Merge branch 'drop-masked-neighborhoods'

* exclude self-neighborhoods at masked-away sites
* test OverlapCalculator::neighborhoods with various masks

Resolve #25

Author: pavoljuhas

src/diffpy/srreal/OverlapCalculator.cpp

@@ -344,18 +344,33 @@ vector< unordered_set<int> > OverlapCalculator::neighborhoods() const
             rvptr[*idx1] = rvptr[j0];
         }
     }
-    // replace any unassigned items with a self-neighborhoods
-    for (int i = 0; i < cntsites; ++i)
+    // helper function that initializes neighbor set at site i
+    auto initsiteset = [&](int i, int& counter) {
+        if (!rvptr[i]) {
+            rvptr[i].reset(new SiteSet(&i, &i + 1));
+            ++counter;
+        }
+    };
+    // count initialized items in rvptr
+    int cnt = count_if(rvptr.begin(), rvptr.end(),
+            [](SiteSetPointers::value_type& p) { return bool(p); });
+    // create self-neighborhoods unless prohibited by mask
+    for (int j0 = 0; j0 < cntsites && cnt < cntsites; ++j0)
     {
-        if (rvptr[i].get())  continue;
-        rvptr[i].reset(new SiteSet(&i, &i + 1));
+        for (int j1 = j0; j1 < cntsites; ++j1)
+        {
+            if (rvptr[j0] && rvptr[j1])  continue;
+            if (!this->getPairMask(j0, j1))  continue;
+            initsiteset(j0, cnt);
+            initsiteset(j1, cnt);
+        }
     }
     unordered_set<const SiteSet*> duplicate;
     vector< unordered_set<int> > rv;
     SiteSetPointers::const_iterator ssp;
     for (ssp = rvptr.begin(); ssp != rvptr.end(); ++ssp)
     {
-        if (duplicate.count(ssp->get()))  continue;
+        if (!ssp->get() || duplicate.count(ssp->get()))  continue;
         duplicate.insert(ssp->get());
         rv.push_back(**ssp);
     }

src/tests/TestOverlapCalculator.hpp

@@ -270,16 +270,35 @@ class TestOverlapCalculator : public CxxTest::TestSuite
 
         void test_neighborhoods()
         {
+            auto tb = molc->getAtomRadiiTable();
             molc->eval(mnacl);
             auto nbhood = molc->neighborhoods();
             TS_ASSERT_EQUALS(1u, nbhood.size());
             TS_ASSERT_EQUALS(8u, nbhood[0].size());
-            molc->getAtomRadiiTable()->resetAll();
+            tb->resetAll();
             molc->eval(mnacl);
             auto nbsep = molc->neighborhoods();
             TS_ASSERT_EQUALS(8u, nbsep.size());
             int nb5site = *(nbsep[5].begin());
             TS_ASSERT_EQUALS(5, nb5site);
+            molc->maskAllPairs(false);
+            molc->eval(mnacl);
+            auto nbdark = molc->neighborhoods();
+            TS_ASSERT(nbdark.empty());
+            molc->setTypeMask("Na1+", "Na1+", true);
+            molc->eval(mnacl);
+            auto nbnanasep = molc->neighborhoods();
+            TS_ASSERT_EQUALS(4u, nbnanasep.size());
+            int nb3site = *(nbnanasep[3].begin());
+            TS_ASSERT_EQUALS(3, nb3site);
+            tb->setCustom("Na1+", 5);
+            tb->setCustom("Cl1-", 5);
+            molc->eval(mnacl);
+            auto nbnana = molc->neighborhoods();
+            TS_ASSERT_EQUALS(1u, nbnana.size());
+            TS_ASSERT_EQUALS(4u, nbnana[0].size());
+            TS_ASSERT(nbnana[0].count(0));
+            TS_ASSERT(!nbnana[0].count(4));
         }