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

Inheritance diagram for gmx::AbstractAverageHistogram:

Collaboration diagram for gmx::AbstractAverageHistogram:

Description

Base class for representing histograms averaged over frames.

The averaging module for a per-frame histogram is always created by the histogram module class (e.g., AnalysisDataSimpleHistogramModule), and can be accessed using, e.g., AnalysisDataSimpleHistogramModule::averager(). The user can alter some properties of the average histogram directly, but the main use of the object is to postprocess the histogram once the calculation is finished.

This class can represent multiple histograms in one object: each column in the data is an independent histogram. The X values correspond to center of the bins, except for a cumulative histogram made with makeCumulative().

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

AverageHistogramPointer	resampleDoubleBinWidth (bool bIntegerBins) const
	Creates a copy of the histogram with double the bin width. More...

AverageHistogramPointer	clone () const
	Creates a deep copy of the histogram. More...

void	normalizeProbability ()
	Normalizes the histogram such that the integral over it is one.

void	makeCumulative ()
	Makes the histograms cumulative by summing up each bin to all bins after it. More...

void	scaleSingle (int index, real factor)
	Scales a single histogram by a uniform scaling factor.

void	scaleAll (real factor)
	Scales all histograms by a uniform scaling factor.

void	scaleAllByVector (const real factor[])
	Scales the value of each bin by a different scaling factor.

void	done ()
	Notifies attached modules of the histogram data. More...

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.

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
	AbstractAverageHistogram ()
	Creates a histogram module with undefined bins. More...

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

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

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

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

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

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

void	setDataSetCount (int dataSetCount)
	Sets the number of data sets. 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
static void	copyContents (const AbstractAnalysisArrayData src, AbstractAnalysisArrayData dest)
	Copies the contents into a new object. More...

Constructor & Destructor Documentation

gmx::AbstractAverageHistogram::AbstractAverageHistogram ( )

protected

Creates a histogram module with undefined bins.

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

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::AbstractAnalysisArrayData::allocateValues ( )

protectedinherited

Allocates memory for the values.

Exceptions

std::bad_alloc if memory allocation fails.

setColumnCount() and setRowCount() must have been called.

Strong exception safety guarantee.

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).

AverageHistogramPointer gmx::AbstractAverageHistogram::clone ( ) const

Creates a deep copy of the histogram.

Exceptions

std::bad_alloc if out of memory.

The returned histogram is not necessarily of the same dynamic type as the original object, but contains the same data from the point of view of the AbstractAverageHistogram interface.

The caller is responsible of deleting the returned object.

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)

void gmx::AbstractAnalysisArrayData::copyContents	(	const AbstractAnalysisArrayData *	src,
		AbstractAnalysisArrayData *	dest
	)

staticprotectedinherited

Copies the contents into a new object.

Parameters

[in]	src	Object to copy data from.
[in,out]	dest	Empty array data object to copy data to.

Exceptions

std::bad_alloc if memory allocation for dest fails.

dest should not have previous contents.

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::AbstractAverageHistogram::done ( )

inline

Notifies attached modules of the histogram data.

After this function has been called, it is no longer possible to alter the histogram.

int gmx::AbstractAnalysisArrayData::frameCount ( ) const

inlineoverridevirtualinherited

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.

void gmx::AbstractAverageHistogram::makeCumulative ( )

Makes the histograms cumulative by summing up each bin to all bins after it.

The X values in the data are adjusted such that they match the right edges of bins instead of bin centers.

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()

AverageHistogramPointer gmx::AbstractAverageHistogram::resampleDoubleBinWidth ( bool bIntegerBins ) const

Creates a copy of the histogram with double the bin width.

Parameters

[in] bIntegerBins If true, the first bin in the result will cover the first bin from the source. Otherwise, the first bin will cover first two bins from the source.

Exceptions

std::bad_alloc if out of memory.

The caller is responsible of deleting the returned object.

int gmx::AbstractAnalysisArrayData::rowCount ( ) const

inlineinherited

Returns the number of rows in the data array.

This function is identical to frameCount(), except that frameCount() returns 0 before valuesReady() has been called.

void gmx::AbstractAnalysisArrayData::setColumnCount ( int ncols )

protectedinherited

Sets the number of columns in the data array.

Parameters

[in] ncols Number of columns in the data.

Cannot be called after allocateValues().

See AbstractAnalysisData::setColumnCount() for exception behavior.

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

protectedinherited

Sets the number of columns for a data set.

Parameters

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

Exceptions

APIError if modules have been added that are not compatible with the new column count.

Must be called at least once for each data set before AnalysisDataModuleManager::notifyDataStart(). Can be called only before AnalysisDataModuleManager::notifyDataStart(). Multiple calls are allowed before that point; the last call takes effect.

Strong exception safety.

See Also: columnCount()

void gmx::AbstractAnalysisData::setDataSetCount ( int dataSetCount )

protectedinherited

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.

It not called, the data object has a single data set. Can be called only before AnalysisDataModuleManager::notifyDataStart(). Multiple calls are allowed before that point; the last call takes effect.

Strong exception safety.

See Also: dataSetCount()

void gmx::AbstractAnalysisData::setMultipoint ( bool bMultipoint )

protectedinherited

Sets whether the data has multiple points per column in a frame.

Parameters

[in] bMultipoint Whether multiple points per column are possible.

Exceptions

APIError if modules have been added that are not compatible with the new setting.

If not called, only a single point per column is allowed. Can be called only before AnalysisDataModuleManager::notifyDataStart(). Multiple calls are allowed before that point; the last call takes effect.

Strong exception safety.

See Also: isMultipoint()

void gmx::AbstractAnalysisArrayData::setRowCount ( int rowCount )

protectedinherited

Sets the number of rows in the data array.

Parameters

[in] rowCount Number of rows in the data.

Cannot be called after allocateValues().

Does not throw.

void gmx::AbstractAnalysisArrayData::setXAxis	(	real	start,
		real	step
	)

protectedinherited

Sets the values reported as x values for frames.

Parameters

[in]	start	x value for the first frame.
[in]	step	Step between x values of successive frames.

Must not be called after valuesReady(). Any values set with setXAxisValue() are overwritten.

Does not throw.

void gmx::AbstractAnalysisArrayData::setXAxisValue	(	int	row,
		real	value
	)

protectedinherited

Sets a single value reported as x value for frames.

Parameters

[in]	row	Row/frame for which to set the value.
[in]	value	x value for the frame specified by `row`.

Must not be called after valuesReady().

Does not throw.

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()

void gmx::AbstractAnalysisArrayData::valuesReady ( )

protectedinherited

Notifies modules of the data.

Exceptions

unspecified Any exception thrown by attached data modules in data notification methods.

This function should be called once the values in the array have been initialized. The values should not be changed after this function has been called.

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 Member Functions

Protected Member Functions

Static Protected Member Functions

Constructor & Destructor Documentation

Member Function Documentation