From d09f49d6150c91f15e314e2ff221278b4ba69048 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Alejandro=20S=C3=A1nchez=20Castillo?=
 <asanchezcastillo@ugr.es>
Date: Fri, 17 Jan 2025 07:44:06 -0600
Subject: [PATCH 1/4] Change type pmtana::Waveform_t to raw::OpDetWaveform for
 OpHitFinder algorithms

---
 larana/OpticalDetector/OpHitFinder/AlgoCFD.cxx           | 2 +-
 larana/OpticalDetector/OpHitFinder/AlgoCFD.h             | 2 +-
 larana/OpticalDetector/OpHitFinder/AlgoFixedWindow.cxx   | 2 +-
 larana/OpticalDetector/OpHitFinder/AlgoFixedWindow.h     | 2 +-
 larana/OpticalDetector/OpHitFinder/AlgoSiPM.cxx          | 2 +-
 larana/OpticalDetector/OpHitFinder/AlgoSiPM.h            | 2 +-
 larana/OpticalDetector/OpHitFinder/AlgoSlidingWindow.cxx | 2 +-
 larana/OpticalDetector/OpHitFinder/AlgoSlidingWindow.h   | 2 +-
 larana/OpticalDetector/OpHitFinder/AlgoThreshold.cxx     | 2 +-
 larana/OpticalDetector/OpHitFinder/AlgoThreshold.h       | 2 +-
 larana/OpticalDetector/OpHitFinder/PMTPulseRecoBase.cxx  | 2 +-
 larana/OpticalDetector/OpHitFinder/PMTPulseRecoBase.h    | 5 +++--
 larana/OpticalDetector/OpHitFinder/PulseRecoManager.cxx  | 2 +-
 larana/OpticalDetector/OpHitFinder/PulseRecoManager.h    | 3 ++-
 14 files changed, 17 insertions(+), 15 deletions(-)

diff --git a/larana/OpticalDetector/OpHitFinder/AlgoCFD.cxx b/larana/OpticalDetector/OpHitFinder/AlgoCFD.cxx
index f244e6f8..af41a31a 100644
--- a/larana/OpticalDetector/OpHitFinder/AlgoCFD.cxx
+++ b/larana/OpticalDetector/OpHitFinder/AlgoCFD.cxx
@@ -48,7 +48,7 @@ namespace pmtana {
   }
 
   //***************************************************************
-  bool AlgoCFD::RecoPulse(const pmtana::Waveform_t& wf,
+  bool AlgoCFD::RecoPulse(const raw::OpDetWaveform& wf,
                           const pmtana::PedestalMean_t& mean_v,
                           const pmtana::PedestalSigma_t& sigma_v)
   //***************************************************************
diff --git a/larana/OpticalDetector/OpHitFinder/AlgoCFD.h b/larana/OpticalDetector/OpHitFinder/AlgoCFD.h
index 02206ef3..bbac5921 100644
--- a/larana/OpticalDetector/OpHitFinder/AlgoCFD.h
+++ b/larana/OpticalDetector/OpHitFinder/AlgoCFD.h
@@ -50,7 +50,7 @@ namespace pmtana {
 
   protected:
     /// Implementation of AlgoCFD::reco() method
-    bool RecoPulse(const pmtana::Waveform_t&,
+    bool RecoPulse(const raw::OpDetWaveform&,
                    const pmtana::PedestalMean_t&,
                    const pmtana::PedestalSigma_t&);
 
diff --git a/larana/OpticalDetector/OpHitFinder/AlgoFixedWindow.cxx b/larana/OpticalDetector/OpHitFinder/AlgoFixedWindow.cxx
index d6be6d14..68df0e3f 100644
--- a/larana/OpticalDetector/OpHitFinder/AlgoFixedWindow.cxx
+++ b/larana/OpticalDetector/OpHitFinder/AlgoFixedWindow.cxx
@@ -49,7 +49,7 @@ namespace pmtana {
   }
 
   //***************************************************************
-  bool AlgoFixedWindow::RecoPulse(const Waveform_t& wf,
+  bool AlgoFixedWindow::RecoPulse(const raw::OpDetWaveform& wf,
                                   const PedestalMean_t& mean_v,
                                   const PedestalSigma_t& sigma_v)
   //***************************************************************
diff --git a/larana/OpticalDetector/OpHitFinder/AlgoFixedWindow.h b/larana/OpticalDetector/OpHitFinder/AlgoFixedWindow.h
index 8b4b9009..60e36494 100644
--- a/larana/OpticalDetector/OpHitFinder/AlgoFixedWindow.h
+++ b/larana/OpticalDetector/OpHitFinder/AlgoFixedWindow.h
@@ -52,7 +52,7 @@ namespace pmtana {
 
   protected:
     /// Implementation of AlgoFixedWindow::reco() method
-    bool RecoPulse(const pmtana::Waveform_t&,
+    bool RecoPulse(const raw::OpDetWaveform&,
                    const pmtana::PedestalMean_t&,
                    const pmtana::PedestalSigma_t&);
 
diff --git a/larana/OpticalDetector/OpHitFinder/AlgoSiPM.cxx b/larana/OpticalDetector/OpHitFinder/AlgoSiPM.cxx
index ff001e24..e41a684c 100644
--- a/larana/OpticalDetector/OpHitFinder/AlgoSiPM.cxx
+++ b/larana/OpticalDetector/OpHitFinder/AlgoSiPM.cxx
@@ -34,7 +34,7 @@ namespace pmtana {
   }
 
   //---------------------------------------------------------------------------
-  bool AlgoSiPM::RecoPulse(const pmtana::Waveform_t& wf,
+  bool AlgoSiPM::RecoPulse(const raw::OpDetWaveform& wf,
                            const pmtana::PedestalMean_t& ped_mean,
                            const pmtana::PedestalSigma_t& ped_rms)
   {
diff --git a/larana/OpticalDetector/OpHitFinder/AlgoSiPM.h b/larana/OpticalDetector/OpHitFinder/AlgoSiPM.h
index c3666ffb..33f90068 100644
--- a/larana/OpticalDetector/OpHitFinder/AlgoSiPM.h
+++ b/larana/OpticalDetector/OpHitFinder/AlgoSiPM.h
@@ -39,7 +39,7 @@ namespace pmtana {
     //      void SetNSigma(double v) {_nsigma = v;};
 
   protected:
-    bool RecoPulse(const pmtana::Waveform_t&,
+    bool RecoPulse(const raw::OpDetWaveform&,
                    const pmtana::PedestalMean_t&,
                    const pmtana::PedestalSigma_t&);
 
diff --git a/larana/OpticalDetector/OpHitFinder/AlgoSlidingWindow.cxx b/larana/OpticalDetector/OpHitFinder/AlgoSlidingWindow.cxx
index 83b2fa5b..4563455b 100644
--- a/larana/OpticalDetector/OpHitFinder/AlgoSlidingWindow.cxx
+++ b/larana/OpticalDetector/OpHitFinder/AlgoSlidingWindow.cxx
@@ -298,4 +298,4 @@ namespace pmtana {
     return true;
   }
 
-}
+}
\ No newline at end of file
diff --git a/larana/OpticalDetector/OpHitFinder/AlgoSlidingWindow.h b/larana/OpticalDetector/OpHitFinder/AlgoSlidingWindow.h
index 11fd39d8..47e38199 100644
--- a/larana/OpticalDetector/OpHitFinder/AlgoSlidingWindow.h
+++ b/larana/OpticalDetector/OpHitFinder/AlgoSlidingWindow.h
@@ -69,4 +69,4 @@ namespace pmtana {
 }
 #endif
 
-/** @} */ // end of doxygen group
+/** @} */ // end of doxygen group
\ No newline at end of file
diff --git a/larana/OpticalDetector/OpHitFinder/AlgoThreshold.cxx b/larana/OpticalDetector/OpHitFinder/AlgoThreshold.cxx
index 1789f24d..d9a2eac4 100644
--- a/larana/OpticalDetector/OpHitFinder/AlgoThreshold.cxx
+++ b/larana/OpticalDetector/OpHitFinder/AlgoThreshold.cxx
@@ -49,7 +49,7 @@ namespace pmtana {
   }
 
   //***************************************************************
-  bool AlgoThreshold::RecoPulse(const Waveform_t& wf,
+  bool AlgoThreshold::RecoPulse(const raw::OpDetWaveform& wf,
                                 const PedestalMean_t& mean_v,
                                 const PedestalSigma_t& sigma_v)
   //***************************************************************
diff --git a/larana/OpticalDetector/OpHitFinder/AlgoThreshold.h b/larana/OpticalDetector/OpHitFinder/AlgoThreshold.h
index dac6a587..42b70c0a 100644
--- a/larana/OpticalDetector/OpHitFinder/AlgoThreshold.h
+++ b/larana/OpticalDetector/OpHitFinder/AlgoThreshold.h
@@ -50,7 +50,7 @@ namespace pmtana {
 
   protected:
     /// Implementation of AlgoThreshold::reco() method
-    bool RecoPulse(const pmtana::Waveform_t& wf,
+    bool RecoPulse(const raw::OpDetWaveform& wf,
                    const pmtana::PedestalMean_t& mean_v,
                    const pmtana::PedestalSigma_t& sigma_v);
 
diff --git a/larana/OpticalDetector/OpHitFinder/PMTPulseRecoBase.cxx b/larana/OpticalDetector/OpHitFinder/PMTPulseRecoBase.cxx
index 32ae9929..5bea9ee5 100644
--- a/larana/OpticalDetector/OpHitFinder/PMTPulseRecoBase.cxx
+++ b/larana/OpticalDetector/OpHitFinder/PMTPulseRecoBase.cxx
@@ -33,7 +33,7 @@ namespace pmtana {
   }
 
   //******************************************************************
-  bool PMTPulseRecoBase::Reconstruct(const Waveform_t& wf,
+  bool PMTPulseRecoBase::Reconstruct(const raw::OpDetWaveform& wf,
                                      const PedestalMean_t& mean_v,
                                      const PedestalSigma_t& sigma_v)
   //******************************************************************
diff --git a/larana/OpticalDetector/OpHitFinder/PMTPulseRecoBase.h b/larana/OpticalDetector/OpHitFinder/PMTPulseRecoBase.h
index 759d7a0f..fcddcd7e 100644
--- a/larana/OpticalDetector/OpHitFinder/PMTPulseRecoBase.h
+++ b/larana/OpticalDetector/OpHitFinder/PMTPulseRecoBase.h
@@ -21,6 +21,7 @@
 
 #include "OpticalRecoTypes.h"
 #include "larana/OpticalDetector/OpHitFinder/RiseTimeTools/RiseTimeCalculatorBase.h"
+#include "lardataobj/RawData/OpDetWaveform.h"
 
 #include <memory>
 
@@ -84,7 +85,7 @@ namespace pmtana {
     /** A core method: this executes the algorithm and stores reconstructed parameters
       in the pulse_param struct object.
     */
-    bool Reconstruct(const pmtana::Waveform_t&,
+    bool Reconstruct(const raw::OpDetWaveform&,
                      const pmtana::PedestalMean_t&,
                      const pmtana::PedestalSigma_t&);
 
@@ -108,7 +109,7 @@ namespace pmtana {
     bool _status;
 
   protected:
-    virtual bool RecoPulse(const pmtana::Waveform_t&,
+    virtual bool RecoPulse(const raw::OpDetWaveform&,
                            const pmtana::PedestalMean_t&,
                            const pmtana::PedestalSigma_t&) = 0;
 
diff --git a/larana/OpticalDetector/OpHitFinder/PulseRecoManager.cxx b/larana/OpticalDetector/OpHitFinder/PulseRecoManager.cxx
index 1517f6b4..bf7ea60a 100644
--- a/larana/OpticalDetector/OpHitFinder/PulseRecoManager.cxx
+++ b/larana/OpticalDetector/OpHitFinder/PulseRecoManager.cxx
@@ -38,7 +38,7 @@ namespace pmtana {
   }
 
   //**********************************************************************
-  bool PulseRecoManager::Reconstruct(const pmtana::Waveform_t& wf) const
+  bool PulseRecoManager::Reconstruct(const raw::OpDetWaveform& wf) const
   //**********************************************************************
   {
     if (_reco_algo_v.empty() && !_ped_algo)
diff --git a/larana/OpticalDetector/OpHitFinder/PulseRecoManager.h b/larana/OpticalDetector/OpHitFinder/PulseRecoManager.h
index 60e9171a..a8027cc4 100644
--- a/larana/OpticalDetector/OpHitFinder/PulseRecoManager.h
+++ b/larana/OpticalDetector/OpHitFinder/PulseRecoManager.h
@@ -16,6 +16,7 @@
 #define PULSERECOMANAGER_H
 
 #include "larana/OpticalDetector/OpHitFinder/OpticalRecoTypes.h"
+#include "lardataobj/RawData/OpDetWaveform.h"
 
 #include <vector>
 
@@ -37,7 +38,7 @@ namespace pmtana {
     PulseRecoManager();
 
     /// Implementation of ana_base::analyze method
-    bool Reconstruct(const pmtana::Waveform_t&) const;
+    bool Reconstruct(const raw::OpDetWaveform&) const;
 
     /// A method to set pulse reconstruction algorithm
     void AddRecoAlgo(pmtana::PMTPulseRecoBase* algo, PMTPedestalBase* ped_algo = nullptr);

From 885fe73bc59bc9a959334f6ef5f9ff2a0c6aba09 Mon Sep 17 00:00:00 2001
From: Lynn Garren <garren@fnal.gov>
Date: Tue, 29 Oct 2024 14:32:28 -0500
Subject: [PATCH 2/4] larana v09_15_15 for larsoft v09_93_01

---
 CMakeLists.txt | 1 +
 1 file changed, 1 insertion(+)

diff --git a/CMakeLists.txt b/CMakeLists.txt
index 9fbeb59f..423f6f6c 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -11,6 +11,7 @@ cmake_minimum_required(VERSION 3.20 FATAL_ERROR)
 find_package(cetmodules 3.12.00 REQUIRED)
 project(larana VERSION 10.00.05 LANGUAGES CXX)
 
+
 # cetbuildtools contains our cmake modules
 
 include(CetCMakeEnv)

From 4a8cca33c04ef5c0b89d96d02720665aa29d90c8 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Alejandro=20S=C3=A1nchez=20Castillo?=
 <asanchezcastillo@ugr.es>
Date: Fri, 17 Jan 2025 10:42:46 -0600
Subject: [PATCH 3/4] Add individual channel threshold for ophitfinding
 algorithms

---
 larana/OpticalDetector/OpHitFinder/AlgoCFD.cxx   | 10 ++++++++++
 larana/OpticalDetector/OpHitFinder/AlgoCFD.h     |  4 ++++
 larana/OpticalDetector/OpHitFinder/AlgoSiPM.cxx  | 10 +++++++++-
 larana/OpticalDetector/OpHitFinder/AlgoSiPM.h    |  6 ++++++
 .../OpHitFinder/AlgoSlidingWindow.cxx            | 16 +++++++++++++++-
 .../OpHitFinder/AlgoSlidingWindow.h              |  9 ++++++++-
 6 files changed, 52 insertions(+), 3 deletions(-)

diff --git a/larana/OpticalDetector/OpHitFinder/AlgoCFD.cxx b/larana/OpticalDetector/OpHitFinder/AlgoCFD.cxx
index af41a31a..12d6bb4e 100644
--- a/larana/OpticalDetector/OpHitFinder/AlgoCFD.cxx
+++ b/larana/OpticalDetector/OpHitFinder/AlgoCFD.cxx
@@ -31,6 +31,8 @@ namespace pmtana {
     _D = pset.get<int>("Delay");
 
     //_number_presample = pset.get<int>   ("BaselinePreSample");
+    _peak_thresh_by_channel = pset.get<bool>("ThreshByChannel", false);
+    _peak_thresh_vector = pset.get<std::vector<double>>("PeakThreshVector", {});
     _peak_thresh = pset.get<double>("PeakThresh");
     _start_thresh = pset.get<double>("StartThresh");
     _end_thresh = pset.get<double>("EndThresh");
@@ -56,6 +58,14 @@ namespace pmtana {
 
     Reset();
 
+    if(_peak_thresh_by_channel)
+    {
+      uint ChannelNumber = wf.ChannelNumber();
+      if(ChannelNumber>=_peak_thresh_vector.size()) throw cet::exception("OpHitFinder") << "Threshold not found for channel " << ChannelNumber << "\n";
+      _peak_thresh = _peak_thresh_vector[ChannelNumber];
+    }
+
+
     std::vector<double> cfd;
     cfd.reserve(wf.size());
 
diff --git a/larana/OpticalDetector/OpHitFinder/AlgoCFD.h b/larana/OpticalDetector/OpHitFinder/AlgoCFD.h
index bbac5921..8f088ff6 100644
--- a/larana/OpticalDetector/OpHitFinder/AlgoCFD.h
+++ b/larana/OpticalDetector/OpHitFinder/AlgoCFD.h
@@ -64,6 +64,10 @@ namespace pmtana {
     double _peak_thresh;
     double _start_thresh;
     double _end_thresh;
+    //Whether to apply an individual threshold for each channel
+    bool _peak_thresh_by_channel;
+    //Vector of thresholds for each channel
+    std::vector<double> _peak_thresh_vector;
   };
 
 }
diff --git a/larana/OpticalDetector/OpHitFinder/AlgoSiPM.cxx b/larana/OpticalDetector/OpHitFinder/AlgoSiPM.cxx
index e41a684c..636426d0 100644
--- a/larana/OpticalDetector/OpHitFinder/AlgoSiPM.cxx
+++ b/larana/OpticalDetector/OpHitFinder/AlgoSiPM.cxx
@@ -14,7 +14,8 @@ namespace pmtana {
                      const std::string name)
     : PMTPulseRecoBase(name)
   {
-
+    _adc_thres_by_channel = pset.get<bool>("ADCThresholdByChannel", false);
+    _adc_thres_vector = pset.get<std::vector<float>>("ADCThresVector", {});
     _adc_thres = pset.get<float>("ADCThreshold");
     _min_width = pset.get<float>("MinWidth");
     _2nd_thres = pset.get<float>("SecondThreshold");
@@ -49,6 +50,13 @@ namespace pmtana {
       ped_mean
         .front(); //Switch pedestal definition to incoroprate pedestal finder - K.S. 04/18/2019
 
+    if(_adc_thres_by_channel)
+    {
+      uint ChannelNumber = wf.ChannelNumber();
+      if(ChannelNumber>=_adc_thres_vector.size()) throw cet::exception("OpHitFinder") << "ADC Threshold not found for channel " << ChannelNumber << "\n";
+      _adc_thres = _adc_thres_vector[ChannelNumber];
+    }
+
     double threshold = _adc_thres;
     threshold += pedestal;
     double pre_threshold = _2nd_thres;
diff --git a/larana/OpticalDetector/OpHitFinder/AlgoSiPM.h b/larana/OpticalDetector/OpHitFinder/AlgoSiPM.h
index 33f90068..bcffbb85 100644
--- a/larana/OpticalDetector/OpHitFinder/AlgoSiPM.h
+++ b/larana/OpticalDetector/OpHitFinder/AlgoSiPM.h
@@ -43,6 +43,9 @@ namespace pmtana {
                    const pmtana::PedestalMean_t&,
                    const pmtana::PedestalSigma_t&);
 
+    //Whether to apply an individual threshold for each channel
+    bool _adc_thres_by_channel;
+
     // A variable holder for a user-defined absolute ADC threshold value
     double _adc_thres;
 
@@ -55,6 +58,9 @@ namespace pmtana {
     // Use this pedestal instead of the one given by the pedestal algorithm
     double _pedestal;
 
+    // Vector of ADCThreshold to be used for each channel
+    std::vector<float> _adc_thres_vector;
+
     // A variable holder for a multiplicative factor for the pedestal
     // standard deviation to define the threshold
     //      double _nsigma;
diff --git a/larana/OpticalDetector/OpHitFinder/AlgoSlidingWindow.cxx b/larana/OpticalDetector/OpHitFinder/AlgoSlidingWindow.cxx
index 4563455b..d7931ddc 100644
--- a/larana/OpticalDetector/OpHitFinder/AlgoSlidingWindow.cxx
+++ b/larana/OpticalDetector/OpHitFinder/AlgoSlidingWindow.cxx
@@ -26,6 +26,10 @@ namespace pmtana {
   {
     _positive = pset.get<bool>("PositivePolarity", true);
 
+    _adc_thres_by_channel = pset.get<bool>("ADCThresholdByChannel", false);
+
+    _adc_thres_vector = pset.get<std::vector<float>>("ADCThresVector", {});
+    
     _adc_thres = pset.get<float>("ADCThreshold");
 
     _tail_adc_thres = pset.get<float>("TailADCThreshold", _adc_thres);
@@ -59,7 +63,7 @@ namespace pmtana {
   }
 
   //***************************************************************
-  bool AlgoSlidingWindow::RecoPulse(const pmtana::Waveform_t& wf,
+  bool AlgoSlidingWindow::RecoPulse(const raw::OpDetWaveform& wf,
                                     const pmtana::PedestalMean_t& mean_v,
                                     const pmtana::PedestalSigma_t& sigma_v)
   //***************************************************************
@@ -87,6 +91,16 @@ namespace pmtana {
 
     Reset();
 
+
+    if(_adc_thres_by_channel)
+    {
+      uint ChannelNumber = wf.ChannelNumber();
+      if(ChannelNumber>=_adc_thres_vector.size()) throw cet::exception("OpHitFinder") << "ADC Threshold not found for channel " << ChannelNumber << "\n";
+      _adc_thres = _adc_thres_vector[ChannelNumber];
+    }
+
+    std::cout << " The channel number is " << wf.ChannelNumber() <<  " and the adc threshold is " << _adc_thres << std::endl;
+
     for (size_t i = 0; i < wf.size(); ++i) {
 
       double value = 0.;
diff --git a/larana/OpticalDetector/OpHitFinder/AlgoSlidingWindow.h b/larana/OpticalDetector/OpHitFinder/AlgoSlidingWindow.h
index 47e38199..e1a7701d 100644
--- a/larana/OpticalDetector/OpHitFinder/AlgoSlidingWindow.h
+++ b/larana/OpticalDetector/OpHitFinder/AlgoSlidingWindow.h
@@ -21,6 +21,7 @@ namespace fhicl {
 }
 
 #include "larana/OpticalDetector/OpHitFinder/OpticalRecoTypes.h"
+#include "lardataobj/RawData/OpDetWaveform.h"
 
 #include <string>
 
@@ -47,13 +48,16 @@ namespace pmtana {
 
   protected:
     /// Implementation of AlgoSlidingWindow::reco() method
-    bool RecoPulse(const pmtana::Waveform_t&,
+    bool RecoPulse(const raw::OpDetWaveform&,
                    const pmtana::PedestalMean_t&,
                    const pmtana::PedestalSigma_t&);
 
     /// A boolean to set waveform positive/negative polarity
     bool _positive;
 
+    //Whether to apply an individual threshold for each channel
+    bool _adc_thres_by_channel;
+
     /// A variable holder for a user-defined absolute ADC threshold value
     float _adc_thres, _tail_adc_thres, _end_adc_thres;
 
@@ -64,6 +68,9 @@ namespace pmtana {
     float _nsigma, _tail_nsigma, _end_nsigma;
     bool _verbose;
     size_t _num_presample, _num_postsample;
+
+    // Vector of ADCThreshold to be used for each channel
+    std::vector<float> _adc_thres_vector;
   };
 
 }

From 9d845ccf09052408f082d422c310a358032710e5 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Alejandro=20S=C3=A1nchez=20Castillo?=
 <asanchezcastillo@ugr.es>
Date: Mon, 27 Jan 2025 08:30:27 -0600
Subject: [PATCH 4/4] Format code

---
 larana/OpticalDetector/OpHitFinder/AlgoCFD.cxx      |  8 ++++----
 larana/OpticalDetector/OpHitFinder/AlgoSiPM.cxx     |  7 ++++---
 .../OpHitFinder/AlgoSlidingWindow.cxx               | 13 +++++++------
 3 files changed, 15 insertions(+), 13 deletions(-)

diff --git a/larana/OpticalDetector/OpHitFinder/AlgoCFD.cxx b/larana/OpticalDetector/OpHitFinder/AlgoCFD.cxx
index 12d6bb4e..337ac233 100644
--- a/larana/OpticalDetector/OpHitFinder/AlgoCFD.cxx
+++ b/larana/OpticalDetector/OpHitFinder/AlgoCFD.cxx
@@ -58,14 +58,14 @@ namespace pmtana {
 
     Reset();
 
-    if(_peak_thresh_by_channel)
-    {
+    if (_peak_thresh_by_channel) {
       uint ChannelNumber = wf.ChannelNumber();
-      if(ChannelNumber>=_peak_thresh_vector.size()) throw cet::exception("OpHitFinder") << "Threshold not found for channel " << ChannelNumber << "\n";
+      if (ChannelNumber >= _peak_thresh_vector.size())
+        throw cet::exception("OpHitFinder")
+          << "Threshold not found for channel " << ChannelNumber << "\n";
       _peak_thresh = _peak_thresh_vector[ChannelNumber];
     }
 
-
     std::vector<double> cfd;
     cfd.reserve(wf.size());
 
diff --git a/larana/OpticalDetector/OpHitFinder/AlgoSiPM.cxx b/larana/OpticalDetector/OpHitFinder/AlgoSiPM.cxx
index 636426d0..d223266b 100644
--- a/larana/OpticalDetector/OpHitFinder/AlgoSiPM.cxx
+++ b/larana/OpticalDetector/OpHitFinder/AlgoSiPM.cxx
@@ -50,10 +50,11 @@ namespace pmtana {
       ped_mean
         .front(); //Switch pedestal definition to incoroprate pedestal finder - K.S. 04/18/2019
 
-    if(_adc_thres_by_channel)
-    {
+    if (_adc_thres_by_channel) {
       uint ChannelNumber = wf.ChannelNumber();
-      if(ChannelNumber>=_adc_thres_vector.size()) throw cet::exception("OpHitFinder") << "ADC Threshold not found for channel " << ChannelNumber << "\n";
+      if (ChannelNumber >= _adc_thres_vector.size())
+        throw cet::exception("OpHitFinder")
+          << "ADC Threshold not found for channel " << ChannelNumber << "\n";
       _adc_thres = _adc_thres_vector[ChannelNumber];
     }
 
diff --git a/larana/OpticalDetector/OpHitFinder/AlgoSlidingWindow.cxx b/larana/OpticalDetector/OpHitFinder/AlgoSlidingWindow.cxx
index d7931ddc..3d64f9dd 100644
--- a/larana/OpticalDetector/OpHitFinder/AlgoSlidingWindow.cxx
+++ b/larana/OpticalDetector/OpHitFinder/AlgoSlidingWindow.cxx
@@ -29,7 +29,7 @@ namespace pmtana {
     _adc_thres_by_channel = pset.get<bool>("ADCThresholdByChannel", false);
 
     _adc_thres_vector = pset.get<std::vector<float>>("ADCThresVector", {});
-    
+
     _adc_thres = pset.get<float>("ADCThreshold");
 
     _tail_adc_thres = pset.get<float>("TailADCThreshold", _adc_thres);
@@ -91,15 +91,16 @@ namespace pmtana {
 
     Reset();
 
-
-    if(_adc_thres_by_channel)
-    {
+    if (_adc_thres_by_channel) {
       uint ChannelNumber = wf.ChannelNumber();
-      if(ChannelNumber>=_adc_thres_vector.size()) throw cet::exception("OpHitFinder") << "ADC Threshold not found for channel " << ChannelNumber << "\n";
+      if (ChannelNumber >= _adc_thres_vector.size())
+        throw cet::exception("OpHitFinder")
+          << "ADC Threshold not found for channel " << ChannelNumber << "\n";
       _adc_thres = _adc_thres_vector[ChannelNumber];
     }
 
-    std::cout << " The channel number is " << wf.ChannelNumber() <<  " and the adc threshold is " << _adc_thres << std::endl;
+    std::cout << " The channel number is " << wf.ChannelNumber() << " and the adc threshold is "
+              << _adc_thres << std::endl;
 
     for (size_t i = 0; i < wf.size(); ++i) {