Gromacs
2024.4
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#include <gromacs/analysisdata/modules/histogram.h>
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 | 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... | |
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protected |
Creates a histogram module with undefined bins.
Bin parameters must be defined with init() before data input is started.
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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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protectedinherited |
Allocates memory for the values.
std::bad_alloc | if memory allocation fails. |
setColumnCount() and setRowCount() must have been called.
Strong exception safety guarantee.
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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). AverageHistogramPointer gmx::AbstractAverageHistogram::clone | ( | ) | const |
Creates a deep copy of the histogram.
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.
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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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staticprotectedinherited |
Copies the contents into a new object.
[in] | src | Object to copy data from. |
[in,out] | dest | Empty array data object to copy data to. |
std::bad_alloc | if memory allocation for dest fails. |
dest
should not have previous contents.
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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.
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inline |
Notifies attached modules of the histogram data.
After this function has been called, it is no longer possible to alter the histogram.
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inlineoverridevirtualinherited |
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.
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.
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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.
AverageHistogramPointer gmx::AbstractAverageHistogram::resampleDoubleBinWidth | ( | bool | bIntegerBins | ) | const |
Creates a copy of the histogram with double the bin width.
[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. |
std::bad_alloc | if out of memory. |
The caller is responsible of deleting the returned object.
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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.
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protectedinherited |
Sets the number of columns in the data array.
[in] | ncols | Number of columns in the data. |
Cannot be called after allocateValues().
See AbstractAnalysisData::setColumnCount() for exception behavior.
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protectedinherited |
Sets the number of rows in the data array.
[in] | rowCount | Number of rows in the data. |
Cannot be called after allocateValues().
Does not throw.
Sets the values reported as x values for frames.
[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.
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protectedinherited |
Sets a single value reported as x value for frames.
[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.
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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.
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protectedinherited |
Notifies modules of the data.
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.