src/gromacs/analysisdata/modules/plot.cpp

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  35 /*! \internal \file
  36  * \brief
  37  * Implements classes in plot.h.
  38  *
  39  * \ingroup module_analysisdata
  40  * \author Teemu Murtola <teemu.murtola@gmail.com>
  41  */
  42 #include "gmxpre.h"
  43
  44 #include "plot.h"
  45
  46 #include <cstdio>
  47 #include <cstring>
  48
  49 #include <string>
  50 #include <vector>
  51
  52 #include "gromacs/analysisdata/dataframe.h"
  53 #include "gromacs/fileio/gmxfio.h"
  54 #include "gromacs/fileio/oenv.h"
  55 #include "gromacs/fileio/xvgr.h"
  56 #include "gromacs/math/vec.h"
  57 #include "gromacs/options/basicoptions.h"
  58 #include "gromacs/options/ioptionscontainer.h"
  59 #include "gromacs/options/timeunitmanager.h"
  60 #include "gromacs/selection/selectioncollection.h"
  61 #include "gromacs/utility/exceptions.h"
  62 #include "gromacs/utility/gmxassert.h"
  63 #include "gromacs/utility/programcontext.h"
  64 #include "gromacs/utility/stringutil.h"
  65 #include "gromacs/utility/unique_cptr.h"
  66
  67 namespace
  68 {
  69
  70 //! Enum values for plot formats.
  71 const char *const g_plotFormats[] = {
  72     "none", "xmgrace", "xmgr"
  73 };
  74
  75 } // namespace
  76
  77 namespace gmx
  78 {
  79
  80 /********************************************************************
  81  * AnalysisDataPlotSettings
  82  */
  83
  84 AnalysisDataPlotSettings::AnalysisDataPlotSettings()
  85     : selections_(nullptr), timeUnit_(TimeUnit_Default), plotFormat_(1)
  86 {
  87 }
  88
  89 void
  90 AnalysisDataPlotSettings::setSelectionCollection(const SelectionCollection *selections)
  91 {
  92     selections_ = selections;
  93 }
  94
  95
  96 void
  97 AnalysisDataPlotSettings::initOptions(IOptionsContainer *options)
  98 {
  99     options->addOption(EnumIntOption("xvg").enumValue(g_plotFormats)
 100                            .store(&plotFormat_)
 101                            .description("Plot formatting"));
 102 }
 103
 104
 105 /********************************************************************
 106  * AbstractPlotModule::Impl
 107  */
 108
 109 class AbstractPlotModule::Impl
 110 {
 111     public:
 112         explicit Impl(const AnalysisDataPlotSettings &settings);
 113         ~Impl();
 114
 115         void closeFile();
 116
 117         AnalysisDataPlotSettings  settings_;
 118         std::string               filename_;
 119         FILE                     *fp_;
 120
 121         bool                      bPlain_;
 122         bool                      bOmitX_;
 123         bool                      bErrorsAsSeparateColumn_;
 124         std::string               title_;
 125         std::string               subtitle_;
 126         std::string               xlabel_;
 127         std::string               ylabel_;
 128         std::vector<std::string>  legend_;
 129         char                      xformat_[15];
 130         char                      yformat_[15];
 131         real                      xscale_;
 132 };
 133
 134 AbstractPlotModule::Impl::Impl(const AnalysisDataPlotSettings &settings)
 135     : settings_(settings), fp_(nullptr), bPlain_(false), bOmitX_(false),
 136       bErrorsAsSeparateColumn_(false), xscale_(1.0)
 137 {
 138     strcpy(xformat_, "%11.3f");
 139     strcpy(yformat_, " %8.3f");
 140 }
 141
 142 AbstractPlotModule::Impl::~Impl()
 143 {
 144     closeFile();
 145 }
 146
 147
 148 void
 149 AbstractPlotModule::Impl::closeFile()
 150 {
 151     if (fp_ != nullptr)
 152     {
 153         if (bPlain_)
 154         {
 155             gmx_fio_fclose(fp_);
 156         }
 157         else
 158         {
 159             xvgrclose(fp_);
 160         }
 161         fp_ = nullptr;
 162     }
 163 }
 164
 165
 166 /********************************************************************
 167  * AbstractPlotModule
 168  */
 169 /*! \cond libapi */
 170 AbstractPlotModule::AbstractPlotModule()
 171     : impl_(new Impl(AnalysisDataPlotSettings()))
 172 {
 173 }
 174
 175 AbstractPlotModule::AbstractPlotModule(const AnalysisDataPlotSettings &settings)
 176     : impl_(new Impl(settings))
 177 {
 178 }
 179 //! \endcond
 180
 181 AbstractPlotModule::~AbstractPlotModule()
 182 {
 183 }
 184
 185
 186 void
 187 AbstractPlotModule::setSettings(const AnalysisDataPlotSettings &settings)
 188 {
 189     impl_->settings_ = settings;
 190 }
 191
 192
 193 void
 194 AbstractPlotModule::setFileName(const std::string &filename)
 195 {
 196     impl_->filename_ = filename;
 197 }
 198
 199
 200 void
 201 AbstractPlotModule::setPlainOutput(bool bPlain)
 202 {
 203     impl_->bPlain_ = bPlain;
 204 }
 205
 206
 207 void
 208 AbstractPlotModule::setErrorsAsSeparateColumn(bool bSeparate)
 209 {
 210     impl_->bErrorsAsSeparateColumn_ = bSeparate;
 211 }
 212
 213
 214 void
 215 AbstractPlotModule::setOmitX(bool bOmitX)
 216 {
 217     impl_->bOmitX_ = bOmitX;
 218 }
 219
 220
 221 void
 222 AbstractPlotModule::setTitle(const char *title)
 223 {
 224     impl_->title_ = title;
 225 }
 226
 227 void
 228 AbstractPlotModule::setTitle(const std::string &title)
 229 {
 230     impl_->title_ = title;
 231 }
 232
 233
 234 void
 235 AbstractPlotModule::setSubtitle(const char *subtitle)
 236 {
 237     impl_->subtitle_ = subtitle;
 238 }
 239
 240
 241 void
 242 AbstractPlotModule::setSubtitle(const std::string &subtitle)
 243 {
 244     impl_->subtitle_ = subtitle;
 245 }
 246
 247
 248 void
 249 AbstractPlotModule::setXLabel(const char *label)
 250 {
 251     impl_->xlabel_ = label;
 252 }
 253
 254
 255 void
 256 AbstractPlotModule::setXAxisIsTime()
 257 {
 258     TimeUnitManager manager(impl_->settings_.timeUnit());
 259     impl_->xlabel_ = formatString("Time (%s)", manager.timeUnitAsString());
 260     impl_->xscale_ = manager.inverseTimeScaleFactor();
 261 }
 262
 263
 264 void
 265 AbstractPlotModule::setYLabel(const char *label)
 266 {
 267     impl_->ylabel_ = label;
 268 }
 269
 270
 271 void
 272 AbstractPlotModule::setLegend(int nsets, const char * const *setname)
 273 {
 274     impl_->legend_.reserve(impl_->legend_.size() + nsets);
 275     for (int i = 0; i < nsets; ++i)
 276     {
 277         appendLegend(setname[i]);
 278     }
 279 }
 280
 281
 282 void
 283 AbstractPlotModule::appendLegend(const char *setname)
 284 {
 285     impl_->legend_.emplace_back(setname);
 286 }
 287
 288
 289 void
 290 AbstractPlotModule::appendLegend(const std::string &setname)
 291 {
 292     impl_->legend_.push_back(setname);
 293 }
 294
 295
 296 void
 297 AbstractPlotModule::setXFormat(int width, int precision, char format)
 298 {
 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) != nullptr,
 303                        "Invalid format specifier");
 304     sprintf(impl_->xformat_, "%%%d.%d%c", width, precision, format);
 305 }
 306
 307
 308 void
 309 AbstractPlotModule::setYFormat(int width, int precision, char format)
 310 {
 311     GMX_RELEASE_ASSERT(width >= 0 && precision >= 0
 312                        && width <= 99 && precision <= 99,
 313                        "Invalid width or precision");
 314     GMX_RELEASE_ASSERT(strchr("eEfFgG", format) != nullptr,
 315                        "Invalid format specifier");
 316     sprintf(impl_->yformat_, " %%%d.%d%c", width, precision, format);
 317 }
 318
 319
 320 int
 321 AbstractPlotModule::flags() const
 322 {
 323     return efAllowMissing | efAllowMulticolumn | efAllowMultipoint
 324            | efAllowMultipleDataSets;
 325 }
 326
 327
 328 void
 329 AbstractPlotModule::dataStarted(AbstractAnalysisData * /* data */)
 330 {
 331     if (!impl_->filename_.empty())
 332     {
 333         if (impl_->bPlain_)
 334         {
 335             impl_->fp_ = gmx_fio_fopen(impl_->filename_.c_str(), "w");
 336         }
 337         else
 338         {
 339             time_unit_t  time_unit
 340                 = static_cast<time_unit_t>(impl_->settings_.timeUnit() + 1); // NOLINT(misc-misplaced-widening-cast)
 341             xvg_format_t xvg_format
 342                 = (impl_->settings_.plotFormat() > 0
 343                    ? static_cast<xvg_format_t>(impl_->settings_.plotFormat())
 344                    : exvgNONE);
 345             gmx_output_env_t                                    *oenv;
 346             output_env_init(&oenv, getProgramContext(), time_unit, FALSE, xvg_format, 0);
 347             const unique_cptr<gmx_output_env_t, output_env_done> oenvGuard(oenv);
 348             impl_->fp_ = xvgropen(impl_->filename_.c_str(), impl_->title_.c_str(),
 349                                   impl_->xlabel_, impl_->ylabel_,
 350                                   oenv);
 351             const SelectionCollection *selections
 352                 = impl_->settings_.selectionCollection();
 353             if (selections != nullptr && output_env_get_xvg_format(oenv) != exvgNONE)
 354             {
 355                 selections->printXvgrInfo(impl_->fp_);
 356             }
 357             if (!impl_->subtitle_.empty())
 358             {
 359                 xvgr_subtitle(impl_->fp_, impl_->subtitle_.c_str(), oenv);
 360             }
 361             if (output_env_get_print_xvgr_codes(oenv)
 362                 && !impl_->legend_.empty())
 363             {
 364                 std::vector<const char *> legend;
 365                 legend.reserve(impl_->legend_.size());
 366                 for (size_t i = 0; i < impl_->legend_.size(); ++i)
 367                 {
 368                     legend.push_back(impl_->legend_[i].c_str());
 369                 }
 370                 xvgr_legend(impl_->fp_, legend.size(), legend.data(), oenv);
 371             }
 372         }
 373     }
 374 }
 375
 376
 377 void
 378 AbstractPlotModule::frameStarted(const AnalysisDataFrameHeader &frame)
 379 {
 380     if (!isFileOpen())
 381     {
 382         return;
 383     }
 384     if (!impl_->bOmitX_)
 385     {
 386         std::fprintf(impl_->fp_, impl_->xformat_, frame.x() * impl_->xscale_);
 387     }
 388 }
 389
 390
 391 void
 392 AbstractPlotModule::frameFinished(const AnalysisDataFrameHeader & /*header*/)
 393 {
 394     if (!isFileOpen())
 395     {
 396         return;
 397     }
 398     std::fprintf(impl_->fp_, "\n");
 399 }
 400
 401
 402 void
 403 AbstractPlotModule::dataFinished()
 404 {
 405     impl_->closeFile();
 406 }
 407
 408 /*! \cond libapi */
 409 bool
 410 AbstractPlotModule::isFileOpen() const
 411 {
 412     return impl_->fp_ != nullptr;
 413 }
 414
 415
 416 void
 417 AbstractPlotModule::writeValue(const AnalysisDataValue &value) const
 418 {
 419     GMX_ASSERT(isFileOpen(), "File not opened, but write attempted");
 420     const real y = value.isSet() ? value.value() : 0.0;
 421     std::fprintf(impl_->fp_, impl_->yformat_, y);
 422     if (impl_->bErrorsAsSeparateColumn_)
 423     {
 424         const real dy = value.isSet() ? value.error() : 0.0;
 425         std::fprintf(impl_->fp_, impl_->yformat_, dy);
 426     }
 427 }
 428 //! \endcond
 429
 430 /********************************************************************
 431  * DataPlotModule
 432  */
 433
 434 AnalysisDataPlotModule::AnalysisDataPlotModule()
 435 {
 436 }
 437
 438 AnalysisDataPlotModule::AnalysisDataPlotModule(
 439         const AnalysisDataPlotSettings &settings)
 440     : AbstractPlotModule(settings)
 441 {
 442 }
 443
 444
 445 void
 446 AnalysisDataPlotModule::pointsAdded(const AnalysisDataPointSetRef &points)
 447 {
 448     if (!isFileOpen())
 449     {
 450         return;
 451     }
 452     for (int i = 0; i < points.columnCount(); ++i)
 453     {
 454         writeValue(points.values()[i]);
 455     }
 456 }
 457
 458
 459 /********************************************************************
 460  * DataVectorPlotModule
 461  */
 462
 463 AnalysisDataVectorPlotModule::AnalysisDataVectorPlotModule()
 464 {
 465     for (int i = 0; i < DIM; ++i)
 466     {
 467         bWrite_[i] = true;
 468     }
 469     bWrite_[DIM] = false;
 470 }
 471
 472
 473 AnalysisDataVectorPlotModule::AnalysisDataVectorPlotModule(
 474         const AnalysisDataPlotSettings &settings)
 475     : AbstractPlotModule(settings)
 476 {
 477     for (int i = 0; i < DIM; ++i)
 478     {
 479         bWrite_[i] = true;
 480     }
 481     bWrite_[DIM] = false;
 482 }
 483
 484
 485 void
 486 AnalysisDataVectorPlotModule::setWriteX(bool bWrite)
 487 {
 488     bWrite_[XX] = bWrite;
 489 }
 490
 491
 492 void
 493 AnalysisDataVectorPlotModule::setWriteY(bool bWrite)
 494 {
 495     bWrite_[YY] = bWrite;
 496 }
 497
 498
 499 void
 500 AnalysisDataVectorPlotModule::setWriteZ(bool bWrite)
 501 {
 502     bWrite_[ZZ] = bWrite;
 503 }
 504
 505
 506 void
 507 AnalysisDataVectorPlotModule::setWriteNorm(bool bWrite)
 508 {
 509     bWrite_[DIM] = bWrite;
 510 }
 511
 512
 513 void
 514 AnalysisDataVectorPlotModule::setWriteMask(const bool bWrite[DIM + 1])
 515 {
 516     for (int i = 0; i < DIM + 1; ++i)
 517     {
 518         bWrite_[i] = bWrite[i];
 519     }
 520 }
 521
 522
 523 void
 524 AnalysisDataVectorPlotModule::pointsAdded(const AnalysisDataPointSetRef &points)
 525 {
 526     if (points.firstColumn() % DIM != 0 || points.columnCount() % DIM != 0)
 527     {
 528         GMX_THROW(APIError("Partial data points"));
 529     }
 530     if (!isFileOpen())
 531     {
 532         return;
 533     }
 534     for (int i = 0; i < points.columnCount(); i += 3)
 535     {
 536         for (int d = 0; d < DIM; ++d)
 537         {
 538             if (bWrite_[d])
 539             {
 540                 writeValue(points.values()[i + d]);
 541             }
 542         }
 543         if (bWrite_[DIM])
 544         {
 545             const rvec        y = { points.y(i), points.y(i + 1), points.y(i + 2) };
 546             AnalysisDataValue value(norm(y));
 547             writeValue(value);
 548         }
 549     }
 550 }
 551
 552 } // namespace gmx