merged master

src/modules/AnalysisDUT/AnalysisDUT.cpp

@@ -37,15 +37,43 @@ AnalysisDUT::AnalysisDUT(Configuration& config, std::shared_ptr<Detector> detect
 void AnalysisDUT::initialize() {
 
     if(correlations_) {
-        hTrackCorrelationX = new TH1F(
-            "hTrackCorrelationX", "Track residual X, all clusters;x_{track}-x_{hit} [#mum];# entries", 8000, -1000.5, 999.5);
-        hTrackCorrelationY = new TH1F(
-            "hTrackCorrelationY", "Track residual Y, all clusters;y_{track}-y_{hit} [#mum];# entries", 8000, -1000.5, 999.5);
-        hTrackCorrelationTime = new TH1F("hTrackCorrelationTime",
-                                         "Track time residual, all clusters;time_{track}-time_{hit} [ns];# entries",
-                                         n_timebins_,
-                                         -(n_timebins_ + 1) / 2. * time_binning_,
-                                         (n_timebins_ - 1) / 2. * time_binning_);
+        trackCorrelationX_beforeCuts =
+            new TH1F("trackCorrelationX_beforeCuts",
+                     "Track residual X (tracks before cuts), all clusters;x_{track}-x_{hit} [#mum];# entries",
+                     8000,
+                     -1000.5,
+                     999.5);
+        trackCorrelationY_beforeCuts =
+            new TH1F("trackCorrelationY_beforeCuts",
+                     "Track residual Y (tracks before cuts), all clusters;y_{track}-y_{hit} [#mum];# entries",
+                     8000,
+                     -1000.5,
+                     999.5);
+        trackCorrelationTime_beforeCuts =
+            new TH1F("trackCorrelationTime_beforeCuts",
+                     "Track time residual (tracks before cuts), all clusters;time_{track}-time_{hit} [ns];# entries",
+                     n_timebins_,
+                     -(n_timebins_ + 1) / 2. * time_binning_,
+                     (n_timebins_ - 1) / 2. * time_binning_);
+
+        trackCorrelationX_afterCuts =
+            new TH1F("trackCorrelationX_afterCuts",
+                     "Track residual X (tracks after cuts), all clusters;x_{track}-x_{hit} [#mum];# entries",
+                     8000,
+                     -1000.5,
+                     999.5);
+        trackCorrelationY_afterCuts =
+            new TH1F("trackCorrelationY_afterCuts",
+                     "Track residual Y (tracks after cuts), all clusters;y_{track}-y_{hit} [#mum];# entries",
+                     8000,
+                     -1000.5,
+                     999.5);
+        trackCorrelationTime_afterCuts =
+            new TH1F("trackCorrelationTime_afterCuts",
+                     "Track time residual (tracks after cuts), all clusters;time_{track}-time_{hit} [ns];# entries",
+                     n_timebins_,
+                     -(n_timebins_ + 1) / 2. * time_binning_,
+                     (n_timebins_ - 1) / 2. * time_binning_);
     }
 
     hClusterMapAssoc = new TH2F("clusterMapAssoc",
@@ -391,6 +419,54 @@ void AnalysisDUT::initialize() {
                           -pitch_y / 2.,
                           pitch_y / 2.);
 
+    title = "Mean cluster charge map (1-pixel);" + mod_axes + "<cluster charge> [ke]";
+    qvsxmym_1px = new TProfile2D("qvsxmym_1px",
+                                 title.c_str(),
+                                 static_cast<int>(pitch_x),
+                                 -pitch_x / 2.,
+                                 pitch_x / 2.,
+                                 static_cast<int>(pitch_y),
+                                 -pitch_y / 2.,
+                                 pitch_y / 2.,
+                                 0,
+                                 250);
+
+    title = "Mean cluster charge map (2-pixel);" + mod_axes + "<cluster charge> [ke]";
+    qvsxmym_2px = new TProfile2D("qvsxmym_2px",
+                                 title.c_str(),
+                                 static_cast<int>(pitch_x),
+                                 -pitch_x / 2.,
+                                 pitch_x / 2.,
+                                 static_cast<int>(pitch_y),
+                                 -pitch_y / 2.,
+                                 pitch_y / 2.,
+                                 0,
+                                 250);
+
+    title = "Mean cluster charge map (3-pixel);" + mod_axes + "<cluster charge> [ke]";
+    qvsxmym_3px = new TProfile2D("qvsxmym_3px",
+                                 title.c_str(),
+                                 static_cast<int>(pitch_x),
+                                 -pitch_x / 2.,
+                                 pitch_x / 2.,
+                                 static_cast<int>(pitch_y),
+                                 -pitch_y / 2.,
+                                 pitch_y / 2.,
+                                 0,
+                                 250);
+
+    title = "Mean cluster charge map (4-pixel);" + mod_axes + "<cluster charge> [ke]";
+    qvsxmym_4px = new TProfile2D("qvsxmym_4px",
+                                 title.c_str(),
+                                 static_cast<int>(pitch_x),
+                                 -pitch_x / 2.,
+                                 pitch_x / 2.,
+                                 static_cast<int>(pitch_y),
+                                 -pitch_y / 2.,
+                                 pitch_y / 2.,
+                                 0,
+                                 250);
+
     residualsTime = new TH1F("residualsTime",
                              "Time residual;time_{track}-time_{hit} [ns];#entries",
                              n_timebins_,
@@ -525,15 +601,15 @@ StatusCode AnalysisDUT::run(const std::shared_ptr<Clipboard>& clipboard) {
         auto globalIntercept = m_detector->getIntercept(track.get());
         auto localIntercept = m_detector->globalToLocal(globalIntercept);
 
-        // Fill correlation plots before applying any cuts:
+        // Fill correlation plots BEFORE applying any cuts:
         if(correlations_) {
             auto clusters = clipboard->getData<Cluster>(m_detector->getName());
             for(auto& cls : clusters) {
                 double xdistance_um = (globalIntercept.X() - cls->global().x()) * 1000.;
                 double ydistance_um = (globalIntercept.Y() - cls->global().y()) * 1000.;
-                hTrackCorrelationX->Fill(xdistance_um);
-                hTrackCorrelationY->Fill(ydistance_um);
-                hTrackCorrelationTime->Fill(track->timestamp() - cls->timestamp());
+                trackCorrelationX_beforeCuts->Fill(xdistance_um);
+                trackCorrelationY_beforeCuts->Fill(ydistance_um);
+                trackCorrelationTime_beforeCuts->Fill(track->timestamp() - cls->timestamp());
             }
         }
 
@@ -550,7 +626,6 @@ StatusCode AnalysisDUT::run(const std::shared_ptr<Clipboard>& clipboard) {
         }
 
         // Check if it intercepts the DUT
-
         if(!m_detector->hasIntercept(track.get(), 0.5)) {
             LOG(DEBUG) << " - track outside DUT area";
             hCutHisto->Fill(2);
@@ -571,6 +646,18 @@ StatusCode AnalysisDUT::run(const std::shared_ptr<Clipboard>& clipboard) {
             continue;
         }
 
+        // Fill correlation plots after applying cuts:
+        if(correlations_) {
+            auto clusters = clipboard->getData<Cluster>(m_detector->getName());
+            for(auto& cls : clusters) {
+                double xdistance_um = (globalIntercept.X() - cls->global().x()) * 1000.;
+                double ydistance_um = (globalIntercept.Y() - cls->global().y()) * 1000.;
+                trackCorrelationX_afterCuts->Fill(xdistance_um);
+                trackCorrelationY_afterCuts->Fill(ydistance_um);
+                trackCorrelationTime_afterCuts->Fill(track->timestamp() - cls->timestamp());
+            }
+        }
+
         // Get the event:
         auto event = clipboard->getEvent();
 
@@ -595,8 +682,8 @@ StatusCode AnalysisDUT::run(const std::shared_ptr<Clipboard>& clipboard) {
 
         // Calculate in-pixel position of track in microns
         auto inpixel = m_detector->inPixel(localIntercept);
-        auto xmod = inpixel.X() * 1000.; // convert mm -> um
-        auto ymod = inpixel.Y() * 1000.; // convert mm -> um
+        auto xmod_um = inpixel.X() * 1000.; // convert mm -> um
+        auto ymod_um = inpixel.Y() * 1000.; // convert mm -> um
 
         // Loop over all associated DUT clusters:
         for(auto assoc_cluster : track->getAssociatedClusters(m_detector->getName())) {
@@ -713,11 +800,11 @@ StatusCode AnalysisDUT::run(const std::shared_ptr<Clipboard>& clipboard) {
             clusterWidthColAssoc->Fill(static_cast<double>(assoc_cluster->columnWidth()));
 
             // Fill in-pixel plots: (all as function of track position within pixel cell)
-            qvsxmym->Fill(xmod, ymod, cluster_charge);                     // cluster charge profile
-            qMoyalvsxmym->Fill(xmod, ymod, exp(-normalized_charge / 3.5)); // norm. cluster charge profile
+            qvsxmym->Fill(xmod_um, ymod_um, cluster_charge);                     // cluster charge profile
+            qMoyalvsxmym->Fill(xmod_um, ymod_um, exp(-normalized_charge / 3.5)); // norm. cluster charge profile
 
             // mean charge of cluster seed
-            pxqvsxmym->Fill(xmod, ymod, assoc_cluster->getSeedPixel()->charge());
+            pxqvsxmym->Fill(xmod_um, ymod_um, assoc_cluster->getSeedPixel()->charge());
 
             if(assoc_cluster->size() > 1) {
                 for(auto& px : assoc_cluster->pixels()) {
@@ -751,20 +838,28 @@ StatusCode AnalysisDUT::run(const std::shared_ptr<Clipboard>& clipboard) {
             }
 
             // mean cluster size
-            npxvsxmym->Fill(xmod, ymod, static_cast<double>(assoc_cluster->size()));
-            if(assoc_cluster->size() == 1)
-                npx1vsxmym->Fill(xmod, ymod);
-            if(assoc_cluster->size() == 2)
-                npx2vsxmym->Fill(xmod, ymod);
-            if(assoc_cluster->size() == 3)
-                npx3vsxmym->Fill(xmod, ymod);
-            if(assoc_cluster->size() == 4)
-                npx4vsxmym->Fill(xmod, ymod);
+            npxvsxmym->Fill(xmod_um, ymod_um, static_cast<double>(assoc_cluster->size()));
+            if(assoc_cluster->size() == 1) {
+                npx1vsxmym->Fill(xmod_um, ymod_um);
+                qvsxmym_1px->Fill(xmod_um, ymod_um, cluster_charge);
+            }
+            if(assoc_cluster->size() == 2) {
+                npx2vsxmym->Fill(xmod_um, ymod_um);
+                qvsxmym_2px->Fill(xmod_um, ymod_um, cluster_charge);
+            }
+            if(assoc_cluster->size() == 3) {
+                npx3vsxmym->Fill(xmod_um, ymod_um);
+                qvsxmym_3px->Fill(xmod_um, ymod_um, cluster_charge);
+            }
+            if(assoc_cluster->size() == 4) {
+                npx4vsxmym->Fill(xmod_um, ymod_um);
+                qvsxmym_4px->Fill(xmod_um, ymod_um, cluster_charge);
+            }
 
             // residual MAD x, y, combined (sqrt(x*x + y*y))
-            rmsxvsxmym->Fill(xmod, ymod, xabsdistance);
-            rmsyvsxmym->Fill(xmod, ymod, yabsdistance);
-            rmsxyvsxmym->Fill(xmod, ymod, fabs(sqrt(xdistance * xdistance + ydistance * ydistance)));
+            rmsxvsxmym->Fill(xmod_um, ymod_um, xabsdistance);
+            rmsyvsxmym->Fill(xmod_um, ymod_um, yabsdistance);
+            rmsxyvsxmym->Fill(xmod_um, ymod_um, fabs(sqrt(xdistance * xdistance + ydistance * ydistance)));
 
             hAssociatedTracksGlobalPosition->Fill(globalIntercept.X(), globalIntercept.Y());
             hAssociatedTracksLocalPosition->Fill(m_detector->getColumn(localIntercept), m_detector->getRow(localIntercept));

src/modules/AnalysisDUT/AnalysisDUT.h

@@ -38,9 +38,8 @@ namespace corryvreckan {
         std::shared_ptr<Detector> m_detector;
 
         // Histograms
-        TH1F* hTrackCorrelationX;
-        TH1F* hTrackCorrelationY;
-        TH1F* hTrackCorrelationTime;
+        TH1F *trackCorrelationX_beforeCuts, *trackCorrelationY_beforeCuts, *trackCorrelationTime_beforeCuts;
+        TH1F *trackCorrelationX_afterCuts, *trackCorrelationY_afterCuts, *trackCorrelationTime_afterCuts;
 
         TH2F *hClusterMapAssoc, *hHitMapAssoc;
         TProfile2D *hClusterSizeMapAssoc, *hClusterChargeMapAssoc;
@@ -75,6 +74,7 @@ namespace corryvreckan {
 
         TProfile2D *rmsxvsxmym, *rmsyvsxmym, *rmsxyvsxmym;
         TProfile2D *qvsxmym, *qMoyalvsxmym, *pxqvsxmym;
+        TProfile2D *qvsxmym_1px, *qvsxmym_2px, *qvsxmym_3px, *qvsxmym_4px;
         TProfile2D* npxvsxmym;
         TH2F *npx1vsxmym, *npx2vsxmym, *npx3vsxmym, *npx4vsxmym;
 

src/modules/AnalysisDUT/README.md

@@ -14,7 +14,7 @@ If a region of interest (ROI) is defined for the detector under investigation, o
 * `use_closest_cluster`: If `true` the cluster with the smallest distance to the track is used if a track has more than one associated cluster. If `false`, loop over all associated clusters. Defaults to `true`.
 * `n_time_bins`: Number of bins in the time residual and correlation histograms. Defaults to `20000`.
 * `time_binning`: Bin width in the time residual and correlation histograms. Defaults to `0.1ns`.
-* `correlations`: If `true`, correlation plots between all tracks and all clusters on the DUT (i.e. associated + non-associated) are created. Defaults to `false`.
+* `correlations`: If `true`, correlation plots between all (before and after applying cuts) tracks and all clusters on the DUT (i.e. associated + non-associated) are created. Defaults to `false`.
 
 ### Plots produced
 

src/modules/AnalysisEfficiency/AnalysisEfficiency.cpp

@@ -23,11 +23,15 @@ AnalysisEfficiency::AnalysisEfficiency(Configuration& config, std::shared_ptr<De
     config_.setDefault<double>("time_cut_frameedge", Units::get<double>(20, "ns"));
     config_.setDefault<double>("chi2ndof_cut", 3.);
     config_.setDefault<double>("inpixel_bin_size", Units::get<double>(1.0, "um"));
+    config_.setDefault<XYVector>("inpixel_cut_edge", {Units::get(5.0, "um"), Units::get(5.0, "um")});
+    config_.setDefault<double>("masked_pixel_distance_cut", 1.);
 
     m_timeCutFrameEdge = config_.get<double>("time_cut_frameedge");
     m_chi2ndofCut = config_.get<double>("chi2ndof_cut");
     m_inpixelBinSize = config_.get<double>("inpixel_bin_size");
     require_associated_cluster_on_ = config_.getArray<std::string>("require_associated_cluster_on", {});
+    m_inpixelEdgeCut = config_.get<XYVector>("inpixel_cut_edge");
+    m_maskedPixelDistanceCut = config_.get<int>("masked_pixel_distance_cut");
 }
 
 void AnalysisEfficiency::initialize() {
@@ -35,6 +39,12 @@ void AnalysisEfficiency::initialize() {
     hPixelEfficiency = new TH1D(
         "hPixelEfficiency", "hPixelEfficiency; single pixel efficiency; # entries", 201, 0, 1.005); // get 0.5%-wide bins
 
+    hPixelEfficiencyMatrix = new TH1D("hPixelEfficiencyMatrix",
+                                      "hPixelEfficiencyMatrix; single pixel efficiency; # entries",
+                                      201,
+                                      0,
+                                      1.005); // get 0.5%-wide bins
+
     auto pitch_x = static_cast<double>(Units::convert(m_detector->getPitch().X(), "um"));
     auto pitch_y = static_cast<double>(Units::convert(m_detector->getPitch().Y(), "um"));
 
@@ -64,6 +74,19 @@ void AnalysisEfficiency::initialize() {
                                                    -pitch_y / 2.,
                                                    pitch_y / 2.);
 
+    title = m_detector->getName() +
+            " Pixel efficiency map (in-pixel ROI);in-pixel x_{track} [#mum];in-pixel y_{track} #mum;#epsilon";
+    hPixelEfficiencyMap_inPixelROI_trackPos_TProfile = new TProfile2D("pixelEfficiencyMap_inPixelROI_trackPos_TProfile",
+                                                                      title.c_str(),
+                                                                      nbins_x,
+                                                                      -pitch_x / 2.,
+                                                                      pitch_x / 2.,
+                                                                      nbins_y,
+                                                                      -pitch_y / 2.,
+                                                                      pitch_y / 2.,
+                                                                      0,
+                                                                      1);
+
     title = m_detector->getName() + " Chip efficiency map;x [px];y [px];#epsilon";
     hChipEfficiencyMap_trackPos_TProfile = new TProfile2D("chipEfficiencyMap_trackPos_TProfile",
                                                           title.c_str(),
@@ -84,6 +107,18 @@ void AnalysisEfficiency::initialize() {
                                                   -0.5,
                                                   m_detector->nPixels().Y() - 0.5);
 
+    title = m_detector->getName() + " Pixel efficiency matrix;x [px];y [px];#epsilon";
+    hPixelEfficiencyMatrix_TProfile = new TProfile2D("hPixelEfficiencyMatrix",
+                                                     title.c_str(),
+                                                     m_detector->nPixels().X(),
+                                                     -0.5,
+                                                     m_detector->nPixels().X() - 0.5,
+                                                     m_detector->nPixels().Y(),
+                                                     -0.5,
+                                                     m_detector->nPixels().Y() - 0.5,
+                                                     0,
+                                                     1);
+
     title = m_detector->getName() + " Global efficiency map;x [mm];y [mm];#epsilon";
     hGlobalEfficiencyMap_trackPos_TProfile = new TProfile2D("globalEfficiencyMap_trackPos_TProfile",
                                                             title.c_str(),
@@ -158,6 +193,8 @@ void AnalysisEfficiency::initialize() {
                                       -1.5 * m_detector->getPitch().y(),
                                       1.5 * m_detector->getPitch().y());
     eTotalEfficiency = new TEfficiency("eTotalEfficiency", "totalEfficiency;;#epsilon", 1, 0, 1);
+    eTotalEfficiency_inPixelROI = new TEfficiency(
+        "eTotalEfficiency_inPixelROI", "eTotalEfficiency_inPixelROI;;#epsilon (within in-pixel ROI)", 1, 0, 1);
 
     efficiencyColumns = new TEfficiency("efficiencyColumns",
                                         "Efficiency vs. column number; column; #epsilon",
@@ -169,6 +206,7 @@ void AnalysisEfficiency::initialize() {
                                      m_detector->nPixels().Y(),
                                      -0.5,
                                      m_detector->nPixels().Y() - 0.5);
+    efficiencyVsTime = new TEfficiency("efficiencyVsTime", "Efficiency vs. time; time [s]; #epsilon", 3000, 0, 3000);
 
     hTrackTimeToPrevHit_matched =
         new TH1D("trackTimeToPrevHit_matched", "trackTimeToPrevHit_matched;time to prev hit [us];# events", 1e6, 0, 1e6);
@@ -245,6 +283,9 @@ StatusCode AnalysisEfficiency::run(const std::shared_ptr<Clipboard>& clipboard)
     // Get the telescope tracks from the clipboard
     auto tracks = clipboard->getData<Track>();
 
+    auto pitch_x = m_detector->getPitch().X();
+    auto pitch_y = m_detector->getPitch().Y();
+
     // Loop over all tracks
     for(auto& track : tracks) {
         n_track++;
@@ -281,7 +322,7 @@ StatusCode AnalysisEfficiency::run(const std::shared_ptr<Clipboard>& clipboard)
 
         // Check that it doesn't go through/near a masked pixel
         LOG(TRACE) << " Checking if track is close to masked pixel";
-        if(m_detector->hitMasked(track.get(), 1.)) {
+        if(m_detector->hitMasked(track.get(), m_maskedPixelDistanceCut)) {
             n_masked++;
             LOG(DEBUG) << " - track close to masked pixel";
             continue;
@@ -327,8 +368,13 @@ StatusCode AnalysisEfficiency::run(const std::shared_ptr<Clipboard>& clipboard)
 
         // Calculate in-pixel position of track in microns
         auto inpixel = m_detector->inPixel(localIntercept);
-        auto xmod = static_cast<double>(Units::convert(inpixel.X(), "um"));
-        auto ymod = static_cast<double>(Units::convert(inpixel.Y(), "um"));
+        auto xmod = inpixel.X();
+        auto ymod = inpixel.Y();
+        auto xmod_um = xmod * 1000.; // mm->um (for plotting)
+        auto ymod_um = ymod * 1000.; // mm->um (for plotting)
+
+        bool isWithinInPixelROI =
+            (pitch_x - abs(xmod * 2) > m_inpixelEdgeCut.x()) && (pitch_y - abs(ymod * 2) > m_inpixelEdgeCut.y());
 
         // Get the DUT clusters from the clipboard, that are assigned to the track
         auto associated_clusters = track->getAssociatedClusters(m_detector->getName());
@@ -336,6 +382,16 @@ StatusCode AnalysisEfficiency::run(const std::shared_ptr<Clipboard>& clipboard)
             auto cluster = track->getClosestCluster(m_detector->getName());
             has_associated_cluster = true;
             matched_tracks++;
+            auto pixels = cluster->pixels();
+            for(auto& pixel : pixels) {
+                if((pixel->column() == static_cast<int>(m_detector->getColumn(localIntercept)) &&
+                    pixel->row() == static_cast<int>(m_detector->getRow(localIntercept))) &&
+                   isWithinInPixelROI) {
+                    hPixelEfficiencyMatrix_TProfile->Fill(pixel->column(), pixel->row(), 1);
+                    break; // There cannot be a second pixel within the cluster through which the track goes.
+                }
+            }
+
             auto clusterLocal = m_detector->globalToLocal(cluster->global());
 
             auto distance =
@@ -353,6 +409,11 @@ StatusCode AnalysisEfficiency::run(const std::shared_ptr<Clipboard>& clipboard)
                 has_associated_cluster, m_detector->getColumn(clusterLocal), m_detector->getRow(clusterLocal));
         }
 
+        if(!has_associated_cluster && isWithinInPixelROI) {
+            hPixelEfficiencyMatrix_TProfile->Fill(
+                m_detector->getColumn(localIntercept), m_detector->getRow(localIntercept), 0);
+        }
+
         hGlobalEfficiencyMap_trackPos_TProfile->Fill(globalIntercept.X(), globalIntercept.Y(), has_associated_cluster);
         hGlobalEfficiencyMap_trackPos->Fill(has_associated_cluster, globalIntercept.X(), globalIntercept.Y());
 
@@ -363,11 +424,17 @@ StatusCode AnalysisEfficiency::run(const std::shared_ptr<Clipboard>& clipboard)
 
         // For pixels, only look at the ROI:
         if(is_within_roi) {
-            hPixelEfficiencyMap_trackPos_TProfile->Fill(xmod, ymod, has_associated_cluster);
-            hPixelEfficiencyMap_trackPos->Fill(has_associated_cluster, xmod, ymod);
+            hPixelEfficiencyMap_trackPos_TProfile->Fill(xmod_um, ymod_um, has_associated_cluster);
+            hPixelEfficiencyMap_trackPos->Fill(has_associated_cluster, xmod_um, ymod_um);
             eTotalEfficiency->Fill(has_associated_cluster, 0); // use 0th bin for total efficiency
             efficiencyColumns->Fill(has_associated_cluster, m_detector->getColumn(localIntercept));
             efficiencyRows->Fill(has_associated_cluster, m_detector->getRow(localIntercept));
+            efficiencyVsTime->Fill(has_associated_cluster, track->timestamp() / 1e9); // convert nanoseconds to seconds
+
+            if(isWithinInPixelROI) {
+                hPixelEfficiencyMap_inPixelROI_trackPos_TProfile->Fill(xmod_um, ymod_um, has_associated_cluster);
+                eTotalEfficiency_inPixelROI->Fill(has_associated_cluster, 0); // use 0th bin for total efficiency
+            }
         }
 
         auto intercept_col = static_cast<size_t>(m_detector->getColumn(localIntercept));
@@ -447,11 +514,16 @@ void AnalysisEfficiency::finalize(const std::shared_ptr<ReadonlyClipboard>&) {
         for(int irow = 1; irow < m_detector->nPixels().Y() + 1; irow++) {
             // calculate total efficiency: (just to double check the other calculation)
             const int bin = hChipEfficiencyMap_trackPos->GetGlobalBin(icol, irow);
-            const double eff = hChipEfficiencyMap_trackPos->GetEfficiency(bin);
+            double eff = hChipEfficiencyMap_trackPos->GetEfficiency(bin);
             if(eff > 0) {
                 LOG(TRACE) << "col/row = " << icol << "/" << irow << ", binContent = " << eff;
                 hPixelEfficiency->Fill(eff);
             }
+            eff = hPixelEfficiencyMatrix_TProfile->GetBinContent(bin);
+            if(eff > 0) {
+                LOG(TRACE) << "col/row = " << icol << "/" << irow << ", binContent = " << eff;
+                hPixelEfficiencyMatrix->Fill(eff);
+            }
         }
     }
 }

src/modules/AnalysisEfficiency/AnalysisEfficiency.h

@@ -44,10 +44,13 @@ namespace corryvreckan {
         std::shared_ptr<Detector> m_detector;
 
         TH1D* hPixelEfficiency;
+        TH1D* hPixelEfficiencyMatrix;
 
         // Profile version
         TProfile2D* hPixelEfficiencyMap_trackPos_TProfile;
+        TProfile2D* hPixelEfficiencyMap_inPixelROI_trackPos_TProfile;
         TProfile2D* hChipEfficiencyMap_trackPos_TProfile;
+        TProfile2D* hPixelEfficiencyMatrix_TProfile;
         TProfile2D* hGlobalEfficiencyMap_trackPos_TProfile;
         TProfile2D* hChipEfficiencyMap_clustPos_TProfile;
         TProfile2D* hGlobalEfficiencyMap_clustPos_TProfile;
@@ -59,8 +62,10 @@ namespace corryvreckan {
         TEfficiency* hGlobalEfficiencyMap_clustPos;
 
         TEfficiency* eTotalEfficiency;
+        TEfficiency* eTotalEfficiency_inPixelROI;
         TEfficiency* efficiencyColumns;
         TEfficiency* efficiencyRows;
+        TEfficiency* efficiencyVsTime;
 
         TH1D* hDistanceCluster;
         TH1D* hTimeDiffPrevTrack_assocCluster;
@@ -76,6 +81,8 @@ namespace corryvreckan {
         TH2D* hPosDiffPrevTrack_noAssocCluster;
         TH2D* hDistanceCluster_track;
         double m_chi2ndofCut, m_timeCutFrameEdge, m_inpixelBinSize;
+        XYVector m_inpixelEdgeCut;
+        int m_maskedPixelDistanceCut = 1;
         int total_tracks = 0;
         int matched_tracks = 0;
 

src/modules/AnalysisEfficiency/README.md

@@ -19,6 +19,8 @@ More information can be found in the ROOT `TEfficiency` class reference, section
 * `time_cut_frameedge`: Parameter to discard telescope tracks at the frame edges (start and end of the current event window). Defaults to `20ns`.
 * `chi2ndof_cut`: Acceptance criterion for telescope tracks, defaults to a value of `3`.
 * `inpixel_bin_size`: Parameter to set the bin size of the in-pixel 2D efficiency histogram. This should be given in units of distance and the same value is used in both axes. Defaults to `1.0um`.
+* `inpixel_cut_edge`: Parameter to exclude tracks going within a cut-distance to the pixel edge. Effectively defines an in-pixel ROI. Defaults to `5um`.
+* `masked_pixel_distance_cut`: Distance (in pixels) to exclude tracks passing close to masked pixel. Defaults to `1`.
 * `require_associated_cluster_on`: Names of detectors which are required to have an associated cluster to the telescope tracks. Detectors listed here must be marked as `role = DUT` in the detector configuration file. Only tracks satisfying this requirement are accepted for the efficiency measurement. If empty, no detector is required. Default is empty.
 
 ### Plots produced
@@ -26,8 +28,9 @@ More information can be found in the ROOT `TEfficiency` class reference, section
 For the DUT, the following plots are produced:
 
 * 2D histograms:
-  * 2D Map of in-pixel efficiency
+  * 2D Map of in-pixel efficiency and in-pixel efficiency within in-pixel ROI
   * 2D Maps of chip efficiency in local and global coordinates, filled at the position of the track intercept point or at the position of the associated cluster center
+  * 2D Map of pixel efficiency, for the full matrix, filled at the pixel (of the associated cluster) through which the track goes, constrained to an in-pixel ROI defined by `inpixel_cut_edge`.
   * 2D Maps of the position difference of a track with and without associated cluster to the previous track
   * 2D Map of the distance between track intersection and associated cluster
 
@@ -39,8 +42,8 @@ For the DUT, the following plots are produced:
   * Distribution of cluster-track distances
 
 * Other:
-  * Value of total efficiency as `TEfficiency` including (asymmetric) error bars
-  * Efficiency as function of column and row
+  * Value of total efficiency as `TEfficiency` including (asymmetric) error bars (total and restricted to in-pixel ROI)
+  * Efficiency as function of column and row, and vs. time
 
 
 ### Usage

src/modules/DUTAssociation/DUTAssociation.cpp

@@ -31,15 +31,15 @@ DUTAssociation::DUTAssociation(Configuration& config, std::shared_ptr<Detector>
     }
 
     // timing cut, relative (x * time_resolution) or absolute:
-    timeCut = corryvreckan::calculate_cut<double>("time_cut", config_, m_detector);
+    time_cut_ = corryvreckan::calculate_cut<double>("time_cut", config_, m_detector);
 
     // spatial cut, relative (x * spatial_resolution) or absolute:
-    spatialCut = corryvreckan::calculate_cut<XYVector>("spatial_cut", config_, m_detector);
-    useClusterCentre = config_.get<bool>("use_cluster_centre");
+    spatial_cut_ = corryvreckan::calculate_cut<XYVector>("spatial_cut", config_, m_detector);
+    use_cluster_centre_ = config_.get<bool>("use_cluster_centre");
 
-    LOG(DEBUG) << "time_cut = " << Units::display(timeCut, {"ms", "us", "ns"});
-    LOG(DEBUG) << "spatial_cut = " << Units::display(spatialCut, {"um", "mm"});
-    LOG(DEBUG) << "use_cluster_centre = " << useClusterCentre;
+    LOG(DEBUG) << "time_cut = " << Units::display(time_cut_, {"ms", "us", "ns"});
+    LOG(DEBUG) << "spatial_cut = " << Units::display(spatial_cut_, {"um", "mm"});
+    LOG(DEBUG) << "use_cluster_centre = " << use_cluster_centre_;
 }
 
 void DUTAssociation::initialize() {
@@ -99,7 +99,7 @@ void DUTAssociation::initialize() {
     // Nr of associated clusters per track
     title = m_detector->getName() + ": number of associated clusters per track;associated clusters;events";
     hNoAssocCls = new TH1F("no_assoc_cls", title.c_str(), 10, -0.5, 9.5);
-    LOG(DEBUG) << "DUT association time cut = " << Units::display(timeCut, {"ms", "ns"});
+    LOG(DEBUG) << "DUT association time cut = " << Units::display(time_cut_, {"ms", "ns"});
 }
 
 StatusCode DUTAssociation::run(const std::shared_ptr<Clipboard>& clipboard) {
@@ -165,8 +165,8 @@ StatusCode DUTAssociation::run(const std::shared_ptr<Clipboard>& clipboard) {
             }
 
             // Check if the cluster is close in space (either use cluster centre of closest pixel to track)
-            auto xdistance = (useClusterCentre ? xdistance_centre : xdistance_nearest);
-            auto ydistance = (useClusterCentre ? ydistance_centre : ydistance_nearest);
+            auto xdistance = (use_cluster_centre_ ? xdistance_centre : xdistance_nearest);
+            auto ydistance = (use_cluster_centre_ ? ydistance_centre : ydistance_nearest);
             auto distance = sqrt(xdistance * xdistance + ydistance * ydistance);
             // Check if track-cluster distance lies within ellipse defined by spatial cuts, following this example:
             // https://www.geeksforgeeks.org/check-if-a-point-is-inside-outside-or-on-the-ellipse/
@@ -175,8 +175,8 @@ StatusCode DUTAssociation::run(const std::shared_ptr<Clipboard>& clipboard) {
             //                                       > 1: outside,
             //                                       < 1: inside
             // Discard track if outside of ellipse:
-            auto norm = (xdistance * xdistance) / (spatialCut.x() * spatialCut.x()) +
-                        (ydistance * ydistance) / (spatialCut.y() * spatialCut.y());
+            auto norm = (xdistance * xdistance) / (spatial_cut_.x() * spatial_cut_.x()) +
+                        (ydistance * ydistance) / (spatial_cut_.y() * spatial_cut_.y());
             if(norm > 1) {
                 LOG(DEBUG) << "Discarding DUT cluster with distance (" << Units::display(std::abs(xdistance), {"um", "mm"})
                            << "," << Units::display(std::abs(ydistance), {"um", "mm"}) << ")"
@@ -187,7 +187,7 @@ StatusCode DUTAssociation::run(const std::shared_ptr<Clipboard>& clipboard) {
             }
 
             // Check if the cluster is close in time
-            if(std::abs(cluster->timestamp() - track->timestamp()) > timeCut) {
+            if(std::abs(cluster->timestamp() - track->timestamp()) > time_cut_) {
                 LOG(DEBUG) << "Discarding DUT cluster with time difference "
                            << Units::display(std::abs(cluster->timestamp() - track->timestamp()), {"ms", "s"});
                 hCutHisto->Fill(2);

src/modules/DUTAssociation/DUTAssociation.h

@@ -37,9 +37,9 @@ namespace corryvreckan {
 
     private:
         std::shared_ptr<Detector> m_detector;
-        double timeCut;
-        ROOT::Math::XYVector spatialCut;
-        bool useClusterCentre;
+        double time_cut_;
+        ROOT::Math::XYVector spatial_cut_;
+        bool use_cluster_centre_;
 
         TH1F* hCutHisto;
 

src/modules/EventLoaderATLASpix/EventLoaderATLASpix.cpp

@@ -82,6 +82,14 @@ void EventLoaderATLASpix::initialize() {
     m_file.open(m_filename.c_str(), ios::in | ios::binary);
     LOG(DEBUG) << "Opening file " << m_filename;
 
+    std::string title = m_detector->getName() + ": number of different messages;message type;# events";
+    hMessages = new TH1F("hMessages", title.c_str(), 5, 1, 6);
+    hMessages->GetXaxis()->SetBinLabel(1, "UNKNOWN_MESSAGE");
+    hMessages->GetXaxis()->SetBinLabel(2, "BUFFER_OVERFLOW");
+    hMessages->GetXaxis()->SetBinLabel(3, "SERDES_LOCK_ESTABLISHED");
+    hMessages->GetXaxis()->SetBinLabel(4, "SERDES_LOCK_LOST");
+    hMessages->GetXaxis()->SetBinLabel(5, "WEIRD_DATA");