Merge branch 'hotfix/3.1.1' into develop

Readme.md

@@ -55,6 +55,11 @@ in the `ci-scripts` directory where `<prefix>` 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 <options> && 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
+#### v3.1.1
+Fixes:
+* Minuit precision fixed
+* Minor fit interface fixes
+
 #### v3.1
 Additions:
 * Wrappers to NLopt and GSL minimisers.

configure.ac

@@ -2,7 +2,7 @@
 
 # Initialization
 AC_PREREQ([2.63])
-AC_INIT([LatAnalyze],[3.1-dev],[antonin.portelli@me.com],[LatAnalyze])
+AC_INIT([LatAnalyze],[3.1.1-dev],[antonin.portelli@me.com],[LatAnalyze])
 AC_CONFIG_AUX_DIR([.buildutils])
 AC_CONFIG_SRCDIR([lib/Global.cpp])
 AC_CONFIG_SRCDIR([utils/sample_read.cpp])

lib/AsciiFile.cpp

@@ -170,7 +170,7 @@ void AsciiFile::open(const string &name, const unsigned int mode)
 
 std::string AsciiFile::load(const string &name)
 {
-    if ((mode_ & Mode::read)&&(isOpen()))
+    if ((mode_ & Mode::read) and (isOpen()))
     {
         if (!isParsed_)
         {

lib/File.cpp

@@ -57,7 +57,7 @@ void File::deleteData(void)
 
 void File::checkWritability(void)
 {
-    if (!((mode_ & Mode::write)||(mode_ & Mode::append))||!isOpen())
+    if (!((mode_ & Mode::write) or (mode_ & Mode::append)) or !isOpen())
     {
         LATAN_ERROR(Io, "file '" + name_ + "' is not writable");
     }

lib/File.hpp

@@ -110,6 +110,12 @@ const IoT& File::getData(const std::string &name) const
         LATAN_ERROR(Definition, "no data with name '" + name + "' in file "
                     + name_);
     }
+    catch(std::bad_cast)
+    {
+        LATAN_ERROR(Definition, "data with name '" + name + "' in file "
+                    + name_ + " does not have type '" + typeid(IoT).name()
+                    + "'");
+    }
 }
 
 END_LATAN_NAMESPACE

lib/FitInterface.cpp

@@ -58,7 +58,7 @@ void FitInterface::addXDim(const Index nData, const string name,
         scheduleDataCoordInit();
         if (!name.empty())
         {
-            xName().setName(getNXDim(), name);
+            xName().setName(getNXDim() - 1, name);
         }
     }
 }
@@ -70,7 +70,7 @@ void FitInterface::addYDim(const string name)
     scheduleLayoutInit();
     if (!name.empty())
     {
-        yName().setName(getNYDim(), name);
+        yName().setName(getNYDim() - 1, name);
     }
 }
 

lib/Function.cpp

@@ -183,7 +183,7 @@ DoubleFunction & DoubleFunction::operator op##=(const DoubleFunction &f)\
     setFunction(res, getNArg());\
     return *this;\
 }\
-DoubleFunction & DoubleFunction::operator op##=(const DoubleFunction &&f)\
+DoubleFunction & DoubleFunction::operator op##=(const DoubleFunction  and f)\
 {\
     *this op##= f;\
     return *this;\

lib/GslHybridRootFinder.cpp

@@ -122,7 +122,7 @@ GslHybridRootFinder::operator()(const vector<DoubleFunction *> &func)
             break;
         }
         status = gsl_multiroot_test_residual(solver_->f, getPrecision());
-    } while ((status == GSL_CONTINUE)&&(iter < getMaxIteration()));
+    } while ((status == GSL_CONTINUE) and (iter < getMaxIteration()));
     if (verbosity >= Verbosity::Debug)
     {
         cout << "--- done" << endl;

lib/Hdf5File.cpp

@@ -207,14 +207,14 @@ string Hdf5File::getFirstGroupName(void)
 {
     string res;
 
-    if ((mode_ & Mode::read)&&(isOpen()))
+    if ((mode_ & Mode::read) and (isOpen()))
     {
         auto firstGroupName = [](hid_t loc_id, const char *name, void *fname)
         {
             H5G_stat_t statbuf;
 
             H5Gget_objinfo(loc_id, name, 0, &statbuf);
-            if ((statbuf.type == H5G_GROUP) && (strlen((char *)fname) == 0))
+            if ((statbuf.type == H5G_GROUP) and (strlen((char *)fname) == 0))
             {
                 strncpy((char *)fname, name, maxGroupNameSize);
             }
@@ -268,7 +268,7 @@ void Hdf5File::load(DSample &ds, const DataSet &d)
 
 string Hdf5File::load(const string &name)
 {
-    if ((mode_ & Mode::read)&&(isOpen()))
+    if ((mode_ & Mode::read) and (isOpen()))
     {
         string           groupName;
         Group            group;

lib/Histogram.cpp

@@ -165,7 +165,7 @@ double Histogram::operator()(const double x) const
 // percentiles & confidence interval ///////////////////////////////////////////
 double Histogram::percentile(const double p) const
 {
-    if ((p < 0.0)||(p > 100.0))
+    if ((p < 0.0) or (p > 100.0))
     {
         LATAN_ERROR(Range, "percentile (" + strFrom(p) + ")"
                     " is outside the [0, 100] range");

lib/Io.cpp

@@ -38,7 +38,7 @@ unique_ptr<File> Io::open(const std::string &fileName, const unsigned int mode)
 {
     string ext = extension(fileName);
     
-    if ((ext == "dat")||(ext == "sample")||(ext == "seed"))
+    if ((ext == "dat") or (ext == "sample") or (ext == "seed"))
     {
         return unique_ptr<File>(new AsciiFile(fileName, mode));
     }

lib/MathInterpreter.cpp

@@ -478,7 +478,7 @@ void SemicolonNode::compile(Program &program, RunContext &context) const
         bool isSemiColumn = isDerivedFrom<SemicolonNode>(&n[i]);
         bool isKeyword    = isDerivedFrom<KeywordNode>(&n[i]);
         
-        if (isAssign||isSemiColumn||isKeyword)
+        if (isAssign or isSemiColumn or isKeyword)
         {
             n[i].compile(program, context);
         }
@@ -513,7 +513,7 @@ void AssignNode::compile(Program &program, RunContext &context) const
 }
 
 // MathOpNode compile //////////////////////////////////////////////////////////
-#define IFNODE(name, nArg) if ((n.getName() == (name))&&(n.getNArg() == nArg))
+#define IFNODE(name, nArg) if ((n.getName() == (name)) and (n.getNArg() == nArg))
 #define ELIFNODE(name, nArg) else IFNODE(name, nArg)
 #define ELSE else
 
@@ -703,7 +703,7 @@ void MathInterpreter::compile(RunContext &context)
                 }
             }
         }
-        if (!root_||!gotReturn)
+        if (!root_ or !gotReturn)
         {
             LATAN_ERROR(Syntax, "expected 'return' in program '" + codeName_
                         + "'");

lib/MinuitMinimizer.cpp

@@ -61,6 +61,7 @@ const DVec & MinuitMinimizer::operator()(const DoubleFunction &f)
     DVec           &x = getState();
     int            printLevel = 0;
     EMinimizerType minuitAlg  = kCombined;
+    double         prec = getPrecision();
     
     // convert Latan parameters to Minuit parameters
     switch (getVerbosity())
@@ -75,16 +76,21 @@ const DVec & MinuitMinimizer::operator()(const DoubleFunction &f)
             printLevel = 3;
             break;
     }
+    // The factor of 0.002 here is to compensate the dirty hack in Minuit
+    // source used to match the C++ and F77 versions
+    // (cf. VariableMetricBuilder.cxx)
     switch (getAlgorithm())
     {
         case Algorithm::migrad:
             minuitAlg  = kMigrad;
+            prec      /= 0.002;
             break;
         case Algorithm::simplex:
             minuitAlg = kSimplex;
             break;
         case Algorithm::combined:
             minuitAlg  = kCombined;
+            prec      /= 0.002;
             break;
     }
     
@@ -99,7 +105,7 @@ const DVec & MinuitMinimizer::operator()(const DoubleFunction &f)
     
     min.SetStrategy(2);
     min.SetMaxFunctionCalls(getMaxIteration());
-    min.SetTolerance(getPrecision());
+    min.SetTolerance(prec);
     min.SetPrintLevel(printLevel);
     
     // set function and variables
@@ -146,7 +152,7 @@ const DVec & MinuitMinimizer::operator()(const DoubleFunction &f)
         min.Minimize();
         status = min.Status();
         n++;
-    } while (status and (n < getMaxPass()));
+    } while ((status >= 2) and (n < getMaxPass()));
     if (getVerbosity() >= Verbosity::Normal)
     {
         cout << "=================================================" << endl;
@@ -154,7 +160,8 @@ const DVec & MinuitMinimizer::operator()(const DoubleFunction &f)
     switch (status)
     {
         case 1:
-            LATAN_WARNING("invalid minimum: covariance matrix was made positive");
+            // covariance matrix was made positive, the minimum is still good
+            // it just means that Minuit error analysis is inaccurate
             break;
         case 2:
             LATAN_WARNING("invalid minimum: Hesse analysis is not valid");

lib/Plot.cpp

@@ -458,7 +458,7 @@ void Plot::getProgramPath(void)
         {
             for (i=0;path[i];)
             {
-                for (j=i;(path[j])&&(path[j]!=':');j++);
+                for (j=i;(path[j]) and (path[j]!=':');j++);
                 lg = j - i;
                 strncpy(buf,path + i,(size_t)(lg));
                 if (lg == 0)

lib/StatArray.hpp

@@ -262,7 +262,7 @@ namespace ReducOp
     inline Mat<double> tensProd(const Mat<double>  &v1,
                                 const Mat<double>  &v2)
     {
-        if ((v1.cols() != 1)||(v2.cols() != 1))
+        if ((v1.cols() != 1) or (v2.cols() != 1))
         {
             LATAN_ERROR(Size,
                         "tensorial product is only valid with column vectors");

lib/TabFunction.cpp

@@ -65,7 +65,7 @@ double TabFunction::operator()(const double *arg) const
     double result = 0.0, x = arg[0];
 
 
-    if ((x < value_.begin()->first) || (x >= value_.rbegin()->first)) {
+    if ((x < value_.begin()->first) or (x >= value_.rbegin()->first)) {
         LATAN_ERROR(Range, "tabulated function variable out of range "
                                "(x= " + strFrom(x) + " not in ["
                            + strFrom(value_.begin()->first) + ", "

utils/sample_combine.cpp

@@ -187,7 +187,7 @@ int main(int argc, char *argv[])
     {
         process<DSample>(outFileName, fileName, code);
     }
-    catch (bad_cast &e)
+    catch (Exceptions::Definition)
     {
         process<DMatSample>(outFileName, fileName, code);
     }

utils/sample_read.cpp

@@ -24,7 +24,7 @@ using namespace Latan;
 
 int main(int argc, char *argv[])
 {
-    if ((argc < 2) || (argc > 3))
+    if ((argc < 2) or (argc > 3))
     {
         cerr << "usage: " << argv[0] << " <file> [<copy>]" << endl;
 
@@ -46,7 +46,7 @@ int main(int argc, char *argv[])
             Io::save(s, copy, File::Mode::write, name);
         }
     }
-    catch (bad_cast &e)
+    catch (Exceptions::Definition)
     {
         DSample s    = Io::load<DSample>(fileName);
         string  name = Io::getFirstName(fileName);