Add support for cumulative histograms

Now the final, averaged histograms computed by the analysisdata
histogram modules can also be made cumulative.  This is needed to
preserve some functionality of 'gmx rdf' when moving to the C++
framework.  For now, only the unit test is using the function.

Change-Id: Iaf7175dd904f9a615b8bd887d677aa8dc1e10f0d

diff --git a/src/gromacs/analysisdata/modules/histogram.cpp b/src/gromacs/analysisdata/modules/histogram.cpp
index 24f67024a74217c8391166d56b187ce72c51080b..fd6727ff91aa53d4fec623f54db339cde280a4e9 100644 (file)
--- a/src/gromacs/analysisdata/modules/histogram.cpp
+++ b/src/gromacs/analysisdata/modules/histogram.cpp
@@ -333,6 +333,7 @@ AbstractAverageHistogram::clone() const
 {
     AverageHistogramPointer dest(new StaticAverageHistogram());
     copyContents(this, dest.get());
+    dest->settings_ = settings_;
     return dest;
 }
 
@@ -354,6 +355,24 @@ AbstractAverageHistogram::normalizeProbability()
     }
 }
 
+void
+AbstractAverageHistogram::makeCumulative()
+{
+    for (int c = 0; c < columnCount(); ++c)
+    {
+        double sum = 0;
+        for (int i = 0; i < rowCount(); ++i)
+        {
+            sum += value(i, c).value();
+            // Clear the error, as we don't cumulate that.
+            value(i, c).clear();
+            value(i, c).setValue(sum);
+        }
+    }
+    setXAxis(settings().firstEdge() + settings().binWidth(),
+             settings().binWidth());
+}
+
 
 void
 AbstractAverageHistogram::scaleSingle(int index, real factor)

diff --git a/src/gromacs/analysisdata/modules/histogram.h b/src/gromacs/analysisdata/modules/histogram.h
index fe47fe0840a1363049ead744ab0226a60035b997..0717b4b822d1c68b76a5f0397f7700af3cfd90c8 100644 (file)
--- a/src/gromacs/analysisdata/modules/histogram.h
+++ b/src/gromacs/analysisdata/modules/histogram.h
@@ -255,6 +255,8 @@ typedef boost::shared_ptr<AbstractAverageHistogram>
  *
  * This class can represent multiple histograms in one object: each column in
  * the data is an independent histogram.
+ * The X values correspond to center of the bins, except for a cumulative
+ * histogram made with makeCumulative().
  *
  * \inpublicapi
  * \ingroup module_analysisdata
@@ -289,6 +291,14 @@ class AbstractAverageHistogram : public AbstractAnalysisArrayData
         AverageHistogramPointer clone() const;
         //! Normalizes the histogram such that the integral over it is one.
         void normalizeProbability();
+        /*! \brief
+         * Makes the histograms cumulative by summing up each bin to all bins
+         * after it.
+         *
+         * The X values in the data are adjusted such that they match the right
+         * edges of bins instead of bin centers.
+         */
+        void makeCumulative();
         //! Scales a single histogram by a uniform scaling factor.
         void scaleSingle(int index, real factor);
         //! Scales all histograms by a uniform scaling factor.

diff --git a/src/gromacs/analysisdata/tests/histogram.cpp b/src/gromacs/analysisdata/tests/histogram.cpp
index f210b4b7adba43a839c4afec591959ef1063674f..3fef0ef42ceab21d90eb0770ea561cefdc9660f5 100644 (file)
--- a/src/gromacs/analysisdata/tests/histogram.cpp
+++ b/src/gromacs/analysisdata/tests/histogram.cpp
@@ -523,6 +523,24 @@ TEST_F(AbstractAverageHistogramTest, ClonesCorrectly)
 }
 
 
+TEST_F(AbstractAverageHistogramTest, ComputesCumulativeHistogram)
+{
+    const AnalysisDataTestInput &input = AverageInputData::get();
+    MockAverageHistogram         data(
+            gmx::histogramFromBins(1.0, input.frameCount(), 0.5).integerBins());
+    setupArrayData(input, &data);
+
+    ASSERT_NO_THROW_GMX(addStaticCheckerModule(input, &data));
+    ASSERT_NO_THROW_GMX(addReferenceCheckerModule("InputData", &data));
+    ASSERT_NO_THROW_GMX(data.done());
+
+    gmx::AverageHistogramPointer cumulative(data.clone());
+    cumulative->makeCumulative();
+    ASSERT_NO_THROW_GMX(addReferenceCheckerModule("CumulativeHistogram", cumulative.get()));
+    ASSERT_NO_THROW_GMX(cumulative->done());
+}
+
+
 TEST_F(AbstractAverageHistogramTest, ResamplesAtDoubleBinWidth)
 {
     const AnalysisDataTestInput &input = AverageInputData::get();

diff --git a/src/gromacs/analysisdata/tests/refdata/AbstractAverageHistogramTest_ComputesCumulativeHistogram.xml b/src/gromacs/analysisdata/tests/refdata/AbstractAverageHistogramTest_ComputesCumulativeHistogram.xml
new file mode 100644 (file)
index 0000000..e7bd9d2
--- /dev/null
+++ b/src/gromacs/analysisdata/tests/refdata/AbstractAverageHistogramTest_ComputesCumulativeHistogram.xml
@@ -0,0 +1,141 @@
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+  <AnalysisData Name="InputData">
+    <DataFrame Name="Frame0">
+      <Real Name="X">1</Real>
+      <DataValues>
+        <Int Name="Count">1</Int>
+        <DataValue>
+          <Real Name="Value">2</Real>
+          <Real Name="Error">1</Real>
+        </DataValue>
+      </DataValues>
+    </DataFrame>
+    <DataFrame Name="Frame1">
+      <Real Name="X">1.5</Real>
+      <DataValues>
+        <Int Name="Count">1</Int>
+        <DataValue>
+          <Real Name="Value">1</Real>
+          <Real Name="Error">1</Real>
+        </DataValue>
+      </DataValues>
+    </DataFrame>
+    <DataFrame Name="Frame2">
+      <Real Name="X">2</Real>
+      <DataValues>
+        <Int Name="Count">1</Int>
+        <DataValue>
+          <Real Name="Value">3</Real>
+          <Real Name="Error">2</Real>
+        </DataValue>
+      </DataValues>
+    </DataFrame>
+    <DataFrame Name="Frame3">
+      <Real Name="X">2.5</Real>
+      <DataValues>
+        <Int Name="Count">1</Int>
+        <DataValue>
+          <Real Name="Value">4</Real>
+          <Real Name="Error">2</Real>
+        </DataValue>
+      </DataValues>
+    </DataFrame>
+    <DataFrame Name="Frame4">
+      <Real Name="X">3</Real>
+      <DataValues>
+        <Int Name="Count">1</Int>
+        <DataValue>
+          <Real Name="Value">2</Real>
+          <Real Name="Error">1</Real>
+        </DataValue>
+      </DataValues>
+    </DataFrame>
+    <DataFrame Name="Frame5">
+      <Real Name="X">3.5</Real>
+      <DataValues>
+        <Int Name="Count">1</Int>
+        <DataValue>
+          <Real Name="Value">0</Real>
+          <Real Name="Error">3</Real>
+        </DataValue>
+      </DataValues>
+    </DataFrame>
+    <DataFrame Name="Frame6">
+      <Real Name="X">4</Real>
+      <DataValues>
+        <Int Name="Count">1</Int>
+        <DataValue>
+          <Real Name="Value">1</Real>
+          <Real Name="Error">3</Real>
+        </DataValue>
+      </DataValues>
+    </DataFrame>
+  </AnalysisData>
+  <AnalysisData Name="CumulativeHistogram">
+    <DataFrame Name="Frame0">
+      <Real Name="X">1.25</Real>
+      <DataValues>
+        <Int Name="Count">1</Int>
+        <DataValue>
+          <Real Name="Value">2</Real>
+        </DataValue>
+      </DataValues>
+    </DataFrame>
+    <DataFrame Name="Frame1">
+      <Real Name="X">1.75</Real>
+      <DataValues>
+        <Int Name="Count">1</Int>
+        <DataValue>
+          <Real Name="Value">3</Real>
+        </DataValue>
+      </DataValues>
+    </DataFrame>
+    <DataFrame Name="Frame2">
+      <Real Name="X">2.25</Real>
+      <DataValues>
+        <Int Name="Count">1</Int>
+        <DataValue>
+          <Real Name="Value">6</Real>
+        </DataValue>
+      </DataValues>
+    </DataFrame>
+    <DataFrame Name="Frame3">
+      <Real Name="X">2.75</Real>
+      <DataValues>
+        <Int Name="Count">1</Int>
+        <DataValue>
+          <Real Name="Value">10</Real>
+        </DataValue>
+      </DataValues>
+    </DataFrame>
+    <DataFrame Name="Frame4">
+      <Real Name="X">3.25</Real>
+      <DataValues>
+        <Int Name="Count">1</Int>
+        <DataValue>
+          <Real Name="Value">12</Real>
+        </DataValue>
+      </DataValues>
+    </DataFrame>
+    <DataFrame Name="Frame5">
+      <Real Name="X">3.75</Real>
+      <DataValues>
+        <Int Name="Count">1</Int>
+        <DataValue>
+          <Real Name="Value">12</Real>
+        </DataValue>
+      </DataValues>
+    </DataFrame>
+    <DataFrame Name="Frame6">
+      <Real Name="X">4.25</Real>
+      <DataValues>
+        <Int Name="Count">1</Int>
+        <DataValue>
+          <Real Name="Value">13</Real>
+        </DataValue>
+      </DataValues>
+    </DataFrame>
+  </AnalysisData>
+</ReferenceData>