From e7fd245c10a38cbf0ae6d896ff928c6dc352b431 Mon Sep 17 00:00:00 2001 From: Antonin Portelli Date: Wed, 13 Apr 2016 12:54:05 +0100 Subject: [PATCH 01/20] start of 3.1 unstable branch --- configure.ac | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/configure.ac b/configure.ac index 31b871f..897806f 100644 --- a/configure.ac +++ b/configure.ac @@ -2,7 +2,7 @@ # Initialization AC_PREREQ([2.63]) -AC_INIT([LatAnalyze],[3.1],[antonin.portelli@me.com],[LatAnalyze]) +AC_INIT([LatAnalyze],[3.1-dev],[antonin.portelli@me.com],[LatAnalyze]) AC_CONFIG_AUX_DIR([.buildutils]) AC_CONFIG_SRCDIR([lib/Global.cpp]) AC_CONFIG_SRCDIR([utils/sample_read.cpp]) From 1a6b877f4ecd7666a10acba66fe72ea1279fe8be Mon Sep 17 00:00:00 2001 From: Antonin Portelli Date: Fri, 15 Apr 2016 18:21:40 +0100 Subject: [PATCH 02/20] more precise output for fit results --- lib/XYSampleData.cpp | 2 +- lib/XYStatData.cpp | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/lib/XYSampleData.cpp b/lib/XYSampleData.cpp index 5253fef..0e71825 100644 --- a/lib/XYSampleData.cpp +++ b/lib/XYSampleData.cpp @@ -98,7 +98,7 @@ void SampleFitResult::print(const bool printXsi, ostream &out) const Index pMax = printXsi ? size() : nPar_; DMat err = this->variance().cwiseSqrt(); - sprintf(buf, "chi^2/dof= %.1f/%d= %.2f -- p-value= %.2e", getChi2(), + sprintf(buf, "chi^2/dof= %.1e/%d= %.2e -- p-value= %.2e", getChi2(), static_cast(getNDof()), getChi2PerDof(), getPValue()); out << buf << endl; for (Index p = 0; p < pMax; ++p) diff --git a/lib/XYStatData.cpp b/lib/XYStatData.cpp index 74aa728..710f1a4 100644 --- a/lib/XYStatData.cpp +++ b/lib/XYStatData.cpp @@ -66,7 +66,7 @@ void FitResult::print(const bool printXsi, ostream &out) const char buf[256]; Index pMax = printXsi ? size() : nPar_; - sprintf(buf, "chi^2/dof= %.1f/%d= %.2f -- p-value= %.2e", getChi2(), + sprintf(buf, "chi^2/dof= %.1e/%d= %.2e -- p-value= %.2e", getChi2(), static_cast(getNDof()), getChi2PerDof(), getPValue()); out << buf << endl; for (Index p = 0; p < pMax; ++p) From fe0f32e42c5c0050d1ae888bc4fbff0933765fdb Mon Sep 17 00:00:00 2001 From: Antonin Portelli Date: Fri, 27 May 2016 13:40:57 +0100 Subject: [PATCH 03/20] XYSampleData: more stable fit initialisation strategy --- lib/XYSampleData.cpp | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/lib/XYSampleData.cpp b/lib/XYSampleData.cpp index 0e71825..bd47452 100644 --- a/lib/XYSampleData.cpp +++ b/lib/XYSampleData.cpp @@ -277,12 +277,12 @@ SampleFitResult XYSampleData::fit(std::vector &minimizer, if (s == central) { sampleResult = data_.fit(minimizer, initCopy, v); + initCopy = sampleResult.segment(0, initCopy.size()); } else { sampleResult = data_.fit(*(minimizer.back()), initCopy, v); } - initCopy = sampleResult.segment(0, initCopy.size()); result[s] = sampleResult; result.chi2_[s] = sampleResult.getChi2(); for (unsigned int j = 0; j < v.size(); ++j) From 1f3a8c27a15c5b817fa3a93ba8c97ac157ab1aee Mon Sep 17 00:00:00 2001 From: Matt Spraggs Date: Tue, 7 Jun 2016 18:11:01 +0100 Subject: [PATCH 04/20] Utils: Added little utility to flatten 1x1 DMatSamples --- utils/Makefile.am | 5 +++++ utils/sample_flatten.cpp | 31 +++++++++++++++++++++++++++++++ 2 files changed, 36 insertions(+) create mode 100644 utils/sample_flatten.cpp diff --git a/utils/Makefile.am b/utils/Makefile.am index 1eba782..b7b200a 100644 --- a/utils/Makefile.am +++ b/utils/Makefile.am @@ -9,6 +9,7 @@ endif bin_PROGRAMS = \ latan_make_fake_sample\ latan_sample_combine \ + latan_sample_flatten \ latan_sample_plot_corr\ latan_sample_read \ latan_resample @@ -21,6 +22,10 @@ latan_sample_combine_SOURCES = sample_combine.cpp latan_sample_combine_CXXFLAGS = $(COM_CXXFLAGS) latan_sample_combine_LDFLAGS = -L../lib/.libs -lLatAnalyze +latan_sample_flatten_SOURCES = sample_flatten.cpp +latan_sample_flatten_CXXFLAGS = $(COM_CXXFLAGS) +latan_sample_flatten_LDFLAGS = -L../lib/.libs -lLatAnalyze + latan_sample_plot_corr_SOURCES = sample_plot_corr.cpp latan_sample_plot_corr_CXXFLAGS = $(COM_CXXFLAGS) latan_sample_plot_corr_LDFLAGS = -L../lib/.libs -lLatAnalyze diff --git a/utils/sample_flatten.cpp b/utils/sample_flatten.cpp new file mode 100644 index 0000000..46f68b3 --- /dev/null +++ b/utils/sample_flatten.cpp @@ -0,0 +1,31 @@ +#include +#include + +#include +#include + + +namespace La = Latan; + +int main(int argc, char* argv[]) +{ + if (argc != 4) { + std::cout << "Usage: " << argv[0] << " " << std::endl; + return -1; + } + + std::string inFileName = argv[1]; + std::string outFileName = argv[2]; + auto nSamples = La::strTo(argv[3]); + + La::DMatSample inputData(nSamples, 1, 1); + La::DSample outputData(nSamples); + + inputData = La::Io::load(inFileName); + + FOR_STAT_ARRAY(inputData, s) { + outputData[s] = inputData[s](0, 0); + } + + La::Io::save(outputData, outFileName); +} From 82d020c82fb0a3ac8f1b56da8b3e00a0fff4716d Mon Sep 17 00:00:00 2001 From: Matt Spraggs Date: Thu, 9 Jun 2016 17:38:41 +0100 Subject: [PATCH 05/20] Utils: Renamed sample_flatten.cpp to sample_element.cpp as suggested --- utils/Makefile.am | 8 ++++---- utils/sample_element.cpp | 39 +++++++++++++++++++++++++++++++++++++++ utils/sample_flatten.cpp | 31 ------------------------------- 3 files changed, 43 insertions(+), 35 deletions(-) create mode 100644 utils/sample_element.cpp delete mode 100644 utils/sample_flatten.cpp diff --git a/utils/Makefile.am b/utils/Makefile.am index b7b200a..bc38c79 100644 --- a/utils/Makefile.am +++ b/utils/Makefile.am @@ -9,7 +9,7 @@ endif bin_PROGRAMS = \ latan_make_fake_sample\ latan_sample_combine \ - latan_sample_flatten \ + latan_sample_element \ latan_sample_plot_corr\ latan_sample_read \ latan_resample @@ -22,9 +22,9 @@ latan_sample_combine_SOURCES = sample_combine.cpp latan_sample_combine_CXXFLAGS = $(COM_CXXFLAGS) latan_sample_combine_LDFLAGS = -L../lib/.libs -lLatAnalyze -latan_sample_flatten_SOURCES = sample_flatten.cpp -latan_sample_flatten_CXXFLAGS = $(COM_CXXFLAGS) -latan_sample_flatten_LDFLAGS = -L../lib/.libs -lLatAnalyze +latan_sample_element_SOURCES = sample_element.cpp +latan_sample_element_CXXFLAGS = $(COM_CXXFLAGS) +latan_sample_element_LDFLAGS = -L../lib/.libs -lLatAnalyze latan_sample_plot_corr_SOURCES = sample_plot_corr.cpp latan_sample_plot_corr_CXXFLAGS = $(COM_CXXFLAGS) diff --git a/utils/sample_element.cpp b/utils/sample_element.cpp new file mode 100644 index 0000000..9797bd2 --- /dev/null +++ b/utils/sample_element.cpp @@ -0,0 +1,39 @@ +#include +#include + +#include +#include + + +int main(int argc, char* argv[]) +{ + using namespace std; + using namespace Latan; + + if (argc != 4 and argc != 5) { + cout << "Usage: " << argv[0] << " "; + cout << "[output filename]" << endl; + return -1; + } + + string inFileName = argv[1]; + auto row = strTo(argv[2]); + auto col = strTo(argv[3]); + string outFileName = (argc == 5) ? argv[4] : ""; + + auto inputData = Io::load(inFileName); + cout << scientific; + cout << "central value:\n" << inputData[central](row, col) << endl; + cout << "standard deviation:\n"; + cout << inputData.variance().cwiseSqrt()(row, col) << endl; + + if (not outFileName.empty()) + { + DSample outputData(inputData.size()); + FOR_STAT_ARRAY(inputData, s) { + outputData[s] = inputData[s](row, col); + } + + Io::save(outputData, outFileName); + } +} diff --git a/utils/sample_flatten.cpp b/utils/sample_flatten.cpp deleted file mode 100644 index 46f68b3..0000000 --- a/utils/sample_flatten.cpp +++ /dev/null @@ -1,31 +0,0 @@ -#include -#include - -#include -#include - - -namespace La = Latan; - -int main(int argc, char* argv[]) -{ - if (argc != 4) { - std::cout << "Usage: " << argv[0] << " " << std::endl; - return -1; - } - - std::string inFileName = argv[1]; - std::string outFileName = argv[2]; - auto nSamples = La::strTo(argv[3]); - - La::DMatSample inputData(nSamples, 1, 1); - La::DSample outputData(nSamples); - - inputData = La::Io::load(inFileName); - - FOR_STAT_ARRAY(inputData, s) { - outputData[s] = inputData[s](0, 0); - } - - La::Io::save(outputData, outFileName); -} From b925a365e2a9f00cc9aa71e54c52d7859a0136cb Mon Sep 17 00:00:00 2001 From: Antonin Portelli Date: Tue, 14 Jun 2016 12:33:27 +0100 Subject: [PATCH 06/20] Plot: bands --- lib/Plot.cpp | 14 ++++++++++++++ lib/Plot.hpp | 10 ++++++++++ 2 files changed, 24 insertions(+) diff --git a/lib/Plot.cpp b/lib/Plot.cpp index 039d3c3..13c6f4b 100644 --- a/lib/Plot.cpp +++ b/lib/Plot.cpp @@ -183,6 +183,20 @@ PlotHLine::PlotHLine(const double y) setCommand(strFrom(y)); } +// PlotHBand constructor /////////////////////////////////////////////////////// +PlotBand::PlotBand(const double xMin, const double xMax, const double yMin, + const double yMax, const double opacity) +{ + setCommand("'< printf \"%e %e\\n%e %e\\n%e %e\\n%e %e\\n%e %e\\n\" " + + strFrom(xMin) + " " + strFrom(yMin) + " " + + strFrom(xMax) + " " + strFrom(yMin) + " " + + strFrom(xMax) + " " + strFrom(yMax) + " " + + strFrom(xMin) + " " + strFrom(yMax) + " " + + strFrom(xMin) + " " + strFrom(yMin) + + "' u 1:2 w filledcurves closed fs solid " + strFrom(opacity) + + " noborder"); +} + // PlotFunction constructor //////////////////////////////////////////////////// PlotFunction::PlotFunction(const DoubleFunction &function, const double xMin, const double xMax, const unsigned int nPoint) diff --git a/lib/Plot.hpp b/lib/Plot.hpp index 1ae7cf0..a6d9e81 100644 --- a/lib/Plot.hpp +++ b/lib/Plot.hpp @@ -106,6 +106,16 @@ public: virtual ~PlotHLine(void) = default; }; +class PlotBand: public PlotObject +{ +public: + // constructor + PlotBand(const double xMin, const double xMax, const double yMin, + const double yMax, const double opacity = 0.15); + // destructor + virtual ~PlotBand(void) = default; +}; + class PlotFunction: public PlotObject { public: From 85d76052ce8aac7dc62d31c7cac5f8877556ed5a Mon Sep 17 00:00:00 2001 From: Antonin Portelli Date: Tue, 14 Jun 2016 12:34:46 +0100 Subject: [PATCH 07/20] more consistent naming of utilities --- utils/Makefile.am | 24 +++++++++---------- ...{sample_combine.cpp => sample-combine.cpp} | 0 .../{make_fake_sample.cpp => sample-fake.cpp} | 0 ...ple_plot_corr.cpp => sample-plot-corr.cpp} | 1 + utils/{sample_read.cpp => sample-read.cpp} | 0 5 files changed, 13 insertions(+), 12 deletions(-) rename utils/{sample_combine.cpp => sample-combine.cpp} (100%) rename utils/{make_fake_sample.cpp => sample-fake.cpp} (100%) rename utils/{sample_plot_corr.cpp => sample-plot-corr.cpp} (96%) rename utils/{sample_read.cpp => sample-read.cpp} (100%) diff --git a/utils/Makefile.am b/utils/Makefile.am index 1eba782..2f76091 100644 --- a/utils/Makefile.am +++ b/utils/Makefile.am @@ -7,25 +7,25 @@ endif endif bin_PROGRAMS = \ - latan_make_fake_sample\ - latan_sample_combine \ - latan_sample_plot_corr\ - latan_sample_read \ - latan_resample + latan-sample-combine \ + latan-sample-fake \ + latan-sample-plot-corr\ + latan-sample-read \ + latan-resample -latan_make_fake_sample_SOURCES = make_fake_sample.cpp -latan_make_fake_sample_CXXFLAGS = $(COM_CXXFLAGS) -latan_make_fake_sample_LDFLAGS = -L../lib/.libs -lLatAnalyze - -latan_sample_combine_SOURCES = sample_combine.cpp +latan_sample_combine_SOURCES = sample-combine.cpp latan_sample_combine_CXXFLAGS = $(COM_CXXFLAGS) latan_sample_combine_LDFLAGS = -L../lib/.libs -lLatAnalyze -latan_sample_plot_corr_SOURCES = sample_plot_corr.cpp +latan_sample_fake_SOURCES = sample-fake.cpp +latan_sample_fake_CXXFLAGS = $(COM_CXXFLAGS) +latan_sample_fake_LDFLAGS = -L../lib/.libs -lLatAnalyze + +latan_sample_plot_corr_SOURCES = sample-plot-corr.cpp latan_sample_plot_corr_CXXFLAGS = $(COM_CXXFLAGS) latan_sample_plot_corr_LDFLAGS = -L../lib/.libs -lLatAnalyze -latan_sample_read_SOURCES = sample_read.cpp +latan_sample_read_SOURCES = sample-read.cpp latan_sample_read_CXXFLAGS = $(COM_CXXFLAGS) latan_sample_read_LDFLAGS = -L../lib/.libs -lLatAnalyze diff --git a/utils/sample_combine.cpp b/utils/sample-combine.cpp similarity index 100% rename from utils/sample_combine.cpp rename to utils/sample-combine.cpp diff --git a/utils/make_fake_sample.cpp b/utils/sample-fake.cpp similarity index 100% rename from utils/make_fake_sample.cpp rename to utils/sample-fake.cpp diff --git a/utils/sample_plot_corr.cpp b/utils/sample-plot-corr.cpp similarity index 96% rename from utils/sample_plot_corr.cpp rename to utils/sample-plot-corr.cpp index 12c22e8..638abd2 100644 --- a/utils/sample_plot_corr.cpp +++ b/utils/sample-plot-corr.cpp @@ -42,6 +42,7 @@ int main(int argc, char *argv[]) cout << "-- computing variance matrix from '" << fileName << "'..." << endl; name = Io::getFirstName(fileName); sample = Io::load(fileName); + sample = sample.block(0, 0, sample[central].rows(), 1); var = sample.varianceMatrix(); p << PlotMatrix(varToCorr(var)); p.display(); diff --git a/utils/sample_read.cpp b/utils/sample-read.cpp similarity index 100% rename from utils/sample_read.cpp rename to utils/sample-read.cpp From 83afc7901b6cc77390d227942b8d24a495ca58e8 Mon Sep 17 00:00:00 2001 From: Antonin Portelli Date: Tue, 14 Jun 2016 12:35:17 +0100 Subject: [PATCH 08/20] 2-pt fitter moved here from UKAnalyze --- Makefile.am | 2 +- configure.ac | 3 +- physics/2pt-fit.cpp | 332 ++++++++++++++++++++++++++++++++++++++++++++ physics/LatAnalyze | 1 + physics/Makefile.am | 15 ++ 5 files changed, 351 insertions(+), 2 deletions(-) create mode 100644 physics/2pt-fit.cpp create mode 120000 physics/LatAnalyze create mode 100644 physics/Makefile.am diff --git a/Makefile.am b/Makefile.am index c531723..16742b8 100644 --- a/Makefile.am +++ b/Makefile.am @@ -1,3 +1,3 @@ -SUBDIRS = lib utils examples +SUBDIRS = lib utils physics examples ACLOCAL_AMFLAGS = -I .buildutils/m4 diff --git a/configure.ac b/configure.ac index 90569c3..38c1473 100644 --- a/configure.ac +++ b/configure.ac @@ -131,7 +131,8 @@ AC_SUBST([LIBS]) AC_SUBST([AM_CFLAGS]) AC_SUBST([AM_LDFLAGS]) -AC_CONFIG_FILES([Makefile lib/Makefile utils/Makefile examples/Makefile]) +AC_CONFIG_FILES([Makefile lib/Makefile utils/Makefile physics/Makefile + examples/Makefile]) AC_OUTPUT echo "*********************************************" diff --git a/physics/2pt-fit.cpp b/physics/2pt-fit.cpp new file mode 100644 index 0000000..11f4328 --- /dev/null +++ b/physics/2pt-fit.cpp @@ -0,0 +1,332 @@ +#include +#include +#include +#include +#include +#include +#include +#include +#include + +using namespace std; +using namespace Latan; + +int main(int argc, char *argv[]) +{ + // parse arguments ///////////////////////////////////////////////////////// + OptParser opt; + bool parsed, doPlot, doHeatmap, doCorr, fold; + string corrFileName, model, outFileName, outFmt; + Index ti, tf, shift, nPar, thinning; + double svdTol; + Minimizer::Verbosity verbosity; + + opt.addOption("" , "ti" , OptParser::OptType::value , false, + "initial fit time"); + opt.addOption("" , "tf" , OptParser::OptType::value , false, + "final fit time"); + opt.addOption("t" , "thinning", OptParser::OptType::value , true, + "thinning of the time interval", "1"); + opt.addOption("s", "shift" , OptParser::OptType::value , true, + "time variable shift", "0"); + opt.addOption("m", "model" , OptParser::OptType::value , true, + "fit model (exp|exp2|exp3|cosh|cosh2|cosh3|)", "cosh"); + opt.addOption("" , "nPar" , OptParser::OptType::value , true, + "number of model parameters for custom models " + "(-1 if irrelevant)", "-1"); + opt.addOption("" , "svd" , OptParser::OptType::value , true, + "singular value elimination threshold", "0."); + opt.addOption("v", "verbosity", OptParser::OptType::value , true, + "minimizer verbosity level (0|1|2)", "0"); + opt.addOption("o", "output", OptParser::OptType::value , true, + "output file", ""); + opt.addOption("" , "uncorr" , OptParser::OptType::trigger, true, + "only do the uncorrelated fit"); + opt.addOption("" , "fold" , OptParser::OptType::trigger, true, + "fold the correlator"); + opt.addOption("p", "plot" , OptParser::OptType::trigger, true, + "show the fit plot"); + opt.addOption("h", "heatmap" , OptParser::OptType::trigger, true, + "show the fit correlation heatmap"); + opt.addOption("", "help" , OptParser::OptType::trigger, true, + "show this help message and exit"); + parsed = opt.parse(argc, argv); + if (!parsed or (opt.getArgs().size() != 1) or opt.gotOption("help")) + { + cerr << "usage: " << argv[0] << " " << endl; + cerr << endl << "Possible options:" << endl << opt << endl; + + return EXIT_FAILURE; + } + corrFileName = opt.getArgs().front(); + ti = opt.optionValue("ti"); + tf = opt.optionValue("tf"); + thinning = opt.optionValue("t"); + shift = opt.optionValue("s"); + model = opt.optionValue("m"); + nPar = opt.optionValue("nPar"); + svdTol = opt.optionValue("svd"); + outFileName = opt.optionValue("o"); + doCorr = !opt.gotOption("uncorr"); + fold = opt.gotOption("fold"); + doPlot = opt.gotOption("p"); + doHeatmap = opt.gotOption("h"); + switch (opt.optionValue("v")) + { + case 0: + verbosity = Minimizer::Verbosity::Silent; + break; + case 1: + verbosity = Minimizer::Verbosity::Normal; + break; + case 2: + verbosity = Minimizer::Verbosity::Debug; + break; + default: + cerr << "error: wrong verbosity level" << endl; + return EXIT_FAILURE; + } + + // load correlator ///////////////////////////////////////////////////////// + DMatSample tmp, corr; + Index nSample, nt; + + tmp = Io::load(corrFileName); + nSample = tmp.size(); + nt = tmp[central].rows(); + tmp = tmp.block(0, 0, nt, 1); + corr = tmp; + FOR_STAT_ARRAY(corr, s) + { + for (Index t = 0; t < nt; ++t) + { + corr[s]((t - shift + nt)%nt) = tmp[s](t); + } + } + if (fold) + { + tmp = corr; + FOR_STAT_ARRAY(corr, s) + { + for (Index t = 0; t < nt; ++t) + { + corr[s](t) = 0.5*(tmp[s](t) + tmp[s]((nt - t) % nt)); + } + } + } + + // make model ////////////////////////////////////////////////////////////// + DoubleModel mod; + bool coshModel = false; + + if ((model == "exp") or (model == "exp1")) + { + nPar = 2; + mod.setFunction([](const double *x, const double *p) + { + return p[1]*exp(-p[0]*x[0]); + }, 1, nPar); + } + else if (model == "exp2") + { + nPar = 4; + mod.setFunction([](const double *x, const double *p) + { + return p[1]*exp(-p[0]*x[0]) + p[3]*exp(-p[2]*x[0]); + }, 1, nPar); + } + else if (model == "exp3") + { + nPar = 6; + mod.setFunction([](const double *x, const double *p) + { + return p[1]*exp(-p[0]*x[0]) + p[3]*exp(-p[2]*x[0]) + + p[5]*exp(-p[4]*x[0]); + }, 1, nPar); + } + else if ((model == "cosh") or (model == "cosh1")) + { + coshModel = true; + nPar = 2; + mod.setFunction([nt](const double *x, const double *p) + { + return p[1]*(exp(-p[0]*x[0])+exp(-p[0]*(nt-x[0]))); + }, 1, nPar); + } + else if (model == "cosh2") + { + coshModel = true; + nPar = 4; + mod.setFunction([nt](const double *x, const double *p) + { + return p[1]*(exp(-p[0]*x[0])+exp(-p[0]*(nt-x[0]))) + + p[3]*(exp(-p[2]*x[0])+exp(-p[2]*(nt-x[0]))); + }, 1, nPar); + } + else if (model == "cosh3") + { + coshModel = true; + nPar = 6; + mod.setFunction([nt](const double *x, const double *p) + { + return p[1]*(exp(-p[0]*x[0])+exp(-p[0]*(nt-x[0]))) + + p[3]*(exp(-p[2]*x[0])+exp(-p[2]*(nt-x[0]))) + + p[5]*(exp(-p[2]*x[0])+exp(-p[4]*(nt-x[0]))); + }, 1, nPar); + } + else + { + if (nPar > 0) + { + mod = compile(model, 1, nPar); + } + else + { + cerr << "error: please specify the number of model parameter" + " using the --nPar function" << endl; + + return EXIT_FAILURE; + } + } + + // fit ///////////////////////////////////////////////////////////////////// + DMatSample tvec(nSample); + XYSampleData data(nSample); + SampleFitResult fit; + DVec init(nPar); + NloptMinimizer globMin(NloptMinimizer::Algorithm::GN_CRS2_LM); + MinuitMinimizer locMin; + vector unCorrMin{&globMin, &locMin}; + + FOR_STAT_ARRAY(tvec, s) + { + tvec[s] = DVec::LinSpaced(nt, 0, nt - 1); + } + data.addXDim(nt, "t/a", true); + data.addYDim("C(t)"); + data.setUnidimData(tvec, corr); + for (Index p = 0; p < nPar; p += 2) + { + mod.parName().setName(p, "E_" + strFrom(p/2)); + mod.parName().setName(p + 1, "Z_" + strFrom(p/2)); + } + init(0) = log(data.y(nt/4, 0)[central]/data.y(nt/4 + 1, 0)[central]); + init(1) = data.y(nt/4, 0)[central]/(exp(-init(0)*nt/4)); + for (Index p = 2; p < nPar; p += 2) + { + init(p) = 2*init(p - 2); + init(p + 1) = init(p - 1)/2.; + } + for (Index p = 0; p < nPar; p += 2) + { + globMin.setLowLimit(p, 0.); + globMin.setHighLimit(p, 10.*init(p)); + globMin.setLowLimit(p + 1, -10.*init(p + 1)); + globMin.setHighLimit(p + 1, 10.*init(p + 1)); + locMin.setLowLimit(p, 0.); + } + globMin.setPrecision(0.001); + globMin.setMaxIteration(100000); + globMin.setVerbosity(verbosity); + locMin.setMaxIteration(1000000); + locMin.setVerbosity(verbosity); + for (Index t = 0; t < nt; ++t) + { + data.fitPoint((t >= ti) and (t <= tf) + and ((t - ti) % thinning == 0), t); + } + if (doCorr) + { + cout << "-- uncorrelated fit..." << endl; + } + cout << "using model '" << model << "'" << endl; + data.setSvdTolerance(svdTol); + data.assumeYYCorrelated(false, 0, 0); + fit = data.fit(unCorrMin, init, mod); + fit.print(); + if (doCorr) + { + cout << "-- correlated fit..." << endl; + cout << "using model '" << model << "'" << endl; + init = fit[central]; + data.assumeYYCorrelated(true, 0, 0); + fit = data.fit(locMin, init, mod); + fit.print(); + } + + // plots /////////////////////////////////////////////////////////////////// + if (doPlot) + { + Plot p; + DMatSample effMass(nSample); + DVec effMassT, fitErr; + Index maxT = (coshModel) ? (nt - 2) : (nt - 1); + double e0, e0Err; + + p << PlotRange(Axis::x, 0, nt - 1); + p << LogScale(Axis::y); + p << Color("rgb 'blue'") << PlotPredBand(fit.getModel(_), 0, nt - 1); + p << Color("rgb 'blue'") << PlotFunction(fit.getModel(), 0, nt - 1); + p << Color("rgb 'red'") << PlotData(data.getData()); + p.display(); + effMass.resizeMat(maxT, 1); + effMassT.setLinSpaced(maxT, 1, maxT); + fitErr = fit.variance().cwiseSqrt(); + e0 = fit[central](0); + e0Err = fitErr(0); + if (coshModel) + { + FOR_STAT_ARRAY(effMass, s) + { + for (Index t = 1; t < nt - 1; ++t) + { + effMass[s](t - 1) = acosh((corr[s](t-1) + corr[s](t+1)) + /(2.*corr[s](t))); + } + } + } + else + { + FOR_STAT_ARRAY(effMass, s) + { + for (Index t = 1; t < nt; ++t) + { + effMass[s](t - 1) = log(corr[s](t-1)/corr[s](t)); + } + } + } + p.reset(); + p << PlotRange(Axis::x, 1, maxT); + p << PlotRange(Axis::y, e0 - 20.*e0Err, e0 + 20.*e0Err); + p << Color("rgb 'blue'") << PlotBand(0, maxT, e0 - e0Err, e0 + e0Err); + p << Color("rgb 'blue'") << PlotHLine(e0); + p << Color("rgb 'red'") << PlotData(effMassT, effMass); + p.display(); + p.save("test"); + } + if (doHeatmap) + { + Plot p; + Index n = data.getFitVarMat().rows(); + DMat id = DMat::Identity(n, n); + + p << PlotMatrix(Math::varToCorr(data.getFitVarMat())); + p << Caption("correlation matrix"); + p.display(); + if (svdTol > 0.) + { + p.reset(); + p << PlotMatrix(id - data.getFitVarMat()*data.getFitVarMatPInv()); + p << Caption("singular space projector"); + p.display(); + } + } + + // output ////////////////////////////////////////////////////////////////// + if (!outFileName.empty()) + { + Io::save(fit, outFileName); + } + + return EXIT_SUCCESS; +} diff --git a/physics/LatAnalyze b/physics/LatAnalyze new file mode 120000 index 0000000..dc598c5 --- /dev/null +++ b/physics/LatAnalyze @@ -0,0 +1 @@ +../lib \ No newline at end of file diff --git a/physics/Makefile.am b/physics/Makefile.am new file mode 100644 index 0000000..51f34e7 --- /dev/null +++ b/physics/Makefile.am @@ -0,0 +1,15 @@ +if CXX_GNU + COM_CXXFLAGS = -Wall -W -pedantic -Wno-deprecated-declarations +else +if CXX_INTEL + COM_CXXFLAGS = -wd1682 -Wall +endif +endif + +bin_PROGRAMS = latan-2pt-fit + +latan_2pt_fit_SOURCES = 2pt-fit.cpp +latan_2pt_fit_CXXFLAGS = $(COM_CXXFLAGS) +latan_2pt_fit_LDFLAGS = -L../lib/.libs -lLatAnalyze + +ACLOCAL_AMFLAGS = -I .buildutils/m4 From 1bede86547ef4a99dab4798d5d37f2dcd630033a Mon Sep 17 00:00:00 2001 From: Antonin Portelli Date: Tue, 14 Jun 2016 14:06:59 +0100 Subject: [PATCH 09/20] systematically using LatCore argument parser for utilities --- utils/resample.cpp | 90 ++++++++++++++++++---------------------- utils/sample-combine.cpp | 73 +++++++++++++------------------- 2 files changed, 69 insertions(+), 94 deletions(-) diff --git a/utils/resample.cpp b/utils/resample.cpp index 61d8917..8e3117d 100644 --- a/utils/resample.cpp +++ b/utils/resample.cpp @@ -17,74 +17,66 @@ * along with LatAnalyze 3. If not, see . */ +#include #include #include +#include #ifndef DEF_NSAMPLE -#define DEF_NSAMPLE 100 +#define DEF_NSAMPLE "100" +#endif + +#ifdef HAVE_HDF5 +#define DEF_FMT "h5" +#else +#define DEF_FMT "sample" #endif using namespace std; using namespace Latan; -static void usage(const string &cmdName) -{ - cerr << "usage: " << cmdName; - cerr << " [-n -b -r -o -f {h5|sample}]"; - cerr << " "; - cerr << endl; - exit(EXIT_FAILURE); -} - int main(int argc, char *argv[]) { // argument parsing //////////////////////////////////////////////////////// - int c; + OptParser opt; + bool parsed; random_device rd; SeedType seed = rd(); - string manFileName, nameFileName, cmdName, outDirName = "."; - string ext = "h5"; - Index binSize = 1, nSample = DEF_NSAMPLE; + string manFileName, nameFileName, outDirName; + string ext; + Index binSize, nSample; - opterr = 0; - cmdName = basename(argv[0]); - while ((c = getopt(argc, argv, "b:n:r:o:f:")) != -1) + opt.addOption("n", "nsample" , OptParser::OptType::value, true, + "number of samples", DEF_NSAMPLE); + opt.addOption("b", "bin" , OptParser::OptType::value, true, + "bin size", "1"); + opt.addOption("r", "seed" , OptParser::OptType::value, true, + "random generator seed (default: random)"); + opt.addOption("o", "output-dir", OptParser::OptType::value, true, + "output directory", "."); + opt.addOption("f", "format" , OptParser::OptType::value, true, + "output file format", DEF_FMT); + opt.addOption("" , "help" , OptParser::OptType::trigger, true, + "show this help message and exit"); + parsed = opt.parse(argc, argv); + if (!parsed or (opt.getArgs().size() != 1) or opt.gotOption("help")) { - switch (c) - { - case 'b': - binSize = strTo(optarg); - break; - case 'n': - nSample = strTo(optarg); - break; - case 'o': - outDirName = optarg; - break; - case 'r': - seed = strTo(optarg); - break; - case 'f': - ext = optarg; - break; - case '?': - cerr << "error parsing option -" << char(optopt) << endl; - usage(cmdName); - break; - default: - usage(cmdName); - break; - } + cerr << "usage: " << argv[0]; + cerr << " " << endl; + cerr << endl << "Possible options:" << endl << opt << endl; + + return EXIT_FAILURE; } - if (argc - optind == 2) + nSample = opt.optionValue("n"); + binSize = opt.optionValue("b"); + if (opt.gotOption("r")) { - manFileName = argv[optind]; - nameFileName = argv[optind+1]; - } - else - { - usage(cmdName); + seed = opt.optionValue("r"); } + ext = opt.optionValue("f"); + outDirName = opt.optionValue("o"); + manFileName = opt.getArgs()[0]; + nameFileName = opt.getArgs()[1]; // parameter parsing /////////////////////////////////////////////////////// vector dataFileName, name; diff --git a/utils/sample-combine.cpp b/utils/sample-combine.cpp index e24c432..453434c 100644 --- a/utils/sample-combine.cpp +++ b/utils/sample-combine.cpp @@ -17,28 +17,19 @@ * along with LatAnalyze 3. If not, see . */ +#include #include #include using namespace std; using namespace Latan; -static void usage(const string &cmdName) -{ - cerr << "usage: " << cmdName; - cerr << " [-o ]"; - cerr << " ... "; - cerr << endl; - exit(EXIT_FAILURE); -} - template static void loadAndCheck(vector &sample, const vector &fileName) { const unsigned int n = sample.size(); Index nSample = 0; - cout << "-- loading data..." << endl; for (unsigned int i = 0; i < n; ++i) { sample[i] = Io::load(fileName[i]); @@ -137,49 +128,41 @@ void process(const string &outFileName, const vector &fileName, int main(int argc, char *argv[]) { // argument parsing //////////////////////////////////////////////////////// + OptParser opt; + bool parsed; string cmdName, outFileName = "", code; vector fileName; - int c; unsigned int n = 0; - opterr = 0; - cmdName = basename(argv[0]); - while ((c = getopt(argc, argv, "o:")) != -1) + opt.addOption("o", "output", OptParser::OptType::value , true, + "output file name (default: result not saved)"); + opt.addOption("" , "help" , OptParser::OptType::trigger, true, + "show this help message and exit"); + parsed = opt.parse(argc, argv); + if (opt.getArgs().size() >= 1) { - switch (c) - { - case 'o': - outFileName = optarg; - break; - case '?': - cerr << "error parsing option -" << char(optopt) << endl; - usage(cmdName); - break; - default: - usage(cmdName); - break; - } - } - if (argc - optind >= 1) - { - n = strTo(argv[optind]); - if (argc - optind == static_cast(n + 2)) - { - fileName.resize(n); - code = argv[optind + 1]; - for (unsigned int i = 0; i < n; ++i) - { - fileName[i] = argv[optind + 2 + i]; - } - } - else - { - usage(cmdName); - } + n = strTo(opt.getArgs()[0]); } else { - usage(cmdName); + parsed = false; + } + if (!parsed or (opt.getArgs().size() != n + 2) or opt.gotOption("help")) + { + cerr << "usage: " << argv[0]; + cerr << " ... " << endl; + cerr << endl << "Possible options:" << endl << opt << endl; + + return EXIT_FAILURE; + } + if (opt.gotOption("o")) + { + outFileName = opt.optionValue("o"); + } + code = opt.getArgs()[1]; + for (unsigned int i = 0; i < n; ++i) + { + fileName.push_back(opt.getArgs()[2 + i]); } // process data //////////////////////////////////////////////////////////// From 2976f6f3476691671e4abc800db88dee0b1d8698 Mon Sep 17 00:00:00 2001 From: Antonin Portelli Date: Tue, 14 Jun 2016 14:08:02 +0100 Subject: [PATCH 10/20] preparing for 3.2 --- configure.ac | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/configure.ac b/configure.ac index 38c1473..9191118 100644 --- a/configure.ac +++ b/configure.ac @@ -2,7 +2,7 @@ # Initialization AC_PREREQ([2.63]) -AC_INIT([LatAnalyze],[3.1.1-dev],[antonin.portelli@me.com],[LatAnalyze]) +AC_INIT([LatAnalyze],[3.2],[antonin.portelli@me.com],[LatAnalyze]) AC_CONFIG_AUX_DIR([.buildutils]) AC_CONFIG_SRCDIR([lib/Global.cpp]) AC_CONFIG_SRCDIR([utils/sample_read.cpp]) From 05ac1cc3adaee89c6282749985c49562878a97cb Mon Sep 17 00:00:00 2001 From: Antonin Portelli Date: Tue, 14 Jun 2016 17:31:47 +0100 Subject: [PATCH 11/20] Travis: fix for Linux clang builds --- .travis.yml | 10 ++++------ 1 file changed, 4 insertions(+), 6 deletions(-) diff --git a/.travis.yml b/.travis.yml index 638670f..f051d34 100644 --- a/.travis.yml +++ b/.travis.yml @@ -7,6 +7,7 @@ notifications: cache: directories: - ci-scripts/local + - ci-scripts/clang matrix: include: @@ -44,27 +45,24 @@ matrix: apt: sources: - ubuntu-toolchain-r-test - - llvm-toolchain-precise-3.6 packages: - - clang-3.6 - libgsl0-dev - flex - bison - env: VERSION=-3.6 + env: CLANG_LINK=http://llvm.org/releases/3.6.0/clang+llvm-3.6.0-x86_64-linux-gnu-ubuntu-14.04.tar.xz - compiler: clang addons: apt: sources: - ubuntu-toolchain-r-test - - llvm-toolchain-precise-3.7 packages: - - clang-3.7 - libgsl0-dev - flex - bison - env: VERSION=-3.7 + env: CLANG_LINK=http://llvm.org/releases/3.7.0/clang+llvm-3.7.0-x86_64-linux-gnu-ubuntu-14.04.tar.xz before_install: + - if [[ "$TRAVIS_OS_NAME" == "linux" ]] && [[ "$CC" == "clang" ]] && [ ! -e clang ]; then wget $CLANG_LINK; tar -xf `basename $CLANG_LINK`; mv clang* clang; cd clang; export PATH="`pwd`/bin:${PATH}"; cd -; fi - if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then brew update; fi - if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then brew install gsl; fi - if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then brew install bison flex; export PATH="/usr/local/opt/flex/bin:/usr/local/opt/bison/bin:$PATH"; fi From 16ea3e753a9ef6e8fda702e074949f568b4c228b Mon Sep 17 00:00:00 2001 From: Antonin Portelli Date: Tue, 14 Jun 2016 17:39:45 +0100 Subject: [PATCH 12/20] Travis fix --- .travis.yml | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/.travis.yml b/.travis.yml index f051d34..f864d88 100644 --- a/.travis.yml +++ b/.travis.yml @@ -62,7 +62,9 @@ matrix: env: CLANG_LINK=http://llvm.org/releases/3.7.0/clang+llvm-3.7.0-x86_64-linux-gnu-ubuntu-14.04.tar.xz before_install: - - if [[ "$TRAVIS_OS_NAME" == "linux" ]] && [[ "$CC" == "clang" ]] && [ ! -e clang ]; then wget $CLANG_LINK; tar -xf `basename $CLANG_LINK`; mv clang* clang; cd clang; export PATH="`pwd`/bin:${PATH}"; cd -; fi + - cd ci-scripts + - if [[ "$TRAVIS_OS_NAME" == "linux" ]] && [[ "$CC" == "clang" ]] && [ ! -e clang ]; then wget $CLANG_LINK; tar -xf `basename $CLANG_LINK`; mv clang* clang; fi + - if [[ "$TRAVIS_OS_NAME" == "linux" ]] && [[ "$CC" == "clang" ]]; then export PATH="`pwd`/clang/bin:${PATH}"; fi - if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then brew update; fi - if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then brew install gsl; fi - if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then brew install bison flex; export PATH="/usr/local/opt/flex/bin:/usr/local/opt/bison/bin:$PATH"; fi @@ -72,7 +74,6 @@ install: - export LATDIR=`pwd` - export CC=$CC$VERSION - export CXX=$CXX$VERSION - - cd ci-scripts - ./install-deps.sh `pwd`/local - cd .. - if [[ "$TRAVIS_OS_NAME" == "linux" ]]; then export LD_LIBRARY_PATH=${LATDIR}/ci-scripts/local/lib:$LD_LIBRARY_PATH; fi From 3603d67d97103c9c24b82d8a8fd0c85cc6571b07 Mon Sep 17 00:00:00 2001 From: Antonin Portelli Date: Tue, 14 Jun 2016 17:46:04 +0100 Subject: [PATCH 13/20] Travis fix --- .travis.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.travis.yml b/.travis.yml index f864d88..55822eb 100644 --- a/.travis.yml +++ b/.travis.yml @@ -63,7 +63,7 @@ matrix: before_install: - cd ci-scripts - - if [[ "$TRAVIS_OS_NAME" == "linux" ]] && [[ "$CC" == "clang" ]] && [ ! -e clang ]; then wget $CLANG_LINK; tar -xf `basename $CLANG_LINK`; mv clang* clang; fi + - if [[ "$TRAVIS_OS_NAME" == "linux" ]] && [[ "$CC" == "clang" ]] && [ ! -e clang/bin ]; then wget $CLANG_LINK; tar -xf `basename $CLANG_LINK`; mv clang* clang; fi - if [[ "$TRAVIS_OS_NAME" == "linux" ]] && [[ "$CC" == "clang" ]]; then export PATH="`pwd`/clang/bin:${PATH}"; fi - if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then brew update; fi - if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then brew install gsl; fi From 3bff42b55408f3065d8d66a15a6117a555ae95b9 Mon Sep 17 00:00:00 2001 From: Antonin Portelli Date: Tue, 14 Jun 2016 17:58:24 +0100 Subject: [PATCH 14/20] Travis fix --- .travis.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.travis.yml b/.travis.yml index 55822eb..342ab29 100644 --- a/.travis.yml +++ b/.travis.yml @@ -63,7 +63,7 @@ matrix: before_install: - cd ci-scripts - - if [[ "$TRAVIS_OS_NAME" == "linux" ]] && [[ "$CC" == "clang" ]] && [ ! -e clang/bin ]; then wget $CLANG_LINK; tar -xf `basename $CLANG_LINK`; mv clang* clang; fi + - if [[ "$TRAVIS_OS_NAME" == "linux" ]] && [[ "$CC" == "clang" ]] && [ ! -e clang/bin ]; then wget $CLANG_LINK; tar -xf `basename $CLANG_LINK`; mv clang+* clang; fi - if [[ "$TRAVIS_OS_NAME" == "linux" ]] && [[ "$CC" == "clang" ]]; then export PATH="`pwd`/clang/bin:${PATH}"; fi - if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then brew update; fi - if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then brew install gsl; fi From 9631a2565f0855867b1897b8b9e7ba7596fe44a1 Mon Sep 17 00:00:00 2001 From: Antonin Portelli Date: Tue, 14 Jun 2016 18:03:17 +0100 Subject: [PATCH 15/20] Travis fix --- .travis.yml | 9 +++++++-- 1 file changed, 7 insertions(+), 2 deletions(-) diff --git a/.travis.yml b/.travis.yml index 342ab29..7334b99 100644 --- a/.travis.yml +++ b/.travis.yml @@ -62,18 +62,23 @@ matrix: env: CLANG_LINK=http://llvm.org/releases/3.7.0/clang+llvm-3.7.0-x86_64-linux-gnu-ubuntu-14.04.tar.xz before_install: + - export LATDIR=`pwd` - cd ci-scripts - if [[ "$TRAVIS_OS_NAME" == "linux" ]] && [[ "$CC" == "clang" ]] && [ ! -e clang/bin ]; then wget $CLANG_LINK; tar -xf `basename $CLANG_LINK`; mv clang+* clang; fi - - if [[ "$TRAVIS_OS_NAME" == "linux" ]] && [[ "$CC" == "clang" ]]; then export PATH="`pwd`/clang/bin:${PATH}"; fi + - if [[ "$TRAVIS_OS_NAME" == "linux" ]] && [[ "$CC" == "clang" ]]; then export PATH="${LATDIR}/ci-scripts/clang/bin:${PATH}"; fi - if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then brew update; fi - if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then brew install gsl; fi - if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then brew install bison flex; export PATH="/usr/local/opt/flex/bin:/usr/local/opt/bison/bin:$PATH"; fi - if [[ "$TRAVIS_OS_NAME" == "osx" ]] && [[ "$CC" == "gcc" ]]; then brew install gcc5; fi install: - - export LATDIR=`pwd` - export CC=$CC$VERSION - export CXX=$CXX$VERSION + - echo $PATH + - which $CC + - $CC --version + - which $CXX + - $CXX --version - ./install-deps.sh `pwd`/local - cd .. - if [[ "$TRAVIS_OS_NAME" == "linux" ]]; then export LD_LIBRARY_PATH=${LATDIR}/ci-scripts/local/lib:$LD_LIBRARY_PATH; fi From b6a96619d2d505372d369335192df4adef7d23e2 Mon Sep 17 00:00:00 2001 From: Antonin Portelli Date: Tue, 14 Jun 2016 18:07:08 +0100 Subject: [PATCH 16/20] Travis debug --- .travis.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/.travis.yml b/.travis.yml index 7334b99..b8830bc 100644 --- a/.travis.yml +++ b/.travis.yml @@ -72,6 +72,7 @@ before_install: - if [[ "$TRAVIS_OS_NAME" == "osx" ]] && [[ "$CC" == "gcc" ]]; then brew install gcc5; fi install: + - ls /home/travis/build/aportelli/LatAnalyze/ci-scripts/clang/bin - export CC=$CC$VERSION - export CXX=$CXX$VERSION - echo $PATH From 6a37baaf2890e11b438add5e01ecda4a7072e90a Mon Sep 17 00:00:00 2001 From: Antonin Portelli Date: Tue, 14 Jun 2016 18:12:32 +0100 Subject: [PATCH 17/20] Travis debug --- .travis.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.travis.yml b/.travis.yml index b8830bc..9f5489e 100644 --- a/.travis.yml +++ b/.travis.yml @@ -64,7 +64,7 @@ matrix: before_install: - export LATDIR=`pwd` - cd ci-scripts - - if [[ "$TRAVIS_OS_NAME" == "linux" ]] && [[ "$CC" == "clang" ]] && [ ! -e clang/bin ]; then wget $CLANG_LINK; tar -xf `basename $CLANG_LINK`; mv clang+* clang; fi + - if [[ "$TRAVIS_OS_NAME" == "linux" ]] && [[ "$CC" == "clang" ]] && [ ! -e clang/bin ]; then wget $CLANG_LINK; tar -xf `basename $CLANG_LINK`; mv clang+* clang; pwd; ls; fi - if [[ "$TRAVIS_OS_NAME" == "linux" ]] && [[ "$CC" == "clang" ]]; then export PATH="${LATDIR}/ci-scripts/clang/bin:${PATH}"; fi - if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then brew update; fi - if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then brew install gsl; fi From 761d68bc823f77c547a79994571326c34b0c561e Mon Sep 17 00:00:00 2001 From: Antonin Portelli Date: Tue, 14 Jun 2016 18:19:41 +0100 Subject: [PATCH 18/20] Travis debug --- .travis.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.travis.yml b/.travis.yml index 9f5489e..15a66f0 100644 --- a/.travis.yml +++ b/.travis.yml @@ -64,7 +64,7 @@ matrix: before_install: - export LATDIR=`pwd` - cd ci-scripts - - if [[ "$TRAVIS_OS_NAME" == "linux" ]] && [[ "$CC" == "clang" ]] && [ ! -e clang/bin ]; then wget $CLANG_LINK; tar -xf `basename $CLANG_LINK`; mv clang+* clang; pwd; ls; fi + - if [[ "$TRAVIS_OS_NAME" == "linux" ]] && [[ "$CC" == "clang" ]] && [ ! -e clang/bin ]; then wget $CLANG_LINK; tar -xf `basename $CLANG_LINK`; mkdir clang; mv clang+*/* clang/; pwd; ls; ls clang; fi - if [[ "$TRAVIS_OS_NAME" == "linux" ]] && [[ "$CC" == "clang" ]]; then export PATH="${LATDIR}/ci-scripts/clang/bin:${PATH}"; fi - if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then brew update; fi - if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then brew install gsl; fi From 553181787fdcde3ce0918909deebedefce7bf68c Mon Sep 17 00:00:00 2001 From: Antonin Portelli Date: Tue, 14 Jun 2016 18:28:51 +0100 Subject: [PATCH 19/20] more Travis fix --- .travis.yml | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/.travis.yml b/.travis.yml index 15a66f0..a7dcd36 100644 --- a/.travis.yml +++ b/.travis.yml @@ -46,6 +46,7 @@ matrix: sources: - ubuntu-toolchain-r-test packages: + - g++-4.8 - libgsl0-dev - flex - bison @@ -56,6 +57,7 @@ matrix: sources: - ubuntu-toolchain-r-test packages: + - g++-4.8 - libgsl0-dev - flex - bison @@ -64,15 +66,15 @@ matrix: before_install: - export LATDIR=`pwd` - cd ci-scripts - - if [[ "$TRAVIS_OS_NAME" == "linux" ]] && [[ "$CC" == "clang" ]] && [ ! -e clang/bin ]; then wget $CLANG_LINK; tar -xf `basename $CLANG_LINK`; mkdir clang; mv clang+*/* clang/; pwd; ls; ls clang; fi + - if [[ "$TRAVIS_OS_NAME" == "linux" ]] && [[ "$CC" == "clang" ]] && [ ! -e clang/bin ]; then wget $CLANG_LINK; tar -xf `basename $CLANG_LINK`; mkdir clang; mv clang+*/* clang/; fi - if [[ "$TRAVIS_OS_NAME" == "linux" ]] && [[ "$CC" == "clang" ]]; then export PATH="${LATDIR}/ci-scripts/clang/bin:${PATH}"; fi + - if [[ "$TRAVIS_OS_NAME" == "linux" ]] && [[ "$CC" == "clang" ]]; then export LD_LIBRARY_PATH="${LATDIR}/ci-scripts/clang/lib:${LD_LIBRARY_PATH}"; fi - if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then brew update; fi - if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then brew install gsl; fi - if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then brew install bison flex; export PATH="/usr/local/opt/flex/bin:/usr/local/opt/bison/bin:$PATH"; fi - if [[ "$TRAVIS_OS_NAME" == "osx" ]] && [[ "$CC" == "gcc" ]]; then brew install gcc5; fi install: - - ls /home/travis/build/aportelli/LatAnalyze/ci-scripts/clang/bin - export CC=$CC$VERSION - export CXX=$CXX$VERSION - echo $PATH From 77a585ac4ba4a2759e582d7527c529ca531ed90d Mon Sep 17 00:00:00 2001 From: Antonin Portelli Date: Tue, 14 Jun 2016 18:55:51 +0100 Subject: [PATCH 20/20] Readme update --- Readme.md | 12 +++++++++++- 1 file changed, 11 insertions(+), 1 deletion(-) diff --git a/Readme.md b/Readme.md index 8dbbdb0..397d877 100644 --- a/Readme.md +++ b/Readme.md @@ -55,11 +55,21 @@ in the `ci-scripts` directory where `` is where you want LatAnalyze (and For a more customised installation, one first needs to generate the build system by running `./bootstrap.sh` in the root directory. Then the library can be built and installed through the usual GNU mantra `./configure && make && make install`. Use `./configure --help` to obtain a list of possible options for `./configure`. Because Eigen expressions rely a lot on inlining and compiler optimisations it is strongly recommended to set the `CXXFLAGS` variable to `-O3 -march=native -mtune=native`. ## History +#### v3.2 (needs LatCore 1.1) +Additions: +* 2-pt function fitter `latan-2pt-fit` +* Tool to extract one element of a matrix sample `latan-sample-element` +* Band plotting + +Changes: +* Sample utilities renamed `latan-sample-*` +* Resample utility renamed `latan-resample` + #### v3.1.2 Fixes: * HDF5 archive URL update in build scripts -#### v3.1.1 +#### v3.1.1 (needs LatCore 1.0) Fixes: * Minuit precision fixed * Minor fit interface fixes