Gromacs
2024.3
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#include <gromacs/analysisdata/analysisdata.h>
Parallelizable data container for raw data.
This is the main class used to implement parallelizable data processing in analysis tools. It is used by first creating an object and setting its properties using setDataSetCount(), setColumnCount() and setMultipoint(), and attaching necessary modules using addModule() etc. Then one or more AnalysisDataHandle objects can be created using startData(). Each data handle can then be independently used to provide data frames (each frame must be provided by a single handle, but different frames can be freely mixed between the handles). The finishFrameSerial() method must be called in serial for each frame, after one of the handles has been used to provide the data for that frame. When all data has been provided, the handles are destroyed using finishData() (or AnalysisDataHandle::finishData()).
When used through the trajectory analysis framework, calls to startData(), finishFrameSerial(), and finishData() are handled by the framework.
Public Member Functions | |
AnalysisData () | |
Creates an empty analysis data object. More... | |
void | setDataSetCount (int dataSetCount) |
Sets the number of data sets. More... | |
void | setColumnCount (int dataSet, int columnCount) |
Sets the number of columns in a data set. More... | |
void | setMultipoint (bool bMultipoint) |
Sets whether the data contains multiple points per column per frame. More... | |
int | frameCount () const override |
Returns the total number of frames in the data. More... | |
AnalysisDataHandle | startData (const AnalysisDataParallelOptions &opt) |
Creates a handle for adding data. More... | |
void | finishFrameSerial (int frameIndex) |
Performs in-order sequential processing for the next frame. More... | |
void | finishData (AnalysisDataHandle handle) |
Destroys a handle after all data has been added. 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... | |
gmx::AnalysisData::AnalysisData | ( | ) |
Creates an empty analysis data object.
std::bad_alloc | if out of memory. |
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inherited |
Adds a module that processes only a subset of the columns.
[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.
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inherited |
Adds a module to process the data.
module | Module to add. |
std::bad_alloc | if out of memory. |
APIError | if
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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.
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inherited |
Applies a module to process data that is ready.
module | Module to apply. |
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.
module
requests storage (addModule() has the same problem if called after data is started).
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inherited |
Returns the number of columns in a data set.
[in] | dataSet | Zero-based index of the data set to query. |
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.
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inherited |
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.
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inherited |
Returns the number of data sets in the data object.
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::AnalysisData::finishData | ( | AnalysisDataHandle | handle | ) |
Destroys a handle after all data has been added.
[in] | handle | Handle to destroy. |
unspecified | Any exception thrown by attached data modules in IAnalysisDataModule::dataFinished(). |
handle
must have been obtained from startData() of this object. The order of the calls with respect to the corresponding startData() calls is not important.
The handle
(and any copies) are invalid after the call.
void gmx::AnalysisData::finishFrameSerial | ( | int | frameIndex | ) |
Performs in-order sequential processing for the next frame.
[in] | frameIndex | Index of the frame that has been finished. |
unspecified | Any exception thrown by attached data modules in IAnalysisDataModule::frameFinishedSerial(). |
This method should be called sequentially for each frame, after data for that frame has been produced. It is not necessary to call this method if there is no parallelism, i.e., if only a single data handle is created and the parallelization options provided at that time do not indicate parallelism.
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overridevirtual |
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.
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inherited |
Access stored data.
[in] | index | Zero-based frame index to access. |
index
. APIError | if the requested frame is not accessible. |
If the data is not certainly available, use tryGetDataFrame().
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inherited |
Whether the data can have multiple points in the same column in the same frame.
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.
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inherited |
Request storage of frames.
[in] | nframes | Request storing at least nframes previous frames (-1 = request storing all). Must be >= -1. |
If called multiple times, the largest request is honored.
Does not throw. Failure to honor the request is indicated through the return value.
void gmx::AnalysisData::setColumnCount | ( | int | dataSet, |
int | columnCount | ||
) |
Sets the number of columns in a data set.
[in] | dataSet | Zero-based data set index. |
[in] | columnCount | Number of columns in the data (must be > 0). |
APIError | if modules have been added that are not compatible with the new column count. |
Must be called before startData() for each data set. Must not be called after startData() has been called. If called multiple times for a data set, the last call takes effect.
void gmx::AnalysisData::setDataSetCount | ( | int | dataSetCount | ) |
Sets the number of data sets.
[in] | dataSetCount | Number of data sets (must be > 0). |
std::bad_alloc | if out of memory. |
APIError | if modules have been added that are not compatible with the new data set count. |
Must not be called after startData() has been called. If not called, a single data set is assumed. If called multiple times, the last call takes effect.
void gmx::AnalysisData::setMultipoint | ( | bool | bMultipoint | ) |
Sets whether the data contains multiple points per column per frame.
[in] | bMultipoint | Whether the data will allow multiple points per column within a single frame. |
APIError | if modules have been added that are not compatible with the new setting. |
If this method is not called, the data is not multipoint.
Must not be called after startData() has been called.
AnalysisDataHandle gmx::AnalysisData::startData | ( | const AnalysisDataParallelOptions & | opt | ) |
Creates a handle for adding data.
[in] | opt | Options for setting how this handle will be used. |
std::bad_alloc | if out of memory. |
APIError | if any attached data module is not compatible. |
unspecified | Any exception thrown by attached data modules in IAnalysisDataModule::dataStarted(). |
The caller should retain the returned handle (or a copy of it), and pass it to finishData() after successfully adding all data. The caller should discard the returned handle if an error occurs; memory allocated for the handle will be freed when the AnalysisData object is destroyed.
The opt
options should be the same for all calls to this method, and the number of calls should match the parallelization factor defined in opt
.
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inherited |
Access stored data.
[in] | index | Zero-based frame index to access. |
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.