Index: trunk/tests/time_stamp.hh
===================================================================
--- trunk/tests/time_stamp.hh	(revision 563)
+++ trunk/tests/time_stamp.hh	(revision 564)
@@ -1,29 +0,0 @@
-#ifndef TIME_STAMP_H_
-#define TIME_STAMP_H_
-
-//
-// Return the string representing current time in the format hh:mm:ss
-//
-// I. Volobouev
-// March 2013
-//
-
-#include <ctime>
-#include <cstdio>
-#include <string>
-
-inline std::string time_stamp()
-{
-    struct tm *current;
-    time_t now;
-
-    time(&now);
-    current = localtime(&now);
-
-    char buf[10];
-    sprintf(buf, "%02i:%02i:%02i", current->tm_hour,
-            current->tm_min, current->tm_sec);
-    return std::string(buf);
-}
-
-#endif // TIME_STAMP_H_
Index: trunk/tests/jacobiEpsPseudoExp.cc
===================================================================
--- trunk/tests/jacobiEpsPseudoExp.cc	(revision 563)
+++ trunk/tests/jacobiEpsPseudoExp.cc	(revision 564)
@@ -1,325 +0,0 @@
-#include <string>
-#include <sstream>
-#include <iostream>
-#include <fstream>
-#include <cerrno>
-#include <utility>
-
-#include <string.h>
-#include <unistd.h>
-
-#include <sys/stat.h>
-#include <sys/types.h>
-
-#include "test_utils.hh"
-#include "time_stamp.hh"
-
-#include "npstat/nm/ClassicalOrthoPolys1D.hh"
-#include "npstat/nm/ContOrthoPoly1D.hh"
-#include "npstat/nm/GaussLegendreQuadrature.hh"
-
-#include "npstat/stat/Distributions1D.hh"
-#include "npstat/stat/SampleAccumulator.hh"
-#include "npstat/stat/orthoPoly1DVProducts.hh"
-
-#include "npstat/rng/MersenneTwister.hh"
-
-using namespace npstat;
-using namespace std;
-
-
-inline static double kdelta(const unsigned i,
-                            const unsigned j)
-{
-    return i == j ? 1.0 : 0.0;
-}
-
-
-static double calculateExpectation(
-    const JacobiOrthoPoly1D& jac, const unsigned nPoints,
-    const unsigned m, const unsigned n,
-    const unsigned maxdeg, const bool highOrder)
-{
-    const unsigned sumdeg = (unsigned)(jac.alpha()) + (unsigned)(jac.beta()) + 4U*maxdeg;
-    const unsigned nGood = GaussLegendreQuadrature::minimalExactRule(sumdeg);
-    assert(nGood);
-    GaussLegendreQuadrature glq(nGood);
-    return oracleEpsExpectation(jac, glq, nPoints, m, n, highOrder);
-}
-
-
-static double calculateCovariance(
-    const JacobiOrthoPoly1D& jac, const unsigned nPoints,
-    const unsigned m1, const unsigned n1,
-    const unsigned m2, const unsigned n2,
-    const unsigned maxdeg, const bool highOrder)
-{
-    const unsigned sumdeg = (unsigned)(jac.alpha()) + (unsigned)(jac.beta()) + 8U*maxdeg;
-    const unsigned nGood = GaussLegendreQuadrature::minimalExactRule(sumdeg);
-    assert(nGood);
-    GaussLegendreQuadrature glq(nGood);
-    return oracleEpsCovariance(jac, glq, nPoints, m1, n1, m2, n2, highOrder);
-}
-
-
-static string eps_name(const unsigned m, const unsigned n,
-                       const char* prefix)
-{
-    ostringstream os;
-    os << prefix << "_eps_" << m << '_' << n;
-    return os.str();
-}
-
-
-static string cov_columns(const unsigned maxdeg)
-{
-    ostringstream os;
-    unsigned colnum = 0;
-
-    for (unsigned j=0; j<=maxdeg; ++j)
-        for (unsigned i=0; i<=j; ++i)
-            for (unsigned n=0; n<=maxdeg; ++n)
-                for (unsigned m=0; m<=n; ++m)
-                    if (std::make_pair(m,n) <= std::make_pair(i,j))
-                    {
-                        if (colnum++)
-                            os << ' ';
-                        os << "cov_" << m << '_' << n << '_' << i << '_' << j;
-                    }
-
-    return os.str();
-}
-
-
-static string pseudo_exp_columns(const unsigned maxdeg)
-{
-    ostringstream os;
-    unsigned colnum = 0;
-
-    for (unsigned j=0; j<=maxdeg; ++j)
-        for (unsigned i=0; i<=j; ++i, ++colnum)
-        {
-            if (colnum)
-                os << ' ';
-            os << eps_name(i, j, "real") << ' '
-               << eps_name(i, j, "ora") << ' '
-               << eps_name(i, j, "est");
-        }
-
-    os << ' ' << cov_columns(maxdeg);
-    return os.str();
-}
-
-
-static string ora_columns(const unsigned maxdeg)
-{
-    ostringstream os;
-    unsigned colnum = 0;
-
-    for (unsigned j=0; j<=maxdeg; ++j)
-        for (unsigned i=0; i<=j; ++i, ++colnum)
-        {
-            if (colnum)
-                os << ' ';
-            os << "eps_" << i << '_' << j;
-        }
-
-    os << ' ' << cov_columns(maxdeg);
-    return os.str();
-}
-
-
-template <class Acc>
-static void print_accumulator(const string& which,
-                              const Acc& acc, const double expMean)
-{
-    const double m = acc.mean();
-    const double u = acc.meanUncertainty();
-    const double nsig = (m - expMean)/u;
-    
-    cout << which << " average is " << m << " +- " << u
-         << ", expected " << expMean << " (" << nsig << " sigma)" << endl;
-}
-
-
-#define dump_parameter(str, value) do {             \
-    str << "set parameters(" << #value << ") " << value << '\n';\
-} while(0);
-
-
-int main(int argc, char const* argv[])
-{
-    const unsigned reportFrequency = 100;
-
-    if (argc != 9)
-    {
-        cout << "Usage: " << parse_progname(argv[0])
-             << " alpha beta pointsPerPseudo nPseudo maxdeg highOrder_eps highOrder_cov dirname" << endl;
-        exit(1);
-    }
-
-    unsigned alpha, beta;
-    if (parse_unsigned(argv[1], &alpha)) exit(1);
-    if (parse_unsigned(argv[2], &beta)) exit(1);
-
-    unsigned perpseudo;
-    if (parse_unsigned(argv[3], &perpseudo)) exit(1);
-    if (!perpseudo)
-    {
-        cerr << "pointsPerPseudo must be positive" << endl;
-        exit(1);
-    }
-
-    unsigned npseudo;
-    if (parse_unsigned(argv[4], &npseudo)) exit(1);
-    if (npseudo < 2)
-    {
-        cerr << "nPseudo must be at least 2" << endl;
-        exit(1);
-    }
-
-    unsigned maxdeg;
-    if (parse_unsigned(argv[5], &maxdeg)) exit(1);
-    if (!maxdeg)
-    {
-        cerr << "maxdeg must be positive" << endl;
-        exit(1);
-    }
-
-    bool highOrder_eps, highOrder_cov;
-    if (parse_bool(argv[6], &highOrder_eps)) exit(1);
-    if (parse_bool(argv[7], &highOrder_cov)) exit(1);
-
-    // Make a new directory and go there
-    const char* dirname = argv[8];
-    if (mkdir(dirname, S_IRWXU | S_IRWXG | S_IROTH | S_IXOTH))
-    {
-        cerr << "Failed to make directory \"" << dirname << "\": "
-             << strerror(errno) << endl;
-        exit(1);
-    }
-    if (chdir(dirname))
-    {
-        cerr << "Failed to change working directory to \"" << dirname << "\": "
-             << strerror(errno) << endl;
-        exit(1);
-    }
-
-    // Print the command used and parsed argument values
-    {
-        ofstream cmdfile("parameters.tcl");
-        assert(cmdfile.is_open());
-        cmdfile << "# " << argv[0];
-        for (int i=1; i<argc; ++i)
-            cmdfile << ' ' << argv[i];
-        cmdfile << '\n';
-
-        cmdfile << "set parameters(executable) \"" << argv[0] << "\"\n";
-        dump_parameter(cmdfile, alpha);
-        dump_parameter(cmdfile, beta);
-        dump_parameter(cmdfile, perpseudo);
-        dump_parameter(cmdfile, npseudo);
-        dump_parameter(cmdfile, maxdeg);
-        dump_parameter(cmdfile, highOrder_eps);
-        dump_parameter(cmdfile, highOrder_cov);
-        cmdfile << "set parameters(dirname) \"" << dirname << "\"\n";
-    }
-
-    // File for saving results of pseudo experiments
-    ofstream outfile("pseudo.txt");
-    assert(outfile.is_open());
-    outfile << "# " << pseudo_exp_columns(maxdeg) << '\n';
-    outfile.precision(10);
-
-    // Various objects needed for calculations
-    Beta1D distro(-1.0, 2.0, beta+1, alpha+1);
-    MersenneTwister rng;
-    JacobiOrthoPoly1D jac(alpha, beta);
-    OrthoPoly1DWeight jacWeight(jac);
-    vector<double> rn;
-    rn.reserve(perpseudo);
-
-    const unsigned integPoints = GaussLegendreQuadrature::minimalExactRule(
-        (unsigned)(jac.alpha()) + (unsigned)(jac.beta()) + 2U*maxdeg);
-
-    for (unsigned ips=0; ips<npseudo; ++ips)
-    {
-        if (reportFrequency > 0)
-            if (ips % reportFrequency == 0)
-                cout << time_stamp() << " running pseudo exp " << ips << endl;
-
-        rn.clear();
-        double tmp;
-        for (unsigned i=0; i<perpseudo; ++i)
-        {
-            distro.random(rng, &tmp);
-            rn.push_back(tmp);
-        }
-
-        // Calculate actual and estimated eps values
-        ContOrthoPoly1D samplePoly(maxdeg, rn);
-
-        for (unsigned j=0; j<=maxdeg; ++j)
-            for (unsigned i=0; i<=j; ++i)
-            {
-                // Actual eps value for this sample (orthonormality uncertainty)
-                const double real_eps = samplePoly.integrateEWPolyProduct(
-                    jacWeight, i, j, -1.0, 1.0, integPoints) - kdelta(i, j);
-                outfile << real_eps << ' ';
-
-                // Oracle eps approximation for this sample
-                const double ora_eps = sampleEpsValue(
-                    jac, &rn[0], perpseudo, i, j, highOrder_eps);
-                outfile << ora_eps << ' ';
-
-                // Chaos poly eps approximation for this sample
-                const double est_eps = samplePoly.epsExpectation(i, j, highOrder_eps);
-                outfile << est_eps << ' ';
-            }
-
-        // Covariances estimated from the sample
-        for (unsigned j=0; j<=maxdeg; ++j)
-            for (unsigned i=0; i<=j; ++i)
-                for (unsigned n=0; n<=maxdeg; ++n)
-                   for (unsigned m=0; m<=n; ++m)
-                        // Calculate only if (m,n) <= (i,j)
-                        if (std::make_pair(m,n) <= std::make_pair(i,j))
-                        {
-                            const double cov = samplePoly.epsCovariance(
-                                m, n, i, j, highOrder_cov);
-                            outfile << cov << ' ';
-                        }
-
-        outfile << '\n';
-    }
-
-    // File for saving oracle predictions
-    ofstream orafile("oracle.txt");
-    assert(orafile.is_open());
-    orafile << "# " << ora_columns(maxdeg) << '\n';
-    orafile.precision(10);
-
-    // Expected eps values with O(N^{-1}) or O(N^{-3/2}) approximation
-    for (unsigned j=0; j<=maxdeg; ++j)
-        for (unsigned i=0; i<=j; ++i)
-        {
-            const double exp_eps = calculateExpectation(
-                jac, perpseudo, i, j, maxdeg, highOrder_eps);
-            orafile << exp_eps << ' ';
-        }
-
-    // Expected eps covariances
-    for (unsigned j=0; j<=maxdeg; ++j)
-        for (unsigned i=0; i<=j; ++i)
-            for (unsigned n=0; n<=maxdeg; ++n)
-                for (unsigned m=0; m<=n; ++m)
-                    if (std::make_pair(m,n) <= std::make_pair(i,j))
-                    {
-                        const double ecov = calculateCovariance(
-                            jac, perpseudo, m, n, i, j, maxdeg, highOrder_cov);
-                        orafile << ecov << ' ';
-                    }
-
-    orafile << '\n';
-    return 0;
-}
Index: trunk/tests/Makefile
===================================================================
--- trunk/tests/Makefile	(revision 563)
+++ trunk/tests/Makefile	(revision 564)
@@ -1,119 +1,118 @@
 
 # Set the following two variables correctly
 UTESTPP_DIR = /home/igv/Code/UnitTest++
 FFTW_LIBDIR = /usr/local/lib
 
 
 OFILES_COMMON = test_utils.o
 
 OTESTS_FAST = test_ArrayND.o test_OrthoPoly1D.o test_OrthoPolyND.o \
               test_Functors.o test_interpolation.o test_LocalPolyFilterND.o \
               test_Distributions1D.o test_InterpolatedDistribution1D.o \
               test_EmpiricalCopula.o test_BoxNDScanner.o \
               test_QuadraticOrthoPolyND.o test_LocalLogisticRegression.o \
               test_randomPermutation.o test_gegenbauerSeriesSum.o \
               test_GaussHermiteQuadrature.o test_SpecialFunctions.o \
               test_GaussLegendreQuadrature.o test_WeightedStatAccumulator.o \
               test_RandomSequenceRepeater.o test_logLikelihoodPeak.o \
               test_legendreSeriesSum.o test_solveCubic.o test_HistoND.o \
               test_SampleAccumulator.o test_GridInterpolatedDistribution.o \
               test_GridAxis.o test_Matrix.o test_StatUtils.o \
               test_amiseOptimalBandwidth.o test_OrderedPointND.o \
               test_CompositeDistributionND.o test_CompositeBuilder.o \
               test_ArchiveIO.o test_Ntuples.o test_LocalQuantileRegression.o \
               test_rectangleQuadrature.o test_RegularSampler1D.o \
               test_Instantiations.o test_chebyshevSeriesSum.o \
               test_dawsonIntegral.o test_NMCombinationSequencer.o \
               test_CrossCovarianceAccumulator.o test_StatAccumulatorPair.o \
               test_findPeak2D.o test_StatAccumulatorArr.o \
               test_goldenSectionSearch.o test_empiricalQuantile.o \
               test_StatAccumulator.o test_binomialCoefficient.o \
               test_CircularMapper1d.o test_LinInterpolatedTableND.o \
               test_StorableMultivariateFunctor.o test_NeymanPearsonWindow1D.o \
               test_hermiteSeriesSum.o test_hermiteSeriesSumPhys.o \
               test_DiscreteDistributions1D.o test_LocalPolyFilter1D.o \
               test_definiteIntegrals.o test_ExpMapper1d.o test_MathUtils.o \
               test_MemoizingSymbetaFilterProvider.o test_ResponseMatrix.o \
               test_gaussianResponseMatrix.o LogLogQuadratic1D.o \
               WeightedTestAccumulator.o TestAccumulator.o test_histoUtils.o \
               test_LocalMultiFilter1D.o test_InterpolatedCompositeBuilder.o \
               test_DensityAveScanND.o test_Distro1DBuilder.o \
               test_findRootNewtonRaphson.o test_Uncertainties.o \
               test_ClassicalOrthoPolys1D.o test_ContOrthoPoly1D.o \
               test_findRootUsingBisections.o test_orthoPoly1DVProducts.o
 
 OTESTS_COMPREHENSIVE = test_ArrayND_cmh.o test_DiscreteBernstein.o \
                        test_KDTree.o test_rescanArray_cmh.o test_lorpeMise1D.o 
 
 # OPTIMIZE = -g
 OPTIMIZE = -std=c++11 -O3
 
 INCLUDES = -I. -I.. -I$(UTESTPP_DIR)/src -I$(FFTW_LIBDIR)/../include
 CPPFLAGS = $(OPTIMIZE) $(INCLUDES) -Wall -W -Werror -Wno-unused-parameter
 
 LIBS = -L../npstat/.libs -lnpstat -L$(UTESTPP_DIR) -lUnitTest++ \
        -L$(FFTW_LIBDIR) -L/usr/lib64 -lfftw3 -llapack -lblas \
        -L/usr/local/lib -lrk -lgeners -lbz2 -lz -lkstest -lm
 
 %.o : %.cc
 	g++ -c $(CPPFLAGS) -fPIC -MD $< -o $@
 	@sed -i 's,\($*\.o\)[:]*\(.*\),$@: $$\(wildcard\2\)\n\1:\2,g' $*.d
 
 # Change the "all" target below to suit your development needs.
 # Useful targets which can be included are:
 #
 #   fast fast_run
 #   comprehensive comprehensive_run
 #   regression regression_run
 #
 # The tests inside the "fast" target are a subset of tests from the
 # "comprehensive" target
 
 all: fast fast_run
 # all: fast regression fast_run regression_run
 # all: comprehensive comprehensive_run regression regression_run
 
 fast: test_main.o $(OTESTS_FAST) $(OFILES_COMMON)
 	rm -f $@
 	g++ $(OPTIMIZE) -fPIC -o $@ $^ $(LIBS)
 
 fast_run: fast
 	./fast
 
 comprehensive: test_main.o $(OTESTS_FAST) \
                $(OTESTS_COMPREHENSIVE) $(OFILES_COMMON)
 	rm -f $@
 	g++ $(OPTIMIZE) -fPIC -o $@ $^ $(LIBS)
 
 comprehensive_run: comprehensive
 	./comprehensive
 
 regression:
 
 regression_run: regression
 	@ echo Running regression tests.
 
 PROGRAMS = kdtree_speed.cc quantileBinFromCdf.cc incompleteGamma.cc \
            convertToSpherical.cc printPermutations.cc showIOTraits.cc \
            hugeNtuple.cc hugeNtupleRead.cc histoStdev.cc effectiveDim.cc \
            buildInterpolatedCheck.cc legendreRoots.cc jacobiPolyStats.cc \
-           jacobiVProducts.cc jacobiEpsTest.cc jacobiEpsPseudoExp.cc \
-           gauss2DRandom.cc
+           jacobiVProducts.cc jacobiEpsTest.cc gauss2DRandom.cc
 
 PROGRAMS += cpp11Random.cc
 
 BINARIES = $(PROGRAMS:.cc=)
 
 binaries: $(BINARIES)
 
 $(BINARIES): % : %.o $(OFILES_COMMON); g++ $(OPTIMIZE) -fPIC -o $@ $^ $(LIBS)
 
 clean:
 	rm -f fast comprehensive $(BINARIES) \
             *.out core.* *.o *.d *~ *.gsbd *.gsbmf
 
 -include test_main.d
 -include $(OFILES_COMMON:.o=.d)
 -include $(OTESTS_FAST:.o=.d)
 -include $(OTESTS_COMPREHENSIVE:.o=.d)
 -include $(PROGRAMS:.cc=.d)