From 6ebc098c9bbf233b5a4325faec04236feedab191 Mon Sep 17 00:00:00 2001 From: vrouvrea Date: Fri, 17 Aug 2018 14:48:08 +0000 Subject: Code review : rename max_plots and max_barcodes as max_intervals for peristence_graphical_tools git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/plot_persistence_density_vincent@3803 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: ad73f7e6cc6d72c3ba24b5ac947265c78a29f387 --- src/cython/cython/persistence_graphical_tools.py | 43 ++++++++++++++---------- 1 file changed, 26 insertions(+), 17 deletions(-) diff --git a/src/cython/cython/persistence_graphical_tools.py b/src/cython/cython/persistence_graphical_tools.py index 96b579bd..85d2a5ad 100755 --- a/src/cython/cython/persistence_graphical_tools.py +++ b/src/cython/cython/persistence_graphical_tools.py @@ -62,7 +62,8 @@ try: import os def plot_persistence_barcode(persistence=[], persistence_file='', alpha=0.6, - max_barcodes=1000, inf_delta=0.1, legend=False): + max_intervals=1000, 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 `. @@ -74,10 +75,10 @@ try: :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 max_intervals: maximal number of intervals to display. + Selected points are those with the longest life time. Set it + to 0 to see all. Default value is 1000. + :type max_intervals: int. :param inf_delta: Infinity is placed at ((max_death - min_birth) x inf_delta) above the highest point. A reasonable value is between 0.05 and 0.5 - default is 0.1. @@ -99,9 +100,13 @@ try: 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] + if max_barcodes is not 1000: + print('Deprecated parameter. It has been replaced by max_intervals') + max_intervals = max_barcodes + + if max_intervals > 0 and max_intervals < len(persistence): + # Sort by life time, then takes only the max_intervals elements + persistence = sorted(persistence, key=lambda life_time: life_time[1][1]-life_time[1][0], reverse=True)[:max_intervals] persistence = sorted(persistence, key=lambda birth: birth[1][0]) @@ -139,7 +144,7 @@ try: return plt def plot_persistence_diagram(persistence=[], persistence_file='', alpha=0.6, - band=0., max_plots=1000, inf_delta=0.1, legend=False): + band=0., max_intervals=1000, 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 `. @@ -153,10 +158,10 @@ try: :type alpha: float. :param band: band (not displayed if :math:`\leq` 0. - default is 0.) :type band: float. - :param max_plots: maximal number of points to display. Selected points - are those with the longest life time. Set it to 0 to see all, - default value is 1000. - :type max_plots: int. + :param max_intervals: maximal number of intervals to display. + Selected points are those with the longest life time. Set it + to 0 to see all. Default value is 1000. + :type max_intervals: int. :param inf_delta: Infinity is placed at ((max_death - min_birth) x inf_delta) above the highest point. A reasonable value is between 0.05 and 0.5 - default is 0.1. @@ -178,9 +183,13 @@ try: 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] + if max_plots is not 1000: + print('Deprecated parameter. It has been replaced by max_intervals') + max_intervals = max_plots + + if max_intervals > 0 and max_intervals < len(persistence): + # Sort by life time, then takes only the max_intervals elements + persistence = sorted(persistence, key=lambda life_time: life_time[1][1]-life_time[1][0], reverse=True)[:max_intervals] (min_birth, max_death) = __min_birth_max_death(persistence, band) delta = ((max_death - min_birth) * inf_delta) @@ -227,7 +236,7 @@ try: def plot_persistence_density(persistence=[], persistence_file='', nbins=300, bw_method=None, - max_plots=1000, dimension=None, + max_intervals=1000, dimension=None, cmap=plt.cm.hot_r, legend=False): """This function plots the persistence density from persistence values list or from a :doc:`persistence file `. Be -- cgit v1.2.3