diff options
Diffstat (limited to 'cython/cython/persistence_graphical_tools.py')
| -rwxr-xr-x | cython/cython/persistence_graphical_tools.py | 220 |
1 files changed, 0 insertions, 220 deletions
diff --git a/cython/cython/persistence_graphical_tools.py b/cython/cython/persistence_graphical_tools.py deleted file mode 100755 index 314bd6db..00000000 --- a/cython/cython/persistence_graphical_tools.py +++ /dev/null @@ -1,220 +0,0 @@ -"""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" - -try: - import matplotlib.pyplot as plt - import matplotlib.patches as mpatches - import numpy as np - import os - - def __min_birth_max_death(persistence, band=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: band - :type band: 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 > 0.: - max_death += band - 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 plot_persistence_barcode(persistence=[], persistence_file='', alpha=0.6, - max_barcodes=1000, inf_delta=0.1, legend=False): - """This function plots the persistence bar code from persistence values list - or from a :doc:`persistence file <fileformats>`. - - :param persistence: Persistence values list. - :type persistence: list of tuples(dimension, tuple(birth, death)). - :param persistence_file: A :doc:`persistence file <fileformats>` style name - (reset persistence if both are set). - :type persistence_file: string - :param alpha: barcode transparency value (0.0 transparent through 1.0 opaque - default is 0.6). - :type alpha: float. - :param max_barcodes: number of maximal barcodes to be displayed. - Set it to 0 to see all, Default value is 1000. - (persistence will be sorted by life time if max_barcodes is set) - :type max_barcodes: int. - :param inf_delta: Infinity is placed at ((max_death - min_birth) x inf_delta). - A reasonable value is between 0.05 and 0.5 - default is 0.1. - :type inf_delta: float. - :returns: A matplotlib object containing horizontal bar plot of persistence - (launch `show()` method on it to display it). - """ - 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] - - persistence = sorted(persistence, key=lambda birth: birth[1][0]) - - (min_birth, max_death) = __min_birth_max_death(persistence) - ind = 0 - delta = ((max_death - min_birth) * inf_delta) - # 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]], - linewidth=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]], - linewidth=0) - ind = ind + 1 - - if legend: - dimensions = list(set(item[0] for item in persistence)) - plt.legend(handles=[mpatches.Patch(color=palette[dim], - label=str(dim)) for dim in dimensions], - loc='lower right') - 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=0., max_plots=1000, inf_delta=0.1, legend=False): - """This function plots the persistence diagram from persistence values list - or from a :doc:`persistence file <fileformats>`. - - :param persistence: Persistence values list. - :type persistence: list of tuples(dimension, tuple(birth, death)). - :param persistence_file: A :doc:`persistence file <fileformats>` style name - (reset persistence if both are set). - :type persistence_file: string - :param alpha: plot transparency value (0.0 transparent through 1.0 opaque - default is 0.6). - :type alpha: float. - :param band: band (not displayed if :math:`\leq` 0. - default is 0.) - :type band: float. - :param max_plots: number of maximal plots to be displayed - Set it to 0 to see all, Default value is 1000. - (persistence will be sorted by life time if max_plots is set) - :type max_plots: int. - :param inf_delta: Infinity is placed at ((max_death - min_birth) x inf_delta). - A reasonable value is between 0.05 and 0.5 - default is 0.1. - :type inf_delta: float. - :returns: A matplotlib object containing diagram plot of persistence - (launch `show()` method on it to display it). - """ - 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) - ind = 0 - delta = ((max_death - min_birth) * inf_delta) - # 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 > 0.: - plt.fill_between(x, x, x+band, 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 - - if legend: - dimensions = list(set(item[0] for item in persistence)) - plt.legend(handles=[mpatches.Patch(color=palette[dim], label=str(dim)) for dim in dimensions]) - - 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 - -except ImportError: - # Continue in case of import error, functions won't be available - pass |