trackpy.plots

These functions generate handy plots.

Functions

annotate(centroids, image[, circle_size, ...])

Mark identified features with white circles.

annotate3d(centroids, image, **kwargs)

Annotates a 3D image and returns a scrollable stack for display in IPython.

examine_jumps(data, jumps)

fit(data, fits[, inverted_model, logx, logy, ax])

invert_yaxis(ax)

Inverts the y-axis of an axis object.

make_axes(func)

A decorator for plotting functions. NORMALLY: Direct the plotting function to the current axes, gca(). When it's done, make the legend and show that plot. (Instant gratificaiton!) The axes have to be 2d or else the current figure will be cleared. BUT: If the uses passes axes to plotting function, write on those axes and return them. The user has the option to draw a more complex plot in multiple steps.

make_axes3d(func)

A decorator for plotting 3d functions. NORMALLY: Direct the plotting function to the current axes, gca(). When it's done, make the legend and show that plot. (Instant gratificaiton!) The axes have to be 3d or else the current figure will be cleared. BUT: If the uses passes axes to plotting function, write on those axes and return them. The user has the option to draw a more complex plot in multiple steps.

make_fig(func)

See make_axes.

mass_ecc(f[, ax])

Plot each particle's mass versus eccentricity.

mass_size(f[, ax])

Plot each particle's mass versus size.

plot_density_profile(f, binsize[, blocks, ...])

Plot a histogram showing the density profile in one direction.

plot_displacements(t, frame1, frame2[, ...])

Plot arrows showing particles displacements between two frames.

plot_principal_axes(img, x_bar, y_bar, cov)

Plot bars with a length of 2 stddev along the principal axes.

plot_traj(traj[, colorby, mpp, label, ...])

Plot traces of trajectories for each particle.

plot_traj3d(*args, **kwargs)

The 3D equivalent of plot_traj.

ptraj(traj[, colorby, mpp, label, ...])

Plot traces of trajectories for each particle.

ptraj3d(*args, **kwargs)

The 3D equivalent of plot_traj.

scatter(centroids[, mpp, cmap, ax, ...])

Scatter plot of all particles.

scatter3d(*args, **kwargs)

The 3D equivalent of scatter.

subpx_bias(f[, pos_columns])

Histogram the fractional part of the x and y position.