Fix issues #113 (replace 'is not' with '!=') and #109 (replace palette with a more visible one)

1 files changed, 25 insertions, 32 deletions

diff --git a/src/python/gudhi/persistence_graphical_tools.py b/src/python/gudhi/persistence_graphical_tools.py
index 181bc8ea..a8e2051b 100644
--- a/src/python/gudhi/persistence_graphical_tools.py
+++ b/src/python/gudhi/persistence_graphical_tools.py
@@ -44,27 +44,6 @@ def __min_birth_max_death(persistence, band=0.0):
         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="",
@@ -73,6 +52,7 @@ def plot_persistence_barcode(
     max_barcodes=1000,
     inf_delta=0.1,
     legend=False,
+    colormap=None
 ):
     """This function plots the persistence bar code from persistence values list
     or from a :doc:`persistence file <fileformats>`.
@@ -95,6 +75,9 @@ def plot_persistence_barcode(
     :type inf_delta: float.
     :param legend: Display the dimension color legend (default is False).
     :type legend: boolean.
+    :param colormap: A matplotlib-like qualitative colormaps. Default is None
+        which means :code:`matplotlib.cm.Set1.colors`.
+    :type colormap: tuple of colors (3-tuple of float between 0. and 1.).
     :returns: A matplotlib object containing horizontal bar plot of persistence
         (launch `show()` method on it to display it).
     """
@@ -102,7 +85,7 @@ def plot_persistence_barcode(
         import matplotlib.pyplot as plt
         import matplotlib.patches as mpatches
 
-        if persistence_file is not "":
+        if persistence_file != "":
             if path.isfile(persistence_file):
                 # Reset persistence
                 persistence = []
@@ -116,7 +99,7 @@ def plot_persistence_barcode(
                 print("file " + persistence_file + " not found.")
                 return None
 
-        if max_barcodes is not 1000:
+        if max_barcodes != 1000:
             print("Deprecated parameter. It has been replaced by max_intervals")
             max_intervals = max_barcodes
 
@@ -127,6 +110,9 @@ def plot_persistence_barcode(
                 key=lambda life_time: life_time[1][1] - life_time[1][0],
                 reverse=True,
             )[:max_intervals]
+        
+        if colormap == None:
+            colormap = plt.cm.Set1.colors
 
         persistence = sorted(persistence, key=lambda birth: birth[1][0])
 
@@ -147,7 +133,7 @@ def plot_persistence_barcode(
                     height=0.8,
                     left=interval[1][0],
                     alpha=alpha,
-                    color=palette[interval[0]],
+                    color=colormap[interval[0]],
                     linewidth=0,
                 )
             else:
@@ -158,7 +144,7 @@ def plot_persistence_barcode(
                     height=0.8,
                     left=interval[1][0],
                     alpha=alpha,
-                    color=palette[interval[0]],
+                    color=colormap[interval[0]],
                     linewidth=0,
                 )
             ind = ind + 1
@@ -167,7 +153,7 @@ def plot_persistence_barcode(
             dimensions = list(set(item[0] for item in persistence))
             plt.legend(
                 handles=[
-                    mpatches.Patch(color=palette[dim], label=str(dim))
+                    mpatches.Patch(color=colormap[dim], label=str(dim))
                     for dim in dimensions
                 ],
                 loc="lower right",
@@ -190,6 +176,7 @@ def plot_persistence_diagram(
     max_plots=1000,
     inf_delta=0.1,
     legend=False,
+    colormap=None
 ):
     """This function plots the persistence diagram from persistence values
     list or from a :doc:`persistence file <fileformats>`.
@@ -214,6 +201,9 @@ def plot_persistence_diagram(
     :type inf_delta: float.
     :param legend: Display the dimension color legend (default is False).
     :type legend: boolean.
+    :param colormap: A matplotlib-like qualitative colormaps. Default is None
+        which means :code:`matplotlib.cm.Set1.colors`.
+    :type colormap: tuple of colors (3-tuple of float between 0. and 1.).
     :returns: A matplotlib object containing diagram plot of persistence
         (launch `show()` method on it to display it).
     """
@@ -221,7 +211,7 @@ def plot_persistence_diagram(
         import matplotlib.pyplot as plt
         import matplotlib.patches as mpatches
 
-        if persistence_file is not "":
+        if persistence_file != "":
             if path.isfile(persistence_file):
                 # Reset persistence
                 persistence = []
@@ -235,7 +225,7 @@ def plot_persistence_diagram(
                 print("file " + persistence_file + " not found.")
                 return None
 
-        if max_plots is not 1000:
+        if max_plots != 1000:
             print("Deprecated parameter. It has been replaced by max_intervals")
             max_intervals = max_plots
 
@@ -247,6 +237,9 @@ def plot_persistence_diagram(
                 reverse=True,
             )[:max_intervals]
 
+        if colormap == None:
+            colormap = plt.cm.Set1.colors
+
         (min_birth, max_death) = __min_birth_max_death(persistence, band)
         delta = (max_death - min_birth) * inf_delta
         # Replace infinity values with max_death + delta for diagram to be more
@@ -272,19 +265,19 @@ def plot_persistence_diagram(
                     interval[1][0],
                     interval[1][1],
                     alpha=alpha,
-                    color=palette[interval[0]],
+                    color=colormap[interval[0]],
                 )
             else:
                 # Infinite death case for diagram to be nicer
                 plt.scatter(
-                    interval[1][0], infinity, alpha=alpha, color=palette[interval[0]]
+                    interval[1][0], infinity, alpha=alpha, color=colormap[interval[0]]
                 )
 
         if legend:
             dimensions = list(set(item[0] for item in persistence))
             plt.legend(
                 handles=[
-                    mpatches.Patch(color=palette[dim], label=str(dim))
+                    mpatches.Patch(color=colormap[dim], label=str(dim))
                     for dim in dimensions
                 ]
             )
@@ -354,7 +347,7 @@ def plot_persistence_density(
         import matplotlib.pyplot as plt
         from scipy.stats import kde
 
-        if persistence_file is not "":
+        if persistence_file != "":
             if dimension is None:
                 # All dimension case
                 dimension = -1