fish2eod.xdmf package

Submodules

fish2eod.xdmf.load module

Load solutions in a filterable form from xdmf/manifests.

class fish2eod.xdmf.load.DataSolution(domain_map, variables, data, s_var=None)

Bases: Solution

load_data()
spawn_from_variable(new_selected_variable, new_data)
class fish2eod.xdmf.load.H5Solution(h5_file, parameter_levels, domain_map, variables, data, s_param=(), s_var=None)

Bases: Solution

Store the solution or filtered subset.

A solution is a collection of datasets. This can be filtered on parameter or variable. Once subset further processing sub setting is needed until a single solution remains

Parameters:

  • h5_file (Path) – Path to the h5 data set

  • parameter_levels (Dict[str, Tuple[int]]) – Dictionary of parameter : levels of parameter

  • variables (Tuple[str]) – Possible variables

  • data (List[DataSet]) – List of DataSet objects

  • s_param (Tuple[str, ...]) – List of selected_parameters if any else None

  • s_var (Optional[str]) – Selected variable if selected else None

filter_parameters(parameter, value)

Filter the solution where parameter = value.

Parameters:

  • parameter (str) – Name of the parameter

  • value (str) – String of selected parameter index

Return type:

H5Solution

Returns:

Filtered solution

load_data()

Load data.

Checks if loadable i.e. no other parameters or variables to select Loads either a namedtuple for misc data or a tuple of arrays for fem dataset

Returns:

Loaded data

property parameters: Tuple[str]

Get the parameter names.

Return type:

Tuple[str]

Returns:

Tuple of parameter names - no particular order

spawn_from_variable(new_selected_variable, new_data)
class fish2eod.xdmf.load.Solution

Bases: object

filter_variables(variable)

Extract the variable from the solution.

Parameters:

variable (str) – Name of the variable

Return type:

Solution

Returns:

Filtered solution

abstract load_data()
abstract spawn_from_variable(new_selected_variable, new_data)
fish2eod.xdmf.load.domain_map_from_data(path)

Extract the domain map from the data.

TODO duplication in constant map across time steps

Parameters:

path (Path) – Path to the manifest

Return type:

Dict[str, int]

Returns:

Map of domains name to number

fish2eod.xdmf.load.extract_all_data(path)

Load data from each xdmf file.

Parameters:

path (Path) – Path to manifest

Return type:

Iterator[DataSet]

Returns:

Iterator of DataSets

fish2eod.xdmf.load.extract_path_from_grid(grid, parent)

Extract h5 data paths from the grid.

Parameters:

  • grid – The grid to search (et.Element)

  • parent (str) – The parent to get paths of (Attribute for example for data)

Return type:

Iterator[Tuple[str, Optional[str]]]

Returns:

Sequence of child paths and the name of the dataset or None if not available

fish2eod.xdmf.load.extract_unique_from_grid(grid, term)

Extract a unique term from the grid.

A unique term like <Time /> or <Metadata /> only is entered once per grid

Parameters:

  • grid – The grid (et.Element) to search

  • term (str) – The term to search for

Return type:

Dict[str, Any]

Returns:

The attributes of the found element

fish2eod.xdmf.load.find_manifest(path, search_name='manifest.xml')

Find the manifest file in the given path.

Since the path can be specified as either the path to the manifest or the containing directory this will check if the specified path is the manifest or if the folder given contains the manifest.

Parameters:

  • path (Union[str, Path]) – Path to manifest or search path

  • search_name – Name of file to search for

Return type:

Path

Returns:

Path to the manifest

fish2eod.xdmf.load.load_fem_data(h5_file, data_set)

Load fem data from the h5 file.

FEM data is a topology, geometry and an array representation of function TODO named tuple

Parameters:

  • h5_file (Path) – Path to the h5 file

  • data_set (DataSet) – DataSet to load

Return type:

Tuple[ndarray, ...]

Returns:

The tuple of data topology, geometry, data

fish2eod.xdmf.load.load_from_file(path)

User-facing api to load the data.

Parameters:

path (Union[str, Path]) – Path to manifest.xml or the model folder

Return type:

H5Solution

Returns:

The Solution object

fish2eod.xdmf.load.load_from_h5(h5_file, *data_paths)

Load data from the h5_file with a sequence of paths.

Nx1 data is converted to an array of length N and unsignedintegers are converted to signed integers

Parameters:

  • h5_file (Path) – Path to the h5 file

  • data_paths (str) – Arbitrary number of data_paths to load

Return type:

Iterator[ndarray]

Returns:

Iterator of arrays for each data_path

fish2eod.xdmf.load.load_misc_data(h5_file, data_set)

Load misc data from the h5 file.

Parameters:

  • h5_file (Path) – Path to the h5 file

  • data_set (DataSet) – DataSet to load

Return type:

Tuple

Returns:

The misc_data in its named tuple

fish2eod.xdmf.load.load_xdmf(xdmf_file)

Load an xdmf file.

Parameters:

xdmf_file (Path) – The path to the xdmf file

Return type:

Iterator[DataSet]

Returns:

Sequence of DataSet objects

fish2eod.xdmf.load.misc_attribute_to_data_set(grid)

Return data_set compatible structure from misc attributes.

The goal is for each (super) attribute to have a structure ([(sub_attr1, path1), …], name_of_super_attribute, …) where each super attribute behaves like a normal attribute and the path with be a list of subpaths and subnames

Parameters:

grid – Grid to convert (et.Element)

Return type:

Iterator[Tuple[List, str]]

Returns:

Structured misc data

fish2eod.xdmf.load.parameter_levels_from_data(path)

Extract all parameter levels (and parameters) from a dataset.

Parameters:

path (Path) – Path to the manifest

Return type:

Dict[str, Tuple[int]]

Returns:

Parameters and corresponding levels

fish2eod.xdmf.load.parse_manifest(manifest)

Parse the xdmf/h5 files from the manifest.

Parameters:

manifest (Path) – Manifest path

Return type:

Tuple[Iterator[Path], Path]

Returns:

The xdmf paths and the h5 file

fish2eod.xdmf.load.variables_from_data(path)

Extract all the variables from a dataset.

Parameters:

path (Path) – Path to the manifest

Return type:

Tuple[str, ...]

Returns:

Variable names

fish2eod.xdmf.save module

Save solutions to an expandable structure.

Saves 1D data I.e. function defined on boundaries and 2D data I.e. function defined on domains/cells and misc data (see later)

There is one manifest file which stores the the locations of the different data types which are stored in separate XDMF(ish) files for paraview compatibility (not strictly XDMF as they contain additional tags but could be considered a superset of XDMF).

# <Manifest> # <data type=’1d’ path=”PATH_TO_1D_DATA.xdmf”/> # <data type=’2d’ path=”PATH_TO_2D_DATA.xdmf”/> # <data type=’misc’ path=”PATH_TO_misc.xdmf”/> # <h5 path=”PATH_TO_h5_file.h5”/> # </Manifest>

1D dataset contains boundary functions

The XDMF tag contains a domain containing a grid which specifies a “set of parameters” with each parameter being stored in a nested grid tag. Within a simulation the topology (what connects to what) and the geometry (where was is) and the is stored in topology and geometry tags with the function defined on the Attribute tag

# <!DOCTYPE Xdmf SYSTEM “Xdmf.dtd” []> # <Xdmf xmlns:xi=”http://www.w3.org/2001/XInclude” Version=”3.0”> # <Domain> # <Grid Name=”TimeSeries” GridType=”Collection” CollectionType=”Temporal”> # <Grid Name=”mesh” GridType=”Uniform”> # <Time Value=”0”/> # <Metadata TimeName=”ParaViewTime” step=”0” location=”0” amp=”0”/> # <Topology NumberOfElements=”173” TopologyType=”PolyLine” NodesPerElement=”2”> # <DataItem Dimensions=”173 2” NumberType=”UInt” Format=”HDF”>MODEL.h5:/Mesh/2/mesh/edges</DataItem> # </Topology> # <Geometry GeometryType=”XY”> # <DataItem Dimensions=”62 2” Format=”HDF”>MODEL.h5:/Mesh/1/mesh/geometry</DataItem> # </Geometry> # <Attribute Name=”boundary” AttributeType=”Scalar” Center=”Cell”> # <DataItem Dimensions=”173 1” Format=”HDF”>MODEL.h5:/VisualisationVector/3</DataItem> # </Attribute> # </Grid> # </domain> # </Xdmf>

2D dataset contains domain/cell functions

The XDMF tag contains a domain containing a grid which specifies a “set of parameters” with each parameter being stored in a nested grid tag. Within a simulation the topology (what connects to what) and the geometry (where was is) and the is stored in topology and geometry tags with the function defined on the Attribute tag

# <!DOCTYPE Xdmf SYSTEM “Xdmf.dtd” []> # <Xdmf xmlns:xi=”http://www.w3.org/2001/XInclude” Version=”3.0”> # <Domain> # <Grid Name=”mesh” GridType=”Uniform”> # <Time Value=”0”/> # <Metadata TimeName=”ParaViewTime” step=”0” location=”0” amp=”0”/> # <Topology NumberOfElements=”114” TopologyType=”Triangle” NodesPerElement=”3”> # <DataItem Dimensions=”114 3” NumberType=”UInt” Format=”HDF”>MODEL.h5:/Mesh/0/mesh/topology</DataItem> # </Topology> # <Geometry GeometryType=”XY”> # <DataItem Dimensions=”62 2” Format=”HDF”>MODEL.h5:/Mesh/1/mesh/geometry</DataItem> # </Geometry> # <Attribute Name=”V” AttributeType=”Scalar” Center=”Node”> # <DataItem Dimensions=”62 1” Format=”HDF”>MODEL.h5:/VisualisationVector/5</DataItem> # </Attribute> # <Attribute Name=”sigma” AttributeType=”Scalar” Center=”Node”> # <DataItem Dimensions=”62 1” Format=”HDF”>MODEL.h5:/VisualisationVector/6</DataItem> # </Attribute> # <Attribute Name=”domain” AttributeType=”Scalar” Center=”Cell”> # <DataItem Dimensions=”114 1” Format=”HDF”>MODEL.h5:/VisualisationVector/7</DataItem> # </Attribute> # </Grid> # </domain> # </Xdmf>

class fish2eod.xdmf.save.Saver(model_name, save_path)

Bases: object

Saves relevant data from a model into paraview-compatible set of xdmf files.

Parameters:

  • model_name (str) – Name of the model

  • save_path (Union[Path, str]) – Path to save the model to (model will be saves to save_path/model_name)

add_data(f)

Add the dataset to the h5 file and the reference it in the XDMF file.

If the data f is a tuple of misc data its passed to add_misc_data otherwise its passed to add_fencis_data

Parameters:

f – Data to save Meshfunction/function/tuple

Return type:

None

add_fenics_data(f)

Add the dataset to the h5 file and the reference it in the XDMF file.

If the data f is a tuple of misc data its passed to add_misc_data otherwise its passed to add_fencis_data

Parameters:

f – Data to save Meshfunction/function

Return type:

None

add_misc_data(d)

Add the miscellaneous data to the xdmf and the h5 file.

Misc data is treated separately because for each data structure there is an outer Attribute which holds a collection of data sets from d (namedtuple)

Parameters:

d – Miscelaneous data container, must be a namedtuple

Return type:

None

Returns:

None

create_next_grid(num_topology_elements_1d=None, num_topology_elements_2d=None, num_geometry_elements=None, metadata=None, domain_map=None)

Create grid for a the next step for the 1d and 2d xdmf files.

Creates the grid and assigns them as a pointer in current_grid_1d and current_grid_2d attributes

# TODO refactor the duplication out of this function. Any loop right now will be awkward

Parameters:

  • num_geometry_elements – Number of elements in the geometry (number of nodes)

  • num_topology_elements_1d – Number of elements in the 1d topology (lines)

  • num_topology_elements_2d – Number of elements in the 2d topology (triangles)

  • metadata – Metadata dictionary

property geometry_path: str

H5 path for the geometry arrays (/Geometry/step).

Return type:

str

save()

Save the XDMF files.

Because XDMF are so small - this overwrites the entire XDMF file with the new data: which is the old data + new

save_model(model, metadata=None)

Save the specified model to an XDMF representation.

Parameters:

  • model (Model) – The model to save

  • metadata – Metadata (parameter states) to save along with the data

property topology_path_1d: str

H5 path for the 1d topology arrays (/Topology/1d/step).

Return type:

str

property topology_path_2d: str

H5 path for the 2d topology arrays (/Topology/2d/step).

Return type:

str

write_geometry(geometry)

Write the geometry (coordinates) to the h5 file.

Parameters:

geometry (ndarray) – Array of x,y coordinates for the geometry

Return type:

None

write_h5(path, d)

Write to the h5 file.

Parameters:

  • path (str) – Internal h5 path to write to

  • d (ndarray) – Dataset to write

write_topology(topology)

Write the topology to the dimension appropriate h5 file path.

Parameters:

topology (ndarray) – Array of topology

Return type:

None

fish2eod.xdmf.xml_tools module

Common tools for working with XDMF/XML files.

fish2eod.xdmf.xml_tools.create_minimal_xdmf()

Create the minimal XDMF template.

Most of these properties are necessary for Paraview compatibility. Some may not be required but they’re used in the Fenics XDMF files.

fish2eod.xdmf.xml_tools.create_timestep_grid(*, step_number, num_topology_elements, dim, data_location_topology, num_geometry_elements, data_location_geometry, metadata, domain_map)

Create the inner grid defining a time-step.

This function has many inputs which must be specified as keywords. Additionally they must all be specified non-None type. The assert_all_defined decorator ensures this.

Parameters:

  • step_number – Current iteration of the model. Paraview will plot in this order

  • num_topology_elements – Number of elements in the Topology

  • dim – Dimension of the data

  • data_location_topology – h5 location of the Topology

  • num_geometry_elements – Number of elements in the geometry

  • data_location_geometry – h5 location of the geometry

  • metadata – Dictionary of parameter_name:value to be saved along with the simulation

Returns:

Inner grid (et.Element)

fish2eod.xdmf.xml_tools.create_timestep_grid_misc(*, step_number, metadata, domain_map)

Create the grid for a “time-step” in the miscellaneous data-set.

Time step refers to an individual simulation which could be time or some parameter sweep Typical parameters like topology and dimension are not specified due to miscellaneous dataset.

Parameters:

  • step_number – Current iteration of the model. Paraview will plot in this order

  • metadata – Dictionary of parameter_name:value to be saved along with the simulation

Returns:

Newly created grid (et.Element)

fish2eod.xdmf.xml_tools.get_outer_grid(xdmf, parent_tag='Domain')

Get the outer grid element from the XDMF structure.

Parameters:

  • xdmf – The xdmf structure to parse (et.Element)

  • parent_tag – The name of the domain tag (parent)

fish2eod.xdmf.xml_tools.make_geometry(num_elements, location)

Create the XDMF geometry element.

Parameters:

  • num_elements (int) – Number of elements in the geometry (# nodes)

  • location (str) – Location of the geometry in the h5 file

Returns:

The geometry element (et.Element)

fish2eod.xdmf.xml_tools.make_manifest_file(model_name, save_path, data_folder='DATA')

Create the manifest file.

The manifest file holds the paths to the 1d, 2d, misc data as well as the path to the h5 file

Parameters:

  • model_name (str) – Name of the model

  • save_path (Path) – Path of parent folder of the model

  • data_folder – Optional argument specifying name of the sub-folder containing the data

Return type:

None

Returns:

None

fish2eod.xdmf.xml_tools.make_topology(num_elements, dim, location)

Create the XDMF topology element.

Parameters:

  • num_elements (int) – Number of elements in the topology (# triangles/lines)

  • dim (int) – Dimension of the solution

  • location (str) – Location of the topology in the h5 file

Returns:

The topology element (et.Element)

fish2eod.xdmf.xml_tools.write_xml(save_path, xml_obj, xml_declaration=True, doctype=None)

Write an ElementTree object to an xml/xdmf file.

Parameters:

  • save_path (Path) – Path to save the file to

  • xml_obj – The ElementTree to save

  • xml_declaration – Include XML declaration

  • doctype – Optional doctype for XDMF files (None for no doctype)

Return type:

None

Returns:

None