Overdue Ozelot

New

• grsiframe: Replacement for grsiproof, based on ROOT's RDataFrame instead of the obsolete PROOF. grsiframe uses "helpers" instead of "selectors" and a number of the latter that have been translated into the former can be found in the examples directory.
• FastTiminingHistSelector: A selector to create fast timing histograms from a prepared tree of fast timing information.
• checklog.sh script in examples is a quick script to check a log-file to see if the sort of a subrun ended successfully or not. Simply checks if the last line is "bye,bye" (good) or "Deleting thread" (bad).
• sort.sh script in examples can be used to sort files and can be run with multiple instances in parallel. Automatically saves the output of the sorting into log files which can be check with checklog.sh script to see if the sorting finished.
• TLevelScheme: New class to create, plot, and save level schemes. Includes some modification to the behavior of GCanvas if the canvas name is "LevelScheme".
• TEfficiencyCalibrator: New GUI to automatically take spectra created by the effiency helper to calculate efficiency curves, including summing in and summing out. The calculation of the latter still has some bugs in it.
• TRedirect class redirect stdout and stderr to a file as long as the object exists, i.e. until it goes out of scope or is deleted.
• EnableCrosstalkCorrection program allows enabling crosstalk correction for a list of analysis files.
• PlotVsRun allows plotting histograms vs the run number.
• ReadCalFromRoot loops over the provided root files and writes out a .cal file for each one of them.
• SetOdbFromData loops over the provided root files and checks if the PPG information read from the ODB matches the data. Writes out a line for each file whether the information was already correct, some error occured, or if it was updated.
• checkSort loops over the provided analysis root files and checks if any problem with repeated events occured (the bug making this check necessary has been fixed by now).

Improvements

• TGRSIUtilities now provides a trim function and the separate versions in GValue, TChannel, and TRunInfo have been removed.
• GValue: It is now possible to provide a default value to GValue::Value which is used instead of NaN if the requested value is not found.
• Globals.h now provides a function std::string hex(T val, int width = -1) that formats the provided value in hexadecimal with lead 0x and if the provided width is positive pads it with zeroes up to that width. It also provides a void SetGRSIEnv() function to set the environment for grsisort, and for linux systems a void PrintGdbStacktrace() function to print the stack trace using gdb.
• TSinglePeak and all its children now have a working Sigma and FWHM function, and the InitializeParameters function can take a range which is used as limits for the centroid.
• TPeakFitter uses the range as limit for the centroid and doesn't include it when releasing all parameters if the fit failed to give good errors. Also returns the TFitResultPtr to allow users to access e.g. the covariance matrix.
• Made some adjustments to make grsisort work with ROOT 6.24 and 6.26.
• TCalibrationGraphSet: Added options to set marker type, as well as setting line colors and marker colors in one single function and adding axis titles. Also added functions to get minimum and maximum x- and y-values. When adding graphs to the set, the colors are initialized to the current size of the set.
• TChannel now supports multiple ranges for calibrations, corrections for time drifts (if digitizer clocks are not synched properly) and added GetTime function which is now called by TDetectorHit and simply calles the GetTime function of the mnemonic.
• TMnemomic warns if the base class is being used instead of the version defined in the data library. Also includes GetTime function that takes care of the different time stamp units of different digitizer etc.
• Instead of looping over the vector of fragments and adding the fragments on at a time to the UnpackedEvent class, we now simply set the raw data to the whole vector at once.
• TGRSIMaps includes a function to emplace elements.
• Added multiple new options to grsisort, mostly used by grsiproof and grsiframe.
• TGRSISelector includes a check for the size of object to warn if ROOT's limit of 1 GB is reached.
• Replaced (most?) uses of printf with std::cout.
• TNucleus offers option to get the transition sorted by energy or intensity. To that effect two lists of transitions are kept simultaneously.
• TPulseAnalyzer has been ported to the latest version from SFU TIPSort code.
• Updated TScaler to get ratio of two variables of the last scaler entry (used in EMMA). Also scalers are now actually written to file at the end.
• TSortingDiagnostics now includes a map of channels missing in the calibration file.
• TSourceCalibration zooms graph and residual simultaneously, had some bugs fixed as well.
• Improved and unified Print statements for detectors.
• TRunInfo now has a function CreateLabel that returns a string created using the run and sub-run numbers in it. Before this code was copied in multiple places of grsisort.
• Added new event building mode "Skip" that skips the step of sorting the fragments because they are already sorted.
• The makefile honors the c++ standard root-config returns and includes support for HIL data library.
• WriteCalToRoot output updated to show more clearly which files were update successfully and where problems occured.

Bug fixes

• grsiproof: --max-events flag now works, additional options for PROOF added, log file names now include the run and sub-run number(s).
• The use of multiple threads to write the analysis file has led to problems with single events being repeated thousands of times, leading to spikes in the energy or time histograms. So we have reverted now to having TAnalysisWriteLoop write a single TFile directly instead of using the TAnaysisWriteLoopClient class.
• TPeakFitter used to crash when adding and removing peaks between fits.
• TSinglePeak and children now first set the parameter, then the limits, this avoids warnings that the parameter (which is 0 at that point) is outside the limits.

Pandemic Piranha

New

• TCalibrateDescant class allows interactive fitting and calibrating of DESCANT detectors (WIP).
• TSourceCalibration class adds interactive fitting of data from multiple sources (mostly working, some WIP). This includes a new classes TCalibrationGraph and TCalibrationGraphSet.
• Added AlphanumericSelector for use with TSourceCalibration (but also as useful example of using channel addresses as axis labels).

Improvements

• 1D-histograms can now be toggled to logscale using the y key as well (and not just the l key).
• Added simple gaussian peak (TGauss).
• grsiproof retries connecting to proof if first attempt fails. If that fails too the error message suggests running grsiproof again.
• Added function to read energy non-linearities from a root-file as well as a cal-file.
• Also added program WriteNonLinearitiesCal which reads non-linearities froma root-file and creates a cal-file with them in it.
• Expanded usability of TPriorityValue class by adding all (?) std::vector and std::string functions to it.
• Setting word count check to negative value (-1) disabled the word count check. This is now the default setting.
• Parser libraries can now be compiled directly from $GRSISYS.
• Added option to run macro with arguments from command line.
• Read multiple .val files, g-values stored in root file are now named "Values" instead of "GValue".
• Replaced all "master" with "primary", "default", or "main" (includes changing "MSC" to "PSC").
• Added threadsafe printing capabilities and PrintStacktrace function (mainly for ease of debugging).
• Root2Rad can now traverse directories in root-files.
• Changed k-values for piled-up hits after reconstruction of their charge from 1 to the k-values of the first hits.
• Added GriffinKValueSelector and PlotGriffinKValue program for a quick check of k-values.
• Improved documentation of GROOT classes.
• Added comparison operator to TNucleus.
• Improved and updated peak fitting classes (no-print option actually works, more fine-tuning options for output, using Class()->GetName() in parent class instead of individual print statements).
• No longer trying to link xml-libraries if xml isn't present.
• TBGSubtraction has option to select peak type and to rebin the background subtracted histogram.
• Fitting functions check if parameters are near their limits (which means the uncertainty estimates of the fit parameters are wrong). Using "retryfit" option causes the fit to be tried again with all parameters released.
• Added option to write trees with grsiproof including one example selector.

makefile

• Only compiles grsiproof.cxx instead of all .cxx file in GRSIProof directory.
• Added parser library specific cflags, and incdir options.
• Removed -lPyROOT flag which doesn’t work with new root versions (and doesn’t seem to be needed with older versions either?).
• Only setting the -std flag if it is not set already by root-config.

Bug fixes

• Fixed a bug in GCanvas where toggling the z-axis to or from logscale would change the range of the y-axis.
• Removed incorrect use of TPROOF::SetMacroPath in grsiproof.
• TChannel is now correctly written to the grsiproof output file.
• Fixed issue #1154 using cross talk corrections in grsiproof.
• Fixed multiple issues with copying detector hits.
• Fixed a bug in TPPG with conversion from ns to timestamp units.

Riveting Rhino

New

• Added flag to skip sorting input.
• Removed UpdateChannelNumberMap as it's no longer needed (see #1115).

Improvements

• Unified channel address maps to use TParsingDiagnosticsData class to reduce map lookups (see #1113).

• Makefile: changed argument to find/gfind from -links to -maxdepth to fix #1118.

• Fixing #1124:

  Changed GMarker to not store independent x/y coordinates and bins but use values from the TLines instead.

  This means that changing the TLines (by dragging them on the canvas) changes the GMarker values now, e.g. when fitting a histogram. It also means that one has to provide the histogram the marker refers to either
  via the constructor, or afterwards via the GMarker::SetHist function.
  Failure to do so results in a segmentation violation if e.g. asking for the position of the marker in bins (these functions do not yet check if the histogram pointer has been set).

• Deep copy & destructor fixed for TDetector.

• Implemented (temporary) fix for issue #1123 by forcing the setting of TDetector::fChannel regardless of the bit if fChannel is channel is a null pointer. This should be replace by a fix for the transients bits that aren't correctly read as zero from file.

Ominous Osprey

New

• GRSIProof now works with the new split version.
• EDigitizer is not part of TMnemonic anymore but is defined by the data parser libraries.
• Added 8k matrix to Root2Rad.
• New TParserLibrary class handles all loading and initialization of data parsing libraries.
• New flag '--downscaled ' allows to read only every nth MIDAS event from the file (to speed up online sorting with lower statistics).
• New flag '--ignore-odb-channels' does just that, it causes grsisort to ignore any TChannel information in the ODB.
• New flag to sort by timestamps as the new default is to sort by time.
• Timestamps are now stored in the native resolution of the digitizer and the additional information TimeStampUnit is used to convert this into ns. GetTimeStamps returns now in the native unit, and GetTimeStampNs returns timestamp in ns.
• Build windows are now also in ns (and the default was changed from 200 in 10 ns units, to 2000 in ns).
  Added capability to create cuts and use them in GRSIproof …
• GRSIProof reads cuts from all supplied "cut files". The cut files are determined by TGRSIOptions::InputCutFiles which returns all files with extension .cuts provided on the command line. Don't know what these files were originally intended for, but now those are just re-named root-files.
  • TGRSISelector tries to open all files provided by GRSIProof as "cut files" and reads any TCutG object from them. These are stored in a map, mapping the TCutG pointer to the name of the cut.
  • GCanvas now has two more short cuts:
    • i: initialize cut, prompting for a name, using single clicks to add points, and double click to finish/close the cut.
    • c: create the cut, using the previously initialized object "CUTG".
    • s: save cuts, prompting for a file name, default is CutFile.cuts.
• New utility Root2Ascii to create simple ascii files.
• TRunInfo has a run list of all runs added together.

Improvements

• LibraryInit function now automatically sets the mnemonic class of TChannel to the right choice.
• EnumerateDigitizer function creates a warning if string is not recognized (or empty).
• '-H' flag writes now root spectra instead of grsisort spectra so that the resulting files can be used with just root and one doesn't need grsisort to look at them.
• Fixed some bugs in TFragmentMap and changed NPileups to be signed.
• Changed things to get grsisort to work on CentOS 7.
• Made the flag of maximum events to be read actually do that.
• Control-C now causes the program to exit at first press if in interactive mode.
• Warnings about missing channels are suppressed in interactive mode.
• TPeakFitter can now fit ranges outside the current windows range.
• Energy nonlinearity is now stored in TChannel.
• Improved output of TSortingDiagnostics.
• Fixed warnings when using newer compilers.
• Sped the sorting up by a number of fixes:
  • TPriorityValue::Value returns a constant reference instead of a copy.
  • Use unordered_map instead of map where possible/sensible.

Serendipitous Spaniel

This is the first release of the split version of GRSISort.

New

• GRSISort itself now has only analysis classes and the base classes for detectors.
• Separate libraries are needed that provide data parsing and setup specific detector classes.
• The code has been tested with GRIFFIN files (using the GRSIData library), but not with ILL or iThemba files.
• This also implements the last changes discussed in #942, i.e. changing the names of objects written to file not to be the class names of the objects.

Improvements

• New function TChannel::FindChannelByRegEx returns vector of channels that match the supplied regular expression (see #1051).
• Changed default GetArrayNumber function to return detector number. This function is overwritten by detectors that have cyrstals/segments.
• Added full version (with commit) and date of grsisort to TRunInfo (which is also written to sorted files).

Yappy Yak

New

• Using TParallelFileMerger to write analysis trees (see below).
• Added code to sort data from iThemba decay station:
  • Added TTdrFile and TTdrEvent classes as well as data parser for UK midas DAQ
  • Added detector classes TTdrTigress, TTdrClover, TTdrPlastic, and TTdrSiLi
• Added code to parse data from CAEN DT5730 digitizer
• Added option to write analysis histograms w/o writing the analysis tree.

Improvements

• Added TGRSIMap and TGRSIMapException to give a better error message if trying to access non-existing histogram in grsiproof
• Updated ErrorReport.sh to work with new issue template
• Updated grsisort man page
• Added LB as mnemonic for LaBr
• Improved S3 comments and modifications to TIGRESS position
• Added functions to access PPG information read from the ODB
• Fixed a number of TODO things:
  • GCanvas markers work also in log-mode
  • TSharc used std::move when adding hits
  • StoppableThread will throw an exception if a thread with the same
    name as an existing thread is added.
  • Trying to sort analysis histograms from an analysis tree still does
    not work, but added to the error message that grsiproof should be
    used.
• Now there is the ConvolutedDecay2, which allows the fit of a guassian convoluted with 2 exponential decays, a common stituation

TParallelFileMerger
This allows us to use multiple threads to write to the same analysis output file. The code is based of the $ROOTSYS/tutorials/net/parallelMergeServer.C and $ROOTSYS/tutorials/net/parallelMergeClient.C. The analysis write loop now pushes the events it reads from its input queue into the clients input queue and then moves to the next client (round-robin style). Each client sends the events that were written to a TParallelMergingFile back to the server every 100000 events (this number is hard-coded for now).
This means the events are now out of order (which doesn't matter in most cases where we only look at data within one events anyways).

The events can be put back in order if instead of going round-robin we send the first N events to the first client, then the next N events to the next client, and so on. Here N is the number of events each client keeps before sending all of them back to the server.

TSuppressed
Added new TSuppressed class as a base for all detector with BGO suppressors. TSuppressed doesn't do much, it just provides the template functions that allow to create addback vectors and suppressed vectors (and suppressed addback vectors) from a provided hit vector. Two new analysis options were added, one to set the time window between the detector and the BGO, the other to set an energy threshold for the BGO.
This also includes adding classes TBgo/TBgoHit and derived classes for each detector.

This affect all suppressed detector classes except Tigress.

Bug fixes

• grsiproof checks if a tree was found in the input files
• fixed bug in TSingleton when using TGRSIRunInfo from multiple files in grsiproof
• fixed bug in TGRSIRunInfo (parentheses missing after functions)
• fixed TPeak segfault when attempting to fit a range with no data
• fixed description of '-q' flag
• fixed case problem in Tigress by switching mnemonics (could have caused 10% data loss)
• fixed issue with reading calibration from ODB by changing priority from kDefault to kRootFile
• added a check that the charge word is actually in the right format. This was necessary since the stricter data parser didn't have all options for the highest nibble in the switch statement anymore, meaning "default" could mean something where the highest bit is not set (e.g. a footer word).
• Changed all comparisons of DigitizerTypeString to use the existing enumeration class
• Use std::transform to force upper case on string read.
• Made TGRSISelector member variables transient
• decreased memory usage and fixed memory leak warnings for cross talk scripts

Uninspired Urchin

New

• Added Contributing.md, advising people to search old issued, and to use ErrorReport.sh when creating new ones
• Added AngularCorrelationSelector (might need a bit of tweaking to reduce memory usage)
• Added TBgo class (not yet fully functional)
• Added TGenericDetector detector
• Added TPriorityValue template class which enables updating only values that have been changed from the default (e.g. when reading a calibration file)
• New class TSingleton provides templated base-class for singletons
  that are written to file. The Get() function automatically reads
  from the current file, keeping the information updated even in a
  loop over input files (such as used with grsiproof).
  • Adding a new class involves
    • including the TSingleton.h header,
    • changing the base to TSingleton,
    • adding TSingleton as a friend class (might not be needed?),
    • removing old Get() function and static pointer to instance,
    • updating class definition version,
    • adding #pragma link C++ class TSingleton<T>-; to
      libraries/TGRSIFormat/LinkDef.h,
    • constructors must now call TSingleton constructor instead of
      TObject constructor, and
    • existing static WriteToRoot functions must be modified to be
      in the right directory before using Get() so that writing doesn't
      create a new (empty) instance because the directory has been
      changed.
  • TGRSIRunInfo, TPPG, TParsingDiagnostics, and TSortingDiagnostics are now based on TSingleton.
• Writing TGRSIOptions to fragment and analysis files
• Added '--recommended' flag, added colours to printing of options

Improvements

• AtExitHandler for grsiproof gathers log-files when program exits.
• Added flag to force kill grsiproof with second Ctrl-c
• Added stopwatch to grsiproof
• Changed default status width to 120 (corresponds to 6 threads which is standard if sorting from midas-file to analysis-tree)
• Example selectors were updated to gracefully deal with missing branches
• TChannel allows to unset UseCalFileIntegration
• Changed most enums to enum classes. Doing this also caught a few bugs in the code.
• Added possibility to have boolean command line option take argument to un-set it
• Updated ErrorReport.sh to contain a guess of the OS
• TGRSIDetectorHit::GetTime now uses TChannel::CalibratedCFD
• Using argv[0] (program name) to decide which options are added to ArgParser, this allows us to show different options for grsisort and grsiproof when used with '-h' flag
• Added option for WriteCalToRoot program to update calibration instead of replacing them
• Changed TParsingDiagnostics maps to use channel address as keys (instead of channel numbers)
• Added check for channel with single event to TParsingDiagnostics::Print

TBGSubtraction

• Added a second background for gating
• Refactored TBGSubtraction to work more linearly
  • removed many of the connections
  • back-end of interface should be much more easy to follow now
• Added Update check box to BGSubtraction
  • This increases speed when not interested in performing gating-on-the-fly
  • Default is on-the-fly is off
  • Fitting, and writing is disabled when you are not updating the gates.
  • Allows faster window expansion, gate setting etc, especially with multiple backgrounds
  • This was implemented because I'm not sure it's possible to connect to histogram range expansion without also connectiong to the window being expanded.
• BGSubtraction Zoom in connection fix
  • As per James' suggestion, I've fixed the zoom in to ignore window expansion.
  • Now auto-update can be the default, and is set as such
• Squished a bug (peak marker drawing on gating)

SPICE

• added SiLi oscillation fit
• Fixed a crucial small mistake clearing S3
• Multiple S3s
• Added magnet shadow
• Changed various time comparisons and functions. The unit conversions are a bit messy but correct
• TSiLi addback replaced
• Small S3 tweak for mnemonic shuffle
• Fixed BGOs being thrown away and write

Bug fixes

• Fixed an energy/charge calculation issue when using cal file integration parameter
• Fixed error where "dropped" fragments weren't removed from the map
• Fixed TCanvas problem on Ubuntu
• Fixed bug in TPPG when setting patterns (high bits weren't masked out)
• Fixed shadow warnings by changing kNone to kNoneSet in TGRSIDetectorHit::ETimeFlag
• Change .grsirc prompt color based on root version. Fixes #958
• Fixed warnings by using static_cast<std::underlying_type::type>(enum-class)
• Added check to use rootcling if rootcint is not available
• Fixed bug when writing very small energy calibration coefficients (changed format of print statement)
• Added checks that file were successfully opened, e.g. in TAnalysisOptions::ReadFromFile
• Updated order of libraries in grsi-config for Ubuntu (fixes #979)
• Fixed bug when executing macros from command line
• Getting TGRSIRunInfo and TGRSIOptions instances before opening output file in TGRSISelector

Peekaboo Puffin

• Histograms & Graphics

  • Fixed errors in symmetric 2D histogram class GHSym
  • Added GCube, a symmetric 3D histogram class
  • shift-f fits a peak using TPeak, f fits it using GPeak
  • arrow keys now also work on 2D histograms
  • Ryan remodeled the peak fitting making it easier to add new peak fit functions. This now includes a function to fit addback peaks.
  • Updates to TBGSubtraction:
    • can fit peaks,
    • now has a status bar,
    • a background option,
    • an axis option,
    • and a skewed gaussian option

• New Functionality

  • James worked on improvements to TSiLiHit, TPulseAnalyzer
  • Added functionality to deal with non-linearities of ADCs
  • TTACHit can have temperature corrections applied
  • Bruno added his TAC calibrator script (might be changed to a Selector in the future?)
  • Function to describe decay convoluted with gaussian was added
  • Started adding an angular correlations selector, had to be split up due to the large size of the histograms in memory

• Data Parsing & Analysis Options

  • Changed data parsing:
    • store reason for error and the word, but continue to try and parse the event until the next header is found
    • store bad fragments in their own class, including the word the parser failed on and the data up to and including the next header
    • data parser throws expection with the word it failed on and why it failed
    • added option to reconstruct missing high timestamp bits
  • PPG information is read from ODB
  • Analysis options are written to the files but can be overwritten by using command line options
  • We had a problem with data taken in May and June this year where the number of words in a GRIFFIN event didn't match the number of words reported in the header, for this a new flag --word-count-offset has been introduced
  • TGRSIRunInfo now stores the run start, run stop, and run length and merges them correctly (this was lost from earlier version of GRSISort)

• Program control

  • GRSISort now always prints it's version, even when using -l flag, and the version is now always updated
  • Added stopwatch to report how long GRSISort has been running
  • Change reaction to cltr-c:
    • Using ctrl-c once stops the input queue but not the output queue
    • Using ctrl-c twice clears all queues (but still waits for a normal end of the sorting)
    • Using ctrl-c thrice exits the program without trying to close files
  • Using an unknown command line flag now causes the program to exit and display the help message
  • using ctrl-c on grisproof now also kills all workers

• Programming

  • Fixed problems using make -j after make clean
  • Used clang-format to bring formatting of code up to out standard, can't be used automatically
  • Ran clang-tidy over the code to fixed coding:
    • replaced deprecated C-headers with c++-headers
    • converted for loops to range-based loops
    • string literals with escaped characters were replaced by raw string literals, R"()"
    • uses "auto" for iterators, new expressions, or cast expressions
    • replaced integer literals cast to bool with true or false
    • uses emplace_back instead of push_back on vectors, deques, and lists
    • uses nullptr instead of 0 or NULL
    • replaces typedefs with using
    • converted constructors member initialization with default member initializers
    • uses override and removes virtual where applicable
  • We broke ROOT 5 compatibility with versions newer than v.3.1.3.2 (leaping lion)

• Documentation

  • Ryan updated some documentation for TGRSIOptions and TGRSIint
  • Fixed ErrorReport.sh script, this script is now also reference in our CONTRIBUTING.md which is shown when creating a new issue

Leaping Lion

Last version that works with ROOT 5!

• The analysis options are now written to the root files, and read at the start of grsisort. Commandline options overwrite anything in the analysis options that were read from file.
• This also required some changes to the argument parser:
  • Moved the definition of the output streamer into a (new) source file.
  • Created two different versions of the member function parse, one takes the original int argc, char** argv as arguments, and puts any unknown flags (and their arguments) into a vector of strings. The second one takes that vector of strings as argument and does throw exceptions if unknown flags are encountered.
• Moved the stopwatch to grsisort.cxx itself, this eliminated the double "bye.bye" message and guarantees printing the message after the last command prompt.
• Added multiple axes and BG on/off to TBGSubtraction.
• Updated network packet plot in AnalyzeDataLoss.

current

v3.1.2.0