diff options
| author | ROUVREAU Vincent <vincent.rouvreau@inria.fr> | 2019-05-21 18:08:38 +0200 |
|---|---|---|
| committer | ROUVREAU Vincent <vincent.rouvreau@inria.fr> | 2019-05-21 18:08:38 +0200 |
| commit | 7e8685458f684f347b2aa6a77a288c249c722f25 (patch) | |
| tree | e24dc5ab73159ba1b878d63017f04fdc5552d49a /src | |
| parent | aedd6928abdcb3057ce7d48f254f8e698d7c7a79 (diff) | |
Use numpy to speed computations for plot_persistence_density and fix code review
Diffstat (limited to 'src')
| -rw-r--r-- | src/cython/cython/persistence_graphical_tools.py | 30 |
1 files changed, 14 insertions, 16 deletions
diff --git a/src/cython/cython/persistence_graphical_tools.py b/src/cython/cython/persistence_graphical_tools.py index 98cd355c..7bb69840 100644 --- a/src/cython/cython/persistence_graphical_tools.py +++ b/src/cython/cython/persistence_graphical_tools.py @@ -291,32 +291,30 @@ def plot_persistence_density(persistence=[], persistence_file='', from scipy.stats import kde if persistence_file is not '': + if dimension is None: + # All dimension case + dimension = -1 if 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)) + persistence_dim = read_persistence_intervals_in_dimension(persistence_file=persistence_file, + only_this_dim=dimension) + print(persistence_dim) else: print("file " + persistence_file + " not found.") return None - persistence_dim = [] - if dimension is not None: - persistence_dim = [(dim_interval) for dim_interval in persistence if (dim_interval[0] == dimension)] - else: - persistence_dim = persistence + if len(persistence) > 0: + persistence_dim = np.array([(dim_interval[1][0], dim_interval[1][1]) for dim_interval in persistence if (dim_interval[0] == dimension) or (dimension is None)]) + persistence_dim = persistence_dim[np.isfinite(persistence_dim[:,1])] if max_intervals > 0 and max_intervals < len(persistence_dim): # Sort by life time, then takes only the max_intervals elements - persistence_dim = sorted(persistence_dim, - key=lambda life_time: life_time[1][1]-life_time[1][0], - reverse=True)[:max_intervals] + persistence_dim = np.array(sorted(persistence_dim, + key=lambda life_time: life_time[1]-life_time[0], + reverse=True)[:max_intervals]) # Set as numpy array birth and death (remove undefined values - inf and NaN) - birth = np.asarray([(interval[1][0]) for interval in persistence_dim if (isfinite(interval[1][1]) and isfinite(interval[1][0]))]) - death = np.asarray([(interval[1][1]) for interval in persistence_dim if (isfinite(interval[1][1]) and isfinite(interval[1][0]))]) + birth = persistence_dim[:,0] + death = persistence_dim[:,1] # line display of equation : birth = death x = np.linspace(death.min(), birth.max(), 1000) |