Merge pull request #50 from willp240/formatting

Formatting
snoplus · Aug 27, 2024 · c96170f · c96170f
2 parents 93b4f81 + 24aab8d
commit c96170f
Showing 227 changed files with 9,791 additions and 8,638 deletions.
diff --git a/HOWTO.md b/HOWTO.md
diff --git a/README.md b/README.md
@@ -1,7 +1,6 @@
 <h1> OXSX </h1>
 Signal Extraction framework for the SNO+ experiment
 
-
 <h2> Dependencies </h2>
 1. GCC compiler capable of compiling C++ code to the C++17 standard
 
@@ -11,7 +10,7 @@ Signal Extraction framework for the SNO+ experiment
 
 4. [SCons](http://www.scons.org/) Is used for the build, also a dependency for RAT
 
-5. [HDF5](https://www.hdfgroup.org/HDF5/release/obtain5.html) Should be configured to install with c++ support ```./configure --enable-cxx && make && make install```
+5. [HDF5](https://www.hdfgroup.org/HDF5/release/obtain5.html) Should be configured to install with c++ support `./configure --enable-cxx && make && make install`
 
 6. [ROOT](https://root.cern.ch/downloading-root) Should be installed with Minuit2 enabled `./configure --enable-minuit2`
 
@@ -28,35 +27,32 @@ Signal Extraction framework for the SNO+ experiment
 <h2>Installation Instructions </h2>
 Follow the installation instructions for each of the above using either the default install location or a different directory if you would prefer. Be careful to start the install with a clean environment.
 
-1. Clone this repository with ```git clone https://github.com/snoplus/oxsx.git```
+1. Clone this repository with `git clone https://github.com/snoplus/oxsx.git`
 
 2. If your dependencies are somewhere the compiler can't find them, copy `config/userconfig.ini.template` to `config/userconfig.ini` and add the relevant paths. Missing entries are assumed to be in standard locations. e.g.
-    ```
-    [root]
-    header_path : <path/to/headers>
-    lib_path    : <path/to/libraries>
-     ```
-  
-3. Run ```scons && scons units```: this will compile the OXSX library and subsequently the unit tests.
 
-4. Test the build was sucessful with ```./test/RunUnits```
+   ```
+   [root]
+   header_path : <path/to/headers>
+   lib_path    : <path/to/libraries>
+   ```
+
+3. Run `scons && scons units`: this will compile the OXSX library and subsequently the unit tests.
 
+4. Test the build was sucessful with `./test/RunUnits`
 
 <h3> Compiling Your Own Scripts</h3>
 
-scons auto-generates a script that compiles and links your c++ against the source code and dependencies just run ```. <oxsx root>/bin/compile.sh <your cpp file>``` to produce an executible of the same name
+scons auto-generates a script that compiles and links your c++ against the source code and dependencies just run `. <oxsx root>/bin/compile.sh <your cpp file>` to produce an executible of the same name
 
 Look in `<oxsx root>/examples` for help getting started
 
-
-
 <h2> Creating ntuples </h2>
 One way to read in data is using a ROOT ntuple. If you are looking at SNO+ data, you probably have a flat root tree that can be easily pruned down into this format with only the branches you are interested in.
 
-To create ntuples for oxsx run ```./util/prune_flat_tree <path_to_file_to_convert> -treename <name_of_the_tree> <branch1> <branch2> <branch3> -newtreename <name_of_your_tree> -outfile <name_of_your_file> -nevents <number_of_events>```
-
- * The name of the tree in an input file is optional, as a default it is "output"
- * The name of the output file is optional, as a default is is <the_name_of_input_file>+"_oxsx.root"
- * The name of the tree in an output file is optional, as a default it is "oxsx"
- * The number of events of an output file is optional 
+To create ntuples for oxsx run `./util/prune_flat_tree <path_to_file_to_convert> -treename <name_of_the_tree> <branch1> <branch2> <branch3> -newtreename <name_of_your_tree> -outfile <name_of_your_file> -nevents <number_of_events>`
 
+- The name of the tree in an input file is optional, as a default it is "output"
+- The name of the output file is optional, as a default is is <the_name_of_input_file>+"\_oxsx.root"
+- The name of the tree in an output file is optional, as a default it is "oxsx"
+- The number of events of an output file is optional
diff --git a/bench/Bench.cpp b/bench/Bench.cpp
@@ -3,17 +3,19 @@
 #include "Bench.h"
 #include <iostream>
 
-/* Taken from SO 
-http://stackoverflow.com/questions/1861294/how-to-calculate-execution-time-of-a-code-snippet-in-c. Answer 
+/* Taken from SO
+http://stackoverflow.com/questions/1861294/how-to-calculate-execution-time-of-a-code-snippet-in-c. Answer
 from Andreas Bonini */
 
 /* Remove if already defined */
-typedef long long int64; typedef unsigned long long uint64;
+typedef long long int64;
+typedef unsigned long long uint64;
 
 /* Returns the amount of milliseconds elapsed since the UNIX epoch.*/
 
-uint64 
-Bench::GetTimeMs64() const{
+uint64
+Bench::GetTimeMs64() const
+{
     /* Linux */
     struct timeval tv;
 
@@ -29,31 +31,34 @@ Bench::GetTimeMs64() const{
     return ret;
 }
 
-uint64 
-Bench::TimeElapsed() const{
+uint64
+Bench::TimeElapsed() const
+{
     uint64 start = GetTimeMs64();
     fFunction();
     return GetTimeMs64() - start;
 }
 
-long double 
-Bench::TimeRepetitions(unsigned iterations_){
+long double
+Bench::TimeRepetitions(unsigned iterations_)
+{
     fIterations = iterations_;
     fMeanTime = 0;
-    for(unsigned i = 0; i < iterations_; i++){
+    for (unsigned i = 0; i < iterations_; i++)
+    {
         double timeElapsed = TimeElapsed();
         fMeanTime += timeElapsed;
 
-        if(!i || timeElapsed < fMinTime)
-            fMinTime = timeElapsed;                
+        if (!i || timeElapsed < fMinTime)
+            fMinTime = timeElapsed;
     }
 
-    fMeanTime = (double)(fMeanTime)/iterations_;
+    fMeanTime = (double)(fMeanTime) / iterations_;
     return fMeanTime;
 }
 
-void 
-Bench::PrintResult() const{
+void Bench::PrintResult() const
+{
     std::cout << "Test " << fName << " Results: " << std::endl;
     std::cout << "Average of " << fMeanTime << "ms over " << fIterations << " iterations" << std::endl;
     std::cout << "Min execution time " << fMinTime << "ms" << std::endl;

diff --git a/bench/Bench.h b/bench/Bench.h
@@ -5,18 +5,20 @@
 #define __BENCH__
 #include <string>
 
-class Bench{
- public:
- Bench(void (*func_)(), const std::string& name_ = " ") : fFunction(func_), 
-        fMeanTime(-1), fName(name_), fMinTime(-1) {}
+class Bench
+{
+public:
+    Bench(void (*func_)(), const std::string &name_ = " ") : fFunction(func_),
+                                                             fMeanTime(-1), fName(name_), fMinTime(-1) {}
 
-    typedef long long int64; 
+    typedef long long int64;
     typedef unsigned long long uint64;
-    
+
     long double TimeRepetitions(unsigned iterations_);
     void PrintResult() const;
- private:
-    void (*fFunction)(); 
+
+private:
+    void (*fFunction)();
     uint64 GetTimeMs64() const;
     uint64 TimeElapsed() const;
     double fMeanTime;

diff --git a/bench/BenchTests/PdfBuild.cpp b/bench/BenchTests/PdfBuild.cpp
@@ -7,7 +7,8 @@
 const std::string fileName = "/Users/Jack/snoplus/bbplus/ntuples/fake_pu_ntup.root";
 const std::string treeName = "T";
 
-void BuildAPdf(){
+void BuildAPdf()
+{
     // Build the pdf
     AxisCollection ax;
     ax.AddAxis(BinAxis("energy", 0, 3, 100));
@@ -22,24 +23,23 @@ void BuildAPdf(){
     indicies.push_back(3);
     pdf.SetObservables(ObsSet(indicies));
 
-
     // Get the data
     ROOTNtuple rHandle(fileName, treeName);
     unsigned nEntries = rHandle.GetNEntries();
     std::cout << nEntries << " Entries to fill" << std::endl;
     // Fill the Pdf
-    for(size_t i = 0; i < nEntries; i++){
+    for (size_t i = 0; i < nEntries; i++)
+    {
         pdf.Fill(rHandle.GetEntry(i));
     }
-    
+
     return;
 }
 
-
-int main(){
+int main()
+{
     Bench b(&BuildAPdf, "Filling ");
     b.TimeRepetitions(100);
     b.PrintResult();
     return 0;
-
 }
diff --git a/examples/Cuts.cpp b/examples/Cuts.cpp
@@ -2,7 +2,7 @@
 Cuts are functions that take an event and return true or false, depending on whether the event passes the cut or not.
 
 Cuts can be grouped together into a cut collection, which returns true if all cuts are satisfied.
-The CutCollection object is used to FillPdfs or generate data sets, only taking events that pass 
+The CutCollection object is used to FillPdfs or generate data sets, only taking events that pass
 */
 #include <BoxCut.h>
 #include <BoolCut.h>
@@ -11,12 +11,13 @@ The CutCollection object is used to FillPdfs or generate data sets, only taking
 #include <Event.h>
 #include <iostream>
 
-int main(){
+int main()
+{
     // Names for observables
     const std::vector<std::string> observables = {"radius", "energy", "external_tag"};
     // cut if radius is bigger than two i.e. a lower limit
     LineCut lineCut("fv_cut", "radius", 2, "lower");
-    
+
     // cut if second observable is between 5 and 10
     BoxCut boxCut("energy_cut", "energy", 5, 10);
 
@@ -39,22 +40,21 @@ int main(){
     fakeEvent.SetObservableNames(&observables);
 
     // test it
-    std::cout << "Event passes line cut " 
+    std::cout << "Event passes line cut "
               << lineCut.PassesCut(fakeEvent)
               << std::endl;
 
-    std::cout << "Event passes box cut " 
+    std::cout << "Event passes box cut "
               << boxCut.PassesCut(fakeEvent)
               << std::endl;
 
-    std::cout << "Event passes bool cut " 
+    std::cout << "Event passes bool cut "
               << boolCut.PassesCut(fakeEvent)
               << std::endl;
 
-    std::cout << "Event passes all cuts " 
+    std::cout << "Event passes all cuts "
               << combinedCuts.PassesCuts(fakeEvent)
               << std::endl;
 
     return 0;
-
 }
diff --git a/examples/DataSetGeneration.cpp b/examples/DataSetGeneration.cpp
@@ -1,28 +1,29 @@
-#include <DataSetGenerator.h>        
-#include <OXSXDataSet.h>         
+#include <DataSetGenerator.h>
+#include <OXSXDataSet.h>
 #include <ROOTNtuple.h>
-int main(){        
-    // (filename, tree name)        
+int main()
+{
+    // (filename, tree name)
     ROOTNtuple zeroNuMC("<filename1>", "treename");
-    ROOTNtuple twoNuMC( "<filename2>", "treename");
-    ROOTNtuple b8NuMC(  "<filename3>", "treename");
+    ROOTNtuple twoNuMC("<filename2>", "treename");
+    ROOTNtuple b8NuMC("<filename3>", "treename");
 
     std::vector<bool> bootstraps;
-    
-    // DataSetGenerator        
-    DataSetGenerator dataGen;        
-    dataGen.AddDataSet(&zeroNuMC, 5, false);  // second arg is the expected rate
+
+    // DataSetGenerator
+    DataSetGenerator dataGen;
+    dataGen.AddDataSet(&zeroNuMC, 5, false); // second arg is the expected rate
     bootstraps.push_back(true);
     dataGen.AddDataSet(&twoNuMC, 50, false);
     bootstraps.push_back(true);
     dataGen.AddDataSet(&b8NuMC, 100, false);
     bootstraps.push_back(true);
 
     dataGen.SetBootstrap(bootstraps);
-    
-    // Generate a data set        
-    OXSXDataSet fakeData  = dataGen.PoissonFluctuatedDataSet();
+
+    // Generate a data set
+    OXSXDataSet fakeData = dataGen.PoissonFluctuatedDataSet();
     OXSXDataSet fakeData2 = dataGen.ExpectedRatesDataSet();
-                
-    return 0;        
+
+    return 0;
 }
diff --git a/examples/beestonBarlowLHH.cpp b/examples/beestonBarlowLHH.cpp
@@ -13,15 +13,16 @@
 #include <BinnedNLLH.h>
 #include <ParameterDict.h>
 
-const std::string bgMCfile    = "";
-const std::string sigMCfile   = "";
-const std::string bgTreeName  = "";
+const std::string bgMCfile = "";
+const std::string sigMCfile = "";
+const std::string bgTreeName = "";
 const std::string sigTreeName = "";
 
 const std::string dataFile = "";
 const std::string dataTreeName = "";
 
-int main(){
+int main()
+{
   ////////////////////
   // 1. Set Up PDFs //
   ////////////////////
@@ -35,17 +36,17 @@ int main(){
   dataObs.push_back("energy");
 
   // Set up pdf with these bins in this observable
-  BinnedED bgPdf("bgPDF",axes);
+  BinnedED bgPdf("bgPDF", axes);
   bgPdf.SetObservables(dataObs);
 
-  //Hard code bin contents of PDF
-  bgPdf.SetBinContent(0,20);
-  bgPdf.SetBinContent(1,35);
-  bgPdf.SetBinContent(2,30);
-  bgPdf.SetBinContent(3,15);
+  // Hard code bin contents of PDF
+  bgPdf.SetBinContent(0, 20);
+  bgPdf.SetBinContent(1, 35);
+  bgPdf.SetBinContent(2, 30);
+  bgPdf.SetBinContent(3, 15);
   bgPdf.Normalise();
 
-  //Hard code generated number of events
+  // Hard code generated number of events
   const int gen_rate = 1000;
 
   std::cout << "Initialised PDF" << std::endl;
@@ -54,14 +55,14 @@ int main(){
   // 2. Fill with data and normalise //
   /////////////////////////////////////
 
-  BinnedED bgData("bgData",axes);
+  BinnedED bgData("bgData", axes);
   bgData.SetObservables(dataObs);
 
-  //Hard code bin contents of data
-  bgData.SetBinContent(0,25);
-  bgData.SetBinContent(1,30);
-  bgData.SetBinContent(2,40);
-  bgData.SetBinContent(3,10);
+  // Hard code bin contents of data
+  bgData.SetBinContent(0, 25);
+  bgData.SetBinContent(1, 30);
+  bgData.SetBinContent(2, 40);
+  bgData.SetBinContent(3, 10);
 
   std::cout << "Filled data " << std::endl;
 
@@ -79,10 +80,10 @@ int main(){
 
   ParameterDict parameterValues;
 
-  //Set normalisation of PDF
+  // Set normalisation of PDF
   parameterValues["bgPDF"] = 100;
 
-  //Calculate and print likelihood
+  // Calculate and print likelihood
   lhFunction.SetParameters(parameterValues);
   std::cout << "Total LogL = " << lhFunction.Evaluate() << std::endl;