Trapping correction module and app by sophieehaight · Pull Request #184 · cositools/nuclearizer

sophieehaight · 2026-07-24T17:54:22Z

Contains a new module for applying depth-based charge trapping correction to individual hit energies along with modules with GUI options and GUI expos. The branch also includes an app for characterizing trapping with Cs-137 data. The trapping correction module requires a csv parameter file as input:
detector_0_trapping_parameters.csv
This file can also be found in resource/dee

fhagemann · 2026-07-28T21:23:43Z

This is what I'm getting if I'm plotting the content of the file (parsing the base CCE curve, and applying the calibration parameters from the first line):

fhagemann

It looks like the units of depth_val (mm) and m_Depths (cm) do not match..

fhagemann · 2026-07-30T00:28:34Z

I looked at applying the inverse of the charge trapping correction to the DEE, and with the latest file, I would say that it gives reasonable results.

fhagemann · 2026-08-14T21:51:34Z

Can we also remove HasCalibratedTiming() == true from the trapping app and replace by something like HasFastTiming() == true && HasNearestNeighbor() == false (in an effort to completely get rid of HasCalibratedTiming)?

fhagemann

Here is my feedback from just looking at the code.
I will also try to compile and run both the module and the app to provide more feedback on that as well! :)

fhagemann · 2026-08-17T20:01:42Z

The example file in resource/dee and the results after applying the inverse charge trapping in the DEE looks reasonable:

codecov-commenter · 2026-08-17T23:47:52Z

Welcome to Codecov 🎉

Once you merge this PR into your default branch, you're all set! Codecov will compare coverage reports and display results in all future pull requests.

ℹ️ You can also turn on project coverage checks and project coverage reporting on Pull Request comment

Thanks for integrating Codecov - We've got you covered ☂️

fhagemann

Final code-style review, will give it a run to see that it compiles.
But then this should be good to go (tackling reading trapping parameters for multiple detectors in a follow-up PR)

fhagemann · 2026-08-24T19:18:32Z

+  m_Name = "Trapping Correction"; // - correcting energies for charge trapping (by Sophie);
+
+  // Set the XML tag --- has to be unique --- no spaces allowed
+  m_XmlTag = "TrappingCorrection";


Let's be consistent with XML tag naming here (see #193)

Suggested change

m_XmlTag = "TrappingCorrection";

m_XmlTag = "XmlTagTrappingCorrection";

I'm actually not seeing this convention in the depth or energy calibration modules? It looks like the XML tag is just the name of the module

This is tackled in #197 once it is merged

Once I change the name of the xml tag, nuclearizer can no longer recognize the module. Is there somewhere else in assembly I need to update the xml tag? I was looking but I couldn't find anything

This will affect reading in a nuclearizer config file (*.cfg). In those, you might need to update all occurences of TrappingCorrection with XmlTrappingCorrection.

So either update the .nuclearizer.cfg in your home directory, or the respective .cfg that you load when running nuclearizer.

fhagemann · 2026-08-24T19:22:48Z

+    cout << "\n" << m_XmlTag << " --- " << titleLabel << " ---" << endl;
+    cout << "  Centroid (Mu)        : " << mu << " keV" << endl;
+    cout << "  Fitted Gaussian FWHM : " << fwhm << " keV" << endl;
+    cout << "  Direct Histogram FWHM: " << directFWHM << " keV" << endl;


Put this in c_Info?

I use this output to evaluate how well the trapping correction is working. If I change the verbosity to info, the comand line becomes overloaded (I believe w info from the depth cal) and nuclearizer crashes. I agree this info doesn't need to be repeated so I can change the verbosity for the following comments but I do need it read out somewhere.

I think we probably need to clean up the outputs for the info verbosity right now because right now it's outputting so much info that I can't receive the info I'm trying to get from the trapping correction.

@zoglauer maybe we can introduce the chatty verbosity from megalib also to nuclearizer, and move some of the info messages to chatty?

yeah that could be a good idea!

fhagemann

This would be good from my side. Just gathering here the open TODOs (for follow-up PRs):

Allow for a charge trapping parameters file for multiple detectors, at not just one
Think about flushing output to c_Info without overloading the output
Maybe find an alternative to Interpolate to avoid code duplication (maybe from an existing package or another module --> the depth calibration also used some sort of interpolation algorithm to interpolate the CTD-to-depth spline).

fhagemann

Some code-style and some more major comments.

One general comment:
you are using a lot of snake-case when assigning variable names, we might want to use camel-case consistently here (e.g. SimCCESortedHoles instead of sim_cce_sorted_h)

fhagemann · 2026-09-05T23:59:08Z

+    // Evaluate full function FWHM over the fit window (645 keV to 675 keV)
+    double xMinFit = 645.0;
+    double xMaxFit = 675.0;


This seems to be tailored to Cs137. Is this what we want? What if we pass data from other isotopes through MModuleTrappingCorrection?

I set it up in commits 8f30f9b, b95dc1e, and f191838 (took a couple tries to get my axes to update correctly here). I let the user define the energy of the photopeak they are tryting to fit on the nuclearizer expo. The trapping correction module then takes that input and uses it to define the Mu and min and max energies for the photopeak fits measuring resolutions pre and post trapping correction. I kept the default energy for Cs-137 as a benchmark.

fhagemann · 2026-09-21T23:46:59Z

@@ -605,7 +600,7 @@ TF1* MModuleTrappingCorrection::GeneratePhotopeakFunction()

  // Provide initial sensible guesses for a Cs137 photopeak
  PhotopeakFunction->SetParameter("Amplitude", 1000);
-  PhotopeakFunction->SetParameter("x0 (Mu)", muInitial);
+  PhotopeakFunction->SetParameter("x0 (Mu)", 661.7);
  PhotopeakFunction->SetParameter("Sigma Gauss", 2.0);
  PhotopeakFunction->SetParameter("BoverA", 0.05);
  PhotopeakFunction->SetParameter("Gamma", 0.5);
@@ -615,7 +610,7 @@ TF1* MModuleTrappingCorrection::GeneratePhotopeakFunction()

  // Set boundary limits to stabilize convergence
  PhotopeakFunction->SetParLimits(0, 1, 1e8);
-  PhotopeakFunction->SetParLimits(1, fitMin, fitMax);     // Keeps peak centered around Mu 
+  PhotopeakFunction->SetParLimits(1, 645, 675);     // Keeps peak centered around 662 keV


Your last pushes reverted back to the fixed window around 662keV.
Is this intended?

my mistake! I was testing the fit with and without the dynamic fitting window. This is fixed in 6321870

fhagemann · 2026-09-21T23:47:33Z

I've lost track. Is this ready for a final review?

fhagemann · 2026-09-21T23:48:24Z

Do you also plan to add the individual detector files to resource/calibration/COSISMEX/unit?

yes, I will do this today

fhagemann · 2026-09-25T10:59:10Z

If the last changes conclude this PR, we might want to clean up the commit history and reduce the ~100 commits to a few major commits (adding the module, adding the GUI options, adding example files, ...), as this PR changes only a handful of files and adds a handful to the resource folder.

Happy to help here!

created app to return depth dep centroid energy shift for Cs-137 data

Created charge trapping correction module with GUI options

cleaned up outputs and added a check for events with calibrated timing

Created a trapping correction expo

Added trapping parameter files for unit level as well as dummy payload and single detector files

Record a local position in depth cal to access in trapping correction

changed depth cal functions to public for use in the trapping correction

fhagemann

Comments on the Cs137 trapping app only:

fhagemann · 2026-09-26T16:42:28Z

+double g_MinCTD = -250;
+double g_MaxCTD = 250;


Is there ever a scenario where this range might no be enough?
For payload calibrations, we will have slightly higher temperatures than in unit-level calibrations, resulting in lower charge carrier mobilities, that might push the CTD out of the [-250,250] range (maybe?)

fhagemann · 2026-09-26T16:43:25Z

+  MString m_TACCalFile;
+  MString m_TACCalibrationFile;


What is the difference between TACCalFile and TACCalibrationFile?
Edit: looks like m_TACCalibrationFile is used for what used to be the TAC cut file, so this can go:

Suggested change

MString m_TACCalFile;

MString m_TACCalibrationFile;

MString m_TACCalFile;

fhagemann · 2026-09-26T16:44:03Z

+  Usage<<"         --emax:   maximum Event energy (default 700 kev)"<<endl;
+  Usage<<"         -e:   energy calibration file (.ecal)"<<endl;
+  Usage<<"         --tcal:   TAC calibration file"<<endl;
+  Usage<<"         --tcut:   TAC cut file"<<endl;


I don't think that we need TAC cut files anymore with the latest changes in #194

fhagemann · 2026-09-26T16:44:55Z

+
+    // First check if each option has sufficient arguments:
+    // Single argument
+    if ((Option == "-i") || (Option == "-o") || (Option == "--emin") || (Option == "--emax") || (Option == "--tcal") || (Option == "--tcut") || (Option == "-m") || (Option == "--ctdmin") || (Option == "--ctdmax")) {


Suggested change

if ((Option == "-i") || (Option == "-o") || (Option == "--emin") || (Option == "--emax") || (Option == "--tcal") || (Option == "--tcut") || (Option == "-m") || (Option == "--ctdmin") || (Option == "--ctdmax")) {

if ((Option == "-i") || (Option == "-o") || (Option == "--emin") || (Option == "--emax") || (Option == "--tcal") || (Option == "-m") || (Option == "--ctdmin") || (Option == "--ctdmax")) {

fhagemann · 2026-09-26T16:45:15Z

+    if (Option == "--tcut") {
+      m_TACCalibrationFile = argv[++i];
+      cout<<"Accepting file name: "<<m_TACCalibrationFile<<endl;
+    } 
+


Suggested change

if (Option == "--tcut") {

m_TACCalibrationFile = argv[++i];

cout<<"Accepting file name: "<<m_TACCalibrationFile<<endl;

}

fhagemann · 2026-09-26T16:53:02Z

+    cout << "Creating energy calibrator" << endl;
+    EnergyCalibrator = new MModuleEnergyCalibration();
+    EnergyCalibrator->SetFileName(m_EcalFile);
+    S->SetModule(EnergyCalibrator, MNumber);
+    ++MNumber;


Do you require any sort of energy (slow) thresholds to be set here?

fhagemann · 2026-09-26T16:55:32Z

+    unsigned int MNumber = 0;
+    cout << "Creating HDF5 loader" << endl;
+    Loader = new MModuleLoaderMeasurementsHDF();
+    Loader->SetFileNameStripMap(m_StripMapFile);
+    Loader->SetFileName(File);
+    Loader->SetLoadContinuationFiles(m_ContinueHDF5);
+    S->SetModule(Loader, MNumber);
+    ++MNumber;


Would it make sense to filter out nearest neighbor strip hits here?
Something like

Loader->SetIncludeNearestNeighbor(false);

or you do use them later?

fhagemann · 2026-09-26T17:01:11Z

+  PhotopeakFunction->SetParName(7, "D (Lin Slope)");
+
+  // Provide initial sensible guesses for a Cs137 photopeak
+  PhotopeakFunction->SetParameter("Amplitude", 1000);


Is the Amplitude initial guess and ranges something that would make sense to determine from the actual data? I assume this number might change if you're passing a lot of / very few files.

fhagemann · 2026-09-26T17:03:35Z

+MStripHit* TrappingCorrectionCs137::GetDominantStrip(vector<MStripHit*>& Strips, double& EnergyFraction)
+{
+  double MaxEnergy = -numeric_limits<double>::max(); 
+  double TotalEnergy = 0.0;
+  MStripHit* MaxStrip = nullptr;
+
+  // Iterate through strip hits and get the strip with highest energy
+  for (const auto SH : Strips) {
+    double Energy = SH->GetEnergy();
+    TotalEnergy += Energy;
+    if (Energy > MaxEnergy) {
+      MaxStrip = SH;
+      MaxEnergy = Energy;
+    }
+  }
+  if (TotalEnergy == 0) {
+    EnergyFraction = 0;
+  } else {
+    EnergyFraction = MaxEnergy/TotalEnergy;
+  }
+  return MaxStrip;
+}


This seems like it's an identical copy of MModuleDepthCalibration::GetDominantStrip, which is a public function, so you can probably use that here instead:

Load #include "MModuleDepthCalibration.h"

In Analyze, define (with all other modules) MModuleDepthCalibration* Depth = new MModuleDepthCalibration, maybe with a comment that you're not running the module, just using its functions here.

Call Depth->GetDominantStrip where you just have GetDominantStrip.

Remove this function here (plus its declaration in the class).

fhagemann · 2026-09-26T17:09:55Z

+  signal(SIGINT, CatchSignal);
+
+  // Initialize global MEGALIB variables, especially mgui, etc.
+  MGlobal::Initialize("Standalone", "a standalone example program");


You could be more explicit here:

Suggested change

MGlobal::Initialize("Standalone", "a standalone example program");

MGlobal::Initialize("TrappingCorrectionCs137", "A standalone program to determine CTD-dependent shifts of the Cs137 peak");

or something like that.

fhagemann · 2026-09-26T17:16:38Z

+#include "MString.h"
+
+// Nuclearizer libs:
+#include "MGUIOptionsTrappingCorrection.h"


I'm currently getting an error when trying to compile this app, because MGUIOptionsTrappingCorrection.h is missing.
I guess they got lost while stashing the commits.
Could you add this file back? 😇

fhagemann

And some general comment on the file format (header lines starting with # or not)

fhagemann · 2026-09-26T17:18:10Z

@@ -0,0 +1,154 @@
+# A_HV,A_LV,B,C 
+1.0009264205609762,1.00084829470918,1.288689028046797,0.3010529785474152
+# z_depth_cm,e_CCE_HV,h_CCE_HV,e_CCE_LV,h_CCE_LV


The example files here in resource/dee and in resource/calibration are a bit inconsistent when it comes to the line defining the headers z_depth (in terms of if they should start with a # or not).

I would prefer the line to always start with a #,

fhagemann · 2026-09-26T17:18:26Z

I guess this file won't work because it doesn't start with ### 0 ?

fhagemann · 2026-09-26T17:18:50Z

@@ -0,0 +1,154 @@
+### 0
+1.0008508757266585,1.0009808031358887,1.1384578503113774,0.3538332986513531
+z_depth_cm,e_CCE_HV,h_CCE_HV,e_CCE_LV,h_CCE_LV


Here and elsewhere in resource/calibration:

Suggested change

z_depth_cm,e_CCE_HV,h_CCE_HV,e_CCE_LV,h_CCE_LV

# z_depth_cm,e_CCE_HV,h_CCE_HV,e_CCE_LV,h_CCE_LV

fhagemann · 2026-09-26T17:20:06Z

+    // Skip text column headers 
+    if (Line.BeginsWith("z_depth")) continue;


This could go if we force the header lines to start with #.
Or is there any reason you chose not to?

Created header file missing in previous commit

troubleshooting trapping app

3aee0c3

sophieehaight requested review from ckierans and fhagemann July 24, 2026 17:54

sophieehaight marked this pull request as ready for review July 24, 2026 17:56

fhagemann reviewed Jul 24, 2026

View reviewed changes

Comment thread apps/TrappingCorrectionCs137.cxx Outdated

fhagemann reviewed Jul 24, 2026

View reviewed changes

Comment thread src/MModuleTrappingCorrection.cxx Outdated

fhagemann reviewed Jul 28, 2026

View reviewed changes

Comment thread include/MModuleTrappingCorrection.h Outdated

fhagemann reviewed Jul 28, 2026

View reviewed changes

Comment thread resource/dee/dummy_trapping_parameters_singledetector.csv

fhagemann requested changes Jul 28, 2026

View reviewed changes

Comment thread src/MModuleTrappingCorrection.cxx Outdated

Comment thread src/MModuleTrappingCorrection.cxx Outdated

Comment thread src/MModuleTrappingCorrection.cxx Outdated

fhagemann reviewed Jul 30, 2026

View reviewed changes

Comment thread src/MModuleTrappingCorrection.cxx Outdated

This was referenced Aug 4, 2026

FIX: Assign correct DetIDs to strip detectors when loading detector dimensions #182

Merged

ADD: Inverse charge trapping for the DEE #187

Draft

fhagemann reviewed Aug 7, 2026

View reviewed changes

Comment thread src/MModuleTrappingCorrection.cxx Outdated

fhagemann reviewed Aug 10, 2026

View reviewed changes

Comment thread src/MModuleTrappingCorrection.cxx Outdated

cositools deleted a comment from codecov-commenter Aug 17, 2026

fhagemann reviewed Aug 17, 2026

View reviewed changes

fhagemann mentioned this pull request Aug 17, 2026

StripEnergyThresholdFinder for per-strip slow and fast threshold extraction with diagnostics #166

Open

fhagemann reviewed Aug 18, 2026

View reviewed changes

Comment thread src/MModuleTrappingCorrection.cxx Outdated

fhagemann reviewed Aug 18, 2026

View reviewed changes

Comment thread src/MGUIOptionsLoaderMeasurementsHDF.cxx

fhagemann linked an issue Aug 18, 2026 that may be closed by this pull request

Implement Charge Trapping correction #41

Open

fhagemann mentioned this pull request Aug 18, 2026

Implement Charge Trapping correction #41

Open

fhagemann reviewed Aug 24, 2026

View reviewed changes

fhagemann approved these changes Aug 25, 2026

View reviewed changes

fhagemann reviewed Sep 6, 2026

View reviewed changes

fhagemann reviewed Sep 21, 2026

View reviewed changes

sophieehaight added 7 commits September 25, 2026 14:05

Create TrappingCorrectionCs137.cxx

dfddc6b

created app to return depth dep centroid energy shift for Cs-137 data

Created trapping correction module

0ffc58f

Created charge trapping correction module with GUI options

Update TrappingCorrectionAm241.cxx

5d5f49d

cleaned up outputs and added a check for events with calibrated timing

Created trapping correction expo

4da4f5c

Created a trapping correction expo

Added trapping parameter files

322fbb3

Added trapping parameter files for unit level as well as dummy payload and single detector files

added local position

c852c22

Record a local position in depth cal to access in trapping correction

Changed depth functions to public

4aba2dc

changed depth cal functions to public for use in the trapping correction

sophieehaight force-pushed the trapping_correction_branch branch from 33d2a05 to 4aba2dc Compare September 25, 2026 21:43

fhagemann reviewed Sep 26, 2026

View reviewed changes

fhagemann requested changes Sep 26, 2026

View reviewed changes

fhagemann reviewed Sep 26, 2026

View reviewed changes

Create MGUIOptionsTrappingCorrection.h

ba643dc

Created header file missing in previous commit

sophieehaight force-pushed the trapping_correction_branch branch from 5809849 to ba643dc Compare September 26, 2026 23:36

	m_XmlTag = "TrappingCorrection";
	m_XmlTag = "XmlTagTrappingCorrection";

	MString m_TACCalFile;
	MString m_TACCalibrationFile;
	MString m_TACCalFile;

	if ((Option == "-i") \|\| (Option == "-o") \|\| (Option == "--emin") \|\| (Option == "--emax") \|\| (Option == "--tcal") \|\| (Option == "--tcut") \|\| (Option == "-m") \|\| (Option == "--ctdmin") \|\| (Option == "--ctdmax")) {
	if ((Option == "-i") \|\| (Option == "-o") \|\| (Option == "--emin") \|\| (Option == "--emax") \|\| (Option == "--tcal") \|\| (Option == "-m") \|\| (Option == "--ctdmin") \|\| (Option == "--ctdmax")) {

	MGlobal::Initialize("Standalone", "a standalone example program");
	MGlobal::Initialize("TrappingCorrectionCs137", "A standalone program to determine CTD-dependent shifts of the Cs137 peak");

	z_depth_cm,e_CCE_HV,h_CCE_HV,e_CCE_LV,h_CCE_LV
	# z_depth_cm,e_CCE_HV,h_CCE_HV,e_CCE_LV,h_CCE_LV

		// Skip text column headers
		if (Line.BeginsWith("z_depth")) continue;

Conversation

sophieehaight commented Jul 24, 2026

Uh oh!

Uh oh!

Uh oh!

Uh oh!

Uh oh!

fhagemann commented Jul 28, 2026 • edited Loading Uh oh! There was an error while loading. Please reload this page.

Uh oh!

Uh oh!

fhagemann left a comment

Choose a reason for hiding this comment

Uh oh!

Uh oh!

Uh oh!

Uh oh!

fhagemann commented Jul 30, 2026 • edited Loading Uh oh! There was an error while loading. Please reload this page.

Uh oh!

Uh oh!

Uh oh!

Uh oh!

Uh oh!

fhagemann commented Aug 14, 2026

Uh oh!

fhagemann left a comment

Choose a reason for hiding this comment

Uh oh!

Uh oh!

Uh oh!

Uh oh!

Uh oh!

Uh oh!

Uh oh!

Uh oh!

Uh oh!

Uh oh!

Uh oh!

fhagemann commented Aug 17, 2026

Uh oh!

codecov-commenter commented Aug 17, 2026

Welcome to Codecov 🎉

Uh oh!

Uh oh!

Uh oh!

fhagemann left a comment

Choose a reason for hiding this comment

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Uh oh!

Uh oh!

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Uh oh!

Uh oh!

fhagemann left a comment • edited by sophieehaight Loading Uh oh! There was an error while loading. Please reload this page.

Uh oh!

Choose a reason for hiding this comment

Uh oh!

fhagemann left a comment

Choose a reason for hiding this comment

Uh oh!

Uh oh!

fhagemann commented Jul 28, 2026 •

edited

Loading

fhagemann commented Jul 30, 2026 •

edited

Loading

fhagemann left a comment •

edited by sophieehaight

Loading