#include <gromacs/analysisdata/modules/average.h>

Inheritance diagram for gmx::AnalysisDataAverageModule:

Collaboration diagram for gmx::AnalysisDataAverageModule:

Description

Data module for independently averaging each column in input data.

Computes the average and standard deviation independently for each column in the input data. Multipoint data, multiple data sets, and missing data points are all supported. The average is always calculated over all frames and data points for a column.

Output data contains a column for each data set in the input data, and a frame for each column in the input data. If different data sets have different number of columns, the frame count accommodates the largest data set. Other columns are padded with zero values that are additionally marked as missing. Each value in the output data is the average of the corresponding input column in the corresponding input data set. The error value for each value provides the standard deviation of the corresponding input column. average(), standardDeviation(), and sampleCount() methods are also provided for convenient access to these properties.

The output data becomes available only after the input data has been finished.

Examples:: template.cpp.

Public Member Functions
void	setAverageDataSets (bool bDataSets)
	Sets the averaging to happen over entire data sets. More...

int	flags () const override
	Returns properties supported by the module. More...

void	dataStarted (AbstractAnalysisData *data) override
	Called (once) when the data has been set up properly. More...

void	frameStarted (const AnalysisDataFrameHeader &header) override
	Called at the start of each data frame. More...

void	pointsAdded (const AnalysisDataPointSetRef &points) override
	Called one or more times during each data frame. More...

void	frameFinished (const AnalysisDataFrameHeader &header) override
	Called when a data frame is finished. More...

void	dataFinished () override
	Called (once) when no more data is available. More...

real	average (int dataSet, int column) const
	Convenience access to the average of a data column. More...

real	standardDeviation (int dataSet, int column) const
	Convenience access to the standard deviation of a data column. More...

int	sampleCount (int dataSet, int column) const
	Access the number of samples for a data column. More...

Public Member Functions inherited from gmx::AbstractAnalysisArrayData
int	frameCount () const override
	Returns the total number of frames in the data. More...

int	rowCount () const
	Returns the number of rows in the data array. More...

bool	isAllocated () const
	Returns true if values have been allocated.

real	xstart () const
	Returns the x value of the first frame.

real	xstep () const
	Returns the step between frame x values.

real	xvalue (int row) const
	Returns the x value of a row.

const AnalysisDataValue &	value (int row, int col) const
	Returns a given array element.

Public Member Functions inherited from gmx::AbstractAnalysisData
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...

Additional Inherited Members
Public Types inherited from gmx::IAnalysisDataModule
enum	Flag { efAllowMultipoint = 1 << 0, efOnlyMultipoint = 1 << 1, efAllowMulticolumn = 1 << 2, efAllowMissing = 1 << 3, efAllowMultipleDataSets = 1 << 4 }
	Possible flags for flags(). More...

Protected Member Functions inherited from gmx::AbstractAnalysisArrayData
	AbstractAnalysisArrayData ()
	Initializes an empty array data object. More...

void	setColumnCount (int ncols)
	Sets the number of columns in the data array. More...

void	setRowCount (int rowCount)
	Sets the number of rows in the data array. More...

void	allocateValues ()
	Allocates memory for the values. More...

void	setXAxis (real start, real step)
	Sets the values reported as x values for frames. More...

void	setXAxisValue (int row, real value)
	Sets a single value reported as x value for frames. More...

AnalysisDataValue &	value (int row, int col)
	Returns a reference to a given array element.

void	valuesReady ()
	Notifies modules of the data. More...

Protected Member Functions inherited from gmx::AbstractAnalysisData
	AbstractAnalysisData ()
	Initializes a new 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 for a data set. More...

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

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.

Static Protected Member Functions inherited from gmx::AbstractAnalysisArrayData
static void	copyContents (const AbstractAnalysisArrayData src, AbstractAnalysisArrayData dest)
	Copies the contents into a new object. More...

Member Function Documentation

real gmx::AnalysisDataAverageModule::average	(	int	dataSet,
		int	column
	)		const

Convenience access to the average of a data column.

Note that the interpretation of the parameters follows their naming: with setAverageDataSets(false), dataSet corresponds to a column in the output, but with setAverageDataSets(false) it corresponds to an output row. In both cases, it selects the data set; with setAverageDataSets(false), column should always be zero as there is only one value per data set.

void gmx::AnalysisDataAverageModule::dataFinished ( )

overridevirtual

Called (once) when no more data is available.

Exceptions

unspecified Can throw any exception required by the implementing class to report errors.

Implements gmx::AnalysisDataModuleSerial.

void gmx::AnalysisDataAverageModule::dataStarted ( AbstractAnalysisData * data )

overridevirtual

Called (once) when the data has been set up properly.

Parameters

[in] data Data object to which the module is added.

Exceptions

APIError	if the provided data is not compatible.
unspecified	Can throw any exception required by the implementing class to report errors.

When the data is ready, either this method or parallelDataStarted() is called, depending on the nature of the input data. If this method is called, the input data will always present the frames in sequential order.

The data to which the module is attached is passed as an argument to provide access to properties of the data for initialization and/or validation. The module can also call AbstractAnalysisData::requestStorage() if needed.

This is the only place where the module gets access to the data; if properties of the data are required later, the module should store them internally. It is guaranteed that the data properties (column count, whether it's multipoint) do not change once this method has been called.

Notice that data will be a proxy object if the module is added as a column module, not the data object for which AbstractAnalysisData::addColumnModule() was called.

Implements gmx::AnalysisDataModuleSerial.

int gmx::AnalysisDataAverageModule::flags ( ) const

overridevirtual

Returns properties supported by the module.

The return value of this method should not change after the module has been added to a data (this responsibility can, and in most cases must, be delegated to the user of the module).

The purpose of this method is to remove the need for common checks for data compatibility in the classes that implement the interface. Instead, AbstractAnalysisData performs these checks based on the flags provided.

Does not throw.

Implements gmx::AnalysisDataModuleSerial.

void gmx::AnalysisDataAverageModule::frameFinished ( const AnalysisDataFrameHeader & header )

overridevirtual

Called when a data frame is finished.

Parameters

[in] header Header information for the frame that is ending.

Exceptions

unspecified Can throw any exception required by the implementing class to report errors.

Implements gmx::AnalysisDataModuleSerial.

void gmx::AnalysisDataAverageModule::frameStarted ( const AnalysisDataFrameHeader & frame )

overridevirtual

Called at the start of each data frame.

Parameters

[in] frame Header information for the frame that is starting.

Exceptions

unspecified Can throw any exception required by the implementing class to report errors.

Implements gmx::AnalysisDataModuleSerial.

void gmx::AnalysisDataAverageModule::pointsAdded ( const AnalysisDataPointSetRef & points )

overridevirtual

Called one or more times during each data frame.

Parameters

[in] points Set of points added (also provides access to frame-level data).

Exceptions

APIError	if the provided data is not compatible.
unspecified	Can throw any exception required by the implementing class to report errors.

Can be called once or multiple times for a frame. For all data objects currently implemented in the library (and all objects that will use AnalysisDataStorage for internal implementation), it is called exactly once for each frame if the data is not multipoint, but currently this restriction is not enforced.

Implements gmx::AnalysisDataModuleSerial.

int gmx::AnalysisDataAverageModule::sampleCount	(	int	dataSet,
		int	column
	)		const

Access the number of samples for a data column.

See average() for the interpretation of the parameters.

void gmx::AnalysisDataAverageModule::setAverageDataSets ( bool bDataSets )

Sets the averaging to happen over entire data sets.

If bDataSets is false (the default), the module averages each column separately. The output will have a column for each data set, and a row for each column.

If bDataSets is true, the module averages all values within a single data set into a single average/standard deviation. The output will have only one column, with one row for each data set.

real gmx::AnalysisDataAverageModule::standardDeviation	(	int	dataSet,
		int	column
	)		const

Convenience access to the standard deviation of a data column.

See average() for the interpretation of the parameters.

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

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

Description

Public Member Functions

Additional Inherited Members

Member Function Documentation