sitator.visualization package¶
Submodules¶
sitator.visualization.atoms module¶
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sitator.visualization.atoms.
plot_atoms
(atoms, positions=None, hide_species=(), wrap=False, fig=None, ax=None, i=None)¶
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sitator.visualization.atoms.
plot_points
(points, marker='x', fig=None, ax=None, i=None, **kwargs)¶
sitator.visualization.common module¶
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sitator.visualization.common.
color_for_species
(species)¶
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sitator.visualization.common.
grid
(*args, **kwargs)¶
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sitator.visualization.common.
layers
(*args, **fax)¶
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sitator.visualization.common.
plotter
(is3D=True, **outer)¶
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sitator.visualization.common.
set_axes_equal
(ax)¶ Make axes of 3D plot have equal scale so that spheres appear as spheres, cubes as cubes, etc.. This is one possible solution to Matplotlib’s ax.set_aspect(‘equal’) and ax.axis(‘equal’) not working for 3D.
- Input
- ax: a matplotlib axis, e.g., as output from plt.gca().
Module contents¶
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class
sitator.visualization.
SiteNetworkPlotter
(site_mappings={'marker': 'site_types'}, edge_mappings={}, markers=['x', '+', 'v', '<', '^', '>', '*', 'd', 'h', 'p'], plot_points_params={}, minmax_linewidth=(1.5, 7), minmax_edge_alpha=(0.15, 0.75), minmax_markersize=(20.0, 80.0), min_color_threshold=0.0, min_width_threshold=0.0, title='')¶ Bases:
object
Plot a
SiteNetwork
.Note that for edges, the average of the edge property for i -> j and j -> i is often used for visual clarity; if your edge properties are not almost symmetric, the visualization might not be useful.
Parameters: - site_mappings (dict) – defines how to show different properties. Each entry maps a visual aspect (‘marker’, ‘color’, ‘size’) to the name of a site attribute including ‘site_type’. The markers can also be arbitrary text (key “text”) in which case the value can also be a 2-tuple of an attribute name and a % format string.
- edge_mappings (dict) – each key maps a visual property (‘intensity’, ‘color’, ‘width’, ‘linestyle’) to an edge attribute in the SiteNetwork.
- markers (list of str) – What matplotlib markers to use for sites.
- plot_points_params (dict) – User options for plotting site points.
- minmax_linewidth (2-tuple) – Minimum and maximum linewidth to use.
- minmax_edge_alpha (2-tuple) – Similar, for edge line alphas.
- minmax_markersize (2-tuple) – Similar, for markersize.
- min_color_threshold (float) – Minimum (normalized) color intensity for the corresponding line to be shown. Defaults to zero, i.e., all nonzero edges will be drawn.
- min_width_threshold (float) – Minimum normalized edge width for the corresponding edge to be shown. Defaults to zero, i.e., all nonzero edges will be drawn.
- title (str) – Title for the figure.
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DEFAULT_LINESTYLES
= ['--', ':', '-.', '-']¶
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DEFAULT_MARKERS
= ['x', '+', 'v', '<', '^', '>', '*', 'd', 'h', 'p']¶
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DEFAULT_SITE_MAPPINGS
= {'marker': 'site_types'}¶
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EDGE_GROUP_COLORS
= ['b', 'g', 'm', 'crimson', 'lightseagreen', 'darkorange', 'sandybrown', 'gold', 'hotpink', 'gray']¶
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class
sitator.visualization.
SiteTrajectoryPlotter
¶ Bases:
object
Produce various plots of a
SiteTrajectory
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plot_frame
(st, frame, **kwargs)¶ Plot sites and instantaneous positions from a given frame.
Parameters: - st (SiteTrajectory) –
- frame (int) –
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plot_particle_trajectory
(st, particle, ax=None, fig=None, **kwargs)¶ Plot the sites occupied by a mobile particle over time.
Parameters: - st (SiteTrajectory) –
- particle (int) –
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plot_site
(st, site, **kwargs)¶ Plot all real space positions associated with a site.
Parameters: - st (SiteTrajectory) –
- site (int) –
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