Changeset 45f4f96

Timestamp:

Nov 8, 2012, 1:13:52 PM (12 years ago)

Author:

Frederik Heber <heber@…>

Branches:

Action_Thermostats, Add_AtomRandomPerturbation, Add_FitFragmentPartialChargesAction, Add_RotateAroundBondAction, Add_SelectAtomByNameAction, Added_ParseSaveFragmentResults, AddingActions_SaveParseParticleParameters, Adding_Graph_to_ChangeBondActions, Adding_MD_integration_tests, Adding_ParticleName_to_Atom, Adding_StructOpt_integration_tests, AtomFragments, Automaking_mpqc_open, AutomationFragmentation_failures, Candidate_v1.5.4, Candidate_v1.6.0, Candidate_v1.6.1, ChangeBugEmailaddress, ChangingTestPorts, ChemicalSpaceEvaluator, CombiningParticlePotentialParsing, Combining_Subpackages, Debian_Package_split, Debian_package_split_molecuildergui_only, Disabling_MemDebug, Docu_Python_wait, EmpiricalPotential_contain_HomologyGraph, EmpiricalPotential_contain_HomologyGraph_documentation, Enable_parallel_make_install, Enhance_userguide, Enhanced_StructuralOptimization, Enhanced_StructuralOptimization_continued, Example_ManyWaysToTranslateAtom, Exclude_Hydrogens_annealWithBondGraph, FitPartialCharges_GlobalError, Fix_BoundInBox_CenterInBox_MoleculeActions, Fix_ChargeSampling_PBC, Fix_ChronosMutex, Fix_FitPartialCharges, Fix_FitPotential_needs_atomicnumbers, Fix_ForceAnnealing, Fix_IndependentFragmentGrids, Fix_ParseParticles, Fix_ParseParticles_split_forward_backward_Actions, Fix_PopActions, Fix_QtFragmentList_sorted_selection, Fix_Restrictedkeyset_FragmentMolecule, Fix_StatusMsg, Fix_StepWorldTime_single_argument, Fix_Verbose_Codepatterns, Fix_fitting_potentials, Fixes, ForceAnnealing_goodresults, ForceAnnealing_oldresults, ForceAnnealing_tocheck, ForceAnnealing_with_BondGraph, ForceAnnealing_with_BondGraph_continued, ForceAnnealing_with_BondGraph_continued_betteresults, ForceAnnealing_with_BondGraph_contraction-expansion, FragmentAction_writes_AtomFragments, FragmentMolecule_checks_bonddegrees, GeometryObjects, Gui_Fixes, Gui_displays_atomic_force_velocity, ImplicitCharges, IndependentFragmentGrids, IndependentFragmentGrids_IndividualZeroInstances, IndependentFragmentGrids_IntegrationTest, IndependentFragmentGrids_Sole_NN_Calculation, JobMarket_RobustOnKillsSegFaults, JobMarket_StableWorkerPool, JobMarket_unresolvable_hostname_fix, MoreRobust_FragmentAutomation, ODR_violation_mpqc_open, PartialCharges_OrthogonalSummation, PdbParser_setsAtomName, PythonUI_with_named_parameters, QtGui_reactivate_TimeChanged_changes, Recreated_GuiChecks, Rewrite_FitPartialCharges, RotateToPrincipalAxisSystem_UndoRedo, SaturateAtoms_findBestMatching, SaturateAtoms_singleDegree, StoppableMakroAction, Subpackage_CodePatterns, Subpackage_JobMarket, Subpackage_LinearAlgebra, Subpackage_levmar, Subpackage_mpqc_open, Subpackage_vmg, Switchable_LogView, ThirdParty_MPQC_rebuilt_buildsystem, TrajectoryDependenant_MaxOrder, TremoloParser_IncreasedPrecision, TremoloParser_MultipleTimesteps, TremoloParser_setsAtomName, Ubuntu_1604_changes, stable

Children:

22c4f57

Parents:

bb68c0

git-author:

Frederik Heber <heber@…> (07/27/12 12:35:40)

git-committer:

Frederik Heber <heber@…> (11/08/12 13:13:52)

Message:

FIX: Bins are initialized as normalized from samples.

• Bins are now initialized as normalized from samples.
• the addition to the histogram by one sample always equals a surface area of one, i.e. we add 1 / binwidth.
• only then may we sensibly add and subtract different histograms with different binwidths.
• also added Histogram::area() function and unit test.

Location:

src/Fragmentation/Histogram

Files:

• Histogram.cpp (modified) (2 diffs)
• Histogram.hpp (modified) (3 diffs)
• unittests/HistogramUnitTest.cpp (modified) (1 diff)
• unittests/HistogramUnitTest.hpp (modified) (2 diffs)

src/Fragmentation/Histogram/Histogram.cpp

@@ -119 +119 @@
     bins.insert(vectorbins.begin(), vectorbins.end());
 
-    // 4. place each sample into bin
+    // 4. place each sample into bin (make count normalized, i.e. always equal to
+    // surface area of 1)
     BOOST_FOREACH( double value, samples) {
       const Bins_t::iterator biniter = getLowerEndBin(value);
       ASSERT( biniter != bins.end(),
           "Histogram::Histogram() - cannot find bin for value from given samples.");
-      biniter->second += 1.;
+      biniter->second += 1./binwidth;
     }
     LOG(2, "DEBUG: Bins are " << printBins() << ".");
@@ -189 +190 @@
   return iter;
 }
+
+double Histogram::area() const
+{
+  double area = 0.;
+  for(Bins_t::const_iterator iter = bins.begin(); iter != bins.end(); ++iter)
+    area += iter->second*binwidth;
+  return area;
+}

src/Fragmentation/Histogram/Histogram.hpp

@@ -56 +56 @@
   /** Adding another histogram onto this one.
    *
+   * \note The operation is area-conserving, i.e. the new area is the sum of
+   * both areas.
+   *
    * @param other other histogram
    * @return ref to this instance
@@ -62 +65 @@
 
   /** Subtracting another histogram from this one.
+   *
+   * \note The operation is area-conserving, i.e. the new area is the
+   * difference of both areas.
    *
    * @param other other histogram
@@ -73 +79 @@
    */
   bool isEmpty() const;
+
+  /** Sums all found weights times the Histogram::binwidth.
+   *
+   * @return sum over all weights times width.
+   */
+  double area() const;
 
 private:

src/Fragmentation/Histogram/unittests/HistogramUnitTest.cpp

@@ -173 +173 @@
 }
 
+/** UnitTest for area()
+ */
+void HistogramTest::areaTest()
+{
+  histogram = new Histogram(std::vector<double>());
+  // test on empty histogramgram
+  CPPUNIT_ASSERT_EQUAL( 0., histogram->area() );
+
+  // create non-empty histogram and sum up
+  Histogram::samples_t sampled_values;
+  sampled_values += 1.,2.,3.,4., 4.;
+  delete histogram;
+  histogram = new Histogram(sampled_values, 4);
+  CPPUNIT_ASSERT_EQUAL( 5., histogram->area() );
+  Histogram::samples_t more_values;
+  more_values += 1.75,2.5,3.;
+  Histogram otherhistogram(more_values, 3);
+  CPPUNIT_ASSERT_EQUAL( 3., otherhistogram.area() );
+
+}
+
 /** UnitTest for operator+=(), operator-=()
  */

src/Fragmentation/Histogram/unittests/HistogramUnitTest.hpp

@@ -29 +29 @@
     CPPUNIT_TEST ( isEmpty_Test );
     CPPUNIT_TEST ( operator_Test );
+    CPPUNIT_TEST ( areaTest );
     CPPUNIT_TEST_SUITE_END();
 
@@ -39 +40 @@
       void isEmpty_Test();
       void operator_Test();
+      void areaTest();
 
 private: