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/*! \file
* \brief
- * Declares gmx::AnalysisData and related classes.
+ * Declares gmx::AnalysisData and gmx::AnalysisDataHandle.
*
- * \author Teemu Murtola <teemu.murtola@cbr.su.se>
+ * \author Teemu Murtola <teemu.murtola@gmail.com>
* \inpublicapi
* \ingroup module_analysisdata
*/
#ifndef GMX_ANALYSISDATA_ANALYSISDATA_H
#define GMX_ANALYSISDATA_ANALYSISDATA_H
-#include "abstractdata.h"
+#include "gromacs/analysisdata/abstractdata.h"
+#include "gromacs/utility/real.h"
namespace gmx
{
/*! \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). When all data has been provided, the handles
+ * are destroyed using finishData() (or AnalysisDataHandle::finishData()).
+ * The AnalysisData object takes care of internally sorting the frames and
+ * passing them to the attached modules in the order in which the modules
+ * expect them.
+ *
+ * \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
* 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.
+ * provide it. With the current registration mechanism in
+ * TrajectoryAnalysisModule, this should be straightforward.
* \endif
*
* \inpublicapi
class AnalysisData : public AbstractAnalysisData
{
public:
- //! Creates an empty analysis data object.
+ /*! \brief
+ * Creates an empty analysis data object.
+ *
+ * \throws std::bad_alloc if out of memory.
+ */
AnalysisData();
virtual ~AnalysisData();
/*! \brief
- * Sets the number of columns in the data.
+ * 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 ncol);
+ 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
* Create 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
* Destroy 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.
*/
namespace internal
{
class AnalysisDataHandleImpl;
-} // namespace internal
+} // 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.
- *
- * Several handles can exist concurrently.
+ * 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
* 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();
- //! Start data for a new frame.
+ //! 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);
- //! Set a value for a single column for the current frame.
- void setPoint(int col, real y, real dy = 0.0, bool present = true);
- //! Set values for consecutive columns for the current frame.
- void setPoints(int firstcol, int n, const real *y);
- //! Finish data for the current point set.
+ /*! \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();
- //! Finish data for the current frame.
+ /*! \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();
/*! \brief
* Creates a new data handle associated with \p data.
*
- * \param data Data to associate the handle with.
+ * \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);
*/
internal::AnalysisDataHandleImpl *impl_;
+ /*! \brief
+ * Needed to access the non-public implementation.
+ */
friend class AnalysisData;
};
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff