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37 * Implements classes in plot.h.
39 * \ingroup module_analysisdata
40 * \author Teemu Murtola <teemu.murtola@gmail.com>
44 #include "gromacs/analysisdata/modules/plot.h"
52 #include <boost/shared_ptr.hpp>
54 #include "gromacs/legacyheaders/oenv.h"
56 #include "gromacs/analysisdata/dataframe.h"
57 #include "gromacs/fileio/gmxfio.h"
58 #include "gromacs/fileio/xvgr.h"
59 #include "gromacs/math/vec.h"
60 #include "gromacs/options/basicoptions.h"
61 #include "gromacs/options/options.h"
62 #include "gromacs/options/timeunitmanager.h"
63 #include "gromacs/selection/selectioncollection.h"
64 #include "gromacs/utility/exceptions.h"
65 #include "gromacs/utility/gmxassert.h"
66 #include "gromacs/utility/programcontext.h"
67 #include "gromacs/utility/stringutil.h"
72 //! Enum values for plot formats.
73 const char *const g_plotFormats[] = {
74 "none", "xmgrace", "xmgr"
82 /********************************************************************
83 * AnalysisDataPlotSettings
86 AnalysisDataPlotSettings::AnalysisDataPlotSettings()
87 : selections_(NULL), timeUnit_(eTimeUnit_ps), plotFormat_(1)
92 AnalysisDataPlotSettings::setSelectionCollection(const SelectionCollection *selections)
94 selections_ = selections;
99 AnalysisDataPlotSettings::addOptions(Options *options)
101 options->addOption(StringOption("xvg").enumValue(g_plotFormats)
102 .defaultValue("xmgrace")
103 .storeEnumIndex(&plotFormat_)
104 .description("Plot formatting"));
108 /********************************************************************
109 * AbstractPlotModule::Impl
112 class AbstractPlotModule::Impl
115 explicit Impl(const AnalysisDataPlotSettings &settings);
120 AnalysisDataPlotSettings settings_;
121 std::string filename_;
126 bool bErrorsAsSeparateColumn_;
128 std::string subtitle_;
131 std::vector<std::string> legend_;
137 AbstractPlotModule::Impl::Impl(const AnalysisDataPlotSettings &settings)
138 : settings_(settings), fp_(NULL), bPlain_(false), bOmitX_(false),
139 bErrorsAsSeparateColumn_(false), xscale_(1.0)
141 strcpy(xformat_, "%11.3f");
142 strcpy(yformat_, " %8.3f");
145 AbstractPlotModule::Impl::~Impl()
152 AbstractPlotModule::Impl::closeFile()
169 /********************************************************************
173 AbstractPlotModule::AbstractPlotModule()
174 : impl_(new Impl(AnalysisDataPlotSettings()))
178 AbstractPlotModule::AbstractPlotModule(const AnalysisDataPlotSettings &settings)
179 : impl_(new Impl(settings))
184 AbstractPlotModule::~AbstractPlotModule()
190 AbstractPlotModule::setSettings(const AnalysisDataPlotSettings &settings)
192 impl_->settings_ = settings;
197 AbstractPlotModule::setFileName(const std::string &filename)
199 impl_->filename_ = filename;
204 AbstractPlotModule::setPlainOutput(bool bPlain)
206 impl_->bPlain_ = bPlain;
211 AbstractPlotModule::setErrorsAsSeparateColumn(bool bSeparate)
213 impl_->bErrorsAsSeparateColumn_ = bSeparate;
218 AbstractPlotModule::setOmitX(bool bOmitX)
220 impl_->bOmitX_ = bOmitX;
225 AbstractPlotModule::setTitle(const char *title)
227 impl_->title_ = title;
232 AbstractPlotModule::setSubtitle(const char *subtitle)
234 impl_->subtitle_ = subtitle;
239 AbstractPlotModule::setXLabel(const char *label)
241 impl_->xlabel_ = label;
246 AbstractPlotModule::setXAxisIsTime()
248 TimeUnitManager manager(impl_->settings_.timeUnit());
249 impl_->xlabel_ = formatString("Time (%s)", manager.timeUnitAsString());
250 impl_->xscale_ = manager.inverseTimeScaleFactor();
255 AbstractPlotModule::setYLabel(const char *label)
257 impl_->ylabel_ = label;
262 AbstractPlotModule::setLegend(int nsets, const char * const *setname)
264 impl_->legend_.reserve(impl_->legend_.size() + nsets);
265 for (int i = 0; i < nsets; ++i)
267 appendLegend(setname[i]);
273 AbstractPlotModule::appendLegend(const char *setname)
275 impl_->legend_.push_back(setname);
280 AbstractPlotModule::appendLegend(const std::string &setname)
282 impl_->legend_.push_back(setname);
287 AbstractPlotModule::setXFormat(int width, int precision, char format)
289 GMX_RELEASE_ASSERT(width >= 0 && precision >= 0
290 && width <= 99 && precision <= 99,
291 "Invalid width or precision");
292 GMX_RELEASE_ASSERT(strchr("eEfFgG", format) != NULL,
293 "Invalid format specifier");
294 sprintf(impl_->xformat_, "%%%d.%d%c", width, precision, format);
299 AbstractPlotModule::setYFormat(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_->yformat_, " %%%d.%d%c", width, precision, format);
311 AbstractPlotModule::flags() const
313 return efAllowMissing | efAllowMulticolumn | efAllowMultipoint
314 | efAllowMultipleDataSets;
319 AbstractPlotModule::dataStarted(AbstractAnalysisData * /* data */)
321 if (!impl_->filename_.empty())
325 impl_->fp_ = gmx_fio_fopen(impl_->filename_.c_str(), "w");
329 time_unit_t time_unit
330 = static_cast<time_unit_t>(impl_->settings_.timeUnit() + 1);
331 xvg_format_t xvg_format
332 = (impl_->settings_.plotFormat() > 0
333 ? static_cast<xvg_format_t>(impl_->settings_.plotFormat())
336 output_env_init(&oenv, getProgramContext(), time_unit, FALSE, xvg_format, 0);
337 boost::shared_ptr<output_env> oenvGuard(oenv, &output_env_done);
338 impl_->fp_ = xvgropen(impl_->filename_.c_str(), impl_->title_.c_str(),
339 impl_->xlabel_.c_str(), impl_->ylabel_.c_str(),
341 const SelectionCollection *selections
342 = impl_->settings_.selectionCollection();
343 if (selections != NULL)
345 selections->printXvgrInfo(impl_->fp_, oenv);
347 if (!impl_->subtitle_.empty())
349 xvgr_subtitle(impl_->fp_, impl_->subtitle_.c_str(), oenv);
351 if (output_env_get_print_xvgr_codes(oenv)
352 && !impl_->legend_.empty())
354 std::vector<const char *> legend;
355 legend.reserve(impl_->legend_.size());
356 for (size_t i = 0; i < impl_->legend_.size(); ++i)
358 legend.push_back(impl_->legend_[i].c_str());
360 xvgr_legend(impl_->fp_, legend.size(), &legend[0], oenv);
368 AbstractPlotModule::frameStarted(const AnalysisDataFrameHeader &frame)
376 std::fprintf(impl_->fp_, impl_->xformat_, frame.x() * impl_->xscale_);
382 AbstractPlotModule::frameFinished(const AnalysisDataFrameHeader & /*header*/)
388 std::fprintf(impl_->fp_, "\n");
393 AbstractPlotModule::dataFinished()
400 AbstractPlotModule::isFileOpen() const
402 return impl_->fp_ != NULL;
407 AbstractPlotModule::writeValue(const AnalysisDataValue &value) const
409 GMX_ASSERT(isFileOpen(), "File not opened, but write attempted");
410 const real y = value.isSet() ? value.value() : 0.0;
411 std::fprintf(impl_->fp_, impl_->yformat_, y);
412 if (impl_->bErrorsAsSeparateColumn_)
414 const real dy = value.isSet() ? value.error() : 0.0;
415 std::fprintf(impl_->fp_, impl_->yformat_, dy);
420 /********************************************************************
424 AnalysisDataPlotModule::AnalysisDataPlotModule()
428 AnalysisDataPlotModule::AnalysisDataPlotModule(
429 const AnalysisDataPlotSettings &settings)
430 : AbstractPlotModule(settings)
436 AnalysisDataPlotModule::pointsAdded(const AnalysisDataPointSetRef &points)
442 for (int i = 0; i < points.columnCount(); ++i)
444 writeValue(points.values()[i]);
449 /********************************************************************
450 * DataVectorPlotModule
453 AnalysisDataVectorPlotModule::AnalysisDataVectorPlotModule()
455 for (int i = 0; i < DIM; ++i)
459 bWrite_[DIM] = false;
463 AnalysisDataVectorPlotModule::AnalysisDataVectorPlotModule(
464 const AnalysisDataPlotSettings &settings)
465 : AbstractPlotModule(settings)
467 for (int i = 0; i < DIM; ++i)
471 bWrite_[DIM] = false;
476 AnalysisDataVectorPlotModule::setWriteX(bool bWrite)
478 bWrite_[XX] = bWrite;
483 AnalysisDataVectorPlotModule::setWriteY(bool bWrite)
485 bWrite_[YY] = bWrite;
490 AnalysisDataVectorPlotModule::setWriteZ(bool bWrite)
492 bWrite_[ZZ] = bWrite;
497 AnalysisDataVectorPlotModule::setWriteNorm(bool bWrite)
499 bWrite_[DIM] = bWrite;
504 AnalysisDataVectorPlotModule::setWriteMask(bool bWrite[DIM + 1])
506 for (int i = 0; i < DIM + 1; ++i)
508 bWrite_[i] = bWrite[i];
514 AnalysisDataVectorPlotModule::pointsAdded(const AnalysisDataPointSetRef &points)
516 if (points.firstColumn() % DIM != 0 || points.columnCount() % DIM != 0)
518 GMX_THROW(APIError("Partial data points"));
524 for (int i = 0; i < points.columnCount(); i += 3)
526 for (int d = 0; d < DIM; ++d)
530 writeValue(points.values()[i + d]);
535 const rvec y = { points.y(i), points.y(i + 1), points.y(i + 2) };
536 AnalysisDataValue value(norm(y));