src/gromacs/analysisdata/datastorage.h

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  35 /*! \libinternal \file
  36  * \brief
  37  * Declares gmx::AnalysisDataStorage.
  38  *
  39  * \author Teemu Murtola <teemu.murtola@gmail.com>
  40  * \inlibraryapi
  41  * \ingroup module_analysisdata
  42  */
  43 #ifndef GMX_ANALYSISDATA_DATASTORAGE_H
  44 #define GMX_ANALYSISDATA_DATASTORAGE_H
  45
  46 #include <vector>
  47
  48 #include "gromacs/analysisdata/dataframe.h"
  49 #include "gromacs/utility/classhelpers.h"
  50 #include "gromacs/utility/gmxassert.h"
  51 #include "gromacs/utility/real.h"
  52
  53 namespace gmx
  54 {
  55
  56 class AbstractAnalysisData;
  57 class AnalysisDataFrameHeader;
  58 class AnalysisDataFrameRef;
  59 class AnalysisDataModuleManager;
  60 class AnalysisDataParallelOptions;
  61
  62 class AnalysisDataStorage;
  63
  64 namespace internal
  65 {
  66 class AnalysisDataStorageImpl;
  67 class AnalysisDataStorageFrameData;
  68 }   // namespace internal
  69
  70 /*! \libinternal \brief
  71  * Allows assigning values for a data frame in AnalysisDataStorage.
  72  *
  73  * This class implements the necessary methods to add new data into the
  74  * storage.  AnalysisDataStorage::startFrame() returns an object of this type,
  75  * which can be used to add one or more point sets to that data frame.
  76  * When all data has been added, finishFrame() needs to be called.
  77  *
  78  * \inlibraryapi
  79  * \ingroup module_analysisdata
  80  */
  81 class AnalysisDataStorageFrame
  82 {
  83     public:
  84         /*! \brief Frees the frame object.
  85          *
  86          * Should not be called outside AnalysisDataStorage.
  87          */
  88         ~AnalysisDataStorageFrame();
  89
  90         /*! \brief
  91          * Select data set that all other methods operate on.
  92          *
  93          * \param[in] index  Zero-based data set index to select.
  94          *
  95          * With multipoint data, a single point set can only contain values in
  96          * a single data set.
  97          * With non-multipoint data, arbitrary sequences of selectDataSet() and
  98          * setValue() are supported.  The full frame is notified to the modules
  99          * once it is finished.
 100          *
 101          * Does not throw.
 102          */
 103         void selectDataSet(int index);
 104
 105         //! Returns number of columns for the frame.
 106         int columnCount() const { return columnCount_; }
 107
 108         /*! \brief
 109          * Sets value for a column.
 110          *
 111          * \param[in] column  Zero-based column index.
 112          * \param[in] value   Value to set for the column.
 113          * \param[in] bPresent Present flag to set for the column.
 114          *
 115          * If called multiple times for a column (within one point set for
 116          * multipoint data), old values are overwritten.
 117          *
 118          * Does not throw.
 119          */
 120         void setValue(int column, real value, bool bPresent = true)
 121         {
 122             GMX_ASSERT(column >= 0 && column < columnCount(),
 123                        "Invalid column index");
 124             values_[currentOffset_ + column].setValue(value, bPresent);
 125             bPointSetInProgress_ = true;
 126         }
 127         /*! \brief
 128          * Sets value for a column.
 129          *
 130          * \param[in] column  Zero-based column index.
 131          * \param[in] value   Value to set for the column.
 132          * \param[in] error   Error estimate to set for the column.
 133          * \param[in] bPresent Present flag to set for the column.
 134          *
 135          * If called multiple times for a column (within one point set for
 136          * multipoint data), old values are overwritten.
 137          *
 138          * Does not throw.
 139          */
 140         void setValue(int column, real value, real error, bool bPresent = true)
 141         {
 142             GMX_ASSERT(column >= 0 && column < columnCount(),
 143                        "Invalid column index");
 144             values_[currentOffset_ + column].setValue(value, error, bPresent);
 145             bPointSetInProgress_ = true;
 146         }
 147         /*! \brief
 148          * Access value for a column.
 149          *
 150          * \param[in] column  Zero-based column index.
 151          *
 152          * Should only be called after the column value has been set using
 153          * setValue(); assigning a value to \c value(i) does not mark the
 154          * column as set.
 155          *
 156          * Does not throw.
 157          */
 158         real &value(int column)
 159         {
 160             GMX_ASSERT(column >= 0 && column < columnCount(),
 161                        "Invalid column index");
 162             return values_[currentOffset_ + column].value();
 163         }
 164         /*! \brief
 165          * Access value for a column.
 166          *
 167          * \param[in] column  Zero-based column index.
 168          *
 169          * Should only be called after the column value has been set using
 170          * setValue().
 171          *
 172          * Does not throw.
 173          */
 174         real value(int column) const
 175         {
 176             GMX_ASSERT(column >= 0 && column < columnCount(),
 177                        "Invalid column index");
 178             return values_[currentOffset_ + column].value();
 179         }
 180         /*! \brief
 181          * Mark point set as finished for multipoint data.
 182          *
 183          * Must be called after each point set for multipoint data, including
 184          * the last (i.e., no values must be set between the last call to this
 185          * method and AnalysisDataStorage::finishFrame()).
 186          * Must not be called for non-multipoint data.
 187          *
 188          * After this method has been called, all values appear as not set.
 189          *
 190          * May call AnalysisDataModuleManager::notifyPointsAdd() and
 191          * AnalysisDataModuleManager::notifyParallelPointsAdd(), and may throw
 192          * any exception these methods throw.
 193          */
 194         void finishPointSet();
 195         /*! \brief
 196          * Finish storing a frame.
 197          *
 198          * Must be called exactly once for each frame returned by startFrame(),
 199          * after the corresponding call.
 200          * The frame object must not be accessed after the call.
 201          *
 202          * Calls notification methods in AnalysisDataModuleManager, and may
 203          * throw any exceptions these methods throw.
 204          */
 205         void finishFrame();
 206
 207     private:
 208
 209         /*! \brief
 210          * Create a new storage frame.
 211          *
 212          * \param[in] data  Data object for which the frame is for
 213          *      (used for data set and column counts).
 214          */
 215         explicit AnalysisDataStorageFrame(const AbstractAnalysisData &data);
 216
 217         //! Clear all column values from the frame.
 218         void clearValues();
 219
 220         //! Implementation data.
 221         internal::AnalysisDataStorageFrameData *data_;
 222         //! Values for the currently in-progress point set.
 223         std::vector<AnalysisDataValue>          values_;
 224
 225         //! Index of the currently active dataset.
 226         int                                     currentDataSet_;
 227         //! Offset of the first value in \a values_ for the current data set.
 228         int                                     currentOffset_;
 229         //! Number of columns in the current data set.
 230         int                                     columnCount_;
 231
 232         //! Whether any values have been set in the current point set.
 233         bool                                    bPointSetInProgress_;
 234
 235         //! Needed for access to the constructor.
 236         friend class internal::AnalysisDataStorageImpl;
 237         //! Needed for managing the frame the object points to.
 238         friend class internal::AnalysisDataStorageFrameData;
 239
 240         GMX_DISALLOW_COPY_AND_ASSIGN(AnalysisDataStorageFrame);
 241 };
 242
 243 /*! \libinternal \brief
 244  * Helper class that implements storage of data.
 245  *
 246  * This class implements a standard way of storing data to avoid implementing
 247  * storage in each class derived from AbstractAnalysisData separately.
 248  * To use this class in a class derived from AbstractAnalysisData, a member
 249  * variable of this type should be declared and the pure virtual methods
 250  * forwarded to frameCount(), tryGetDataFrame() and requestStorage().
 251  * Storage properties should be set up, and then startDataStorage() or
 252  * startParallelDataStorage() called.
 253  * New frames can then be added using startFrame(), currentFrame(),
 254  * finishFrame(), and finishFrameSerial() methods (the last is only necessary
 255  * if startParallelDataStorage() is used).  When all frames are ready,
 256  * finishDataStorage() must be called.  These methods (and
 257  * AnalysisDataStorageFrame::finishPointSet()) take the responsibility of
 258  * calling all the notification methods in AnalysisDataModuleManager,
 259  *
 260  * \todo
 261  * Proper multi-threaded implementation.
 262  *
 263  * \inlibraryapi
 264  * \ingroup module_analysisdata
 265  */
 266 class AnalysisDataStorage
 267 {
 268     public:
 269         //! Constructs a storage object.
 270         AnalysisDataStorage();
 271         ~AnalysisDataStorage();
 272
 273         /*! \brief
 274          * Returns the number of ready frames.
 275          *
 276          * This method is designed such that calls to
 277          * AbstractAnalysisData::frameCount() can be directly forwarded to this
 278          * method.  See that method for more documentation.
 279          *
 280          * If this method returns N, this means that the first N frames have
 281          * all been finished.
 282          *
 283          * \see AbstractAnalysisData::frameCount()
 284          */
 285         int frameCount() const;
 286         /*! \brief
 287          * Implements access to data frames.
 288          *
 289          * This method is designed such that calls to
 290          * AbstractAnalysisData::tryGetDataFrameInternal() can be directly
 291          * forwarded to this method.  See that method for more documentation.
 292          *
 293          * A valid reference for a frame will be returned after finishFrame()
 294          * has been called for that frame.
 295          *
 296          * \see AbstractAnalysisData::tryGetDataFrameInternal()
 297          */
 298         AnalysisDataFrameRef tryGetDataFrame(int index) const;
 299         /*! \brief
 300          * Implements storage requests.
 301          *
 302          * This method is designed such that calls to
 303          * AbstractAnalysisData::requestStorageInternal() can be directly
 304          * forwarded to this method.  See that method for more documentation.
 305          *
 306          * \see AbstractAnalysisData::requestStorageInternal()
 307          */
 308         bool requestStorage(int nframes);
 309
 310         /*! \brief
 311          * Start storing data.
 312          *
 313          * \param[in] data    AbstractAnalysisData object containing this
 314          *      storage.
 315          * \param     modules Module manager for \p data.
 316          * \exception std::bad_alloc if storage allocation fails.
 317          *
 318          * Typically called as \c startDataStorage(this, &moduleManager())
 319          * from a member of \p data when the data is ready to be started.
 320          * The storage object will take responsibility of calling all
 321          * module notification methods in AnalysisDataModuleManager using
 322          * \p modules.
 323          *
 324          * Lifetime of \p data and \p modules must exceed the lifetime of the
 325          * storage object
 326          * (typically, the storage object will be a member in \p data).
 327          *
 328          * Calls AnalysisDataModuleManager::notifyDataStart(), and throws any
 329          * exceptions this method throws.
 330          */
 331         void startDataStorage(AbstractAnalysisData      *data,
 332                               AnalysisDataModuleManager *modules);
 333         /*! \brief
 334          * Start storing data in parallel.
 335          *
 336          * \param[in] data    AbstractAnalysisData object containing this
 337          *      storage.
 338          * \param[in] options Parallelization options to use.
 339          * \param     modules Module manager for \p data.
 340          * \exception std::bad_alloc if storage allocation fails.
 341          *
 342          * Should be called instead of startDataStorage() if the data will be
 343          * produced in parallel.  Works as startDataStorage(), but additionally
 344          * initializes the storage and the attached modules to prepare for
 345          * out-of-order data frames.
 346          *
 347          * Calls AnalysisDataModuleManager::notifyParallelDataStart(), and
 348          * throws any exceptions this method throws.
 349          */
 350         void startParallelDataStorage(
 351             AbstractAnalysisData              *data,
 352             AnalysisDataModuleManager         *modules,
 353             const AnalysisDataParallelOptions &options);
 354         /*! \brief
 355          * Starts storing a new frame.
 356          *
 357          * \param[in] header  Header for the new frame.
 358          * \retval  Frame object corresponding to the started frame.
 359          * \exception std::bad_alloc if storage reallocation fails
 360          *      (only possible if storage of all frames has been requested).
 361          * \exception APIError if frame is too far in the future.
 362          *
 363          * The returned object will be valid until the corresponding
 364          * finishFrame() call.
 365          *
 366          * Must be called exactly once for each frame index.
 367          *
 368          * Currently, the implementation only works if the new frame is not too
 369          * far in the future:
 370          * If \c i is the index of the last frame such that all frames from
 371          * 0, ..., \c i have been finished, then \p header().index() should be
 372          * at most \c parallelizationFactor larger than \c i, where
 373          * parallelizationFactor is the parallelization factor passed to
 374          * setParallelOptions().
 375          * Throws APIError if this constraint is violated.
 376          *
 377          * Calls AnalysisDataModuleManager::notifyFrameStart() (in certain
 378          * cases) and AnalysisDataModuleManager::notifyParallelFrameStart(),
 379          * and throws any exceptions these methods throw.
 380          */
 381         AnalysisDataStorageFrame &startFrame(const AnalysisDataFrameHeader &header);
 382         /*! \brief
 383          * Convenience method to start storing a new frame.
 384          *
 385          * Identical to \c startFrame(AnalysisDataFrameHeader(index, x, dx));
 386          */
 387         AnalysisDataStorageFrame &startFrame(int index, real x, real dx);
 388         /*! \brief
 389          * Obtains a frame object for an in-progress frame.
 390          *
 391          * \param[in] index  Frame index.
 392          * \retval  Frame object corresponding to \p index.
 393          *
 394          * startFrame() should have been called for the frame with index
 395          * \p index, and finishFrame() should not yet have been called.
 396          * Returns the same object as returned by the original startFrame()
 397          * call for the same index.
 398          *
 399          * Does not throw.
 400          */
 401         AnalysisDataStorageFrame &currentFrame(int index);
 402         /*! \brief
 403          * Convenience method for finishing a data frame.
 404          *
 405          * \param[in] index  Frame index.
 406          *
 407          * Identical to \c currentFrame(index).finishFrame().
 408          *
 409          * \see AnalysisDataStorageFrame::finishFrame()
 410          */
 411         void finishFrame(int index);
 412         /*! \brief
 413          * Performs in-order sequential processing for a data frame.
 414          *
 415          * \param[in] index  Frame index.
 416          *
 417          * If startParallelDataStorage() has been called with options that
 418          * indicate parallelism, this method must be called after
 419          * `finishFrame(index)` (or the equivalent call in
 420          * AnalysisDataStorageFrame), such that it is called in the correct
 421          * order sequentially for each frame.
 422          *
 423          * If there is no parallelism, this method does nothing; the equivalent
 424          * processing is done already during finishFrame().
 425          */
 426         void finishFrameSerial(int index);
 427         /*! \brief
 428          * Finishes storing data.
 429          *
 430          * Calls AnalysisDataModuleManager::notifyDataFinish(), and throws any
 431          * exceptions this method throws.
 432          */
 433         void finishDataStorage();
 434
 435     private:
 436         typedef internal::AnalysisDataStorageImpl Impl;
 437
 438         PrivateImplPointer<Impl> impl_;
 439 };
 440
 441 } // namespace gmx
 442
 443 #endif