Remove using namespace std from Parameters header

src/algorithms/Alignment.C

@@ -3,6 +3,7 @@
 #include <TVirtualFitter.h>
 
 using namespace corryvreckan;
+using namespace std;
 
 Alignment::Alignment(Configuration config, Clipboard* clipboard) : Algorithm(std::move(config), clipboard) {
     m_numberOfTracksForAlignment = 20000;

src/algorithms/BasicTracking.C

@@ -3,6 +3,7 @@
 #include "objects/KDTree.h"
 
 using namespace corryvreckan;
+using namespace std;
 
 BasicTracking::BasicTracking(Configuration config, Clipboard* clipboard) : Algorithm(std::move(config), clipboard) {
     // Default values for cuts
@@ -229,7 +230,7 @@ StatusCode BasicTracking::run(Clipboard* clipboard) {
     }
 
     nTracksTotal += tracks->size();
-    cout << ", produced " << (int)nTracksTotal << " tracks";
+    LOG_PROGRESS(STATUS, "basic_tracking") << "Produced " << (int)nTracksTotal << " tracks";
 
     // Clean up tree objects
     for(int det = 0; det < parameters->nDetectors; det++) {

src/algorithms/BasicTracking.h

@@ -35,8 +35,8 @@ namespace corryvreckan {
         TH1F* tracksPerEvent;
         TH1F* trackAngleX;
         TH1F* trackAngleY;
-        map<string, TH1F*> residualsX;
-        map<string, TH1F*> residualsY;
+        std::map<std::string, TH1F*> residualsX;
+        std::map<std::string, TH1F*> residualsY;
 
         // Cuts for tracking
         double timingCut;

src/algorithms/CLICpixEventLoader.C

 #include "CLICpixEventLoader.h"
 
 using namespace corryvreckan;
+using namespace std;
 
 CLICpixEventLoader::CLICpixEventLoader(Configuration config, Clipboard* clipboard)
     : Algorithm(std::move(config), clipboard) {

src/algorithms/CLICpixEventLoader.h

@@ -29,8 +29,8 @@ namespace corryvreckan {
 
         // Member variables
         int m_eventNumber;
-        string m_filename;
-        ifstream m_file;
+        std::string m_filename;
+        std::ifstream m_file;
 
         TH2F* hHitMap;
         TH1F* hPixelToT;

src/algorithms/Clicpix2Correlator.C

 #include "Clicpix2Correlator.h"
 
 using namespace corryvreckan;
+using namespace std;
 
 Clicpix2Correlator::Clicpix2Correlator(Configuration config, Clipboard* clipboard)
     : Algorithm(std::move(config), clipboard) {}

src/algorithms/Clicpix2Correlator.h

@@ -26,14 +26,14 @@ namespace corryvreckan {
 
         // Member variables
         int m_eventNumber;
-        string dutID;
-        map<int, Clusters> m_eventClusters;
-        map<int, Tracks> m_eventTracks;
+        std::string dutID;
+        std::map<int, Clusters> m_eventClusters;
+        std::map<int, Tracks> m_eventTracks;
         double angleStart, angleStop, angleStep;
 
         // Histograms
-        map<string, TH1F*> hTrackDiffX;
-        map<string, TH1F*> hTrackDiffY;
+        std::map<std::string, TH1F*> hTrackDiffX;
+        std::map<std::string, TH1F*> hTrackDiffY;
     };
 }
 #endif // Clicpix2Correlator_H

src/algorithms/Clicpix2EventLoader.C

 #include "Clicpix2EventLoader.h"
 
 using namespace corryvreckan;
+using namespace std;
 
 Clicpix2EventLoader::Clicpix2EventLoader(Configuration config, Clipboard* clipboard)
     : Algorithm(std::move(config), clipboard) {}

src/algorithms/Clicpix2EventLoader.h

@@ -29,15 +29,15 @@ namespace corryvreckan {
         void finalise();
 
         // Histograms for several devices
-        map<string, TH2F*> plotPerDevice;
+        std::map<std::string, TH2F*> plotPerDevice;
 
         // Single histograms
         TH1F* singlePlot;
 
         // Member variables
         int m_eventNumber;
-        string m_filename;
-        ifstream m_file;
+        std::string m_filename;
+        std::ifstream m_file;
 
         TH2F* hHitMap;
         TH1F* hPixelToT;

src/algorithms/ClicpixAnalysis.C

@@ -4,6 +4,7 @@
 #include "objects/Track.h"
 
 using namespace corryvreckan;
+using namespace std;
 
 ClicpixAnalysis::ClicpixAnalysis(Configuration config, Clipboard* clipboard) : Algorithm(std::move(config), clipboard) {
     m_associationCut = 0.05; // 100 um

src/algorithms/ClicpixAnalysis.h

@@ -119,8 +119,8 @@ namespace corryvreckan {
         // Member variables
         int m_eventNumber;
         int m_triggerNumber;
-        string dutID;
-        map<int, double> m_hitPixels;
+        std::string dutID;
+        std::map<int, double> m_hitPixels;
         double m_associationCut;
         double m_proximityCut;
         double m_lostHits;

src/algorithms/DataDump.C

 #include "DataDump.h"
 
 using namespace corryvreckan;
+using namespace std;
 
 DataDump::DataDump(Configuration config, Clipboard* clipboard) : Algorithm(std::move(config), clipboard) {
     m_detector = "DeviceToDumpData";

src/algorithms/DataDump.h

@@ -29,7 +29,7 @@ namespace corryvreckan {
 
         // Member variables
         int m_eventNumber;
-        string m_detector;
+        std::string m_detector;
     };
 }
 #endif // DataDump_H

src/algorithms/FileReader.C

@@ -4,6 +4,7 @@
 #include "objects/Timepix3Track.h"
 
 using namespace corryvreckan;
+using namespace std;
 
 FileReader::FileReader(Configuration config, Clipboard* clipboard) : Algorithm(std::move(config), clipboard) {
     m_onlyDUT = false;

src/algorithms/FileReader.h

@@ -21,7 +21,7 @@ namespace corryvreckan {
 
         // Member variables
         int m_eventNumber;
-        string m_fileName;
+        std::string m_fileName;
         TFile* m_inputFile;
 
         // Flags for which data types to write out
@@ -31,19 +31,19 @@ namespace corryvreckan {
         bool m_onlyDUT;
 
         // Map of trees which holds the output objects
-        map<string, TTree*> m_inputTrees;
+        std::map<std::string, TTree*> m_inputTrees;
 
         // Objects which the trees will point to (when
         // the branch address is set
         long long int m_time;
-        map<string, TestBeamObject*> m_objects;
+        std::map<std::string, TestBeamObject*> m_objects;
 
         // List of objects to write out
-        vector<string> m_objectList;
+        std::vector<std::string> m_objectList;
 
         // Variables to keep track of time and file reading
         long long int m_currentTime;
-        map<string, long long int> m_currentPosition;
+        std::map<std::string, long long int> m_currentPosition;
         double m_timeWindow;
     };
 }

src/algorithms/FileWriter.C

 #include "FileWriter.h"
 
 using namespace corryvreckan;
+using namespace std;
 
 FileWriter::FileWriter(Configuration config, Clipboard* clipboard) : Algorithm(std::move(config), clipboard) {
     m_onlyDUT = true;

src/algorithms/FileWriter.h

@@ -21,7 +21,7 @@ namespace corryvreckan {
 
         // Member variables
         int m_eventNumber;
-        string m_fileName;
+        std::string m_fileName;
         TFile* m_outputFile;
 
         // Flags for which data types to write out
@@ -31,15 +31,15 @@ namespace corryvreckan {
         bool m_onlyDUT;
 
         // Map of trees which holds the output objects
-        map<string, TTree*> m_outputTrees;
+        std::map<std::string, TTree*> m_outputTrees;
 
         // Objects which the trees will point to (when
         // the branch address is set
         long long int m_time;
-        map<string, TestBeamObject*> m_objects;
+        std::map<std::string, TestBeamObject*> m_objects;
 
         // List of objects to write out
-        vector<string> m_objectList;
+        std::vector<std::string> m_objectList;
     };
 }
 #endif // FileWriter_H

src/algorithms/GUI.C

@@ -5,6 +5,7 @@
 #include "TSystem.h"
 
 using namespace corryvreckan;
+using namespace std;
 
 GUI::GUI(Configuration config, Clipboard* clipboard) : Algorithm(std::move(config), clipboard) {
     updateNumber = 500;

src/algorithms/GUI.h

@@ -29,12 +29,12 @@ namespace corryvreckan {
         void finalise();
 
         // Plot holders
-        vector<TCanvas*> canvases;
-        map<TCanvas*, vector<TH1*>> histograms;
-        map<TH1*, string> styles;
+        std::vector<TCanvas*> canvases;
+        std::map<TCanvas*, std::vector<TH1*>> histograms;
+        std::map<TH1*, std::string> styles;
 
         // Add plots and canvases
-        void addPlot(TCanvas*, string, string style = "");
+        void addPlot(TCanvas*, std::string, std::string style = "");
         void addCanvas(TCanvas*);
 
         // Application to allow display of canvases

src/algorithms/GenericAlgorithm.C

 #include "GenericAlgorithm.h"
 
 using namespace corryvreckan;
+using namespace std;
 
 GenericAlgorithm::GenericAlgorithm(Configuration config, Clipboard* clipboard) : Algorithm(std::move(config), clipboard) {}