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37 * Declares gmx::AnalysisData and gmx::AnalysisDataHandle.
39 * \author Teemu Murtola <teemu.murtola@gmail.com>
41 * \ingroup module_analysisdata
43 #ifndef GMX_ANALYSISDATA_ANALYSISDATA_H
44 #define GMX_ANALYSISDATA_ANALYSISDATA_H
46 #include "gromacs/analysisdata/abstractdata.h"
47 #include "gromacs/utility/real.h"
52 class AnalysisDataHandle;
53 class AnalysisDataParallelOptions;
56 * Parallelizable data container for raw data.
58 * This is the main class used to implement parallelizable data processing in
59 * analysis tools. It is used by first creating an object and setting its
60 * properties using setDataSetCount(), setColumnCount() and setMultipoint(),
61 * and attaching necessary modules using addModule() etc. Then one or more
62 * AnalysisDataHandle objects can be created using startData(). Each data
63 * handle can then be independently used to provide data frames (each frame
64 * must be provided by a single handle, but different frames can be freely
65 * mixed between the handles). The finishFrameSerial() method must be called
66 * in serial for each frame, after one of the handles has been used to provide
67 * the data for that frame. When all data has been provided, the handles
68 * are destroyed using finishData() (or AnalysisDataHandle::finishData()).
70 * When used through the trajectory analysis framework, calls to startData(),
71 * finishFrameSerial(), and finishData() are handled by the framework.
74 * Parallel implementation is not complete.
77 * Special note for MPI implementation: assuming that the initialization of
78 * data objects is identical in all processes, associating the data objects
79 * in different MPI processes should be possible without changes in the
81 * Alternative, more robust implementation could get a unique ID as parameter
82 * to the constructor or a separate function, but would require all tools to
83 * provide it. With the current registration mechanism in
84 * TrajectoryAnalysisModule, this should be straightforward.
88 * \ingroup module_analysisdata
90 class AnalysisData : public AbstractAnalysisData
94 * Creates an empty analysis data object.
96 * \throws std::bad_alloc if out of memory.
99 virtual ~AnalysisData();
102 * Sets the number of data sets.
104 * \param[in] dataSetCount Number of data sets (must be > 0).
105 * \throws std::bad_alloc if out of memory.
106 * \throws APIError if modules have been added that are not
107 * compatible with the new data set count.
109 * Must not be called after startData() has been called.
110 * If not called, a single data set is assumed.
111 * If called multiple times, the last call takes effect.
113 void setDataSetCount(int dataSetCount);
115 * Sets the number of columns in a data set.
117 * \param[in] dataSet Zero-based data set index.
118 * \param[in] columnCount Number of columns in the data (must be > 0).
119 * \throws APIError if modules have been added that are not
120 * compatible with the new column count.
122 * Must be called before startData() for each data set.
123 * Must not be called after startData() has been called.
124 * If called multiple times for a data set, the last call takes effect.
126 void setColumnCount(int dataSet, int columnCount);
128 * Sets whether the data contains multiple points per column per frame.
130 * \param[in] bMultipoint Whether the data will allow multiple points
131 * per column within a single frame.
132 * \throws APIError if modules have been added that are not
133 * compatible with the new setting.
135 * If this method is not called, the data is not multipoint.
137 * Must not be called after startData() has been called.
139 * \see isMultipoint()
141 void setMultipoint(bool bMultipoint);
143 virtual int frameCount() const;
146 * Creates a handle for adding data.
148 * \param[in] opt Options for setting how this handle will be
150 * \returns The created handle.
151 * \throws std::bad_alloc if out of memory.
152 * \throws APIError if any attached data module is not compatible.
153 * \throws unspecified Any exception thrown by attached data modules
154 * in AnalysisDataModuleInterface::dataStarted().
156 * The caller should retain the returned handle (or a copy of it), and
157 * pass it to finishData() after successfully adding all data.
158 * The caller should discard the returned handle if an error occurs;
159 * memory allocated for the handle will be freed when the AnalysisData
160 * object is destroyed.
162 * The \p opt options should be the same for all calls to this method,
163 * and the number of calls should match the parallelization factor
166 AnalysisDataHandle startData(const AnalysisDataParallelOptions &opt);
168 * Performs in-order sequential processing for the next frame.
170 * \param[in] frameIndex Index of the frame that has been finished.
171 * \throws unspecified Any exception thrown by attached data modules
172 * in AnalysisDataModuleInterface::frameFinishedSerial().
174 * This method should be called sequentially for each frame, after data
175 * for that frame has been produced. It is not necessary to call this
176 * method if there is no parallelism, i.e., if only a single data
177 * handle is created and the parallelization options provided at that
178 * time do not indicate parallelism.
180 void finishFrameSerial(int frameIndex);
182 * Destroys a handle after all data has been added.
184 * \param[in] handle Handle to destroy.
185 * \throws unspecified Any exception thrown by attached data modules
186 * in AnalysisDataModuleInterface::dataFinished().
188 * \p handle must have been obtained from startData() of this object.
189 * The order of the calls with respect to the corresponding startData()
190 * calls is not important.
192 * The \p handle (and any copies) are invalid after the call.
194 void finishData(AnalysisDataHandle handle);
197 virtual AnalysisDataFrameRef tryGetDataFrameInternal(int index) const;
198 virtual bool requestStorageInternal(int nframes);
202 PrivateImplPointer<Impl> impl_;
204 friend class AnalysisDataHandle;
209 class AnalysisDataHandleImpl;
210 } // namespace internal
213 * Handle for inserting data into AnalysisData.
215 * This class provides an interface for adding data frames into an AnalysisData
216 * object. After a handle is obtained from AnalysisData::startData(), new
217 * frames can be added using startFrame(). Then values for that frame are set
218 * using provided methods (see below), and finishFrame() is called. After all
219 * frames have been added, finishData() (or AnalysisData::finishData()) must be
222 * For simple (non-multipoint) data, within a frame values can be set using
223 * selectDataSet(), setPoint() and setPoints(). Setting the same column in the
224 * same data set multiple times overrides previously set values.
225 * When the frame is finished, attached modules are notified.
227 * Multipoint data works otherwise similarly, but requires finishPointSet() to
228 * be called for each set of points for which the modules need to be notified.
229 * Each point set starts empty (after startFrame() or finishPointSet()), and
230 * values can be set using setPoint()/setPoints().
231 * A single point set can contain values only for a single data set, which must
232 * be selected with selectDataSet() before setting any values.
233 * finishPointSet() must also be called for the last point set just before
236 * This class works like a pointer type: copying and assignment is lightweight,
237 * and all copies work interchangeably, accessing the same internal handle.
238 * However, normally you should only keep one copy of a handle, i.e., treat
239 * this type as movable.
240 * Several handles created from the same AnalysisData object can exist
241 * concurrently, but must currently operate on separate frames.
244 * \ingroup module_analysisdata
246 class AnalysisDataHandle
250 * Constructs an invalid data handle.
252 * This constructor is provided for convenience in cases where it is
253 * easiest to declare an AnalysisDataHandle without immediately
254 * assigning a value to it. Any attempt to call methods without first
255 * assigning a value from AnalysisData::startData() to the handle
260 AnalysisDataHandle();
262 //! Returns whether this data handle is valid.
263 bool isValid() const { return impl_ != NULL; }
266 * Start data for a new frame.
268 * \param[in] index Zero-based index for the frame to start.
269 * \param[in] x x value for the frame.
270 * \param[in] dx Error in x for the frame if applicable.
272 * \throws unspecified Any exception thrown by attached data
273 * modules in AnalysisDataModuleInterface::frameStarted().
275 * Each \p index value 0, 1, ..., N (where N is the total number of
276 * frames) should be started exactly once by exactly one handle of an
277 * AnalysisData object. The frames may be started out of order, but
278 * currently the implementation places some limitations on how far
279 * the index can be in the future (as counted from the first frame that
282 void startFrame(int index, real x, real dx = 0.0);
284 * Selects a data set for subsequent setPoint()/setPoints() calls.
286 * \param[in] index Zero-based data set index.
288 * After startFrame(), the first data set is always selected.
289 * The set value is remembered until the end of the current frame, also
290 * across finishPointSet() calls.
294 void selectDataSet(int index);
296 * Set a value for a single column for the current frame.
298 * \param[in] column Zero-based column index.
299 * \param[in] value Value to set for the column.
300 * \param[in] bPresent Present flag to set for the column.
302 * If called multiple times for a column (within one point set for
303 * multipoint data), old values are overwritten.
307 void setPoint(int column, real value, bool bPresent = true);
309 * Set a value and its error estimate for a single column for the
312 * \param[in] column Zero-based column index.
313 * \param[in] value Value to set for the column.
314 * \param[in] error Error estimate to set for the column.
315 * \param[in] bPresent Present flag to set for the column.
317 * If called multiple times for a column (within one point set for
318 * multipoint data), old values are overwritten.
322 void setPoint(int column, real value, real error, bool bPresent = true);
324 * Set values for consecutive columns for the current frame.
326 * \param[in] firstColumn Zero-based column index.
327 * \param[in] count Number of columns to set.
328 * \param[in] values Value array of \p column items.
330 * Equivalent to calling setPoint(firstColumn + i, values[i]) for
335 void setPoints(int firstColumn, int count, const real *values);
337 * Finish data for the current point set.
339 * \throws APIError if any attached data module is not compatible.
340 * \throws unspecified Any exception thrown by attached data
341 * modules in AnalysisDataModuleInterface::pointsAdded().
343 * Must be called after each point set for multipoint data, including
344 * the last (i.e., no values must be set between the last call to this
345 * method and AnalysisDataStorage::finishFrame()).
346 * Must not be called for non-multipoint data.
348 void finishPointSet();
350 * Finish data for the current frame.
352 * \throws APIError if any attached data module is not compatible.
353 * \throws unspecified Any exception thrown by attached data
354 * modules in frame notification methods.
357 //! Calls AnalysisData::finishData() for this handle.
362 * Creates a new data handle associated with \p data.
364 * \param impl Data to associate the handle with.
366 * The constructor is private because data handles should only be
367 * constructed through AnalysisData::startData().
371 explicit AnalysisDataHandle(internal::AnalysisDataHandleImpl *impl);
374 * Pointer to the internal implementation class.
376 * The memory for this object is managed by the AnalysisData object,
377 * and AnalysisDataHandle simply provides a public interface for
378 * accessing the implementation.
380 internal::AnalysisDataHandleImpl *impl_;
383 * Needed to access the non-public implementation.
385 friend class AnalysisData;