Merge branch 'master' into 'master'

small updates to fix zero-tot events, alignment output, etc.

See merge request !7

src/algorithms/Alignment.cpp

@@ -123,15 +123,22 @@ void Alignment::MinimiseResiduals(Int_t& npar, Double_t* grad, Double_t& result,
 
     // Apply new alignment conditions
     globalDetector->update();
+  LOG(DEBUG) << "Updated parameters for "<<detectorToAlign;
 
     // The chi2 value to be returned
     result = 0.;
 
+  LOG(DEBUG) << "Looping over "<<globalTracks.size()<<" tracks";
+
     // Loop over all tracks
     for(auto& track : globalTracks) {
         // Get all clusters on the track
         Clusters associatedClusters = track->associatedClusters();
 
+      LOG(DEBUG) << "- track has chi2 "<<track->chi2();
+      LOG(DEBUG) << "- track has gradient x "<<track->m_direction.X();
+      LOG(DEBUG) << "- track has gradient y "<<track->m_direction.Y();
+
         // Find the cluster that needs to have its position recalculated
         for(auto& associatedCluster : associatedClusters) {
             string detectorID = associatedCluster->detectorID();
@@ -147,8 +154,13 @@ void Alignment::MinimiseResiduals(Int_t& npar, Double_t* grad, Double_t& result,
             double residualX = intercept.X() - positionGlobal.X();
             double residualY = intercept.Y() - positionGlobal.Y();
             double error = associatedCluster->error();
+          LOG(DEBUG) << "- track has intercept ("<<intercept.X()<<","<<intercept.Y()<<")";
+          LOG(DEBUG) << "- cluster has position ("<<positionGlobal.X()<<","<<positionGlobal.Y()<<")";
+          double deltachi2 = ((residualX * residualX + residualY * residualY) / (error * error));
+          LOG(DEBUG) << "- delta chi2 = "<<deltachi2;
             // Add the new residual2
-            result += ((residualX * residualX + residualY * residualY) / (error * error));
+            result += deltachi2;
+          LOG(DEBUG) << "- result is now "<<result;
         }
     }
 }
@@ -300,8 +312,10 @@ void Alignment::finalise() {
     for(auto& detector : get_detectors()) {
         string detectorID = detector->name();
         // Do not align the reference plane
-        if(detectorID == m_config.get<std::string>("reference"))
-            continue;
+      if(detectorID == m_config.get<std::string>("reference") ||
+         detectorID == m_config.get<std::string>("DUT")) {
+        continue;
+      }
 
         // Get the alignment parameters
         double displacementX = residualFitter->GetParameter(det * 6 + 0);

src/algorithms/DUTAnalysis.cpp

@@ -51,8 +51,8 @@ StatusCode DUTAnalysis::run(Clipboard* clipboard) {
     LOG(TRACE) << "Power on time: " << m_powerOnTime / (4096. * 40000000.);
     LOG(TRACE) << "Power off time: " << m_powerOffTime / (4096. * 40000000.);
 
-    if(clipboard->get_persistent("currentTime") < 13.5)
-        return Success;
+//    if(clipboard->get_persistent("currentTime") < 13.5)
+//        return Success;
 
     // Timing cut for association
     double timingCut = 200. / 1000000000.; // 200 ns

src/algorithms/Timepix3Clustering.cpp

@@ -176,9 +176,14 @@ void Timepix3Clustering::calculateClusterCentre(Cluster* cluster) {
 
     // Loop over all pixels
     for(int pix = 0; pix < pixels->size(); pix++) {
-        tot += (*pixels)[pix]->m_adc;
-        row += ((*pixels)[pix]->m_row * (*pixels)[pix]->m_adc);
-        column += ((*pixels)[pix]->m_column * (*pixels)[pix]->m_adc);
+      double pixelToT = (*pixels)[pix]->m_adc;
+      if(pixelToT == 0){
+        LOG(DEBUG) << "Pixel with ToT 0!";
+        pixelToT = 1;
+      }
+        tot += pixelToT;
+        row += ((*pixels)[pix]->m_row * pixelToT);
+        column += ((*pixels)[pix]->m_column * pixelToT);
         if((*pixels)[pix]->m_timestamp < timestamp)
             timestamp = (*pixels)[pix]->m_timestamp;
     }

src/core/Analysis.cpp

@@ -102,8 +102,8 @@ void Analysis::load_detectors() {
     LOG(STATUS) << "Loaded " << detectors.size() << " detectors";
 
     // Finally, sort the list of detectors by z position (from lowest to highest)
-    // FIXME reimplement - std::sort(m_parameters->detectors.begin(), m_parameters->detectors.end(), sortByZ);
-    //
+  std::sort(detectors.begin(), detectors.end(), [](Detector* det1, Detector* det2){ return det1->displacementZ() < det2->displacementZ();});
+  
 }
 
 void Analysis::load_algorithms() {