Merge branch 'master' into dependabot/github_actions/actions/upload-p…

…ages-artifact-3

.github/CODEOWNERS

@@ -1,5 +1,8 @@
-.github/ @lobis
+.github/* @lobis
 * @jgalan
+* @juanangp
+* @lobis
+* @nkx111
 *.py @lobis
 *.cmake @lobis
 CMakelists.txt @lobis

.github/workflows/validation.yml

@@ -248,7 +248,7 @@ jobs:
         run: |
           source ${{ env.REST_PATH }}/thisREST.sh
           cd framework/pipeline/trex
-          wget https://sultan.unizar.es/trexdm-readouts/readouts_v2.4.root
+          wget https://rest-for-physics.github.io/trexdm-readouts/readouts_v2.4.root
           restManager --c 01_raw.rml --f R01928_tagTest_Vm_250_Vd_160_Pr_6_Gain_0x0_Shape_0xF_Clock_0x4-068.aqs
           restManager --c 02_signal.rml --f RawData_01928.root
           restManager --c 03_hits.rml --f Signals_01928.root

CMakeLists.txt

@@ -188,6 +188,27 @@ else ()
     set(REST_MPFR OFF)
 endif (${REST_MPFR} MATCHES "ON")
 
+if (((${REST_ALL_LIBS} MATCHES "ON") AND (NOT DEFINED RESTLIB_AXION))
+    OR (${RESTLIB_AXION} MATCHES "ON"))
+    # GSL #### Find GSL
+    find_package(GSL REQUIRED)
+
+    # Include GSL directories
+    set(external_include_dirs ${external_include_dirs} ${GSL_INCLUDE_DIRS})
+
+    # Link GSL libraries
+    set(external_libs ${external_libs};${GSL_LIBRARIES})
+
+    message(STATUS "Found GSL libraries : ${GSL_LIBRARIES}")
+    message(STATUS "GSL headers : ${GSL_INCLUDE_DIRS}")
+
+    set(REST_GSL ON)
+else ()
+    set(REST_GSL OFF)
+    message(STATUS "GSL libraries not required")
+endif (((${REST_ALL_LIBS} MATCHES "ON") AND (NOT DEFINED RESTLIB_AXION))
+       OR (${RESTLIB_AXION} MATCHES "ON"))
+
 # CURL  #####
 find_library(CURL_LIB curl)
 if (NOT ${CURL_LIB} STREQUAL "CURL_LIB-NOTFOUND")

macros/REST_AddComponentDataSet.C

@@ -0,0 +1,46 @@
+#include "TRestComponent.h"
+#include "TRestTask.h"
+
+#ifndef RestTask_AddComponent
+#define RestTask_AddComponent
+
+//*******************************************************************************************************
+//*** Description: This macro will load from an RML the component chosen in the arguments and it
+//*** will write it inside the file given as outputFile
+//***
+//*** --------------
+//*** Usage: restManager AddComponentDataSet components.rml sectionName [outputFile] [componentName] [update]
+//***
+//*** Arguments description:
+//***
+//*** - cfgFile: The RML configuration file where the component definition can be found.
+//*** - sectionName: The section name used to select a component inside the RML file.
+//*** - outputFile: The file where the component is written, by default is components.root.
+//*** - componentName: This argument allows to change the component name stored in the output file.
+//***                  By default it will take the same value as section name.
+//*** - update: If disabled it will create a new file erasing any other previously added components.
+//***           It is enabled by default.
+//***
+//*******************************************************************************************************
+
+Int_t REST_AddComponentDataSet(std::string cfgFile, std::string sectionName,
+                               std::string outputFile = "components.root", std::string componentName = "",
+                               Bool_t update = true) {
+    TRestComponentDataSet comp(cfgFile.c_str(), sectionName.c_str());
+    comp.Initialize();
+
+    TFile* f;
+    if (update)
+        f = TFile::Open(outputFile.c_str(), "UPDATE");
+    else
+        f = TFile::Open(outputFile.c_str(), "RECREATE");
+
+    if (componentName == "") componentName = sectionName;
+
+    comp.Write(componentName.c_str());
+
+    f->Close();
+
+    return 0;
+}
+#endif

macros/REST_AddComponentFormula.C

@@ -0,0 +1,46 @@
+#include "TRestComponent.h"
+#include "TRestTask.h"
+
+#ifndef RestTask_AddComponentFormula
+#define RestTask_AddComponentFormula
+
+//*******************************************************************************************************
+//*** Description: This macro will load from an RML the component chosen in the arguments and it
+//*** will write it inside the file given as outputFile
+//***
+//*** --------------
+//*** Usage: restManager AddComponentFormula components.rml sectionName [outputFile] [componentName] [update]
+//***
+//*** Arguments description:
+//***
+//*** - cfgFile: The RML configuration file where the component definition can be found.
+//*** - sectionName: The section name used to select a component inside the RML file.
+//*** - outputFile: The file where the component is written, by default is components.root.
+//*** - componentName: This argument allows to change the component name stored in the output file.
+//***                  By default it will take the same value as section name.
+//*** - update: If disabled it will create a new file erasing any other previously added components.
+//***           It is enabled by default.
+//***
+//*******************************************************************************************************
+
+Int_t REST_AddComponentFormula(std::string cfgFile, std::string sectionName,
+                               std::string outputFile = "components.root", std::string componentName = "",
+                               Bool_t update = true) {
+    TRestComponentFormula comp(cfgFile.c_str(), sectionName.c_str());
+    comp.Initialize();
+
+    TFile* f;
+    if (update)
+        f = TFile::Open(outputFile.c_str(), "UPDATE");
+    else
+        f = TFile::Open(outputFile.c_str(), "RECREATE");
+
+    if (componentName == "") componentName = sectionName;
+
+    comp.Write(componentName.c_str());
+
+    f->Close();
+
+    return 0;
+}
+#endif

macros/REST_CheckValidRuns.C

@@ -37,15 +37,14 @@ namespace fs = std::filesystem;
 //*** CAUTION: Be aware that any non-REST file in the list will be removed if you use purge=1
 //***
 //*******************************************************************************************************
-Int_t REST_CheckValidRuns(TString namePattern, Bool_t purge = false) {
+Int_t REST_CheckValidRuns(std::string namePattern, Bool_t purge = false) {
     TGeoManager::SetVerboseLevel(0);
 
     vector<std::string> filesNotWellClosed;
 
     TRestStringOutput RESTLog;
 
-    string a = TRestTools::Execute((string)("ls -d -1 " + namePattern));
-    vector<string> b = Split(a, "\n");
+    std::vector<std::string> b = TRestTools::GetFilesMatchingPattern(namePattern, true);
 
     Double_t totalTime = 0;
     int cont = 0;
@@ -76,11 +75,12 @@ Int_t REST_CheckValidRuns(TString namePattern, Bool_t purge = false) {
         }
 
         RESTLog << "Run time (hours) : " << run->GetRunLength() / 3600. << RESTendl;
-        if (run->GetRunLength() > 0) totalTime += run->GetRunLength() / 3600.;
+        RESTLog << "Entries : " << run->GetEntries() << RESTendl;
 
-        if (run->GetEndTimestamp() == 0 || run->GetRunLength() < 0) {
+        if (run->GetEndTimestamp() == 0 || run->GetRunLength() < 0 || run->GetEntries() == 0) {
             filesNotWellClosed.push_back(filename);
-        }
+        } else if (run->GetRunLength() > 0)
+            totalTime += run->GetRunLength() / 3600.;
 
         delete run;
 
@@ -100,7 +100,6 @@ Int_t REST_CheckValidRuns(TString namePattern, Bool_t purge = false) {
         if (purge) {
             RESTLog << "---------------------------" << RESTendl;
             RESTLog << "The files have been removed" << RESTendl;
-            RESTLog << "---------------------------" << RESTendl;
         }
     }
 

macros/REST_OpenInputFile.C

@@ -46,6 +46,7 @@ void REST_OpenInputFile(const std::string& fileName) {
         printf("\n%s\n", " - dSet->PrintMetadata()");
         printf("%s\n", " - dSet->GetDataFrame().GetColumnNames()");
         printf("%s\n\n", " - dSet->GetTree()->GetEntries()");
+        printf("%s\n", " - dSet->GetDataFrame().Display(\"\")->Print()");
         printf("%s\n\n", " - dSet->GetDataFrame().Display({\"colName1,colName2\"})->Print()");
         if (dSet) delete dSet;
         dSet = new TRestDataSet();

pipeline/panda-x/P3AutoChain.rml

@@ -1,5 +1,4 @@
-<?xml version="1.0" encoding="UTF-8" standalone="no" ?>
-
+<?xml version="1.0" encoding="UTF-8" standalone="no"?>
 <!--In this example, when launching the analysis, we are doing following operations inside TRestManager:
 1. Initialize TRestRun
 1.1 set input and output file for TRestRun(here input and output is in "globals")
@@ -13,25 +12,17 @@
 2.4.1 add additional observables in the process
 3. Add a task to call TRestProcessRunner to run
 -->
-
 <TRestManager name="CoBoDataAnalysis" title="Example" verboseLevel="info">
-
-    <TRestRun name="SJTU_Proto">
-        <parameter name="runNumber" value="auto"/>//change this value to "auto" to enable database
-        <parameter name="inputFileName" value="auto"/>
-    </TRestRun>
-
+    <TRestRun name="SJTU_Proto"><parameter name="runNumber" value="auto"/>//change this value to "auto" to enable database
+        <parameter name="inputFileName" value="auto"/></TRestRun>
     <TRestProcessRunner name="Processor" verboseLevel="info">
         <parameter name="eventsToProcess" value="0"/>
         <parameter name="threadNumber" value="2"/>
-
         <parameter name="inputAnalysisStorage" value="on"/>
         <parameter name="inputEventStorage" value="off"/>
         <parameter name="outputEventStorage" value="on"/>
-
         <addProcess type="TRestRawMultiCoBoAsAdToSignalProcess" name="virtualDAQ" value="ON"/>
-        <addProcess type="TRestRawSignalAnalysisProcess" name="sAna" value="ON">
-            <parameter name="pointsOverThreshold" value="3"/>
+        <addProcess type="TRestRawSignalAnalysisProcess" name="sAna" value="ON"><parameter name="pointsOverThreshold" value="3"/>
             /// We define all observables except MinValue because it is not yet in validation chain
             <observable name="BaseLineMean" value="ON"/>
             <observable name="BaseLineSigmaMean" value="ON"/>
@@ -61,31 +52,20 @@
             <parameter name="zeroSuppression" value="true"/>
             <parameter name="nPointsOverThreshold" value="3"/>
         </addProcess>
-
         <addProcess type="TRestRealTimeDrawingProcess" name="rD" value="ON" drawInterval="1000">
             <TRestAnalysisPlot name="TriggerRatePlot" previewPlot="false">
                 <canvas size="(1000,800)" save="TriggerRate.png"/>
-                <plot name="TriggerRate" title="Trigger Rate" xlabel="Seconds From Start" ylabel="Counts" value="ON"
-                      stats="ON">
+                <plot name="TriggerRate" title="Trigger Rate" xlabel="Seconds From Start" ylabel="Counts" value="ON" stats="ON">
                     <variable name="rateAna_SecondsFromStart" range="auto" nbins="100"/>
                 </plot>
             </TRestAnalysisPlot>
         </addProcess>
-
-
     </TRestProcessRunner>
-
     <addTask type="processEvents" value="ON"/>
-
-
     <globals>
         <searchPath value="$ENV{REST_INPUTDATA}/definitions/"/>
         <parameter name="mainDataPath" value=""/>
-
         <parameter name="pointThreshold" value="3"/>
     </globals>
-
 </TRestManager>
-
-
-        <!--parameter here is accessible to all the classes-->
+<!--parameter here is accessible to all the classes-->

source/bin/restRoot.cxx

@@ -61,7 +61,7 @@ int main(int argc, char* argv[]) {
                     printf("\n");
                     printf(" restRoot --m [0,1]\n");
                     printf("\n");
-                    printf(" Option 0 will disable macro loading. Option 1 is the default.\n");
+                    printf(" Option 0 will disable macro loading. Option 0 is the default.\n");
                     printf("\n");
                     exit(0);
             }
@@ -81,7 +81,18 @@ int main(int argc, char* argv[]) {
     gROOT->ProcessLine("#include <TRestPhysics.h>");
     gROOT->ProcessLine("#include <TRestSystemOfUnits.h>");
     if (loadMacros) {
-        if (!silent) printf("= Loading macros ...\n");
+        if (!silent) {
+            printf("= Loading macros ...\n");
+            printf(
+                "= HINT. Loading all macros may require a long time till you get access to the interactive "
+                "shell\n");
+            printf("= HINT. You may use `restListMacros` outside `restRoot` to check the available macros\n");
+            printf(
+                "= HINT. Then, you may execute the macro externally by using: `restManager MacroName "
+                "[ARGUMENTS]\n");
+            printf("= HINT. `MacroName` is the name of the macro after removing the macro name header\n");
+            printf("= HINT. E.g. REST_Detector_XYZ(arg1,arg2) may be called as: restManager XYZ arg1 arg2\n");
+        }
         vector<string> macroFiles;
         const vector<string> patterns = {
             REST_PATH + "/macros/REST_*.C",   // framework

source/framework/CMakeLists.txt

@@ -4,7 +4,7 @@ link_libraries("-fPIC")
 
 add_subdirectory(external)
 
-set(contents external/tinyxml tools core analysis masks)
+set(contents external/tinyxml tools core analysis masks sensitivity)
 
 file(GLOB_RECURSE addon_src "tiny*cpp" "startup.cpp")
 

source/framework/core/inc/TRestDataSet.h

@@ -82,7 +82,7 @@ class TRestDataSet : public TRestMetadata {
     std::map<std::string, RelevantQuantity> fQuantity;  //<
 
     /// Parameter cuts over the selected dataset
-    TRestCut* fCut = nullptr;
+    TRestCut* fCut = nullptr;  //<
 
     /// The total integrated run time of selected files
     Double_t fTotalDuration = 0;  //<
@@ -103,12 +103,14 @@ class TRestDataSet : public TRestMetadata {
     std::vector<std::string> fImportedFiles;  //<
 
     /// A list of new columns together with its corresponding expressions added to the dataset
-    std::vector<std::pair<std::string, std::string>> fColumnNameExpressions;
+    std::vector<std::pair<std::string, std::string>> fColumnNameExpressions;  //<
 
     /// A flag to enable Multithreading during dataframe generation
     Bool_t fMT = false;  //<
 
-    inline auto GetAddedColumns() const { return fColumnNameExpressions; }
+    // If the dataframe was defined externally it will be true
+    Bool_t fExternal = false;  //<
+
     /// The resulting RDF::RNode object after initialization
     ROOT::RDF::RNode fDataSet = ROOT::RDataFrame(0);  //!
 
@@ -123,20 +125,28 @@ class TRestDataSet : public TRestMetadata {
    public:
     /// Gives access to the RDataFrame
     ROOT::RDF::RNode GetDataFrame() const {
-        if (fTree == nullptr) RESTWarning << "DataFrame has not been yet initialized" << RESTendl;
+        if (!fExternal && fTree == nullptr)
+            RESTWarning << "DataFrame has not been yet initialized" << RESTendl;
         return fDataSet;
     }
 
-    void SetDataFrame(const ROOT::RDF::RNode& dS) { fDataSet = dS; }
-
     void EnableMultiThreading(Bool_t enable = true) { fMT = enable; }
 
     /// Gives access to the tree
     TTree* GetTree() const {
+        if (fTree == nullptr && fExternal) {
+            RESTInfo << "The tree is not accessible. Only GetDataFrame can be used in an externally "
+                        "generated dataset"
+                     << RESTendl;
+            RESTInfo << "You may write a tree using GetDataFrame()->Snapshot(\"MyTree\", \"output.root\");"
+                     << RESTendl;
+            return fTree;
+        }
+
         if (fTree == nullptr) {
             RESTError << "Tree has not been yet initialized" << RESTendl;
-            RESTError << "You should invoke TRestDataSet::GenerateDataSet() before trying to access the tree"
-                      << RESTendl;
+            RESTError << "You should invoke TRestDataSet::GenerateDataSet() or " << RESTendl;
+            RESTError << "TRestDataSet::Import( fname ) before trying to access the tree" << RESTendl;
         }
         return fTree;
     }
@@ -167,21 +177,27 @@ class TRestDataSet : public TRestMetadata {
     inline auto GetFilterLowerThan() const { return fFilterLowerThan; }
     inline auto GetFilterEqualsTo() const { return fFilterEqualsTo; }
     inline auto GetQuantity() const { return fQuantity; }
+    inline auto GetAddedColumns() const { return fColumnNameExpressions; }
     inline auto GetCut() const { return fCut; }
     inline auto IsMergedDataSet() const { return fMergedDataset; }
 
     inline void SetObservablesList(const std::vector<std::string>& obsList) { fObservablesList = obsList; }
     inline void SetFilePattern(const std::string& pattern) { fFilePattern = pattern; }
     inline void SetQuantity(const std::map<std::string, RelevantQuantity>& quantity) { fQuantity = quantity; }
 
+    void SetTotalTimeInSeconds(Double_t seconds) { fTotalDuration = seconds; }
+    void SetDataFrame(const ROOT::RDF::RNode& dS) {
+        fDataSet = dS;
+        fExternal = true;
+    }
+
     TRestDataSet& operator=(TRestDataSet& dS);
     Bool_t Merge(const TRestDataSet& dS);
     void Import(const std::string& fileName);
     void Import(std::vector<std::string> fileNames);
-    void Export(const std::string& filename);
+    void Export(const std::string& filename, std::vector<std::string> excludeColumns = {});
 
     ROOT::RDF::RNode MakeCut(const TRestCut* cut);
-
     ROOT::RDF::RNode DefineColumn(const std::string& columnName, const std::string& formula);
 
     void PrintMetadata() override;
@@ -193,6 +209,6 @@ class TRestDataSet : public TRestMetadata {
     TRestDataSet(const char* cfgFileName, const std::string& name = "");
     ~TRestDataSet();
 
-    ClassDefOverride(TRestDataSet, 5);
+    ClassDefOverride(TRestDataSet, 7);
 };
 #endif