Make soft dependency for matplotlib and numpy dependencies

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/ninja_cmake_warning_fix_vincent@3756 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: 13a2e6e3eea8a36d0b9bdb4ab1c34f940a8932dc

3 files changed, 249 insertions, 238 deletions

diff --git a/src/cython/CMakeLists.txt b/src/cython/CMakeLists.txt
index 8b5d231a..1849a6ec 100644
--- a/src/cython/CMakeLists.txt
+++ b/src/cython/CMakeLists.txt
@@ -16,11 +16,13 @@ endfunction( add_gudhi_cython_lib )
 
 # THE_TEST is the python test file name (without .py extension) containing tests functions
 function( add_gudhi_py_test THE_TEST )
-  # use ${PYTHON_EXECUTABLE} -B, otherwise a __pycache__ directory is created in sources by python
-  # use py.test no cache provider, otherwise a .cache file is created in sources by py.test
-  add_test(NAME ${THE_TEST}_py_test
-           WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
-           COMMAND ${PYTHON_EXECUTABLE} -B -m pytest -p no:cacheprovider ${CMAKE_CURRENT_SOURCE_DIR}/test/${THE_TEST}.py)
+  if(PYTEST_FOUND)
+    # use ${PYTHON_EXECUTABLE} -B, otherwise a __pycache__ directory is created in sources by python
+    # use py.test no cache provider, otherwise a .cache file is created in sources by py.test
+    add_test(NAME ${THE_TEST}_py_test
+             WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
+             COMMAND ${PYTHON_EXECUTABLE} -B -m pytest -p no:cacheprovider ${CMAKE_CURRENT_SOURCE_DIR}/test/${THE_TEST}.py)
+  endif()
 endfunction( add_gudhi_py_test )
 
 # Set gudhi.__debug_info__
@@ -47,10 +49,10 @@ if(CYTHON_FOUND)
     add_gudhi_debug_info("Pytest version ${PYTEST_VERSION}")
   endif()
   if(MATPLOTLIB_FOUND)
-  add_gudhi_debug_info("Matplotlib version ${MATPLOTLIB_VERSION}")
+    add_gudhi_debug_info("Matplotlib version ${MATPLOTLIB_VERSION}")
   endif()
   if(NUMPY_FOUND)
-  add_gudhi_debug_info("Numpy version ${NUMPY_VERSION}")
+    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;")
@@ -213,27 +215,29 @@ if(CYTHON_FOUND)
              ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/alpha_rips_persistence_bottleneck_distance.py"
              -f ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off -t 0.15 -d 3)
 
-    # Tangential
-    add_test(NAME tangential_complex_plain_homology_from_off_file_example_py_test
-             WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
-             COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
-             ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/tangential_complex_plain_homology_from_off_file_example.py"
-             --no-diagram -i 2 -f ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off)
-
-    add_gudhi_py_test(test_tangential_complex)
-
-    # Witness complex AND Subsampling
-    add_test(NAME euclidean_strong_witness_complex_diagram_persistence_from_off_file_example_py_test
-             WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
-             COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
-             ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/euclidean_strong_witness_complex_diagram_persistence_from_off_file_example.py"
-             --no-diagram -f ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off -a 1.0 -n 20 -d 2)
-
-    add_test(NAME euclidean_witness_complex_diagram_persistence_from_off_file_example_py_test
-             WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
-             COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
-             ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/euclidean_witness_complex_diagram_persistence_from_off_file_example.py"
-             --no-diagram -f ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off -a 1.0 -n 20 -d 2)
+    if(MATPLOTLIB_FOUND AND NUMPY_FOUND)
+      # Tangential
+      add_test(NAME tangential_complex_plain_homology_from_off_file_example_py_test
+               WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
+               COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
+               ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/tangential_complex_plain_homology_from_off_file_example.py"
+               --no-diagram -i 2 -f ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off)
+
+      add_gudhi_py_test(test_tangential_complex)
+
+      # Witness complex AND Subsampling
+      add_test(NAME euclidean_strong_witness_complex_diagram_persistence_from_off_file_example_py_test
+               WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
+               COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
+               ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/euclidean_strong_witness_complex_diagram_persistence_from_off_file_example.py"
+               --no-diagram -f ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off -a 1.0 -n 20 -d 2)
+
+      add_test(NAME euclidean_witness_complex_diagram_persistence_from_off_file_example_py_test
+               WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
+               COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
+               ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/euclidean_witness_complex_diagram_persistence_from_off_file_example.py"
+               --no-diagram -f ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off -a 1.0 -n 20 -d 2)
+    endif()
 
     # Subsampling
     add_gudhi_py_test(test_subsampling)
@@ -287,11 +291,13 @@ if(CYTHON_FOUND)
              COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
              ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/alpha_complex_from_points_example.py")
 
-    add_test(NAME alpha_complex_diagram_persistence_from_off_file_example_py_test
+    if(MATPLOTLIB_FOUND AND NUMPY_FOUND)
+      add_test(NAME alpha_complex_diagram_persistence_from_off_file_example_py_test
              WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
              COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
              ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/alpha_complex_diagram_persistence_from_off_file_example.py"
              --no-diagram -f ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off -a 0.6)
+    endif()
 
     add_gudhi_py_test(test_alpha_complex)
 
@@ -310,26 +316,30 @@ if(CYTHON_FOUND)
            ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/periodic_cubical_complex_barcode_persistence_from_perseus_file_example.py"
            --no-barcode -f ${CMAKE_SOURCE_DIR}/data/bitmap/CubicalTwoSphere.txt)
 
-  add_test(NAME random_cubical_complex_persistence_example_py_test
-           WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
-           COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
-           ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/random_cubical_complex_persistence_example.py"
-           10 10 10)
+  if(NUMPY_FOUND)
+    add_test(NAME random_cubical_complex_persistence_example_py_test
+             WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
+             COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
+             ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/random_cubical_complex_persistence_example.py"
+             10 10 10)
+  endif()
 
   add_gudhi_py_test(test_cubical_complex)
 
   # Rips
-  add_test(NAME rips_complex_diagram_persistence_from_distance_matrix_file_example_py_test
-           WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
-           COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
-           ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/rips_complex_diagram_persistence_from_distance_matrix_file_example.py"
-           --no-diagram -f ${CMAKE_SOURCE_DIR}/data/distance_matrix/lower_triangular_distance_matrix.csv -e 12.0 -d 3)
-
-  add_test(NAME rips_complex_diagram_persistence_from_off_file_example_py_test
-           WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
-           COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
-           ${PYTHON_EXECUTABLE} ${CMAKE_CURRENT_SOURCE_DIR}/example/rips_complex_diagram_persistence_from_off_file_example.py
-           --no-diagram -f ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off  -e 0.25 -d 3)
+  if(MATPLOTLIB_FOUND AND NUMPY_FOUND)
+    add_test(NAME rips_complex_diagram_persistence_from_distance_matrix_file_example_py_test
+             WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
+             COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
+             ${PYTHON_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/example/rips_complex_diagram_persistence_from_distance_matrix_file_example.py"
+             --no-diagram -f ${CMAKE_SOURCE_DIR}/data/distance_matrix/lower_triangular_distance_matrix.csv -e 12.0 -d 3)
+    
+    add_test(NAME rips_complex_diagram_persistence_from_off_file_example_py_test
+             WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
+             COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
+             ${PYTHON_EXECUTABLE} ${CMAKE_CURRENT_SOURCE_DIR}/example/rips_complex_diagram_persistence_from_off_file_example.py
+             --no-diagram -f ${CMAKE_SOURCE_DIR}/data/points/tore3D_300.off  -e 0.25 -d 3)
+  endif()
 
   add_test(NAME rips_complex_from_points_example_py_test
            WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
@@ -358,7 +368,7 @@ if(CYTHON_FOUND)
   add_gudhi_py_test(test_reader_utils)
 
   # Documentation generation is available through sphinx - requires all modules
-  if(SPHINX_PATH AND NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1)
+  if(SPHINX_PATH AND MATPLOTLIB_FOUND AND NUMPY_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
@@ -378,5 +388,5 @@ if(CYTHON_FOUND)
              COMMAND ${CMAKE_COMMAND} -E env "PYTHONPATH=${CMAKE_CURRENT_BINARY_DIR}"
              ${SPHINX_PATH} -b doctest ${CMAKE_CURRENT_SOURCE_DIR}/doc ${CMAKE_CURRENT_BINARY_DIR}/doctest)
 
-  endif(SPHINX_PATH AND NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.8.1)
+  endif()
 endif(CYTHON_FOUND)
diff --git a/src/cython/cython/persistence_graphical_tools.py b/src/cython/cython/persistence_graphical_tools.py
index 216ab8d6..314bd6db 100755
--- a/src/cython/cython/persistence_graphical_tools.py
+++ b/src/cython/cython/persistence_graphical_tools.py
@@ -1,8 +1,3 @@
-import matplotlib.pyplot as plt
-import matplotlib.patches as mpatches
-import numpy as np
-import os
-
 """This file is part of the Gudhi Library. The Gudhi library
    (Geometric Understanding in Higher Dimensions) is a generic C++
    library for computational topology.
@@ -29,187 +24,197 @@ __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)
+try:
+    import matplotlib.pyplot as plt
+    import matplotlib.patches as mpatches
+    import numpy as np
+    import os
+
+    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):
-    """This function plots the persistence bar code from persistence values list
-    or from a :doc:`persistence file <fileformats>`.
-
-    :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 alpha: barcode transparency value (0.0 transparent through 1.0 opaque - default is 0.6).
-    :type alpha: float.
-    :param max_barcodes: number of maximal barcodes to be displayed.
-        Set it to 0 to see all, Default value is 1000.
-        (persistence will be sorted by life time if max_barcodes is set)
-    :type max_barcodes: int.
-    :param inf_delta: Infinity is placed at ((max_death - min_birth) x inf_delta).
-        A reasonable value is between 0.05 and 0.5 - default is 0.1.
-    :type inf_delta: float.
-    :returns: A matplotlib object containing horizontal bar 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_barcodes > 0 and max_barcodes < 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_barcodes]
-
-    persistence = sorted(persistence, key=lambda birth: birth[1][0])
-
-    (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
-    # Draw horizontal bars in loop
-    for interval in reversed(persistence):
-        if float(interval[1][1]) != float('inf'):
-            # Finite death case
-            plt.barh(ind, (interval[1][1] - interval[1][0]), height=0.8,
-                     left = interval[1][0], alpha=alpha,
-                     color = palette[interval[0]],
-                     linewidth=0)
-        else:
-            # Infinite death case for diagram to be nicer
-            plt.barh(ind, (infinity - interval[1][0]), height=0.8,
-                     left = interval[1][0], alpha=alpha,
-                     color = palette[interval[0]],
-                     linewidth=0)
-        ind = ind + 1
-
-    if legend:
-        dimensions = list(set(item[0] for item in persistence))
-        plt.legend(handles=[mpatches.Patch(color=palette[dim],
-                                           label=str(dim)) for dim in dimensions],
-                   loc='lower right')
-    plt.title('Persistence barcode')
-    # Ends plot on infinity value and starts a little bit before min_birth
-    plt.axis([axis_start, infinity, 0, ind])
-    return plt
-
-def plot_persistence_diagram(persistence=[], persistence_file='', alpha=0.6,
-        band=0., max_plots=1000, inf_delta=0.1, legend=False):
-    """This function plots the persistence diagram from persistence values list
-    or from a :doc:`persistence file <fileformats>`.
-
-    :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 alpha: plot transparency value (0.0 transparent through 1.0 opaque - default is 0.6).
-    :type alpha: float.
-    :param band: band (not displayed if :math:`\leq` 0. - default is 0.)
-    :type band: float.
-    :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 inf_delta: Infinity is placed at ((max_death - min_birth) x inf_delta).
-        A reasonable value is between 0.05 and 0.5 - default is 0.1.
-    :type inf_delta: float.
-    :returns: A matplotlib object containing diagram plot of persistence
-        (launch `show()` method on it to display it).
+    Only 13 colors for the palette
     """
-    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]
-
-    (min_birth, max_death) = __min_birth_max_death(persistence, band)
-    ind = 0
-    delta = ((max_death - min_birth) * inf_delta)
-    # Replace infinity values with max_death + delta for diagram to be more
-    # readable
-    infinity = max_death + delta
-    axis_start = min_birth - delta
-
-    # line display of equation : birth = death
-    x = np.linspace(axis_start, infinity, 1000)
-    # infinity line and text
-    plt.plot(x, x, color='k', linewidth=1.0)
-    plt.plot(x, [infinity] * len(x), linewidth=1.0, color='k', alpha=alpha)
-    plt.text(axis_start, infinity, r'$\infty$', color='k', alpha=alpha)
-    # bootstrap band
-    if band > 0.:
-        plt.fill_between(x, x, x+band, alpha=alpha, facecolor='red')
-
-    # Draw points in loop
-    for interval in reversed(persistence):
-        if float(interval[1][1]) != float('inf'):
-            # Finite death case
-            plt.scatter(interval[1][0], interval[1][1], alpha=alpha,
-                        color = palette[interval[0]])
-        else:
-            # Infinite death case for diagram to be nicer
-            plt.scatter(interval[1][0], infinity, alpha=alpha,
-                        color = palette[interval[0]])
-        ind = ind + 1
-
-    if legend:
-        dimensions = list(set(item[0] for item in persistence))
-        plt.legend(handles=[mpatches.Patch(color=palette[dim], label=str(dim)) for dim in dimensions])
-
-    plt.title('Persistence diagram')
-    plt.xlabel('Birth')
-    plt.ylabel('Death')
-    # Ends plot on infinity value and starts a little bit before min_birth
-    plt.axis([axis_start, infinity, axis_start, infinity + delta])
-    return plt
+    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):
+        """This function plots the persistence bar code from persistence values list
+        or from a :doc:`persistence file <fileformats>`.
+
+        :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 alpha: barcode transparency value (0.0 transparent through 1.0 opaque - default is 0.6).
+        :type alpha: float.
+        :param max_barcodes: number of maximal barcodes to be displayed.
+            Set it to 0 to see all, Default value is 1000.
+            (persistence will be sorted by life time if max_barcodes is set)
+        :type max_barcodes: int.
+        :param inf_delta: Infinity is placed at ((max_death - min_birth) x inf_delta).
+            A reasonable value is between 0.05 and 0.5 - default is 0.1.
+        :type inf_delta: float.
+        :returns: A matplotlib object containing horizontal bar 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_barcodes > 0 and max_barcodes < 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_barcodes]
+
+        persistence = sorted(persistence, key=lambda birth: birth[1][0])
+
+        (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
+        # Draw horizontal bars in loop
+        for interval in reversed(persistence):
+            if float(interval[1][1]) != float('inf'):
+                # Finite death case
+                plt.barh(ind, (interval[1][1] - interval[1][0]), height=0.8,
+                         left = interval[1][0], alpha=alpha,
+                         color = palette[interval[0]],
+                         linewidth=0)
+            else:
+                # Infinite death case for diagram to be nicer
+                plt.barh(ind, (infinity - interval[1][0]), height=0.8,
+                         left = interval[1][0], alpha=alpha,
+                         color = palette[interval[0]],
+                         linewidth=0)
+            ind = ind + 1
+
+        if legend:
+            dimensions = list(set(item[0] for item in persistence))
+            plt.legend(handles=[mpatches.Patch(color=palette[dim],
+                                               label=str(dim)) for dim in dimensions],
+                       loc='lower right')
+        plt.title('Persistence barcode')
+        # Ends plot on infinity value and starts a little bit before min_birth
+        plt.axis([axis_start, infinity, 0, ind])
+        return plt
+
+    def plot_persistence_diagram(persistence=[], persistence_file='', alpha=0.6,
+            band=0., max_plots=1000, inf_delta=0.1, legend=False):
+        """This function plots the persistence diagram from persistence values list
+        or from a :doc:`persistence file <fileformats>`.
+
+        :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 alpha: plot transparency value (0.0 transparent through 1.0 opaque - default is 0.6).
+        :type alpha: float.
+        :param band: band (not displayed if :math:`\leq` 0. - default is 0.)
+        :type band: float.
+        :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 inf_delta: Infinity is placed at ((max_death - min_birth) x inf_delta).
+            A reasonable value is between 0.05 and 0.5 - default is 0.1.
+        :type inf_delta: float.
+        :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]
+
+        (min_birth, max_death) = __min_birth_max_death(persistence, band)
+        ind = 0
+        delta = ((max_death - min_birth) * inf_delta)
+        # Replace infinity values with max_death + delta for diagram to be more
+        # readable
+        infinity = max_death + delta
+        axis_start = min_birth - delta
+
+        # line display of equation : birth = death
+        x = np.linspace(axis_start, infinity, 1000)
+        # infinity line and text
+        plt.plot(x, x, color='k', linewidth=1.0)
+        plt.plot(x, [infinity] * len(x), linewidth=1.0, color='k', alpha=alpha)
+        plt.text(axis_start, infinity, r'$\infty$', color='k', alpha=alpha)
+        # bootstrap band
+        if band > 0.:
+            plt.fill_between(x, x, x+band, alpha=alpha, facecolor='red')
+
+        # Draw points in loop
+        for interval in reversed(persistence):
+            if float(interval[1][1]) != float('inf'):
+                # Finite death case
+                plt.scatter(interval[1][0], interval[1][1], alpha=alpha,
+                            color = palette[interval[0]])
+            else:
+                # Infinite death case for diagram to be nicer
+                plt.scatter(interval[1][0], infinity, alpha=alpha,
+                            color = palette[interval[0]])
+            ind = ind + 1
+
+        if legend:
+            dimensions = list(set(item[0] for item in persistence))
+            plt.legend(handles=[mpatches.Patch(color=palette[dim], label=str(dim)) for dim in dimensions])
+
+        plt.title('Persistence diagram')
+        plt.xlabel('Birth')
+        plt.ylabel('Death')
+        # Ends plot on infinity value and starts a little bit before min_birth
+        plt.axis([axis_start, infinity, axis_start, infinity + delta])
+        return plt
+
+except ImportError:
+    # Continue in case of import error, functions won't be available
+    pass
diff --git a/src/cython/setup.py.in b/src/cython/setup.py.in
index ee381a1b..4037aab6 100644
--- a/src/cython/setup.py.in
+++ b/src/cython/setup.py.in
@@ -46,9 +46,5 @@ setup(
     version='@GUDHI_VERSION@',
     url='http://gudhi.gforge.inria.fr/',
     ext_modules = cythonize(gudhi),
-    install_requires = [
-        "matplotlib",
-        "numpy",
-        "cython",
-        ],
+    install_requires = ["cython",],
 )