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37 * Implements classes in analysismodule.h.
39 * \author Teemu Murtola <teemu.murtola@gmail.com>
40 * \ingroup module_trajectoryanalysis
42 #include "gromacs/trajectoryanalysis/analysismodule.h"
46 #include "gromacs/analysisdata/analysisdata.h"
47 #include "gromacs/selection/selection.h"
48 #include "gromacs/utility/exceptions.h"
49 #include "gromacs/utility/gmxassert.h"
54 /********************************************************************
55 * TrajectoryAnalysisModule::Impl
59 * Private implementation class for TrajectoryAnalysisModule.
61 * \ingroup module_trajectoryanalysis
63 class TrajectoryAnalysisModule::Impl
66 //! Container that associates a data set with its name.
67 typedef std::map<std::string, AbstractAnalysisData *> DatasetContainer;
68 //! Container that associates a AnalysisData object with its name.
69 typedef std::map<std::string, AnalysisData *> AnalysisDatasetContainer;
71 //! Initializes analysis module data with given name and description.
72 Impl(const char *name, const char *description)
73 : name_(name), description_(description)
77 //! Name of the module.
79 //! Description of the module.
80 std::string description_;
81 //! List of registered data set names.
82 std::vector<std::string> datasetNames_;
84 * Keeps all registered data sets.
86 * This container also includes datasets from \a analysisDatasets_.
88 DatasetContainer datasets_;
89 //! Keeps registered AnalysisData objects.
90 AnalysisDatasetContainer analysisDatasets_;
93 /********************************************************************
94 * TrajectoryAnalysisModuleData::Impl
98 * Private implementation class for TrajectoryAnalysisModuleData.
100 * \ingroup module_trajectoryanalysis
102 class TrajectoryAnalysisModuleData::Impl
105 //! Container that associates a data handle to its AnalysisData object.
106 typedef std::map<const AnalysisData *, AnalysisDataHandle>
109 //! \copydoc TrajectoryAnalysisModuleData::TrajectoryAnalysisModuleData()
110 Impl(TrajectoryAnalysisModule *module,
111 const AnalysisDataParallelOptions &opt,
112 const SelectionCollection &selections);
114 //! Checks whether the given AnalysisData has been initialized.
115 bool isInitialized(const AnalysisData &data) const;
117 //! Keeps a data handle for each AnalysisData object.
118 HandleContainer handles_;
119 //! Stores thread-local selections.
120 const SelectionCollection &selections_;
123 TrajectoryAnalysisModuleData::Impl::Impl(
124 TrajectoryAnalysisModule *module,
125 const AnalysisDataParallelOptions &opt,
126 const SelectionCollection &selections)
127 : selections_(selections)
129 TrajectoryAnalysisModule::Impl::AnalysisDatasetContainer::const_iterator i;
130 for (i = module->impl_->analysisDatasets_.begin();
131 i != module->impl_->analysisDatasets_.end(); ++i)
133 AnalysisDataHandle handle;
134 if (isInitialized(*i->second))
136 handle = i->second->startData(opt);
138 handles_.insert(std::make_pair(i->second, handle));
142 bool TrajectoryAnalysisModuleData::Impl::isInitialized(
143 const AnalysisData &data) const
145 for (int i = 0; i < data.dataSetCount(); ++i)
147 if (data.columnCount(i) > 0)
149 // If not all of the column counts are set, startData() in the
150 // constructor asserts, so that does not need to be checked here.
158 /********************************************************************
159 * TrajectoryAnalysisModuleData
162 TrajectoryAnalysisModuleData::TrajectoryAnalysisModuleData(
163 TrajectoryAnalysisModule *module,
164 const AnalysisDataParallelOptions &opt,
165 const SelectionCollection &selections)
166 : impl_(new Impl(module, opt, selections))
171 TrajectoryAnalysisModuleData::~TrajectoryAnalysisModuleData()
176 void TrajectoryAnalysisModuleData::finishDataHandles()
178 // FIXME: Call finishData() for all handles even if one throws
179 Impl::HandleContainer::iterator i;
180 for (i = impl_->handles_.begin(); i != impl_->handles_.end(); ++i)
182 if (i->second.isValid())
184 i->second.finishData();
187 impl_->handles_.clear();
192 TrajectoryAnalysisModuleData::dataHandle(const AnalysisData &data)
194 Impl::HandleContainer::const_iterator i = impl_->handles_.find(&data);
195 GMX_RELEASE_ASSERT(i != impl_->handles_.end(),
196 "Data handle requested on unknown dataset");
201 Selection TrajectoryAnalysisModuleData::parallelSelection(const Selection &selection)
203 // TODO: Implement properly.
209 TrajectoryAnalysisModuleData::parallelSelections(const SelectionList &selections)
211 // TODO: Consider an implementation that does not allocate memory every time.
212 SelectionList newSelections;
213 newSelections.reserve(selections.size());
214 SelectionList::const_iterator i = selections.begin();
215 for (; i != selections.end(); ++i)
217 newSelections.push_back(parallelSelection(*i));
219 return newSelections;
223 /********************************************************************
224 * TrajectoryAnalysisModuleDataBasic
231 * Basic thread-local trajectory analysis data storage class.
233 * Most simple tools should only require data handles and selections to be
234 * thread-local, so this class implements just that.
236 * \ingroup module_trajectoryanalysis
238 class TrajectoryAnalysisModuleDataBasic : public TrajectoryAnalysisModuleData
242 * Initializes thread-local storage for data handles and selections.
244 * \param[in] module Analysis module to use for data objects.
245 * \param[in] opt Data parallelization options.
246 * \param[in] selections Thread-local selection collection.
248 TrajectoryAnalysisModuleDataBasic(TrajectoryAnalysisModule *module,
249 const AnalysisDataParallelOptions &opt,
250 const SelectionCollection &selections);
252 virtual void finish();
255 TrajectoryAnalysisModuleDataBasic::TrajectoryAnalysisModuleDataBasic(
256 TrajectoryAnalysisModule *module,
257 const AnalysisDataParallelOptions &opt,
258 const SelectionCollection &selections)
259 : TrajectoryAnalysisModuleData(module, opt, selections)
265 TrajectoryAnalysisModuleDataBasic::finish()
273 /********************************************************************
274 * TrajectoryAnalysisModule
277 TrajectoryAnalysisModule::TrajectoryAnalysisModule(const char *name,
278 const char *description)
279 : impl_(new Impl(name, description))
284 TrajectoryAnalysisModule::~TrajectoryAnalysisModule()
289 void TrajectoryAnalysisModule::optionsFinished(
290 Options * /*options*/,
291 TrajectoryAnalysisSettings * /*settings*/)
296 void TrajectoryAnalysisModule::initAfterFirstFrame(const t_trxframe & /*fr*/)
301 TrajectoryAnalysisModuleDataPointer
302 TrajectoryAnalysisModule::startFrames(const AnalysisDataParallelOptions &opt,
303 const SelectionCollection &selections)
305 return TrajectoryAnalysisModuleDataPointer(
306 new TrajectoryAnalysisModuleDataBasic(this, opt, selections));
310 void TrajectoryAnalysisModule::finishFrames(TrajectoryAnalysisModuleData * /*pdata*/)
315 const char *TrajectoryAnalysisModule::name() const
317 return impl_->name_.c_str();
321 const char *TrajectoryAnalysisModule::description() const
323 return impl_->description_.c_str();
327 int TrajectoryAnalysisModule::datasetCount() const
329 return impl_->datasetNames_.size();
333 const std::vector<std::string> &TrajectoryAnalysisModule::datasetNames() const
335 return impl_->datasetNames_;
339 AbstractAnalysisData &TrajectoryAnalysisModule::datasetFromIndex(int index) const
341 if (index < 0 || index >= datasetCount())
343 GMX_THROW(APIError("Out of range data set index"));
345 Impl::DatasetContainer::const_iterator item
346 = impl_->datasets_.find(impl_->datasetNames_[index]);
347 GMX_RELEASE_ASSERT(item != impl_->datasets_.end(),
348 "Inconsistent data set names");
349 return *item->second;
353 AbstractAnalysisData &TrajectoryAnalysisModule::datasetFromName(const char *name) const
355 Impl::DatasetContainer::const_iterator item = impl_->datasets_.find(name);
356 if (item == impl_->datasets_.end())
358 GMX_THROW(APIError("Unknown data set name"));
360 return *item->second;
364 void TrajectoryAnalysisModule::registerBasicDataset(AbstractAnalysisData *data,
367 GMX_RELEASE_ASSERT(data != NULL, "Attempting to register NULL data");
368 // TODO: Strong exception safety should be possible to implement.
369 GMX_RELEASE_ASSERT(impl_->datasets_.find(name) == impl_->datasets_.end(),
370 "Duplicate data set name registered");
371 impl_->datasets_[name] = data;
372 impl_->datasetNames_.push_back(name);
376 void TrajectoryAnalysisModule::registerAnalysisDataset(AnalysisData *data,
379 // TODO: Strong exception safety should be possible to implement.
380 registerBasicDataset(data, name);
381 impl_->analysisDatasets_[name] = data;