Tags

- Fixed some typos and mistakes after significant changes of v8.0.0
- Added scripts for condor job submission, under jobSubmission/. Scripts for outputTree, rawSampicData; only one run at the time or all runs in use at once.
- Adapted app and utility scripts to work in condor, tuned settings
- Improved initialize.sh
- Gitignoring all user-dependent output
- Updated source-lxplus.sh, sourcing also when in a bigbird machine
- Added list of runs in use under parameters/runsInUse.dat, for which to produce the outputTree and rawSampicData files.

This version is a rebase of the scripts, and some source code has been modified accordingly.
To see full history of commits and changes, refer to branch feature/addJsonSettings, the commits have been squashed when merging to main.

- dropping the separate repository tof-reco-settings. Now all settings are in here, under `settings/`.
-- Note that all files are gigignored, so anybody can put their settings with local paths here.
-- Only settings of common utility have to be force added.
-- See `docs/code-description` for more information.
- changed names of input and output folders, now called `midasDirectory`, `rootDirectory` (for outputTree and rawSampicData), `appOutputDirectory`. The default is to use the paths in our eos space.
- new script findSettings, that can be used alone and is used in all other app scripts.
-- After flag `-s`, no need to give full path anymore, the name of the settings file is enough at it will be searched inside `settings/`.
-- See `docs/code-description` for more information, or just the -h option.
- new script `initialize.sh`, called at the beginning of every other script.
-- Now we have some environment variables like $REPO_HOME, that can also be used in the source code with `getenv`.
-- No impact for the user.
- finished updating the scripts `findRun.sh` and `compile.sh`, no impact for user.
- updated all app scripts with the new utilities scripts above. No impact for the user, there are just more flags that can be used.
- minor updates in source code of all apps, now all of them have a `AppVerboseMode` and `AppDebugMode` that can be used to manage the printouts, and a `DisplayPlots` option.
- removed usage of cout and cerr, replaced with Logger in some apps.
- removed default geometry file from source code, always reading from settings.
- changed behavior of `createOutputTree.sh` and `batch-createOutputTree.sh`.
-- The outputTree is not recreated if already existing unless `--recreate` is parsed.
-- subruns are analyzed one at the time in sequence, fixing the non-optimal behavior of before.
- rawRootConverter is now able to handle more subruns and merge them together, if present.
- added docs/tof-reco-version.txt, where you can find the current version of the code.
-- This is used to create a subfolder in the output and prevent confusing different code versions.
-- All outputs of all apps are going to be under outputFolder/v8.0.0, with the code version being updated over time.
-- The version here is updated automatically when tagging a new code version with script `tagNewVersion.sh` (Emanuele takes care of using it).
- added placeholder for history of versions, not in use yet
- added a test/ subfolder with a simple script that can test all apps after some change is applied. Usage is extremely simple: `./test/testAllApps.sh` and it will do everything automatically.

Another test of tagNewVersion.sh

- added channel maps in easily readable format
- added special channel mapping for run 2637 (?)
- added ChannelMapping utility functions
- fixed bug in geometry, a plane was flipped
- fixed some flags in scripts to properly use the --no-compile option

- fixes in scripts, all should now run properly
- dynamically extending coincidence window to always include coincidences within 25ns

Read hits even when MIDAS event contains more than one trigger (very wrong for MCB runs, ok for local runs). Should never go in main branch, this is a special tag

- added script compile.sh, used in all other scripts (includes automatic sourcing of environment when running in lxplus)
- added script findRun.sh, for consistent searching of runs. Possibility to select the run type (local, gdaq, dog1) and the subrun. Not yet used for createOutputTree.
- fixed bug in montorDataQuality in the plot of the average waveforms 
- updated way to read and write outputTree
- added new app triggerStudies
- misc improvements

- replaced `manage-submodules.sh` with `update.sh`, which has more functionalities
- renamed executables to have `tof` at the beginning of their name, source and scripts remain unchanged
- removed concept of Gate everywhere, replaced with Trigger Timestamp
- adding reading of trigger serial word in `TofMidasEvent.h`, added Trigger Type
- fixed a bug in the creation of events, some hits might escape the loop where they are stored in signals
- removing limit on number of hits in rawRootConverter
- more plots in monitorDataQuality (midas and trigger), cleanup
- updated documentation

- included all the apps that were being developed in branches: `analysisPrime`, `sandMuonsSelection`, `cosmicsAnalysis`. `analysisPrime` not fully working though, and it will need renaming.
- improvements in `investigateBaselines` and `investigateSingleHist`
- improved geometry 
- fixed all CMakeLists
- changes to work in fedora: removed all [] when using vectors, using at()
- safety conditions for linear interpolation out of range results
- small fixes in `rawRootConverter`
- fix: correctly updating all FitParameters so that they are correct in the outputTree
- initializing more variables in classes to allow easier out-of-context use
- added fit plotting when using `displayWaveform`
- look for new naming of tof local files in scripts

Added search for new naming convention 'tof_*_*.daq.mid.gz' in all scripts that read MIDAS files.

Minor improvements. Main one: change manage-submodules to hopefully work better with old git versions.

- Added new apps by Raphael for baseline and single hit studies. They come with libraries. Already properly included in cmake structure
- Added trigger gate timestamps to TofHit and in outputTree.

Now the software is meant to run on lxplus9 (the new default). This means that `source-lxplus.sh` loads an image for el9. 
You can still use lxplus7, but HTCondor jobs need a different configuration than the one proposed in the template in `condor-job-submission.md`.

This version is the same as 5.3.0, just giving it a new name to make the change clear.

IMPORTANT: Now sourcing lxplus9 environment, not lxplus7 anymore.
Changed scripts to run properly in HTCondor considering this and the new containerization methods. In particular, using awk instead of jq to read json files from bash scripts.
Improved scripts to handle 'file not found' and clean repositories. 
Updated documentation and template script in condor.

Added functionality to read the subruns. 
It looks for all filename formats. It simply loads in an array all the files containing a certain run number and then iterates over them, finally merging into one root file with hadd.

Improved Debug and Verbose options for TofSignal, set through EventCreateSignals.
Cleaned up comments and syntax in some cases. No changes to functionalities.

- changed scripts in order to be able to run `batch-createOutputTree` as a HTCondor job
- added documentation and an example to run batch jobs
- fixed names of executables

- tofUtils has been updated to be aligned to ND280. This includes utility functions, maps, structs to handle the TTree
- structs to handle the outputTree and the variables in it have been changed or improved. Documentation added in docs/code-description.md
- added documentation about how to use condor to submit grid jobs in lxplus
- changed way CfTime is computed, now by default it tries with the fit and then with the linear interpolation, no need to call them separately. What was used can be deduced by looking at HitCfSuccess and HitCfSuccess, refer to the docs
- fixing bugs along the way, including for variables SignalBar and SignalPlane
- removed outdated root scripts

- improved compareTofRuns, now plotting all variables
- added HitCfTime variables to HitStruct and in output tree, used for rising time

MIDAS ODB settings are read directly from the MIDAS file, both if it is JSON or XML format. 
We don't use anymore the .json file that was created by the DAQ.