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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/legacyheaders/oenv.h"
54 #include "gromacs/analysisdata/dataframe.h"
55 #include "gromacs/fileio/gmxfio.h"
56 #include "gromacs/fileio/xvgr.h"
57 #include "gromacs/math/vec.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/programcontext.h"
65 #include "gromacs/utility/stringutil.h"
70 //! Enum values for plot formats.
71 const char *const g_plotFormats[] = {
72 "none", "xmgrace", "xmgr"
80 /********************************************************************
81 * AnalysisDataPlotSettings
84 AnalysisDataPlotSettings::AnalysisDataPlotSettings()
85 : selections_(NULL), timeUnit_(eTimeUnit_ps), plotFormat_(1)
90 AnalysisDataPlotSettings::setSelectionCollection(const SelectionCollection *selections)
92 selections_ = selections;
97 AnalysisDataPlotSettings::addOptions(Options *options)
99 options->addOption(StringOption("xvg").enumValue(g_plotFormats)
100 .defaultValue("xmgrace")
101 .storeEnumIndex(&plotFormat_)
102 .description("Plot formatting"));
106 /********************************************************************
107 * AbstractPlotModule::Impl
110 class AbstractPlotModule::Impl
113 explicit Impl(const AnalysisDataPlotSettings &settings);
118 AnalysisDataPlotSettings settings_;
119 std::string filename_;
124 bool bErrorsAsSeparateColumn_;
126 std::string subtitle_;
129 std::vector<std::string> legend_;
135 AbstractPlotModule::Impl::Impl(const AnalysisDataPlotSettings &settings)
136 : settings_(settings), fp_(NULL), bPlain_(false), bOmitX_(false),
137 bErrorsAsSeparateColumn_(false), xscale_(1.0)
139 strcpy(xformat_, "%11.3f");
140 strcpy(yformat_, " %8.3f");
143 AbstractPlotModule::Impl::~Impl()
150 AbstractPlotModule::Impl::closeFile()
167 /********************************************************************
171 AbstractPlotModule::AbstractPlotModule()
172 : impl_(new Impl(AnalysisDataPlotSettings()))
176 AbstractPlotModule::AbstractPlotModule(const AnalysisDataPlotSettings &settings)
177 : impl_(new Impl(settings))
182 AbstractPlotModule::~AbstractPlotModule()
188 AbstractPlotModule::setSettings(const AnalysisDataPlotSettings &settings)
190 impl_->settings_ = settings;
195 AbstractPlotModule::setFileName(const std::string &filename)
197 impl_->filename_ = filename;
202 AbstractPlotModule::setPlainOutput(bool bPlain)
204 impl_->bPlain_ = bPlain;
209 AbstractPlotModule::setErrorsAsSeparateColumn(bool bSeparate)
211 impl_->bErrorsAsSeparateColumn_ = bSeparate;
216 AbstractPlotModule::setOmitX(bool bOmitX)
218 impl_->bOmitX_ = bOmitX;
223 AbstractPlotModule::setTitle(const char *title)
225 impl_->title_ = title;
230 AbstractPlotModule::setSubtitle(const char *subtitle)
232 impl_->subtitle_ = subtitle;
237 AbstractPlotModule::setXLabel(const char *label)
239 impl_->xlabel_ = label;
244 AbstractPlotModule::setXAxisIsTime()
246 TimeUnitManager manager(impl_->settings_.timeUnit());
247 impl_->xlabel_ = formatString("Time (%s)", manager.timeUnitAsString());
248 impl_->xscale_ = manager.inverseTimeScaleFactor();
253 AbstractPlotModule::setYLabel(const char *label)
255 impl_->ylabel_ = label;
260 AbstractPlotModule::setLegend(int nsets, const char * const *setname)
262 impl_->legend_.reserve(impl_->legend_.size() + nsets);
263 for (int i = 0; i < nsets; ++i)
265 appendLegend(setname[i]);
271 AbstractPlotModule::appendLegend(const char *setname)
273 impl_->legend_.push_back(setname);
278 AbstractPlotModule::appendLegend(const std::string &setname)
280 impl_->legend_.push_back(setname);
285 AbstractPlotModule::setXFormat(int width, int precision, char format)
287 GMX_RELEASE_ASSERT(width >= 0 && precision >= 0
288 && width <= 99 && precision <= 99,
289 "Invalid width or precision");
290 GMX_RELEASE_ASSERT(strchr("eEfFgG", format) != NULL,
291 "Invalid format specifier");
292 sprintf(impl_->xformat_, "%%%d.%d%c", width, precision, format);
297 AbstractPlotModule::setYFormat(int width, int precision, char format)
299 GMX_RELEASE_ASSERT(width >= 0 && precision >= 0
300 && width <= 99 && precision <= 99,
301 "Invalid width or precision");
302 GMX_RELEASE_ASSERT(strchr("eEfFgG", format) != NULL,
303 "Invalid format specifier");
304 sprintf(impl_->yformat_, " %%%d.%d%c", width, precision, format);
309 AbstractPlotModule::flags() const
311 return efAllowMissing | efAllowMulticolumn | efAllowMultipoint
312 | efAllowMultipleDataSets;
317 AbstractPlotModule::dataStarted(AbstractAnalysisData * /* data */)
319 if (!impl_->filename_.empty())
323 impl_->fp_ = gmx_fio_fopen(impl_->filename_.c_str(), "w");
327 time_unit_t time_unit
328 = static_cast<time_unit_t>(impl_->settings_.timeUnit() + 1);
329 xvg_format_t xvg_format
330 = (impl_->settings_.plotFormat() > 0
331 ? static_cast<xvg_format_t>(impl_->settings_.plotFormat())
334 output_env_init(&oenv, getProgramContext(), time_unit, FALSE, xvg_format, 0);
335 boost::shared_ptr<output_env> oenvGuard(oenv, &output_env_done);
336 impl_->fp_ = xvgropen(impl_->filename_.c_str(), impl_->title_.c_str(),
337 impl_->xlabel_.c_str(), impl_->ylabel_.c_str(),
339 const SelectionCollection *selections
340 = impl_->settings_.selectionCollection();
341 if (selections != NULL)
343 selections->printXvgrInfo(impl_->fp_, oenv);
345 if (!impl_->subtitle_.empty())
347 xvgr_subtitle(impl_->fp_, impl_->subtitle_.c_str(), oenv);
349 if (output_env_get_print_xvgr_codes(oenv)
350 && !impl_->legend_.empty())
352 std::vector<const char *> legend;
353 legend.reserve(impl_->legend_.size());
354 for (size_t i = 0; i < impl_->legend_.size(); ++i)
356 legend.push_back(impl_->legend_[i].c_str());
358 xvgr_legend(impl_->fp_, legend.size(), &legend[0], oenv);
366 AbstractPlotModule::frameStarted(const AnalysisDataFrameHeader &frame)
374 std::fprintf(impl_->fp_, impl_->xformat_, frame.x() * impl_->xscale_);
380 AbstractPlotModule::frameFinished(const AnalysisDataFrameHeader & /*header*/)
386 std::fprintf(impl_->fp_, "\n");
391 AbstractPlotModule::dataFinished()
398 AbstractPlotModule::isFileOpen() const
400 return impl_->fp_ != NULL;
405 AbstractPlotModule::writeValue(const AnalysisDataValue &value) const
407 GMX_ASSERT(isFileOpen(), "File not opened, but write attempted");
408 const real y = value.isSet() ? value.value() : 0.0;
409 std::fprintf(impl_->fp_, impl_->yformat_, y);
410 if (impl_->bErrorsAsSeparateColumn_)
412 const real dy = value.isSet() ? value.error() : 0.0;
413 std::fprintf(impl_->fp_, impl_->yformat_, dy);
418 /********************************************************************
422 AnalysisDataPlotModule::AnalysisDataPlotModule()
426 AnalysisDataPlotModule::AnalysisDataPlotModule(
427 const AnalysisDataPlotSettings &settings)
428 : AbstractPlotModule(settings)
434 AnalysisDataPlotModule::pointsAdded(const AnalysisDataPointSetRef &points)
440 for (int i = 0; i < points.columnCount(); ++i)
442 writeValue(points.values()[i]);
447 /********************************************************************
448 * DataVectorPlotModule
451 AnalysisDataVectorPlotModule::AnalysisDataVectorPlotModule()
453 for (int i = 0; i < DIM; ++i)
457 bWrite_[DIM] = false;
461 AnalysisDataVectorPlotModule::AnalysisDataVectorPlotModule(
462 const AnalysisDataPlotSettings &settings)
463 : AbstractPlotModule(settings)
465 for (int i = 0; i < DIM; ++i)
469 bWrite_[DIM] = false;
474 AnalysisDataVectorPlotModule::setWriteX(bool bWrite)
476 bWrite_[XX] = bWrite;
481 AnalysisDataVectorPlotModule::setWriteY(bool bWrite)
483 bWrite_[YY] = bWrite;
488 AnalysisDataVectorPlotModule::setWriteZ(bool bWrite)
490 bWrite_[ZZ] = bWrite;
495 AnalysisDataVectorPlotModule::setWriteNorm(bool bWrite)
497 bWrite_[DIM] = bWrite;
502 AnalysisDataVectorPlotModule::setWriteMask(bool bWrite[DIM + 1])
504 for (int i = 0; i < DIM + 1; ++i)
506 bWrite_[i] = bWrite[i];
512 AnalysisDataVectorPlotModule::pointsAdded(const AnalysisDataPointSetRef &points)
514 if (points.firstColumn() % DIM != 0 || points.columnCount() % DIM != 0)
516 GMX_THROW(APIError("Partial data points"));
522 for (int i = 0; i < points.columnCount(); i += 3)
524 for (int d = 0; d < DIM; ++d)
528 writeValue(points.values()[i + d]);
533 const rvec y = { points.y(i), points.y(i + 1), points.y(i + 2) };
534 AnalysisDataValue value(norm(y));