plot_util
Short description
@author: Moritz F P Becker
- pyrid.observables.plot_util.cuboid_data(origin, size=[1, 1, 1])[source]
Returns the vertex array of a cuboid given an origin vector.
- Parameters
- originfloat64[3]
Origin of the cuboid
- sizefloat64[3]
Extend of the cuboid in each dimension. Default = [1,1,1]
- pyrid.observables.plot_util.draw_cuboid(positions, sizes=None, colors=None, edgecolor='k', edgewidth=1, edgealpha=1)[source]
Draws a cuboid of a given size at a given position.
- Parameters
- positionsfloat[:]
Position vector
- sizefloat[3]
Extend of the cuboid in each dimension. Default = [1,1,1]
- colorsarray_like
Array of face colors
- edgecolorstring
Edge color. Default = k
- edgewidthfloat
Width of the cuboid edges. Default = 1
- edgealphafloat
Opacity of the cuboid edges. Default = 1
- Returns
- tuple(object, object)
Poly3DCollection, Line3DCollection
- pyrid.observables.plot_util.draw_sphere(ax, pos, radius, col)[source]
Draws a sphere of given radius and centered at a given position vector.
- Parameters
- axobject
Axis object of a matplotlib figure
- posfloat[3]
Position of the sphere center
- radiusfloat
Sphere radius
- colstring
Sphere color
- Returns
- float[2,3]
Lower left and upper right sphere vertices (Used to set figure aspect ratio).
- pyrid.observables.plot_util.plot_cell_grid(Simulation, save_fig=False, fig_name=None, fig_path=None, Compartments=None, show=True)[source]
Visualization of the cell grid that divides the simulation box into different cells/voxels.
- Parameters
- Simulationobject
Instance of the Simulation class.
- save_figboolean
If True, the plot is exported to a .png file.
- fig_namestring
Name of the figure
- fig_pathstring
Path to which the figure is exported
- Compartmentsnb.types.DictType(nb.int64, Compartment.class_type.instance_type)
Dictionary keeping the index of each compartment in the simulation and the corresponding instances of the Compartment class.
- showboolean
If True, the plot is shown directly, otherwise only after the simulation has ended.
- pyrid.observables.plot_util.plot_compartment_0(Simulation, System, vertices, triangles, Compartments, comp_name, save_fig=False, fig_name=None, fig_path=None, face_groups=True, show_normals=True, mol_traj=None, indices=None, projection='orthographic', plot_cube=True, plane='-xz', alpha=None, show=True)[source]
Plots a compartment mesh and highlights any face groups and borders/edges using the plotly library. Also plots the triangle normal vectors.
- Parameters
- Simulationobject
Instance of the Simulation class
- Systemobject
Instance of the System class
- verticesfloat64[N,3]
Coordinates of the N vertices in each dimension.
- trianglesint64[N,3]
Indices of the vertices that make up each triangle (3 vertices per triangle).
- Compartmentsnb.types.DictType(nb.int64, Compartment.class_type.instance_type)
Dictionary keeping the index of each compartment in the simulation and the corresponding instances of the Compartment class.
- save_figboolean
If True, the plot is exported to a .png file.
- fig_namestring
Name of the figure
- fig_pathstring
Path to which the figure is exported
- comp_namestring
Name of the compartment which to plot
- face_groupsboolean
If True, the face groups of the compartment are highlighted
- show_normalsboolean
If True, the triangle normal vectors are plotted
- mol_trajfloat64[T,N,3]
Molecule trajectories can be passed which are then plotted as lines in 3D. T is the number of time steps, N the number of molecules. Molecules whose trajectory to plot can also be selected in addition by the parameter indces.
- indicesint64[:]
Indices of the molecules whose trajectory to plot
- projectionstring
Projection type. Default = orthographic
- plot_cube = `boolean`
If True, the simulation box is visualized in addition to the selected compartment
- planestring (‘-xy’, ‘xy’, ‘-yz’, ‘yz’, ‘-xz’, ‘xz’)
Defines the plane to which the camera is oriented. Default = -xz
- alphafloat64 in [0,1]
Sets the opacity of the mesh faces.
- showboolean
If True, the plot is shown directly, otherwise only after the simualtion has ended.
- pyrid.observables.plot_util.plot_compartments(Simulation, save_fig=False, fig_name=None, fig_path=None, comp_name=None, face_groups=True, show_normals=True, mol_traj=None, indices=None, projection='orthographic', plot_cube=True, plane='-xz', alpha=None, show=True)[source]
Plots the compartment meshes and highlights any face groups and borders/edges using the plotly library. Also plots the triangle normal vectors.
- Parameters
- Simulationobject
Instance of the Simulation class
- save_figboolean
If True, the plot is exported to a .png file.
- fig_namestring
Name of the figure
- fig_pathstring
Path to which the figure is exported
- comp_namestring
Name of the compartment which to plot
- face_groupsboolean
If True, the face groups of the compartment are highlighted
- show_normalsboolean
If True, the triangle normal vectors are plotted
- mol_trajfloat64[T,N,3]
Molecule trajectories can be passed which are then plotted as lines in 3D. T is the number of time steps, N the number of molecules. Molecules whose trajectory to plot can also be selected in addition by the parameter indces.
- indicesint64[:]
Indices of the molecules whose trajectory to plot
- projectionstring
Projection type. Default = orthographic
- plot_cube = `boolean`
If True, the simulation box is visualized in addition to the selected compartment
- planestring (‘-xy’, ‘xy’, ‘-yz’, ‘yz’, ‘-xz’, ‘xz’)
Defines the plane to which the camera is oriented. Default = -xz
- alphafloat64 in [0,1]
Sets the opacity of the mesh faces.
- showboolean
If True, the plot is shown directly, otherwise only after the simulation has ended.
- pyrid.observables.plot_util.plot_concentration_profile(Simulation, axis=0, save_fig=False, fig_name=None, fig_path=None, show=True)[source]
Plots the concentration/density profile of molecules along a given axes.
- Parameters
- Simulationobject
Instance of the Simulation class.
- axis0, 1 or 2
Axes along which to plot the concentration profile.
- save_figboolean
If True, the plot is exported to a .png file.
- fig_namestring
Name of the figure
- fig_pathstring
Path to which the figure is exported
- showboolean
If True, the plot is shown directly, otherwise only after the simulation has ended.
- pyrid.observables.plot_util.plot_mobility_matrix(molecule, Simulation, save_fig=False, fig_name=None, fig_path=None, color_scheme='colored', show=True)[source]
Plots the mobility tensor (also see diffusion tensor) of a molecule type.
- Parameters
- moleculestring
Name of the molecule type
- Simulationobject
Instance of the Simulation class.
- save_figboolean
If True, the plot is exported to a .png file.
- fig_namestring
Name of the figure
- fig_pathstring
Path to which the figure is exported
- color_schemestring
Available color schemes: ‘colored’, ‘flat’. Default = ‘colored’
- showboolean
If True, the plot is shown directly, otherwise only after the simulation has ended.
- pyrid.observables.plot_util.plot_path(file_path, molecule, indices, show=True)[source]
Plots the trajectory of one or several molecules of a specific type in 3D.
- Parameters
- file_pathstring
Directory of the hdf5 file that contains the molecule trajectory data.
- moleculestring
Name of the molecule type.
- indicesint64[:]
List of molecule indices for which to plot the molecule trajectory
- showboolean
If False, the plot is not shown. Default = True
- pyrid.observables.plot_util.plot_path_mesh(file_path, molecule, indices, show=True)[source]
Plots the trajectory of one or several molecules of a specific type in 3D and includes a 3d mesh compartment.
- Parameters
- file_pathstring
Directory of the hdf5 file that contains the molecule trajectory data.
- moleculestring
Name of the molecule type.
- indicesint64[:]
List of molecule indices for which to plot the molecule trajectory
- showboolean
If False, the plot is not shown. Default = True
- pyrid.observables.plot_util.plot_potential(Simulation, Potentials, yU_limits=None, yF_limits=None, r_limits=None, show=True, save_fig=False)[source]
Plots a range of given energy potential functions and the corresponding force functions.
- Parameters
- Simulationobject
Instance of the Simulation class.
- Potentialslist
List of functions which to plot.
- yU_limitsfloat64[2]
Lower and upper limits for the y axes of the potential energy plot. Default = None
- yF_limitsfloat64[2]
Lower and upper limits for the y axes of the force plot. Default = None
- r_limitsfloat64[2]
Lower and upper limits for the inter-particle distance. Default = None
- showboolean
If True, the plot is shown directly, otherwise only after the simulation has ended.
- save_figboolean
If True, the plot is exported to a .png file.
- pyrid.observables.plot_util.plot_scene(Simulation, save_fig=False, fig_name=None, fig_path=None, projection='orthographic', plane='-xz', show=True)[source]
Plots the simulation scene with all its compartments and molecule positions. Molecule positions are represented by a scatter plot.
- Parameters
- Simulationobject
Instance of the Simulation class
- save_figboolean
If True, the plot is exported to a .png file.
- fig_namestring
Name of the figure
- fig_pathstring
Path to which the figure is exported
- projectionstring
Projection type. Default = orthographic
- planestring (‘-xy’, ‘xy’, ‘-yz’, ‘yz’, ‘-xz’, ‘xz’)
Defines the plane to which the camera is oriented. Default = -xz
- showboolean
If True, the plot is shown directly, otherwise only after the simualtion has ended.
- pyrid.observables.plot_util.plot_sphere_packing(Compartment_Number, Simulation, points, ptype, save_fig=False, fig_name=None, fig_path=None, show=True)[source]
Visualization of the molecule distribution where molecules are represented as spheres.
- Parameters
- Compartmentsint64
Index of the compartment which to include in the plot.
- Simulationobject
Instance of the Simulation class.
- pointsfloat64[:,3]
Coordinates of the molecules.
- ptypeint64[:]
List of molecule type indices corresponding to the molecule coordinates given by the parameter points.
- save_figboolean
If True, the plot is exported to a .png file.
- fig_namestring
Name of the figure
- fig_pathstring
Path to which the figure is exported
- showboolean
If True, the plot is shown directly, otherwise only after the simulation has ended.