Code review : More explicit message when import fails in plot persistence graphical tools

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/plot_persistence_density_vincent@3881 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: 96f9e3da3bd68d6cba65242b9890c4beb463c863

1 files changed, 161 insertions, 148 deletions

diff --git a/src/cython/cython/persistence_graphical_tools.py b/src/cython/cython/persistence_graphical_tools.py
index f5550e3a..e66643d2 100755
--- a/src/cython/cython/persistence_graphical_tools.py
+++ b/src/cython/cython/persistence_graphical_tools.py
@@ -55,39 +55,39 @@ 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
-    import os
-
-    def plot_persistence_barcode(persistence=[], persistence_file='', alpha=0.6,
-                                 max_intervals=1000, 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_intervals: maximal number of intervals to display.
-            Selected points are those with the longest life time. Set it
-            to 0 to see all. Default value is 1000.
-        :type max_intervals: int.
-        :param inf_delta: Infinity is placed at ((max_death - min_birth) x
-            inf_delta) above the highest point. A reasonable value is between
-            0.05 and 0.5 - default is 0.1.
-        :type inf_delta: float.
-        :param legend: Display the dimension color legend (default is False).
-        :type legend: boolean.
-        :returns: A matplotlib object containing horizontal bar plot of persistence
-            (launch `show()` method on it to display it).
-        """
+def plot_persistence_barcode(persistence=[], persistence_file='', alpha=0.6,
+                             max_intervals=1000, 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_intervals: maximal number of intervals to display.
+        Selected points are those with the longest life time. Set it
+        to 0 to see all. Default value is 1000.
+    :type max_intervals: int.
+    :param inf_delta: Infinity is placed at ((max_death - min_birth) x
+        inf_delta) above the highest point. A reasonable value is between
+        0.05 and 0.5 - default is 0.1.
+    :type inf_delta: float.
+    :param legend: Display the dimension color legend (default is False).
+    :type legend: boolean.
+    :returns: A matplotlib object containing horizontal bar plot of persistence
+        (launch `show()` method on it to display it).
+    """
+    try:
+        import matplotlib.pyplot as plt
+        import matplotlib.patches as mpatches
+        import numpy as np
+        import os
+
         if persistence_file is not '':
             if os.path.isfile(persistence_file):
                 # Reset persistence
@@ -143,34 +143,43 @@ try:
         plt.axis([axis_start, infinity, 0, ind])
         return plt
 
-    def plot_persistence_diagram(persistence=[], persistence_file='', alpha=0.6,
-            band=0., max_intervals=1000, 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_intervals: maximal number of intervals to display.
-            Selected points are those with the longest life time. Set it
-            to 0 to see all. Default value is 1000.
-        :type max_intervals: int.
-        :param inf_delta: Infinity is placed at ((max_death - min_birth) x
-            inf_delta) above the highest point. A reasonable value is between
-            0.05 and 0.5 - default is 0.1.
-        :type inf_delta: float.
-        :param legend: Display the dimension color legend (default is False).
-        :type legend: boolean.
-        :returns: A matplotlib object containing diagram plot of persistence
-            (launch `show()` method on it to display it).
-        """
+    except ImportError:
+        print("This function is not available, you may be missing numpy and/or matplotlib.")
+
+def plot_persistence_diagram(persistence=[], persistence_file='', alpha=0.6,
+        band=0., max_intervals=1000, 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_intervals: maximal number of intervals to display.
+        Selected points are those with the longest life time. Set it
+        to 0 to see all. Default value is 1000.
+    :type max_intervals: int.
+    :param inf_delta: Infinity is placed at ((max_death - min_birth) x
+        inf_delta) above the highest point. A reasonable value is between
+        0.05 and 0.5 - default is 0.1.
+    :type inf_delta: float.
+    :param legend: Display the dimension color legend (default is False).
+    :type legend: boolean.
+    :returns: A matplotlib object containing diagram plot of persistence
+        (launch `show()` method on it to display it).
+    """
+    try:
+        import matplotlib.pyplot as plt
+        import matplotlib.patches as mpatches
+        import numpy as np
+        import os
+
         if persistence_file is not '':
             if os.path.isfile(persistence_file):
                 # Reset persistence
@@ -230,104 +239,108 @@ try:
         plt.axis([axis_start, infinity, axis_start, infinity + delta])
         return plt
 
+    except ImportError:
+        print("This function is not available, you may be missing numpy and/or matplotlib.")
+
+def plot_persistence_density(persistence=[], persistence_file='',
+                             nbins=300, bw_method=None,
+                             max_intervals=1000, dimension=None,
+                             cmap=None, 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 bw_method: The method used to calculate the estimator
+        bandwidth. This can be 'scott', 'silverman', a scalar constant
+        or a callable. If a scalar, this will be used directly as
+        kde.factor. If a callable, it should take a gaussian_kde
+        instance as only parameter and return a scalar. If None
+        (default), 'scott' is used. See
+        `scipy.stats.gaussian_kde documentation
+        <http://scipy.github.io/devdocs/generated/scipy.stats.gaussian_kde.html>`_
+        for more details.
+    :type bw_method: str, scalar or callable, optional.
+    :param max_intervals: maximal number of intervals to display.
+        Selected points are those with the longest life time. Set it
+        to 0 to see all. Default value is 1000.
+    :type max_intervals: int.
+    :param dimension: the dimension to be selected in the intervals
+        (default is None to mix all dimensions).
+    :type dimension: 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).
+    """
     try:
+        import matplotlib.pyplot as plt
+        import numpy as np
         from scipy.stats import kde
+        import os
         import math
 
-        def plot_persistence_density(persistence=[], persistence_file='',
-                                     nbins=300, bw_method=None,
-                                     max_intervals=1000, dimension=None,
-                                     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 bw_method: The method used to calculate the estimator
-                bandwidth. This can be 'scott', 'silverman', a scalar constant
-                or a callable. If a scalar, this will be used directly as
-                kde.factor. If a callable, it should take a gaussian_kde
-                instance as only parameter and return a scalar. If None
-                (default), 'scott' is used. See
-                `scipy.stats.gaussian_kde documentation
-                <http://scipy.github.io/devdocs/generated/scipy.stats.gaussian_kde.html>`_
-                for more details.
-            :type bw_method: str, scalar or callable, optional.
-            :param max_intervals: maximal number of intervals to display.
-                Selected points are those with the longest life time. Set it
-                to 0 to see all. Default value is 1000.
-            :type max_intervals: int.
-            :param dimension: the dimension to be selected in the intervals
-                (default is None to mix all dimensions).
-            :type dimension: 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
-
-            persistence_dim = []
-            if dimension is not None:
-                persistence_dim = [(dim_interval) for dim_interval in persistence if (dim_interval[0] == dimension)]
+        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:
-                persistence_dim = persistence
+                print("file " + persistence_file + " not found.")
+                return None
 
-            if max_intervals > 0 and max_intervals < len(persistence_dim):
-                # Sort by life time, then takes only the max_intervals elements
-                persistence_dim = sorted(persistence_dim,
-                                     key=lambda life_time: life_time[1][1]-life_time[1][0],
-                                     reverse=True)[:max_intervals]
+        persistence_dim = []
+        if dimension is not None:
+            persistence_dim = [(dim_interval) for dim_interval in persistence if (dim_interval[0] == dimension)]
+        else:
+            persistence_dim = persistence
 
-            # Set as numpy array birth and death (remove undefined values - inf and NaN)
-            birth = np.asarray([(interval[1][0]) for interval in persistence_dim if (math.isfinite(interval[1][1]) and math.isfinite(interval[1][0]))])
-            death = np.asarray([(interval[1][1]) for interval in persistence_dim if (math.isfinite(interval[1][1]) and math.isfinite(interval[1][0]))])
+        if max_intervals > 0 and max_intervals < len(persistence_dim):
+            # Sort by life time, then takes only the max_intervals elements
+            persistence_dim = sorted(persistence_dim,
+                                 key=lambda life_time: life_time[1][1]-life_time[1][0],
+                                 reverse=True)[:max_intervals]
 
-            # line display of equation : birth = death
-            x = np.linspace(death.min(), birth.max(), 1000)
-            plt.plot(x, x, color='k', linewidth=1.0)
+        # Set as numpy array birth and death (remove undefined values - inf and NaN)
+        birth = np.asarray([(interval[1][0]) for interval in persistence_dim if (math.isfinite(interval[1][1]) and math.isfinite(interval[1][0]))])
+        death = np.asarray([(interval[1][1]) for interval in persistence_dim if (math.isfinite(interval[1][1]) and math.isfinite(interval[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()]))
+        # line display of equation : birth = death
+        x = np.linspace(death.min(), birth.max(), 1000)
+        plt.plot(x, x, color='k', linewidth=1.0)
 
-            # Make the plot
-            plt.pcolormesh(xi, yi, zi.reshape(xi.shape), cmap=cmap)
+        # 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()]))
 
-            if legend:
-                plt.colorbar()
+        # default cmap value cannot be done at argument definition level as matplotlib is not yet defined.
+        if cmap is None:
+            cmap = plt.cm.hot_r
+        # Make the plot
+        plt.pcolormesh(xi, yi, zi.reshape(xi.shape), cmap=cmap)
 
-            plt.title('Persistence density')
-            plt.xlabel('Birth')
-            plt.ylabel('Death')
-            return plt
+        if legend:
+            plt.colorbar()
 
-    except ImportError:
-        # Continue in case of import error, functions won't be available
-        pass
+        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:
+        print("This function is not available, you may be missing numpy, matplotlib and/or scipy.")