Core module

A module containing core tools and wrappers for vtk data containers used in simphony_mayavi.

Classes

CubaData(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 docstrings 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_cuba()	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.

Description

class simphony_mayavi.core.cuba_data.CubaData(attribute_data, stored_cuba=None, size=None, masks=None)

Bases: _abcoll.MutableSequence

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 array 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 tvtk 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 then 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 “<CUBA.name>-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_=<AttributeSetType.POINTS: 1>, size=0)

Return an empty sequence based wrapping a vtkAttributeDataSet.

Parameters:

• size (int) – The virtual size of the container.
• 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. Unsupported 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.

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 < sequence length.

class simphony_mayavi.core.cuba_data_accumulator.CUBADataAccumulator(keys=None)

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 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

>>> accumulator = CUBADataAccumulator():
>>> accumulator.append(DataContainer(TEMPERATURE=34))
>>> accumulator.keys()
{CUBA.TEMPERATURE}
>>> accumulator.append(DataContainer(VELOCITY=(0.1, 0.1, 0.1))
>>> accumulator.append(DataContainer(TEMPERATURE=56))
>>> accumulator.keys()
{CUBA.TEMPERATURE, CUBA.VELOCITY}
>>> accumulator[CUBA.TEMPERATURE]
[34, None, 56]
>>> accumulator[CUBA.VELOCITY]
[None, (0.1, 0.1, 0.1), None]

fixed operation

>>> accumulator = CUBADataAccumulator([CUBA.TEMPERATURE, CUBA.PRESSURE]):
>>> accumulator.keys()
{CUBA.TEMPERATURE, CUBA.PRESSURE}
>>> accumulator.append(DataContainer(TEMPERATURE=34))
>>> accumulator.append(DataContainer(VELOCITY=(0.1, 0.1, 0.1))
>>> accumulator.append(DataContainer(TEMPERATURE=56))
>>> accumulator.keys()
{CUBA.TEMPERATURE, CUBA.PRESSURE}
>>> accumulator[CUBA.TEMPERATURE]
[34, None, 56]
>>> accumulator[CUBA.PRESSURE]
[None, None, None]
>>> 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. An empty list is acceptable, and returns a trivial accumulator providing no data. If None is passed, then the 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 (list) – 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 values 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.

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 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 -> 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 one dimensional array based on the following template:

[n, id0, id1, id2, ..., idn, m, id0, ...]

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.