InterpolateXDMF API reference documentation!

InterpolateXDMF is a python package for easy accessing XDMF/HDF5 files as outputed by Finite Element software like OpenGeoSys. It uses the VTK python wrapper and linear interpolation between time steps and grid points access any points in and and time within the simulation domain.

Copyright (c) 2012-2022, OpenGeoSys Community (http://www.opengeosys.org)
Distributed under a Modified BSD License.

See accompanying file LICENSE or http://www.opengeosys.org/project/license

class InterpolateXDMF.InterpolateXDMF.VTUIOObject(obj, points, h5_data, nneighbors=20, dim=3, one_d_axis=0, two_d_planenormal=2, interpolation_backend='scipy')

Bases: VTUIO

delete_cell_field()

delete cell field(s) and write data to disk

Parameters:

  • fieldnames (str or list) –

  • ofilename (str) –

delete_point_field()

delete point field(s) and write data to disk

Parameters:

  • fieldnames (str or list) –

  • ofilename (str) –

func_to_field()

Add a field to the vtu file (which will be saved directly as “ofilename” by providing a three argument function(x,y,z)

Parameters:

  • function (function) –

  • fieldname (str) –

  • ofilename (str) –

  • cell (bool) –

func_to_m_dim_field()

Add a multidimensional field to the vtu file (which will be saved directly as “ofilename” by providing am array of three argument functions.

Parameters:

  • functionarray (array of objects) –

  • fieldname (str) –

  • ofilename (str) –

get_cell_field(fieldname)

Return vtu point field as numpy array.

Parameters:

fieldname (str) –

get_cell_field_names()

Get names of all cell fields in the vtu file.

get_point_field(fieldname)

Return vtu cell field as numpy array.

Parameters:

fieldname (str) –

get_point_field_names()

Get names of all point fields in the vtu file.

point_data_to_cell_data()

convert pointdata to cell data of field “fieldname”

Parameters:

  • fieldname (str) –

  • ofilename (str) –

write()

Write data as file “filename”.

Parameters:

filename (str) –

write_cell_field()

Write a field (numpy array of correct size) to field “fieldname” as file “ofilename”.

Parameters:

  • field (array) –

  • fieldname (str) –

  • ofilename (str) –

write_point_field()

Write a field (numpy array of correct size) to field “fieldname” as file “ofilename”.

Parameters:

  • field (array) –

  • fieldname (str) –

  • ofilename (str) –

class InterpolateXDMF.InterpolateXDMF.XDMFReader(filename, nneighbors=20, dim=3, one_d_axis=0, two_d_planenormal=2, interpolation_backend='scipy')

Bases: object

Interface for XDMF data

Parameters:

  • filename (str) –

  • nneighbors (int, optional) – default: 20

  • dim (int, optional) – default: 3

  • one_d_axis (int) – between 0 and 2, default: 0

  • two_d_planenormal (int) – between 0 and 2, default: 2

  • interpolation_backend (str) – scipy or vtk

property cell_center_points

Method for obtaining cell center points

property data_arrays
get_cell_field(fieldname, timestep=0)

Return vtu cell field as numpy array.

Parameters:

  • fieldname (str) –

  • timestep (int) –

get_cell_field_names(timestep=0)

Get names of all cell fields in the vtu file. :param timestep: default: 0 :type timestep: int, optional

get_point_field(fieldname, timestep=0)

Return vtu point field as numpy array.

Parameters:

  • fieldname (str) –

  • timestep (int) –

get_point_field_names(timestep=0)

Get names of all point fields in the vtu file.

Parameters:

timestep (int, optional) – default: 0

property header
read_aggregate(fieldname, agg_fct, data_type='point', pointsetarray=None)

Return time series data of an aggregate function for field “fieldname”.

Parameters:

  • fieldname (str or list) –

  • agg_fct (str,) – can be: “min”, “max” or “mean”

  • data_type (str optional) – “point” or “cell”

  • pointsetarray (str, list or numpy.ndarray) – defines a submesh if str pointsetarray is construed as filename containing the mesh

read_set_data(time, fieldname, pointsetarray=None, data_type='point', interpolation_method='linear')

Get data of field “fieldname” at time “time” alon a given “pointsetarray”.

Parameters:

  • time (float) –

  • fieldname (str) –

  • pointsetarray (list, numpy.ndarray or str) – containing a list of 3-tuples

  • interpolation_method (str) – default: ‘linear’

read_time_series(fieldname, pts=None, data_type='point', interpolation_method='linear')

Return time series data of field “fieldname” at points pts. Also a list of fieldnames can be provided as “fieldname”

Parameters:

  • fieldname (str) –

  • pts (dict, optional) –

  • data_type (str optional) – “point” or “cell”

  • interpolation_method (str, optional) – default: ‘linear

read_time_slice(time, fieldname)

Print field “fieldname” at time “time”.

Parameters:

  • time (float) –

  • fieldname (str) –

write_pvd(filename)

Writes data to PVD/VTU

Parameters:

filename (str) –

Indices and tables