Adapt to new interface of Cluster class

src/core/detector/Detector.cpp

@@ -363,7 +363,7 @@ bool Detector::isWithinROI(Cluster* cluster) const {
     }
 
     // Loop over all pixels of the cluster
-    for(auto& pixel : (*cluster->pixels())) {
+    for(auto& pixel : cluster->pixels()) {
         if(winding_number(pixel->coordinates(), m_roi) == 0) {
             return false;
         }

src/modules/AnalysisCLICpix/AnalysisCLICpix.cpp

@@ -388,8 +388,8 @@ StatusCode AnalysisCLICpix::run(std::shared_ptr<Clipboard> clipboard) {
                 hClusterChargeAssociated4pix->Fill((bestCluster)->charge());
                 hInterceptClusterSize4->Fill(pixelInterceptX, pixelInterceptY);
             }
-            Pixels* pixels = bestCluster->pixels();
-            for(auto& pixel : (*pixels)) {
+            auto pixels = bestCluster->pixels();
+            for(auto& pixel : pixels) {
                 hPixelToTMap->Fill(pixel->column(), pixel->row(), pixel->raw());
             }
 
@@ -541,23 +541,22 @@ void AnalysisCLICpix::fillClusterHistos(std::shared_ptr<Clusters> clusters) {
     for(itc = clusters->begin(); itc != clusters->end(); ++itc) {
 
         // Loop over pixels and check if there are pixels not known
-        Pixels* pixels = (*itc)->pixels();
-        Pixels::iterator itp;
-        for(itp = pixels->begin(); itp != pixels->end(); itp++) {
+        auto pixels = (*itc)->pixels();
+        for(auto& itp : pixels) {
             // Check if this clicpix frame is still the current
-            int pixelID = (*itp)->column() + nCols * (*itp)->row();
-            if(m_hitPixels[pixelID] != (*itp)->raw()) {
+            int pixelID = itp->column() + nCols * itp->row();
+            if(m_hitPixels[pixelID] != itp->raw()) {
                 // New frame! Reset the stored pixels and trigger number
                 if(!newFrame) {
                     m_hitPixels.clear();
                     newFrame = true;
                 }
-                m_hitPixels[pixelID] = (*itp)->raw();
+                m_hitPixels[pixelID] = itp->raw();
                 m_triggerNumber = 0;
             }
-            hHitPixels->Fill((*itp)->column(), (*itp)->row());
-            hColumnHits->Fill((*itp)->column());
-            hRowHits->Fill((*itp)->row());
+            hHitPixels->Fill(itp->column(), itp->row());
+            hColumnHits->Fill(itp->column());
+            hRowHits->Fill(itp->row());
         }
 
         // Fill cluster histograms
@@ -578,12 +577,8 @@ void AnalysisCLICpix::fillResponseHistos(double trackInterceptX, double trackInt
 
     // Loop over pixels in the cluster and show their distance from the track
     // intercept
-    Pixels* pixels = cluster->pixels();
-    Pixels::iterator itp;
-    for(itp = pixels->begin(); itp != pixels->end(); itp++) {
-
-        // Get the pixel
-        Pixel* pixel = (*itp);
+    auto pixels = cluster->pixels();
+    for(auto& pixel : pixels) {
         // Get the pixel local then global position
         PositionVector3D<Cartesian3D<double>> pixelPositionLocal =
             m_detector->getLocalPosition(pixel->column(), pixel->row());

src/modules/AnalysisDUT/AnalysisDUT.cpp

@@ -315,7 +315,7 @@ StatusCode AnalysisDUT::run(std::shared_ptr<Clipboard> clipboard) {
                     m_detector->getColumn(clusterLocal), m_detector->getRow(clusterLocal), cluster->charge());
 
                 // Fill per-pixel histograms
-                for(auto& pixel : (*cluster->pixels())) {
+                for(auto& pixel : cluster->pixels()) {
                     hHitMapAssoc->Fill(pixel->column(), pixel->row());
                     if(is_within_roi) {
                         hHitMapROI->Fill(pixel->column(), pixel->row());

src/modules/AnalysisTimingATLASpix/AnalysisTimingATLASpix.cpp

@@ -474,7 +474,7 @@ StatusCode AnalysisTimingATLASpix::run(std::shared_ptr<Clipboard> clipboard) {
                     }
 
                     // 2D histograms: --> fill for all pixels from cluster
-                    for(auto& pixel : (*cluster->pixels())) {
+                    for(auto& pixel : cluster->pixels()) {
 
                         // to check that cluster timestamp = earliest pixel timestamp
                         if(cluster->size() > 1) {
@@ -752,13 +752,14 @@ void AnalysisTimingATLASpix::correctClusterTimestamp(Cluster* cluster, int mode)
      */
 
     // Get the pixels on this cluster
-    Pixels* pixels = cluster->pixels();
+    auto pixels = cluster->pixels();
+    auto first_pixel = pixels.front();
     double correction = 0;
 
     if(mode == 0) {
-        correction = gRowCorr->Eval((*pixels)[0]->row());
+        correction = gRowCorr->Eval(first_pixel->row());
     } else if(mode == 1) {
-        correction = gTimeWalkCorr->Eval((*pixels)[0]->raw());
+        correction = gTimeWalkCorr->Eval(first_pixel->raw());
     } else {
         LOG(ERROR) << "Mode " << mode << " does not exist!\n"
                    << "Choose\n\t0 --> row correction \n\t1-->timewalk correction";
@@ -766,10 +767,12 @@ void AnalysisTimingATLASpix::correctClusterTimestamp(Cluster* cluster, int mode)
     }
 
     // Initial guess for cluster timestamp:
-    double timestamp = (*pixels)[0]->timestamp() + correction;
+    double timestamp = first_pixel->timestamp() + correction;
 
     // Loop over all pixels:
-    for(auto& pixel : (*pixels)) {
+    for(auto& pixel : pixels) {
+        // FIXME ugly hack
+        auto px = const_cast<Pixel*>(pixel);
 
         if(mode == 0) {
             correction = gRowCorr->Eval(pixel->row());
@@ -780,7 +783,7 @@ void AnalysisTimingATLASpix::correctClusterTimestamp(Cluster* cluster, int mode)
         }
 
         // Override pixel timestamps:
-        pixel->setTimestamp(pixel->timestamp() + correction);
+        px->setTimestamp(pixel->timestamp() + correction);
 
         // timestamp = earliest pixel:
         if(pixel->timestamp() < timestamp) {

src/modules/Clustering4D/Clustering4D.cpp

@@ -122,7 +122,7 @@ bool Clustering4D::touching(Pixel* neighbour, Cluster* cluster) {
 
     bool Touching = false;
 
-    for(auto pixel : (*cluster->pixels())) {
+    for(auto pixel : cluster->pixels()) {
         int row_distance = abs(pixel->row() - neighbour->row());
         int col_distance = abs(pixel->column() - neighbour->column());
 
@@ -142,10 +142,10 @@ bool Clustering4D::closeInTime(Pixel* neighbour, Cluster* cluster) {
 
     bool CloseInTime = false;
 
-    Pixels* pixels = cluster->pixels();
-    for(size_t iPix = 0; iPix < pixels->size(); iPix++) {
+    auto pixels = cluster->pixels();
+    for(auto& px : pixels) {
 
-        double timeDifference = abs(neighbour->timestamp() - (*pixels)[iPix]->timestamp());
+        double timeDifference = abs(neighbour->timestamp() - px->timestamp());
         if(timeDifference < timingCut)
             CloseInTime = true;
     }
@@ -159,13 +159,13 @@ void Clustering4D::calculateClusterCentre(Cluster* cluster) {
     double column(0), row(0), charge(0);
 
     // Get the pixels on this cluster
-    Pixels* pixels = cluster->pixels();
-    string detectorID = (*pixels)[0]->detectorID();
-    double timestamp = (*pixels)[0]->timestamp();
-    LOG(DEBUG) << "- cluster has " << (*pixels).size() << " pixels";
+    auto pixels = cluster->pixels();
+    string detectorID = pixels.front()->detectorID();
+    double timestamp = pixels.front()->timestamp();
+    LOG(DEBUG) << "- cluster has " << pixels.size() << " pixels";
 
     // Loop over all pixels
-    for(auto& pixel : (*pixels)) {
+    for(auto& pixel : pixels) {
         charge += pixel->charge();
         column += (pixel->column() * pixel->charge());
         row += (pixel->row() * pixel->charge());

src/modules/ClusteringSpatial/ClusteringSpatial.cpp

@@ -161,12 +161,12 @@ void ClusteringSpatial::calculateClusterCentre(Cluster* cluster) {
     double column(0), row(0), charge(0);
 
     // Get the pixels on this cluster
-    Pixels* pixels = cluster->pixels();
-    string detectorID = (*pixels)[0]->detectorID();
-    LOG(DEBUG) << "- cluster has " << (*pixels).size() << " pixels";
+    auto pixels = cluster->pixels();
+    string detectorID = pixels.front()->detectorID();
+    LOG(DEBUG) << "- cluster has " << pixels.size() << " pixels";
 
     // Loop over all pixels
-    for(auto& pixel : (*pixels)) {
+    for(auto& pixel : pixels) {
         charge += pixel->charge();
         column += (pixel->column() * pixel->charge());
         row += (pixel->row() * pixel->charge());

src/modules/TreeWriterDUT/TreeWriterDUT.cpp

@@ -118,11 +118,11 @@ StatusCode TreeWriterDUT::run(std::shared_ptr<Clipboard> clipboard) {
         LOG(DEBUG) << "Gets cluster eventID = " << eventID;
 
         // Get the pixels in the current cluster
-        Pixels* pixels = cluster->pixels();
+        auto pixels = cluster->pixels();
 
         // Iterate through all pixels in the cluster
         numPixels = 0;
-        for(auto& pixel : (*pixels)) {
+        for(auto& pixel : pixels) {
             // Increase counter for number of pixels in the cluster
             numPixels++;