pyoptics.plot_tools

Plot helpers: intensities, complex fields (amplitude and phase) and image stacks through focus. Importing this module sets matplotlib’s font size and family.

Functions

plot_field	Plot a complex field.
plot_imstack	Plot an image stack.
plot_imstack_alternative	Plot an image stack.
plot_intensity	Plot an intensity image.

pyoptics.plot_tools.plot_intensity(psi, x, y, xlabel=None, ylabel=None, title=None, colorbar=True, use_intensity=False, n=1.0, ax=None, **kwargs)

Plot an intensity image.

Parameters:

psiarray

Complex field or intensity image. psi is considered to be an intensity already is if is of complex type, otherwise it’s considered to be an in intensity.

x, yarrays

Linear coordinate arrays the image is sampled on.

xlabel, ylabel, titlestrings, optional

Matplotlib options.

colorbarboolean, optional

If True, a colorbar is added.

use_intensityboolean, optional

If True, use physical intensity for the plot. Otherwise, use abs(psi)**2 [default].

ndouble, optional

Refractive index of embedding medium. Defaults to n=1.0. Used if psi is complex.

axmatplotlib axes, optional

If given, use this axes to plot to.

**kwargskeyword arguments

Propagated to matplotlib imshow() call.

pyoptics.plot_tools.plot_field(field, x, y, xlabel=None, ylabel=None, title=None, colorbar=True, use_intensity=False, amp_title=None, phase_title=None, horizontal_layout=True, use_rad=False, n=1.0, **kwargs)

Plot a complex field.

Parameters:

psiarray

Complex field.

x, yarrays

Linear coordinate arrays the field is sampled on.

xlabel, ylabel, titlestrings, optional

Matplotlib options.

colorbarboolean, optional

If True, a colorbar is added.

use_intensityboolean, optional

If True, use intensity for the amplitude plot. Otherwise, use abs(psi) [default].

ndouble, optional

Refractive index of embedding medium. Defaults to n=1.0. Used if psi is complex.

**kwargskeyword arguments

Propagated to matplotlib imshow() call. If given, phase_cmap is mapped to cmap for the phase plot.

pyoptics.plot_tools.plot_imstack_alternative(imstack, x, y, z_vals, cmap=<matplotlib.colors.LinearSegmentedColormap object>, normalize=False)

Plot an image stack.

Parameters:

imstackarray

Array of dimension (Nz, Nx, Ny).

x, yarrays

Linear or 2d coordinate arrays.

z_valsarray

cmapMPL colormap, optional

Colormap to use. Defaults to cm.Blues.

normalizeboolean, optional

If True, normalize each image slice individually to [0, 1]. Use this if the individual images differ a lot in maximum intensity. Defaults to False.

pyoptics.plot_tools.plot_imstack(imstack, x, y, z_vals, cmap=<matplotlib.colors.LinearSegmentedColormap object>, normalize=False, alpha=0.5)

Plot an image stack.

Parameters:

imstackarray

Array of dimension (Nz, Nx, Ny).

x, yarrays

Linear or 2d coordinate arrays.

z_valsarray

cmapMPL colormap, optional

Colormap to use. Defaults to cm.Blues.

normalizeboolean, optional

If True, normalize each image slice individually to [0, 1]. Use this if the individual images differ a lot in maximum intensity. Defaults to False.

alphafloat, optional