSelectionHandler()) self.registerVtkWebProtocol( pv_protocols.ParaViewWebWidgetManager()) self.registerVtkWebProtocol( pv_protocols.ParaViewWebKeyValuePairStore()) self.registerVtkWebProtocol( pv_protocols.ParaViewWebSaveData( baseSavePath=_VisualizerServer.dataDir)) # Disable interactor-based render calls simple.GetRenderView().EnableRenderOnInteraction = 0 simple.GetRenderView().Background = [0, 0, 0] # Update interaction mode pxm = simple.servermanager.ProxyManager() interactionProxy = pxm.GetProxy('settings', 'RenderViewInteractionSettings') interactionProxy.Camera3DManipulators = [ 'Rotate', 'Pan', 'Zoom', 'Pan', 'Roll', 'Pan', 'Zoom', 'Rotate', 'Zoom' ] args = Options() if pm.GetPartitionId() == 0: producer = simple.DistributedTrivialProducer() producer.UpdateDataset = '' producer.UpdateDataset = 'Spark' server.start_webserver(options=args, protocol=_VisualizerServer) pm.GetGlobalController().TriggerBreakRMIs() yield (idx, targetPartition)
def unstructured_from_composite_arrays(points, arrays, controller=None): """Given a set of VTKCompositeDataArrays, creates a vtkUnstructuredGrid. The main goal of this function is to transform the output of XXX_per_block() methods to a single dataset that can be visualized and further processed. Here arrays is an iterable (e.g. list) of (array, name) pairs. Here is an example: centroid = mean_per_block(composite_data.Points) T = mean_per_block(composite_data.PointData['Temperature']) ug = unstructured_from_composite_arrays(centroid, (T, 'Temperature')) When called in parallel, this function makes sure that each array in the input dataset is represented only on 1 process. This is important because methods like mean_per_block() return the same value for blocks that are partitioned on all of the participating processes. If the same point were to be created across multiple processes in the output, filters like histogram would report duplicate values erroneously. """ try: dataset = points.DataSet except AttributeError: dataset = None if dataset is None and points is not dsa.NoneArray: raise ValueError( "Expecting a points arrays with an associated dataset.") if points is dsa.NoneArray: cpts = [] else: cpts = points.Arrays ownership = numpy.zeros(len(cpts), dtype=numpy.int32) rank = 0 # Let's first create a map of array index to composite ids. if dataset is None: ids = [] else: it = dataset.NewIterator() it.UnRegister(None) itr = cpts.__iter__() ids = numpy.empty(len(cpts), dtype=numpy.int32) counter = 0 while not it.IsDoneWithTraversal(): _id = it.GetCurrentFlatIndex() ids[counter] = _id counter += 1 it.GoToNextItem() if controller is None and vtkMultiProcessController is not None: controller = vtkMultiProcessController.GetGlobalController() if controller and controller.IsA("vtkMPIController"): from mpi4py import MPI comm = vtkMPI4PyCommunicator.ConvertToPython( controller.GetCommunicator()) rank = comm.Get_rank() # Determine the max id to use for reduction # operations # Get all ids from dataset, including empty ones. lmax_id = numpy.int32(0) if dataset is not None: it = dataset.NewIterator() it.UnRegister(None) it.SetSkipEmptyNodes(False) while not it.IsDoneWithTraversal(): _id = it.GetCurrentFlatIndex() lmax_id = numpy.max((lmax_id, _id)).astype(numpy.int32) it.GoToNextItem() max_id = numpy.array(0, dtype=numpy.int32) mpitype = _lookup_mpi_type(numpy.int32) comm.Allreduce([lmax_id, mpitype], [max_id, mpitype], MPI.MAX) # Now we figure out which processes have which ids lownership = numpy.empty(max_id, dtype=numpy.int32) lownership.fill(numpy.iinfo(numpy.int32).max) ownership = numpy.empty(max_id, dtype=numpy.int32) if dataset is not None: it = dataset.NewIterator() it.UnRegister(None) it.InitTraversal() itr = cpts.__iter__() while not it.IsDoneWithTraversal(): _id = it.GetCurrentFlatIndex() if itr.next() is not dsa.NoneArray: lownership[_id] = rank it.GoToNextItem() mpitype = _lookup_mpi_type(numpy.int32) # The process with the lowest id containing a block will # produce the output for that block. comm.Allreduce([lownership, mpitype], [ownership, mpitype], MPI.MIN) # Iterate over blocks to produce points and arrays from vtk.vtkCommonDataModel import vtkUnstructuredGrid from vtk.vtkCommonCore import vtkDoubleArray, vtkPoints ugrid = vtkUnstructuredGrid() da = vtkDoubleArray() da.SetNumberOfComponents(3) pts = vtkPoints() pts.SetData(da) counter = 0 for pt in cpts: if ownership[ids[counter]] == rank: pts.InsertNextPoint(tuple(pt)) counter += 1 ugrid.SetPoints(pts) for ca, name in arrays: if ca is not dsa.NoneArray: da = vtkDoubleArray() ncomps = ca.Arrays[0].flatten().shape[0] da.SetNumberOfComponents(ncomps) counter = 0 for a in ca.Arrays: if ownership[ids[counter]] == rank: a = a.flatten() for i in range(ncomps): da.InsertNextValue(a[i]) counter += 1 if len(a) > 0: da.SetName(name) ugrid.GetPointData().AddArray(da) return ugrid
def unstructured_from_composite_arrays(points, arrays, controller=None): """Given a set of VTKCompositeDataArrays, creates a vtkUnstructuredGrid. The main goal of this function is to transform the output of XXX_per_block() methods to a single dataset that can be visualized and further processed. Here arrays is an iterable (e.g. list) of (array, name) pairs. Here is an example: centroid = mean_per_block(composite_data.Points) T = mean_per_block(composite_data.PointData['Temperature']) ug = unstructured_from_composite_arrays(centroid, (T, 'Temperature')) When called in parallel, this function makes sure that each array in the input dataset is represented only on 1 process. This is important because methods like mean_per_block() return the same value for blocks that are partitioned on all of the participating processes. If the same point were to be created across multiple processes in the output, filters like histogram would report duplicate values erroneously. """ try: dataset = points.DataSet except AttributeError: dataset = None if dataset is None and points is not dsa.NoneArray: raise ValueError, "Expecting a points arrays with an associated dataset." if points is dsa.NoneArray: cpts = [] else: cpts = points.Arrays ownership = numpy.zeros(len(cpts), dtype=numpy.int32) rank = 0 # Let's first create a map of array index to composite ids. if dataset is None: ids = [] else: it = dataset.NewIterator() it.UnRegister(None) itr = cpts.__iter__() ids = numpy.empty(len(cpts), dtype=numpy.int32) counter = 0 while not it.IsDoneWithTraversal(): _id = it.GetCurrentFlatIndex() ids[counter] = _id counter += 1 it.GoToNextItem() if controller is None and vtkMultiProcessController is not None: controller = vtkMultiProcessController.GetGlobalController() if controller and controller.IsA("vtkMPIController"): from mpi4py import MPI comm = vtkMPI4PyCommunicator.ConvertToPython(controller.GetCommunicator()) rank = comm.Get_rank() # Determine the max id to use for reduction # operations # Get all ids from dataset, including empty ones. lmax_id = numpy.int32(0) if dataset is not None: it = dataset.NewIterator() it.UnRegister(None) it.SetSkipEmptyNodes(False) while not it.IsDoneWithTraversal(): _id = it.GetCurrentFlatIndex() lmax_id = numpy.max((lmax_id, _id)).astype(numpy.int32) it.GoToNextItem() max_id = numpy.array(0, dtype=numpy.int32) mpitype = _lookup_mpi_type(numpy.int32) comm.Allreduce([lmax_id, mpitype], [max_id, mpitype], MPI.MAX) # Now we figure out which processes have which ids lownership = numpy.empty(max_id, dtype = numpy.int32) lownership.fill(numpy.iinfo(numpy.int32).max) ownership = numpy.empty(max_id, dtype = numpy.int32) if dataset is not None: it = dataset.NewIterator() it.UnRegister(None) it.InitTraversal() itr = cpts.__iter__() while not it.IsDoneWithTraversal(): _id = it.GetCurrentFlatIndex() if itr.next() is not dsa.NoneArray: lownership[_id] = rank it.GoToNextItem() mpitype = _lookup_mpi_type(numpy.int32) # The process with the lowest id containing a block will # produce the output for that block. comm.Allreduce([lownership, mpitype], [ownership, mpitype], MPI.MIN) # Iterate over blocks to produce points and arrays from vtk.vtkCommonDataModel import vtkUnstructuredGrid from vtk.vtkCommonCore import vtkDoubleArray, vtkPoints ugrid = vtkUnstructuredGrid() da = vtkDoubleArray() da.SetNumberOfComponents(3) pts = vtkPoints() pts.SetData(da) counter = 0 for pt in cpts: if ownership[ids[counter]] == rank: pts.InsertNextPoint(tuple(pt)) counter += 1 ugrid.SetPoints(pts) for ca, name in arrays: if ca is not dsa.NoneArray: da = vtkDoubleArray() ncomps = ca.Arrays[0].flatten().shape[0] da.SetNumberOfComponents(ncomps) counter = 0 for a in ca.Arrays: if ownership[ids[counter]] == rank: a = a.flatten() for i in range(ncomps): da.InsertNextValue(a[i]) counter += 1 if len(a) > 0: da.SetName(name) ugrid.GetPointData().AddArray(da) return ugrid