open_viewmin

`open_viewmin`#

Subpackages#

Submodules#

open_viewmin.open_viewmin

Package Contents#

Classes#

`FilterFormula`	Class for reusable PyVista filters.
`FilterTreePlot`	Extend PyVista Plotter class to organize meshes into a "filter tree" so that
`FilterTreePlotQt`	Implement some PyVista functionality, with filter trees, in the PyVistaQt
`NematicPlot`	Plotter class for nematic liquid crystals visualization, with the
`NematicPlotNoQt`	Plotter class for nematic liquid crystals visualization, with the
`WidgetFormula`	Class for creating re-usable widgets

class open_viewmin.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 (open_viewmin.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).

property array_names#

Get mesh’s dataset names

Return type:: list[str]

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

property normal#

property orientations#

property origin#

property parent_filter_formula#

Get parent mesh’s filter formula

Return type:: FilterFormula

property parent_mesh#

Get parent mesh

Return type:: pyvista.dataset

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#

__getitem__(key)#: Access mesh’s datasets in dictionary-like manner

__repr__()#

Print keyword arguments to self.__init__ and their current values

Return type:: str

__setitem__(key, set_to)#: Set mesh’s datasets in dictionary-like manner

_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 filter_formula’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)#

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()

inherit(filter_kwarg)#

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 self.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 actors

Return type:

list of vtkmodules.vtkRenderingOpenGL2.vtkOpenGLActor

update_children()#

Update child meshes

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

class open_viewmin.FilterTreePlot(filenames=None, user_settings=None, theme=None, reader=ovm_utilities.fast_import, dims=None, data_stride=1, **kwargs)#

Bases: pyvista.Plotter

Extend PyVista Plotter class to organize meshes into a “filter tree” so that 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

property actor_names#

Names of all actors in filters tree.

Returns:: List of actor names.
Return type:: list[str]

property array_dims#

System array-size dimensions.

Returns:: (array_Lx, array_Ly, array_Lz)
Return type:: tuple(int)

property colorbar_titles#

Get titles of all scalar bars

Returns:: List of scalar bar titles
Return type:: list[str]

property colorbars#

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

Return type:: list of VTK scalar bar actors

property default_mesh#

property default_mesh_name#

property dims#

System linear dimensions.

Returns:: (Lx, Ly, Lz)
Return type:: tuple(int)

property filter_tree_roots#

property fullmesh#

property mesh_names#

Names of all meshes in filters tree.

Returns:: List of mesh names.
Return type:: list[str]

property 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]

property num_frames#: Number of frames in timeseries data.

property points#

Get array of coordinates belonging to root mesh “fullmesh”

Returns:: Array of point coordinates.
Return type:: numpy.ndarray

__getitem__(mesh_name)#

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

Parameters:: mesh_name (str) –
Return type:: open_viewmin.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:

open_viewmin.FilterFormula

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

_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)#

_set_pyvista_plotter_properties()#: Initialization choices for PyVista Plotter

_visibility_callback(actor_name)#

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 open_viewmin.FilterFormula.__init__.

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

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

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 open_viewmin.WidgetFormula.__init__

Returns:

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

Return type:

open_viewmin.WidgetFormula or None

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 (numpy.ndarray) –
filename (str) –
do_load_frame (bool, optional) – Whether to view the frame

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 (numpy.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

disable_eye_dome_lighting()#

disable_shows()#

do_orbit()#

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/api/ plotting/_autosummary/pyvista.themes.DefaultTheme.jupyter_backend .html.
Returns:: New PyVista plotter containing this plotter’s actors.
Return type:: pyvista.Plotter

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_widget(widget_name)#

get_widget_formula(widget_name)#

hide_all_actors()#

hide_all_meshes()#

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 open_viewmin.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.

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.

static organize_filenames(filenames, mpi_group=True)#

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)#

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)#

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_lights_intensity(intensity)#

Rescale intensity of all lights.

Parameters:: intensity (float) –

set_orbit(**kwargs)#

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

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_eye_dome_lighting()#

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()#

toggle_stereo_render()#

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:

actor_name (str) – Name of filter formula
**kwargs – Keyword arguments to `open_viewmin.FilterFormula.set

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

Update a filter formula.

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

Parameters:

mesh_name (str) – Name of filter formula
update_actor (bool, optional) – Whether to update an actor immediately after updating its mesh.
kwargs (dict, optional) – Keyword arguments to open_viewmin.FilterFormula.update

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.

class open_viewmin.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

property actor_control_toolbars#

Get toolbars controlling individual actors

Returns:: Dictionary of toolbars
Return type:: dict

_assign_keypress_events()#: Assign actions to keyboard keys.

_enable_3_lights(only_active=False)#

_enable_lightkit(only_active=False)#

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:

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 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 open_viewmin.FilterFormula.__init__.

Returns:

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

Return type:

pyvista.dataset or None

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)#

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 open_viewmin.WidgetFormula.__init__

Returns:

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

Return type:

open_viewmin.WidgetFormula or None

customize_controls_dock()#: Modify settings of controls area

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)#

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.

open_files_dialog(sort=True)#

Launch GUI widget for selecting files to import

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

refresh()#: Re-apply all filter formulas to refresh meshes

remove_actor_completely(actor_name)#

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=False)#

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_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 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_orbit_dlg(**kwargs)#

show_editor()#: Show editor widget controlling actors’ visibility

update_actor(actor_name, **kwargs)#

Update a filter formula’s mesh visualization options.

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

Parameters:

actor_name (str) – Name of filter formula
**kwargs – Keyword arguments to `open_viewmin.FilterFormula.set

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

Update a filter formula.

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

Parameters:

mesh_name (str) – Name of filter formula
update_actor (bool, optional) – Whether to update an actor immediately after updating its mesh.
kwargs (dict, optional) – Keyword arguments to open_viewmin.FilterFormula.update

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

class open_viewmin.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, NematicPlotNoQt

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 open_viewmin.FilterTreePlot

auto_setup(notebook=False)#: Routines to run after first importing data.

finish_setup_calculate_menu()#: Add nematic-specific items to the “Calculate” menu

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) –
Returns:: callback that refreshes Jones planes by re-applying the control slider widgets
Return type:: callable()

class open_viewmin.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 open_viewmin.FilterTreePlot

property num_boundaries#: returns: Number of boundary objects :rtype: int

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[numpy.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)#

analyze_disclination_at_picked_point(**kwargs)#

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

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

auto_setup(notebook=True)#: Routines to run after first importing data.

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_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_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_rotation_vector_n()#

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

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:

numpy.ndarray

load(filenames, **kwargs)#

max_re_eigval(a)#

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

Parameters:: a (numpy.ndarray | pyvista.pyvista_ndarray) – Array of 3x3 matrices
Returns:: Maximum real part of eigenvalues
Return type:: numpy.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 (numpy.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) –

pick_point_analyze_disclination(**kwargs)#

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

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 (numpy.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 (numpy.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:

numpy.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)#

class open_viewmin.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 (open_viewmin.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.

property widget#

Get widget

Return type:: VTK widget

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)#

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.

open_viewmin

Contents

open_viewmin#

Subpackages#

Submodules#

Package Contents#

Classes#

`open_viewmin`#