open_viewmin

Contents

open_viewmin#

open-ViewMin project top-level module

Subpackages#

Submodules#

Classes#

FilterFormula

Class for reusable PyVista filters.

FilterTreePlot

PyVista Plotter with meshes organized into a "filter tree".

FilterTreePlotQt

Implement some PyVista functionality, with filter trees, in the PyVistaQt

NematicPlot

Plotter class for nematic liquid crystals visualization,

NematicPlotNoQt

Plotter class for nematic liquid crystals visualization, with the

WidgetFormula

Class for creating re-usable widgets

Package Contents#

class FilterFormula(plotter, name=None, parent_mesh_name=None, filter_callable=None, filter_kwargs=None, mesh_kwargs=None, random=None, has_actor=True, in_place=False, ovm_info=None, widget_name=None, apply_upon_creation=True, children=None, colorbar=None, **extra_filter_kwargs)#

Class for reusable PyVista filters.

Parameters:

  • plotter (FilterTreePlot) – Parent plotter

  • name (str or None) – Name of filter formula and its mesh. Pass None to default to plotter’s default mesh name.

  • parent_mesh_name (str or None) – Name of parent mesh. Pass None to default to plotter’s default mesh name.

  • filter_callable (callable(), str, or None) – Function of parent mesh that returns a callable, which when called applies a filter to (re-)create a child mesh. Pass None to use an “identity filter”, making the parent its own child.

  • filter_kwargs (dict or None, optional) – Dictionary of keyword arguments supplied to the function returned by filter_callable. None is equivalent to dict().

  • mesh_kwargs (dict or None, optional) – Dictionary of keyword arguments to pyvista.Plotter.add_mesh for customization of mesh visualization. None is equivalent to dict().

  • random (bool or None, optional) – Whether to use random sampling, if applicable.

  • has_actor (bool, optional) – Whether to create an actor visualizing the mesh.

  • in_place (bool, optional) – Whether to modify a mesh in-place rather than creating a child mesh.

  • ovm_info (dict or None) – Dictionary of keyword arguments for ad-hoc purposes. None is equivalent to dict().

  • widget_name (str or None) – Name of widget, if applicable, that creates this filter formula

  • apply_upon_creation (bool, optional) – Whether to apply the filter formula, creating its mesh, immediately upon creating the filter formula.

  • children (list of str, or None, optional) – List of names of child meshes. None is equivalent to [].

  • colorbar (VTK scalar bar actor or None, optional) – Existing colorbar actor, if applicable.

  • **extra_filter_kwargs (dict, optional) – Extra keyword arguments to append to filter_kwargs (for convenience).

__getitem__(key)#

Access mesh’s datasets in dictionary-like manner

__repr__()#

Print keyword arguments to FilterFormula and their current values

Return type:

str

__setitem__(key, set_to)#

Set mesh’s datasets in dictionary-like manner

_inherit(filter_kwarg)#

If this FilterFormula has no value currently assigned to filter_kwarg, try to inherit the value from an ancestor FilterFormula

Parameters:

filter_kwarg (str)

Return type:

inherited_filter_keyword_argument

_interpret_color_or_scalars(mesh_kwargs)#

Check if mesh coloring should be updated as a solid color or color array.

Parameters:

mesh_kwargs (dict) – Mesh visualizing settings

Returns:

Whether to update solid color, whether to update color array, and mesh visualizing settings dictionary

Return type:

(bool, bool, dict)

_remove_bad_mesh_kwargs(mesh_kwargs)#

Remove unexpected keyword arguments to pyvista.Plotter.add_mesh

Parameters:

mesh_kwargs (dict) – Mesh visualization settings

Returns:

Mesh visualization settings with bad keyword arguments removed

Return type:

dict

_update_actor_color_array()#

Visualize mesh with color array

_update_actor_solid_color()#

Visualize mesh with solid color

add_calculation(name, calc_callable)#

Create a data array for this mesh that is recalculated whenever the mesh is updated. The function accomplishing this is added to the FilterFormula’s do_after_update list.

Example: If we have a NematicPlot p, with a glyphs filter_formula called “director”, the following creates a scalar data array holding the normal component of the “director” orientation field.

>>> p["director"].add_calculation("normal_component", lambda a: np.inner(a.orientations, a.normal))

Equivalently, you can assign calc_callable as the value corresponding to key name:

>>> p["director"]["normal_component"] = lambda a: np.inner(a.orientations, a.normal)
Parameters:

  • name (str)

  • calc_callable (callable()) – Function mapping filter_formula to calculated data array.

add_filter(filter_callable, **kwargs)#

Create a callable that returns a filter formula whose parent mesh is this formula’s child mesh

Used for dictionary-style assignment of new filter formula to plotter.

Parameters:

  • filter_callable (callable()) – Function mapping new mesh name to new filter formula

  • kwargs (dict, optional) – Keyword arguments to FilterFormula

Return type:

callable()

add_glyphs(**kwargs)#

Create a glyphs child filter formula

Parameters:

kwargs (dict, optional)

Returns:

Function of new mesh name; adds glyphs filter formula

Return type:

callable()

color_by_active_scalars(categories=None)#

Set mesh’s color array to most recently used scalar dataset

Parameters:

categories (bool, optional)

get_auto_color()#

Get next color in plotter’s color sequence

Returns:

color rgb values

Return type:

tuple(float)

get_centroids(num_centroids=10, ref_pt_idx=0, mesh_name_to_probe=None)#

Add centroids filter formula

Child filter formula probes a given mesh at centroids calculated from the points of this filter formula’s mesh.

Parameters:

  • num_centroids (int, optional) – Number of centroids

  • ref_pt_idx (int, optional) – Index of starting point for calculating centroids

  • mesh_name_to_probe (str or None, optional) – Name of mesh to probe (source of datasets). Pass None to default to self.plotter.default_mesh_name.

Returns:

Name of sampled (child) mesh

Return type:

str

get_circuits(mesh_to_probe_name=None, normals_name=None, radius=3, n_samples=100, use_ints=False)#

Add circuits filter formula

Parameters:

  • mesh_to_probe_name (str) – Name of mesh to probe

  • normals_name (str or None, optional) – Name of vectors dataset defined on mesh_of_circuit_centers to be used as normal directions to circuits. Pass None to default to name of active_vectors dataset of parent mesh.

  • radius (float, optional) – Radius of each circuit

  • n_samples (int, optional) – Number of circuits

  • use_ints (bool, optional) – Whether to round coordinates of circuit points to integers

Returns:

Name of sampled (child) mesh, or None if no child mesh was created.

Return type:

str or None

get_eigenvec(tensors_name=None, evec_idx=-1, new_dataset_name=None)#

Calculate an eigenvector of symmetric second-rank tensor dataset

Parameters:

  • tensors_name (str or None, optional) – Name of symmetric rank-2 tensors dataset. Pass None to default to name of most recently created symmetric rank-2 tensors dataset.

  • evec_idx (int, optional) – Index of eigenvector to take, ordered by ascending eigenvalues

  • new_dataset_name (str or None) – Name of vector dataset storing eigenvector. Pass None to default to “_eigenvec” appended to tensors_name.

Return type:

numpy.ndarray

give_colorbar_unique_title()#

Check if color bar lacks a title, and assign one if so

Returns:

Color bar title

Return type:

str

static handle_filter_or_numpy(filter_result, parent_mesh, filter_name)#

Properly handle filter results that may be mesh or array

If the filter result is an array, assigns the filter result as a new dataset on a copy of the parent mesh.

Parameters:

  • filter_result (pyvista.dataset or numpy.ndarray) – Result of filter

  • parent_mesh (pyvista.dataset) – Parent mesh

  • filter_name (str) – Name for new dataset in case filter_result is an array.

Returns:

New child mesh

Return type:

pyvista.dataset

hide()#

Make mesh’s actor invisible

static identity_callable(mesh)#

Get a filter formula callable that simply copies the parent mesh

Parameters:

mesh (pyvista.dataset)

Return type:

callable()

make_sure_parent_knows_about_me()#

Make sure that this filter formula’s name is in the parent mesh filter formula’s list of children

remove_child_relationship_to_all_parents()#

Cause any meshes claiming this mesh as a child to forget that relationship, a prerequisite for deleting this mesh.

remove_colorbar()#

Remove color bar for this filter formula’s mesh

set(**mesh_kwargs)#

Shorthand for update_actor()

Parameters:

**mesh_kwargs – New or modified keyword arguments to pyvista.Plotter.add_mesh

Returns:

Updated actor

Return type:

vtkmodules.vtkRenderingOpenGL2.vtkOpenGLActor

set_glyph_shape(new_shape, **geom_args)#

Modify shape of glyphs

Parameters:

  • new_shape (str) – Shape name

  • geom_args (dict, optional) – Keyword arguments for shape

set_glyphs_scale(new_scale)#

Set global scale factor for glyphs

Parameters:

new_scale (float) – New scale factor

set_glyphs_stride(new_stride)#

Set spacing between glyphs

Parameters:

new_stride (int) – New spacing

static string_to_filter(filter_string)#

Convert filter name to callable

Convert string name of PyVista filter to a callable that produces that filter. If the argument is not a string, return the argument (for cases where the filter callable is passed rather than its string name).

Parameters:

filter_string (str or object)

Returns:

  • callable() – Function mapping existing mesh to a new mesh via the named filter.

  • object – If filter_string is not a string, returns filter_string

update(update_actor=True, ovm_info=None, **filter_kwargs)#

Update a mesh by calling its creator filter

Parameters:

  • update_actor (bool, optional) – Whether to update the actor visualizing the mesh

  • ovm_info (dict or None, optional) – New or modified items for mesh settings dictionary

  • **filter_kwargs – New or modified keyword arguments for filter callable

Returns:

Updated child mesh

Return type:

pyvista.dataset

update_actor(is_new=False, **mesh_kwargs)#

Update or create mesh visualizing actor

Parameters:

  • is_new (bool, optional) – Whether actor has just been created (to avoid duplicate warnings)

  • mesh_kwargs (dict, optional) – New or modified keyword arguments to pyvista.Plotter.add_mesh

Returns:

Updated actor

Return type:

vtkmodules.vtkRenderingOpenGL2.vtkOpenGLActor

update_children()#

Update child meshes

Calls update function of each filter formula named in self.children

_allowed_args_to_add_mesh#
property array_names#
Get mesh's dataset names
Return type:

list[str]

colorbar#
do_after_update = []#
filter_kwargs#
has_actor#
in_place#
property is_filter_tree_root#
Check whether mesh is a root of the filter tree
Return type:

bool

property is_glyphs#
Check whether mesh is glyphs
Return type:

bool

property mesh#
Get child mesh
Return type:

pyvista.dataset

mesh_kwargs#
property normal#
Normal vector to plane
Return type:

numpy.ndarray

property orientations#
Get orientations data array for glyphs; `None` for non-glyphs
property origin#
Origin of plane
Return type:

numpy.ndarray

ovm_info#
property parent_filter_formula#
Get parent mesh's filter formula
Return type:

FilterFormula

property parent_mesh#
Get parent mesh
Return type:

pyvista.dataset

parent_mesh_name#
plotter#
property points#
Get mesh's points
Return type:

numpy.ndarray

property random#
Check whether random sampling has been selected
Return type:

bool

property root_ancestor#
root (possibly self) of filter tree from which this filter formula
property descends#
widget_name#
class FilterTreePlot(filenames=None, user_settings=None, theme=None, reader=ovm_utilities.fast_import, dims=None, data_stride=1, **kwargs)#

Bases: pyvista.Plotter

PyVista Plotter with meshes organized into a “filter tree”.

Updates to any mesh are automatically followed by updates to its child meshes and actors, recursively.

Parameters:

  • filenames (list[str], str, or None, optional) – Files to import.

  • user_settings (dict or None, optional) – Customizations to default plotter settings.

  • theme (['dark' | 'document' | 'paraview' | None], optional) – PyVista plot theme

  • reader (callable()) – Function to import and process data files

  • dims (tuple of ints or None, optional) – System dimensions used if no filenames are given.

  • data_stride (int, optional) – Spacing between grid sites used if no filenames are given.

  • kwargs (dict, optional) – Keyword arguments to pyvista.Plotter()

__getitem__(mesh_name)#

Mimic dictionary key-value behavior for mesh names and meshes.

Parameters:

mesh_name (str)

Return type:

FilterFormula

__repr__()#

Represent plotter as a textual representation of its filters tree.

Returns:

Textual representation of filters tree.

Return type:

str

__setitem__(mesh_name, filter_formula_lambda)#

Mimic dictionary key-value behavior for mesh names and meshes.

Parameters:

  • mesh_name (str)

  • filter_formula_lambda (callable()) – Callable that creates filter formula

Return type:

FilterFormula

_add_checkbox_generic(callback, current_val, size=50, position=None, color_on=None, **kwargs)#

Add checkbox

Parameters:

  • callback (callable)

  • current_val (bool)

  • size (int)

  • position (tuple(float), optional)

  • color_on (pyvista.plotting.colors.Color, optional)

  • kwargs – keyword arguments to :meth:pyvista.Plotter.add_checkbox_button_widget

_add_inplot_slider(callback, mesh_name, current_val=None, min_val=None, max_val=None, title=None, title_height=0.03, style='classic', label_height=0.03, pointa=None, pointb=None, loc='top right', **kwargs)#
Parameters:

  • callback (callable)

  • mesh_name (str)

  • current_val (float, optional)

  • min_val (float, optional)

  • max_val (float, optional)

  • title (str, optional)

  • title_height (float, optional)

  • style (str, optional) – Options in pyvista.global_theme.slider_styles

  • label_height (float)

  • pointa (tuple(float), optional)

  • pointb (tuple(float), optional)

  • loc (str, optional) – Slider location by keyword; options are “top left”, “bottom left”, “bottom right”. If any other string or None is given, slider is positioned in top right.

  • kwargs – keyword arguments to pyvista.Plotter.add_slider_widget()

Return type:

vtk.vtkSliderWidget

_set_pyvista_plotter_properties()#

Initialization choices for PyVista Plotter

_visibility_callback(actor_name)#
actor_names()#

Names of all actors in filters tree.

Returns:

List of actor names.

Return type:

list[str]

add_axes()#

Add x,y,z axes widget.

add_filter_formula(name=None, **kwargs)#

Add a filter formula to the plotter.

Parameters:

  • name (str or None, optional) – Name of new mesh. Pass None to do nothing.

  • **kwargs – Keyword arguments to FilterFormula

Returns:

New child mesh created by filter formula, or None if no filter formula was created.

Return type:

pyvista.dataset or None

add_isosurface_slider(mesh_name, min_val=None, max_val=None, title=None, title_height=0.02, style='classic', label_height=0.02, pointa=None, pointb=None, loc='top right', **kwargs)#

Add isosurface slider

Parameters:

  • mesh_name (str)

  • min_val (float, optional)

  • max_val (float, optional)

  • title (str, optional)

  • title_height (float)

  • style (str, optional) – Options in pyvista.global_theme.slider_styles

  • label_height (float, optional)

  • pointa (tuple(float), optional)

  • pointb (tuple(float), optional)

  • loc (str, optional) – Slider location by keyword; options are “top left”, “bottom left”, “bottom right”. If any other string or None is given, slider is positioned in top right.

  • kwargs – keyword arguments to _add_inplot_slider()

Return type:

vtk.vtkSliderWidget

add_plane_widget(*args, **kwargs)#

Overload add_plane_widget to take a string argument as name of mesh controlled by widget.

Parameters:

  • *args (tuple, optional)

  • **kwargs (dict, optional)

Return type:

vtkmodules.vtkInteractionWidgets.vtkImplicitPlaneWidget

add_root_mesh(mesh, mesh_name='fullmesh')#

Add a filter formula as a new root of the filter tree.

Parameters:

  • mesh (pyvista.DataSet) – PyVista mesh

  • mesh_name (str, optional) – Name of the new root mesh.

Returns:

Name of the new root mesh (possibly altered to avoid overwriting existing mesh names).

Return type:

str

add_threshold_slider(mesh_name, min_val=None, max_val=None, title=None, title_height=0.02, style='classic', label_height=0.02, pointa=None, pointb=None, loc='top right', **kwargs)#

Add slider for threshold

Parameters:

  • mesh_name (str)

  • min_val (float, optional)

  • max_val (float, optional)

  • title (str, optional)

  • title_height (float, optional)

  • style (str, optional) – Options in pyvista.global_theme.slider_styles

  • label_height (float, optional)

  • pointa (tuple(float), optional)

  • pointb (tuple(float), optional)

  • loc (str, optional) – Slider location by keyword; options are “top left”, “bottom left”, “bottom right”. If any other string or None is given, slider is positioned in top right.

  • kwargs – keyword arguments to _add_inplot_slider()

add_visibility_checkbox(actor_name, size=50, position=None, **kwargs)#

Add checkbox to toggle an actor’s visibility

Parameters:

  • actor_name (str)

  • size (int)

  • position (tuple(float), optional)

  • kwargs – Keyword arguments to _add_checkbox_generic()

add_widget_checkbox(widget_name, size=50, position=None, background_color='red', **kwargs)#

Add checkbox that activates/deactivates a widget

Parameters:

  • widget_name (str)

  • size (int)

  • position (tuple(float), optional)

  • background_color (str)

  • kwargs – Keyword arguments to _add_checkbox_generic()

add_widget_formula(name=None, **kwargs)#

Add a widget formula to the plotter.

Parameters:

  • name (str or None, optional) – Name of new widget. Pass None to do nothing.

  • **kwargs (dict, optional) – Keyword arguments to WidgetFormula

Returns:

The new widget formula, or None if none was created.

Return type:

WidgetFormula or None

array_dims()#

System array-size dimensions.

Returns:

(array_Lx, array_Ly, array_Lz)

Return type:

tuple(int)

assign_file_data_to_frame(file_data, filename, do_load_frame=True)#

Store data from a file as a new frame in the plotter’s timeseries data.

Parameters:

  • file_data (np.ndarray)

  • filename (str)

  • do_load_frame (bool, optional) – Whether to view the frame

colorbar_titles()#

Get titles of all scalar bars

Returns:

List of scalar bar titles

Return type:

list[str]

colorbars()#

Get list of all existing colorbars (scalar bars) for filter tree actors.

Return type:

list of VTK scalar bar actors

copy_all_actors(to_plotter)#

Copy actors to another plotter, such as for displaying in Jupyter notebooks.

Parameters:

to_plotter (pyvista.Plotter)

Return type:

None

create_fullmesh(dat=None, mesh_name='fullmesh', frame_num=None)#

Create a uniform grid mesh as a root mesh for the filter tree.

Parameters:

  • dat (np.ndarray, optional) – Data array, with first three columns holding integer coordinates X, Y, Z.

  • mesh_name (str, optional) – Name of root mesh.

  • frame_num (int or None, optional) – Frame number for this root mesh. Pass None to append as a new frame.

Returns:

Frame number and new root mesh.

Return type:

int, pyvista.dataset

dims()#

System linear dimensions.

Returns:

(Lx, Ly, Lz)

Return type:

tuple(int)

disable_eye_dome_lighting()#
disable_shadows()#
do_orbit()#

Move camera along orbit path

Removes actor named “orbit”, if it exists, before starting the motion.

enable_eye_dome_lighting()#
enable_shadows()#
extract_actors(jupyter_backend='trame')#

Set up a new PyVista plotter with a copy of all this plotter’s actors.

Parameters:

jupyter_backend (str, optional) – PyVista plotting backend. See https://docs.pyvista.org/version/stable/user-guide/themes.

Returns:

New PyVista Plotter containing this Plotter’s actors.

Return type:

pyvista.Plotter

filter_tree_roots()#

Names of meshes whose generating FilterFormula ‘s are roots of the filter tree

Return type:

list[str]

find_actor_for_scalar_bar(scalar_bar)#

Get the name of the filter tree mesh corresponding to a given scalar bar.

Parameters:

scalar_bar (VTK scalar bar actor)

Returns:

Mesh name

Return type:

str

first_frame()#

View first frame in data timeseries.

get_actor(actor_name)#

Return actor with a given name, if it exists.

Parameters:

actor_name (str) – Name of actor.

Returns:

PyVista actor.

Return type:

vtkmodules.vtkRenderingOpenGL2.vtkOpenGLActor

get_actor_name(actor)#

Given an actor, return its name.

Parameters:

actor (vtkOpenGLActor) – PyVista actor.

Returns:

Name of actor.

Return type:

str

get_filter_formula(actor_name)#

Get the formula needed to re-create an actor from its parent mesh.

Parameters:

actor_name (str) – Name of the actor.

Returns:

Actor recipe.

Return type:

types.SimpleNamespace

get_grandparent_mesh_name(actor_or_mesh_name)#

Get the name of the parent of the parent of a given actor or mesh.

Parameters:

actor_or_mesh_name (str) – Name of actor of mesh

Returns:

Name of grandparent mesh.

Return type:

str

get_mesh(mesh_name)#

Return mesh with a given name, if it exists. For non-mesh actors, return parent mesh.

Parameters:

mesh_name (str)

Returns:

PyVista mesh

Return type:

pyvista.DataSet

get_mesh_name(mesh)#

Get the name of a given mesh.

Parameters:

mesh (pyvista.DataSet)

Returns:

name of the mesh

Return type:

str

get_points()#

Get array of coordinates belonging to root mesh “fullmesh”

Returns:

Array of point coordinates.

Return type:

np.ndarray

get_widget(widget_name)#

Get widget by name

Parameters:

widget_name (str)

Return type:

vtkmodules.vtkInteractionWidgets.vtk3DWidget

get_widget_formula(widget_name)#

Get WidgetFormula by name

Parameters:

widget_name (str)

Return type:

WidgetFormula

hide_all_actors()#

Make all actors invisible

hide_all_meshes()#

Make actors of all meshes invisible

hide_orbit()#

Remove the mesh visualizing the camera orbit.

initialize_plotter(**kwargs)#

Run pyvista.Plotter initialization.

Note: This is removed from __init__() for purposes of multiple inheritance of NematicPlot.

last_frame()#

View last frame in data timeseries.

load(filenames, reader=ovm_utilities.fast_import, mpi_group=True, do_load_frame=True)#

Import a file or files.

Parameters:

  • filenames (str or list[str]) – Files to load.

  • reader (callable, optional) – Function to read each file.

  • mpi_group (bool, optional) – Whether to stitch files together as separate outputs from the same timestep from an MPI run.

  • do_load_frame (bool, optional) – Whether to view the frame containing the loaded data.

mesh_names()#

Names of all meshes in filters tree.

Returns:

List of mesh names.

Return type:

list[str]

name_mesh_without_overwriting(mesh_name)#

Modify a proposed new mesh name to be distinct from existing mesh names

Parameters:

mesh_name (str) – Proposed mesh name

Returns:

Distinct mesh name to use

Return type:

str

name_widget_without_overwriting(widget_name)#
Modify a proposed new widget name to be distinct from existing

widget names

Parameters:

widget_name (str) – Proposed widget name

Returns:

Distinct widget name to use

Return type:

str

next_frame()#

View next frame in data timeseries.

non_filter_tree_actor_names()#

List actors that don’t belong to open_viewmin’s filter tree.

Returns:

List of actor names.

Return type:

list[str]

num_frames()#

Number of frames in timeseries data.

static organize_filenames(filenames, mpi_group=True)#

For data to be imported, sort filenames alphabetically after grouping MPI files appropriately.

Parameters:

  • filenames (list[str] | str)

  • mpi_group (bool)

Return type:

list[str]

play(pause_time=0.5)#

In-GUI animation; will be slow because it loads and renders on the fly

previous_frame()#

View previous frame in data timeseries.

probe_at_picked_surface_point(result_name=None)#

Create a FilterFormula with the sample filter probing a picked mesh at a picked point

Parameters:

result_name (str, optional) – Name of new FilterFormula; defaults to “_probed” appended to name of picked mesh

Returns:

result_name – Name of new FilterFormula

Return type:

str

refresh()#

Re-apply all filter formulas to refresh meshes

remove_mesh_completely(mesh_name, remove_children=True)#

Remove a mesh (filter or actor) from the plotter and from the filters tree.

Parameters:

  • mesh_name (str) – Name of mesh to remove.

  • remove_children (bool, optional) – Whether to recursively remove all meshes descended from this mesh in the filters tree.

Return type:

None

rename_mesh(from_name, to_name, do_refresh=True)#

Copy a mesh in the filters tree by copying its recipe.

Parameters:

  • from_name (str) – Name of mesh to copy.

  • to_name (str) – Name of new mesh.

  • do_refresh (bool, optional) – Whether to create the mesh anew from its filter after renaming.

Return type:

None

save_meshes(file_prefix)#

Save all meshes to .vtk files

Parameters:

file_prefix (str) – File location will be [mesh_name].vtk appended to this.

scalar_fields(mesh_name='fullmesh')#

List names of datasets with one value at each site.

Parameters:

mesh_name (str or pyvista.DataSet) – PyVista mesh or its name.

Returns:

List of array names.

Return type:

list[str]

set_actor_visibility(actor, visibility: bool)#

Set visibility of a mesh or meshes

Parameters:

  • actor (str, sequence of str, VTK actor, or sequence of VTK actors)

  • visibility (bool) – Whether mesh(es) are to be visible.

set_background(*args, **kwargs)#

Set plotter’s background color(s)

If called with no arguments, retrieves color from FilterTreePlot.settings[“background_color”], defaulting to black. Otherwise, args and kwargs are sent to pyvista.Plotter.set_background.

Parameters:

  • args

  • kwargs

set_lights_intensity(intensity)#

Rescale intensity of all lights.

Parameters:

intensity (float)

set_orbit(**kwargs)#

Set orbit properties and get its camera locations

Parameters:

kwargs – keyword arguments to set_orbit_kwargs()

Returns:

Orbit points

Return type:

pyvista.core.pointset.PolyData

set_orbit_kwargs(factor=3.0, n_points=20, viewup=None, shift=0.0, step=0.1)#

Modify camera orbit

Parameters:

  • factor (float) – orbit radius relative to data extent

  • n_points (int) – number of points subdividing circle at which to generate images

  • viewup (iterable[float], optional) – orientation vector for camera’s up direction

  • shift (float) – translation of camera location along viewup

  • step (float) – orbit speed in seconds per frame

Returns:

vis – Visibility of orbit points actor

Return type:

bool

show_orbit()#

Add a mesh of points visualizing the camera orbit.

symmetric_tensor_fields(mesh_name='fullmesh')#

List names of datasets with nine values at each site, whose corresponding 3x3 matrix is everywhere symmetric.

Parameters:

mesh_name (str or pyvista.DataSet) – PyVista mesh or its name.

Returns:

List of array names.

Return type:

list[str]

tensor_fields(mesh_name='fullmesh')#

List names of datasets with nine values at each site.

Parameters:

mesh_name (str or pyvista.DataSet) – PyVista mesh or its name.

Returns:

List of array names.

Return type:

list[str]

static toggle_actor_visibility(actor)#

Toggle visibility of an actor

Parameters:

actor (VTK actor)

Returns:

new_visibility

Return type:

bool

toggle_eye_dome_lighting()#

Switch eye dome lighting on/off

toggle_filter_tree_actor_visibility(actor_name)#

Toggle visibility of a mesh in the filter tree.

Parameters:

actor_name (str) – Name of mesh

toggle_floor()#

Toggle visibility of floor (-z) plane.

toggle_last_colorbar()#

Toggle visibility of most recently modified colorbar.

toggle_orbit_visibility(toggle=True)#

Toggle visibility of mesh visualizing camera orbit.

toggle_scalar_bar_visibility(scalar_bar_actor)#

Toggle visibility of a scalar bar

Parameters:

scalar_bar_actor (VTK scalar bar actor)

toggle_shadows()#

Turn shadow rendering on/off

toggle_stereo_render()#

Turn anaglyph stereo 3D effect on/off

unique_array_names(mesh=None)#

Get array names for datasets attached to a mesh, deleting duplicates.

Parameters:

mesh (str or pyvista.DataSet) – PyVista mesh or name of mesh

Returns:

Mesh along with the list of unique array names.

Return type:

(pyvista.DataSet, list[str])

update_actor(actor_name, **kwargs)#

Update a filter formula’s mesh visualization options.

Shorthand for self.get_filter_formula(ellipsoid_mesh_name).set()

Parameters:
update_filter(mesh_name, update_actor=False, **kwargs)#

Update a filter formula.

Shorthand for self.get_filter_formula(parent_mesh_name).update().

Parameters:
vector_fields(mesh='fullmesh')#

List names of datasets with three values at each site.

Parameters:

mesh (str or pyvista.DataSet) – PyVista mesh or its name.

Returns:

List of array names.

Return type:

list[str]

view_frame(frame_num=0, keep_camera_dist=True)#

Use one of the (already imported) sets of data as the source for all PyVista meshes, e.g. for generating a frame of an animation from timeseries data.

Parameters:

  • frame_num (int, optional) – Index in self.data of the timeframe to display.

  • keep_camera_dist (bool, optional) – Whether to force camera to maintain position after frame load.

actors_color_cycle#
array_dims_defined = False#
axes = None#
data = []#
data_stride#
property default_mesh#
default_mesh_name#
filenames = []#
filter_formulas#
frame_data = []#
frame_num#
property fullmesh#
geometric_objects#
is_enabled_eye_dome_lighting#
meshes_dict#
oVM_theme#
off_screen#
orbit_kwargs#
orbit_path#
settings#
title#
widget_formulas#
widgets#
class FilterTreePlotQt(filenames=None, user_settings=None, theme=None, reader=ovm_utilities.fast_import, **kwargs)#

Bases: open_viewmin.filter_tree_plot.filter_tree_plot.FilterTreePlot, pyvistaqt.BackgroundPlotter

Implement some PyVista functionality, with filter trees, in the PyVistaQt GUI

Parameters:

  • filenames (list[str], str, or None, optional) – Files to import.

  • user_settings (dict or None, optional) – Customizations to default plotter settings.

  • theme (['dark' | 'document' | 'paraview' | None], optional) – PyVista plot theme

  • reader (callable()) – Function to import and process data files

  • kwargs (dict, optional) – Keyword arguments to open_viewmin.FilterTreePlot

_assign_keypress_events()#

Assign actions to keyboard keys.

static _get_menu(parent, title)#

Get a menu with a given title

Parameters:

  • parent (PyQt5.QtWidgets.QMenuBar) – Menu bar to search

  • title (str) – Title of menu

Returns:

Menu

Return type:

PyQt5.QtWidgets.QMenu

_init_procedures_after_data_import()#

Initialization steps that can be carried out only after some data is imported

add_filter_formula(name=None, **kwargs)#
add_slice_with_controls(scalars_name, mesh_to_slice_name='fullmesh')#

Create a callable that adds a slice filter formula controlled by sliders and buttons in the controls area.

Parameters:

  • scalars_name (str or None) – Name of scalar dataset to use for coloring the slice. Pass None to use a solid color.

  • mesh_to_slice_name (str, optional) – Name of parent mesh to slice

Return type:

callable()

add_widget_formula(name=None, **kwargs)#
customize_controls_dock()#

Modify settings of controls area

enable_pyvista_3_lights(only_active=False)#
enable_pyvista_lightkit(only_active=False)#
initialize_plotter(**kwargs)#

Override parent class’s plotter initialization to use pyvistaqt.BackgroundPlotter instead of pyvista.Plotter

Parameters:

kwargs (dict, optional) – Keyword arguments to pyvistaqt.BackgroundPlotter

load(filenames, **kwargs)#
open_files_dialog(sort=True)#

Launch GUI widget for selecting files to import

Parameters:

sort (bool, optional) – Whether to sort filenames by timestamp

refresh()#
remove_actor_completely(actor_name)#
remove_mesh_completely(mesh_name, remove_children=True)#
rename_mesh(from_name, to_name, do_refresh=False)#
save_html(filename=None)#

Export plotter scene as interactive html widget

Parameters:

filename (str or None) – Filename to write to. Pass None to launch GUI file selector.

save_mesh(mesh_name, mesh_filename=None)#

Export a mesh.

Note that the allowed file types depend on the type of mesh.

Parameters:

  • mesh_name (str) – Mesh name

  • mesh_filename (str or None) – File to write to. Pass None to launch GUI file selector.

save_meshes_launch_dialog(file_prefix=None)#
set_actor_visibility(actor, visibility)#
set_orbit_dlg(**kwargs)#
show_editor()#

Show editor widget controlling actors’ visibility

update_actor(actor_name, **kwargs)#
update_filter(mesh_name, update_actor=False, **kwargs)#
update_filters_tree()#
update_frame_spinbox()#

Update the spinbox controlling the frame

view_frame(frame_num=0, **kwargs)#

Use one of the imported data files as the source for all datasets

property actor_control_toolbars#
Get toolbars controlling individual actors
Returns:

Dictionary of toolbars

Return type:

dict

calculate_menu#
controls_dock_scroll_area#
controls_dock_widget#
controls_dock_window#
dock_widgets#
filters_tree_widget_items#
finished_setup = False#
frame_num = 0#
non_ovm_actors_toggle_menu#
settings_Qt_dict#
the_Add_menu#
the_File_menu#
the_Tools_menu#
the_View_menu#
the_refresh_toolbar#
theme_menu#
toolbars#
window_size#
class NematicPlot(filenames=None, q0=0.0, user_settings=None, data_format='open-Qmin', sep='\t', reader=None, theme=None, dims=None, data_stride=1, **kwargs)#

Bases: open_viewmin.filter_tree_plot_Qt.filter_tree_plot_Qt.FilterTreePlotQt, open_viewmin.nematic.nematic_plot.nematic_plot_no_qt.NematicPlotNoQt

Plotter class for nematic liquid crystals visualization, with the filters tree, in a Qt window.

Parameters:

  • filenames (list[str], str, or None, optional) – Files to import.

  • q0 (float, optional) – Chiral wavenumber for cholesteric (chiral nematic) ground state, used in free energy calculations.

  • user_settings (dict or None, optional) – Customizations to default plotter settings.

  • data_format (['open-Qmin' | 'Qmin' | 'director'], optional) – Formatting style of data text files to import; used only if parameter reader has value None.

  • sep (str, optional) – Column delimiter for imported text file(s)

  • reader (callable() or None, optional) – Function for reading data from text files; set to None to use the data_format (and, optionally, sep) parameters to determine data import behavior.

  • theme (['dark' | 'document' | 'paraview' | None], optional) – PyVista plot theme

  • dims (tuple(int) or None) – System size; used only if filenames is None.

  • data_stride (int, optional) – Data spacing; used only if filenames is None.

  • kwargs (dict, optional) – Keyword arguments to FilterTreePlot

auto_setup(notebook=False)#
finish_setup_calculate_menu()#

Add nematic-specific items to the “Calculate” menu

setup_defects()#

Automatic setup for defects visualization

setup_director()#

Automatic setup for director visualization

show_jones(**kwargs)#

Display optical transmission, calculated from Jones matrices, on three planes.

Parameters:

kwargs (dict, optional)

Returns:

callback that refreshes Jones planes by re-applying the control slider widgets

Return type:

callable()

reader#
class NematicPlotNoQt(filenames=None, q0=0.0, user_settings=None, data_format='open-Qmin', sep='\t', reader=None, theme=None, off_screen=False, notebook=True, **kwargs)#

Bases: open_viewmin.filter_tree_plot.filter_tree_plot.FilterTreePlot

Plotter class for nematic liquid crystals visualization, with the

filters tree but without Qt.

Parameters:

  • filenames (list[str], str, or None, optional) – Files to import.

  • q0 (float, optional) – Chiral wavenumber for cholesteric (chiral nematic) ground state, used in free energy calculations.

  • user_settings (dict or None, optional) – Customizations to default plotter settings.

  • data_format (['open-Qmin' | 'Qmin' | 'director'], optional) – Formatting style of data text files to import; used only if parameter reader has value None.

  • sep (str, optional) – Column delimiter for imported text file(s)

  • reader (callable() or None, optional) – Function for reading data from text files; set to None to use the data_format (and, optionally, sep) parameters to determine data import behavior.

  • theme ([‘dark’ | ‘document’ | ‘paraview’ | None], optional) – PyVista plot theme

  • off_screen (bool, optional) – Whether to render off-screen

  • notebook (bool, optional) – Whether to display inside of a Jupyter notebook

  • **kwargs – Keyword arguments to FilterTreePlot

static Q33_from_Q5(q5)#

Convert 5-component Q-tensor information to 3x3 matrix

static Q_from_n(director_data)#

Create Q-tensor array from director data assuming S_0=1

_legacy_qmin_import(qtensor_filename)#

Reader for output from older Qmin (a.k.a. nematicvXX) code.

Note that while only the “Qtensor_…” files are supplied directly, this routine expects the associated “Qmatrix_…” files to be in the same directory.

Parameters:

qtensor_filename (str) – Filenames of “Qtensor_…”

Returns:

Imported data

Return type:

list[np.ndarray]

_pre_init(q0, data_format, reader, sep)#

Portion of initialization to run before open_viewmin.FilterTreePlot.__init__()

Parameters:

  • q0 (float) – Chiral wavenumber

  • data_format (['open-Qmin' | 'Qmin' | 'director'], optional) – Formatting style of data text files to import; used only if parameter reader has value None.

  • reader (callable() or None, optional) – Function for reading data from text files; set to None to use the data_format (and, optionally, sep) parameters to determine data import behavior.

  • sep (str, optional) – Column delimiter for imported text file(s)

Returns:

Reader

Return type:

callable()

add_circuits_around_points(points_mesh_name, normals_name, radius=3, n_samples=16, use_ints=False)#

Create small, closed-loop meshes around a set of points, for use in plotting director winding near disclinations.

Parameters:

  • points_mesh_name (str)

  • normals_name (str)

  • radius (float)

  • n_samples (int)

  • use_ints (bool)

Return type:

FilterFormula

analyze_disclination_at_picked_point(**kwargs)#

Show director winding character at a picked point on a disclination

Parameters:

**kwargs (dict, optional) – Keyword arguments to analyze_disclinations_at_points()

analyze_disclinations(defects_mesh_name='defects', n_centroids=50, tangents_glyph_name=None, **kwargs)#

For several “centroid” points along disclination lines, show the director winding character.

Parameters:
analyze_disclinations_at_points(points_mesh_name, radius=3, n_samples=16, use_ints=False)#
Parameters:

  • points_mesh_name (str)

  • radius (int)

  • n_samples (int)

  • use_ints (bool)

Return type:

FilterFormula

auto_setup(notebook=True)#

Routines to run after first importing data.

calculate_D_tensor(refresh=True)#

Calculate Schimming-Viñals tensor.

Creates the tensor array “D_tensor”, and the symmetric tensor arrays “D^T D” and “D D^T”.

calculate_Westin_metrics()#

Calculate Westin scalars measures from the Q-tensor.

Creates the scalar arrays “Westin_l”, “Westin_p”, “Westin_s”.

calculate_and_show_defect_tangent(glyph_stride=2, field_name=None, scale='nematic_sites', mesh_name='defects', threshold=0.4)#

Display disclination line tangent vectors as glyphs

Parameters:

  • glyph_stride (int, optional) – Typical spacing between glyphs

  • field_name (str or None, optional) – Proposed name for new tangent vector field array

  • scale (str, optional) – Name of scalar array to use for glyph size scale.

  • mesh_name (str, optional) – Name of defects mesh

  • threshold (float or None, optional) – Minimum value of 1/S for deciding which points to include in tangent calculation.

Returns:

Name of new glyphs mesh

Return type:

str

calculate_chi_tensor(refresh=True)#

Calculate Efrati-Irvine handedness pseudotensor.

Creates the tensor array “Chi”, the symmetric tensor arrays “Chi^T Chi” and “Chi Chi^T”, and the vector array “Omega from Chi”. Note that this calculation extends Efrati and Irvine’s construction to the Q-tensor rather than relying on the director field.

calculate_defect_tangent(threshold=0.4, mesh_name='defects', field_name=None)#

Calculate the unit tangent field to defect lines.

Parameters:

  • threshold (float or None, optional) – Minimum value of 1/S for deciding which points to include in tangent calculation.

  • mesh_name (str, optional) – Name of defects mesh

  • field_name (str or None, optional) – Proposed name for new tangent vector field array

Returns:

Name of new tangent vector field array

Return type:

str

calculate_frank_energy_comps()#

Calculate splay, twist, and bend Frank free energy densities and related quantities.

calculate_n_gradients(refresh=True)#

Calculate gradients of director field

calculate_rotation_vector_n()#

Calculate a combination of derivatives on the director field that, for an ideal disclination, gives the rotation vector (a.k.a. Frank vector) up to sign.

create_fullmesh(dat=None, mesh_name='fullmesh', frame_num=None)#

Create a uniform grid mesh as a root mesh for the filter tree.

Parameters:

  • dat (np.ndarray, optional) – Data array, with first three columns holding integer coordinates X, Y, Z.

  • mesh_name (str, optional) – Name of root mesh.

  • frame_num (int or None, optional) – Frame number for this root mesh. Pass None to append as a new frame.

Returns:

Frame number and new root mesh.

Return type:

int, pyvista.dataset

static director_data_import(filename, sep='\t')#

Import nematic director data and convert it into Q-tensor data in the open-Qmin data_format.

Parameters:

  • filename (str)

  • sep (str, optional)

Returns:

Q-tensor data in the open-Qmin data_format.

Return type:

np.ndarray

load(filenames, **kwargs)#

Import a file or files.

Parameters:

  • filenames (str or list[str]) – Files to load.

  • reader (callable, optional) – Function to read each file.

  • mpi_group (bool, optional) – Whether to stitch files together as separate outputs from the same timestep from an MPI run.

  • do_load_frame (bool, optional) – Whether to view the frame containing the loaded data.

static max_re_eigval(a)#

Maximum real part of eigenvalue for eigenvalues in an array of 3x3 matrices

Parameters:

a (np.ndarray | pyvista.pyvista_ndarray) – Array of 3x3 matrices

Returns:

Maximum real part of eigenvalues

Return type:

np.ndarray

static n_from_Q(q_matrix)#

Get director from 3x3-matrix Q-tensor data

nematic_calculations(dat, mesh)#

Assign Q-tensor and director field data to a mesh, and conduct calculations based on them.

Parameters:

  • dat (np.ndarray) – Data array of floats in the open-Qmin data_format: x y z Qxx Qxy Qxz Qyy Qyz site_type S

  • mesh (pyvista.DataSet)

num_boundaries()#

Number of boundary objects

Returns:

Number of boundary objects

Return type:

int

pick_point_analyze_disclination(**kwargs)#

Enable surface picking mode and analyze director winding about the picked point, assumed to be on a disclination.

Parameters:

**kwargs (dict, optional) – Keyword arguments to analyze_disclinations_at_points()

plot_director_glyphs_on_circuits(points_mesh_name, circuits_formula, result_name='director_on_circuits', defects_mesh_name='defects')#

Show director glyphs on small, closed-loop measuring circuits around disclinations at given points.

Parameters:

  • points_mesh_name (str)

  • circuits_formula (FilterFormula)

  • result_name (str)

  • defects_mesh_name (str)

Return type:

FilterFormula

post_init()#

Portion of initialization to run after open_viewmin.FilterTreePlot.__init__()

set_director(director_data, mesh_name=None)#

Set director orientation data directly from an array.

Parameters:

  • director_data (np.ndarray)

  • mesh_name (str or None, optional) – Name of mesh on which to define director

set_q0(q0)#

Set energetically preferred cholesteric wavenumber.

(Re)calculates arrays that depend on q0.

Parameters:

q0 (float) – Chiral wavenumber

set_qtensor(q_data, mesh)#

Set Q-tensor data directly from an array.

Parameters:

  • q_data (np.ndarray) – Q-tensor data with each row formatted as [Qxx, Qxy, Qxz, Qyy, Qyz]

  • mesh (pyvista.DataSet)

Returns:

Q-tensor data reformatted such that each row contains the nine elements of the symmetric Q-tensor matrix, flattened.

Return type:

np.ndarray

setup_boundaries(separate_meshes=False)#

Add isosurface or isosurfaces for boundaries.

Parameters:

separate_meshes (bool, optional) – Whether to create a separate isosurface mesh for each boundary.

setup_defects()#

Add single-value isosurface of uniaxial order to visualize defects

setup_director()#

Add glyphs to visualize nematic director on a plane controlled by a plane widget

show_jones(**kwargs)#

Display optical transmission, calculated from Jones matrices, on three planes.

Parameters:

**kwargs (dict, optional)

do_auto_setup = False#
q0#
reader#
xyz_arrays#
class WidgetFormula(plotter, name=None, mesh_name=None, enabled=True, callback=None, creator=None, configure=None, widget_args=None, **kwargs)#

Class for creating re-usable widgets

Parameters:

  • plotter (FilterTreePlot)

  • name (str or None) – Name of widget. Pass None to default to “_widget” appended to parent_mesh_name.

  • mesh_name (str or None) – Name of mesh controlled by widget. Pass None to default to plotter’s default mesh name.

  • enabled (bool, optional) – Whether to initialize widget as enabled.

  • callback (callable()) – Function mapping (plotter, parent_mesh_name) to a callable that applies the widget to update its mesh.

  • creator (callable()) – Function creating the widget. First argument must be a function of the kind created by callback(plotter, parent_mesh_name). Must also accept all arguments in widget_args and keyword arguments in kwargs.

  • configure (callable() or None, optional) – Function configuring a widget based on previously existing widget, mapping the widget to a two-element tuple (enabled: bool, widget_args: tuple). Pass None to ignore.

  • widget_args (tuple or None) – Positional arguments, besides callback, to creator. None is equivalent to empty tuple.

  • kwargs (dict, optional) – Keyword arguments to creator.

apply()#

Create the widget and apply it to create the mesh it controls

check_existing_widget_configuration()#

Get information to configure widget according to previous settings

Returns:

Whether widget is enabled; widget arguments.

Return type:

(bool, tuple)

get_creator_func()#

If self.creator is a string, get the corresponding callable

Return type:

callable()

set_color(*widget_color)#

Set widget color

Note that this does not control the color of any mesh.

Parameters:

widget_color (tuple) – Color as rgb floats, or as one-element tuple containing string of color name or hex value.

set_outline_visibility(visibility: int)#

Set visibility of a widget’s box outline

Parameters:

visibility (int) – Make outline visible unless visibility equals 0.

update()#

Update mesh controlled by widget.

Configure widget according to previous settings, then apply the widget’s callback.

callback#
color = None#
configure#
creator#
enabled#
plotter#
property widget#
Get widget
Return type:

VTK widget

widget_kwargs#
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