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37 * Declares gmx::TrajectoryAnalysisModule and
38 * gmx::TrajectoryAnalysisModuleData.
40 * \author Teemu Murtola <teemu.murtola@gmail.com>
42 * \ingroup module_trajectoryanalysis
44 #ifndef GMX_TRAJECTORYANALYSIS_ANALYSISMODULE_H
45 #define GMX_TRAJECTORYANALYSIS_ANALYSISMODULE_H
50 #include "../legacyheaders/typedefs.h"
52 #include "../selection/selection.h" // For gmx::SelectionList
53 #include "../utility/common.h"
54 #include "../utility/uniqueptr.h"
59 class AbstractAnalysisData;
61 class AnalysisDataHandle;
62 class AnalysisDataParallelOptions;
64 class SelectionCollection;
65 class TopologyInformation;
66 class TrajectoryAnalysisModule;
67 class TrajectoryAnalysisSettings;
70 * Base class for thread-local data storage during trajectory analysis.
72 * Thread-local storage of data handles and selections is implemented in this
73 * class; TrajectoryAnalysisModule instances can access the thread-local values
74 * in their TrajectoryAnalysisModule::analyzeFrame() method using dataHandle()
75 * and parallelSelection().
77 * \see TrajectoryAnalysisModule::startFrames()
78 * \see TrajectoryAnalysisModule::analyzeFrame()
79 * \see TrajectoryAnalysisModule::finishFrames()
82 * \ingroup module_trajectoryanalysis
84 class TrajectoryAnalysisModuleData
87 virtual ~TrajectoryAnalysisModuleData();
90 * Performs any finishing actions after all frames have been processed.
92 * \throws unspecified Implementation may throw exceptions to indicate
95 * This function is called immediately before the destructor, after
96 * TrajectoryAnalysisModule::finishFrames().
97 * Derived classes should implement any final operations that need to
98 * be done after successful analysis.
99 * All implementations should call finishDataHandles().
101 virtual void finish() = 0;
104 * Returns a data handle for a given dataset.
106 * \param[in] data Analysis data object.
107 * \returns Data handle for \p data stored in this thread-local data.
109 * \p data should have previously been registered with
110 * TrajectoryAnalysisModule::registerAnalysisDataset().
111 * If \p data has zero columns in all data sets, the returned data
116 AnalysisDataHandle dataHandle(const AnalysisData &data);
118 * Returns a selection that corresponds to the given selection.
120 * \param[in] selection Global selection object.
121 * \returns Selection object corresponding to this thread-local data.
123 * \p selection is the selection object that was obtained from
124 * SelectionOption. The return value is the corresponding selection
125 * in the selection collection with which this data object was
130 Selection parallelSelection(const Selection &selection);
132 * Returns a set of selection that corresponds to the given selections.
134 * \throws std::bad_alloc if out of memory.
136 * Works as parallelSelection(), but for a list of selections at once.
138 * \see parallelSelection()
140 SelectionList parallelSelections(const SelectionList &selections);
144 * Initializes thread-local storage for data handles and selections.
146 * \param[in] module Analysis module to use for data objects.
147 * \param[in] opt Data parallelization options.
148 * \param[in] selections Thread-local selection collection.
149 * \throws std::bad_alloc if out of memory.
150 * \throws unspecified Can throw any exception thrown by
151 * AnalysisData::startData().
153 * Calls AnalysisData::startData() on all data objects registered with
154 * TrajectoryAnalysisModule::registerAnalysisDataset() in \p module.
155 * The handles are accessible through dataHandle().
157 TrajectoryAnalysisModuleData(TrajectoryAnalysisModule *module,
158 const AnalysisDataParallelOptions &opt,
159 const SelectionCollection &selections);
162 * Calls finishData() on all data handles.
164 * \throws unspecified Can throw any exception thrown by
165 * AnalysisDataHandle::finishData().
167 * This function should be called from the implementation of finish()
170 void finishDataHandles();
175 PrivateImplPointer<Impl> impl_;
178 //! Smart pointer to manage a TrajectoryAnalysisModuleData object.
179 typedef gmx_unique_ptr<TrajectoryAnalysisModuleData>::type
180 TrajectoryAnalysisModuleDataPointer;
183 * Base class for trajectory analysis modules.
185 * Trajectory analysis methods should derive from this class and override the
186 * necessary virtual methods to implement initialization (initOptions(),
187 * optionsFinished(), initAnalysis(), initAfterFirstFrame()), per-frame analysis
188 * (analyzeFrame()), and final processing (finishFrames(), finishAnalysis(),
191 * For parallel analysis using threads, only a single object is constructed,
192 * but the methods startFrames(), analyzeFrame() and finishFrames() are called
193 * in each thread. Frame-local data should be initialized in startFrames() and
194 * stored in a class derived from TrajectoryAnalysisModuleData that is passed
195 * to the other methods. The default implementation of startFrames() can be
196 * used if only data handles and selections need to be thread-local.
198 * To get the full benefit from this class,
199 * \ref module_analysisdata "analysis data objects" and
200 * \ref module_selection "selections" should be used in the implementation.
201 * See the corresponding modules' documentation for details of how they work.
203 * Typical way of using AnalysisData in derived classes is to have the
204 * AnalysisData object as a member variable and register it using
205 * registerAnalysisDataset(). Analysis modules are initialized in
206 * initAnalysis() and the processing chain is initialized. If any of the
207 * modules is required, e.g., for post-processing in finishAnalysis(), it can
208 * be stored in a member variable. To add data to the data object in
209 * analyzeFrame(), a data handle is obtained using
210 * TrajectoryAnalysisModuleData::dataHandle().
212 * Typical way of using selections in derived classes is to have the required
213 * \ref Selection objects (or ::SelectionList objects) as member variables, and
214 * add the required selection options in initOptions(). These member variables
215 * can be accessed in initAnalysis() to get general information about the
216 * selections. In analyzeFrame(), these selection objects should not be used
217 * directly, but instead TrajectoryAnalysisModuleData::parallelSelection()
218 * should be used to obtain a selection object that works correctly also for
221 * Derived classes should use exceptions to indicate errors in the virtual
225 * \ingroup module_trajectoryanalysis
227 class TrajectoryAnalysisModule
230 virtual ~TrajectoryAnalysisModule();
233 * Initializes options understood by the module.
235 * \param[in,out] options Options object to add the options to.
236 * \param[in,out] settings Settings to pass to and from the module.
238 * This method is called first after the constructor, and it should
239 * add options understood by the module to \p options. Output values
240 * from options (including selections) should be stored in member
243 * In addition to initializing the options, this method can also
244 * provide information about the module's requirements using the
245 * \p settings object; see TrajectoryAnalysisSettings for more details.
247 * If settings depend on the option values provided by the user, see
250 virtual void initOptions(Options *options,
251 TrajectoryAnalysisSettings *settings) = 0;
253 * Called after all option values have been set.
255 * \param[in,out] options Options object in which options are stored.
256 * \param[in,out] settings Settings to pass to and from the module.
258 * This method is called after option values have been assigned (but
259 * interactive selection input has not yet been performed).
261 * If the module needs to change settings that affect topology loading
262 * (can be done using the \p settings object) or selection
263 * initialization (can be done using SelectionOptionInfo) based on
264 * option values, this method has to be overridden.
266 * The default implementation does nothing.
268 virtual void optionsFinished(Options *options,
269 TrajectoryAnalysisSettings *settings);
271 * Initializes the analysis.
273 * \param[in] settings Settings to pass to and from the module.
274 * \param[in] top Topology information.
276 * When this function is called, selections have been initialized based
277 * on user input, and a topology has been loaded if provided by the
278 * user. For dynamic selections, the selections have been evaluated to
279 * the largest possible selection, i.e., the selections passed to
280 * analyzeFrame() are always a subset of the selections provided here.
282 virtual void initAnalysis(const TrajectoryAnalysisSettings &settings,
283 const TopologyInformation &top) = 0;
285 * Performs additional initialization after reading the first frame.
287 * When this function is called, selections are the same as in
288 * initAnalysis(), i.e., they have not been evaluated for the first
291 * It is necessary to override this method only if the module needs to
292 * do initialization for which it requires data from the first frame.
294 * The default implementation does nothing.
296 virtual void initAfterFirstFrame(const t_trxframe &fr);
299 * Starts the analysis of frames.
302 * \param[in] selections Frame-local selection collection object.
303 * \returns Data structure for thread-local data.
305 * This function is necessary only for threaded parallelization.
306 * It is called once for each thread and should initialize a class that
307 * contains any required frame-local data in the returned value.
308 * The default implementation creates a basic data structure that holds
309 * thread-local data handles for all data objects registered with
310 * registerAnalysisDataset(), as well as the thread-local selection
311 * collection. These can be accessed in analyzeFrame() using the
312 * methods in TrajectoryAnalysisModuleData.
313 * If other thread-local data is needed, this function should be
314 * overridden and it should create an instance of a class derived from
315 * TrajectoryAnalysisModuleData.
317 * \see TrajectoryAnalysisModuleData
319 virtual TrajectoryAnalysisModuleDataPointer startFrames(
320 const AnalysisDataParallelOptions &opt,
321 const SelectionCollection &selections);
323 * Analyzes a single frame.
325 * \param[in] frnr Frame number, a zero-based index that
326 * uniquely identifies the frame.
327 * \param[in] fr Current frame.
328 * \param[in] pbc Periodic boundary conditions for \p fr.
329 * \param[in,out] pdata Data structure for frame-local data.
331 * This method is called once for each frame to be analyzed, and should
332 * analyze the positions provided in the selections. Data handles and
333 * selections should be obtained from the \p pdata structure.
335 * For threaded analysis, this method is called asynchronously in
336 * different threads to analyze different frames. The \p pdata
337 * structure is one of the structures created with startFrames(),
338 * but no assumptions should be made about which of these data
339 * structures is used. It is guaranteed that two instances of
340 * analyzeFrame() are not running concurrently with the same \p pdata
342 * Any access to data structures not stored in \p pdata should be
343 * designed to be thread-safe.
345 virtual void analyzeFrame(int frnr, const t_trxframe &fr, t_pbc *pbc,
346 TrajectoryAnalysisModuleData *pdata) = 0;
348 * Finishes the analysis of frames.
350 * \param[in] pdata Data structure for thread-local data.
352 * This method is called once for each call of startFrames(), with the
353 * data structure returned by the corresponding startFrames().
354 * The \p pdata object should be destroyed by the caller after this
355 * function has been called.
357 * You only need to override this method if you need custom
358 * operations to combine data from the frame-local data structures
359 * to get the final result. In such cases, the data should be
360 * aggregated in this function and stored in a member attribute.
362 * The default implementation does nothing.
366 virtual void finishFrames(TrajectoryAnalysisModuleData *pdata);
369 * Postprocesses data after frames have been read.
371 * \param[in] nframes Total number of frames processed.
373 * This function is called after all finishFrames() calls have been
375 * \p nframes will equal the number of calls to analyzeFrame() that
378 virtual void finishAnalysis(int nframes) = 0;
380 * Writes output into files and/or standard output/error.
382 * All output from the module, excluding data written out for each
383 * frame during analyzeFrame(), should be confined into this function.
384 * This function is guaranteed to be called only after
387 virtual void writeOutput() = 0;
390 * Returns the name of the analysis module.
394 const char *name() const;
396 * Returns short description for the analysis module.
400 const char *description() const;
402 * Returns the number of datasets provided by the module.
406 int datasetCount() const;
408 * Returns a vector with the names of datasets provided by the module.
412 const std::vector<std::string> &datasetNames() const;
414 * Returns a pointer to the data set \p index.
416 * \param[in] index Data set to query for.
417 * \returns Reference to the requested data set.
418 * \throws APIError if \p index is not valid.
420 * \p index should be >= 0 and < datasetCount().
422 * The return value is not const to allow callers to add modules to the
423 * data sets. However, the AbstractAnalysisData interface does not
424 * provide any means to alter the data, so the module does not need to
425 * care about external modifications.
427 AbstractAnalysisData &datasetFromIndex(int index) const;
429 * Returns a pointer to the data set with name \p name
431 * \param[in] name Data set to query for.
432 * \returns Reference to the requested data set.
433 * \throws APIError if \p name is not valid.
435 * \p name should be one of the names returned by datasetNames().
437 * The return value is not const to allow callers to add modules to the
438 * data sets. However, the AbstractAnalysisData interface does not
439 * provide any means to alter the data, so the module does not need to
440 * care about external modifications.
442 AbstractAnalysisData &datasetFromName(const char *name) const;
446 * Initializes the dataset registration mechanism.
448 * \param[in] name Name for the module.
449 * \param[in] description One-line description for the module.
450 * \throws std::bad_alloc if out of memory.
452 TrajectoryAnalysisModule(const char *name, const char *description);
455 * Registers a dataset that exports data.
457 * \param data Data object to register.
458 * \param[in] name Name to register the dataset with.
459 * \throws std::bad_alloc if out of memory.
461 * Registers \p data as a dataset that provides output from the
462 * analysis module. Callers for the module can access the dataset
463 * with datasetFromName() using \p name as an AbstractAnalysisData
464 * object. This allows them to add their own data modules to do extra
467 * \p name must be unique across all calls within the same
468 * TrajectoryAnalysisModule instance.
470 void registerBasicDataset(AbstractAnalysisData *data, const char *name);
472 * Registers a parallelized dataset that exports data.
474 * \param data AnalysisData object to register.
475 * \param[in] name Name to register the dataset with.
476 * \throws std::bad_alloc if out of memory.
478 * This method works as registerBasicDataset(), but additionally allows
479 * data handles for \p data to be accessed using
480 * TrajectoryAnalysisData.
482 * \see registerBasicDataset()
484 void registerAnalysisDataset(AnalysisData *data, const char *name);
489 PrivateImplPointer<Impl> impl_;
492 * Needed to access the registered analysis data sets.
494 friend class TrajectoryAnalysisModuleData;
497 //! Smart pointer to manage a TrajectoryAnalysisModule.
498 typedef gmx_unique_ptr<TrajectoryAnalysisModule>::type
499 TrajectoryAnalysisModulePointer;