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gmx::AnalysisDataWeightedHistogramModule Class Reference

#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 colums, 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...
 
AbstractAverageHistogramaverager ()
 Returns the average histogram over all frames. More...
 
const AnalysisHistogramSettingssettings () const
 Returns bin properties for the histogram. More...
 
virtual int frameCount () const
 Returns the total number of frames in the data. More...
 
virtual int flags () const
 Returns properties supported by the module. More...
 
virtual bool parallelDataStarted (AbstractAnalysisData *data, const AnalysisDataParallelOptions &options)
 Called (once) for parallel data when the data has been set up. More...
 
virtual void frameStarted (const AnalysisDataFrameHeader &header)
 Called at the start of each data frame. More...
 
virtual void pointsAdded (const AnalysisDataPointSetRef &points)
 Called one or more times during each data frame. More...
 
virtual void frameFinished (const AnalysisDataFrameHeader &header)
 Called when a data frame is finished. More...
 
virtual void frameFinishedSerial (int frameIndex)
 Called in sequential order for each frame after they are finished. More...
 
virtual void dataFinished ()
 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 (AnalysisDataModulePointer module)
 Adds a module to process the data. More...
 
void addColumnModule (int col, int span, 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

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...
 
AnalysisDataModuleManagermoduleManager ()
 Returns the module manager to use for calling notification methods.
 
const AnalysisDataModuleManagermoduleManager () const
 Returns the module manager to use for calling notification methods.
 

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.

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,
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 ( 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::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).
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]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. 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::AnalysisDataWeightedHistogramModule::dataFinished ( )
virtual

Called (once) when no more data is available.

Exceptions
unspecifiedCan 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. Derived classes should set the number of columns with setDataSetCount(), within the above limitations.

Does not throw.

int gmx::AnalysisDataWeightedHistogramModule::flags ( ) const
virtual

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
virtual

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::AnalysisDataWeightedHistogramModule::frameFinished ( const AnalysisDataFrameHeader header)
virtual

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::AnalysisDataModuleParallel.

void gmx::AnalysisDataWeightedHistogramModule::frameFinishedSerial ( int  frameIndex)
virtual

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

Parameters
[in]frameIndexIndex of the next finished frame.
Exceptions
unspecifiedCan 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 downsteam 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)
virtual

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::AnalysisDataModuleParallel.

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()
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. 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.

bool gmx::AnalysisDataWeightedHistogramModule::parallelDataStarted ( AbstractAnalysisData data,
const AnalysisDataParallelOptions options 
)
virtual

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

Parameters
[in]dataData object to which the module is added.
[in]optionsParallelization properties of the input data.
Returns
true if the module can process the input in non-sequential order.
Exceptions
APIErrorif the provided data is not compatible.
unspecifiedCan 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)
virtual

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::AnalysisDataModuleParallel.

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

Sets the number of columns for a data set.

Parameters
[in]dataSetZero-based index of the data set.
[in]columnCountNumber of columns in dataSet (must be > 0).
Exceptions
APIErrorif 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]dataSetCountNumber of data sets (must be > 0).
Exceptions
std::bad_allocif out of memory.
APIErrorif 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]bMultipointWhether multiple points per column are possible.
Exceptions
APIErrorif 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()
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]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()

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