Commit ce3e40af authored by Simon Spannagel's avatar Simon Spannagel
Browse files

Merge branch 'data_output' into 'master'

Data output

See merge request !12
parents 95208d10 af78cfeb
Pipeline #248472 passed with stages
in 4 minutes and 31 seconds
# Define module and return the generated name as ALGORITHM_NAME
# Add source files to library
# Provide standard install target
#include "DataOutput.h"
#include <vector>
using namespace corryvreckan;
using namespace std;
DataOutput::DataOutput(Configuration config, std::vector<Detector*> detectors)
: Algorithm(std::move(config), std::move(detectors)) {
m_fileName = m_config.get<std::string>("fileName", "outputTuples.root");
m_treeName = m_config.get<std::string>("treeName", "tree");
This algorithm writes an output file and fills it with trees containing
the following information for the DUT:
1)size in x of each cluster,
2)size in y of each cluster,
3)the event ID of each cluster,
4)a list of the X positions of the pixels of each cluster,
5)a list of the Y positions of the pixels of each cluster,
6)a list of the ToT of the pixels of each cluster,
7)a list of the timestamp/ToA of the pixels of each cluster,
the number of pixels in each cluster (so that in the analysis the lists
of pixel X positions etc. can be split into their respective clusters).
8)the intercept with the DUT for each track
void DataOutput::initialise() {
LOG(DEBUG) << "Initialised DataOutput";
// Create output file and directories
m_outputFile = new TFile(m_fileName.c_str(), "RECREATE");
LOG(DEBUG) << "Made and moved to output file: " << m_fileName;
m_outputTree = new TTree(m_treeName.c_str(), m_treeName.c_str());
LOG(DEBUG) << "Created tree: " << m_treeName;
eventID = 0;
filledEvents = 0;
// Create the output branches
m_outputTree->Branch("EventID", &v_clusterEventID);
m_outputTree->Branch("clusterSizeX", &v_clusterSizeX);
m_outputTree->Branch("clusterSizeY", &v_clusterSizeY);
m_outputTree->Branch("pixelX", &v_pixelX);
m_outputTree->Branch("pixelY", &v_pixelY);
m_outputTree->Branch("pixelToT", &v_pixelToT);
m_outputTree->Branch("pixelToA", &v_pixelToA);
m_outputTree->Branch("clusterNumPixels", &v_clusterNumPixels);
// Branch for track intercepts
m_outputTree->Branch("intercepts", &v_intercepts);
StatusCode DataOutput::run(Clipboard* clipboard) {
// Counter for cluster event ID
// Get the DUT
auto DUT = get_detector(m_config.get<std::string>("DUT"));
// Clear data vectors before storing the cluster information for
// this event
// Getting tracks from the clipboard
Tracks* tracks = (Tracks*)clipboard->get("tracks");
if(tracks == NULL) {
LOG(DEBUG) << "No tracks on the clipboard";
return Success;
// Iterate through tracks found
for(auto& track : (*tracks)) {
// CHeck if we have associated clusters:
Clusters associatedClusters = track->associatedClusters();
if(associatedClusters.empty()) {
LOG(TRACE) << "No associated clusters, skipping track.";
// Drop events with more than one cluster associated
else if(associatedClusters.size() > 1) {
LOG(DEBUG) << "More than one associated cluster, dropping track.";
LOG(DEBUG) << "Found track with associated cluster";
// Get track intercept with DUT in global coordinates
trackIntercept = DUT->getIntercept(track);
// Calculate the intercept in local coordinates
trackInterceptLocal = *(DUT->globalToLocal()) * trackIntercept;
Cluster* cluster = associatedClusters.front();
// x size
LOG(DEBUG) << "Gets column width = " << cluster->columnWidth();
// y size
LOG(DEBUG) << "Gets row width = " << cluster->rowWidth();
// eventID
LOG(DEBUG) << "Gets cluster eventID = " << eventID;
// Get the pixels in the current cluster
Pixels* pixels = cluster->pixels();
// Iterate through all pixels in the cluster
numPixels = 0;
for(auto& pixel : (*pixels)) {
// Increase counter for number of pixels in the cluster
// x position
LOG(DEBUG) << "Gets pixel column = " << pixel->m_column;
// y position
LOG(DEBUG) << "Gets pixel row = " << pixel->m_row;
// ToT
LOG(DEBUG) << "Gets pixel tot = " << pixel->m_adc;
// ToA
LOG(DEBUG) << "Gets pixel timestamp = " << pixel->m_timestamp;
if(v_intercepts.empty()) {
return NoData;
if(filledEvents % 100 == 0) {
LOG(DEBUG) << "Events with single associated cluster: " << filledEvents;
// Fill the tree with the information for this event
// Return value telling analysis to keep running
return Success;
void DataOutput::finalise() {
LOG(DEBUG) << "Finalise";
// DUT angles for output
auto DUT = get_detector(m_config.get<std::string>("DUT"));
auto directory = m_outputFile->mkdir("Directory");
auto orientation = DUT->rotation();
directory->WriteObject(&orientation, "DUTorientation");
// Writing out outputfile
#define DATAOUTPUT_H 1
#include <iostream>
#include "Math/Point3D.h"
#include "Math/Vector3D.h"
#include "TFile.h"
#include "TTree.h"
#include "core/algorithm/Algorithm.h"
#include "objects/Track.h"
namespace corryvreckan {
class DataOutput : public Algorithm {
// Constructors and destructors
DataOutput(Configuration config, std::vector<Detector*> detectors);
~DataOutput() {}
// Functions
void initialise();
StatusCode run(Clipboard* clipboard);
void finalise();
// Member variables
int numPixels;
int eventID;
int filledEvents;
PositionVector3D<Cartesian3D<double>> trackIntercept;
PositionVector3D<Cartesian3D<double>> trackInterceptLocal;
std::vector<int> v_clusterEventID;
std::vector<int> v_pixelX;
std::vector<int> v_pixelY;
std::vector<int> v_pixelToT;
std::vector<int> v_clusterNumPixels;
std::vector<long long int> v_pixelToA;
std::vector<double> v_clusterSizeX;
std::vector<double> v_clusterSizeY;
std::vector<std::string> m_objectList;
std::vector<PositionVector3D<Cartesian3D<double>>> v_intercepts;
std::map<std::string, TestBeamObject*> m_objects;
TFile* m_outputFile;
TTree* m_outputTree{};
// Config parameters
std::string m_fileName;
std::string m_treeName;
#endif // DATAOUTPUT_H
## DataOutput
**Maintainer**: Morag Williams (<>)
**Status**: Functional
#### Description
This algorithm writes out data from a Timepix3 DUT for timing analysis. The outputted ROOT TTree contains data in branches. This is intended for analysis of the timing capabilities of Timepix3 devices of different thicknesses.
For each track associated DUT `cluster` object the following information is written out:
* Event ID
* Size in X
* Size in Y
* Number of pixels in the cluster
For each `pixel` object in an associated `cluster` the follwing information is written out:
* X position
* Y position
* ToT
* ToA
For each `track` with associated DUT `clusters` the following information is written out:
* Intercept with the DUT (3D position vector)
#### Parameters
* `DUT`: Name of the DUT plane.
* `fileName`: Name of the outputted ROOT file. Default value is `outputTuples`.
* `treeName`: Name of the tree inside the outputted ROOT file. Default value is `tree`.
#### Plots produced
No plots are produced.
#### Usage
DUT = "W0005_H03"
fileName = "myOutputFile.root"
treeName = "myTree"
Parameters to be used in multiple algorithms can also be defined globally at the top of the configuration file. This is highly encouraged for parameters such as `DUT` and `reference`.
......@@ -69,6 +69,8 @@ namespace corryvreckan {
double rotationX() { return m_orientation.X(); }
double rotationY() { return m_orientation.Y(); }
double rotationZ() { return m_orientation.Z(); }
ROOT::Math::XYZVector rotation() { return m_orientation; }
void rotation(ROOT::Math::XYZVector rotation) { m_orientation = rotation; }
// Functions to set and check channel masking
void setMaskFile(std::string file);
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