DensitySpace.VoxelSpace

DensitySpace.VoxelSpace#

DensitySpace.VoxelSpace.py

get_meshgrid(N)#

Create a meshgrid for the electron density space.

Parameters:

N (int) – The size of the grid along each axis.

Returns:

A tuple containing the meshgrid arrays (x, y, z).

Return type:

tuple

draw_voxles_as_dots_impl(ax, image, cmap=<matplotlib.colors.ListedColormap object>, min_value=0, colorbar=False, limits=None, alpha=1, s=30)#

Draw voxels as dots in a 3D plot.

Parameters:

  • ax (matplotlib.axes.Axes) – The axes to plot on.

  • image (np.ndarray) – The 3D density array.

  • min_value (float) – The minimum density value to consider for plotting.

  • colorbar (bool) – Whether to display a colorbar.

  • limits (tuple or None) – The limits for the axes in the form (xlim, ylim, zlim). If None, the limits will be set to the size of the image.

  • alpha (float) – The alpha value for the dots.

  • s (float) – The size of the dots.

Return type:

None

add_center_plane(ax, N, k=None, alpha=0.2, color='gray')#

Add a plane at z=k to the 3D axes.

Parameters:

  • ax (matplotlib.axes.Axes) – The axes to plot on.

  • N (int) – The size of the grid along each axis.

  • k (int or None) – The z value for the plane. If None, it will be set to N//2

  • alpha (float) – The alpha value for the plane.

compute_rg_impl(rho, min_value=0)#

Compute the radius of gyration for a 3D density array. (This code was generated by Copilot)

Parameters:

  • rho (np.ndarray) – 3D density array.

  • min_value (float) – Minimum density value to include in calculation.

Returns:

Radius of gyration.

Return type:

float

class VoxelSpace(N, shape=None, density=None)#

Bases: object

VoxelSpace class to handle voxel-based density spaces. It can be initialized with a shape or a density array.

rho#

3D density array.

Type:

np.ndarray

plot_as_dots(ax=None, cmap=<matplotlib.colors.ListedColormap object>, min_value=0, colorbar=False, alpha=1, s=30)#

Plot the voxel space.

Parameters:

  • ax (matplotlib.axes.Axes) – The axes to plot on.

  • min_value (float) – The minimum density value to consider for plotting.

plot_with_density(axes=None, cmap=<matplotlib.colors.ListedColormap object>, min_value=0.0001, colorbar=True, alpha=0.3, s=1, k=None)#

Plot the voxel space.

Parameters:

  • axes (matplotlib.axes.Axes) – The axes to plot on.

  • min_value (float) – The minimum density value to consider for plotting.

  • colorbar (bool) – Whether to display a colorbar.

  • alpha (float) – The alpha value for the plots.

  • s (float) – The size of the dots.

  • k (int or None) – The z value for the cross-sectional plane. If None, it will be set to N//2

Return type:

None

compute_rg(min_value=0)#

Compute the radius of gyration of the voxel space.

Parameters:

min_value (float) – Minimum density value to include in calculation.

Returns:

The radius of gyration.

Return type:

float

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