SimPhoNy-Mayavi Documentation
Contents
1. 18 Chapter 8 User Manual SimPhoNy Mayavi Documentation Release 0 1 2 dev240 Lattice example import numpy from simphony cuds lattice import make_cubic_lattice from simphony core cuba import CUBA lattice make_cubic_lattice test 0 1 5 10 12 for node in lattice iter_nodes index numpy array node index 1 0 node data CUBA TEMPERATURE numpy prod index lattice update_node node if name n main o from simphony visualisation import mayavi_tools Visualise the Lattice object mayavi_tools show lattice PHEMMOOTSB 242 aS Particles example from numpy import array from simphony cuds particles import Particles Particle Bond from simphony core data_container import DataContainer points array 0 0 0 1 0 0 bonds array 0 1 0 3 1 3 temperature array 10 20 30 40 particles Particles test 8 1 SimPhoNy 19 SimPhoNy Mayavi Documentation Release 0 1 2 dev240 uids for index point in enumerate points uid particles add_particle Particle coordinates point data DataContainer TEMPERATURE temperature index uids append uid for indices in bonds particles add_bond Bond particles uids index for index in indices if name main from simphony visualisation import mayavi_tools Visualise the Particles object mayavi_tools show pa2. Contents 1 SimPhoNy Mayavi Documentation Release 0 1 2 dev240 2 Contents CHAPTER 1 Repository Simphony mayavi is hosted on github https github com simphony simphony mayavi SimPhoNy Mayavi Documentation Release 0 1 2 dev240 4 Chapter 1 Repository CHAPTER 2 Requirements e mayavi gt 4 4 0 e simphony gt 0 1 3 2 1 Optional requirements To support the documentation built you need the following packages e sphinx gt 1 2 3 e sectiondoc commit 8a0c2be https github com enthought sectiondoc e trait documenter https github com enthought trait documenter e mock Alternative running pip install r doc_requirements should install the minimum necessary components for the documentation built SimPhoNy Mayavi Documentation Release 0 1 2 dev240 6 Chapter 2 Requirements CHAPTER 3 Installation The package requires python 2 7 x installation is based on setuptools build and install python setup py install or build for in place development python setup py develop SimPhoNy Mayavi Documentation Release 0 1 2 dev240 8 Chapter 3 Installation CHAPTER 4 Testing To run the full test suite run python m unittest discover SimPhoNy Mayavi Documentation Release 0 1 2 dev240 10 Chapter 4 Testing CHAPTER 5 Documentation To build the documentation in the doc bui
3. Checks if a bond with the given uid already exists in the container has_particle uid Checks if a particle with the given uid already exists in the container index2bond None The reverse mapping from index to bond uid index2particle None The reverse mapping from index to point uid iter_bonds uids None Generator method for iterating over the bonds of the container It can receive any kind of sequence of bond ids to iterate over those concrete bond If nothing is passed as parameter it will iterate over all the bonds uids iterable of uuid UUID optional sequence containing the id s of the bond that will be iterated When the uids are provided then the bonds are returned in the same order the uids are returned by the iterable If uids is None then all bonds are returned by the interable and there is no restriction on the order that they are returned Yields bond Bond The next Bond item Raises KeyError if any of the ids passed as parameters are not in the container Examples It can be used with a sequence as parameter or without it gt gt gt particles Particles name foo gt ras gt gt gt for bond in particles iter_bonds idl id2 id3 do stuff take the bond back to the container so it will be updated in case we need it particles update_bond bond gt gt gt for bond in particles iter_bond do stuff it will iterate over all the bond take the bond back to the con
4. 2 Type help copyright credits or license for more information gt Logger Python Fig 8 2 Use the provided example to create a CUDS Lattice and visualise directly in Mayavi2 container add_bond Bond particles uids index for index in indices Now view the data mayavi2 standalone def view from mayavi modules surface import Surface from mayavi modules glyph import Glyph from simphony mayavi sources api import CUDSSource mayavi new_scene noga src CUDSSource cuds container mayavi add_source src noga g Glyph gs g glyph glyph_source gs glyph source gs glyph_dict sphere_source g glyph glyph scale_factor 0 05 g glyph scale_mode data_scaling_off s Surface s actor mapper scalar_visibility False mayavi add_module g noga mayavi add_module s noga Lf name _ main view 28 Chapter 8 User Manual SimPhoNy Mayavi Documentation Release 0 1 2 dev240 File Visualize View Tools Help Mayavi Bx Mayavi Scene 1 EJ Python ax EA S Python 2 7 3 Master 2 0 0 devi463 albb912 64 bit default Nov 8 24 NAO e e eo 2014 14 05 41 MSC v 1500 64 bit AMD64 on win32 E Type help copyright credits or license for more information gt gt gt import simphony gt gt gt 4 Mayavi Scene 1 4 TI VTK Data PolyData 48 Colors and legends Glyph M Surface
5. Scalar LUT vectorLur ModuleManager LUT Look Up Table Manager Lut mode pluered Mi Number of colors 256 Reverse lut 7 Edit LUT properties Edit Legend representation l Launch LUT editor Show legend F Number of labels 0 64 B Shadow Use default name Data name TEMPERATURE Edit bar Title Edit bar Text Edit bar Actor Edit bar Widget Use default range Y 10 0 Data range ano togger Python Fig 8 3 Use the provided example to create a CUDS Particles and visualise directly in Mayavi2 Source from a CUDS File from contextlib import closing from mayavi scripts import mayavi2 import numpy from numpy import array from simphony core data_container import DataContainer from simphony core cuba import CUBA from simphony cuds particles import Particles Particle Bond from simphony cuds lattice import make_hexagonal_lattice make_cubic_lattice make_square_lattice from simphony cuds mesh import Mesh Point Cell Edge Face from simphony io h5_cuds import H5CUDS points array 0 0 0 1 0 0 I bonds array 0 1 0 3 1 3 2 0 r 2 temperature array 10 20 30 40 1 particles Particles particles_example uids for index point in enumerate points uid particles add_particle Particle coordinates point data DataContainer TEMPERATURE temper
6. accumulator append DataContainer TEMPERATURE 56 gt gt gt accumulator keys CUBA TEMPERATURE CUBA PRESSURE gt gt gt accumulator CUBA TEMPERATURE 34 None 56 gt gt gt accumulator CUBA PRESSURE None None None gt gt gt accumulator CUBA VELOCITY KeyError Constructor Parameters keys list The list of keys that the accumulator should care about Providing this value at initialisation sets up the accumulator to operate in fixed mode If no keys are provided then accumulator operates in expand mode __getitem_ key Get the list of accumulated values for the CUBA key Parameters key CUBA A CUBA Enum value Returns result dist A list of data values collected for key Missing values are designated with None __len__ The number of values that are stored per key Note Behaviour is temporary and will probably change soon append data Append info from a DataContainer Parameters data DataContainer The data information to append If the accumulator operates in fixed mode Any keys in self keys that have values in data will be stored appended to the related key lits Missing keys will be stored as None If the accumulator operates in expand mode Any new keys in Data will be added to the self keys list and the related list of v
7. gt gt fdo whatever you want with the particle gt gt gt part_container update_particle part class simphony_mayavi cuds vtk_mesh VTKMesh name data None data_set None map pings None Bases simphony cuds abstractmesh ABCMesh Constructor 9 3 Cuds module 39 SimPhoNy Mayavi Documentation Release 0 1 2 dev240 Parameters e name string The name of the container e data DataContainer The data attribute to attach to the container Default is None e data set tvtk DataSet The dataset to wrap in the CUDS api Default is None which will create a tvtk UnstructuredGrid e mappings dict A dictionary of mappings for the point2index index2point ele ment2index and index2element Should be provided if the points and elements described in data_set are already assigned uids Default is None and will result in the uid lt gt index mappings being generated at construction add cell cell add edge edge add face face add point point data Easy access to the vtk PointData structure data set None The vtk PolyData dataset element2indez None The mapping from uid to bond index element_data None Easy access to the vtk CellData structure classmethod from_dataset name data set data None Wrap a plain dataset into a new VTKMesh The constructor makes some sanity checks to make sure that the tvtk DataSet is compatible and all the information can be properly used Raises
8. the per item mapping of data values in a CUDS container to a per CUBA key mapping of the data values useful for coping data to vtk array containers The Accumulator has two modes of operation fixed and expand fixed means that data will be stored for a predefined set of keys on every append call and missing values will be saved as None Where expand will extend the internal table of values whenever a new key is introduced expand operation gt gt gt accumulator CUBADataAccumulator gt gt gt accumulator append DataContainer TEMPERATURE 34 gt gt gt accumulator keys CUBA TEMPERATURE gt gt gt accumulator append DataContainer VELOCITY 0 1 0 1 0 1 gt gt gt accumulator append DataContainer TEMPERATURE 56 gt gt gt accumulator keys CUBA TEMPERATURE CUBA VELOCITY gt gt gt accumulator CUBA TEMPERATURE 34 None 56 gt gt gt accumulator CUBA VELOCITY None 0 1 0 1 0 1 None 44 Chapter 9 API Reference SimPhoNy Mayavi Documentation Release 0 1 2 dev240 fixed operation gt gt gt accumulator CUBADataAccumulator CUBA TEMPERATURE CUBA PRESSURE gt gt gt accumulator keys CUBA TEMPERATURE CUBA PRESSURE gt gt gt accumulator append DataContainer TEMPERATURE 34 gt gt gt accumulator append DataContainer VELOCITY 0 1 0 1 0 1 gt gt gt
9. F imPhoNy SimPhoNy Mayavi Documentation Release 0 1 2 dev240 SimPhoNy FP7 Collaboration August 05 2015 Contents 10 Repository Requirements 21 Optional requirements 0 25 cristal Che Se ew Ree ae Installation Testing Documentation Usage Directory structure User Manual 8 1 8 2 SUMPHONY situa be ea Sc da A SAK a wtb e ek Oe DS be eo MWAI 26k eo ae eee EERE RA AER ARE ee EEE A EO API Reference 9 1 9 2 9 3 9 4 Plugin module 24654222 4 24642200 P60 5b 4 28 2424604 04 6S RSG betas SOUNCES MOU S migis y Be Soe WA ER eR eee A ee ee 6 SE eee Ye eS Cudsmodule lt ca s 224434 25 4 eX RS eGR eA REPRE Pe RE PEE HOSS BARS Core module e io io a Seen Det dn a Jb atti he agian aoe na a a ay Ane Jee es ap aes Simphony Mayavi 10 1 10 2 10 3 10 4 10 5 10 6 10 7 REPOSO e kaka ide wea ee wa aaa eee ea hee ee ek ee we SY REQUITements ula e Ate Gh et or A alee Hee a Ghee ee ee ot ae EAS Installation 4 g4 554 m4 beh ooo Ga bh eae eb es bw ee ee ied de gee eS Tesino st Bae oe ee hae Bee ee A Pe See EEE SSE eS Documenta o s s 4 8 soe e oY Gee elke E Be oe 4 ee Ss eo a ees MWS AS Cia 20 eset o a atte a ar Se Bae ok a Sng et Ai ee ghee ge Ge Wa Bie a 11 13 15 17 17 24 SimPhoNy Mayavi Documentation Release 0 1 2 dev240 A plugin library for the Simphony framework http www simphony project eu to provide visualization support of the CUDS highlevel components
10. ON 12 cell types array tetra_type hex_type cell array tvtk CellArray cell_array set_cells 2 cells ug tvtk UnstructuredGrid points points ug set_cells cell_types offset cell_array scalars random random points shape 0 ug point_data scalars scalars ug point_data scalars name array_name scalars random random 2 1 ug cell_data scalars scalars ug cell_data scalars name array_name return ug Create an example vtk_dataset create_unstructured_grid Adapt to a mesh by converting the scalars attribute to TEMPERATURE container mayavi_tools adapt2cuds vtk_dataset test rename_arrays scalars CUBA TEMPERATURE if name _ main E Visualise the Lattice object mayavi_tools show container 8 1 4 Loading into CUDS The load function is available to load mayavi readable files e g VTK xml format into top level CUDS contain ers Using load the user can import inside their simulation scripts files that have been created by other simulation application and export data into one of the Mayavi supported formats 8 1 SimPhoNy 23 SimPhoNy Mayavi Documentation Release 0 1 2 dev240 CH meee setae 7 8 2 Mayavi2 The Simphony Mayavi library provides a plugin for Mayavi2 easily create mayavi Source instances from SimPhoNy CUDS containers and files With the provided tools one can use the SimPhoNy libraries to work inside the Mayavi2 appl
11. TypeError When the sanity checks fail classmethod from_mesh mesh Create a new VTKMesh copy from a CUDS mesh instance get_cell uid get_edge uid get_face uid get_point uid has_cells has_edges has_faces index2element None The reverse mapping from index to bond uid index2point None The reverse mapping from index to point uid iter cells uids None 40 Chapter 9 API Reference SimPhoNy Mayavi Documentation Release 0 1 2 dev240 iter_edges uids None iter_faces uids None iter_points uids None point2index None The mapping from uid to point index supported_cuba None The currently supported and stored CUBA keywords update cell element update edge element update face element update point point class simphony_mayavi cuds vtk_lattice VIKLattice name type data set data None Bases simphony cuds abstractlattice ABCLattice Constructor Parameters e name string The name of the container e type string The type of the container e data set tvtk DataSet The dataset to wrap in the CUDS api e data DataContainer The data attribute to attach to the container Default is None base_vect data The container data classmethod empty name type_ base_vector size origin data None Create a new empty Lattice classmethod from_dataset name data set data None Create a new Lattice and try to guess the type classmethod from_lattice lattic
12. a CUDS Mesh and visualise directly in Mayavi2 Source from a CUDS Lattice import numpy from mayavi scripts import mayavi2 from simphony cuds lattice import make_hexagonal_lattice make_cubic_lattice make_square_lattice from simphony core cuba import CUBA 26 Chapter 8 User Manual SimPhoNy Mayavi Documentation Release 0 1 2 dev240 hexagonal make_hexagonal_lattice test 0 1 5 4 square make_square_lattice test 0 1 5 4 cubic make_cubic_lattice test 0 1 5 10 12 def add_temperature lattice for node in lattice iter_nodes index numpy array node index 1 0 node data CUBA TEMPERATURE numpy prod index lattice update_node node add_temperature hexagonal add_temperature cubic add_temperature square Now view the data mayavi2 standalone def view lattice from mayavi modules glyph import Glyph from simphony mayavi sources api import CUDSSource mayavi new_scene noga src CUDSSource cuds lattice mayavi add_source src noga g Glyph gs g glyph glyph_source gs glyph_source gs glyph_dict sphere_source g glyph glyph scale_factor 0 02 g glyph scale_mode data_scaling_off mayavi add_module g noga if name _ main Ya view cubic Source for a CUDS Particles from numpy import array from mayavi scripts import mayavi2 from simphony cuds particles import Particles Particle Bo
13. alues with length equal to the current record size will be initialised with values of None Any keys in the modified self keys that have values in data will be stored appended to the list of the related key Missing keys will be store as None keys The set of CUBA keys that this accumulator contains 9 4 Core module 45 SimPhoNy Mayavi Documentation Release 0 1 2 dev240 load_onto_vtk vtk_data Load the stored information onto a vtk data container Parameters vtk_data vtkPointData or vtkCellData The vtk container to load the value onto Data are loaded onto the vtk container based on their data type The name of the added array is the name of the CUBA key i e CUBA name Currently only scalars and three dimensional vectors are supported class simphony_mayavi core cuba_data_extractor CUBADataExtractor traits Bases traits has_traits HasStrictTraits Extract cuba data from cuds items iterable The class that supports extracting data values of a specific CUBA key from an iterable that returns low level CUDS objects e g Point available Property Set CUBATrait depends_on _available The list of cuba keys that are available read only The value is recalculated at initialialisation and when the reset method is called data Property Dict UUID Any depends_on _data The dictionary mapping of item uid to the extracted data value A change Event is fired for data when selected or
14. ature index uids append uid for indices in bonds particles add_bond Bond particles uids index for index in indices 8 2 Mayavi2 29 SimPhoNy Mayavi Documentation Release 0 1 2 dev240 hexagonal make_hexagonal_lattice hexagonal 0 1 5 4 square make_square_lattice square 0 1 5 4 cubic make_cubic_lattice cubic 0 1 5 10 12 def add temperature lattice for node in lattice iter_nodes index numpy array node index 1 0 node data CUBA TEMPERATURE numpy prod index lattice update_node node def add _velocity lattice for node in lattice iter_nodes node data CUBA VELOCITY node index lattice update_node node add_temperature hexagonal add_temperature cubic add_temperature square add_velocity hexagonal add_velocity cubic add_velocity square points array iO O Ol TL 0 0 LO Ly 017 CO 0 11 EE Oe Oly Sy Op O 18 1y Oly Te 1y 0J EX 07 Lla Sy 0 De le y tle 2 2 1 er cells IO 1 2 31 tetra 4 5 6 Tr 8 9 LO Lay hex faces 2 7 11 edges 1 4 3 8 mesh Mesh mesh_example add points uids mesh add_point Point coordinates point data DataContainer TEMPERATURE index for index point in enumerate points add edges edge_uids mesh add_edge Edge points uids index for index in element data Da
15. cell_collection 43 ___getitem__ simphony_mayavi core cuba_data_accumulubaDBA DetaAcenmsitafdrony_mayavi core cuba_data method 45 42 _ len _ simphony_mayavi core cell_collection CellColletH BA DataAccumulator class in sim method 44 phony_mayavi core cuba_data_accumulator __len__ simphony_mayavi core cuba_data_accumulator CUBADatalAccumulator method 45 CUBADataExtractor class in sim __setitem__ simphony_mayavi core cell_collection CellCollection phony_mayavi core cuba_data_extractor method 44 46 cubas simphony_mayavi core cuba_data CubaData at A tribute 43 adapt2cuds in module simphony_mayavi adapt2cuds cuds simphony_mayavi sources cuds_source CUDSSource 33 attribute 34 add_bond simphony_mayavi cuds vtk_particles VTKPartfelePSFileSource class in sim method 35 phony_mayavi sources cuds_file_source add_cell simphony_mayavi cuds vtk_mesh VTKMesh 34 method 40 CUDSSource class in sim add_edge simphony_mayavi cuds vtk_mesh VTKMesh phony_mayavi sources cuds_source 34 method 40 add_face simphony_mayavi cuds vtk_mesh VTKMesh D method 40 data simphony_mayavi core cuba_data_extractor CUBADataExtractor add_particle simphony_mayavi cuds vtk_particles VTKParticles attribute 46 method 36 data simphony_mayavi cuds vtk_lattice VTKLattice at add_point simphony_mayavi cuds vtk_mesh VTKMesh tribute 41 method 40 data simphony_mayavi cuds vtk_mesh VTKMesh append simphony_ma
16. d Replaces an existing bond Takes the uid of bond and searches inside the container for that bond If the bond exists it is replaced with the new bond passed as parameter If the bond doesn t exist it will raise an exception Parameters bond Bond the bond that will be replaced Raises ValueError If the bond doesn t exist Examples Given a Bond that already exists in the Particles container taken with the get_bond method for example just call the function passing the Bond as parameter gt gt gt particles Particles name foo gt gt A gt gt gt bond particles get_bond uid gt gt gt fdo whatever you want with the bond gt gt gt particles update_bond bond update_particle particle Replaces an existing particle Takes the uid of particle and searches inside the container for that particle If the particle exists it is replaced with the new particle passed as parameter If the particle doesn t exist it will raise an exception Parameters particle Particle the particle that will be replaced Raises ValueError If the particle does not exist Examples Given a Particle that already exists in the Particles container taken with the get_particle method for example just call the function passing the Particle as parameter gt gt gt part_container Particles name foo 35 gt ca gt gt gt part part_container get_particle uid gt
17. ds_source CUDSSource A mayavi source of a SimPhoNy CUDS File dataset DEnum values_name datasets The name of the CUDS container that is currently loaded datasets ListStr The names of the contained datasets 34 Chapter 9 API Reference SimPhoNy Mayavi Documentation Release 0 1 2 dev240 file path Instance FilePath desc the current file name The file path of the cuds file to read initialize filename Initialise the CUDS file source start update 9 3 Cuds module A module containing tvtk dataset wrappers to simphony CUDS containers Classes VTKParticles namel data data set mappings Constructor VTKMesh name data data set mappings Constructor VTKLatt ice name type data_set data Constructor 9 3 1 Description class simphony_mayavi cuds vtk_particles VTKParticles name data None data_set None map pings None Bases simphony cuds abstractparticles ABCParticles Constructor Parameters e name string The name of the container e data DataContainer The data attribute to attach to the container Default is None e data set tvtk DataSet The dataset to wrap in the CUDS api Default is None which will create a tvtk PolyData e mappings dict A dictionary of mappings for the particle2index index2particle bond2index and bond2element Should be provided if the particles and bonds described in data_set are already assigned uids De
18. e Create a new Lattice from the provided one get_coordinate index Get coordinate of the given index coordinate index int 3 node index coordinate Returns coordinates float 3 get_node index Get the lattice node corresponding to the given index index int 3 node index coordinate Returns node LatticeNode 9 3 Cuds module 41 SimPhoNy Mayavi Documentation Release 0 1 2 dev240 iter_nodes indices None Get an iterator over the LatticeNodes described by the indices indices iterable set of int 3 optional When indices i e node index coordinates are provided then nodes are returned in the same order of the provided indices If indices is None there is no restriction on the order the nodes that are returned Returns iterator An iterator over LatticeNode objects origin point_data None Easy access to the vtk PointData structure size supported_cuba None The currently supported and stored CUBA keywords type update_node node Update the corresponding lattice node Parameters node LatticeNode 9 4 Core module A module containing core tools and wrappers for vtk data containers used in simphony_mayavi Classes CubaDat a attribute_data stored_cuba Map a vtkCellData or vtkPointData object to a sequence of DataContainers CellCollection cell_array A mutable sequence of cells wrapping a tvtk CellArray mergedocs other Merge the docst
19. e Visualize View Tools Help tayavi ax Mayavi Scene 1 EJ 4 Mayavi Scene 1 REMUS s Hae 4 CUDS File cubic CUDS Lattice 4 Colors and legends Glyph ki ie oo Pont scalars name TEMPERATURE Point vectors name VELOCITY oe Call vectors name y Data Data pos WA LFF EET Lib EEC ee Ie a a E E 4 if y i ff yd yA gt 47 PD ph y pp YA a AO A Aa Pp Pp LO AA IAM JIJI EAN A ad hdd MLA y P SOLU B GN gD e hid Fig 8 5 When loaded a CUDSFile is converted into a Mayavi Source and the user can add normal Mayavi modules to visualise the currently selected CUDS container from the available containers in the file In the example we load the container named cubic and attach the Glyph module to draw a cone at each point to visualise TEMPERATURE and VELOCITY in the Mayavi Scene 32 Chapter 8 User Manual CHAPTER 9 API Reference 9 1 Plugin module This module simphony_mayavi plugin provides a set of tools to visualize CUDS objects The tools are also available as a visualisation plug in to the simphony library simphony_mayavi show show cuds Show the cuds objects using the default visualisation Parameters cuds A top level cuds object e g a mesh The method will detect the type of object and create the appropriate visualisation simphony_mayavi snapshot snapshot cuds filename Shave a snapshot of the cuds
20. e dimensional array based on the following template 46 Chapter 9 API Reference SimPhoNy Mayavi Documentation Release 0 1 2 dev240 En 1d0 201 102 e p LA my LAO KA The iterator takes a cell array and returns the point indices for each cell simphony_mayavi core doc_utils mergedoc function other Merge the docstring from the other function to the decorated function 9 4 Core module 47 SimPhoNy Mayavi Documentation Release 0 1 2 dev240 48 Chapter 9 API Reference CHAPTER 10 Simphony Mayavi A plugin library for the Simphony framework http www simphony project eu to provide visualization support of the CUDS highlevel components 10 1 Repository Simphony mayavi is hosted on github https github com simphony simphony mayavi 10 2 Requirements e mayavi gt 4 4 0 e simphony gt 0 1 3 10 2 1 Optional requirements To support the documentation built you need the following packages e sphinx gt 1 2 3 e sectiondoc commit 8a0c2be https github com enthought sectiondoc e trait documenter https github com enthought trait documenter e mock Alternative running pip install r doc_requirements should install the minimum necessary components for the documentation built 10 3 Installation The package requires python 2 7 x installation is based on setuptools build and install python setup py install or 49 SimPhoNy Mayavi Documentati
21. fault is None and will result in the uid lt gt index mappings being generated at construction add_bond bond Adds the bond to the container Also like with particles if the bond has a defined uid it won t add the bond if a bond with the same uid already exists and if the bond has no uid the particle container will generate an uid If the user wants to replace an existing bond in the container there is an update_bond method for that purpose Parameters bond Bond the new bond that will be included in the container Returns uid uuid UID The uid of the added bond Raises ValueError When the new particle already exists in the container 9 3 Cuds module 35 SimPhoNy Mayavi Documentation Release 0 1 2 dev240 Examples Add a bond to a Particles container gt gt gt bond Bond gt gt gt particles Particles name foo gt gt gt particles add_bond bond add_particle particle Adds the particle to the container If the new particle has no uid the particle container will generate a new uid for it If the particle has already an uid it won t add the particle if a particle with the same uid already exists If the user wants to replace an existing particle in the container there is an update_particle method for that purpose Parameters particle Particle the new particle that will be included in the container Returns uid uuid UUID The uid of the added par
22. ication as it is demonstrated in the examples Setup plugin To setup the mayavi2 plugin one needs to make sure that the simpony_mayavi plugin has been selected and activated in the Mayavi2 preferences dialog Source from a CUDS Mesh from numpy import array from mayavi scripts import mayavi2 from simphony cuds mesh import Mesh Point Cell Edge Face from simphony core data_container import DataContainer points array 0 0 0 1 0 0 0 1 0 0 0 1 2 0 01 3 0 0 3 1 0 2 1 0 2 0 1 3 0 1 3 1 1 12 1 1 1 ES cells 0 ly 2 31 tetra l4 Dp Gr Tr Sp 9 10 111 hex faces 2 7 11 24 Chapter 8 User Manual SimPhoNy Mayavi Documentation Release 0 1 2 dev240 General Logger gt Mayavi TVTK Scene Open help in light browser Available contributions General settings Confirm delete Show splash screen Show helper nodes Use ipython Contribution settings Selected contributions simphony_mayavi edges 1 4 container Mesh test add points uids container add_point Point coordinates point for index add edges edge_uids container add_edge Edge points uids index MP data DataContainer TE ERATUR E index point in enumerate points for index in element data DataC
23. it particles update_particle particle particle2index None The mapping from uid to point index remove_bond uid Removes the bond with the uid from the container The uid passed as parameter should exists in the container If it doesn t exists nothing will happen Parameters uid uuid UUID the uid of the bond to be removed Examples Having an uid of an existing bond pass it to the function gt gt gt particles Particles name foo gt gt gt gt gt bond particles get_bond uid gt gt gt gt gt gt particles remove bond bond uid or gt gt gt particles remove_bond uid remove_particle uid Removes the particle with uid from the container The uid passed as parameter should exists in the container Otherwise an exception will be raised Parameters uid uuid UID the uid of the particle to be removed Raises KeyError If the particle doesn t exist Examples Having an uid of an existing particle pass it to the function 38 Chapter 9 API Reference SimPhoNy Mayavi Documentation Release 0 1 2 dev240 gt gt gt particles Particles name foo gt gt gt gt gt gt particle particles get_particle uid ae gt gt gt particles remove_particle part uid or directly gt gt gt particles remove_particle uid supported_cuba None The currently supported and stored CUBA keywords update_bond bon
24. keys change or the reset method is called function ReadOnly The function to call that returns a generator over the desired items e g Mesh iter_points This value cannot be changed after initialisation keys Either None Set UUID The list of uuid keys to restrict the data extraction This attribute is passed to the function generator method to restrict iteration over the provided keys e g Mesh iter_points uids keys reset Reset the available and data attributes selected CUBATrait Currently selected CUBA key Changing the selected key will fire events that will result in executing the generator function and extracting the related values from the CUDS items that the iterator yields The resulting mapping of uid gt value will be stored in data class simphony_mayavi core doc_utils mergedocs other Bases object Merge the docstrings of other class to the decorated simphony_mayavi core cuba_utils supported_cuba Return the list of CUBA keys that can be supported by vtk simphony_mayavi core cuba_utils default_cuba_value cuba Return the default value of the CUBA key as a scalar or numpy array Int type values have 1 as default while float type values have numpy nan Note Only vector and scalar values are currently supported simphony_mayavi core cell_array_tools cell_array_slicer data Iterate over cell components on a vtk cell array VTK stores the associated point index for each cell in a on
25. ld directory run python setup py build_sphinx Note e One can use the help option with a setup py command to see all available options The documentation will be saved in the build directory 11 SimPhoNy Mayavi Documentation Release 0 1 2 dev240 12 Chapter 5 Documentation CHAPTER 6 Usage After installation the user should be able to import the mayavi visualization plugin module by from simphony visualization import mayavi_tools mayavi_tools show cuds 13 SimPhoNy Mayavi Documentation Release 0 1 2 dev240 14 Chapter 6 Usage CHAPTER 7 Directory structure e simphony mayavi Main package folder sources Wrap CUDS objects to provide Mayavi Sources cuds Wrap VTK Dataset objects to provide the CUDS container api core Utility classes and tools to manipulate vtk and cuds objects e examples Holds examples of loading and visualising SimPhoNy objects with simphony mayavi e doc Documentation related files The rst source files for the documentation 15 SimPhoNy Mayavi Documentation Release 0 1 2 dev240 16 Chapter 7 Directory structure CHAPTER 8 User Manual 8 1 SimPhoNy Mayavi tools are available in the simphony library through the visualisation plug in named mayavi_tools e g from simphony visualisation import mayavi_tools 8 1 1 Visualizing CUDS The show fu
26. n the necessary arrays are created and the initial_size info is not used anymore Note Missing values for the attribute arrays are stored in separate attribute arrays named lt CUBA name gt mask as 0 while present values are designated with a 1 Constructor attribute_data tvtk DataSetAttributes The vtk attribute container stored_cuba set The CUBA keys that are going to be stored default is the result of running supported_cuba size int The initial size of the container Default is None Setting a value will activate the virtual size behaviour of the container mask tvtk FieldData A data arrays containing the mask of some of the CUBA data in attribute_data Raises ValueError When a non empty attribute_data container is provided while size None cubas The set of currently stored CUBA keys For each cuba key there is an associated DataArray connected to the PointData or CellData classmethod empty type_ lt AttributeSetType POINTS 1 gt size 0 Return an empty sequence based wrapping a vtkAttributeDataSet Parameters e size int The virtual size of the container e type AttributeSetType The type of the vtkAttributeSet to create insert index value Insert the values of the DataContainer in the arrays at row index If the provided DataContainer contains new but supported cuba keys then a new empty array is created for them and updated with the associated values of value Unsupp
27. nction is available to visualise any top level CUDS container The function will open a window containing a 3D view and a mayavi toolbar Interaction allows the common mayavi operations Mesh example from numpy import array from simphony cuds mesh import Mesh Point Cell Edge Face from simphony core data_container import DataContainer points array 0 0 01 1 0 0 0 1 O 0 O 1 2 0 01 3 0 0 3 1 0 2 1 0 2 0 11 3 0 1 3 1 1 12 1 1 1 Wa A cells 0 1 2 3 tetra 4 5 6 7 8 9 10 11 hex faces 2 7 11 edges 1 4 3 81 mesh Mesh example add points uids mesh add_point 17 SimPhoNy Mayavi Documentation Release 0 1 2 dev240 Point coordinates point data DataContainer TEMPERATURE index for index point in enumerate points add edges edge_uids mesh add_edge Edge points uids index for index in element for index lement in enumerate edges add faces face_uids mesh add_face Face points uids index for index in element for index lement in enumerate faces add cells cell_uids mesh add_cell Cell points uids index for index in element for index lement in enumerate cells if name _main_ from simphony visualisation import mayavi_tools Visualise the Mesh object mayavi_tools show mesh
28. nd from simphony core data_container import DataContainer points array 0 0 0 1 0 0 bonds array 0 1 0 3 1 3 2 temperature array 10 20 30 40 OF Dy Ol HO O aT Se 11 1 container Particles test uids for index point in enumerate points uid container add_particle Particle coordinates point data DataContainer TEMPERATURE temperature index uids append uid for indices in bonds 8 2 Mayavi2 27 SimPhoNy Mayavi Documentation Release 0 1 2 dev240 ayavi2 The 3D data Vi File Visualize View Tools Help Mayavi Bx Mayavi Scene 1 EJ Python 7 2 m Python 2 7 3 Master 2 0 0 dev1463 a1bb912 64 bit 4 Mayavi Scene 1 DANA sk ao 2014 14 05 41 MSC v 1500 64 bit AMD64 on win3 4 1 VTK Data ImageData 4 Colors and legends ma Glyph gt gt import simphony gt gt gt Mayavi object editor Giph Actor Masking Glyph GlyphSource Scale mode data_scaling off Color mode color by sealer 7 View type Basic Clamping Y Fill cell data F Generate point ids 7 Orient Scaling Y Color mode color by scalar 7 denote at z Scale mode data_scaling_off Y Vector mode use_vector Point ids name InputPointids Range FO 0 0 Fi 1 0 Scale factor 0 02 default Nov 8
29. object using the default visualisation Parameters e cuds A top level cuds object e g a mesh The method will detect the type of object and create the appropriate visualisation e filename string The filename to use for the output file simphony_mayavi adapt2cuds adapt2cuds data_set name CUDS container kind None re name_arrays None Adapt a TVTK dataset to a CUDS container Parameters e data set tvtk Dataset The dataset to import and wrap into CUDS container e name string The name of the CUDS container Default is CUDS container kind mesh lattice particles The kind of the container to return Default is None where the function will use some heuristics to infer the most appropriate type of CUDS container to return rename_array dict Dictionary mapping the array names used in the dataset object to their related CUBA keywords that will be used in the returned CUDS container Note When set a shallow copy of the input data_set is created and used by the related vtk gt cuds wrapper Raises ValueError When kind is not a valid CUDS container type 33 SimPhoNy Mayavi Documentation Release 0 1 2 dev240 TypeError When it is not possible to wrap the provided data_set simphony_mayavi load load filename name None kind None rename_arrays None Load the file data into a CUDS container Parameters e filename string The file name of the file
30. on Release 0 1 2 dev240 build for in place development python setup py develop 10 4 Testing To run the full test suite run python m unittest discover 10 5 Documentation To build the documentation in the doc build directory run python setup py build_sphinx Note e One can use the help option with a setup py command to see all available options The documentation will be saved in the build directory 10 6 Usage After installation the user should be able to import the mayavi visualization plugin module by from simphony visualization import mayavi_tools mayavi_tools show cuds 10 7 Directory structure e simphony mayavi Main package folder sources Wrap CUDS objects to provide Mayavi Sources cuds Wrap VTK Dataset objects to provide the CUDS container api core Utility classes and tools to manipulate vtk and cuds objects e examples Holds examples of loading and visualising SimPhoNy objects with simphony mayavi e doc Documentation related files The rst source files for the documentation 50 Chapter 10 Simphony Mayavi Index Symbols C _ delitem__ simphony_mayavi core cell_collection CellGalllectroay_slicer in module sim method 44 phony_mayavi core cell_array_tools 46 getitem__ simphony_mayavi core cell_collection CellGOtlkCidlection class in sim method 44 phony_mayavi core
31. ontainer T for index element in add faces face_uids container add_face Face points uids index EMPERATURE index 20 numerate edges for index in element data DataContainer TE for index element in add cells cell_uids container add_cell Cell MPERATURE index 30 numerate faces 8 2 Mayavi2 25 SimPhoNy Mayavi Documentation Release 0 1 2 dev240 points uids index for index in element data DataContainer TEMPERATURE index 40 for index lement in enumerate cells Now view the data mayavi2 standalone def view from mayavi modules surface import Surface from simphony mayavi sources api import CUDSSource mayavi new_scene noga src CUDSSource cuds container mayavi add_source src noga s Surfacel mayavi add_module s noga if name _ main__ view File Visualize View Tools Help Mayavi BI mayaviScene1 E Python ex TE Noya cee ALLTEL e E 4 El VTK Data UnstructuredGrid a AA for more information 48 Colors and legends M Surface gt gt gt Pa ii Point scalars name TEMPERATURE 7 Point vectors name 2 Point tensors name Cell scalars name TEMPERATURE 7 Cell vectors name z Cell tensors name 72 oa oma Logger Python Fig 8 1 Use the provided example to create
32. orted CUBA keys are ignored Note The underline data structure is better suited for append operations Inserting values in the middle or at the front will be less efficient 9 4 Core module 43 SimPhoNy Mayavi Documentation Release 0 1 2 dev240 class simphony_mayavi core cell_collection CellCollection cell_array None Bases _abcoll MutableSequence A mutable sequence of cells wrapping a tvtk CellArray Constructor Parameters cell_array tvtk CellArray The tvtk object to wrap Default value is an empty tvtk CellArray __ delitem index Remove cell at index Note This operation will need to create temporary arrays in order to keep the data info consistent __getitem__ index Return the connectivity list for the cell at index _ len The number of contained cells __ setitem _ index value Update the connectivity list for cell at index Note If the size of the connectivity list changes a slower path creating temporary arrays is used insert index value Insert cell at index Note This operation needs to use a slower path based on temporary array when index lt sequence length class simphony_mayavi core cuba_data_accumulator CUBADataAccumulator keys Bases object Accumulate data information per CUBA key A collector object that stores class DataContainer data into a list of values per CUBA key By appending DataContainer instanced the user can effectively convert
33. rings of other class to the decorated CUBADataAccumulator keys Accumulate data information per CUBA key CUBADataExtractor traits Extract cuba data from cuds items iterable Functions supported_cubal Return the list of CUBA keys that can be supported by vtk default_cuba_value cuba Return the default value of the CUBA key as a scalar or numpy array cell_array_slicer data Iterate over cell components on a vtk cell array mergedoc function other Merge the docstring from the other function to the decorated function 9 4 1 Description class simphony_mayavi core cuba_data CubaData attribute_data stored_cuba None size None masks None Bases _abcoll MutableSequence 42 Chapter 9 API Reference SimPhoNy Mayavi Documentation Release 0 1 2 dev240 Map a vtkCellData or vtkPointData object to a sequence of DataContainers The class implements the MutableSequence api to wrap a tvtk CellData or tvtk PointData ar ray where each CUBA key is a tvtk DataArray The aim is to help the conversion between column based structure of the vtkCellData or vtkPointData and the row based access provided by a list of DataContainer While the wrapped tvkt container is empty the following behaviour is active Using len will return the initial_size if defined or 0 Using element access will return an empty class DataContainer No field arrays have been allocated When values are first added updated with non empty DataContainers the
34. rticle2index simphony_mayavi cuds vtk_particles VTK Particles attribute 38 point2index simphony_mayavi cuds vtk_mesh VTKMesh attribute 41 point data simphony_mayavi cuds vtk_lattice VTKLattice attribute 42 VTKLattice class in simphony_mayavi cuds vtk_lattice 41 R VTKMesh class in simphony_mayavi cuds vtk_mesh method 41 remove_bond simphony_mayavi cuds vtk_particles VTKRarticles i A cl i articles class in sim PEE a sim phony_mayavi cuds vtk_particles 35 phony_mayavi cuds vtk_particles VT KParticles method 38 reset simphony_mayavi core cuba_data_extractor CUBADataExtractor method 46 S selected simphony_mayavi core cuba_data_extractor CUBADataExtractor attribute 46 show in module simphony_mayavi show 33 size simphony_mayavi cuds vtk_lattice VTKLattice at tribute 42 snapshot in module simphony_mayavi snapshot 33 start simphony_mayavi sources cuds_file_source CUDSFileSource method 35 supported_cuba simphony_mayavi cuds vtk_lattice VTKLattice attribute 42 supported_cuba simphony_mayavi cuds vtk_mesh VTKMesh attribute 41 supported_cuba simphony_mayavi cuds vtk_particles VTKParticles attribute 39 supported_cuba in module sim phony_mayavi core cuba_utils 46 T type simphony_mayavi cuds vtk_lattice VTKLattice at tribute 42 U update simphony_mayavi sources cuds_file_source CUDSFileSource method 35 update bond simphony_maya
35. rticles voya scene ei esa 8 1 2 Create VTK backed CUDS Three objects i e class VTKMesh class VTKLattice VTKParticles that wrap a VTK dataset and provide the CUDS top level container API are also available The vtk backed objects are expected to provide memory and some speed advantages when Mayavi aided visualisation and processing is a major part of the working session The provided examples are equivalent to the ones in section Visualizing CUDS Note Note all CUBA keys are supported for the data attribute of the contained items Please see documentation for more details 20 Chapter 8 User Manual SimPhoNy Mayavi Documentation Release 0 1 2 dev240 VTK Mesh example from numpy import array from simphony cuds mesh import Point Cell Edge Face from simphony core data_container import DataContainer from simphony visualisation import mayavi_tools points array 0 0 0 1 0 0 0 1 0 10 O 1 2 0 01 3 0 0 3 1 0 12 1 0 2 0 1 3 0 1 3 1 1 12 1 1 DEN cells IO 1 2 31 tetra A Sy 6p Tr By 9 10 111 hex faces 2 7 11 edges 1 4 3 8 mesh mayavi_tools VTKMesh example add points uids mesh add_point Point coordinates point for index add edges edge_uids mesh add_edge Edge points uids index for index lement in add faces face_uids mesh add_face Face points uid
36. s for index point in enumerate points uid particles add_particle Particle coordinates point data DataContainer TEMPERATURE temperature index uids append uid for indices in bonds particles add_bond Bond particles uids index for index in indices if name _ main ae Visualise the Particles object mayavi_tools show particles 8 1 3 Adapting VTK datasets The adapt2cuds function is available to wrap common VTK datsets into top level CUDS containers The function will attempt to automatically adapt the t vtk Dataset into a CUDS container But when this fails the user can 22 Chapter 8 User Manual SimPhoNy Mayavi Documentation Release 0 1 2 dev240 always force the kind of the container and mapping of the included attribute data into corresponding CUBA keys Example from numpy import array random from tvtk api import tvtk from simphony core cuba import CUBA from simphony visualisation import mayavi_tools def create_unstructured_grid array_name scalars points array PO TEZ 0 67 1 0 01 0 Ls O15 Ls 1 1 tetra l dy Op O Sl 12 Us 0l 12 LD 101 lOr L Oly ly OY 0 Ls O 2 1 Tier Ly Tels Cty 2 jy tc Hex cells array 4 0 1 2 3 tetra 8 4 By 6 Y 8 9 10 111 hex offset array 0 5 tetra_type tvtk Tetra cell_type VIK_TETRA 10 hez type tvtk Hexahedron cell_type VIK_HEXAHEDR
37. s index for index lement in numerat data DataContainer TEMPERATURE index point in enumerate points for index in element numerate edges for index in element faces add cells cell_uids mesh add_cell Cell points uids index for index lement in af name _ main ng Visualise the Mesh object mayavi_tools show mesh for index in element numerate cells 8 1 SimPhoNy 21 SimPhoNy Mayavi Documentation Release 0 1 2 dev240 VTK Lattice example import numpy from simphony core cuba import CUBA from simphony visualisation import mayavi_tools lattice mayavi_tools VTKLattice empty test Cubic 0 1 Dels 061 5 7 10 12 0 07 OY for node in lattice iter_nodes index numpy array node index 1 0 node data CUBA TEMPERATURE numpy prod index lattice update_node node if name _ main Ya Visualise the Lattice object mayavi_tools show lattice VTK Particles example from numpy import array from simphony core data_container import DataContainer from simphony cuds particles import Particle Bond from simphony visualisation import mayavi_tools points array 0 0 0 1 0 0 1 01 10 0 1 bonds array 0 1 10 3 1 3 2 0 r 2 temperature array 10 20 30 40 r 1 particles mayavi_tools VTKParticles test uid
38. taContainer TEMPERATURE index 20 for index lement in enumerate edges add faces face_uids mesh add_face Face points uids index for index in element 30 Chapter 8 User Manual SimPhoNy Mayavi Documentation Release 0 1 2 dev240 data DataContainer TEMPERATURE index 30 for index lement in enumerate faces add cells cell_uids mesh add_cell Cell points uids index for index in element data DataContainer TEMPERATURE index 40 for index lement in enumerate cells save the data into cuds with closing H5CUDS open example cuds w as handle handle add_mesh mesh handle add_particles particles handle add_lattice hexagonal handle add_lattice cubic handle add_lattice square Now view the data mayavi2 standalone def view mayavi new_scene noga if name _ main view voce aaa mamae 7 O 9 0 1 BN yi My Computer Name Size Type Date Modified R itziakos example cuds 1 7 MB cud ile 03 08 10 56 File name example cuds Files of type CUDS files cuds z Fig 8 4 Cuds files are supported in the Open File dialog After running the provided example load the example cuds file into Mayavi2 8 2 Mayavi2 31 SimPhoNy Mayavi Documentation Release 0 1 2 dev240 Mayavi2 The 3D datavisualizer a Fil
39. tainer so it will be updated in case we need it particles update_bond bond iter_particles uids None Generator method for iterating over the particles of the container It can receive any kind of sequence of particle uids to iterate over those concrete particles If nothing is passed as parameter it will iterate over all the particles uids iterable of uuid UUID optional sequence containing the uids of the particles that will be iterated When the uids are provided then the particles are returned in the same order the uids are returned by the iterable If uids is None then all particles are returned by the interable and there is no restriction on the order that they are returned 9 3 Cuds module 37 SimPhoNy Mayavi Documentation Release 0 1 2 dev240 Yields particle Particle The Particle item Raises KeyError if any of the ids passed as parameters are not in the container Examples It can be used with a sequence as parameter or without it gt gt gt particles Particles name foo SSS poi gt gt gt for particle in particles iter_particles uidl uid2 uid3 do stuff take the particle back to the container so it will be updated in case we need it part_container update_particle particle gt gt gt for particle in particles iter_particles do stuff it will iterate over all the particles take the particle back to the container so it will be updated in case we need
40. ticle Raises ValueError when the new particle already exists in the container Examples Add a particle to a Particles container gt gt gt particle Particle gt gt gt particles Particles name foo gt gt gt particles add_particle part bond2index None The mapping from uid to bond index data Easy access to the vtk CellData structure data_set None The vtk PolyData dataset classmethod from_dataset name data set data None Wrap a plain dataset into a new VTKParticles The constructor makes some sanity checks to make sure that the tvtk DataSet is compatible and all the information can be properly used Raises TypeError When the sanity checks fail classmethod from_particles particles Create a new VTKParticles copy from a CUDS particles instance get_bond uid Returns a copy of the bond with the bond_id id Parameters uid uuid UUID the uid of the bond Raises KeyError when the bond is not in the container Returns bond Bond A copy of the internally stored bond info get_particle uid Returns a copy of the particle with the particle_id id Parameters uid uuid UID the uid of the particle 36 Chapter 9 API Reference SimPhoNy Mayavi Documentation Release 0 1 2 dev240 Raises KeyError when the particle is not in the container Returns particle Particle A copy of the internally stored particle info has_bond uid
41. ticles VTK Particles F attribute 37 file path simphony_mayavi sources cuds_file_source CUDSid sSporoe simphony_mayavi cuds vtk_mesh VTKMesh attribute 34 attribute 40 from_dataset simphony_mayavi cuds vtk_lattice VTKLattiv ialize simphony_mayavi sources cuds_file_source CUDSFileSource class method 41 method 35 from_dataset simphony_mayavi cuds vtk_mesh VTKMestnsert simphony_mayavi core cell_collection CellCollection class method 40 method 44 from_dataset simphony_mayavi cuds vtk_particles VT K Pans rl simphony_mayavi core cuba_data CubaData class method 36 method 43 from_lattice simphony_mayavi cuds vtk_lattice VT KLattiter_bonds simphony_mayavi cuds vtk_particles VTKParticles class method 41 method 37 from_mesh simphony_mayavi cuds vtk_mesh VTKMeshiter_cells simphony_mayavi cuds vtk_mesh VTKMesh class method 40 method 40 from_particles simphony_mayavi cuds vtk_particles VTKiRartadges simphony_mayavi cuds vtk_mesh VTKMesh class method 36 method 40 function simphony_mayavi core cuba_data_extractor CUBAtDathiceaadtmphony_mayavi cuds vtk_mesh VTKMesh attribute 46 method 41 iter_nodes simphony_mayavi cuds vtk_lattice VT KLattice G method 41 get_bond simphony_mayavi cuds vtk_particles VTKParti teg particles simphony_mayavi cuds vtk_particles VT KParticles method 36 method 37 get_cell simphony_mayavi cuds vtk_mesh VTKMesh _ iter_points simphony_maya
42. to load e name string The name of the returned CUDS container Default is CUDS container kind mesh lattice particles The kind of the container to return Default is None where the function will use some heuristics to infer the most appropriate type of CUDS container to return using adapt2cuds rename_array dict Dictionary mapping the array names used in the dataset object to their related CUBA keywords that will be used in the returned CUDS container Note Only CUBA keywords are supported for array names so use this option to provide a translation mapping to the CUBA keys 9 2 Sources module A module containing objects that wrap CUDS objects and files to Mayavi compatible sources Please use the simphony_mayavi sources api module to access the provided tools Classes CUDSSource A mayavi source of a SimPhoNy CUDS container CUDSFileSource A mayavi source of a SimPhoNy CUDS File 9 2 1 Description class simphony_mayavi sources cuds_source CUDSSource Bases mayavi sources vtk_data_source VTKDataSource A mayavi source of a SimPhoNy CUDS container cuds Property depends_on _cuds The CUDS container output info PipelineInfo datasets image_data poly data unstructured_grid attribute_types any attribu Output information for the processing pipeline class simphony_mayavi sources cuds_file_source CUDSFileSource Bases simphony_mayavi sources cu
43. vi cuds vtk_mesh VTKMesh method 40 method 41 get_coordinate ony AA method 41 get_edge simphony_mayavi cuds vtk_mesh VTKMesh keys simphony_mayavi core cuba_data_accumulator CUBADataAccumula method 40 attribute 45 get face simphony_mayavi cuds vtk_mesh VTKMesh keys simphony_mayavi core cuba_data_extractor CUBADataExtractor method 40 attribute 46 get_node simphony_mayavi cuds vtk_lattice VTKLattice method 41 get_particle simphony_mayavi cuds vtk_particles VTK Paygi d in module simphony_mayavi load 34 method 36 load_onto_vtk simphony_mayavi core cuba_data_accumulator CUBADAa get_point simphony_mayavi cuds vtk_mesh VTKMesh method 45 method 40 ji M mergedoc in module sim has_bond simphony_mayavi cuds vtk_particles VTKParticles phony_mayavi core doc_utils 47 method 37 mergedocs class in simphony_mayavi core doc_utils 46 has_cells simphony_mayavi cuds vtk_mesh VTKMesh method 40 52 Index SimPhoNy Mayavi Documentation Release 0 1 2 dev240 O update_edge simphony_mayavi cuds vtk_mesh VTKMesh origin simphony_mayavi cuds vtk_lattice VTKLattice method 41 attribute 42 update_face simphony_mayavi cuds vtk_mesh VTKMesh output_info simphony_mayavi sources cuds_source CUDSSource method 41 attribute 34 update_node simphony_mayavi cuds vtk_lattice VTKLattice method 42 P update_particle simphony_mayavi cuds vtk_particles VTKParticles method 39 pa
44. vi cuds vtk_particles VTKParticles method 39 update_cell simphony_mayavi cuds vtk_mesh VTKMesh method 41 Index 53 update_point simphony_mayavi cuds vtk_mesh VTKMesh
45. yavi core cuba_data_accumulator CUBA Dataatadbntejathr method 45 data simphony_mayavi cuds vtk_particles VTKParticles available simphony_mayavi core cuba_data_extractor CUBADataExteanrtidute 36 attribute 46 data set simphony_mayavi cuds vtk_mesh VTKMesh attribute 40 B data set simphony_mayavi cuds vtk_particles VTKParticles base vect simphony_mayavi cuds vtk_lattice VTKLattice attribute 36 attribute 41 dataset simphony_mayavi sources cuds_file_source CUDSFileSource bond2index simphony_mayavi cuds vtk_particles VTKParticles attribute 34 attribute 36 datasets simphony_mayavi sources cuds_file_source CUDSFileSource attribute 34 51 SimPhoNy Mayavi Documentation Release 0 1 2 dev240 default_cuba_value in module sim has edges simphony_mayavi cuds vtk_mesh VTKMesh phony_mayavi core cuba_utils 46 method 40 has_faces simphony_mayavi cuds vtk_mesh VTKMesh E method 40 element2index simphony_mayavi cuds vtk_mesh VTKMeshas_particle simphony_mayavi cuds vtk_particles VTKParticles attribute 40 method 37 element data simphony_mayavi cuds vtk_mesh VTKMesh attribute 40 empty simphony_mayavi core cuba_data CubaData index2bond simphony_mayavi cuds vtk_particles VTKParticles class method 43 attribute 37 empty simphony_mayavi cuds vtk_lattice VT KLattice index2element simphony mayavi cuds vtk mesh VTKMesh class method 41 attribute 40 index2particle simphony_mayavi cuds vtk_par
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