src/gromacs/analysisdata/modules/average.cpp

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  35 /*! \internal \file
  36  * \brief
  37  * Implements gmx::AnalysisDataAverageModule.
  38  *
  39  * \author Teemu Murtola <teemu.murtola@gmail.com>
  40  * \ingroup module_analysisdata
  41  */
  42 #include "gmxpre.h"
  43
  44 #include "average.h"
  45
  46 #include <cmath>
  47
  48 #include <algorithm>
  49 #include <vector>
  50
  51 #include "gromacs/analysisdata/dataframe.h"
  52 #include "gromacs/analysisdata/datastorage.h"
  53
  54 #include "frameaverager.h"
  55
  56 namespace gmx
  57 {
  58
  59 /********************************************************************
  60  * AnalysisDataAverageModule
  61  */
  62
  63 class AnalysisDataAverageModule::Impl
  64 {
  65     public:
  66         Impl() : bDataSets_(false) {}
  67
  68         //! Averaging helper objects for each input data set.
  69         std::vector<AnalysisDataFrameAverager>  averagers_;
  70         //! Whether to average all columns in a data set into a single value.
  71         bool                                    bDataSets_;
  72 };
  73
  74 AnalysisDataAverageModule::AnalysisDataAverageModule()
  75     : impl_(new Impl())
  76 {
  77 }
  78
  79 AnalysisDataAverageModule::~AnalysisDataAverageModule()
  80 {
  81 }
  82
  83 void AnalysisDataAverageModule::setAverageDataSets(bool bDataSets)
  84 {
  85     impl_->bDataSets_ = bDataSets;
  86 }
  87
  88 int AnalysisDataAverageModule::flags() const
  89 {
  90     return efAllowMultipoint | efAllowMulticolumn | efAllowMissing
  91            | efAllowMultipleDataSets;
  92 }
  93
  94 void
  95 AnalysisDataAverageModule::dataStarted(AbstractAnalysisData *data)
  96 {
  97     if (impl_->bDataSets_)
  98     {
  99         setColumnCount(1);
 100         setRowCount(data->dataSetCount());
 101         impl_->averagers_.resize(1);
 102         impl_->averagers_[0].setColumnCount(data->dataSetCount());
 103     }
 104     else
 105     {
 106         setColumnCount(data->dataSetCount());
 107         impl_->averagers_.resize(data->dataSetCount());
 108         int rowCount = 0;
 109         for (int i = 0; i < data->dataSetCount(); ++i)
 110         {
 111             impl_->averagers_[i].setColumnCount(data->columnCount(i));
 112             rowCount = std::max(rowCount, data->columnCount(i));
 113         }
 114         setRowCount(rowCount);
 115     }
 116 }
 117
 118 void
 119 AnalysisDataAverageModule::frameStarted(const AnalysisDataFrameHeader & /*header*/)
 120 {
 121 }
 122
 123 void
 124 AnalysisDataAverageModule::pointsAdded(const AnalysisDataPointSetRef &points)
 125 {
 126     if (impl_->bDataSets_)
 127     {
 128         const int dataSet = points.dataSetIndex();
 129         for (int i = 0; i < points.columnCount(); ++i)
 130         {
 131             if (points.present(i))
 132             {
 133                 impl_->averagers_[0].addValue(dataSet, points.y(i));
 134             }
 135         }
 136     }
 137     else
 138     {
 139         impl_->averagers_[points.dataSetIndex()].addPoints(points);
 140     }
 141 }
 142
 143 void
 144 AnalysisDataAverageModule::frameFinished(const AnalysisDataFrameHeader & /*header*/)
 145 {
 146 }
 147
 148 void
 149 AnalysisDataAverageModule::dataFinished()
 150 {
 151     allocateValues();
 152     for (int i = 0; i < columnCount(); ++i)
 153     {
 154         impl_->averagers_[i].finish();
 155         int j = 0;
 156         for (; j < impl_->averagers_[i].columnCount(); ++j)
 157         {
 158             value(j, i).setValue(impl_->averagers_[i].average(j),
 159                                  std::sqrt(impl_->averagers_[i].variance(j)));
 160         }
 161         for (; j < rowCount(); ++j)
 162         {
 163             value(j, i).setValue(0.0, 0.0, false);
 164         }
 165     }
 166     valuesReady();
 167 }
 168
 169 real AnalysisDataAverageModule::average(int dataSet, int column) const
 170 {
 171     if (impl_->bDataSets_)
 172     {
 173         GMX_ASSERT(column == 0,
 174                    "Column should be zero with setAverageDataSets(true)");
 175         std::swap(dataSet, column);
 176     }
 177     return value(column, dataSet).value();
 178 }
 179
 180 real AnalysisDataAverageModule::standardDeviation(int dataSet, int column) const
 181 {
 182     if (impl_->bDataSets_)
 183     {
 184         GMX_ASSERT(column == 0,
 185                    "Column should be zero with setAverageDataSets(true)");
 186         std::swap(dataSet, column);
 187     }
 188     return value(column, dataSet).error();
 189 }
 190
 191 int AnalysisDataAverageModule::sampleCount(int dataSet, int column) const
 192 {
 193     if (impl_->bDataSets_)
 194     {
 195         GMX_ASSERT(column == 0,
 196                    "Column should be zero with setAverageDataSets(true)");
 197         std::swap(dataSet, column);
 198     }
 199     return impl_->averagers_[dataSet].sampleCount(column);
 200 }
 201
 202
 203 /********************************************************************
 204  * AnalysisDataFrameAverageModule
 205  */
 206
 207 class AnalysisDataFrameAverageModule::Impl
 208 {
 209     public:
 210         //! Storage implementation object.
 211         AnalysisDataStorage     storage_;
 212         //! Number of samples in a frame for each data set.
 213         std::vector<int>        sampleCount_;
 214 };
 215
 216 AnalysisDataFrameAverageModule::AnalysisDataFrameAverageModule()
 217     : impl_(new Impl())
 218 {
 219 }
 220
 221 AnalysisDataFrameAverageModule::~AnalysisDataFrameAverageModule()
 222 {
 223 }
 224
 225 int
 226 AnalysisDataFrameAverageModule::frameCount() const
 227 {
 228     return impl_->storage_.frameCount();
 229 }
 230
 231 int
 232 AnalysisDataFrameAverageModule::flags() const
 233 {
 234     return efAllowMultipoint | efAllowMulticolumn | efAllowMissing
 235            | efAllowMultipleDataSets;
 236 }
 237
 238 void
 239 AnalysisDataFrameAverageModule::dataStarted(AbstractAnalysisData *data)
 240 {
 241     setColumnCount(0, data->dataSetCount());
 242     impl_->sampleCount_.resize(data->dataSetCount());
 243     impl_->storage_.startDataStorage(this, &moduleManager());
 244 }
 245
 246 void
 247 AnalysisDataFrameAverageModule::frameStarted(const AnalysisDataFrameHeader &header)
 248 {
 249     AnalysisDataStorageFrame &frame = impl_->storage_.startFrame(header);
 250     for (int i = 0; i < columnCount(); ++i)
 251     {
 252         impl_->sampleCount_[i] = 0;
 253         frame.setValue(i, 0.0);
 254     }
 255 }
 256
 257 void
 258 AnalysisDataFrameAverageModule::pointsAdded(const AnalysisDataPointSetRef &points)
 259 {
 260     const int                 dataSet = points.dataSetIndex();
 261     AnalysisDataStorageFrame &frame   =
 262         impl_->storage_.currentFrame(points.frameIndex());
 263     for (int i = 0; i < points.columnCount(); ++i)
 264     {
 265         if (points.present(i))
 266         {
 267             // TODO: Consider using AnalysisDataFrameAverager
 268             const real y     = points.y(i);
 269             const real delta = y - frame.value(dataSet);
 270             impl_->sampleCount_[dataSet] += 1;
 271             frame.value(dataSet)         += delta / impl_->sampleCount_[dataSet];
 272         }
 273     }
 274 }
 275
 276 void
 277 AnalysisDataFrameAverageModule::frameFinished(const AnalysisDataFrameHeader &header)
 278 {
 279     impl_->storage_.finishFrame(header.index());
 280 }
 281
 282 void
 283 AnalysisDataFrameAverageModule::dataFinished()
 284 {
 285     impl_->storage_.finishDataStorage();
 286 }
 287
 288 AnalysisDataFrameRef
 289 AnalysisDataFrameAverageModule::tryGetDataFrameInternal(int index) const
 290 {
 291     return impl_->storage_.tryGetDataFrame(index);
 292 }
 293
 294 bool
 295 AnalysisDataFrameAverageModule::requestStorageInternal(int nframes)
 296 {
 297     return impl_->storage_.requestStorage(nframes);
 298 }
 299
 300 } // namespace gmx