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

Inheritance diagram for gmx::AnalysisDataSimpleHistogramModule:

Collaboration diagram for gmx::AnalysisDataSimpleHistogramModule:

Description

Data module for per-frame histograms.

Output data contains the same number of frames and data sets as the input data. Each frame contains the histogram(s) for the points in that frame. Each input data set is processed independently into the corresponding output data set. Missing values are ignored. All input columns for a data set are averaged into the same histogram. The number of columns for all data sets equals the number of bins in the histogram.

The histograms are accumulated as 64-bit integers within a frame and summed in double precision across frames, even if the output data is in single precision.

Classes
class	Impl
	Private implementation class for AnalysisDataSimpleHistogramModule. More...

Public Member Functions
	AnalysisDataSimpleHistogramModule ()
	Creates a histogram module with undefined bins. More...

	AnalysisDataSimpleHistogramModule (const AnalysisHistogramSettings &settings)
	Creates a histogram module with defined bin parameters.

void	init (const AnalysisHistogramSettings &settings)
	(Re)initializes the histogram from settings.

AbstractAverageHistogram &	averager ()
	Returns the average histogram over all frames. More...

const AnalysisHistogramSettings &	settings () const
	Returns bin properties for the histogram.

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

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

bool	parallelDataStarted (AbstractAnalysisData *data, const AnalysisDataParallelOptions &options) override
	Called (once) for parallel data when the data has been set up. 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	frameFinishedSerial (int frameIndex) override
	Called in sequential order for each frame after they are finished. More...

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

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::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.

Constructor & Destructor Documentation

gmx::AnalysisDataSimpleHistogramModule::AnalysisDataSimpleHistogramModule ( )

Creates a histogram module with undefined bins.

Bin parameters must be defined with init() before data input is started.

Member Function Documentation

AbstractAverageHistogram & gmx::AnalysisDataSimpleHistogramModule::averager ( )

Returns the average histogram over all frames.

Can be called already before the histogram is calculated to customize the way the average histogram is calculated.

See Also: AbstractAverageHistogram

void gmx::AnalysisDataSimpleHistogramModule::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::AnalysisDataModuleParallel.

int gmx::AnalysisDataSimpleHistogramModule::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::AnalysisDataModuleParallel.

int gmx::AnalysisDataSimpleHistogramModule::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.

void gmx::AnalysisDataSimpleHistogramModule::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::AnalysisDataModuleParallel.

void gmx::AnalysisDataSimpleHistogramModule::frameFinishedSerial ( int frameIndex )

overridevirtual

Called in sequential order for each frame after they are finished.

Parameters

[in] frameIndex Index of the next finished frame.

Exceptions

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

This method is called after frameFinished(), but with an additional constraint that it is always called in serial and with an increasing frameIndex. Parallel data modules need this to serialize their data for downstream serial modules; AnalysisDataModuleSerial provides an empty implementation, as there frameFinished() can be used for the same purpose.

Implements gmx::AnalysisDataModuleParallel.

void gmx::AnalysisDataSimpleHistogramModule::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::AnalysisDataModuleParallel.

bool gmx::AnalysisDataSimpleHistogramModule::parallelDataStarted	(	AbstractAnalysisData *	data,
		const AnalysisDataParallelOptions &	options
	)

overridevirtual

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

Parameters

[in]	data	Data object to which the module is added.
[in]	options	Parallelization properties of the input data.

Returns: true if the module can process the input in non-sequential order.

Exceptions

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

This method is called instead of dataStarted() if the input data has the capability to present data in non-sequential order. If the method returns true, then the module accepts this and frame notification methods may be called in that non-sequential order. If the method returns false, then the frame notification methods are called in sequential order, as if dataStarted() had been called.

See dataStarted() for general information on initializing the data. That applies to this method as well, with the exception that calling AbstractAnalysisData::requestStorage() is currently not very well supported (or rather, accessing the requested storage doesn't work).

Implements gmx::AnalysisDataModuleParallel.

void gmx::AnalysisDataSimpleHistogramModule::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::AnalysisDataModuleParallel.

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

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

Description

Classes

Public Member Functions

Additional Inherited Members

Constructor & Destructor Documentation

Member Function Documentation