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37 * Implements classes in plot.h.
39 * \ingroup module_analysisdata
40 * \author Teemu Murtola <teemu.murtola@gmail.com>
42 #include "gromacs/analysisdata/modules/plot.h"
50 #include <boost/shared_ptr.hpp>
52 #include "gromacs/fileio/gmxfio.h"
53 #include "gromacs/legacyheaders/oenv.h"
54 #include "gromacs/legacyheaders/vec.h"
55 #include "gromacs/legacyheaders/xvgr.h"
57 #include "gromacs/analysisdata/dataframe.h"
58 #include "gromacs/options/basicoptions.h"
59 #include "gromacs/options/options.h"
60 #include "gromacs/options/timeunitmanager.h"
61 #include "gromacs/selection/selectioncollection.h"
62 #include "gromacs/utility/exceptions.h"
63 #include "gromacs/utility/gmxassert.h"
64 #include "gromacs/utility/stringutil.h"
69 //! Enum values for plot formats.
70 const char *const g_plotFormats[] = {
71 "none", "xmgrace", "xmgr"
79 /********************************************************************
80 * AnalysisDataPlotSettings
83 AnalysisDataPlotSettings::AnalysisDataPlotSettings()
84 : selections_(NULL), timeUnit_(eTimeUnit_ps), plotFormat_(1)
89 AnalysisDataPlotSettings::setSelectionCollection(const SelectionCollection *selections)
91 selections_ = selections;
96 AnalysisDataPlotSettings::addOptions(Options *options)
98 options->addOption(StringOption("xvg").enumValue(g_plotFormats)
99 .defaultValue("xmgrace")
100 .storeEnumIndex(&plotFormat_)
101 .description("Plot formatting"));
105 /********************************************************************
106 * AbstractPlotModule::Impl
109 class AbstractPlotModule::Impl
112 explicit Impl(const AnalysisDataPlotSettings &settings);
117 AnalysisDataPlotSettings settings_;
118 std::string filename_;
123 bool bErrorsAsSeparateColumn_;
125 std::string subtitle_;
128 std::vector<std::string> legend_;
134 AbstractPlotModule::Impl::Impl(const AnalysisDataPlotSettings &settings)
135 : settings_(settings), fp_(NULL), bPlain_(false), bOmitX_(false),
136 bErrorsAsSeparateColumn_(false), xscale_(1.0)
138 strcpy(xformat_, "%11.3f");
139 strcpy(yformat_, " %8.3f");
142 AbstractPlotModule::Impl::~Impl()
149 AbstractPlotModule::Impl::closeFile()
166 /********************************************************************
170 AbstractPlotModule::AbstractPlotModule()
171 : impl_(new Impl(AnalysisDataPlotSettings()))
175 AbstractPlotModule::AbstractPlotModule(const AnalysisDataPlotSettings &settings)
176 : impl_(new Impl(settings))
181 AbstractPlotModule::~AbstractPlotModule()
187 AbstractPlotModule::setSettings(const AnalysisDataPlotSettings &settings)
189 impl_->settings_ = settings;
194 AbstractPlotModule::setFileName(const std::string &filename)
196 impl_->filename_ = filename;
201 AbstractPlotModule::setPlainOutput(bool bPlain)
203 impl_->bPlain_ = bPlain;
208 AbstractPlotModule::setErrorsAsSeparateColumn(bool bSeparate)
210 impl_->bErrorsAsSeparateColumn_ = bSeparate;
215 AbstractPlotModule::setOmitX(bool bOmitX)
217 impl_->bOmitX_ = bOmitX;
222 AbstractPlotModule::setTitle(const char *title)
224 impl_->title_ = title;
229 AbstractPlotModule::setSubtitle(const char *subtitle)
231 impl_->subtitle_ = subtitle;
236 AbstractPlotModule::setXLabel(const char *label)
238 impl_->xlabel_ = label;
243 AbstractPlotModule::setXAxisIsTime()
245 TimeUnitManager manager(impl_->settings_.timeUnit());
246 impl_->xlabel_ = formatString("Time (%s)", manager.timeUnitAsString());
247 impl_->xscale_ = manager.inverseTimeScaleFactor();
252 AbstractPlotModule::setYLabel(const char *label)
254 impl_->ylabel_ = label;
259 AbstractPlotModule::setLegend(int nsets, const char * const *setname)
261 impl_->legend_.reserve(impl_->legend_.size() + nsets);
262 for (int i = 0; i < nsets; ++i)
264 appendLegend(setname[i]);
270 AbstractPlotModule::appendLegend(const char *setname)
272 impl_->legend_.push_back(setname);
277 AbstractPlotModule::appendLegend(const std::string &setname)
279 impl_->legend_.push_back(setname);
284 AbstractPlotModule::setXFormat(int width, int precision, char format)
286 GMX_RELEASE_ASSERT(width >= 0 && precision >= 0
287 && width <= 99 && precision <= 99,
288 "Invalid width or precision");
289 GMX_RELEASE_ASSERT(strchr("eEfFgG", format) != NULL,
290 "Invalid format specifier");
291 sprintf(impl_->xformat_, "%%%d.%d%c", width, precision, format);
296 AbstractPlotModule::setYFormat(int width, int precision, char format)
298 GMX_RELEASE_ASSERT(width >= 0 && precision >= 0
299 && width <= 99 && precision <= 99,
300 "Invalid width or precision");
301 GMX_RELEASE_ASSERT(strchr("eEfFgG", format) != NULL,
302 "Invalid format specifier");
303 sprintf(impl_->yformat_, " %%%d.%d%c", width, precision, format);
308 AbstractPlotModule::flags() const
310 return efAllowMissing | efAllowMulticolumn | efAllowMultipoint
311 | efAllowMultipleDataSets;
316 AbstractPlotModule::dataStarted(AbstractAnalysisData * /*data*/)
318 if (!impl_->filename_.empty())
322 impl_->fp_ = gmx_fio_fopen(impl_->filename_.c_str(), "w");
326 time_unit_t time_unit
327 = static_cast<time_unit_t>(impl_->settings_.timeUnit() + 1);
328 xvg_format_t xvg_format
329 = (impl_->settings_.plotFormat() > 0
330 ? static_cast<xvg_format_t>(impl_->settings_.plotFormat())
333 output_env_init(&oenv, 0, NULL, time_unit, FALSE, xvg_format, 0, 0);
334 boost::shared_ptr<output_env> oenvGuard(oenv, &output_env_done);
335 impl_->fp_ = xvgropen(impl_->filename_.c_str(), impl_->title_.c_str(),
336 impl_->xlabel_.c_str(), impl_->ylabel_.c_str(),
338 const SelectionCollection *selections
339 = impl_->settings_.selectionCollection();
340 if (selections != NULL)
342 selections->printXvgrInfo(impl_->fp_, oenv);
344 if (!impl_->subtitle_.empty())
346 xvgr_subtitle(impl_->fp_, impl_->subtitle_.c_str(), oenv);
348 if (output_env_get_print_xvgr_codes(oenv)
349 && !impl_->legend_.empty())
351 std::vector<const char *> legend;
352 legend.reserve(impl_->legend_.size());
353 for (size_t i = 0; i < impl_->legend_.size(); ++i)
355 legend.push_back(impl_->legend_[i].c_str());
357 xvgr_legend(impl_->fp_, legend.size(), &legend[0], oenv);
365 AbstractPlotModule::frameStarted(const AnalysisDataFrameHeader &frame)
373 std::fprintf(impl_->fp_, impl_->xformat_, frame.x() * impl_->xscale_);
379 AbstractPlotModule::frameFinished(const AnalysisDataFrameHeader & /*header*/)
385 std::fprintf(impl_->fp_, "\n");
390 AbstractPlotModule::dataFinished()
397 AbstractPlotModule::isFileOpen() const
399 return impl_->fp_ != NULL;
404 AbstractPlotModule::writeValue(const AnalysisDataValue &value) const
406 GMX_ASSERT(isFileOpen(), "File not opened, but write attempted");
407 const real y = value.isSet() ? value.value() : 0.0;
408 std::fprintf(impl_->fp_, impl_->yformat_, y);
409 if (impl_->bErrorsAsSeparateColumn_)
411 const real dy = value.isSet() ? value.error() : 0.0;
412 std::fprintf(impl_->fp_, impl_->yformat_, dy);
417 /********************************************************************
421 AnalysisDataPlotModule::AnalysisDataPlotModule()
425 AnalysisDataPlotModule::AnalysisDataPlotModule(
426 const AnalysisDataPlotSettings &settings)
427 : AbstractPlotModule(settings)
433 AnalysisDataPlotModule::pointsAdded(const AnalysisDataPointSetRef &points)
439 for (int i = 0; i < points.columnCount(); ++i)
441 writeValue(points.values()[i]);
446 /********************************************************************
447 * DataVectorPlotModule
450 AnalysisDataVectorPlotModule::AnalysisDataVectorPlotModule()
452 for (int i = 0; i < DIM; ++i)
456 bWrite_[DIM] = false;
460 AnalysisDataVectorPlotModule::AnalysisDataVectorPlotModule(
461 const AnalysisDataPlotSettings &settings)
462 : AbstractPlotModule(settings)
464 for (int i = 0; i < DIM; ++i)
468 bWrite_[DIM] = false;
473 AnalysisDataVectorPlotModule::setWriteX(bool bWrite)
475 bWrite_[XX] = bWrite;
480 AnalysisDataVectorPlotModule::setWriteY(bool bWrite)
482 bWrite_[YY] = bWrite;
487 AnalysisDataVectorPlotModule::setWriteZ(bool bWrite)
489 bWrite_[ZZ] = bWrite;
494 AnalysisDataVectorPlotModule::setWriteNorm(bool bWrite)
496 bWrite_[DIM] = bWrite;
501 AnalysisDataVectorPlotModule::setWriteMask(bool bWrite[DIM + 1])
503 for (int i = 0; i < DIM + 1; ++i)
505 bWrite_[i] = bWrite[i];
511 AnalysisDataVectorPlotModule::pointsAdded(const AnalysisDataPointSetRef &points)
513 if (points.firstColumn() % DIM != 0 || points.columnCount() % DIM != 0)
515 GMX_THROW(APIError("Partial data points"));
521 for (int i = 0; i < points.columnCount(); i += 3)
523 for (int d = 0; d < DIM; ++d)
527 writeValue(points.values()[i + d]);
532 const rvec y = { points.y(i), points.y(i + 1), points.y(i + 2) };
533 AnalysisDataValue value(norm(y));