def persistence_image(ph,
new_fig=True,
subplot=111,
xlims=None,
ylims=None,
masked=False,
colorbar=False,
norm_factor=None,
threshold=0.01,
vmin=None,
vmax=None,
cmap=jet_map,
bw_method=None,
**kwargs):
'''Plots the gaussian kernel
of the ph diagram that is given.
'''
if xlims is None or xlims is None:
xlims, ylims = analysis.get_limits(ph, coll=False)
# pylint: disable=unexpected-keyword-arg
Zn = analysis.get_persistence_image_data(ph,
norm_factor=norm_factor,
bw_method=bw_method,
xlims=xlims,
ylims=ylims)
fig, ax = cm.get_figure(new_fig=new_fig, subplot=subplot)
if masked:
Zn = np.ma.masked_where((threshold > Zn), Zn)
cax = ax.imshow(np.rot90(Zn),
vmin=vmin,
vmax=vmax,
cmap=cmap,
interpolation='bilinear',
extent=xlims + ylims)
if colorbar:
plt.colorbar(cax)
kwargs['xlim'] = xlims
kwargs['ylim'] = ylims
kwargs['title'] = kwargs.get('title', 'Persistence image')
kwargs['xlabel'] = kwargs.get('xlabel', 'End radial distance from soma')
kwargs['ylabel'] = kwargs.get('ylabel', 'Start radial distance from soma')
return Zn, cm.plot_style(fig=fig, ax=ax, **kwargs)
def persistence_image_average(ph_list,
new_fig=True,
subplot=111,
xlims=None,
ylims=None,
norm_factor=1.0,
vmin=None,
vmax=None,
cmap=jet_map,
weighted=False,
**kwargs):
"""Merges a list of ph diagrams and plots their respective average image.
"""
# pylint: disable=unexpected-keyword-arg
av_imgs = analysis.get_average_persistence_image(ph_list,
xlims=xlims,
ylims=ylims,
norm_factor=norm_factor,
weighted=weighted)
if xlims is None or xlims is None:
xlims, ylims = analysis.get_limits(ph_list)
if vmin is None:
vmin = np.min(av_imgs)
if vmax is None:
vmax = np.max(av_imgs)
fig, ax = cm.get_figure(new_fig=new_fig, subplot=subplot)
ax.imshow(np.rot90(av_imgs),
vmin=vmin,
vmax=vmax,
cmap=cmap,
interpolation='bilinear',
extent=xlims + ylims)
kwargs['xlim'] = xlims
kwargs['ylim'] = ylims
kwargs['title'] = kwargs.get('title', 'Average persistence image')
kwargs['xlabel'] = kwargs.get('xlabel', 'End radial distance from soma')
kwargs['ylabel'] = kwargs.get('ylabel', 'Start radial distance from soma')
return av_imgs, cm.plot_style(fig=fig, ax=ax, **kwargs)