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37 * Implements classes in plot.h.
39 * \ingroup module_analysisdata
40 * \author Teemu Murtola <teemu.murtola@gmail.com>
52 #include <boost/shared_ptr.hpp>
54 #include "gromacs/analysisdata/dataframe.h"
55 #include "gromacs/fileio/gmxfio.h"
56 #include "gromacs/fileio/xvgr.h"
57 #include "gromacs/legacyheaders/oenv.h"
58 #include "gromacs/math/vec.h"
59 #include "gromacs/options/basicoptions.h"
60 #include "gromacs/options/ioptionscontainer.h"
61 #include "gromacs/options/timeunitmanager.h"
62 #include "gromacs/selection/selectioncollection.h"
63 #include "gromacs/utility/exceptions.h"
64 #include "gromacs/utility/gmxassert.h"
65 #include "gromacs/utility/programcontext.h"
66 #include "gromacs/utility/stringutil.h"
71 //! Enum values for plot formats.
72 const char *const g_plotFormats[] = {
73 "none", "xmgrace", "xmgr"
81 /********************************************************************
82 * AnalysisDataPlotSettings
85 AnalysisDataPlotSettings::AnalysisDataPlotSettings()
86 : selections_(NULL), timeUnit_(eTimeUnit_ps), plotFormat_(1)
91 AnalysisDataPlotSettings::setSelectionCollection(const SelectionCollection *selections)
93 selections_ = selections;
98 AnalysisDataPlotSettings::initOptions(IOptionsContainer *options)
100 options->addOption(StringOption("xvg").enumValue(g_plotFormats)
101 .defaultValue("xmgrace")
102 .storeEnumIndex(&plotFormat_)
103 .description("Plot formatting"));
107 /********************************************************************
108 * AbstractPlotModule::Impl
111 class AbstractPlotModule::Impl
114 explicit Impl(const AnalysisDataPlotSettings &settings);
119 AnalysisDataPlotSettings settings_;
120 std::string filename_;
125 bool bErrorsAsSeparateColumn_;
127 std::string subtitle_;
130 std::vector<std::string> legend_;
136 AbstractPlotModule::Impl::Impl(const AnalysisDataPlotSettings &settings)
137 : settings_(settings), fp_(NULL), bPlain_(false), bOmitX_(false),
138 bErrorsAsSeparateColumn_(false), xscale_(1.0)
140 strcpy(xformat_, "%11.3f");
141 strcpy(yformat_, " %8.3f");
144 AbstractPlotModule::Impl::~Impl()
151 AbstractPlotModule::Impl::closeFile()
168 /********************************************************************
172 AbstractPlotModule::AbstractPlotModule()
173 : impl_(new Impl(AnalysisDataPlotSettings()))
177 AbstractPlotModule::AbstractPlotModule(const AnalysisDataPlotSettings &settings)
178 : impl_(new Impl(settings))
183 AbstractPlotModule::~AbstractPlotModule()
189 AbstractPlotModule::setSettings(const AnalysisDataPlotSettings &settings)
191 impl_->settings_ = settings;
196 AbstractPlotModule::setFileName(const std::string &filename)
198 impl_->filename_ = filename;
203 AbstractPlotModule::setPlainOutput(bool bPlain)
205 impl_->bPlain_ = bPlain;
210 AbstractPlotModule::setErrorsAsSeparateColumn(bool bSeparate)
212 impl_->bErrorsAsSeparateColumn_ = bSeparate;
217 AbstractPlotModule::setOmitX(bool bOmitX)
219 impl_->bOmitX_ = bOmitX;
224 AbstractPlotModule::setTitle(const char *title)
226 impl_->title_ = title;
230 AbstractPlotModule::setTitle(const std::string &title)
232 impl_->title_ = title;
237 AbstractPlotModule::setSubtitle(const char *subtitle)
239 impl_->subtitle_ = subtitle;
244 AbstractPlotModule::setSubtitle(const std::string &subtitle)
246 impl_->subtitle_ = subtitle;
251 AbstractPlotModule::setXLabel(const char *label)
253 impl_->xlabel_ = label;
258 AbstractPlotModule::setXAxisIsTime()
260 TimeUnitManager manager(impl_->settings_.timeUnit());
261 impl_->xlabel_ = formatString("Time (%s)", manager.timeUnitAsString());
262 impl_->xscale_ = manager.inverseTimeScaleFactor();
267 AbstractPlotModule::setYLabel(const char *label)
269 impl_->ylabel_ = label;
274 AbstractPlotModule::setLegend(int nsets, const char * const *setname)
276 impl_->legend_.reserve(impl_->legend_.size() + nsets);
277 for (int i = 0; i < nsets; ++i)
279 appendLegend(setname[i]);
285 AbstractPlotModule::appendLegend(const char *setname)
287 impl_->legend_.push_back(setname);
292 AbstractPlotModule::appendLegend(const std::string &setname)
294 impl_->legend_.push_back(setname);
299 AbstractPlotModule::setXFormat(int width, int precision, char format)
301 GMX_RELEASE_ASSERT(width >= 0 && precision >= 0
302 && width <= 99 && precision <= 99,
303 "Invalid width or precision");
304 GMX_RELEASE_ASSERT(strchr("eEfFgG", format) != NULL,
305 "Invalid format specifier");
306 sprintf(impl_->xformat_, "%%%d.%d%c", width, precision, format);
311 AbstractPlotModule::setYFormat(int width, int precision, char format)
313 GMX_RELEASE_ASSERT(width >= 0 && precision >= 0
314 && width <= 99 && precision <= 99,
315 "Invalid width or precision");
316 GMX_RELEASE_ASSERT(strchr("eEfFgG", format) != NULL,
317 "Invalid format specifier");
318 sprintf(impl_->yformat_, " %%%d.%d%c", width, precision, format);
323 AbstractPlotModule::flags() const
325 return efAllowMissing | efAllowMulticolumn | efAllowMultipoint
326 | efAllowMultipleDataSets;
331 AbstractPlotModule::dataStarted(AbstractAnalysisData * /* data */)
333 if (!impl_->filename_.empty())
337 impl_->fp_ = gmx_fio_fopen(impl_->filename_.c_str(), "w");
341 time_unit_t time_unit
342 = static_cast<time_unit_t>(impl_->settings_.timeUnit() + 1);
343 xvg_format_t xvg_format
344 = (impl_->settings_.plotFormat() > 0
345 ? static_cast<xvg_format_t>(impl_->settings_.plotFormat())
348 output_env_init(&oenv, getProgramContext(), time_unit, FALSE, xvg_format, 0);
349 boost::shared_ptr<output_env> oenvGuard(oenv, &output_env_done);
350 impl_->fp_ = xvgropen(impl_->filename_.c_str(), impl_->title_.c_str(),
351 impl_->xlabel_.c_str(), impl_->ylabel_.c_str(),
353 const SelectionCollection *selections
354 = impl_->settings_.selectionCollection();
355 if (selections != NULL)
357 selections->printXvgrInfo(impl_->fp_, oenv);
359 if (!impl_->subtitle_.empty())
361 xvgr_subtitle(impl_->fp_, impl_->subtitle_.c_str(), oenv);
363 if (output_env_get_print_xvgr_codes(oenv)
364 && !impl_->legend_.empty())
366 std::vector<const char *> legend;
367 legend.reserve(impl_->legend_.size());
368 for (size_t i = 0; i < impl_->legend_.size(); ++i)
370 legend.push_back(impl_->legend_[i].c_str());
372 xvgr_legend(impl_->fp_, legend.size(), &legend[0], oenv);
380 AbstractPlotModule::frameStarted(const AnalysisDataFrameHeader &frame)
388 std::fprintf(impl_->fp_, impl_->xformat_, frame.x() * impl_->xscale_);
394 AbstractPlotModule::frameFinished(const AnalysisDataFrameHeader & /*header*/)
400 std::fprintf(impl_->fp_, "\n");
405 AbstractPlotModule::dataFinished()
412 AbstractPlotModule::isFileOpen() const
414 return impl_->fp_ != NULL;
419 AbstractPlotModule::writeValue(const AnalysisDataValue &value) const
421 GMX_ASSERT(isFileOpen(), "File not opened, but write attempted");
422 const real y = value.isSet() ? value.value() : 0.0;
423 std::fprintf(impl_->fp_, impl_->yformat_, y);
424 if (impl_->bErrorsAsSeparateColumn_)
426 const real dy = value.isSet() ? value.error() : 0.0;
427 std::fprintf(impl_->fp_, impl_->yformat_, dy);
432 /********************************************************************
436 AnalysisDataPlotModule::AnalysisDataPlotModule()
440 AnalysisDataPlotModule::AnalysisDataPlotModule(
441 const AnalysisDataPlotSettings &settings)
442 : AbstractPlotModule(settings)
448 AnalysisDataPlotModule::pointsAdded(const AnalysisDataPointSetRef &points)
454 for (int i = 0; i < points.columnCount(); ++i)
456 writeValue(points.values()[i]);
461 /********************************************************************
462 * DataVectorPlotModule
465 AnalysisDataVectorPlotModule::AnalysisDataVectorPlotModule()
467 for (int i = 0; i < DIM; ++i)
471 bWrite_[DIM] = false;
475 AnalysisDataVectorPlotModule::AnalysisDataVectorPlotModule(
476 const AnalysisDataPlotSettings &settings)
477 : AbstractPlotModule(settings)
479 for (int i = 0; i < DIM; ++i)
483 bWrite_[DIM] = false;
488 AnalysisDataVectorPlotModule::setWriteX(bool bWrite)
490 bWrite_[XX] = bWrite;
495 AnalysisDataVectorPlotModule::setWriteY(bool bWrite)
497 bWrite_[YY] = bWrite;
502 AnalysisDataVectorPlotModule::setWriteZ(bool bWrite)
504 bWrite_[ZZ] = bWrite;
509 AnalysisDataVectorPlotModule::setWriteNorm(bool bWrite)
511 bWrite_[DIM] = bWrite;
516 AnalysisDataVectorPlotModule::setWriteMask(bool bWrite[DIM + 1])
518 for (int i = 0; i < DIM + 1; ++i)
520 bWrite_[i] = bWrite[i];
526 AnalysisDataVectorPlotModule::pointsAdded(const AnalysisDataPointSetRef &points)
528 if (points.firstColumn() % DIM != 0 || points.columnCount() % DIM != 0)
530 GMX_THROW(APIError("Partial data points"));
536 for (int i = 0; i < points.columnCount(); i += 3)
538 for (int d = 0; d < DIM; ++d)
542 writeValue(points.values()[i + d]);
547 const rvec y = { points.y(i), points.y(i + 1), points.y(i + 2) };
548 AnalysisDataValue value(norm(y));