diff options
Diffstat (limited to 'src/cython/cython/persistence_graphical_tools.py')
| -rwxr-xr-x | src/cython/cython/persistence_graphical_tools.py | 41 |
1 files changed, 24 insertions, 17 deletions
diff --git a/src/cython/cython/persistence_graphical_tools.py b/src/cython/cython/persistence_graphical_tools.py index fb837e29..f7dadb53 100755 --- a/src/cython/cython/persistence_graphical_tools.py +++ b/src/cython/cython/persistence_graphical_tools.py @@ -28,13 +28,13 @@ __author__ = "Vincent Rouvreau, Bertrand Michel" __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 +48,8 @@ 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) """ @@ -77,16 +77,17 @@ def show_palette_values(alpha=0.6): plt.title('Dimension palette values') return plt -def plot_persistence_barcode(persistence=[], persistence_file='', alpha=0.6, max_barcodes=0): +def plot_persistence_barcode(persistence=[], persistence_file='', alpha=0.6, max_barcodes=1000): """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). + :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. @@ -107,6 +108,8 @@ 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) @@ -120,12 +123,14 @@ 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 plt.title('Persistence barcode') @@ -133,18 +138,20 @@ def plot_persistence_barcode(persistence=[], persistence_file='', alpha=0.6, max 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): +def plot_persistence_diagram(persistence=[], persistence_file='', alpha=0.6, band=0., max_plots=1000): """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). + :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. """ @@ -164,7 +171,7 @@ 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) # Replace infinity values with max_death + delta for diagram to be more @@ -179,8 +186,8 @@ 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): |