Merge pull request #99 from VOD555/cdf

Add cdf function to InterRDF

Author: orbeckst

CHANGELOG

@@ -22,6 +22,8 @@ Enhancements
   * store block information in `_block` attribute (Issue #89)
   * add parallel density class (Issue #8)
   * add parallel RMSF class (Issue #90)
+  * add `cdf` attribute to `pmda.rdf.InterRDF` for cumulative
+    distribution function
 
 Fixes
   * default _conclude() in pmda.custom.AnalysisFromFunction fails with

pmda/leaflet.py

@@ -98,6 +98,7 @@ def _find_connected_components(self, data, cutoff=15.0):
             generated from `data`
 
         """
+        # pylint: disable=unsubscriptable-object
         window, index = data[0]
         num = window[0].shape[0]
         i_index = index[0]
@@ -299,7 +300,6 @@ def run(self,
                                              scheduler_kwargs=scheduler_kwargs,
                                              n_jobs=n_jobs,
                                              cutoff=cutoff)
-
                     timings.append(b_compute.elapsed)
                     leaflet1 = self._atomgroup[components[0]]
                     leaflet2 = self._atomgroup[components[1]]

pmda/rdf.py

@@ -161,6 +161,24 @@ def _conclude(self, ):
         rdf = self.count / (density * vol * self.nf)
         self.rdf = rdf
 
+    @property
+    def cdf(self):
+        """Calculate the cumulative distribution functions (CDF).
+        Note that this is the actual count within a given radius, i.e.,
+        :math:`N(r)`.
+
+        Returns
+        -------
+              cdf : numpy array
+                      a numpy array with the same structure as :attr:`rdf`
+
+
+        .. versionadded:: 0.3.0
+        """
+        cdf = np.cumsum(self.count) / self.nf
+
+        return cdf
+
     @staticmethod
     def _reduce(res, result_single_frame):
         """ 'add' action for an accumulator"""
@@ -318,7 +336,8 @@ def _conclude(self):
 
         self.rdf = rdf
 
-    def get_cdf(self):
+    @property
+    def cdf(self):
         """Calculate the cumulative distribution functions (CDF) for all sites.
         Note that this is the actual count within a given radius, i.e.,
         :math:`N(r)`.
@@ -327,18 +346,20 @@ def get_cdf(self):
         -------
               cdf : list
                       list of arrays with the same structure as :attr:`rdf`
+
+
+        .. versionadded:: 0.3.0
+           Method ``get_cdf()`` was removed and :attr:`cdf` is now a managed
+           attribute that computes the CDF when accessed.
         """
         # Calculate cumulative distribution function
         # Empty list to restore CDF
         cdf = []
 
+        # cdf is a list of cdf between pairs of AtomGroups in ags
         for count in self.count:
             cdf.append(np.cumsum(count, axis=2) / self.nf)
 
-        # Results stored in self.cdf
-        # self.cdf is a list of cdf between pairs of AtomGroups in ags
-        self.cdf = cdf
-
         return cdf
 
     @staticmethod

pmda/test/test_rdf.py

@@ -83,6 +83,14 @@ def test_same_result(sels, n_blocks):
     assert_almost_equal(nrdf.rdf, prdf.rdf)
 
 
+def test_cdf(sels):
+    s1, s2 = sels
+    rdf = InterRDF(s1, s2).run()
+    cdf = np.cumsum(rdf.count) / rdf.nf
+    assert_almost_equal(rdf.cdf[-1], rdf.count.sum()/rdf.nf)
+    assert_almost_equal(rdf.cdf, cdf)
+
+
 def test_reduce(sels):
     # should see numpy.array addtion
     s1, s2 = sels

pmda/test/test_rdf_s.py

@@ -85,8 +85,8 @@ def test_double_run(rdf_s):
 
 
 def test_cdf(rdf_s):
-    rdf_s.get_cdf()
-    assert rdf_s.cdf[0][0][0][-1] == rdf_s.count[0][0][0].sum()/rdf_s.nf
+    assert_almost_equal(rdf_s.cdf[0][0][0][-1],
+                        rdf_s.count[0][0][0].sum()/rdf_s.nf)
 
 
 def test_reduce(rdf_s):
@@ -110,7 +110,7 @@ def test_same_result(u, sels, n_blocks):
 
 
 @pytest.mark.parametrize("density, value", [
-    (True, 13275.775528444701),
+    (True, 13275.775440503656),
     (False, 0.021915460340071267)])
 def test_density(u, sels, density, value):
     rdf = InterRDF_s(u, sels, density=density).run()