Merge branch 'rename_pixelToT_to_pixelValue' into 'master'

Changing Pixel object: renaming "tot" to "value"

See merge request !99

src/modules/AnalysisCLICpix/AnalysisCLICpix.cpp

@@ -50,7 +50,7 @@ void AnalysisCLICpix::initialise() {
                                   0,
                                   maxcounter - 1);
     hClusterSizeAll = new TH1F("hClusterSizeAll", "hClusterSizeAll", 20, 0, 20);
-    hClusterTOTAll = new TH1F("hClusterTOTAll", "hClusterTOTAll", 50, 0, 50);
+    hClusterChargeAll = new TH1F("hClusterChargeAll", "hClusterChargeAll", 50, 0, 50);
     hClustersPerEvent = new TH1F("hClustersPerEvent", "hClustersPerEvent", 500, 0, 500);
     hClustersVersusEventNo = new TH1F("hClustersVersusEventNo", "hClustersVersusEventNo", 60000, 0, 60000);
     hGlobalClusterPositions = new TH2F("hGlobalClusterPositions", "hGlobalClusterPositions", 200, -2.0, 2.0, 300, -1., 2);
@@ -108,11 +108,11 @@ void AnalysisCLICpix::initialise() {
     hClusterWidthRowAssociated = new TH1F("hClusterWidthRowAssociated", "hClusterWidthRowAssociated", 20, 0, 20);
     hClusterWidthColAssociated = new TH1F("hClusterWidthColAssociated", "hClusterWidthColAssociated", 20, 0, 20);
 
-    hClusterTOTAssociated = new TH1F("hClusterTOTAssociated", "hClusterTOTAssociated", 50, 0, 50);
-    hClusterTOTAssociated1pix = new TH1F("hClusterTOTAssociated1pix", "hClusterTOTAssociated1pix", 50, 0, 50);
-    hClusterTOTAssociated2pix = new TH1F("hClusterTOTAssociated2pix", "hClusterTOTAssociated2pix", 50, 0, 50);
-    hClusterTOTAssociated3pix = new TH1F("hClusterTOTAssociated3pix", "hClusterTOTAssociated3pix", 50, 0, 50);
-    hClusterTOTAssociated4pix = new TH1F("hClusterTOTAssociated4pix", "hClusterTOTAssociated4pix", 50, 0, 50);
+    hClusterChargeAssociated = new TH1F("hClusterChargeAssociated", "hClusterChargeAssociated", 50, 0, 50);
+    hClusterChargeAssociated1pix = new TH1F("hClusterChargeAssociated1pix", "hClusterChargeAssociated1pix", 50, 0, 50);
+    hClusterChargeAssociated2pix = new TH1F("hClusterChargeAssociated2pix", "hClusterChargeAssociated2pix", 50, 0, 50);
+    hClusterChargeAssociated3pix = new TH1F("hClusterChargeAssociated3pix", "hClusterChargeAssociated3pix", 50, 0, 50);
+    hClusterChargeAssociated4pix = new TH1F("hClusterChargeAssociated4pix", "hClusterChargeAssociated4pix", 50, 0, 50);
 
     hPixelResponseX = new TH1F("hPixelResponseX", "hPixelResponseX", 600, -0.3, 0.3);
     hPixelResponseY = new TH1F("hPixelResponseY", "hPixelResponseY", 600, -0.3, 0.3);
@@ -130,10 +130,10 @@ void AnalysisCLICpix::initialise() {
 
     hResidualsLocalRow2pix = new TH1F("hResidualsLocalRow2pix", "hResidualsLocalRow2pix", 600, -0.3, 0.3);
     hResidualsLocalCol2pix = new TH1F("hResidualsLocalCol2pix", "hResidualsLocalCol2pix", 600, -0.3, 0.3);
-    hClusterTOTRow2pix = new TH1F("hClusterTOTRow2pix", "hClusterTOTRow2pix", 50, 0, 50);
-    hClusterTOTCol2pix = new TH1F("hClusterTOTCol2pix", "hClusterTOTCol2pix", 50, 0, 50);
-    hClusterTOTRatioRow2pix = new TH1F("hClusterTOTRatioRow2pix", "hClusterTOTRatioRow2pix", 100, 0, 1);
-    hClusterTOTRatioCol2pix = new TH1F("hClusterTOTRatioCol2pix", "hClusterTOTRatioCol2pix", 100, 0, 1);
+    hClusterChargeRow2pix = new TH1F("hClusterChargeRow2pix", "hClusterChargeRow2pix", 50, 0, 50);
+    hClusterChargeCol2pix = new TH1F("hClusterChargeCol2pix", "hClusterChargeCol2pix", 50, 0, 50);
+    hClusterChargeRatioRow2pix = new TH1F("hClusterChargeRatioRow2pix", "hClusterChargeRatioRow2pix", 100, 0, 1);
+    hClusterChargeRatioCol2pix = new TH1F("hClusterChargeRatioCol2pix", "hClusterChargeRatioCol2pix", 100, 0, 1);
     hPixelTOTRow2pix = new TH1F("hPixelTOTRow2pix", "hPixelTOTRow2pix", 50, 0, 50);
     hPixelTOTCol2pix = new TH1F("hPixelTOTCol2pix", "hPixelTOTCol2pix", 50, 0, 50);
 
@@ -209,9 +209,9 @@ void AnalysisCLICpix::initialise() {
     for(int x = 0; x < m_nBinsX; x++) {
         for(int y = 0; y < m_nBinsY; y++) {
             int id = x + y * m_nBinsX;
-            std::string name = "hMapClusterTOTAssociated1pix" + convertToString(id);
-            TH1F* hMapEntryClusterTOTAssociated1pix = new TH1F(name.c_str(), name.c_str(), 50, 0, 50);
-            hMapClusterTOTAssociated1pix[id] = hMapEntryClusterTOTAssociated1pix;
+            std::string name = "hMapClusterChargeAssociated1pix" + convertToString(id);
+            TH1F* hMapEntryClusterChargeAssociated1pix = new TH1F(name.c_str(), name.c_str(), 50, 0, 50);
+            hMapClusterChargeAssociated1pix[id] = hMapEntryClusterChargeAssociated1pix;
         }
     }
 }
@@ -362,35 +362,35 @@ StatusCode AnalysisCLICpix::run(std::shared_ptr<Clipboard> clipboard) {
                 pixelInterceptX, pixelInterceptY, sqrt(xresidualBest * xresidualBest + yresidualBest * yresidualBest));
             hXresidualVersusYresidual->Fill(xresidualBest, yresidualBest);
             hAbsoluteResiduals->Fill(sqrt(xresidualBest * xresidualBest + yresidualBest * yresidualBest));
-            hClusterTOTAssociated->Fill((bestCluster)->tot());
+            hClusterChargeAssociated->Fill((bestCluster)->charge());
             hClusterSizeAssociated->Fill(static_cast<double>(bestCluster->size()));
             //      hClusterWidthColAssociated->Fill((*bestCluster)->colWidth());
             //      hClusterWidthRowAssociated->Fill((*bestCluster)->rowWidth());
 
-            hMapClusterSizeAssociated->Fill(chipInterceptCol, chipInterceptRow, (bestCluster)->tot());
+            hMapClusterSizeAssociated->Fill(chipInterceptCol, chipInterceptRow, (bestCluster)->charge());
 
             if((bestCluster)->size() == 1) {
-                hClusterTOTAssociated1pix->Fill((bestCluster)->tot());
+                hClusterChargeAssociated1pix->Fill((bestCluster)->charge());
                 hInterceptClusterSize1->Fill(pixelInterceptX, pixelInterceptY);
                 int id = static_cast<int>(floor(chipInterceptCol * m_nBinsX / m_detector->nPixels().X()) +
                                           floor(chipInterceptRow * m_nBinsY / m_detector->nPixels().Y()) * m_nBinsX);
-                hMapClusterTOTAssociated1pix[id]->Fill((bestCluster)->tot());
+                hMapClusterChargeAssociated1pix[id]->Fill((bestCluster)->charge());
             }
             if((bestCluster)->size() == 2) {
-                hClusterTOTAssociated2pix->Fill((bestCluster)->tot());
+                hClusterChargeAssociated2pix->Fill((bestCluster)->charge());
                 hInterceptClusterSize2->Fill(pixelInterceptX, pixelInterceptY);
             }
             if((bestCluster)->size() == 3) {
-                hClusterTOTAssociated3pix->Fill((bestCluster)->tot());
+                hClusterChargeAssociated3pix->Fill((bestCluster)->charge());
                 hInterceptClusterSize3->Fill(pixelInterceptX, pixelInterceptY);
             }
             if((bestCluster)->size() == 4) {
-                hClusterTOTAssociated4pix->Fill((bestCluster)->tot());
+                hClusterChargeAssociated4pix->Fill((bestCluster)->charge());
                 hInterceptClusterSize4->Fill(pixelInterceptX, pixelInterceptY);
             }
             Pixels* pixels = bestCluster->pixels();
             for(auto& pixel : (*pixels)) {
-                hPixelToTMap->Fill(pixel->column(), pixel->row(), pixel->adc());
+                hPixelToTMap->Fill(pixel->column(), pixel->row(), pixel->raw());
             }
 
         } else {
@@ -546,13 +546,13 @@ void AnalysisCLICpix::fillClusterHistos(Clusters* clusters) {
         for(itp = pixels->begin(); itp != pixels->end(); itp++) {
             // Check if this clicpix frame is still the current
             int pixelID = (*itp)->column() + nCols * (*itp)->row();
-            if(m_hitPixels[pixelID] != (*itp)->adc()) {
+            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)->adc();
+                m_hitPixels[pixelID] = (*itp)->raw();
                 m_triggerNumber = 0;
             }
             hHitPixels->Fill((*itp)->column(), (*itp)->row());
@@ -562,7 +562,7 @@ void AnalysisCLICpix::fillClusterHistos(Clusters* clusters) {
 
         // Fill cluster histograms
         hClusterSizeAll->Fill(static_cast<double>((*itc)->size()));
-        hClusterTOTAll->Fill((*itc)->tot());
+        hClusterChargeAll->Fill((*itc)->charge());
         hGlobalClusterPositions->Fill((*itc)->global().x(), (*itc)->global().y());
     }
 

src/modules/AnalysisCLICpix/AnalysisCLICpix.h

@@ -36,7 +36,7 @@ namespace corryvreckan {
         TH1F* hRowHits;
 
         TH1F* hClusterSizeAll;
-        TH1F* hClusterTOTAll;
+        TH1F* hClusterChargeAll;
         TH1F* hClustersPerEvent;
         TH1F* hClustersVersusEventNo;
         TH1F* hClusterWidthRow;
@@ -71,11 +71,11 @@ namespace corryvreckan {
         TH1F* hClusterSizeAssociated;
         TH1F* hClusterWidthRowAssociated;
         TH1F* hClusterWidthColAssociated;
-        TH1F* hClusterTOTAssociated;
-        TH1F* hClusterTOTAssociated1pix;
-        TH1F* hClusterTOTAssociated2pix;
-        TH1F* hClusterTOTAssociated3pix;
-        TH1F* hClusterTOTAssociated4pix;
+        TH1F* hClusterChargeAssociated;
+        TH1F* hClusterChargeAssociated1pix;
+        TH1F* hClusterChargeAssociated2pix;
+        TH1F* hClusterChargeAssociated3pix;
+        TH1F* hClusterChargeAssociated4pix;
         TH1F* hPixelResponseX;
         TH1F* hPixelResponseGlobalX;
         TH1F* hPixelResponseXOddCol;
@@ -88,12 +88,12 @@ namespace corryvreckan {
         TH2F* hEtaDistributionY;
         TH1F* hResidualsLocalRow2pix;
         TH1F* hResidualsLocalCol2pix;
-        TH1F* hClusterTOTRow2pix;
-        TH1F* hClusterTOTCol2pix;
+        TH1F* hClusterChargeRow2pix;
+        TH1F* hClusterChargeCol2pix;
         TH1F* hPixelTOTRow2pix;
         TH1F* hPixelTOTCol2pix;
-        TH1F* hClusterTOTRatioRow2pix;
-        TH1F* hClusterTOTRatioCol2pix;
+        TH1F* hClusterChargeRatioRow2pix;
+        TH1F* hClusterChargeRatioCol2pix;
 
         // Maps
         TH2F* hTrackIntercepts;
@@ -118,7 +118,7 @@ namespace corryvreckan {
         TH2F* hMapClusterSizeAssociated;
         int m_nBinsX;
         int m_nBinsY;
-        std::map<int, TH1F*> hMapClusterTOTAssociated1pix;
+        std::map<int, TH1F*> hMapClusterChargeAssociated1pix;
 
         // Member variables
         int m_eventNumber;

src/modules/AnalysisCLICpix/README.md

@@ -13,20 +13,20 @@ This module associates CLICpix2 DUT clusters to tracks using a spatial cut (devi
 * `timepix3_telescope`: Boolean to set whether the Timepix3 telescope is being used. Default value is `false`.
 
 ### Plots produced
-The following plots are produced:
+The following plots are produced: (Quite many of them are not filled currently!)
 
 * 2D hitmap
 * Column hits histogram
 * Row hits histogram
 
 * Cluster size histogram
-* CLuster ToT histogram
+* Cluster charge histogram
 * Clusters per event histogram
 * Clusters vs event number
 * Cluster width histogram (rows, Y-axis)
 * Cluster width histogram (columns, X-axis)
 
-* Global track difference
+* Global track difference in X
 * Global track difference in Y
 * Global residuals in X
 * Global residuals in Y
@@ -55,10 +55,10 @@ The following plots are produced:
 * Associated cluster size
 * Associated cluster width (row)
 * Associated cluster width (column)
-* Associated 1-pixel cluster ToT
-* Associated 2-pixel cluster ToT
-* Associated 3-pixel cluster ToT
-* Associated 4-pixel cluster ToT
+* Associated 1-pixel cluster charge
+* Associated 2-pixel cluster charge
+* Associated 3-pixel cluster charge
+* Associated 4-pixel cluster charge
 * Pixel response in X
 * Pixel response in X in global coordinates
 * Pixel response in X for odd columns
@@ -72,12 +72,12 @@ The following plots are produced:
 
 * Local residual for rows for 2-pixel clusters
 * Local residual for columns for 2-pixel clusters
-* Cluster ToT for rows for 2-pixel clusters
-* Cluster ToT for columns for 2-pixel clusters
+* Cluster charge for rows for 2-pixel clusters
+* Cluster charge for columns for 2-pixel clusters
 * Pixel ToT for rows for 2-pixel clusters
 * Pixel ToT for columns for 2-pixel clusters
-* Cluster ToT ratio for rows for 2-pixel clusters
-* Cluster ToT ratio for rows for 2-pixel clusters
+* Cluster charge ratio for rows for 2-pixel clusters
+* Cluster charge ratio for rows for 2-pixel clusters
 * Local residuals for rows for 2-pixel clusters
 
 * 2D track intercepts

src/modules/AnalysisDUT/AnalysisDUT.cpp

@@ -17,7 +17,7 @@ AnalysisDUT::AnalysisDUT(Configuration config, std::shared_ptr<Detector> detecto
 void AnalysisDUT::initialise() {
 
     hClusterMapAssoc = new TH2F("clusterMapAssoc",
-                                "clusterMapAssoc",
+                                "clusterMapAssoc; cluster col; cluster row",
                                 m_detector->nPixels().X(),
                                 0,
                                 m_detector->nPixels().X(),
@@ -25,7 +25,7 @@ void AnalysisDUT::initialise() {
                                 0,
                                 m_detector->nPixels().Y());
     hClusterSizeMapAssoc = new TProfile2D("clusterSizeMapAssoc",
-                                          "clusterSizeMapAssoc",
+                                          "clusterSizeMapAssoc; cluster size; #entries",
                                           m_detector->nPixels().X(),
                                           0,
                                           m_detector->nPixels().X(),
@@ -34,21 +34,20 @@ void AnalysisDUT::initialise() {
                                           m_detector->nPixels().Y(),
                                           0,
                                           100);
-
-    hClusterToTMapAssoc = new TProfile2D("clusterSizeToTAssoc",
-                                         "clusterToTMapAssoc",
-                                         m_detector->nPixels().X(),
-                                         0,
-                                         m_detector->nPixels().X(),
-                                         m_detector->nPixels().Y(),
-                                         0,
-                                         m_detector->nPixels().Y(),
-                                         0,
-                                         1000);
+    hClusterChargeMapAssoc = new TProfile2D("clusterChargeMapAssoc",
+                                            "clusterSizeChargeAssoc; cluster charge [e]; #entries",
+                                            m_detector->nPixels().X(),
+                                            0,
+                                            m_detector->nPixels().X(),
+                                            m_detector->nPixels().Y(),
+                                            0,
+                                            m_detector->nPixels().Y(),
+                                            0,
+                                            500);
 
     // Per-pixel histograms
     hHitMapAssoc = new TH2F("hitMapAssoc",
-                            "hitMapAssoc",
+                            "hitMapAssoc; hit column; hit row",
                             m_detector->nPixels().X(),
                             0,
                             m_detector->nPixels().X(),
@@ -56,24 +55,24 @@ void AnalysisDUT::initialise() {
                             0,
                             m_detector->nPixels().Y());
     hHitMapROI = new TH2F("hitMapROI",
-                          "hitMapROI",
+                          "hitMapROI; hit column; hit row",
                           m_detector->nPixels().X(),
                           0,
                           m_detector->nPixels().X(),
                           m_detector->nPixels().Y(),
                           0,
                           m_detector->nPixels().Y());
-    hPixelToTAssoc = new TH1F("pixelToTAssoc", "pixelToTAssoc", 32, 0, 31);
-    hPixelToTMapAssoc = new TProfile2D("pixelToTMapAssoc",
-                                       "pixelToTMapAssoc",
-                                       m_detector->nPixels().X(),
-                                       0,
-                                       m_detector->nPixels().X(),
-                                       m_detector->nPixels().Y(),
-                                       0,
-                                       m_detector->nPixels().Y(),
-                                       0,
-                                       255);
+    hPixelRawValueAssoc = new TH1F("pixelRawValueAssoc", "pixelRawValueAssoc", 32, 0, 31);
+    hPixelRawValueMapAssoc = new TProfile2D("pixelRawValueMapAssoc",
+                                            "pixelRawValueMapAssoc",
+                                            m_detector->nPixels().X(),
+                                            0,
+                                            m_detector->nPixels().X(),
+                                            m_detector->nPixels().Y(),
+                                            0,
+                                            m_detector->nPixels().Y(),
+                                            0,
+                                            255);
 
     associatedTracksVersusTime = new TH1F("associatedTracksVersusTime", "associatedTracksVersusTime", 300000, 0, 300);
     residualsX = new TH1F("residualsX", "residualsX", 800, -0.1, 0.1);
@@ -84,8 +83,7 @@ void AnalysisDUT::initialise() {
     residualsX2pix = new TH1F("residualsX2pix", "residualsX2pix", 400, -0.2, 0.2);
     residualsY2pix = new TH1F("residualsY2pix", "residualsY2pix", 400, -0.2, 0.2);
 
-    clusterTotAssoc = new TH1F("clusterTotAssociated", "clusterTotAssociated", 10000, 0, 10000);
-    clusterTotAssocNorm = new TH1F("clusterTotAssociatedNormalized", "clusterTotAssociatedNormalized", 10000, 0, 10000);
+    clusterChargeAssoc = new TH1F("clusterChargeAssociated", "clusterChargeAssociated [e]", 10000, 0, 10000);
     clusterSizeAssoc = new TH1F("clusterSizeAssociated", "clusterSizeAssociated", 30, 0, 30);
     clusterSizeAssocNorm = new TH1F("clusterSizeAssociatedNormalized", "clusterSizeAssociatedNormalized", 30, 0, 30);
 
@@ -305,15 +303,16 @@ StatusCode AnalysisDUT::run(std::shared_ptr<Clipboard> clipboard) {
                 hClusterSizeMapAssoc->Fill(m_detector->getColumn(clusterLocal),
                                            m_detector->getRow(clusterLocal),
                                            static_cast<double>(cluster->size()));
-                hClusterToTMapAssoc->Fill(
-                    m_detector->getColumn(clusterLocal), m_detector->getRow(clusterLocal), cluster->tot());
-
-                clusterTotAssoc->Fill(cluster->tot());
 
                 // Cluster charge normalized to path length in sensor:
                 double norm = 1; // FIXME fabs(cos( turn*wt )) * fabs(cos( tilt*wt ));
-                auto normalized_charge = cluster->tot() * norm;
-                clusterTotAssocNorm->Fill(normalized_charge);
+                // FIXME: what does this mean? To my understanding we have the correct charge here already...
+                auto normalized_charge = cluster->charge() * norm;
+
+                // clusterChargeAssoc->Fill(normalized_charge);
+                clusterChargeAssoc->Fill(cluster->charge());
+                hClusterChargeMapAssoc->Fill(
+                    m_detector->getColumn(clusterLocal), m_detector->getRow(clusterLocal), cluster->charge());
 
                 // Fill per-pixel histograms
                 for(auto& pixel : (*cluster->pixels())) {
@@ -321,8 +320,8 @@ StatusCode AnalysisDUT::run(std::shared_ptr<Clipboard> clipboard) {
                     if(is_within_roi) {
                         hHitMapROI->Fill(pixel->column(), pixel->row());
                     }
-                    hPixelToTAssoc->Fill(pixel->tot());
-                    hPixelToTMapAssoc->Fill(pixel->column(), pixel->row(), pixel->tot());
+                    hPixelRawValueAssoc->Fill(pixel->raw());
+                    hPixelRawValueMapAssoc->Fill(pixel->column(), pixel->row(), pixel->raw());
                 }
 
                 associatedTracksVersusTime->Fill(static_cast<double>(Units::convert(track->timestamp(), "s")));
@@ -343,14 +342,14 @@ StatusCode AnalysisDUT::run(std::shared_ptr<Clipboard> clipboard) {
                 // Time residuals
                 residualsTime->Fill(tdistance);
                 residualsTimeVsTime->Fill(tdistance, track->timestamp());
-                residualsTimeVsSignal->Fill(tdistance, cluster->tot());
+                residualsTimeVsSignal->Fill(tdistance, cluster->charge());
 
                 clusterSizeAssoc->Fill(static_cast<double>(cluster->size()));
                 clusterSizeAssocNorm->Fill(static_cast<double>(cluster->size()));
 
                 // Fill in-pixel plots: (all as function of track position within pixel cell)
                 if(is_within_roi) {
-                    qvsxmym->Fill(xmod, ymod, cluster->tot());                     // cluster charge profile
+                    qvsxmym->Fill(xmod, ymod, cluster->charge());                  // cluster charge profile
                     qMoyalvsxmym->Fill(xmod, ymod, exp(-normalized_charge / 3.5)); // norm. cluster charge profile
 
                     // mean charge of cluster seed

src/modules/AnalysisDUT/AnalysisDUT.h

@@ -28,10 +28,10 @@ namespace corryvreckan {
 
         // Histograms
         TH2F *hClusterMapAssoc, *hHitMapAssoc, *hHitMapROI;
-        TProfile2D *hClusterSizeMapAssoc, *hClusterToTMapAssoc;
+        TProfile2D *hClusterSizeMapAssoc, *hClusterChargeMapAssoc;
 
-        TH1F* hPixelToTAssoc;
-        TProfile2D* hPixelToTMapAssoc;
+        TH1F* hPixelRawValueAssoc;
+        TProfile2D* hPixelRawValueMapAssoc;
 
         TH1F* associatedTracksVersusTime;
         TH1F *residualsX, *residualsY;
@@ -39,7 +39,7 @@ namespace corryvreckan {
         TH1F *residualsX1pix, *residualsY1pix;
         TH1F *residualsX2pix, *residualsY2pix;
 
-        TH1F *clusterTotAssoc, *clusterTotAssocNorm;
+        TH1F* clusterChargeAssoc;
         TH1F* clusterSizeAssoc;
         TH1F* clusterSizeAssocNorm;
 

src/modules/AnalysisDUT/README.md

@@ -5,7 +5,7 @@
 **Status**: Work in progress
 
 ### Description
-Analysis module for CLICpix2 prototypes. This module is still work in progress, changes to functionality and behaviour are to be expected.
+Generic analysis module for all prototypes. This module is still work in progress, changes to functionality and behaviour are to be expected.
 
 ### Parameters
 * `time_cut_frameedge`: Parameter to discard telescope tracks at the frame edges (start and end of the current CLICpix2 frame). Defaults to `20ns`.
@@ -15,16 +15,16 @@ Analysis module for CLICpix2 prototypes. This module is still work in progress,
 ### Plots produced
 * 2D Map of associated cluster positions
 * 2D Map of cluster sizes for associated clusters
-* 2D Map of cluster ToT values from associated clusters
+* 2D Map of cluster charge values from associated clusters
 * 2D Map of associated hits
 * 2D Map of tracks not associated to a cluster
 * 2D Map of associated hits within the defined region-of-interest
-* Distribution of pixel ToT values from associated clusters
-* 2D Map of pixel ToT values from associated clusters
+* Distribution of pixel raw value (ToT, ADC, ...) values from associated clusters
+* 2D Map of pixel raw value (ToT, ADC, ...) values from associated clusters
 * Track residuals in X and Y
 * Track residuals for 1-pixel-clusters in X and Y
 * Track residuals for 2-pixel-clusters in X and Y
-* Distribution of cluster Tot values from associated clusters
+* Distribution of cluster charge values from associated clusters
 * Distribution of sizes from associated clusters
 * Normalised distribution of sizes from associated clusters
 * 2D Map of in-pixel efficiency

src/modules/Clustering4D/Clustering4D.cpp

@@ -21,7 +21,7 @@ void Clustering4D::initialise() {
     title = m_detector->name() + " Cluster Width - Columns;cluster width [columns];events";
     clusterWidthColumn = new TH1F("clusterWidthColumn", title.c_str(), 100, 0, 100);
     title = m_detector->name() + " Cluster Charge;cluster charge [e];events";
-    clusterTot = new TH1F("clusterTot", title.c_str(), 10000, 0, 100000);
+    clusterCharge = new TH1F("clusterCharge", title.c_str(), 10000, 0, 100000);
     title = m_detector->name() + " Cluster Position (Global);x [mm];y [mm];events";
     clusterPositionGlobal = new TH2F("clusterPositionGlobal", title.c_str(), 400, -10., 10., 400, -10., 10.);
 }
@@ -60,10 +60,6 @@ StatusCode Clustering4D::run(std::shared_ptr<Clipboard> clipboard) {
             continue;
         }
 
-        if(pixel->adc() == 0.) {
-            continue;
-        }
-
         // Make the new cluster object
         Cluster* cluster = new Cluster();
         LOG(DEBUG) << "==== New cluster";
@@ -88,9 +84,6 @@ StatusCode Clustering4D::run(std::shared_ptr<Clipboard> clipboard) {
                 if(used[neighbour])
                     continue;
 
-                if(neighbour->adc() == 0.)
-                    continue;
-
                 // Check if they are touching cluster pixels
                 if(!touching(neighbour, cluster))
                     continue;
@@ -111,7 +104,7 @@ StatusCode Clustering4D::run(std::shared_ptr<Clipboard> clipboard) {
         clusterSize->Fill(static_cast<double>(cluster->size()));
         clusterWidthRow->Fill(cluster->rowWidth());
         clusterWidthColumn->Fill(cluster->columnWidth());
-        clusterTot->Fill(cluster->tot());
+        clusterCharge->Fill(cluster->charge());
         clusterPositionGlobal->Fill(cluster->global().x(), cluster->global().y());
 
         deviceClusters->push_back(cluster);
@@ -163,30 +156,33 @@ bool Clustering4D::closeInTime(Pixel* neighbour, Cluster* cluster) {
 
 void Clustering4D::calculateClusterCentre(Cluster* cluster) {
 
+    LOG(DEBUG) << "== Making cluster centre";
     // Empty variables to calculate cluster position
-    double row(0), column(0), tot(0);
+    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";
 
     // Loop over all pixels
     for(auto& pixel : (*pixels)) {
-        double pixelToT = pixel->adc();
-        if(pixelToT == 0) {
-            LOG(DEBUG) << "Pixel with ToT 0!";
-            pixelToT = 1;
-        }
-        tot += pixelToT;
-        row += (pixel->row() * pixelToT);
-        column += (pixel->column() * pixelToT);
-        if(pixel->timestamp() < timestamp)
+        charge += pixel->charge();
+        column += (pixel->column() * pixel->charge());
+        row += (pixel->row() * pixel->charge());
+        if(pixel->timestamp() < timestamp) {
             timestamp = pixel->timestamp();
+        }
     }
-    // Row and column positions are tot-weighted
-    row /= (tot > 0 ? tot : 1);
-    column /= (tot > 0 ? tot : 1);
+
+    // Column and row positions are charge-weighted
+    // If charge == 0 (use epsilon to avoid errors in floating-point arithmetics)
+    // calculate simple arithmetic mean
+    column /= (charge > std::numeric_limits<double>::epsilon() ? charge : 1);
+    row /= (charge > std::numeric_limits<double>::epsilon() ? charge : 1);
+
+    LOG(DEBUG) << "- cluster col, row: " << column << "," << row;
 
     if(detectorID != m_detector->name()) {
         // Should never happen...
@@ -201,9 +197,9 @@ void Clustering4D::calculateClusterCentre(Cluster* cluster) {
     PositionVector3D<Cartesian3D<double>> positionGlobal = m_detector->localToGlobal(positionLocal);
 
     // Set the cluster parameters
-    cluster->setRow(row);
     cluster->setColumn(column);
-    cluster->setTot(tot);
+    cluster->setRow(row);
+    cluster->setCharge(charge);
 
     // Set uncertainty on position from intrinstic detector resolution:
     cluster->setError(m_detector->resolution());

src/modules/Clustering4D/Clustering4D.h

@@ -34,7 +34,7 @@ namespace corryvreckan {
         TH1F* clusterSize;
         TH1F* clusterWidthRow;
         TH1F* clusterWidthColumn;
-        TH1F* clusterTot;
+        TH1F* clusterCharge;
         TH2F* clusterPositionGlobal;
 
         double timingCut;

src/modules/Clustering4D/README.md

@@ -5,7 +5,7 @@
 **Status**: Functional
 
 ### Description
-This module performs clustering on data from a Timepix3 device. The clustering method is a charge-weighted centre of gravity calculation, using a positional cut and a timing cut on proximity.
+This module performs clustering for detectors with valid individual hit timestamps. The clustering method is a charge-weighted centre of gravity calculation, using a positional cut and a timing cut on proximity. If the pixel information is binary (i.e. no valid charge-equivalent information is available), the arithmetic mean is calculated for the position.
 
 Split clusters can be recovered using a larger search radius for neighbouring pixels.
 
@@ -20,7 +20,7 @@ For each detector the following plots are produced:
 * Cluster size histogram
 * Cluster width (rows, in X) histogram
 * Cluster width (columns, in Y) histogram
-* Cluster ToT histogram
+* Cluster charge histogram
 * 2D cluster positions in global coordinates
 
 ### Usage

src/modules/ClusteringSpatial/ClusteringSpatial.cpp

@@ -27,7 +27,7 @@ void ClusteringSpatial::initialise() {
     title = m_detector->name() + " Cluster Width - Columns;cluster width [columns];events";
     clusterWidthColumn = new TH1F("clusterWidthColumn", title.c_str(), 100, 0, 100);
     title = m_detector->name() + " Cluster Charge;cluster charge [ke];events";
-    clusterTot = new TH1F("clusterTot", title.c_str(), 300, 0, 300);
+    clusterCharge = new TH1F("clusterCharge", title.c_str(), 300, 0, 300);
     title = m_detector->name() + " Cluster Position (Global);x [mm];y [mm];events";
     clusterPositionGlobal = new TH2F("clusterPositionGlobal",
                                      title.c_str(),
@@ -135,7 +135,7 @@ StatusCode ClusteringSpatial::run(std::shared_ptr<Clipboard> clipboard) {
         clusterSize->Fill(static_cast<double>(cluster->size()));
         clusterWidthRow->Fill(cluster->rowWidth());
         clusterWidthColumn->Fill(cluster->columnWidth());
-        clusterTot->Fill(cluster->tot() * 1e-3);
+        clusterCharge->Fill(cluster->charge() * 1e-3); //  1e-3 because unit is [ke]
         clusterPositionGlobal->Fill(cluster->global().x(), cluster->global().y());
         clusterPositionLocal->Fill(cluster->local().x(), cluster->local().y());
         LOG(DEBUG) << "cluster local: " << cluster->local();
@@ -158,7 +158,7 @@ void ClusteringSpatial::calculateClusterCentre(Cluster* cluster) {
 
     LOG(DEBUG) << "== Making cluster centre";
     // Empty variables to calculate cluster position
-    double row(0), column(0), tot(0);
+    double column(0), row(0), charge(0);
 
     // Get the pixels on this cluster
     Pixels* pixels = cluster->pixels();
@@ -167,15 +167,18 @@ void ClusteringSpatial::calculateClusterCentre(Cluster* cluster) {