#include <gromacs/analysisdata/analysisdata.h>

Inheritance diagram for gmx::AnalysisData:

Collaboration diagram for gmx::AnalysisData:

Description

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.

Examples:: template.cpp.

Public Member Functions
	AnalysisData ()
	Creates an empty analysis data object. More...

void	setDataSetCount (int dataSetCount)
	Sets the number of data sets. More...

void	setColumnCount (int dataSet, int columnCount)
	Sets the number of columns in a data set. More...

void	setMultipoint (bool bMultipoint)
	Sets whether the data contains multiple points per column per frame. More...

int	frameCount () const override
	Returns the total number of frames in the data. More...

AnalysisDataHandle	startData (const AnalysisDataParallelOptions &opt)
	Creates a handle for adding data. More...

void	finishFrameSerial (int frameIndex)
	Performs in-order sequential processing for the next frame. More...

void	finishData (AnalysisDataHandle handle)
	Destroys a handle after all data has been added. More...

bool	isMultipoint () const
	Whether the data can have multiple points in the same column in the same frame. More...

int	dataSetCount () const
	Returns the number of data sets in the data object. More...

int	columnCount (int dataSet) const
	Returns the number of columns in a data set. More...

int	columnCount () const
	Returns the number of columns in the data. More...

AnalysisDataFrameRef	tryGetDataFrame (int index) const
	Access stored data. More...

AnalysisDataFrameRef	getDataFrame (int index) const
	Access stored data. More...

bool	requestStorage (int nframes)
	Request storage of frames. More...

void	addModule (const AnalysisDataModulePointer &module)
	Adds a module to process the data. More...

void	addColumnModule (int col, int span, const AnalysisDataModulePointer &module)
	Adds a module that processes only a subset of the columns. More...

void	applyModule (IAnalysisDataModule *module)
	Applies a module to process data that is ready. More...

Protected Member Functions
AnalysisDataModuleManager &	moduleManager ()
	Returns the module manager to use for calling notification methods.

const AnalysisDataModuleManager &	moduleManager () const
	Returns the module manager to use for calling notification methods.

Friends
class	AnalysisDataHandle

Constructor & Destructor Documentation

gmx::AnalysisData::AnalysisData ( )

Creates an empty analysis data object.

Exceptions

std::bad_alloc if out of memory.

Member Function Documentation

void gmx::AbstractAnalysisData::addColumnModule	(	int	col,
		int	span,
		const AnalysisDataModulePointer &	module
	)

inherited

Adds a module that processes only a subset of the columns.

Parameters

[in]	col	First column.
[in]	span	Number of columns.
	module	Module to add.

Throws in the same situations as addModule().

Currently, all data sets are filtered using the same column mask.

Todo:: This method doesn't currently work in all cases with multipoint data or with multiple data sets. In particular, if the added module requests storage and uses getDataFrame(), it will behave unpredictably (most likely asserts).

Todo:: Generalize this method to multiple data sets (e.g., for adding modules that only process a single data set).

See Also: addModule()

void gmx::AbstractAnalysisData::addModule ( const AnalysisDataModulePointer & module )

inherited

Adds a module to process the data.

Parameters

module Module to add.

Exceptions

std::bad_alloc	if out of memory.
APIError	if `module` is not compatible with the data object data has already been added to the data object and everything is not available through getDataFrame().
unspecified	Any exception thrown by `module` in its notification methods (if data has been added).

If data has already been added to the data, the new module immediately processes all existing data. APIError is thrown if all data is not available through getDataFrame().

The caller can keep a copy of the module pointer if it requires later access to the module.

If the method throws, the state of the data object is not changed. The state of the data module is indeterminate.

void gmx::AbstractAnalysisData::applyModule ( IAnalysisDataModule * module )

inherited

Applies a module to process data that is ready.

Parameters

module Module to apply.

Exceptions

APIError	in same situations as addModule().
unspecified	Any exception thrown by `module` in its notification methods.

This function works as addModule(), except that it does not keep a reference to module within the data object after it returns. Also, it can only be called after the data is ready, and only if getDataFrame() gives access to all of the data. It is provided for additional flexibility in postprocessing in-memory data.

Todo:: Currently, this method may not work correctly if module requests storage (addModule() has the same problem if called after data is started).

int gmx::AbstractAnalysisData::columnCount ( int dataSet ) const

inherited

Returns the number of columns in a data set.

Parameters

[in] dataSet Zero-based index of the data set to query.

Returns: The number of columns in the data.

If the number of columns is not yet known, returns 0. The returned value does not change after modules have been notified of data start, but may change multiple times before that, depending on the actual data class. Derived classes should set the number of columns with setColumnCount(), within the above limitations.

Does not throw.

int gmx::AbstractAnalysisData::columnCount ( ) const

inherited

Returns the number of columns in the data.

Returns: The number of columns in the data.

This is a convenience method for data objects with a single data set. Can only be called if dataSetCount() == 1.

Does not throw.

See Also: columnCount(int)

int gmx::AbstractAnalysisData::dataSetCount ( ) const

inherited

Returns the number of data sets in the data object.

Returns: The number of data sets in the data.

If the number is not yet known, returns 0. The returned value does not change after modules have been notified of data start, but may change multiple times before that, depending on the actual data class. Derived classes should set the number of columns with setDataSetCount(), within the above limitations.

Does not throw.

void gmx::AnalysisData::finishData ( AnalysisDataHandle handle )

Destroys a handle after all data has been added.

Parameters

[in] handle Handle to destroy.

Exceptions

unspecified Any exception thrown by attached data modules in IAnalysisDataModule::dataFinished().

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 handle (and any copies) are invalid after the call.

void gmx::AnalysisData::finishFrameSerial ( int frameIndex )

Performs in-order sequential processing for the next frame.

Parameters

[in] frameIndex Index of the frame that has been finished.

Exceptions

unspecified Any exception thrown by attached data modules in IAnalysisDataModule::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.

int gmx::AnalysisData::frameCount ( ) const

overridevirtual

Returns the total number of frames in the data.

Returns: The total number of frames in the data.

This function returns the number of frames that the object has produced. If requestStorage() has been successfully called, tryGetDataframe() or getDataFrame() can be used to access some or all of these frames.

Does not throw.

Derived classes should implement this to return the number of frames. The frame count should not be incremented before tryGetDataFrameInternal() can return the new frame. The frame count must be incremented before AnalysisDataModuleManager::notifyFrameFinish() is called.

Implements gmx::AbstractAnalysisData.

AnalysisDataFrameRef gmx::AbstractAnalysisData::getDataFrame ( int index ) const

inherited

Access stored data.

Parameters

[in] index Zero-based frame index to access.

Returns: Frame reference to frame index.

Exceptions

APIError if the requested frame is not accessible.

If the data is not certainly available, use tryGetDataFrame().

See Also: requestStorage(); tryGetDataFrame()

bool gmx::AbstractAnalysisData::isMultipoint ( ) const

inherited

Whether the data can have multiple points in the same column in the same frame.

Returns: true if multiple points in the same column are allowed within a single frame.

This kind of data can appear in many histogramming applications (e.g., RDFs), where each trajectory frame has several data points (possibly a different number for each frame). The current interface doesn't support storing such data, but this should rarely be necessary.

The returned value does not change after modules have been notified of data start. Derived classes can change the type by calling setMultipoint() subject to the above restriction. If this is not done, the function always returns false.

Does not throw.

bool gmx::AbstractAnalysisData::requestStorage ( int nframes )

inherited

Request storage of frames.

Parameters

[in] nframes Request storing at least nframes previous frames (-1 = request storing all). Must be >= -1.

Returns: true if the request could be satisfied.

If called multiple times, the largest request is honored.

Does not throw. Failure to honor the request is indicated through the return value.

See Also: getDataFrame(); tryGetDataFrame()

void gmx::AnalysisData::setColumnCount	(	int	dataSet,
		int	columnCount
	)

Sets the number of columns in a data set.

Parameters

[in]	dataSet	Zero-based data set index.
[in]	columnCount	Number of columns in the data (must be > 0).

Exceptions

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 gmx::AnalysisData::setDataSetCount ( int dataSetCount )

Sets the number of data sets.

Parameters

[in] dataSetCount Number of data sets (must be > 0).

Exceptions

std::bad_alloc	if out of memory.
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 gmx::AnalysisData::setMultipoint ( bool bMultipoint )

Sets whether the data contains multiple points per column per frame.

Parameters

[in] bMultipoint Whether the data will allow multiple points per column within a single frame.

Exceptions

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 Also: isMultipoint()

AnalysisDataHandle gmx::AnalysisData::startData ( const AnalysisDataParallelOptions & opt )

Creates a handle for adding data.

Parameters

[in] opt Options for setting how this handle will be used.

Returns: The created handle.

Exceptions

std::bad_alloc	if out of memory.
APIError	if any attached data module is not compatible.
unspecified	Any exception thrown by attached data modules in IAnalysisDataModule::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 opt options should be the same for all calls to this method, and the number of calls should match the parallelization factor defined in opt.

AnalysisDataFrameRef gmx::AbstractAnalysisData::tryGetDataFrame ( int index ) const

inherited

Access stored data.

Parameters

[in] index Zero-based frame index to access.

Returns: Frame reference to frame index, or an invalid reference if no such frame is available.

Does not throw. Failure to access a frame with the given index is indicated through the return value. Negative index is allowed, and will always result in an invalid reference being returned.

See Also: requestStorage(); getDataFrame()

The documentation for this class was generated from the following files:

api/legacy/include/gromacs/analysisdata/analysisdata.h
src/gromacs/analysisdata/analysisdata.cpp

Description

Public Member Functions

Protected Member Functions

Friends

Constructor & Destructor Documentation

Member Function Documentation