def tree_gaussian_kernel(tree,
plane='xy',
feature='radial_distances',
title='',
diameter=True,
treecol='b',
xlims=None,
ylims=None,
**kwargs):
'''Subplot with ph, barcode
and tree within spheres
'''
from tmd import utils as _utils
from matplotlib.collections import LineCollection
kwargs['output_path'] = kwargs.get('output_path', None)
fig1, ax1 = _view.tree(tree,
new_fig=True,
subplot=121,
plane='xy',
title=title,
treecolor=treecol,
diameter=diameter)
feat = getattr(tree, 'get_section_' + feature)()
segs = tree.get_segments()
def _seg_2d(seg):
"""2d coordinates required for the plotting of a segment"""
horz = _utils.term_dict[plane[0]]
vert = _utils.term_dict[plane[1]]
horz1 = seg[0][horz]
horz2 = seg[1][horz]
vert1 = seg[0][vert]
vert2 = seg[1][vert]
return ((horz1, vert1), (horz2, vert2))
if plane in ['xy', 'yx', 'zx', 'xz', 'yz', 'zy']:
ph = _tm.methods.get_persistence_diagram(tree, feature=feature)
else:
raise Exception('Plane value not recognised')
bounds = max(max(ph))
fig1, ax2 = gaussian_kernel(ph,
new_fig=False,
subplot=122,
xlims=xlims,
ylims=ylims)
_view.common.plt.tight_layout(True)
if kwargs['output_path'] is not None:
fig = _view.common.save_plot(fig=ax1, **kwargs)
return fig1, ax1
def ph_diagram_tree(tree, new_fig=True, plane='xy', output_dir=None, **kwargs):
"""
Generates a 2d figure (barcode) of the persistent homology
of a tree as it has been computed by
Topology.get_persistent_homology method.
"""
if plane in ['xy', 'yx', 'zx', 'xz', 'yz', 'zy']:
ph = _tm.methods.get_persistence_diagram(tree, dim=plane)
else:
raise Exception('Plane value not recognised')
bounds = max(max(ph))
for ip, p in enumerate(ph):
ph[ip].append(_np.abs(p[0] - p[1]))
ph.sort(key=lambda x: x[2])
for ip, p in enumerate(ph):
fig, ax = _view.tree(tree, new_fig=new_fig, subplot=121, plane=plane)
c1 = _view.common.plt.Circle([tree.x[0], tree.y[0]], p[0], alpha=0.2)
c2 = _view.common.plt.Circle([tree.x[0], tree.y[0]], p[1], alpha=0.2)
ax.add_patch(c1) # pylint: disable=no-member
ax.add_patch(c2) # pylint: disable=no-member
fig, ax = _view.common.get_figure(new_fig=False, subplot=122)
for ip1, p1 in enumerate(ph):
if ip1 != ip:
ax.scatter(p1[0], p1[1], c='b')
else:
ax.scatter(p1[0], p1[1], c='r', s=50)
kwargs['title'] = kwargs.get('title', 'P.H. diagram')
kwargs['xlabel'] = kwargs.get('xlabel', 'Birth')
kwargs['ylabel'] = kwargs.get('ylabel', 'Death')
_view.common.plot_style(fig, ax, **kwargs)
_view.common.plt.plot([0, bounds], [0, bounds])
if output_dir is not None:
kwargs['output_path'] = output_dir
kwargs['output_name'] = 'ph_' + '0' * (
2 - len(str(len(tree.get_bifurcations()) - ip))) + str(
len(tree.get_bifurcations()) - ip) + '.png'
_view.common.save_plot(fig, **kwargs)
if output_dir is not None:
kwargs['output_path'] = None
kwargs['output_name'] = None
def ph_on_tree(tree,
new_fig=True,
subplot=False,
plane='xy',
alpha=0.05,
**kwargs):
"""
Generates a 3d figure of the tree and adds
the corresponding spheres that represent
important events in the persistent homology
diagram (birth and death of components).
"""
# Initialization of matplotlib figure and axes.
fig, ax = _view.tree(tree,
new_fig=new_fig,
subplot=subplot,
plane=plane,
**kwargs)
if plane in ['xy', 'yx', 'zx', 'xz', 'yz', 'zy']:
ph = _tm.methods.get_persistence_diagram(tree, dim=plane)
else:
raise Exception('Plane value not recognised')
for p in ph:
c1 = _view.common.plt.Circle([tree.x[0], tree.y[0], tree.z[0]],
p[0],
alpha=alpha)
c2 = _view.common.plt.Circle([tree.x[0], tree.y[0], tree.z[0]],
p[1],
alpha=alpha)
ax.add_patch(c1) # pylint: disable=no-member
ax.add_patch(c2) # pylint: disable=no-member
return _view.common.plot_style(fig=fig, ax=ax, **kwargs)
def tree_instance(tree,
new_fig=True,
plane='xy',
component_num=1,
feature='radial_distances',
diameter=True,
col='r',
treecol='b',
**kwargs):
'''Subplot with ph, barcode and tree within spheres
'''
from tmd import utils as _utils
from matplotlib.collections import LineCollection
if new_fig:
fig1, ax1 = _view.tree(tree,
new_fig=new_fig,
subplot=121,
plane='xy',
title='',
treecolor=treecol,
diameter=diameter)
else:
fig1, ax1 = _view.common.get_figure(new_fig=new_fig, subplot=121)
feat = getattr(tree, 'get_section_' + feature)()
segs = tree.get_segments()
def _seg_2d(seg):
"""2d coordinates required for the plotting of a segment"""
horz = _utils.term_dict[plane[0]]
vert = _utils.term_dict[plane[1]]
horz1 = seg[0][horz]
horz2 = seg[1][horz]
vert1 = seg[0][vert]
vert2 = seg[1][vert]
return ((horz1, vert1), (horz2, vert2))
if plane in ['xy', 'yx', 'zx', 'xz', 'yz', 'zy']:
ph = _tm.methods.get_persistence_diagram(tree, feature=feature)
else:
raise Exception('Plane value not recognised')
bounds = max(max(ph))
if new_fig:
fig1, ax2 = barcode(ph, new_fig=False, subplot=222, color=treecol)
fig1, ax3 = ph_diagram(ph, new_fig=False, subplot=224, color=treecol)
else:
fig1, ax2 = _view.common.get_figure(new_fig=new_fig, subplot=222)
fig1, ax3 = _view.common.get_figure(new_fig=new_fig, subplot=224)
ph = sort_ph(ph)
select_section = ph[component_num]
ax2.plot(select_section[:-1], [component_num, component_num],
color=col,
linewidth=2.)
ax3.scatter(select_section[0], select_section[1], color=col, s=50.)
initial = _np.transpose(
tree.get_sections())[_np.where(feat == select_section[0])[0]]
all_way = _np.array(tree.get_way_to_root(initial[0][1]))
if select_section[1] != -1:
final = _np.transpose(
tree.get_sections())[_np.where(feat == select_section[1])[0]]
until = _np.array(tree.get_way_to_root(final[0][1]))
else:
until = _np.array(tree.get_way_to_root(0))
between = _np.setxor1d(all_way, until)
tmp_segs = _np.array(segs)[between]
toplot_segs = [_seg_2d(seg) for seg in tmp_segs]
linewidth = [2 * d * 2 for d in _np.array(tree.d)[between]]
collection = LineCollection(toplot_segs,
color=col,
linewidth=linewidth,
alpha=1.)
ax1.add_collection(collection)
_view.common.plt.tight_layout(True)
return ax1, collection