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37 * Implements gmx::AnalysisDataAverageModule.
39 * \author Teemu Murtola <teemu.murtola@gmail.com>
40 * \ingroup module_analysisdata
49 #include "gromacs/analysisdata/dataframe.h"
50 #include "gromacs/analysisdata/datastorage.h"
52 #include "frameaverager.h"
57 /********************************************************************
58 * AnalysisDataAverageModule
61 class AnalysisDataAverageModule::Impl
64 Impl() : bDataSets_(false) {}
66 //! Averaging helper objects for each input data set.
67 std::vector<AnalysisDataFrameAverager> averagers_;
68 //! Whether to average all columns in a data set into a single value.
72 AnalysisDataAverageModule::AnalysisDataAverageModule()
77 AnalysisDataAverageModule::~AnalysisDataAverageModule()
81 void AnalysisDataAverageModule::setAverageDataSets(bool bDataSets)
83 impl_->bDataSets_ = bDataSets;
86 int AnalysisDataAverageModule::flags() const
88 return efAllowMultipoint | efAllowMulticolumn | efAllowMissing
89 | efAllowMultipleDataSets;
93 AnalysisDataAverageModule::dataStarted(AbstractAnalysisData *data)
95 if (impl_->bDataSets_)
98 setRowCount(data->dataSetCount());
99 impl_->averagers_.resize(1);
100 impl_->averagers_[0].setColumnCount(data->dataSetCount());
104 setColumnCount(data->dataSetCount());
105 impl_->averagers_.resize(data->dataSetCount());
107 for (int i = 0; i < data->dataSetCount(); ++i)
109 impl_->averagers_[i].setColumnCount(data->columnCount(i));
110 rowCount = std::max(rowCount, data->columnCount(i));
112 setRowCount(rowCount);
117 AnalysisDataAverageModule::frameStarted(const AnalysisDataFrameHeader & /*header*/)
122 AnalysisDataAverageModule::pointsAdded(const AnalysisDataPointSetRef &points)
124 if (impl_->bDataSets_)
126 const int dataSet = points.dataSetIndex();
127 for (int i = 0; i < points.columnCount(); ++i)
129 if (points.present(i))
131 impl_->averagers_[0].addValue(dataSet, points.y(i));
137 impl_->averagers_[points.dataSetIndex()].addPoints(points);
142 AnalysisDataAverageModule::frameFinished(const AnalysisDataFrameHeader & /*header*/)
147 AnalysisDataAverageModule::dataFinished()
150 for (int i = 0; i < columnCount(); ++i)
152 impl_->averagers_[i].finish();
154 for (; j < impl_->averagers_[i].columnCount(); ++j)
156 value(j, i).setValue(impl_->averagers_[i].average(j),
157 std::sqrt(impl_->averagers_[i].variance(j)));
159 for (; j < rowCount(); ++j)
161 value(j, i).setValue(0.0, 0.0, false);
167 real AnalysisDataAverageModule::average(int dataSet, int column) const
169 if (impl_->bDataSets_)
171 GMX_ASSERT(column == 0,
172 "Column should be zero with setAverageDataSets(true)");
173 std::swap(dataSet, column);
175 return value(column, dataSet).value();
178 real AnalysisDataAverageModule::standardDeviation(int dataSet, int column) const
180 if (impl_->bDataSets_)
182 GMX_ASSERT(column == 0,
183 "Column should be zero with setAverageDataSets(true)");
184 std::swap(dataSet, column);
186 return value(column, dataSet).error();
189 int AnalysisDataAverageModule::sampleCount(int dataSet, int column) const
191 if (impl_->bDataSets_)
193 GMX_ASSERT(column == 0,
194 "Column should be zero with setAverageDataSets(true)");
195 std::swap(dataSet, column);
197 return impl_->averagers_[dataSet].sampleCount(column);
201 /********************************************************************
202 * AnalysisDataFrameAverageModule
205 class AnalysisDataFrameAverageModule::Impl
208 //! Storage implementation object.
209 AnalysisDataStorage storage_;
210 //! Number of samples in a frame for each data set.
211 std::vector<int> sampleCount_;
214 AnalysisDataFrameAverageModule::AnalysisDataFrameAverageModule()
219 AnalysisDataFrameAverageModule::~AnalysisDataFrameAverageModule()
224 AnalysisDataFrameAverageModule::frameCount() const
226 return impl_->storage_.frameCount();
230 AnalysisDataFrameAverageModule::flags() const
232 return efAllowMultipoint | efAllowMulticolumn | efAllowMissing
233 | efAllowMultipleDataSets;
237 AnalysisDataFrameAverageModule::dataStarted(AbstractAnalysisData *data)
239 setColumnCount(0, data->dataSetCount());
240 impl_->sampleCount_.resize(data->dataSetCount());
241 impl_->storage_.startDataStorage(this, &moduleManager());
245 AnalysisDataFrameAverageModule::frameStarted(const AnalysisDataFrameHeader &header)
247 AnalysisDataStorageFrame &frame = impl_->storage_.startFrame(header);
248 for (int i = 0; i < columnCount(); ++i)
250 impl_->sampleCount_[i] = 0;
251 frame.setValue(i, 0.0);
256 AnalysisDataFrameAverageModule::pointsAdded(const AnalysisDataPointSetRef &points)
258 const int dataSet = points.dataSetIndex();
259 AnalysisDataStorageFrame &frame =
260 impl_->storage_.currentFrame(points.frameIndex());
261 for (int i = 0; i < points.columnCount(); ++i)
263 if (points.present(i))
265 // TODO: Consider using AnalysisDataFrameAverager
266 const real y = points.y(i);
267 const real delta = y - frame.value(dataSet);
268 impl_->sampleCount_[dataSet] += 1;
269 frame.value(dataSet) += delta / impl_->sampleCount_[dataSet];
275 AnalysisDataFrameAverageModule::frameFinished(const AnalysisDataFrameHeader &header)
277 impl_->storage_.finishFrame(header.index());
281 AnalysisDataFrameAverageModule::dataFinished()
283 impl_->storage_.finishDataStorage();
287 AnalysisDataFrameAverageModule::tryGetDataFrameInternal(int index) const
289 return impl_->storage_.tryGetDataFrame(index);
293 AnalysisDataFrameAverageModule::requestStorageInternal(int nframes)
295 return impl_->storage_.requestStorage(nframes);