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import matplotlib.pyplot as plt
import numpy as np
import os
"""This file is part of the Gudhi Library. The Gudhi library
(Geometric Understanding in Higher Dimensions) is a generic C++
library for computational topology.
Author(s): Vincent Rouvreau, Bertrand Michel
Copyright (C) 2016 INRIA
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
You should have received a copy of the GNU General Public License
along with this program. If not, see <http://www.gnu.org/licenses/>.
"""
__author__ = "Vincent Rouvreau, Bertrand Michel"
__copyright__ = "Copyright (C) 2016 INRIA"
__license__ = "GPL v3"
def __min_birth_max_death(persistence, band_boot=0.):
"""This function returns (min_birth, max_death) from the persistence.
:param persistence: The persistence to plot.
:type persistence: list of tuples(dimension, tuple(birth, death)).
:param band_boot: bootstrap band
:type band_boot: float.
:returns: (float, float) -- (min_birth, max_death).
"""
# Look for minimum birth date and maximum death date for plot optimisation
max_death = 0
min_birth = persistence[0][1][0]
for interval in reversed(persistence):
if float(interval[1][1]) != float('inf'):
if float(interval[1][1]) > max_death:
max_death = float(interval[1][1])
if float(interval[1][0]) > max_death:
max_death = float(interval[1][0])
if float(interval[1][0]) < min_birth:
min_birth = float(interval[1][0])
if band_boot > 0.:
max_death += band_boot
return (min_birth, max_death)
"""
Only 13 colors for the palette
"""
palette = ['#ff0000', '#00ff00', '#0000ff', '#00ffff', '#ff00ff', '#ffff00',
'#000000', '#880000', '#008800', '#000088', '#888800', '#880088',
'#008888']
def show_palette_values(alpha=0.6):
"""This function shows palette color values in function of the dimension.
:param alpha: alpha value in [0.0, 1.0] for horizontal bars (default is 0.6).
:type alpha: float.
:returns: plot the dimension palette values.
"""
colors = []
for color in palette:
colors.append(color)
y_pos = np.arange(len(palette))
plt.barh(y_pos, y_pos + 1, align='center', alpha=alpha, color=colors)
plt.ylabel('Dimension')
plt.title('Dimension palette values')
return plt
def plot_persistence_barcode(persistence=[], persistence_file='', alpha=0.6, max_barcodes=0):
"""This function plots the persistence bar code.
:param persistence: The persistence to plot.
:type persistence: list of tuples(dimension, tuple(birth, death)).
:param persistence_file: A persistence file style name (reset persistence if both are set).
:type persistence_file: string
:param alpha: alpha value in [0.0, 1.0] for horizontal bars (default is 0.6).
:type alpha: float.
:param max_barcodes: number of maximal barcodes to be displayed
(persistence will be sorted by life time if max_barcodes is set)
:type max_barcodes: int.
:returns: plot -- An horizontal bar plot of persistence.
"""
if persistence_file is not '':
if os.path.isfile(persistence_file):
# Reset persistence
persistence = []
diag = read_persistence_intervals_grouped_by_dimension(persistence_file=persistence_file)
for key in diag.keys():
for persistence_interval in diag[key]:
persistence.append((key, persistence_interval))
else:
print("file " + persistence_file + " not found.")
return None
if max_barcodes > 0 and max_barcodes < len(persistence):
# Sort by life time, then takes only the max_plots elements
persistence = sorted(persistence, key=lambda life_time: life_time[1][1]-life_time[1][0], reverse=True)[:max_barcodes]
(min_birth, max_death) = __min_birth_max_death(persistence)
ind = 0
delta = ((max_death - min_birth) / 10.0)
# Replace infinity values with max_death + delta for bar code to be more
# readable
infinity = max_death + delta
axis_start = min_birth - delta
# Draw horizontal bars in loop
for interval in reversed(persistence):
if float(interval[1][1]) != float('inf'):
# Finite death case
plt.barh(ind, (interval[1][1] - interval[1][0]), height=0.8,
left = interval[1][0], alpha=alpha,
color = palette[interval[0]])
else:
# Infinite death case for diagram to be nicer
plt.barh(ind, (infinity - interval[1][0]), height=0.8,
left = interval[1][0], alpha=alpha,
color = palette[interval[0]])
ind = ind + 1
plt.title('Persistence barcode')
# Ends plot on infinity value and starts a little bit before min_birth
plt.axis([axis_start, infinity, 0, ind])
return plt
def plot_persistence_diagram(persistence=[], persistence_file='', alpha=0.6, band_boot=0., max_plots=0):
"""This function plots the persistence diagram with an optional confidence band.
:param persistence: The persistence to plot.
:type persistence: list of tuples(dimension, tuple(birth, death)).
:param persistence_file: A persistence file style name (reset persistence if both are set).
:type persistence_file: string
:param alpha: alpha value in [0.0, 1.0] for points and horizontal infinity line (default is 0.6).
:type alpha: float.
:param band_boot: bootstrap band (not displayed if :math:`\leq` 0.)
:type band_boot: float.
:param max_plots: number of maximal plots to be displayed
:type max_plots: int.
:returns: plot -- A diagram plot of persistence.
"""
if persistence_file is not '':
if os.path.isfile(persistence_file):
# Reset persistence
persistence = []
diag = read_persistence_intervals_grouped_by_dimension(persistence_file=persistence_file)
for key in diag.keys():
for persistence_interval in diag[key]:
persistence.append((key, persistence_interval))
else:
print("file " + persistence_file + " not found.")
return None
if max_plots > 0 and max_plots < len(persistence):
# Sort by life time, then takes only the max_plots elements
persistence = sorted(persistence, key=lambda life_time: life_time[1][1]-life_time[1][0], reverse=True)[:max_plots]
(min_birth, max_death) = __min_birth_max_death(persistence, band_boot)
ind = 0
delta = ((max_death - min_birth) / 10.0)
# Replace infinity values with max_death + delta for diagram to be more
# readable
infinity = max_death + delta
axis_start = min_birth - delta
# line display of equation : birth = death
x = np.linspace(axis_start, infinity, 1000)
# infinity line and text
plt.plot(x, x, color='k', linewidth=1.0)
plt.plot(x, [infinity] * len(x), linewidth=1.0, color='k', alpha=alpha)
plt.text(axis_start, infinity, r'$\infty$', color='k', alpha=alpha)
# bootstrap band
if band_boot > 0.:
plt.fill_between(x, x, x+band_boot, alpha=alpha, facecolor='red')
# Draw points in loop
for interval in reversed(persistence):
if float(interval[1][1]) != float('inf'):
# Finite death case
plt.scatter(interval[1][0], interval[1][1], alpha=alpha,
color = palette[interval[0]])
else:
# Infinite death case for diagram to be nicer
plt.scatter(interval[1][0], infinity, alpha=alpha,
color = palette[interval[0]])
ind = ind + 1
plt.title('Persistence diagram')
plt.xlabel('Birth')
plt.ylabel('Death')
# Ends plot on infinity value and starts a little bit before min_birth
plt.axis([axis_start, infinity, axis_start, infinity + delta])
return plt
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