Code review : Try to import module. Functions are unavailable if not available.

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/plot_persistence_density_vincent@3785 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: 53c89a30f7992aa8d20e8330628c03291cea6473

3 files changed, 108 insertions, 103 deletions

diff --git a/src/cmake/modules/GUDHI_third_party_libraries.cmake b/src/cmake/modules/GUDHI_third_party_libraries.cmake
index f03c2177..1ad0c1fd 100644
--- a/src/cmake/modules/GUDHI_third_party_libraries.cmake
+++ b/src/cmake/modules/GUDHI_third_party_libraries.cmake
@@ -143,6 +143,7 @@ if( PYTHONINTERP_FOUND )
   find_python_module("pytest")
   find_python_module("matplotlib")
   find_python_module("numpy")
+  find_python_module("scipy")
 endif()
 
 if(NOT GUDHI_CYTHON_PATH)
diff --git a/src/cython/CMakeLists.txt b/src/cython/CMakeLists.txt
index 1849a6ec..542be9b0 100644
--- a/src/cython/CMakeLists.txt
+++ b/src/cython/CMakeLists.txt
@@ -54,10 +54,8 @@ if(CYTHON_FOUND)
   if(NUMPY_FOUND)
     add_gudhi_debug_info("Numpy version ${NUMPY_VERSION}")
   endif()
-  if(MATPLOTLIB_FOUND AND NUMPY_FOUND)
-    set(GUDHI_CYTHON_MODULES "${GUDHI_CYTHON_MODULES}persistence_graphical_tools;")
-  else()
-      set(GUDHI_CYTHON_MISSING_MODULES "${GUDHI_CYTHON_MODULES}persistence_graphical_tools;")
+  if(SCIPY_FOUND)
+    add_gudhi_debug_info("Scipy version ${SCIPY_VERSION}")
   endif()
 
   message("++ ${PYTHON_EXECUTABLE} v.${PYTHON_VERSION_STRING} - Cython is ${CYTHON_VERSION} - Sphinx is ${SPHINX_PATH}")
@@ -368,7 +366,7 @@ if(CYTHON_FOUND)
   add_gudhi_py_test(test_reader_utils)
 
   # Documentation generation is available through sphinx - requires all modules
-  if(SPHINX_PATH AND MATPLOTLIB_FOUND AND NUMPY_FOUND AND NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1)
+  if(SPHINX_PATH AND MATPLOTLIB_FOUND AND NUMPY_FOUND AND SCIPY_FOUND AND NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1)
     set (GUDHI_SPHINX_MESSAGE "Generating API documentation with Sphinx in ${CMAKE_CURRENT_BINARY_DIR}/sphinx/")
     # User warning - Sphinx is a static pages generator, and configured to work fine with user_version
     # Images and biblio warnings because not found on developper version
diff --git a/src/cython/cython/persistence_graphical_tools.py b/src/cython/cython/persistence_graphical_tools.py
index e172c65b..e154c0b2 100755
--- a/src/cython/cython/persistence_graphical_tools.py
+++ b/src/cython/cython/persistence_graphical_tools.py
@@ -24,44 +24,42 @@ __author__ = "Vincent Rouvreau, Bertrand Michel"
 __copyright__ = "Copyright (C) 2016 Inria"
 __license__ = "GPL v3"
 
+def __min_birth_max_death(persistence, band=0.):
+    """This function returns (min_birth, max_death) from the persistence.
+
+    :param persistence: The persistence to plot.
+    :type persistence: list of tuples(dimension, tuple(birth, death)).
+    :param band: band
+    :type band: float.
+    :returns: (float, float) -- (min_birth, max_death).
+    """
+    # Look for minimum birth date and maximum death date for plot optimisation
+    max_death = 0
+    min_birth = persistence[0][1][0]
+    for interval in reversed(persistence):
+        if float(interval[1][1]) != float('inf'):
+            if float(interval[1][1]) > max_death:
+                max_death = float(interval[1][1])
+        if float(interval[1][0]) > max_death:
+            max_death = float(interval[1][0])
+        if float(interval[1][0]) < min_birth:
+            min_birth = float(interval[1][0])
+    if band > 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']
+
 try:
     import matplotlib.pyplot as plt
     import matplotlib.patches as mpatches
     import numpy as np
-    from scipy.stats import kde
     import os
-    import math
-
-    def __min_birth_max_death(persistence, band=0.):
-        """This function returns (min_birth, max_death) from the persistence.
-
-        :param persistence: The persistence to plot.
-        :type persistence: list of tuples(dimension, tuple(birth, death)).
-        :param band: band
-        :type band: float.
-        :returns: (float, float) -- (min_birth, max_death).
-        """
-        # Look for minimum birth date and maximum death date for plot optimisation
-        max_death = 0
-        min_birth = persistence[0][1][0]
-        for interval in reversed(persistence):
-            if float(interval[1][1]) != float('inf'):
-                if float(interval[1][1]) > max_death:
-                    max_death = float(interval[1][1])
-            if float(interval[1][0]) > max_death:
-                max_death = float(interval[1][0])
-            if float(interval[1][0]) < min_birth:
-                min_birth = float(interval[1][0])
-        if band > 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='', alpha=0.6,
             max_barcodes=1000, inf_delta=0.1, legend=False):
@@ -220,71 +218,79 @@ try:
         plt.axis([axis_start, infinity, axis_start, infinity + delta])
         return plt
 
-    def plot_persistence_density(persistence=[], persistence_file='', nbins=300,
-                                 max_plots=1000, cmap=plt.cm.hot_r, legend=False):
-        """This function plots the persistence density from persistence values list
-        or from a :doc:`persistence file <fileformats>`. Be aware that this
-        function does not distinguish the dimension, it is up to you to select the
-        required one.
-
-        :param persistence: Persistence values list.
-        :type persistence: list of tuples(dimension, tuple(birth, death)).
-        :param persistence_file: A :doc:`persistence file <fileformats>` style name
-            (reset persistence if both are set).
-        :type persistence_file: string
-        :param nbins: Evaluate a gaussian kde on a regular grid of nbins x nbins
-            over data extents (default is 300)
-        :type nbins: int.
-        :param max_plots: number of maximal plots to be displayed
-            Set it to 0 to see all, Default value is 1000.
-            (persistence will be sorted by life time if max_plots is set)
-        :type max_plots: int.
-        :param cmap: A matplotlib colormap (default is matplotlib.pyplot.cm.hot_r).
-        :type cmap: cf. matplotlib colormap.
-        :param legend: Display the color bar values (default is False).
-        :type legend: boolean.
-        :returns: A matplotlib object containing diagram plot of persistence
-            (launch `show()` method on it to display it).
-        """
-        if persistence_file is not '':
-            if os.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))
-            else:
-                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]
-
-        # Set as numpy array birth and death (remove undefined values - inf and NaN)
-        birth = np.asarray([(interval[1][0]) for interval in persistence if (math.isfinite(interval[1][1]) and math.isfinite(interval[1][0]))])
-        death = np.asarray([(interval[1][1]) for interval in persistence if (math.isfinite(interval[1][1]) and math.isfinite(interval[1][0]))])
-
-        # line display of equation : birth = death
-        x = np.linspace(death.min(), birth.max(), 1000)
-        plt.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])
-        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
-        plt.pcolormesh(xi, yi, zi.reshape(xi.shape), cmap=cmap)
-
-        if legend:
-            plt.colorbar()
-
-        plt.title('Persistence density')
-        plt.xlabel('Birth')
-        plt.ylabel('Death')
-        return plt
+    try:
+        from scipy.stats import kde
+        import math
+
+        def plot_persistence_density(persistence=[], persistence_file='', nbins=300,
+                                     max_plots=1000, cmap=plt.cm.hot_r, legend=False):
+            """This function plots the persistence density from persistence values list
+            or from a :doc:`persistence file <fileformats>`. Be aware that this
+            function does not distinguish the dimension, it is up to you to select the
+            required one.
+
+            :param persistence: Persistence values list.
+            :type persistence: list of tuples(dimension, tuple(birth, death)).
+            :param persistence_file: A :doc:`persistence file <fileformats>` style name
+                (reset persistence if both are set).
+            :type persistence_file: string
+            :param nbins: Evaluate a gaussian kde on a regular grid of nbins x nbins
+                over data extents (default is 300)
+            :type nbins: int.
+            :param max_plots: number of maximal plots to be displayed
+                Set it to 0 to see all, Default value is 1000.
+                (persistence will be sorted by life time if max_plots is set)
+            :type max_plots: int.
+            :param cmap: A matplotlib colormap (default is matplotlib.pyplot.cm.hot_r).
+            :type cmap: cf. matplotlib colormap.
+            :param legend: Display the color bar values (default is False).
+            :type legend: boolean.
+            :returns: A matplotlib object containing diagram plot of persistence
+                (launch `show()` method on it to display it).
+            """
+            if persistence_file is not '':
+                if os.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))
+                else:
+                    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]
+
+            # Set as numpy array birth and death (remove undefined values - inf and NaN)
+            birth = np.asarray([(interval[1][0]) for interval in persistence if (math.isfinite(interval[1][1]) and math.isfinite(interval[1][0]))])
+            death = np.asarray([(interval[1][1]) for interval in persistence if (math.isfinite(interval[1][1]) and math.isfinite(interval[1][0]))])
+
+            # line display of equation : birth = death
+            x = np.linspace(death.min(), birth.max(), 1000)
+            plt.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])
+            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
+            plt.pcolormesh(xi, yi, zi.reshape(xi.shape), cmap=cmap)
+
+            if legend:
+                plt.colorbar()
+
+            plt.title('Persistence density')
+            plt.xlabel('Birth')
+            plt.ylabel('Death')
+            return plt
+
+    except ImportError:
+        # Continue in case of import error, functions won't be available
+        pass
 
 except ImportError:
     # Continue in case of import error, functions won't be available