Tags

- 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.

Fixed missing  - bar_length/2. when using LinearInterpolation

- Fixed bug in monitorDataQuality
- Initialising sample lenght and sampling rate to avoid issues when odb settings are not read
- Histogram ranges
- Fixed cable length correction to match new plane names, also moved to tofUtils / CommonUtils

Misc fixes, see the commits.

Adding more tools to analyse raw data (MIDAS format). Accommodate DAQ changes.

- Added `tofUtils`, new folder in the project. Here there are some CommonUtils that might be split in the future. Started to create enums and maps.
- Changed Plane naming convention to be the same as ND280, in a map in `CommonUtils.cxx`. Now using North and South, not Left and Right
- Changed HitEdge convention in TofHit and TofSignal. Now it's -1 or +1, according to ND280 convention: lower coordinate is -1. Each plane is different depending on how it is mounted.
- Added SignalVerboseMode and Debug, to be completed.
- Find automatically number of cores when compiling, makes it faster.

Note that from a user point of view there are no changes from v3.

- `rawRootConverter` is a renaming of `convertMidasToRoot`, with extended functionalities. Script to run available.
- scripts now can read any current data name format (local old and new, gDAQ, dog1)
- to differentiate between windows and linux runs, the scripts now have a flag --which-software (-w). Default is linux, if you read a windows file you need to parse [-w windows]. All the rest is automatically taken care of. 
- the rule based on the run number greater or smaller than 1000 has been removed everywhere
- no changes needed to tof-reco-settings

- Fixed bug in MidasInterface, in the reading of TFCC and TFCI, and fixed naming convention
- Fixed reading of banks in TofRun, now using variable ChannelIndex (0 to 15) instead of Channel (0 to 63). This was propagated everywhere.
- Added options for HitVerboseMode and HitDebugMode, useful for debugging
- Changed variable HitFebChannel to HitSampicChannel, propagated everywhere
- Improved MatchChannelToTof
- Improved scripts to accept input files having name run_0xxxx_000.gz
-

Improved printouts of errors and options VerboseMode and DebugMode, in particular in constructor of TofSignal. 
Added use of Logger in the classes.
More improvements can be made. 
tof-reco-settings updated as well, as some more options are now working.