Make format - should really install the git hook here...

src/algorithms/GUI.C

@@ -9,7 +9,7 @@ using namespace std;
 
 GUI::GUI(Configuration config, Clipboard* clipboard) : Algorithm(std::move(config), clipboard) {
     // Update every X events:
-    updateNumber = m_config.get<int>("updateNumber",500);
+    updateNumber = m_config.get<int>("updateNumber", 500);
 }
 
 void GUI::initialise(Parameters* par) {
@@ -76,7 +76,8 @@ void GUI::initialise(Parameters* par) {
         for(int iHisto = 0; iHisto < nHistograms; iHisto++) {
             canvas->cd(iHisto + 1);
             string style = styles[histos[iHisto]];
-            if(histos[iHisto] != nullptr) histos[iHisto]->Draw(style.c_str());
+            if(histos[iHisto] != nullptr)
+                histos[iHisto]->Draw(style.c_str());
         }
     }
 

src/algorithms/Timepix3EventLoader.C

@@ -18,8 +18,8 @@ Timepix3EventLoader::Timepix3EventLoader(Configuration config, Clipboard* clipbo
     // Take input directory from global parameters
     m_inputDirectory = m_config.get<std::string>("inputDirectory");
 
-    applyTimingCut = m_config.get<bool>("applyTimingCut",false);
-    m_timingCut = m_config.get<double>("timingCut",0.0);
+    applyTimingCut = m_config.get<bool>("applyTimingCut", false);
+    m_timingCut = m_config.get<double>("timingCut", 0.0);
     m_minNumberOfPlanes = m_config.get<int>("minNumerOfPlanes", 1);
 
     m_currentTime = 0.;
@@ -38,9 +38,8 @@ void Timepix3EventLoader::initialise(Parameters* par) {
     if(directory == NULL) {
         LOG(ERROR) << "Directory " << m_inputDirectory << " does not exist";
         return;
-    }
-    else {
-      LOG(TRACE) << "Found directory " << m_inputDirectory;
+    } else {
+        LOG(TRACE) << "Found directory " << m_inputDirectory;
     }
     dirent* entry;
     dirent* file;
@@ -367,8 +366,7 @@ bool Timepix3EventLoader::loadData(string detectorID, Pixels* devicedata, SpidrS
                 // Stop looking at data if the signal is after the current event window
                 // (and rewind the file
                 // reader so that we start with this signal next event)
-                if(eventLength != 0. &&
-                   ((double)time / (4096. * 40000000.)) > (parameters->currentTime + eventLength)) {
+                if(eventLength != 0. && ((double)time / (4096. * 40000000.)) > (parameters->currentTime + eventLength)) {
                     fseek(m_currentFile[detectorID], -1 * sizeof(ULong64_t), SEEK_CUR);
                     fileNotFinished = true;
                     //          LOG(DEBUG) <<"Signal has a time beyond the current event:
@@ -493,8 +491,7 @@ bool Timepix3EventLoader::loadData(string detectorID, Pixels* devicedata, SpidrS
             // Stop looking at data if the pixel is after the current event window
             // (and rewind the file
             // reader so that we start with this pixel next event)
-            if(eventLength != 0. &&
-               ((double)time / (4096. * 40000000.)) > (parameters->currentTime + eventLength)) {
+            if(eventLength != 0. && ((double)time / (4096. * 40000000.)) > (parameters->currentTime + eventLength)) {
                 fseek(m_currentFile[detectorID], -1 * sizeof(ULong64_t), SEEK_CUR);
                 fileNotFinished = true;
                 break;

src/core/Analysis.C

@@ -8,8 +8,8 @@
 #include "utils/log.h"
 
 #include <dlfcn.h>
-#include <iomanip>
 #include <fstream>
+#include <iomanip>
 
 #define CORRYVRECKAN_ALGORITHM_PREFIX "libCorryvreckanAlgorithm"
 #define CORRYVRECKAN_GENERATOR_FUNCTION "corryvreckan_algorithm_generator"
@@ -343,7 +343,7 @@ void Analysis::run() {
 
         // Check for user termination and stop the event loop:
         if(m_terminate) {
-          break;
+            break;
         }
     }
 
@@ -418,9 +418,9 @@ void Analysis::finaliseAll() {
 void Analysis::timing() {
     LOG(STATUS) << "===============| Wall-clock timing (seconds) |================";
     for(auto& algorithm : m_algorithms) {
-        LOG(STATUS) << std::setw(25) << algorithm->getName() << "  --  "
-                  << std::fixed << std::setprecision(5) << algorithm->getStopwatch()->RealTime() << " = "
-                  << std::setprecision(9) << algorithm->getStopwatch()->RealTime() / m_events << " s/evt";
+        LOG(STATUS) << std::setw(25) << algorithm->getName() << "  --  " << std::fixed << std::setprecision(5)
+                    << algorithm->getStopwatch()->RealTime() << " = " << std::setprecision(9)
+                    << algorithm->getStopwatch()->RealTime() / m_events << " s/evt";
     }
     LOG(STATUS) << "==============================================================";
 }

src/core/Analysis.h

 #ifndef ANALYSIS_H
 #define ANALYSIS_H 1
 
+#include <fstream>
 #include <map>
 #include <vector>
-#include <fstream>
 
 #include "TBrowser.h"
 #include "TDirectory.h"

src/core/Clipboard.h

@@ -48,7 +48,7 @@ public:
 
     // Clear items on the clipboard
     void clear() {
-        for(auto & id : m_dataID) {
+        for(auto& id : m_dataID) {
             TestBeamObjects* collection = m_data[id];
             for(TestBeamObjects::iterator it = collection->begin(); it != collection->end(); it++)
                 delete(*it);
@@ -60,7 +60,7 @@ public:
 
     // Quick function to check what is currently held by the clipboard
     void checkCollections() {
-        for(auto &name : m_dataID)
+        for(auto& name : m_dataID)
             LOG(DEBUG) << "Data held: " << name;
     }
 

src/core/DetectorParameters.h

-#include <string>
 #include <map>
+#include <string>
 
 // Root includes
 #include "Math/Point3D.h"
@@ -17,7 +17,18 @@ namespace corryvreckan {
     public:
         // Constructors and desctructors
         DetectorParameters() {}
-        DetectorParameters(std::string detectorType, int nPixelsX, int nPixelsY, double pitchX, double pitchY, double x, double y, double z, double Rx, double Ry, double Rz, double timingOffset) {
+        DetectorParameters(std::string detectorType,
+                           int nPixelsX,
+                           int nPixelsY,
+                           double pitchX,
+                           double pitchY,
+                           double x,
+                           double y,
+                           double z,
+                           double Rx,
+                           double Ry,
+                           double Rz,
+                           double timingOffset) {
             m_detectorType = detectorType;
             m_nPixelsX = nPixelsX;
             m_nPixelsY = nPixelsY;
@@ -69,7 +80,7 @@ namespace corryvreckan {
         bool masked(int chX, int chY) {
             int channelID = chX + m_nPixelsX * chY;
             if(m_masked.count(channelID) > 0)
-            return true;
+                return true;
             return false;
         }
 
@@ -93,7 +104,8 @@ namespace corryvreckan {
             m_origin = (*m_localToGlobal) * m_origin;
             PositionVector3D<Cartesian3D<double>> localZ(0., 0., 1.);
             localZ = (*m_localToGlobal) * localZ;
-            m_normal = PositionVector3D<Cartesian3D<double>>(localZ.X() - m_origin.X(), localZ.Y() - m_origin.Y(), localZ.Z() - m_origin.Z());
+            m_normal = PositionVector3D<Cartesian3D<double>>(
+                localZ.X() - m_origin.X(), localZ.Y() - m_origin.Y(), localZ.Z() - m_origin.Z());
         }
 
         // Function to update transforms (such as during alignment)
@@ -113,12 +125,12 @@ namespace corryvreckan {
             distance += (m_origin.Y() - track->m_state.Y()) * m_normal.Y();
             distance += (m_origin.Z() - track->m_state.Z()) * m_normal.Z();
             distance /= (track->m_direction.X() * m_normal.X() + track->m_direction.Y() * m_normal.Y() +
-            track->m_direction.Z() * m_normal.Z());
+                         track->m_direction.Z() * m_normal.Z());
 
             // Propagate the track
             PositionVector3D<Cartesian3D<double>> globalIntercept(track->m_state.X() + distance * track->m_direction.X(),
-            track->m_state.Y() + distance * track->m_direction.Y(),
-            track->m_state.Z() + distance * track->m_direction.Z());
+                                                                  track->m_state.Y() + distance * track->m_direction.Y(),
+                                                                  track->m_state.Z() + distance * track->m_direction.Z());
             return globalIntercept;
         }
 
@@ -138,8 +150,8 @@ namespace corryvreckan {
             // Check if the row and column are outside of the chip
             bool intercept = true;
             if(row < (pixelTolerance - 0.5) || row > (this->m_nPixelsY - 0.5 - pixelTolerance) ||
-            column < (pixelTolerance - 0.5) || column > (this->m_nPixelsX - 0.5 - pixelTolerance))
-            intercept = false;
+               column < (pixelTolerance - 0.5) || column > (this->m_nPixelsX - 0.5 - pixelTolerance))
+                intercept = false;
 
             return intercept;
         }
@@ -162,7 +174,7 @@ namespace corryvreckan {
             for(int r = (row - tolerance); r <= (row + tolerance); r++) {
                 for(int c = (column - tolerance); c <= (column + tolerance); c++) {
                     if(this->masked(c, r))
-                    hitmasked = true;
+                        hitmasked = true;
                 }
             }
 
@@ -182,7 +194,8 @@ namespace corryvreckan {
         // Function to get local position from row and column
         PositionVector3D<Cartesian3D<double>> getLocalPosition(double row, double column) {
 
-            PositionVector3D<Cartesian3D<double>> positionLocal(m_pitchX * (column - m_nPixelsX / 2.), m_pitchY * (row - m_nPixelsY / 2.), 0.);
+            PositionVector3D<Cartesian3D<double>> positionLocal(
+                m_pitchX * (column - m_nPixelsX / 2.), m_pitchY * (row - m_nPixelsY / 2.), 0.);
 
             return positionLocal;
         }

src/core/Parameters.C

@@ -15,7 +15,7 @@ Parameters::Parameters() {
     conditionsFile = "cond.dat";
     dutMaskFile = "defaultMask.dat";
     inputDirectory = "";
-    currentTime = 0.;    // seconds
+    currentTime = 0.; // seconds
 }
 
 // Sort function for detectors from low to high z
@@ -61,7 +61,8 @@ bool Parameters::readConditions() {
     conditions.open(conditionsFile.c_str());
     string line;
 
-    LOG(INFO) << "-------------------------------------------- Reading conditions ---------------------------------------------------";
+    LOG(INFO) << "-------------------------------------------- Reading conditions "
+                 "---------------------------------------------------";
     // Loop over file
     while(getline(conditions, line)) {
 
@@ -102,7 +103,7 @@ bool Parameters::readConditions() {
     // Loop over all registered detectors
     for(auto& det : detectors) {
         if(detector.count(det) == 0) {
-            //LOG(INFO) << "Detector " << detectors[det] << " has no conditions loaded";
+            // LOG(INFO) << "Detector " << detectors[det] << " has no conditions loaded";
             unregisteredDetector = true;
         }
     }

src/objects/KDTree.h

@@ -91,7 +91,7 @@ public:
         double time = double(cluster->timestamp()) / (4096. * 40000000.);
         timeKdtree->FindInRange(&time, timeWindow, results);
 
-        LOG(TRACE) <<" -- found: "<<results.size();
+        LOG(TRACE) << " -- found: " << results.size();
 
         // Turn this into a vector of clusters
         Clusters resultClusters;

src/objects/KDTreeTimepix3.h

@@ -55,7 +55,7 @@ public:
     // Function to get back all clusters within a given time period
     Timepix3Clusters getAllClustersInTimeWindow(Timepix3Cluster* cluster, double timeWindow) {
 
-        LOG(TRACE) <<"Getting all clusters in time window" << timeWindow;
+        LOG(TRACE) << "Getting all clusters in time window" << timeWindow;
         // Find out which iterator number this cluster corresponds to
         //    int iterator = iteratorNumber[cluster];
 
@@ -65,7 +65,7 @@ public:
         time[0] = double(cluster->timestamp()) / (4096. * 40000000.);
         timeKdtree->FindInRange(time, timeWindow, results);
 
-        LOG(TRACE) << " -- found: "<<results.size();
+        LOG(TRACE) << " -- found: " << results.size();
 
         // Turn this into a vector of clusters
         Timepix3Clusters resultClusters;

src/objects/TestBeamObject.C

@@ -8,9 +8,9 @@
 
 ClassImp(TestBeamObject)
 
-// Return class type for fixed object types (that don't depend on detector
-// type)
-TestBeamObject* TestBeamObject::Factory(std::string objectType, TestBeamObject* object) {
+    // Return class type for fixed object types (that don't depend on detector
+    // type)
+    TestBeamObject* TestBeamObject::Factory(std::string objectType, TestBeamObject* object) {
 
     // Track class
     if(objectType == "tracks") {
@@ -26,9 +26,9 @@ TestBeamObject* TestBeamObject::Factory(std::string detectorType, std::string ob
     // Timepix types both use generic classes
     if(detectorType == "Timepix1" || detectorType == "Timepix3") {
         if(objectType == "pixels")
-        return (object == NULL) ? new Pixel() : new Pixel(*static_cast<Pixel*>(object));
+            return (object == NULL) ? new Pixel() : new Pixel(*static_cast<Pixel*>(object));
         if(objectType == "clusters")
-        return (object == NULL) ? new Cluster() : new Cluster(*static_cast<Cluster*>(object));
+            return (object == NULL) ? new Cluster() : new Cluster(*static_cast<Cluster*>(object));
     }
 
     return new TestBeamObject();

src/objects/Track.h

@@ -32,7 +32,7 @@ public:
         }
 
         Clusters associatedClusters = track->associatedClusters();
-        for(auto & assoc_cluster : associatedClusters) {
+        for(auto& assoc_cluster : associatedClusters) {
             Cluster* cluster = new Cluster(assoc_cluster);
             m_associatedClusters.push_back(cluster);
         }
@@ -73,7 +73,7 @@ public:
         m_chi2ndof = 0.;
 
         // Loop over all clusters
-        for(auto &cluster : m_trackClusters) {
+        for(auto& cluster : m_trackClusters) {
             // Get the distance^2 and the error^2
             double error2 = cluster->error() * cluster->error();
             m_chi2 += (this->distance2(cluster) / error2);
@@ -110,7 +110,7 @@ public:
         double maty[2][2] = {{0., 0.}, {0., 0.}};
 
         // Loop over all clusters and fill the matrices
-        for(auto & cluster : m_trackClusters) {
+        for(auto& cluster : m_trackClusters) {
             // Get the global point details
             double x = cluster->globalX();
             double y = cluster->globalY();