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Rcnp analysis branch#262

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anthoak13 wants to merge 107 commits intoATTPC:developfrom
RealAurio:RCNPAnalysisBranch
Draft

Rcnp analysis branch#262
anthoak13 wants to merge 107 commits intoATTPC:developfrom
RealAurio:RCNPAnalysisBranch

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…TTPC. Also fixed the padplane-projected hits issue by adding a charge threshold...
…tPatternEvent to the GetModifiedTrack method since it may be useful too.
…make sense to keep in the base class. Also fixed some serious bugs that I found while actually implementing a fitter class in the braggCurveFitter feature branch.
…ber to keep track of the name of the ELossModel.
… in order to implement this, but it was only actually implemented for AtPatternLine.
…nimum range value. If particle has stopped before reaching that range, 0s are added up to that range. This is needed in the case of the Bragg curve fitter so that if the estimated kinetic energy is less than real value, bins with ELoss = 0 are added, which would be compared with the experimental non-zero ones, thus increasing the chi2 and hopefully making the kinetic energy greater in the next iteration.
…l in order to obtain the integrated dE/dx profile over bins of given width.
…because of an infinite loop. Many fixes still needed, as well as checking results with the AtEventDisplay.
…, move contrstuctors, Clone() methods, etc...
…so, started refining some of the parameters for the fitter.
RealAurio and others added 27 commits November 17, 2025 10:43
…RCNP experiments.

Co-authored-by: zhangzc <1534485792@qq.com>
…e with the merger so that there is not GAGG data in all events in the h5 file. Ended up just using the GAGG decoder from evt and matching both files.

Co-authored-by: zhangzc <1534485792@qq.com>
… experiments. Pushing them to have them stored. Good job everyone involved in the campaign!
Co-authored-by: pemi7269 <perine.miriot@orange.fr>
…PID makes sense.

Co-authored-by: pemi7269 <perine.miriot@orange.fr>
…. Also roughly substracted the baseline from the integral of the entire trace.
…as done in the GAGG function. Implemented it to the actual Si function in this commit...
…ADC() of a generic trace returns a vector instead of an array... Some GAGGs have 257 entries, so they were not being analyzed. I drop this condition on the last commits, but when doing so I forgot to set the ADC values to the array...
* Implementation of strip class and position for calibrationv2

* Sync issues, pushing again

* Adding back in missing lines for GAGG analysis in AtPSASi.cxx
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@anthoak13 First of all, sorry for the spam.

I think it may be better to first merge the other feature branches this one is based upon first, so that it is more clear what features have been added in different commits, instead of one giant commit with way too many changes.

I would do the following pull requests first before attempting this one:

  1. fitterRefactor: This has not been merger yet, but I think the pull request is still open, but it may need changes since there were changes in develop. This is the pull request Tentative changes for new base class AtFittedTrack. #254

  2. experimentalBraggCurve: It had 1 last commit after it was merged, since I had to fix how the vertex finder is used. It is a small change that only affects the AtPatternModification and the AtBraggCurveFinder classes, so it is easy to merge I think. I just created the pull request, which is Changed the part of the code that finds the vertex. Also passed the AtPatternEvent to the GetModifiedTrack method since it may be useful too. #263

  3. driftDirectionInversion: It has some changes to the digitalization and PSA logic to allow for the case of the AT-TPC being inversed, such as the RCNP experiments and the S800 experiments. It probably needs reviewing still. Actually, I opened a pull request for this months ago, which is Implemented a way to invert the drift velocity direction inside the ATTPC. Also fixed the padplane-projected hits issue by adding a charge threshold... #258

  4. vetoBeamPads: This feature simply allows to pass the AtMap a list of beam pads, which will prevent the unpacker from reading them. Just opened the pull request Veto beam pads #264

  5. IonChamberAnalysis: Some IC analysis code that we are using in RCNP analysis. It actually does not depend on anything from this branch, so it could also be merged. I just opened the pull request Added IC analysis classes #265

  6. ENCourseMerger: This feature adds a merger class for the ENCourse daq. The pull request is ENCourseMerger #266

  7. AtMapCalibration: Finally this feature branch allows the user to pass calibration functions that may be used in AtPSA for example to give each AtHit a calibrated ELoss value. It is implemented but not really used yet, since people are still working on the analysis and calibrations. I created the pull request anyways, so that we can start iterating on it AtMapCalibration #267

* GAGG processing updates. Added GAGG map (csv, xml), and corresponding GAGG map class. Added GAGGID variables to GAGGEvent class, and made some changes to the FRIBLinkedUnpacker to store the digitizer name as a string in the generic trace object to allow this to be accessible. GAGG pulse analysis follows the same algorithm as the Si, with pre-baseline and post-baseline regions, and an energy integral window between. These windows can now be defined dynamically

* Adding timestamps for GAGG and Si. Fixed overflow issue in processing of GAGG traces

* fixed minor bugs in the Si PSA to correctly process negative traces. Several GAGG channels are saturating the ADC, so (a) detecting and accounting for when overflows happen, and (b) fitting the non-clipped part of the trace to have some estimate of the total energy

* Fitting the clipped traces is an option now

* updates to naming, flags for options to dump traces for fitting diagnostics, better fitting and reconstruction to get energy in a consistent manner

* changes suggested by Josema

* updated GAGG maps with LayerID (0 for front, 1 for back)

* clang-format changes

---------

Co-authored-by: Tim Gray <tgray30@utk.edu>
Reviewed-by: RealAurio <oirua@proton.me>
@RealAurio RealAurio force-pushed the RCNPAnalysisBranch branch from b107cbd to 1e8142e Compare May 5, 2026 15:04
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5 participants