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

Inheritance diagram for gmx::AnalysisDataLifetimeModule:

Collaboration diagram for gmx::AnalysisDataLifetimeModule:

Description

Data module for computing lifetime histograms for columns in input data.

The input data set is treated as a boolean array: each value that is present (AnalysisDataValue::isPresent() returns true) and is >0 is treated as present, other values are treated as absent. For each input data set, analyzes the columns to identify the intervals where a column is continuously present. Produces a histogram from the lengths of these intervals. Input data should have frames with evenly spaced x values.

Output data contains one column for each data set in the input data. This column gives the lifetime histogram for the corresponding data set. x axis in the output is spaced the same as in the input data, and extends as long as required to cover all the histograms. Histograms are padded with zeros as required to be of the same length. setCumulative() can be used to alter the handling of subintervals in the output histogram.

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

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
void	setCumulative (bool bCumulative)
	Sets a cumulative histogram mode. 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...

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
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	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...

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

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).

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::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.

void gmx::AnalysisDataLifetimeModule::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.

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.

void gmx::AnalysisDataLifetimeModule::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::AnalysisDataLifetimeModule::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.

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.

Implements gmx::AbstractAnalysisData.

void gmx::AnalysisDataLifetimeModule::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::AnalysisDataLifetimeModule::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.

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.

Does not throw.

void gmx::AnalysisDataLifetimeModule::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.

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()

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::AnalysisDataLifetimeModule::setCumulative ( bool bCumulative )

Sets a cumulative histogram mode.

Parameters

[in] bCumulative If true, all subintervals of a long interval are also explicitly added into the histogram.

Does not throw.

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

Description

Public Types

Public Member Functions

Protected Member Functions

Static Protected Member Functions

Member Enumeration Documentation

Member Function Documentation