solved scale issue and removed title/aspect as functions return ax

1 files changed, 60 insertions, 17 deletions

diff --git a/src/python/gudhi/persistence_graphical_tools.py b/src/python/gudhi/persistence_graphical_tools.py
index 246280de..8ddfdba8 100644
--- a/src/python/gudhi/persistence_graphical_tools.py
+++ b/src/python/gudhi/persistence_graphical_tools.py
@@ -5,6 +5,7 @@
 # Copyright (C) 2016 Inria
 #
 # Modification(s):
+#   - 2020/02 Theo Lacombe: Added more options for improved rendering and more flexibility.
 #   - YYYY/MM Author: Description of the modification
 
 from os import path
@@ -43,6 +44,7 @@ def __min_birth_max_death(persistence, band=0.0):
         max_death += band
     return (min_birth, max_death)
 
+
 def plot_persistence_barcode(
     persistence=[],
     persistence_file="",
@@ -52,7 +54,8 @@ def plot_persistence_barcode(
     inf_delta=0.1,
     legend=False,
     colormap=None,
-    axes=None
+    axes=None,
+    fontsize=16,
 ):
     """This function plots the persistence bar code from persistence values list
     or from a :doc:`persistence file <fileformats>`.
@@ -81,11 +84,16 @@ def plot_persistence_barcode(
     :param axes: A matplotlib-like subplot axes. If None, the plot is drawn on
         a new set of axes.
     :type axes: `matplotlib.axes.Axes`
+    :param fontsize: Fontsize to use in axis.
+    :type fontsize: int
     :returns: (`matplotlib.axes.Axes`): The axes on which the plot was drawn.
     """
     try:
         import matplotlib.pyplot as plt
         import matplotlib.patches as mpatches
+        from matplotlib import rc
+        plt.rc('text', usetex=True)
+        plt.rc('font', family='serif')
 
         if persistence_file != "":
             if path.isfile(persistence_file):
@@ -163,7 +171,7 @@ def plot_persistence_barcode(
                 loc="lower right",
             )
 
-        axes.set_title("Persistence barcode")
+        axes.set_title("Persistence barcode", fontsize=fontsize)
 
         # Ends plot on infinity value and starts a little bit before min_birth
         axes.axis([axis_start, infinity, 0, ind])
@@ -183,7 +191,9 @@ def plot_persistence_diagram(
     inf_delta=0.1,
     legend=False,
     colormap=None,
-    axes=None
+    axes=None,
+    fontsize=16,
+    greyblock=True
 ):
     """This function plots the persistence diagram from persistence values
     list or from a :doc:`persistence file <fileformats>`.
@@ -214,11 +224,19 @@ def plot_persistence_diagram(
     :param axes: A matplotlib-like subplot axes. If None, the plot is drawn on
         a new set of axes.
     :type axes: `matplotlib.axes.Axes`
+    :param fontsize: Fontsize to use in axis.
+    :type fontsize: int
+    :param greyblock: if we want to plot a grey patch on the lower half plane for nicer rendering. Default True.
+    :type greyblock: boolean
     :returns: (`matplotlib.axes.Axes`): The axes on which the plot was drawn.
     """
     try:
         import matplotlib.pyplot as plt
         import matplotlib.patches as mpatches
+        from matplotlib import rc
+        plt.rc('text', usetex=True)
+        plt.rc('font', family='serif')
+
 
         if persistence_file != "":
             if path.isfile(persistence_file):
@@ -256,18 +274,27 @@ def plot_persistence_diagram(
         # Replace infinity values with max_death + delta for diagram to be more
         # readable
         infinity = max_death + delta
+        axis_end = max_death + delta / 2
         axis_start = min_birth - delta
 
-        # line display of equation : birth = death
-        x = np.linspace(axis_start, infinity, 1000)
         # infinity line and text
-        axes.plot(x, x, color="k", linewidth=1.0)
-        axes.plot(x, [infinity] * len(x), linewidth=1.0, color="k", alpha=alpha)
-        axes.text(axis_start, infinity, r"$\infty$", color="k", alpha=alpha)
+        axes.plot([axis_start, axis_end], [axis_start, axis_end], linewidth=1.0, color="k")
+        axes.plot([axis_start, axis_end], [infinity, infinity], linewidth=1.0, color="k", alpha=alpha)
+        # Infinity label
+        yt = axes.get_yticks()
+        yt = yt[np.where(yt < axis_end)] # to avoid ploting ticklabel higher than infinity
+        yt = np.append(yt, infinity)
+        ytl = ["%.3f" % e for e in yt]  # to avoid float precision error
+        ytl[-1] = r'$+\infty$'
+        axes.set_yticks(yt)
+        axes.set_yticklabels(ytl)
         # bootstrap band
         if band > 0.0:
+            x = np.linspace(axis_start, infinity, 1000)
             axes.fill_between(x, x, x + band, alpha=alpha, facecolor="red")
-
+        # lower diag patch
+        if greyblock:
+            axes.add_patch(mpatches.Polygon([[axis_start, axis_start], [axis_end, axis_start], [axis_end, axis_end]], fill=True, color='lightgrey'))
         # Draw points in loop
         for interval in reversed(persistence):
             if float(interval[1][1]) != float("inf"):
@@ -293,11 +320,11 @@ def plot_persistence_diagram(
                 ]
             )
 
-        axes.set_xlabel("Birth")
-        axes.set_ylabel("Death")
+        axes.set_xlabel("Birth", fontsize=fontsize)
+        axes.set_ylabel("Death", fontsize=fontsize)
+        axes.set_title("Persistence diagram", fontsize=fontsize)
         # Ends plot on infinity value and starts a little bit before min_birth
-        axes.axis([axis_start, infinity, axis_start, infinity + delta])
-        axes.set_title("Persistence diagram")
+        axes.axis([axis_start, axis_end, axis_start, infinity + delta/2])
         return axes
 
     except ImportError:
@@ -313,7 +340,9 @@ def plot_persistence_density(
     dimension=None,
     cmap=None,
     legend=False,
-    axes=None
+    axes=None,
+    fontsize=16,
+    greyblock=True
 ):
     """This function plots the persistence density from persistence
     values list or from a :doc:`persistence file <fileformats>`. Be
@@ -355,11 +384,21 @@ def plot_persistence_density(
     :param axes: A matplotlib-like subplot axes. If None, the plot is drawn on
         a new set of axes.
     :type axes: `matplotlib.axes.Axes`
+    :param fontsize: Fontsize to use in axis.
+    :type fontsize: int
+    :param greyblock: if we want to plot a grey patch on the lower half plane 
+                         for nicer rendering. Default True.
+    :type greyblock: boolean
     :returns: (`matplotlib.axes.Axes`): The axes on which the plot was drawn.
     """
     try:
         import matplotlib.pyplot as plt
+        import matplotlib.patches as mpatches
         from scipy.stats import kde
+        from matplotlib import rc
+        plt.rc('text', usetex=True)
+        plt.rc('font', family='serif')
+
 
         if persistence_file != "":
             if dimension is None:
@@ -418,12 +457,16 @@ def plot_persistence_density(
         # Make the plot
         img = axes.pcolormesh(xi, yi, zi.reshape(xi.shape), cmap=cmap)
 
+        if greyblock:
+            axes.add_patch(mpatches.Polygon([[birth.min(), birth.min()], [death.max(), birth.min()], [death.max(), death.max()]], fill=True, color='lightgrey'))
+
         if legend:
             plt.colorbar(img, ax=axes)
 
-        axes.set_xlabel("Birth")
-        axes.set_ylabel("Death")
-        axes.set_title("Persistence density")
+        axes.set_xlabel("Birth", fontsize=fontsize)
+        axes.set_ylabel("Death", fontsize=fontsize)
+        axes.set_title("Persistence density", fontsize=fontsize)
+
         return axes
 
     except ImportError: