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Macro to build the rejectlist for MID (#13330)
* Macro to build the rejectlist for MID * Add instruction on how to use the macros
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‎Detectors/MUON/MID/Calibration/macros/CMakeLists.txt‎

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o2_add_test_root_macro(
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ccdbUtils.C
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PUBLIC_LINK_LIBRARIES O2::MIDCalibration O2::MathUtils
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PUBLIC_LINK_LIBRARIES O2::MIDFiltering O2::DataFormatsMID O2::CCDB
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LABELS muon mid)
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o2_add_test_root_macro(
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build_rejectlist.C
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PUBLIC_LINK_LIBRARIES O2::MIDFiltering O2::MIDGlobalMapping O2::DataFormatsMID O2::CCDB O2::CommonUtils
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LABELS muon mid)

‎Detectors/MUON/MID/Calibration/macros/README.md‎

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<!-- doxy
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\page refMUONMIDCalibrationMacros MID Calibration macros
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/doxy -->
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# MID calibration macros
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This repository contains macros that can be used to handle calibration objects in the CCDB.
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## ccdbUtils.C
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This macro allows to query a series of MID CCDB objects in the CCDB as well as produce default objects.
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The basic usage is the following:
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Query the list of bad channels from the official CCDB:
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```shell
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root -l
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.x ccdbUtils.C("querybad",1721252719000,"mask.txt",true,"http://alice-ccdb.cern.ch")
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```
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Upload the default list of fake dead channels to the local CCDB (assuming that an instance of the local CCDB is running):
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```shell
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root -l
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.x ccdbUtils.C("uploadfake",1,"mask.txt",true,"localhost:8080")
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```
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The macro is also used to keep track of the fake dead channels, which are generated in `makeFakeDeadChannels()`.
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## buils_rejectList.C
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This macro analyses the Quality flag and the Occupancy plot in the QCCDB and searches for issues appearing in the middle of the run, e.g. local board(s) that become noisy and are then excluded from the data taking by the user logic of the CRU.
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It then correlate this information with the GRPECS object in the CCDB in order to create a reject list that will allow to mask the faulty local board(s) from slightly before the problem appeared till the end of the run.
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Notice that the QCDB is not directly reachable from outside CERN. In that case one needs to first create an ssh tunnel:
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```shell
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ssh -L 8083:ali-qcdb-gpn.cern.ch:8083 lxtunnel.cern.ch
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```
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We also advice to have an instance of the local CCDB running, so that the reject list objects will be saved there.
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One can then scan for issues with:
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```shell
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root -l
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build_rejectlist.C+(1716436103391,1721272208000,"localhost:8083")
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```
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Where the first number is the start timestamp for the scan, and the second is the end timestamp of the scan.
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For each problem found, the macro will ask if one wants to upload the reject list to the (local) CCDB or not.

‎Detectors/MUON/MID/Calibration/macros/build_rejectlist.C‎

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// Copyright 2019-2020 CERN and copyright holders of ALICE O2.
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// See https://alice-o2.web.cern.ch/copyright for details of the copyright holders.
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// All rights not expressly granted are reserved.
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//
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// This software is distributed under the terms of the GNU General Public
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// License v3 (GPL Version 3), copied verbatim in the file "COPYING".
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//
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// In applying this license CERN does not waive the privileges and immunities
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// granted to it by virtue of its status as an Intergovernmental Organization
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// or submit itself to any jurisdiction.
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/// \file MID/Calibration/macros/build_rejectlist.C
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/// \brief Analyse QC output and build reject list
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/// \author Diego Stocco <Diego.Stocco at cern.ch>
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/// \date 26 July 2024
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#include <string>
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#include <iostream>
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#include <sstream>
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#include <map>
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#include <vector>
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#include <limits>
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#include <algorithm>
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#include "TCanvas.h"
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#include "TH1.h"
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#include "TGraph.h"
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#include "TTimeStamp.h"
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#include "CCDB/CcdbApi.h"
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#include "DataFormatsParameters/GRPECSObject.h"
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#include "DetectorsCommonDataFormats/DetID.h"
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#include "DataFormatsMID/ColumnData.h"
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#include "MIDGlobalMapping/ExtendedMappingInfo.h"
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#include "MIDGlobalMapping/GlobalMapper.h"
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#include "MIDFiltering/ChannelMasksHandler.h"
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#if !defined(__CLING__) || defined(__ROOTCLING__)
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#include "CCDB/BasicCCDBManager.h"
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#endif
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static const std::string sPathQCQuality = "qc/MID/MO/MIDQuality/Trends/global/MIDQuality/MIDQuality";
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/// @brief Get timestamp in milliseconds
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/// @param timestamp Input timestamp (in s or ms)
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/// @return Timestamp in ms
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long getTSMS(long timestamp)
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{
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if (timestamp < 1000000000000) {
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return timestamp * 1000;
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}
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return timestamp;
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}
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/// @brief Get timestamp in seconds
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/// @param timestamp Input timestamp (in s or ms)
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/// @return Timestamp in s
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long getTSS(long timestamp)
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{
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if (timestamp < 1000000000000) {
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return timestamp;
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}
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return timestamp / 1000;
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}
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/// @brief Converts timestamp to human-readable string
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/// @param timestamp Timestamp as long
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/// @return Timestamp as human-readable string
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std::string tsToString(long timestamp)
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{
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return TTimeStamp(getTSS(timestamp)).AsString("l");
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}
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/// @brief Converts time range in a human-readable string
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/// @param start Start time
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/// @param end End time
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/// @return Time range as human-readable string
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std::string timeRangeToString(long start, long end)
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{
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std::stringstream ss;
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ss << start << " - " << end << " (" << tsToString(start) << " - " << tsToString(end) << ")";
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return ss.str();
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}
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/// @brief Query the CDB path and search for initial validity of objects
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/// @param start Query objects created not before
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/// @param end Query objects created not after
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/// @param api CDB api
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/// @param path CDB path
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/// @return Vector of start validity of each object sorted in ascending way
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std::vector<long> findObjectsTSInPeriod(long start, long end, const o2::ccdb::CcdbApi& api, const char* path)
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{
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std::vector<long> ts;
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auto out = api.list(path, false, "text/plain", getTSMS(end), getTSMS(start));
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std::stringstream ss(out);
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std::string token;
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while (ss >> token) {
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if (token.find("Validity") != std::string::npos) {
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ss >> token;
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ts.emplace_back(std::atol(token.c_str()));
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}
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}
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ts.erase(std::unique(ts.begin(), ts.end()), ts.end());
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// Sort timestamps in ascending order
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std::sort(ts.begin(), ts.end());
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return ts;
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}
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/// @brief Find the first and last time when the quality was good or bad
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/// @param qcQuality MID QC quality canvas
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/// @param selectBad When true select bad quality
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/// @return Pair with first and last time
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std::pair<uint64_t, uint64_t> findTSRange(TCanvas* qcQuality, bool selectBad = true)
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{
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auto* gr = static_cast<TGraph*>(qcQuality->GetListOfPrimitives()->FindObject("Graph"));
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double xp, yp;
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std::pair<uint64_t, uint64_t> range{std::numeric_limits<uint64_t>::max(), 0};
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for (int ip = 0; ip < gr->GetN(); ++ip) {
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gr->GetPoint(ip, xp, yp);
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if (selectBad == (yp > 1 && yp < 3)) {
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uint64_t xpi = static_cast<uint64_t>(1000 * xp);
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range.first = std::min(range.first, xpi);
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range.second = std::max(range.second, xpi);
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}
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}
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if (range.first == std::numeric_limits<uint64_t>::max()) {
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range.first = 0;
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}
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return range;
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}
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/// @brief Find bad channels from the occupancy histograms
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/// @param hits Occupancy histogram
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/// @param infos Mapping
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/// @return Vector of bad channels
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std::vector<o2::mid::ColumnData> findBadChannels(TH1* hits, std::vector<o2::mid::ExtendedMappingInfo>& infos)
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{
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std::map<uint16_t, o2::mid::ColumnData> badChannelsMap;
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for (int ibin = 1; ibin <= hits->GetNbinsX(); ++ibin) {
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if (hits->GetBinContent(ibin) == 0) {
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auto info = infos[ibin - 1];
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auto uniqueId = o2::mid::getColumnDataUniqueId(info.deId, info.columnId);
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o2::mid::ColumnData col;
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col.deId = info.deId;
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col.columnId = info.columnId;
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auto result = badChannelsMap.emplace(uniqueId, col);
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result.first->second.addStrip(info.stripId, info.cathode, info.lineId);
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}
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}
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std::vector<o2::mid::ColumnData> badChannels;
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for (auto& item : badChannelsMap) {
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badChannels.emplace_back(item.second);
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}
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return badChannels;
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}
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/// @brief Converts the bad channels from the occupancy into a reject list (removing the ones from CCDB)
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/// @param badChannels Bad channels from the analysis of the occupancy histogram
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/// @param badChannelsCCDB Bad channels in the CCDB
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/// @return Reject list
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std::vector<o2::mid::ColumnData> getRejectList(std::vector<o2::mid::ColumnData> badChannels, const std::vector<o2::mid::ColumnData>& badChannelsCCDB)
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{
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o2::mid::ChannelMasksHandler mh;
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mh.switchOffChannels(badChannelsCCDB);
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for (auto& bad : badChannels) {
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mh.applyMask(bad);
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}
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badChannels.erase(std::remove_if(badChannels.begin(), badChannels.end(), [](const o2::mid::ColumnData col) { return col.isEmpty(); }),
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badChannels.end());
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return badChannels;
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}
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/// @brief Builds the reject list for the selected timestamp
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/// @param timestamp Timestamp for query
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/// @param qcdbApi QCDB api
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/// @param ccdbApi CCDB api
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/// @param outCCDBApi api of the CCDB where the reject list will be uploaded
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/// @return Reject list
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std::vector<o2::mid::ColumnData> build_rejectlist(long timestamp, const o2::ccdb::CcdbApi& qcdbApi, const o2::ccdb::CcdbApi& ccdbApi, const o2::ccdb::CcdbApi& outCCDBApi)
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{
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std::map<std::string, std::string> metadata;
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auto* qcQuality = qcdbApi.retrieveFromTFileAny<TCanvas>(sPathQCQuality, metadata, getTSMS(timestamp));
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if (!qcQuality) {
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std::cerr << "Cannot find QC quality for " << tsToString(timestamp) << std::endl;
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return {};
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}
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// Find the first and last timestamp where the quality was bad (if any)
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auto badTSRange = findTSRange(qcQuality);
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if (badTSRange.second == 0) {
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std::cout << "All good" << std::endl;
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return {};
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}
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// Search for the last timestamp for which the run quality was good
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auto goodTSRange = findTSRange(qcQuality, false);
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// Query the CCDB to see to which run the timestamp corresponds
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auto oldestTSInQCQuality = (goodTSRange.first == 0) ? badTSRange.first : goodTSRange.first;
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auto grpecs = *ccdbApi.retrieveFromTFileAny<o2::parameters::GRPECSObject>("GLO/Config/GRPECS", metadata, getTSMS(oldestTSInQCQuality));
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if (!grpecs.isDetReadOut(o2::detectors::DetID::MID)) {
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std::cout << "Error: we are probably reading a parallel run" << std::endl;
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grpecs.print();
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return {};
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}
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if (grpecs.getRunType() != o2::parameters::GRPECS::PHYSICS) {
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std::cout << "This is not a physics run: skip" << std::endl;
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grpecs.print();
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return {};
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}
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auto runRange = o2::ccdb::BasicCCDBManager::getRunDuration(ccdbApi, grpecs.getRun());
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long margin = 120000; // Add a two minutes safety margin
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runRange.first -= margin; // Subtract margin
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runRange.second += margin; // Add margin
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// Search for hits histogram in the period where the QC quality was bad
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auto tsVector = findObjectsTSInPeriod(badTSRange.first, badTSRange.second, qcdbApi, "qc/MID/MO/QcTaskMIDDigits/Hits");
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if (tsVector.empty()) {
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std::cerr << "Cannot find hits in period " << tsToString(badTSRange.first) << " - " << tsToString(badTSRange.second) << std::endl;
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return {};
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}
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// Focus on the first object found
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TH1* occupancy = qcdbApi.retrieveFromTFileAny<TH1F>("qc/MID/MO/QcTaskMIDDigits/Hits", metadata, getTSMS(tsVector.front()));
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o2::mid::GlobalMapper gm;
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auto infos = gm.buildStripsInfo();
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auto badChannels = findBadChannels(occupancy, infos);
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auto badChannelsCCDB = *ccdbApi.retrieveFromTFileAny<std::vector<o2::mid::ColumnData>>("MID/Calib/BadChannels", metadata, getTSMS(timestamp));
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auto rejectList = getRejectList(badChannels, badChannelsCCDB);
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if (rejectList.empty()) {
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std::cout << "Warning: reject list was empty. It probably means that an entire board is already masked in calibration for run " << grpecs.getRun() << std::endl;
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return {};
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}
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// Print some useful information
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std::cout << "Reject list:" << std::endl;
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for (auto& col : rejectList) {
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std::cout << col << std::endl;
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}
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std::cout << "Run number: " << grpecs.getRun() << std::endl;
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std::cout << "SOR - EOR: " << timeRangeToString(grpecs.getTimeStart(), grpecs.getTimeEnd()) << std::endl;
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std::cout << "SOT - EOT: " << timeRangeToString(runRange.first, runRange.second) << std::endl;
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std::cout << "Good: " << timeRangeToString(goodTSRange.first, goodTSRange.second) << std::endl;
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std::cout << "Bad: " << timeRangeToString(badTSRange.first, badTSRange.second) << std::endl;
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// Set the start of the reject list to the last timestamp in which the occupancy was ok
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auto startRL = goodTSRange.second;
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if (goodTSRange.first == 0) {
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// If the quality was bad for the full run, set the start of the reject list to the SOR
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std::cout << "CAVEAT: no good TS found. Will use SOT instead" << std::endl;
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startRL = runRange.first;
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}
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// Set the end of the reject list to the end of run
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auto endRL = runRange.second;
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// Ask if you want to upload the object to the CCDB
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std::cout << "Upload reject list with validity: " << startRL << " - " << endRL << " to " << outCCDBApi.getURL() << "? [y/n]" << std::endl;
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std::string answer;
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std::cin >> answer;
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if (answer == "y") {
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std::cout << "Storing RejectList valid from " << startRL << " to " << endRL << std::endl;
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outCCDBApi.storeAsTFileAny(&rejectList, "MID/Calib/RejectList", metadata, startRL, endRL);
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}
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return rejectList;
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}
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/// @brief Builds the reject list for the selected timestamp
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/// @param timestamp Timestamp for query
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/// @param qcdbUrl QCDB URL
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/// @param ccdbUrl CCDB URL
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/// @param outCCDBUrl URL of the CCDB where the reject list will be uploaded
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/// @return Reject list
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std::vector<o2::mid::ColumnData> build_rejectlist(long timestamp, const char* qcdbUrl = "http://ali-qcdb-gpn.cern.ch:8083", const char* ccdbUrl = "http://alice-ccdb.cern.ch", const char* outCCDBUrl = "http://localhost:8080")
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{
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// Get the QC quality object for the selected timestamp
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o2::ccdb::CcdbApi qcdbApi;
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qcdbApi.init(qcdbUrl);
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o2::ccdb::CcdbApi ccdbApi;
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ccdbApi.init(ccdbUrl);
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o2::ccdb::CcdbApi outCCDBApi;
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outCCDBApi.init(outCCDBUrl);
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return build_rejectlist(timestamp, qcdbApi, ccdbApi, outCCDBApi);
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}
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/// @brief Builds the reject list iin a time range
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/// @param start Start time for query
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/// @param end End time for query
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/// @param qcdbUrl QCDB URL
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/// @param ccdbUrl CCDB URL
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/// @param outCCDBUrl URL of the CCDB where the reject lists will be uploaded
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void build_rejectlist(long start, long end, const char* qcdbUrl = "http://ali-qcdb-gpn.cern.ch:8083", const char* ccdbUrl = "http://alice-ccdb.cern.ch", const char* outCCDBUrl = "http://localhost:8080")
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{
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// Query the MID QC quality objects
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o2::ccdb::CcdbApi qcdbApi;
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qcdbApi.init(qcdbUrl);
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o2::ccdb::CcdbApi ccdbApi;
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ccdbApi.init(ccdbUrl);
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o2::ccdb::CcdbApi outCCDBApi;
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outCCDBApi.init(outCCDBUrl);
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auto objectsTS = findObjectsTSInPeriod(start, end, qcdbApi, sPathQCQuality.c_str());
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for (auto ts : objectsTS) {
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build_rejectlist(ts, qcdbApi, ccdbApi, outCCDBApi);
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}
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}

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