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

Inheritance diagram for gmx::AnalysisDataWeightedHistogramModule:

Collaboration diagram for gmx::AnalysisDataWeightedHistogramModule:

Description

Data module for per-frame weighted 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, interpreted such that the first column passed to pointsAdded() determines the bin and the rest give weights to be added to that bin (input data should have at least two columns, and at least two columns should be added at the same time). Each input data set is processed independently into the corresponding output data set. 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 in double precision, even if the output data is in single precision.

Public Types
enum	Flag { efAllowMultipoint = 1 << 0, efOnlyMultipoint = 1 << 1, efAllowMulticolumn = 1 << 2, efAllowMissing = 1 << 3, efAllowMultipleDataSets = 1 << 4 }
	Possible flags for flags(). More...

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

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

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

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

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

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...

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...

Member Enumeration Documentation

enum gmx::IAnalysisDataModule::Flag

inherited

Possible flags for flags().

Enumerator
efAllowMultipoint	The module can process multipoint data.
efOnlyMultipoint	The module does not make sense for non-multipoint data.
efAllowMulticolumn	The module can process data with more than one column.
efAllowMissing	The module can process data with missing points.
efAllowMultipleDataSets	The module can process data with multiple data sets.

Constructor & Destructor Documentation

gmx::AnalysisDataWeightedHistogramModule::AnalysisDataWeightedHistogramModule ( )

Creates a histogram module with undefined bins.

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

gmx::AnalysisDataWeightedHistogramModule::AnalysisDataWeightedHistogramModule ( const AnalysisHistogramSettings & settings )

explicit

Creates a histogram module with defined bin parameters.

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).

AbstractAverageHistogram & gmx::AnalysisDataWeightedHistogramModule::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

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.

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)

void gmx::AnalysisDataWeightedHistogramModule::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::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.

Does not throw.

int gmx::AnalysisDataWeightedHistogramModule::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::AnalysisDataWeightedHistogramModule::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.

Implements gmx::AbstractAnalysisData.

void gmx::AnalysisDataWeightedHistogramModule::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::AnalysisDataWeightedHistogramModule::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::AnalysisDataWeightedHistogramModule::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.

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()

void gmx::AnalysisDataWeightedHistogramModule::init ( const AnalysisHistogramSettings & settings )

(Re)initializes the histogram from settings.

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.

Does not throw.

bool gmx::AnalysisDataWeightedHistogramModule::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::AnalysisDataWeightedHistogramModule::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.

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()

const AnalysisHistogramSettings & gmx::AnalysisDataWeightedHistogramModule::settings ( ) const

Returns bin properties for the histogram.

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/modules/histogram.h
src/gromacs/analysisdata/modules/histogram.cpp

Description

Public Types

Public Member Functions

Member Enumeration Documentation

Constructor & Destructor Documentation

Member Function Documentation