libgromacs-dev 5.1.2-1ubuntu1 / usr / include / gromacs / analysisdata / analysisdata.h

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/*! \file
 * \brief
 * Declares gmx::AnalysisData and gmx::AnalysisDataHandle.
 *
 * \author Teemu Murtola <teemu.murtola@gmail.com>
 * \inpublicapi
 * \ingroup module_analysisdata
 */
#ifndef GMX_ANALYSISDATA_ANALYSISDATA_H
#define GMX_ANALYSISDATA_ANALYSISDATA_H

#include "gromacs/analysisdata/abstractdata.h"
#include "gromacs/utility/real.h"

namespace gmx
{

class AnalysisDataHandle;
class AnalysisDataParallelOptions;

/*! \brief
 * Parallelizable data container for raw data.
 *
 * This is the main class used to implement parallelizable data processing in
 * analysis tools.  It is used by first creating an object and setting its
 * properties using setDataSetCount(), setColumnCount() and setMultipoint(),
 * and attaching necessary modules using addModule() etc.  Then one or more
 * AnalysisDataHandle objects can be created using startData().  Each data
 * handle can then be independently used to provide data frames (each frame
 * must be provided by a single handle, but different frames can be freely
 * mixed between the handles).  The finishFrameSerial() method must be called
 * in serial for each frame, after one of the handles has been used to provide
 * the data for that frame.  When all data has been provided, the handles
 * are destroyed using finishData() (or AnalysisDataHandle::finishData()).
 *
 * When used through the trajectory analysis framework, calls to startData(),
 * finishFrameSerial(), and finishData() are handled by the framework.
 *
 * \todo
 * Parallel implementation is not complete.
 *
 * \if internal
 * Special note for MPI implementation: assuming that the initialization of
 * data objects is identical in all processes, associating the data objects
 * in different MPI processes should be possible without changes in the
 * interface.
 * Alternative, more robust implementation could get a unique ID as parameter
 * to the constructor or a separate function, but would require all tools to
 * provide it.  With the current registration mechanism in
 * TrajectoryAnalysisModule, this should be straightforward.
 * \endif
 *
 * \inpublicapi
 * \ingroup module_analysisdata
 */
class AnalysisData : public AbstractAnalysisData
{
    public:
        /*! \brief
         * Creates an empty analysis data object.
         *
         * \throws std::bad_alloc if out of memory.
         */
        AnalysisData();
        virtual ~AnalysisData();

        /*! \brief
         * Sets the number of data sets.
         *
         * \param[in] dataSetCount  Number of data sets (must be > 0).
         * \throws    std::bad_alloc if out of memory.
         * \throws    APIError if modules have been added that are not
         *      compatible with the new data set count.
         *
         * Must not be called after startData() has been called.
         * If not called, a single data set is assumed.
         * If called multiple times, the last call takes effect.
         */
        void setDataSetCount(int dataSetCount);
        /*! \brief
         * Sets the number of columns in a data set.
         *
         * \param[in] dataSet      Zero-based data set index.
         * \param[in] columnCount  Number of columns in the data (must be > 0).
         * \throws    APIError if modules have been added that are not
         *      compatible with the new column count.
         *
         * Must be called before startData() for each data set.
         * Must not be called after startData() has been called.
         * If called multiple times for a data set, the last call takes effect.
         */
        void setColumnCount(int dataSet, int columnCount);
        /*! \brief
         * Sets whether the data contains multiple points per column per frame.
         *
         * \param[in] bMultipoint  Whether the data will allow multiple points
         *      per column within a single frame.
         * \throws    APIError if modules have been added that are not
         *      compatible with the new setting.
         *
         * If this method is not called, the data is not multipoint.
         *
         * Must not be called after startData() has been called.
         *
         * \see isMultipoint()
         */
        void setMultipoint(bool bMultipoint);

        virtual int frameCount() const;

        /*! \brief
         * Creates a handle for adding data.
         *
         * \param[in]  opt     Options for setting how this handle will be
         *     used.
         * \returns The created handle.
         * \throws  std::bad_alloc if out of memory.
         * \throws  APIError if any attached data module is not compatible.
         * \throws  unspecified  Any exception thrown by attached data modules
         *      in AnalysisDataModuleInterface::dataStarted().
         *
         * The caller should retain the returned handle (or a copy of it), and
         * pass it to finishData() after successfully adding all data.
         * The caller should discard the returned handle if an error occurs;
         * memory allocated for the handle will be freed when the AnalysisData
         * object is destroyed.
         *
         * The \p opt options should be the same for all calls to this method,
         * and the number of calls should match the parallelization factor
         * defined in \p opt.
         */
        AnalysisDataHandle startData(const AnalysisDataParallelOptions &opt);
        /*! \brief
         * Performs in-order sequential processing for the next frame.
         *
         * \param[in]  frameIndex Index of the frame that has been finished.
         * \throws  unspecified  Any exception thrown by attached data modules
         *      in AnalysisDataModuleInterface::frameFinishedSerial().
         *
         * This method should be called sequentially for each frame, after data
         * for that frame has been produced.  It is not necessary to call this
         * method if there is no parallelism, i.e., if only a single data
         * handle is created and the parallelization options provided at that
         * time do not indicate parallelism.
         */
        void finishFrameSerial(int frameIndex);
        /*! \brief
         * Destroys a handle after all data has been added.
         *
         * \param[in]  handle  Handle to destroy.
         * \throws  unspecified  Any exception thrown by attached data modules
         *      in AnalysisDataModuleInterface::dataFinished().
         *
         * \p handle must have been obtained from startData() of this object.
         * The order of the calls with respect to the corresponding startData()
         * calls is not important.
         *
         * The \p handle (and any copies) are invalid after the call.
         */
        void finishData(AnalysisDataHandle handle);

    private:
        virtual AnalysisDataFrameRef tryGetDataFrameInternal(int index) const;
        virtual bool requestStorageInternal(int nframes);

        class Impl;

        PrivateImplPointer<Impl> impl_;

        friend class AnalysisDataHandle;
};

namespace internal
{
class AnalysisDataHandleImpl;
}   // namespace internal

/*! \brief
 * Handle for inserting data into AnalysisData.
 *
 * This class provides an interface for adding data frames into an AnalysisData
 * object.  After a handle is obtained from AnalysisData::startData(), new
 * frames can be added using startFrame().  Then values for that frame are set
 * using provided methods (see below), and finishFrame() is called.  After all
 * frames have been added, finishData() (or AnalysisData::finishData()) must be
 * called.
 *
 * For simple (non-multipoint) data, within a frame values can be set using
 * selectDataSet(), setPoint() and setPoints().  Setting the same column in the
 * same data set multiple times overrides previously set values.
 * When the frame is finished, attached modules are notified.
 *
 * Multipoint data works otherwise similarly, but requires finishPointSet() to
 * be called for each set of points for which the modules need to be notified.
 * Each point set starts empty (after startFrame() or finishPointSet()), and
 * values can be set using setPoint()/setPoints().
 * A single point set can contain values only for a single data set, which must
 * be selected with selectDataSet() before setting any values.
 * finishPointSet() must also be called for the last point set just before
 * finishFrame().
 *
 * This class works like a pointer type: copying and assignment is lightweight,
 * and all copies work interchangeably, accessing the same internal handle.
 * However, normally you should only keep one copy of a handle, i.e., treat
 * this type as movable.
 * Several handles created from the same AnalysisData object can exist
 * concurrently, but must currently operate on separate frames.
 *
 * \inpublicapi
 * \ingroup module_analysisdata
 */
class AnalysisDataHandle
{
    public:
        /*! \brief
         * Constructs an invalid data handle.
         *
         * This constructor is provided for convenience in cases where it is
         * easiest to declare an AnalysisDataHandle without immediately
         * assigning a value to it.  Any attempt to call methods without first
         * assigning a value from AnalysisData::startData() to the handle
         * causes an assert.
         *
         * Does not throw.
         */
        AnalysisDataHandle();

        //! Returns whether this data handle is valid.
        bool isValid() const { return impl_ != NULL; }

        /*! \brief
         * Start data for a new frame.
         *
         * \param[in] index  Zero-based index for the frame to start.
         * \param[in] x      x value for the frame.
         * \param[in] dx     Error in x for the frame if applicable.
         *
         * \throws    unspecified  Any exception thrown by attached data
         *      modules in AnalysisDataModuleInterface::frameStarted().
         *
         * Each \p index value 0, 1, ..., N (where N is the total number of
         * frames) should be started exactly once by exactly one handle of an
         * AnalysisData object.  The frames may be started out of order, but
         * currently the implementation places some limitations on how far
         * the index can be in the future (as counted from the first frame that
         * is not finished).
         */
        void startFrame(int index, real x, real dx = 0.0);
        /*! \brief
         * Selects a data set for subsequent setPoint()/setPoints() calls.
         *
         * \param[in] index  Zero-based data set index.
         *
         * After startFrame(), the first data set is always selected.
         * The set value is remembered until the end of the current frame, also
         * across finishPointSet() calls.
         *
         * Does not throw.
         */
        void selectDataSet(int index);
        /*! \brief
         * Set a value for a single column for the current frame.
         *
         * \param[in] column  Zero-based column index.
         * \param[in] value   Value to set for the column.
         * \param[in] bPresent Present flag to set for the column.
         *
         * If called multiple times for a column (within one point set for
         * multipoint data), old values are overwritten.
         *
         * Does not throw.
         */
        void setPoint(int column, real value, bool bPresent = true);
        /*! \brief
         * Set a value and its error estimate for a single column for the
         * current frame.
         *
         * \param[in] column  Zero-based column index.
         * \param[in] value   Value to set for the column.
         * \param[in] error   Error estimate to set for the column.
         * \param[in] bPresent Present flag to set for the column.
         *
         * If called multiple times for a column (within one point set for
         * multipoint data), old values are overwritten.
         *
         * Does not throw.
         */
        void setPoint(int column, real value, real error, bool bPresent = true);
        /*! \brief
         * Set values for consecutive columns for the current frame.
         *
         * \param[in] firstColumn  Zero-based column index.
         * \param[in] count        Number of columns to set.
         * \param[in] values       Value array of \p column items.
         *
         * Equivalent to calling setPoint(firstColumn + i, values[i]) for
         * i from 0 to count.
         *
         * Does not throw.
         */
        void setPoints(int firstColumn, int count, const real *values);
        /*! \brief
         * Finish data for the current point set.
         *
         * \throws    APIError if any attached data module is not compatible.
         * \throws    unspecified  Any exception thrown by attached data
         *      modules in AnalysisDataModuleInterface::pointsAdded().
         *
         * Must be called after each point set for multipoint data, including
         * the last (i.e., no values must be set between the last call to this
         * method and AnalysisDataStorage::finishFrame()).
         * Must not be called for non-multipoint data.
         */
        void finishPointSet();
        /*! \brief
         * Finish data for the current frame.
         *
         * \throws    APIError if any attached data module is not compatible.
         * \throws    unspecified  Any exception thrown by attached data
         *      modules in frame notification methods.
         */
        void finishFrame();
        //! Calls AnalysisData::finishData() for this handle.
        void finishData();

    private:
        /*! \brief
         * Creates a new data handle associated with \p data.
         *
         * \param  impl Data to associate the handle with.
         *
         * The constructor is private because data handles should only be
         * constructed through AnalysisData::startData().
         *
         * Does not throw.
         */
        explicit AnalysisDataHandle(internal::AnalysisDataHandleImpl *impl);

        /*! \brief
         * Pointer to the internal implementation class.
         *
         * The memory for this object is managed by the AnalysisData object,
         * and AnalysisDataHandle simply provides a public interface for
         * accessing the implementation.
         */
        internal::AnalysisDataHandleImpl *impl_;

        /*! \brief
         * Needed to access the non-public implementation.
         */
        friend class AnalysisData;
};

} // namespace gmx

#endif