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/*! \file
* \brief
*
* \inpublicapi
* \ingroup module_analysisdata
- * \author Teemu Murtola <teemu.murtola@cbr.su.se>
+ * \author Teemu Murtola <teemu.murtola@gmail.com>
*/
#ifndef GMX_ANALYSISDATA_MODULES_PLOT_H
#define GMX_ANALYSISDATA_MODULES_PLOT_H
#include <string>
-#include "../datamodule.h"
+#include <boost/shared_ptr.hpp>
+
+#include "gromacs/analysisdata/datamodule.h"
+#include "gromacs/options/timeunitmanager.h"
+#include "gromacs/utility/common.h"
namespace gmx
{
+class AnalysisDataValue;
class Options;
+class SelectionCollection;
+
+/*! \brief
+ * Common settings for data plots.
+ *
+ * \inpublicapi
+ * \ingroup module_analysisdata
+ */
+class AnalysisDataPlotSettings
+{
+ public:
+ //! Constructs default analysis plot settings.
+ AnalysisDataPlotSettings();
+
+ //! Returns the selection collection set with setSelectionCollection().
+ const SelectionCollection *selectionCollection() const
+ {
+ return selections_;
+ }
+ //! Returns the time unit set with setTimeUnit().
+ TimeUnit timeUnit() const { return timeUnit_; }
+ /*! \brief
+ * Returns the plot format.
+ *
+ * \todo Use a proper enum.
+ */
+ int plotFormat() const { return plotFormat_; }
+
+ /*! \brief
+ * Set selection collection to print as comments into the output.
+ *
+ * Formatted selection text from all selections in \p selections is
+ * printed as comments in the output file.
+ * If this method is not called, no selection information is written
+ * to the output.
+ */
+ void setSelectionCollection(const SelectionCollection *selections);
+ /*! \brief
+ * Sets the time unit for the plot.
+ *
+ * The value is used only if AbstractPlotModule::setXAxisIsTime() is
+ * called, in which case it is used to print the appropriate axis label
+ * and to scale the values.
+ * If not called, the default time unit is ps.
+ */
+ void setTimeUnit(TimeUnit timeUnit) { timeUnit_ = timeUnit; }
+
+
+ /*! \brief
+ * Adds common options for setting plot options.
+ *
+ * \param[in,out] options Options object to which options are added.
+ */
+ void addOptions(Options *options);
+
+ private:
+ const SelectionCollection *selections_;
+ TimeUnit timeUnit_;
+ int plotFormat_;
+};
/*! \brief
* Abstract data module for writing data into a file.
* straightforward plotting).
*
* By default, the data is written into an xvgr file, according to the
- * options read from the Options object given to the constructor.
+ * options read from the AnalysisDataPlotSettings object given to the
+ * constructor.
* For non-xvgr data, it's possible to skip all headers by calling
* setPlainOutput().
*
- * Multipoint data is supported, in which case all the points are written to
- * the output, in the order in which they are added to the data. A single
- * output line corresponds to a single frame. In most cases with multipoint
- * data, setPlainOutput() should be called since the output does not make sense
- * as an xvgr file, but this is not enforced.
+ * A single output line corresponds to a single frame. In most cases with
+ * multipoint data, setPlainOutput() should be called since the output does not
+ * make sense as an xvgr file, but this is not enforced.
+ *
+ * Multipoint data and multiple data sets are both supported, in which case all
+ * the points are written to the output, in the order in which they are added
+ * to the data.
*
* \ingroup module_analysisdata
*/
-class AbstractPlotModule : public AnalysisDataModuleInterface
+class AbstractPlotModule : public AnalysisDataModuleSerial
{
public:
virtual ~AbstractPlotModule();
+ /*! \brief
+ * Set common settings for the plotting.
+ */
+ void setSettings(const AnalysisDataPlotSettings &settings);
/*! \brief
* Set the output file name.
*
- * If no file name is set (or if \p fnm is NULL), no output occurs.
+ * If no file name is set (or if \p filename is empty), no output occurs.
*/
- void setFileName(const std::string &fnm);
+ void setFileName(const std::string &filename);
/*! \brief
* Set plain output.
*
* methods have any effect on the output.
*/
void setPlainOutput(bool bPlain);
+ /*! \brief
+ * Plot errors as a separate output column after each value column.
+ */
+ void setErrorsAsSeparateColumn(bool bSeparate);
/*! \brief
* Omit the X coordinates from the output.
*
*/
void setXLabel(const char *label);
/*! \brief
- * Set X axis label for time.
+ * Treat X axis as time.
+ *
+ * Sets the label for the axis accordingly and also scales output to
+ * take into account the correct time unit.
*/
- void setXTimeLabel();
+ void setXAxisIsTime();
/*! \brief
* Set Y axis label.
*/
* together.
*/
void appendLegend(const char *setname);
+ //! \copydoc appendLegend(const char *)
+ void appendLegend(const std::string &setname);
/*! \brief
* Set field width and precision for X value output.
*/
- void setXFormat(int width, int prec, char fmt = 'f');
+ void setXFormat(int width, int precision, char format = 'f');
/*! \brief
* Set field width and precision for Y value output.
*/
- void setYFormat(int width, int prec, char fmt = 'f');
+ void setYFormat(int width, int precision, char format = 'f');
virtual int flags() const;
virtual void dataStarted(AbstractAnalysisData *data);
- virtual void frameStarted(real x, real dx);
- virtual void pointsAdded(real x, real dx, int firstcol, int n,
- const real *y, const real *dy,
- const bool *present) = 0;
- virtual void frameFinished();
+ virtual void frameStarted(const AnalysisDataFrameHeader &header);
+ virtual void pointsAdded(const AnalysisDataPointSetRef &points) = 0;
+ virtual void frameFinished(const AnalysisDataFrameHeader &header);
virtual void dataFinished();
protected:
/*! \cond libapi */
- explicit AbstractPlotModule(const Options &options);
+ AbstractPlotModule();
+ //! Creates AbstractPlotModule and assign common settings.
+ explicit AbstractPlotModule(const AnalysisDataPlotSettings &settings);
+ //! Whether an output file has been opened.
bool isFileOpen() const;
- void writeValue(real value) const;
+ /*! \brief
+ * Appends a single value to the current output line.
+ *
+ * \param[in] value Value to append.
+ *
+ * Should be used from pointsAdded() implementations in derived classes
+ * to write out individual y values to the output.
+ *
+ * Must not be called if isFileOpen() returns false.
+ */
+ void writeValue(const AnalysisDataValue &value) const;
//! \endcond
private:
class Impl;
- Impl *_impl;
-
- // Disallow copy and assign.
- AbstractPlotModule(const AbstractPlotModule &);
- void operator =(const AbstractPlotModule &);
+ PrivateImplPointer<Impl> impl_;
};
class AnalysisDataPlotModule : public AbstractPlotModule
{
public:
- explicit AnalysisDataPlotModule(const Options &options);
+ AnalysisDataPlotModule();
+ //! Creates AnalysisDataPlotModule and assign common settings.
+ explicit AnalysisDataPlotModule(const AnalysisDataPlotSettings &settings);
- virtual void pointsAdded(real x, real dx, int firstcol, int n,
- const real *y, const real *dy,
- const bool *present);
+ virtual void pointsAdded(const AnalysisDataPointSetRef &points);
// Copy and assign disallowed by base.
};
class AnalysisDataVectorPlotModule : public AbstractPlotModule
{
public:
- explicit AnalysisDataVectorPlotModule(const Options &options);
+ AnalysisDataVectorPlotModule();
+ //! Creates AnalysisDataVectorPlotModule and assign common settings.
+ explicit AnalysisDataVectorPlotModule(const AnalysisDataPlotSettings &settings);
/*! \brief
* Set whether to write X component.
*/
void setWriteMask(bool bWrite[4]);
- virtual void pointsAdded(real x, real dx, int firstcol, int n,
- const real *y, const real *dy,
- const bool *present);
+ virtual void pointsAdded(const AnalysisDataPointSetRef &points);
private:
- bool _bWrite[4];
+ bool bWrite_[4];
// Copy and assign disallowed by base.
};
+//! Smart pointer to manage an AnalysisDataPlotModule object.
+typedef boost::shared_ptr<AnalysisDataPlotModule>
+ AnalysisDataPlotModulePointer;
+//! Smart pointer to manage an AnalysisDataVectorPlotModule object.
+typedef boost::shared_ptr<AnalysisDataVectorPlotModule>
+ AnalysisDataVectorPlotModulePointer;
+
} // namespace gmx
#endif
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