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gmx::AnalysisDataAverageModule Class Reference

#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 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 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...
 
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 AnalysisDataValuevalue (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

AnalysisDataValuevalue (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

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]colFirst column.
[in]spanNumber of columns.
moduleModule 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
moduleModule to add.
Exceptions
std::bad_allocif out of memory.
APIErrorif
  • module is not compatible with the data object
  • data has already been added to the data object and everything is not available through getDataFrame().
unspecifiedAny 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_allocif 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
moduleModule to apply.
Exceptions
APIErrorin same situations as addModule().
unspecifiedAny 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).
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.

int gmx::AbstractAnalysisData::columnCount ( int  dataSet) const
inherited

Returns the number of columns in a data set.

Parameters
[in]dataSetZero-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]srcObject to copy data from.
[in,out]destEmpty array data object to copy data to.
Exceptions
std::bad_allocif memory allocation for dest fails.

dest should not have previous contents.

void gmx::AnalysisDataAverageModule::dataFinished ( )
overridevirtual

Called (once) when no more data is available.

Exceptions
unspecifiedCan 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::AnalysisDataAverageModule::dataStarted ( AbstractAnalysisData data)
overridevirtual

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

Parameters
[in]dataData object to which the module is added.
Exceptions
APIErrorif the provided data is not compatible.
unspecifiedCan 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.

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::AnalysisDataAverageModule::frameFinished ( const AnalysisDataFrameHeader header)
overridevirtual

Called when a data frame is finished.

Parameters
[in]headerHeader information for the frame that is ending.
Exceptions
unspecifiedCan 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]frameHeader information for the frame that is starting.
Exceptions
unspecifiedCan 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]indexZero-based frame index to access.
Returns
Frame reference to frame index.
Exceptions
APIErrorif 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::AnalysisDataAverageModule::pointsAdded ( const AnalysisDataPointSetRef points)
overridevirtual

Called one or more times during each data frame.

Parameters
[in]pointsSet of points added (also provides access to frame-level data).
Exceptions
APIErrorif the provided data is not compatible.
unspecifiedCan 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]nframesRequest 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.

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.

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

Sets the number of columns in the data array.

Parameters
[in]ncolsNumber of columns in the data.

Cannot be called after allocateValues().

See AbstractAnalysisData::setColumnCount() for exception behavior.

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

Sets the number of rows in the data array.

Parameters
[in]rowCountNumber 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]startx value for the first frame.
[in]stepStep 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]rowRow/frame for which to set the value.
[in]valuex value for the frame specified by row.

Must not be called after valuesReady().

Does not throw.

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.

AnalysisDataFrameRef gmx::AbstractAnalysisData::tryGetDataFrame ( int  index) const
inherited

Access stored data.

Parameters
[in]indexZero-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
unspecifiedAny 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: