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37 * Implements classes in histogram.h.
39 * \author Teemu Murtola <teemu.murtola@gmail.com>
40 * \ingroup module_analysisdata
42 #include "gromacs/analysisdata/modules/histogram.h"
49 #include "gromacs/analysisdata/dataframe.h"
50 #include "gromacs/analysisdata/datastorage.h"
51 #include "gromacs/utility/exceptions.h"
52 #include "gromacs/utility/gmxassert.h"
54 #include "frameaverager.h"
59 //! Value used to signify that a real-valued histogram setting is not set.
60 const real UNDEFINED = std::numeric_limits<real>::max();
61 //! Checks whether \p value is defined.
62 bool isDefined(real value)
64 return value != UNDEFINED;
72 /********************************************************************
73 * AnalysisHistogramSettingsInitializer
76 AnalysisHistogramSettingsInitializer::AnalysisHistogramSettingsInitializer()
77 : min_(UNDEFINED), max_(UNDEFINED), binWidth_(UNDEFINED),
78 binCount_(0), bIntegerBins_(false), bRoundRange_(false),
84 /********************************************************************
85 * AnalysisHistogramSettings
88 AnalysisHistogramSettings::AnalysisHistogramSettings()
89 : firstEdge_(0.0), lastEdge_(0.0), binWidth_(0.0), inverseBinWidth_(0.0),
90 binCount_(0), bAll_(false)
95 AnalysisHistogramSettings::AnalysisHistogramSettings(
96 const AnalysisHistogramSettingsInitializer &settings)
98 GMX_RELEASE_ASSERT(isDefined(settings.min_),
99 "Histogram start value must be defined");
100 GMX_RELEASE_ASSERT(!isDefined(settings.max_) || settings.max_ > settings.min_,
101 "Histogram end value must be larger than start value");
102 GMX_RELEASE_ASSERT(!isDefined(settings.binWidth_) || settings.binWidth_ > 0.0,
103 "Histogram bin width must be positive");
104 GMX_RELEASE_ASSERT(settings.binCount_ >= 0,
105 "Histogram bin count must be positive");
107 if (!isDefined(settings.max_))
109 GMX_RELEASE_ASSERT(isDefined(settings.binWidth_) && settings.binCount_ > 0,
110 "Not all required values provided");
111 GMX_RELEASE_ASSERT(!settings.bRoundRange_,
112 "Rounding only supported for min/max ranges");
114 firstEdge_ = settings.min_;
115 binCount_ = settings.binCount_;
116 binWidth_ = settings.binWidth_;
117 if (settings.bIntegerBins_)
119 firstEdge_ -= 0.5 * binWidth_;
121 lastEdge_ = firstEdge_ + binCount_ * binWidth_;
125 GMX_RELEASE_ASSERT(!(isDefined(settings.binWidth_) && settings.binCount_ > 0),
126 "Conflicting histogram bin specifications");
127 GMX_RELEASE_ASSERT(isDefined(settings.binWidth_) || settings.binCount_ > 0,
128 "Not all required values provided");
130 if (settings.bRoundRange_)
132 GMX_RELEASE_ASSERT(!settings.bIntegerBins_,
133 "Rounding and integer bins cannot be combined");
134 GMX_RELEASE_ASSERT(isDefined(settings.binWidth_),
135 "Rounding only makes sense with defined binwidth");
136 binWidth_ = settings.binWidth_;
137 firstEdge_ = binWidth_ * floor(settings.min_ / binWidth_);
138 lastEdge_ = binWidth_ * ceil(settings.max_ / binWidth_);
139 binCount_ = static_cast<int>((lastEdge_ - firstEdge_) / binWidth_ + 0.5);
143 firstEdge_ = settings.min_;
144 lastEdge_ = settings.max_;
145 if (settings.binCount_ > 0)
147 binCount_ = settings.binCount_;
148 if (settings.bIntegerBins_)
150 GMX_RELEASE_ASSERT(settings.binCount_ > 1,
151 "Bin count must be at least two with integer bins");
152 binWidth_ = (lastEdge_ - firstEdge_) / (binCount_ - 1);
153 firstEdge_ -= 0.5 * binWidth_;
154 lastEdge_ += 0.5 * binWidth_;
158 binWidth_ = (lastEdge_ - firstEdge_) / binCount_;
163 binWidth_ = settings.binWidth_;
164 binCount_ = static_cast<int>((lastEdge_ - firstEdge_) / binWidth_ + 0.5);
165 if (settings.bIntegerBins_)
167 firstEdge_ -= 0.5 * binWidth_;
170 lastEdge_ = firstEdge_ + binCount_ * binWidth_;
175 inverseBinWidth_ = 1.0 / binWidth_;
176 bAll_ = settings.bIncludeAll_;
181 AnalysisHistogramSettings::findBin(real y) const
185 return bAll_ ? 0 : -1;
187 int bin = static_cast<int>((y - firstEdge_) * inverseBinWidth_);
188 if (bin >= binCount_)
190 return bAll_ ? binCount_ - 1 : -1;
196 /********************************************************************
197 * StaticAverageHistogram
204 * Represents copies of average histograms.
206 * Methods in AbstractAverageHistogram that return new histogram instances
207 * return objects of this class.
208 * Initialization of values is handled in those methods.
210 * \ingroup module_analysisdata
212 class StaticAverageHistogram : public AbstractAverageHistogram
215 StaticAverageHistogram();
216 //! Creates an average histogram module with defined bin parameters.
217 explicit StaticAverageHistogram(const AnalysisHistogramSettings &settings);
219 // Copy and assign disallowed by base.
222 StaticAverageHistogram::StaticAverageHistogram()
227 StaticAverageHistogram::StaticAverageHistogram(
228 const AnalysisHistogramSettings &settings)
229 : AbstractAverageHistogram(settings)
236 /********************************************************************
237 * AbstractAverageHistogram
240 AbstractAverageHistogram::AbstractAverageHistogram()
245 AbstractAverageHistogram::AbstractAverageHistogram(
246 const AnalysisHistogramSettings &settings)
247 : settings_(settings)
249 setRowCount(settings.binCount());
250 setXAxis(settings.firstEdge() + 0.5 * settings.binWidth(),
251 settings.binWidth());
255 AbstractAverageHistogram::~AbstractAverageHistogram()
261 AbstractAverageHistogram::init(const AnalysisHistogramSettings &settings)
263 settings_ = settings;
264 setRowCount(settings.binCount());
265 setXAxis(settings.firstEdge() + 0.5 * settings.binWidth(),
266 settings.binWidth());
270 AverageHistogramPointer
271 AbstractAverageHistogram::resampleDoubleBinWidth(bool bIntegerBins) const
276 nbins = (rowCount() + 1) / 2;
280 nbins = rowCount() / 2;
283 AverageHistogramPointer dest(
284 new StaticAverageHistogram(
285 histogramFromBins(xstart(), nbins, 2*xstep())
286 .integerBins(bIntegerBins)));
287 dest->setColumnCount(columnCount());
288 dest->allocateValues();
291 for (i = j = 0; i < nbins; ++i)
293 const bool bFirstHalfBin = (bIntegerBins && i == 0);
294 for (int c = 0; c < columnCount(); ++c)
300 v1 = value(0, c).value();
301 e1 = value(0, c).error();
307 v1 = value(j, c).value();
308 e1 = value(j, c).error();
309 v2 = value(j + 1, c).value();
310 e2 = value(j + 1, c).error();
312 dest->value(i, c).setValue(v1 + v2, std::sqrt(e1 * e1 + e2 * e2));
327 AverageHistogramPointer
328 AbstractAverageHistogram::clone() const
330 AverageHistogramPointer dest(new StaticAverageHistogram());
331 copyContents(this, dest.get());
337 AbstractAverageHistogram::normalizeProbability()
339 for (int c = 0; c < columnCount(); ++c)
342 for (int i = 0; i < rowCount(); ++i)
344 sum += value(i, c).value();
346 scaleSingle(c, 1.0 / (sum * xstep()));
352 AbstractAverageHistogram::scaleSingle(int index, real factor)
354 for (int i = 0; i < rowCount(); ++i)
356 value(i, index).value() *= factor;
357 value(i, index).error() *= factor;
363 AbstractAverageHistogram::scaleAll(real factor)
365 for (int i = 0; i < columnCount(); ++i)
367 scaleSingle(i, factor);
373 AbstractAverageHistogram::scaleAllByVector(real factor[])
375 for (int c = 0; c < columnCount(); ++c)
377 for (int i = 0; i < rowCount(); ++i)
379 value(i, c).value() *= factor[i];
380 value(i, c).error() *= factor[i];
386 /********************************************************************
387 * BasicAverageHistogramModule
394 * Implements average histogram module that averages per-frame histograms.
396 * This class is used for accumulating average histograms in per-frame
397 * histogram modules (those that use BasicHistogramImpl as their implementation
399 * There are two columns, first for the average and second for standard
402 * \ingroup module_analysisdata
404 class BasicAverageHistogramModule : public AbstractAverageHistogram,
405 public AnalysisDataModuleInterface
408 BasicAverageHistogramModule();
409 //! Creates an average histogram module with defined bin parameters.
410 explicit BasicAverageHistogramModule(const AnalysisHistogramSettings &settings);
412 using AbstractAverageHistogram::init;
414 virtual int flags() const;
416 virtual void dataStarted(AbstractAnalysisData *data);
417 virtual void frameStarted(const AnalysisDataFrameHeader &header);
418 virtual void pointsAdded(const AnalysisDataPointSetRef &points);
419 virtual void frameFinished(const AnalysisDataFrameHeader &header);
420 virtual void dataFinished();
423 //! Averaging helper objects for each input data set.
424 std::vector<AnalysisDataFrameAverager> averagers_;
426 // Copy and assign disallowed by base.
429 BasicAverageHistogramModule::BasicAverageHistogramModule()
434 BasicAverageHistogramModule::BasicAverageHistogramModule(
435 const AnalysisHistogramSettings &settings)
436 : AbstractAverageHistogram(settings)
442 BasicAverageHistogramModule::flags() const
444 return efAllowMulticolumn | efAllowMultipleDataSets;
449 BasicAverageHistogramModule::dataStarted(AbstractAnalysisData *data)
451 setColumnCount(data->dataSetCount());
452 averagers_.resize(data->dataSetCount());
453 for (int i = 0; i < data->dataSetCount(); ++i)
455 GMX_RELEASE_ASSERT(rowCount() == data->columnCount(i),
456 "Inconsistent data sizes, something is wrong in the initialization");
457 averagers_[i].setColumnCount(data->columnCount(i));
463 BasicAverageHistogramModule::frameStarted(const AnalysisDataFrameHeader & /*header*/)
469 BasicAverageHistogramModule::pointsAdded(const AnalysisDataPointSetRef &points)
471 averagers_[points.dataSetIndex()].addPoints(points);
476 BasicAverageHistogramModule::frameFinished(const AnalysisDataFrameHeader & /*header*/)
482 BasicAverageHistogramModule::dataFinished()
485 for (int i = 0; i < columnCount(); ++i)
487 averagers_[i].finish();
488 for (int j = 0; j < rowCount(); ++j)
490 value(j, i).setValue(averagers_[i].average(j),
491 std::sqrt(averagers_[i].variance(j)));
497 /********************************************************************
502 * Private implementation class for AnalysisDataSimpleHistogramModule and
503 * AnalysisDataWeightedHistogramModule.
505 * \ingroup module_analysisdata
507 class BasicHistogramImpl
510 //! Smart pointer to manage an BasicAverageHistogramModule object.
511 typedef boost::shared_ptr<BasicAverageHistogramModule>
512 BasicAverageHistogramModulePointer;
514 BasicHistogramImpl();
515 //! Creates an histogram impl with defined bin parameters.
516 explicit BasicHistogramImpl(const AnalysisHistogramSettings &settings);
517 ~BasicHistogramImpl();
520 * (Re)initializes the histogram from settings.
522 void init(const AnalysisHistogramSettings &settings);
524 * Initializes data storage frame when a new frame starts.
526 void initFrame(int dataSetCount, AnalysisDataStorageFrame *frame);
528 //! Storage implementation object.
529 AnalysisDataStorage storage_;
530 //! Settings for the histogram object.
531 AnalysisHistogramSettings settings_;
533 BasicAverageHistogramModulePointer averager_;
536 BasicHistogramImpl::BasicHistogramImpl()
537 : averager_(new BasicAverageHistogramModule())
542 BasicHistogramImpl::BasicHistogramImpl(const AnalysisHistogramSettings &settings)
543 : settings_(settings), averager_(new BasicAverageHistogramModule(settings))
548 BasicHistogramImpl::~BasicHistogramImpl()
553 void BasicHistogramImpl::init(const AnalysisHistogramSettings &settings)
555 settings_ = settings;
556 averager_->init(settings);
561 BasicHistogramImpl::initFrame(int dataSetCount, AnalysisDataStorageFrame *frame)
563 for (int s = 0; s < dataSetCount; ++s)
565 frame->selectDataSet(s);
566 for (int i = 0; i < frame->columnCount(); ++i)
568 frame->setValue(i, 0.0);
571 frame->selectDataSet(0);
574 } // namespace internal
577 /********************************************************************
578 * AnalysisDataSimpleHistogramModule
581 AnalysisDataSimpleHistogramModule::AnalysisDataSimpleHistogramModule()
582 : impl_(new internal::BasicHistogramImpl())
587 AnalysisDataSimpleHistogramModule::AnalysisDataSimpleHistogramModule(
588 const AnalysisHistogramSettings &settings)
589 : impl_(new internal::BasicHistogramImpl(settings))
594 AnalysisDataSimpleHistogramModule::~AnalysisDataSimpleHistogramModule()
599 void AnalysisDataSimpleHistogramModule::init(const AnalysisHistogramSettings &settings)
601 impl_->init(settings);
605 AbstractAverageHistogram &
606 AnalysisDataSimpleHistogramModule::averager()
608 return *impl_->averager_;
612 const AnalysisHistogramSettings &
613 AnalysisDataSimpleHistogramModule::settings() const
615 return impl_->settings_;
620 AnalysisDataSimpleHistogramModule::flags() const
622 return efAllowMulticolumn | efAllowMultipoint | efAllowMissing
623 | efAllowMultipleDataSets;
628 AnalysisDataSimpleHistogramModule::dataStarted(AbstractAnalysisData *data)
630 addModule(impl_->averager_);
631 setDataSetCount(data->dataSetCount());
632 for (int i = 0; i < data->dataSetCount(); ++i)
634 setColumnCount(i, settings().binCount());
637 impl_->storage_.startDataStorage(this);
642 AnalysisDataSimpleHistogramModule::frameStarted(const AnalysisDataFrameHeader &header)
644 AnalysisDataStorageFrame &frame = impl_->storage_.startFrame(header);
645 impl_->initFrame(dataSetCount(), &frame);
650 AnalysisDataSimpleHistogramModule::pointsAdded(const AnalysisDataPointSetRef &points)
652 AnalysisDataStorageFrame &frame =
653 impl_->storage_.currentFrame(points.frameIndex());
654 frame.selectDataSet(points.dataSetIndex());
655 for (int i = 0; i < points.columnCount(); ++i)
657 if (points.present(i))
659 const int bin = settings().findBin(points.y(i));
662 frame.value(bin) += 1;
670 AnalysisDataSimpleHistogramModule::frameFinished(const AnalysisDataFrameHeader &header)
672 impl_->storage_.finishFrame(header.index());
677 AnalysisDataSimpleHistogramModule::dataFinished()
684 AnalysisDataSimpleHistogramModule::tryGetDataFrameInternal(int index) const
686 return impl_->storage_.tryGetDataFrame(index);
691 AnalysisDataSimpleHistogramModule::requestStorageInternal(int nframes)
693 return impl_->storage_.requestStorage(nframes);
697 /********************************************************************
698 * AnalysisDataWeightedHistogramModule
701 AnalysisDataWeightedHistogramModule::AnalysisDataWeightedHistogramModule()
702 : impl_(new internal::BasicHistogramImpl())
707 AnalysisDataWeightedHistogramModule::AnalysisDataWeightedHistogramModule(
708 const AnalysisHistogramSettings &settings)
709 : impl_(new internal::BasicHistogramImpl(settings))
714 AnalysisDataWeightedHistogramModule::~AnalysisDataWeightedHistogramModule()
719 void AnalysisDataWeightedHistogramModule::init(const AnalysisHistogramSettings &settings)
721 impl_->init(settings);
725 AbstractAverageHistogram &
726 AnalysisDataWeightedHistogramModule::averager()
728 return *impl_->averager_;
732 const AnalysisHistogramSettings &
733 AnalysisDataWeightedHistogramModule::settings() const
735 return impl_->settings_;
740 AnalysisDataWeightedHistogramModule::flags() const
742 return efAllowMulticolumn | efAllowMultipoint | efAllowMultipleDataSets;
747 AnalysisDataWeightedHistogramModule::dataStarted(AbstractAnalysisData *data)
749 addModule(impl_->averager_);
750 setDataSetCount(data->dataSetCount());
751 for (int i = 0; i < data->dataSetCount(); ++i)
753 setColumnCount(i, settings().binCount());
756 impl_->storage_.startDataStorage(this);
761 AnalysisDataWeightedHistogramModule::frameStarted(const AnalysisDataFrameHeader &header)
763 AnalysisDataStorageFrame &frame = impl_->storage_.startFrame(header);
764 impl_->initFrame(dataSetCount(), &frame);
769 AnalysisDataWeightedHistogramModule::pointsAdded(const AnalysisDataPointSetRef &points)
771 if (points.firstColumn() != 0 || points.columnCount() < 2)
773 GMX_THROW(APIError("Invalid data layout"));
775 int bin = settings().findBin(points.y(0));
778 AnalysisDataStorageFrame &frame =
779 impl_->storage_.currentFrame(points.frameIndex());
780 frame.selectDataSet(points.dataSetIndex());
781 for (int i = 1; i < points.columnCount(); ++i)
783 frame.value(bin) += points.y(i);
790 AnalysisDataWeightedHistogramModule::frameFinished(const AnalysisDataFrameHeader &header)
792 impl_->storage_.finishFrame(header.index());
797 AnalysisDataWeightedHistogramModule::dataFinished()
804 AnalysisDataWeightedHistogramModule::tryGetDataFrameInternal(int index) const
806 return impl_->storage_.tryGetDataFrame(index);
811 AnalysisDataWeightedHistogramModule::requestStorageInternal(int nframes)
813 return impl_->storage_.requestStorage(nframes);
817 /********************************************************************
818 * AnalysisDataBinAverageModule
821 class AnalysisDataBinAverageModule::Impl
825 explicit Impl(const AnalysisHistogramSettings &settings)
826 : settings_(settings)
830 //! Histogram settings.
831 AnalysisHistogramSettings settings_;
832 //! Averaging helper objects for each input data set.
833 std::vector<AnalysisDataFrameAverager> averagers_;
836 AnalysisDataBinAverageModule::AnalysisDataBinAverageModule()
843 AnalysisDataBinAverageModule::AnalysisDataBinAverageModule(
844 const AnalysisHistogramSettings &settings)
845 : impl_(new Impl(settings))
847 setRowCount(settings.binCount());
848 setXAxis(settings.firstEdge() + 0.5 * settings.binWidth(),
849 settings.binWidth());
853 AnalysisDataBinAverageModule::~AnalysisDataBinAverageModule()
859 AnalysisDataBinAverageModule::init(const AnalysisHistogramSettings &settings)
861 impl_->settings_ = settings;
862 setRowCount(settings.binCount());
863 setXAxis(settings.firstEdge() + 0.5 * settings.binWidth(),
864 settings.binWidth());
868 const AnalysisHistogramSettings &
869 AnalysisDataBinAverageModule::settings() const
871 return impl_->settings_;
876 AnalysisDataBinAverageModule::flags() const
878 return efAllowMulticolumn | efAllowMultipoint | efAllowMultipleDataSets;
883 AnalysisDataBinAverageModule::dataStarted(AbstractAnalysisData *data)
885 setColumnCount(data->dataSetCount());
886 impl_->averagers_.resize(data->dataSetCount());
887 for (int i = 0; i < data->dataSetCount(); ++i)
889 impl_->averagers_[i].setColumnCount(rowCount());
895 AnalysisDataBinAverageModule::frameStarted(const AnalysisDataFrameHeader & /*header*/)
901 AnalysisDataBinAverageModule::pointsAdded(const AnalysisDataPointSetRef &points)
903 if (points.firstColumn() != 0 || points.columnCount() < 2)
905 GMX_THROW(APIError("Invalid data layout"));
907 int bin = settings().findBin(points.y(0));
910 AnalysisDataFrameAverager &averager = impl_->averagers_[points.dataSetIndex()];
911 for (int i = 1; i < points.columnCount(); ++i)
913 averager.addValue(bin, points.y(i));
920 AnalysisDataBinAverageModule::frameFinished(const AnalysisDataFrameHeader & /*header*/)
926 AnalysisDataBinAverageModule::dataFinished()
929 for (int i = 0; i < columnCount(); ++i)
931 AnalysisDataFrameAverager &averager = impl_->averagers_[i];
933 for (int j = 0; j < rowCount(); ++j)
935 value(j, i).setValue(averager.average(j),
936 std::sqrt(averager.variance(j)));