unittests.cpp

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/* unittests.cpp : runs all internal unint tests from the library
 * Copyright (C) 2014  Daniel Haley
 * 
 * This program is free software: you can redistribute it and/or modify
 * it under the terms of the GNU General Public License as published by
 * the Free Software Foundation, either version 3 of the License, or
 * (at your option) any later version.
 * 
 * This program is distributed in the hope that it will be useful,
 * but WITHOUT ANY WARRANTY; without even the implied warranty of
 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 * GNU General Public License for more details.
 * 
 * You should have received a copy of the GNU General Public License
 * along with this program.  If not, see <http://www.gnu.org/licenses/>.
 */
#include <iostream>
#include <cassert>

#include "atomprobe/atomprobe.h"

#ifndef ASSERT
    #define ASSERT(f) assert( (f) );
#endif

#ifdef TEST
#undef TEST
#define TEST(f) { if(!(f))  return false; }
#endif

using namespace std;
using namespace AtomProbe;

vector<string> rangePaths()
{
    //TODO: Replace with proper system to obtain
    // the actual range path, relative to this folder
    // e.g. via a glob
    vector<string> paths;
    paths.push_back("samples/ranges/test10.rng");
    paths.push_back("samples/ranges/test11.rng");
    paths.push_back("samples/ranges/test12.rng");
    paths.push_back("samples/ranges/test1.env");
    paths.push_back("samples/ranges/test1.rng");
    paths.push_back("samples/ranges/test1.rrng");
    paths.push_back("samples/ranges/test2.rng");
    paths.push_back("samples/ranges/test2.rrng");
    paths.push_back("samples/ranges/test3.rng");
    paths.push_back("samples/ranges/test3.rrng");
    paths.push_back("samples/ranges/test4.rng");
    paths.push_back("samples/ranges/test4.rrng");
    paths.push_back("samples/ranges/test5.rng");
    paths.push_back("samples/ranges/test5.rrng");
    paths.push_back("samples/ranges/test6.rrng");
    paths.push_back("samples/ranges/test7.rng");
    paths.push_back("samples/ranges/test8.rng");
    paths.push_back("samples/ranges/test9.rng");

    return paths;
}

#ifdef DEBUG
void gsl_catch_errors(const char *reason, const char *file, int line, int gsl_errno)
{
    cerr << "Failed because :" << reason << " in file " << file << " line" << line << " error number :" << gsl_errno << endl;
    ASSERT(false);
}
#endif

bool runTests()
{
#ifdef DEBUG
    //Disable the GSL error handler.
    //It uses abort() which destroys the stack trace.
    // painful for debugging
    gsl_set_error_handler(gsl_catch_errors);

    bool haveAbundance=false;
    AbundanceData abundance;
    if(!abundance.open("naturalAbundance.xml"))
        haveAbundance=true;

    cerr << "Testing overlap...";
    TEST(testDeconvolve());
    cerr << "\tDone" << endl;
    
    cerr << "Testing rotation...";
    TEST(testRotationAlgorithms());
    cerr << "\tDone" << endl;

//Qhull crashes under cygwin
#ifndef __CYGWIN__
    cerr << "Testing Convex Hull...";
    TEST(testConvexHull());
    cerr << "\tDone" << endl;
#endif
    cerr << "Testing progress bar...";
    TEST(testProgressBar()); //No need for "Done",its built into progress bar.

    cerr << "KD tree...";
    TEST(K3DTreeExact::runUnitTests());
    TEST(K3DTreeApprox::test());
    cerr << "\tDone" << endl;

    cerr << "Mesh tests...";
    TEST(meshTests());
    cerr << "\tDone" << endl;

    cerr << "Testing sampling...";
    TEST(testSampling())
    cerr << "\tDone" << endl;

    cerr << "Isotope tests..." ;
    TEST(AbundanceData::runUnitTests())
    cerr << "\tDone" << endl;
    
    cerr << "Knapsack tests..." ;
    TEST(MassTool::runUnitTests())
    cerr << "\tDone" << endl;

    cerr << "Overlap tests..." ;
    TEST(testOverlapDetect());
    cerr << "\tDone" << endl;

    cerr << "Projection tests..." ;
    TEST(testProjection());
    cerr << "\tDone" << endl;
    
    cerr << "Miller index tests...";
    TEST(millerTest());
    cerr << "\tDone" << endl;
    
    cerr << "Reconstruction tests...";
    TEST(AtomProbe::reconstructTest());
    cerr << "\tDone" << endl;
    
    cerr << "Isotope Filter tests...";
    TEST(AtomProbe::isotopeFilterTests());
    cerr << "\tDone" << endl;

    vector<string> rangeFilePaths;
    rangeFilePaths =rangePaths();
    
    cerr << "Range tests...";
    for(auto ui=0; ui < rangeFilePaths.size();ui++)
    {
        RangeFile rng;
        TEST(rng.open(rangeFilePaths[ui].c_str()));

        TEST(rng.isSelfConsistent());
    }
    TEST(RangeFile::test());
    TEST(MultiRange::test());
    //To test the splitting code n 
    if(haveAbundance)
    {
        cerr << "(+Multi-split)...";
        TEST(MultiRange::testSplit(abundance));
    }
    cerr << "\tDone" << endl;
    
    cerr << "Range check tests...";
    TEST(AtomProbe::testRangeChecking());
    cerr << "\tDone" << endl;

    cerr << "Generation tests....";
    TEST(AtomProbe::runGenerateTests());
    cerr << "\tDone" << endl;
    
    cerr << "Mass<>mol conversion...";
    TEST(AtomProbe::testMassMolConversion());
    cerr << "\tDone" << endl;
    
    cerr << "Composition tests....";
    TEST(AtomProbe::testComposition());
    cerr << "\tDone" << endl;
    
    cerr << "Statistics tests....";
    TEST(AtomProbe::runConfidenceTests());
    cerr << "\tDone" << endl;

    cerr << "Spectrum tests....";
    TEST(AtomProbe::testBackgroundFitMaths());
    cerr << "\tDone" << endl;
    cerr << "Voxel tests....";
    TEST(AtomProbe::runVoxelTests());
    cerr << "\tDone" << endl;

    cerr << "Isosurface tests...";
    TEST(AtomProbe::testIsoSurface());
    cerr << "\tDone" << endl; 

    cerr << "Misc. Maths tests....";
    TEST(AtomProbe::runMiscMathsTests());
    TEST(AtomProbe::testPoint3D());
    TEST(AtomProbe::testIonHit());
    cerr << "\tDone" << endl;

    if(haveAbundance)
    {
        cerr << "Ion Adjacency tests...";
        TEST(AtomProbe::runMiscMathsTests());
        cerr << "\tDone" << endl;
    }
    else
        cerr << "Skipping Ion Adjacency ; no abundance" << endl;

#else
    cerr << "Tests not enabled in release mode. Please recompile in debug mode" << endl;
#endif
    return true;
}

int main()
{
    cerr << "Running test program " << endl;
    if(!runTests())
    {
        cerr << "unit tests failed" << endl;
        return 1;
    }

    return 0;   
}