group = store.addGroup(0, 'Test Group') # Add a volume and 4 faces the hard way: volume = smtk.model.Entity.create(int(smtk.model.CELL_ENTITY), 3) f1 = smtk.model.Entity.create(int(smtk.model.CELL_ENTITY), 2) f2 = smtk.model.Entity.create(int(smtk.model.CELL_ENTITY), 2) f3 = smtk.model.Entity.create(int(smtk.model.CELL_ENTITY), 2) f4 = smtk.model.Entity.create(int(smtk.model.CELL_ENTITY), 2) u01 = store.addEntity(f1) u02 = store.addEntity(f2) u03 = store.addEntity(f3) u04 = store.addEntity(f4) volume.pushRelation(u01).\ pushRelation(u02).\ pushRelation(u03).\ pushRelation(u04).\ pushRelation(model.entity()) u00 = store.addEntity(volume) # Now verify that the faces refer back to the volume: status = False if store.findEntity(u01, True).relations()[ 0] == u00 else True # Add cells to the group, the group and cells to the model, submodels # to the model: [store.findOrAddEntityToGroup(group.entity(), x) for x in [u00, u01, u02, u03, u04]] [model.addCell(smtk.model.CellEntity(x)) for x in group.members()] store.assignDefaultNames() model.addGroup(group) model.addSubmodel(model2) model.addSubmodel(model3) # Does the model contain the cells we just added?
def operateInternal(self): # Access the DEFORM point and element files point_file = self.specification().findFile('point-file').value(0) element_file = self.specification().findFile('element-file').value(0) # Access the timestep to process timestep = self.specification().findInt('timestep').value(0) # Access the Dream3D PipelineRunner exectuable pipeline_executable = self.specification().findFile( 'pipeline-executable').value(0) # Access the name of the attribute to use for zoning attribute = self.specification().findString('attribute').value(0) # Access the microscale statistics parameters stats = self.specification().findGroup('stats') # Access the Dream3D ouptut file output_file = self.specification().findFile('output-file').value(0) # The location of the template pipeline is hard-coded w.r.t. the AFRL # directory template_pipeline_file = AFRLDir.description.replace('\n', '') + \ '/Dream3DPipelines/Pipelines/DREAM3D_Phase1_Pipeline.json' # Extract the parameters into python lists mu = [] sigma = [] min_cutoff = [] max_cutoff = [] for i in range(stats.numberOfGroups()): for p in ['mu', 'sigma', 'min_cutoff', 'max_cutoff']: eval(p).append( smtk.attribute.to_concrete(stats.find(i, p)).value(0)) # Access the Dream3D output file output_file = self.specification().findFile('output-file').value(0) # Ensure that the executable is, in fact, an executable pipeline = Dream3DPipeline.which(pipeline_executable) if pipeline is None: print('Cannot find PipelineRunner') return self.createResult(smtk.model.OPERATION_FAILED) # Generate the Dream3D pipeline for this operation pipeline_file = \ Dream3DPipeline.generate_pipeline(template_pipeline_file, point_file, timestep, element_file, attribute, mu, sigma, min_cutoff, max_cutoff, output_file) # Execute the Dream3D pipeline pipelineargs = [pipeline, '-p', '%s' % os.path.abspath(pipeline_file)] subprocess.call(pipelineargs) # Remove the pipeline file os.remove(pipeline_file) # Read DREAM3D Xdmf file as a VTK data object xdmfReader = vtk.vtkXdmfReader() xdmfReader.SetFileName(os.path.splitext(output_file)[0] + '.xdmf') xdmfReader.Update() dataNames = [ xdmfReader.GetOutputDataObject(0).GetMetaData(i).Get( vtk.vtkCompositeDataSet.NAME()) for i in xrange(xdmfReader.GetNumberOfGrids()) ] volumeDataContainer = xdmfReader.GetOutputDataObject(0).GetBlock( dataNames.index("VolumeDataContainer")) # Import the vtk data object as an SMTK mesh cnvrt = smtk.io.vtk.ImportVTKData() collection = cnvrt(volumeDataContainer, self.meshManager(), 'ZoneIds') # Ensure that the import succeeded if not collection or not collection.isValid(): return self.createResult(smtk.model.OPERATION_FAILED) # Assign its model manager to the one associated with this session collection.modelManager = self.manager() collection.name("DEFORM mesh") # Construct the topology self.activeSession().addTopology(smtk.bridge.mesh.Topology(collection)) # Our collections will already have a UUID, so here we create a model # given the model manager and UUID model = self.manager().insertModel(collection.entity(), 2, 2, "DEFORM model") # Declare the model as "dangling" so it will be transcribed self.session().declareDanglingEntity(model) # Set the model's session to point to the current session model.setSession( smtk.model.SessionRef(self.manager(), self.session().sessionId())) collection.associateToModel(model.entity()) # If we don't call "transcribe" ourselves, it never gets called. self.activeSession().transcribe(model, smtk.model.SESSION_EVERYTHING, False) result = self.createResult(smtk.model.OPERATION_SUCCEEDED) resultModels = result.findModelEntity("model") resultModels.setValue(model) created = result.findModelEntity("created") created.setNumberOfValues(1) created.setValue(model) created.setIsEnabled(True) result.findModelEntity("mesh_created").setValue(model) # Return with success return result
def import_model(self, filepath, resource, model_name): # Create mesh resource mesh_resource = smtk.mesh.Resource.create() # Get the mesh resource from file print('Load file from {}'.format(filepath)) smtk.io.importMesh( filepath, mesh_resource, model_name) # Get dimension if self.dim == 0: self.dim = smtk.mesh.highestDimension(mesh_resource.meshes()) else: model_dim = smtk.mesh.highestDimension(mesh_resource.meshes()) if model_dim != self.dim: raise Exception("Solid model and fluid model dimensions are inconsistent!") print('{}\'s dimension is {}'.format(model_name, self.dim)) if int(self.dim) < 2: raise Exception("1D models are not supported!") # Get meshset for new mesh meshes = mesh_resource.meshes() # Remove the mesh without domains meshes_without_domains = [] for i in range(meshes.size()): submesh = meshes.subset(i) if len(submesh.domains()) == 0: meshes_without_domains.append(submesh) for mesh_without_domain in meshes_without_domains: mesh_resource.removeMeshes(mesh_without_domain) # If no mesh found return failue message if not mesh_resource or not mesh_resource.isValid(): return self.createResult(smtk.operation.Operation.Outcome.FAILED) # Set name on mesh and resource mesh_resource.setName(model_name) # Set association between resource and mesh resource mesh_resource.modelResource = resource resource.setMeshTessellations(mesh_resource) # Create a model model = resource.addModel(self.dim, self.dim) model.setName(model_name) # Construct the topology self.session.addTopology(resource, smtk.session.mesh.Topology( model.entity(), meshes, False)) model.setStringProperty('url', filepath) model.setStringProperty('type', 'gmsh') self.session.declareDanglingEntity(model) model.setSession(smtk.model.SessionRef( resource, self.session.sessionId())) mesh_resource.associateToModel(model.entity()) # transcribe resource.session().transcribe( model, smtk.model.SESSION_EVERYTHING, False) # Set string property to the model and its entities model.setStringProperty('Analysis', model_name) entities = model.cells() for e in entities: e.setStringProperty('Analysis', model_name) # Rename model entities # The bitflag 100 indicates all the edges, faces and volumes sub_entities = resource.findEntitiesOfType(0x00000100) for entity in sub_entities: # Edge entities if entity.entityFlags() == 0x00000102: new_name = re.sub('Domain', model_name + ' Edge', entity.name()) entity.setName(new_name) # Face entities elif entity.entityFlags() == 0x00000104: new_name = re.sub('Domain', model_name + ' Face', entity.name()) entity.setName(new_name) # Volume entities elif entity.entityFlags() == 0x00000108: new_name = re.sub('Domain', model_name + ' Volume', entity.name()) entity.setName(new_name) return model
group = store.addGroup(0, 'Test Group') # Add a volume and 4 faces the hard way: volume = smtk.model.Entity.create(int(smtk.model.CELL_ENTITY), 3) f1 = smtk.model.Entity.create(int(smtk.model.CELL_ENTITY), 2) f2 = smtk.model.Entity.create(int(smtk.model.CELL_ENTITY), 2) f3 = smtk.model.Entity.create(int(smtk.model.CELL_ENTITY), 2) f4 = smtk.model.Entity.create(int(smtk.model.CELL_ENTITY), 2) u01 = store.addEntity(f1) u02 = store.addEntity(f2) u03 = store.addEntity(f3) u04 = store.addEntity(f4) volume.pushRelation(u01).\ pushRelation(u02).\ pushRelation(u03).\ pushRelation(u04).\ pushRelation(model.entity()) u00 = store.addEntity(volume) # Now verify that the faces refer back to the volume: status = False if store.findEntity(u01, True).relations()[ 0] == u00 else True # Add cells to the group, the group and cells to the model, submodels # to the model: [store.findOrAddEntityToGroup(group.entity(), x) for x in [u00, u01, u02, u03, u04]] [model.addCell(smtk.model.CellEntity(x)) for x in group.members()] store.assignDefaultNames() model.addGroup(group) model.addSubmodel(model2) model.addSubmodel(model3) # Does the model contain the cells we just added?