VTUinterface API reference documentation!

VTUinterface is a python package for easy accessing VTU/PVD 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 VTUinterface.vtuIO.PVDIO(filename, nneighbors=20, dim=3, one_d_axis=0, two_d_planenormal=2, interpolation_backend=None)

Bases: object

Class for handling I/O of PVD files

Parameters:

  • filename (str) –

  • nneighbors (int, optional) –

  • dim (int) –

  • 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

append(filename, vtu_rename=False)

appends entries from another PVD file

Parameters:

  • filename (str) –

  • vtu_rename (bool) –

clear_pvd_path(write=True)

Delete relative and absolute directory paths in the vtu filenames of the PVD file.

Parameters:

write (bool) –

static create_pvd_from_pattern(filename, pattern='')
delete_cell_field(fieldnames=None)

delete cell field(s) and write data to disk

Parameters:

fieldnames (str or list) – if None all fields will be deleted

delete_integration_point_field(fieldnames=None, skip_last=False)

delete integration point field(s) and write data to disk

Parameters:

  • fieldnames (str or list) – if None all fields will be deleted

  • skip_last (boolean) –

delete_point_field(fieldnames=None)

delete point field(s) and write data to disk

Parameters:

fieldnames (str or list) – if None all fields will be deleted

get_cell_field_names()

Get names of all cell fields in the vtu file.

get_integration_point_field_names()

Get names of integration point fields in the vtu file.

get_point_field_names()

Get names of all point fields in the vtu file.

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_pvd(filename)

Read in PVD file

Parameters:

filename (str) –

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

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

Parameters:

  • time (float) –

  • fieldname (str) –

  • pointsetarray (list, numpy.ndarray or str) – if str, pointsetarray is construed as a filename of a submesh

  • interpolation_method (str) – default: ‘linear’

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

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) –

rename(newname)

Rename PVD file

Parameters:

newname (str) –

write_prj(filename)

exports input data (if available) as OGS project files

Parameters:

filename (str) –

write_xdmf(filename)

exports data as XDMF/HDF

Parameters:

filename (str) –

class VTUinterface.vtuIO.VTUIO(filename, nneighbors=20, dim=3, one_d_axis=0, two_d_planenormal=2, interpolation_backend=None)

Bases: object

Class for handling I/O of VTU files

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

add_cell_field(field, fieldname, ofilename, writefile=True, array_type=None, datamode=None)

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

Parameters:

  • field (array) –

  • fieldname (str) –

  • ofilename (str) –

  • writefile (bool) –

  • array_type (vtk array type) –

  • datamode (str) –

add_integration_point_field(field, fieldname, ofilename, writefile=True, array_type=None, datamode=None)

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

Parameters:

  • field (array) –

  • fieldname (str) –

  • ofilename (str) –

  • writefile (bool) –

  • array_type (vtk array type) –

  • datamode (str) –

add_point_field(field, fieldname, ofilename, writefile=True, array_type=None, datamode=None)

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

Parameters:

  • field (array) –

  • fieldname (str) –

  • ofilename (str) –

  • writefile (bool) –

  • array_type (vtk array type) –

  • datamode (str) –

property cell_center_points

Method for obtaining cell center points

property data_arrays
delete_cell_field(fieldnames=None, ofilename=None, writefile=True)

delete cell field(s) and write data to disk

Parameters:

  • fieldnames (str or list) – if None all fields will be deleted

  • ofilename (str) –

  • writefile (bool) –

delete_integration_point_field(fieldnames=None, ofilename=None, writefile=True)

delete integration point field(s) and write data to disk

Parameters:

  • fieldnames (str or list) – if None all fields will be deleted

  • ofilename (str) –

  • writefile (bool) –

delete_point_field(fieldnames=None, ofilename=None, writefile=True)

delete point field(s) and write data to disk

Parameters:

  • fieldnames (str or list) – if None all fields will be deleted

  • ofilename (str) –

  • writefile (bool) –

func_to_field(function, fieldname, ofilename=None, cell=False, array_type=None, writefile=True, datamode=None)

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) –

  • datamode (str) –

func_to_m_dim_field(functionarray, fieldname, ofilename=None, cell=False, array_type=None, writefile=True, datamode=None)

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_as_point_data(fieldname)

Return vtu cell field as point field.

Parameters:

fieldname (str) –

get_cell_field_names()

Get names of all cell fields in the vtu file.

get_data(fieldname, pts=None, data_type='point', interpolation_method=None)

Get data of field “fieldname” at all points specified in “pts”.

Parameters:

  • fieldname (str) –

  • pts (dict, optional) – default: {‘pt0’: (0.0,0.0,0.0)}

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

get_data_scipy(neighbors, points_interpol, fieldname, data_type='point', interpolation_method='linear')

Get interpolated data for points_interpol using neighbor points.

get_data_vtk(points_interpol, data_type='point', interpolation_method='probefilter')

Get interpolated data for points_interpol using vtks built-in interpolation methods

get_integration_point_field(fieldname)

Return integration point field.

Parameters:

fieldname (str) –

get_integration_point_field_names()

Get names of all integration point data fields in the vtu file.

get_nearest_indices(points_interpol)

Return a dictionary with closest mesh point indices

Parameters:

points_interpol (dict) –

get_nearest_points(points_interpol)

Return a dictionary with closest mesh points

Parameters:

points_interpol (dict) –

get_neighbors(points_interpol, data_type='point')

Method for obtaining neighbor points for interpolation.

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.

get_set_data(fieldname, pointsetarray=None, data_type='point', interpolation_method=None)

Get data specified in fieldname at all points specified in “pointsetarray”.

Parameters:

  • fieldname (str) –

  • pointsetarray (list, numpy.ndarray or str) – if str, pointsetarray is construed as a filename of a submesh

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

property header
point_data_to_cell_data(fieldname, ofilename=None, writefile=True, datamode=None)

convert pointdata to cell data of field “fieldname”

Parameters:

  • fieldname (str) –

  • ofilename (str) –

  • datamode (str) –

write(filename, datamode=None)

Write data as file “filename”.

Parameters:

  • filename (str) –

  • datamode (str) –

Indices and tables