diff options
Diffstat (limited to 'cython/cython/persistence_graphical_tools.py')
| -rwxr-xr-x | cython/cython/persistence_graphical_tools.py | 107 |
1 files changed, 60 insertions, 47 deletions
diff --git a/cython/cython/persistence_graphical_tools.py b/cython/cython/persistence_graphical_tools.py index fb837e29..216ab8d6 100755 --- a/cython/cython/persistence_graphical_tools.py +++ b/cython/cython/persistence_graphical_tools.py @@ -1,4 +1,5 @@ import matplotlib.pyplot as plt +import matplotlib.patches as mpatches import numpy as np import os @@ -8,7 +9,7 @@ import os Author(s): Vincent Rouvreau, Bertrand Michel - Copyright (C) 2016 INRIA + 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 @@ -25,16 +26,16 @@ import os """ __author__ = "Vincent Rouvreau, Bertrand Michel" -__copyright__ = "Copyright (C) 2016 INRIA" +__copyright__ = "Copyright (C) 2016 Inria" __license__ = "GPL v3" -def __min_birth_max_death(persistence, band_boot=0.): +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_boot: bootstrap band - :type band_boot: float. + :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 @@ -48,8 +49,8 @@ def __min_birth_max_death(persistence, band_boot=0.): 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 + if band > 0.: + max_death += band return (min_birth, max_death) """ @@ -59,37 +60,27 @@ 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. +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 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. + :param persistence: Persistence values list. :type persistence: list of tuples(dimension, tuple(birth, death)). - :param persistence_file: A persistence file style name (reset persistence if both are set). + :param persistence_file: A :doc:`persistence file <fileformats>` 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). + :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 + :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. - :returns: plot -- An horizontal bar plot of persistence. + :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): @@ -107,9 +98,11 @@ def plot_persistence_barcode(persistence=[], persistence_file='', alpha=0.6, max # 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) / 10.0) + 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 @@ -120,33 +113,49 @@ def plot_persistence_barcode(persistence=[], persistence_file='', alpha=0.6, max # 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]]) + 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]]) + 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_boot=0., max_plots=0): - """This function plots the persistence diagram with an optional confidence band. +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: The persistence to plot. + :param persistence: Persistence values list. :type persistence: list of tuples(dimension, tuple(birth, death)). - :param persistence_file: A persistence file style name (reset persistence if both are set). + :param persistence_file: A :doc:`persistence file <fileformats>` 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). + :param alpha: plot transparency value (0.0 transparent through 1.0 opaque - default is 0.6). :type alpha: float. - :param band_boot: bootstrap band (not displayed if :math:`\leq` 0.) - :type band_boot: 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. - :returns: plot -- A diagram plot of persistence. + :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): @@ -164,9 +173,9 @@ def plot_persistence_diagram(persistence=[], persistence_file='', alpha=0.6, ban # 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) + (min_birth, max_death) = __min_birth_max_death(persistence, band) ind = 0 - delta = ((max_death - min_birth) / 10.0) + delta = ((max_death - min_birth) * inf_delta) # Replace infinity values with max_death + delta for diagram to be more # readable infinity = max_death + delta @@ -179,8 +188,8 @@ def plot_persistence_diagram(persistence=[], persistence_file='', alpha=0.6, ban 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') + if band > 0.: + plt.fill_between(x, x, x+band, alpha=alpha, facecolor='red') # Draw points in loop for interval in reversed(persistence): @@ -194,6 +203,10 @@ def plot_persistence_diagram(persistence=[], persistence_file='', alpha=0.6, ban 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') |