Fix #461 and review all error cases (no more prints, warnings and exceptions instead)

2 files changed, 141 insertions, 108 deletions

diff --git a/src/python/CMakeLists.txt b/src/python/CMakeLists.txt
index 98f2b85f..1f0d74d4 100644
--- a/src/python/CMakeLists.txt
+++ b/src/python/CMakeLists.txt
@@ -542,6 +542,10 @@ if(PYTHONINTERP_FOUND)
       add_gudhi_py_test(test_dtm_rips_complex)
     endif()
 
+    # persistence graphical tools
+    if(MATPLOTLIB_FOUND)
+      add_gudhi_py_test(test_persistence_graphical_tools)
+    endif()
 
     # Set missing or not modules
     set(GUDHI_MODULES ${GUDHI_MODULES} "python" CACHE INTERNAL "GUDHI_MODULES")
diff --git a/src/python/gudhi/persistence_graphical_tools.py b/src/python/gudhi/persistence_graphical_tools.py
index b129b375..9bfc19e0 100644
--- a/src/python/gudhi/persistence_graphical_tools.py
+++ b/src/python/gudhi/persistence_graphical_tools.py
@@ -13,6 +13,8 @@ from math import isfinite
 import numpy as np
 from functools import lru_cache
 import warnings
+import errno
+import os
 
 from gudhi.reader_utils import read_persistence_intervals_in_dimension
 from gudhi.reader_utils import read_persistence_intervals_grouped_by_dimension
@@ -45,6 +47,9 @@ def __min_birth_max_death(persistence, band=0.0):
             min_birth = float(interval[1][0])
     if band > 0.0:
         max_death += band
+    # can happen if only points at inf death
+    if min_birth == max_death:
+        max_death = max_death + 1.
     return (min_birth, max_death)
 
 
@@ -54,7 +59,7 @@ def _array_handler(a):
                 persistence-compatible list (padding with 0), so that the
                 plot can be performed seamlessly.
     '''
-    if isinstance(a[0][1], np.float64) or isinstance(a[0][1], float):
+    if isinstance(a[0][1], np.floating) or isinstance(a[0][1], float):
         return [[0, x] for x in a]
     else:
         return a
@@ -88,7 +93,7 @@ def _matplotlib_can_use_tex():
         from matplotlib import checkdep_usetex
         return checkdep_usetex(True)
     except ImportError:
-        print("This function is not available, you may be missing matplotlib.")
+        warnings.warn("This function is not available, you may be missing matplotlib.")
 
 
 def plot_persistence_barcode(
@@ -157,53 +162,58 @@ def plot_persistence_barcode(
                     for persistence_interval in diag[key]:
                         persistence.append((key, persistence_interval))
             else:
-                print("file " + persistence_file + " not found.")
-                return None
+                raise FileNotFoundError(errno.ENOENT, os.strerror(errno.ENOENT), persistence_file)
 
-        persistence = _array_handler(persistence)
-
-        persistence = _limit_to_max_intervals(persistence, max_intervals,
-                                              key = lambda life_time: life_time[1][1] - life_time[1][0])
-
-        if colormap == None:
-            colormap = plt.cm.Set1.colors
-        if axes == None:
-            _, axes = plt.subplots(1, 1)
-
-        persistence = sorted(persistence, key=lambda birth: birth[1][0])
+        try:
+            persistence = _array_handler(persistence)
+            persistence = _limit_to_max_intervals(persistence, max_intervals,
+                                                  key = lambda life_time: life_time[1][1] - life_time[1][0])
+            (min_birth, max_death) = __min_birth_max_death(persistence)
+            persistence = sorted(persistence, key=lambda birth: birth[1][0])
+        except IndexError:
+            min_birth, max_death = 0., 1.
+            pass
 
-        (min_birth, max_death) = __min_birth_max_death(persistence)
-        ind = 0
         delta = (max_death - min_birth) * inf_delta
         # Replace infinity values with max_death + delta for bar code to be more
         # readable
         infinity = max_death + delta
         axis_start = min_birth - delta
+
+        if axes == None:
+            _, axes = plt.subplots(1, 1)
+        if colormap == None:
+            colormap = plt.cm.Set1.colors
+        ind = 0
+
         # Draw horizontal bars in loop
         for interval in reversed(persistence):
-            if float(interval[1][1]) != float("inf"):
-                # Finite death case
-                axes.barh(
-                    ind,
-                    (interval[1][1] - interval[1][0]),
-                    height=0.8,
-                    left=interval[1][0],
-                    alpha=alpha,
-                    color=colormap[interval[0]],
-                    linewidth=0,
-                )
-            else:
-                # Infinite death case for diagram to be nicer
-                axes.barh(
-                    ind,
-                    (infinity - interval[1][0]),
-                    height=0.8,
-                    left=interval[1][0],
-                    alpha=alpha,
-                    color=colormap[interval[0]],
-                    linewidth=0,
-                )
-            ind = ind + 1
+            try:
+                if float(interval[1][1]) != float("inf"):
+                    # Finite death case
+                    axes.barh(
+                        ind,
+                        (interval[1][1] - interval[1][0]),
+                        height=0.8,
+                        left=interval[1][0],
+                        alpha=alpha,
+                        color=colormap[interval[0]],
+                        linewidth=0,
+                    )
+                else:
+                    # Infinite death case for diagram to be nicer
+                    axes.barh(
+                        ind,
+                        (infinity - interval[1][0]),
+                        height=0.8,
+                        left=interval[1][0],
+                        alpha=alpha,
+                        color=colormap[interval[0]],
+                        linewidth=0,
+                    )
+                ind = ind + 1
+            except IndexError:
+                pass
 
         if legend:
             dimensions = list(set(item[0] for item in persistence))
@@ -218,11 +228,12 @@ def plot_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])
+        if ind != 0:
+            axes.axis([axis_start, infinity, 0, ind])
         return axes
 
     except ImportError:
-        print("This function is not available, you may be missing matplotlib.")
+        warnings.warn("This function is not available, you may be missing matplotlib.")
 
 
 def plot_persistence_diagram(
@@ -296,20 +307,17 @@ def plot_persistence_diagram(
                     for persistence_interval in diag[key]:
                         persistence.append((key, persistence_interval))
             else:
-                print("file " + persistence_file + " not found.")
-                return None
-
-        persistence = _array_handler(persistence)
-
-        persistence = _limit_to_max_intervals(persistence, max_intervals,
-                                              key = lambda life_time: life_time[1][1] - life_time[1][0])
+                raise FileNotFoundError(errno.ENOENT, os.strerror(errno.ENOENT), persistence_file)
 
-        if colormap == None:
-            colormap = plt.cm.Set1.colors
-        if axes == None:
-            _, axes = plt.subplots(1, 1)
+        try:
+            persistence = _array_handler(persistence)
+            persistence = _limit_to_max_intervals(persistence, max_intervals,
+                                                  key = lambda life_time: life_time[1][1] - life_time[1][0])
+            min_birth, max_death = __min_birth_max_death(persistence, band)
+        except IndexError:
+            min_birth, max_death = 0., 1.
+            pass
 
-        (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
         # readable
@@ -317,33 +325,43 @@ def plot_persistence_diagram(
         axis_end = max_death + delta / 2
         axis_start = min_birth - delta
 
+        if axes == None:
+            _, axes = plt.subplots(1, 1)
+        if colormap == None:
+            colormap = plt.cm.Set1.colors
         # 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'))
+            axes.add_patch(mpatches.Polygon([[axis_start, axis_start], [axis_end, axis_start], [axis_end, axis_end]],
+                                            fill=True, color='lightgrey'))
+        # line display of equation : birth = death
+        axes.plot([axis_start, axis_end], [axis_start, axis_end], linewidth=1.0, color="k")
+
         # Draw points in loop
         pts_at_infty = False  # Records presence of pts at infty
         for interval in reversed(persistence):
-            if float(interval[1][1]) != float("inf"):
-                # Finite death case
-                axes.scatter(
-                    interval[1][0],
-                    interval[1][1],
-                    alpha=alpha,
-                    color=colormap[interval[0]],
-                )
-            else:
-                pts_at_infty = True
-                # Infinite death case for diagram to be nicer
-                axes.scatter(
-                    interval[1][0], infinity, alpha=alpha, color=colormap[interval[0]]
-                )
+            try:
+                if float(interval[1][1]) != float("inf"):
+                    # Finite death case
+                    axes.scatter(
+                        interval[1][0],
+                        interval[1][1],
+                        alpha=alpha,
+                        color=colormap[interval[0]],
+                    )
+                else:
+                    pts_at_infty = True
+                    # Infinite death case for diagram to be nicer
+                    axes.scatter(
+                        interval[1][0], infinity, alpha=alpha, color=colormap[interval[0]]
+                    )
+            except IndexError:
+                pass
         if pts_at_infty:
             # infinity line and text
-            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()
@@ -371,7 +389,7 @@ def plot_persistence_diagram(
         return axes
 
     except ImportError:
-        print("This function is not available, you may be missing matplotlib.")
+        warnings.warn("This function is not available, you may be missing matplotlib.")
 
 
 def plot_persistence_density(
@@ -461,27 +479,7 @@ def plot_persistence_density(
                     persistence_file=persistence_file, only_this_dim=dimension
                 )
             else:
-                print("file " + persistence_file + " not found.")
-                return None
-
-        if len(persistence) > 0:
-            persistence = _array_handler(persistence)
-            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])]
-
-        persistence_dim = np.array(_limit_to_max_intervals(persistence_dim, max_intervals,
-                                                           key = lambda life_time: life_time[1] - life_time[0]))
-
-        # Set as numpy array birth and death (remove undefined values - inf and NaN)
-        birth = persistence_dim[:, 0]
-        death = persistence_dim[:, 1]
+                raise FileNotFoundError(errno.ENOENT, os.strerror(errno.ENOENT), persistence_file)
 
         # default cmap value cannot be done at argument definition level as matplotlib is not yet defined.
         if cmap is None:
@@ -489,23 +487,56 @@ def plot_persistence_density(
         if axes == None:
             _, axes = plt.subplots(1, 1)
 
+        try:
+            if len(persistence) > 0:
+                # if not read from file but given by an argument
+                persistence = _array_handler(persistence)
+                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])]
+            persistence_dim = np.array(_limit_to_max_intervals(persistence_dim, max_intervals,
+                                                               key = lambda life_time: life_time[1] - life_time[0]))
+
+            # Set as numpy array birth and death (remove undefined values - inf and NaN)
+            birth = persistence_dim[:, 0]
+            death = persistence_dim[:, 1]
+            birth_min = birth.min()
+            birth_max = birth.max()
+            death_min = death.min()
+            death_max = death.max()
+
+            # Evaluate a gaussian kde on a regular grid of nbins x nbins over data extents
+            k = kde.gaussian_kde([birth, death], bw_method=bw_method)
+            xi, yi = np.mgrid[
+                birth_min : birth_max : nbins * 1j,
+                death_min : death_max : nbins * 1j,
+            ]
+            zi = k(np.vstack([xi.flatten(), yi.flatten()]))
+            # Make the plot
+            img = axes.pcolormesh(xi, yi, zi.reshape(xi.shape), cmap=cmap, shading='auto')
+
+        # IndexError on empty diagrams, ValueError on only inf death values
+        except (IndexError, ValueError):
+            birth_min = 0.
+            birth_max = 1.
+            death_min = 0.
+            death_max = 1.
+            pass
+
         # line display of equation : birth = death
-        x = np.linspace(death.min(), birth.max(), 1000)
+        x = np.linspace(death_min, birth_max, 1000)
         axes.plot(x, x, color="k", linewidth=1.0)
 
-        # Evaluate a gaussian kde on a regular grid of nbins x nbins over data extents
-        k = kde.gaussian_kde([birth, death], bw_method=bw_method)
-        xi, yi = np.mgrid[
-            birth.min() : birth.max() : nbins * 1j,
-            death.min() : death.max() : nbins * 1j,
-        ]
-        zi = k(np.vstack([xi.flatten(), yi.flatten()]))
-
-        # Make the plot
-        img = axes.pcolormesh(xi, yi, zi.reshape(xi.shape), cmap=cmap, shading='auto')
-
         if greyblock:
-            axes.add_patch(mpatches.Polygon([[birth.min(), birth.min()], [death.max(), birth.min()], [death.max(), death.max()]], fill=True, color='lightgrey'))
+            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)
@@ -517,6 +548,4 @@ def plot_persistence_density(
         return axes
 
     except ImportError:
-        print(
-            "This function is not available, you may be missing matplotlib and/or scipy."
-        )
+        warnings.warn("This function is not available, you may be missing matplotlib and/or scipy.")