From d05f033ffbe888534b8da5c62229798410be65a2 Mon Sep 17 00:00:00 2001
From: Kris Thielemans <k.thielemans@ucl.ac.uk>
Date: Wed, 10 Jan 2024 21:52:56 +0000
Subject: [PATCH] enable branching ratio in BinNormalisatoonWithCalibration

we were not using the radionuclide in the exam_info used for set_up, but
an (uninitialised) class radionuclide class member, therefore always defaulting
to 1 (afer writing a warning).

However, this means that images will now have a different scale.

Also remove the get/set_branching_ratio members, as they shouldn't really
be part of the normalisation object.

This therefore breaks backwards-compatibility!
---
 documentation/release_6.0.htm                 | 16 +++++++-
 .../BinNormalisationWithCalibration.h         | 12 +++---
 .../BinNormalisationWithCalibration.cxx       | 38 +++++++------------
 3 files changed, 34 insertions(+), 32 deletions(-)

diff --git a/documentation/release_6.0.htm b/documentation/release_6.0.htm
index 5221c56458..7e0660e377 100644
--- a/documentation/release_6.0.htm
+++ b/documentation/release_6.0.htm
@@ -44,7 +44,16 @@ <h2>Patch release info</h2>
     <h2> Summary for end users (also to be read by developers)</h2>
 
     <h3>Changes breaking backwards compatibility from a user-perspective</h3>
-   <ul>
+    <ul>
+      <li>
+        When using ECAT7, ECAT8, GEHDF5 or SPECT normalisation, it will
+        now take the branching ratio of the radionuclide into account, if the radionuclide
+        for the data is known (you can check with <tt>list_projdata_info</tt> and <tt>list_lm_info</tt>.
+        For instance, for F-18 this will make reconstructed images 1/0.9686 larger, but
+        the factor is larger for other radionuclides, certainly in SPECT.
+        <br>
+        This was actually already supposed to be the case in previous version, but a bug disabled it.
+        </li>
      <li>
        When parsing Interfile headers for projection data and the <tt>originating system</tt>
        is not recognised, the previous version of STIR tried to guess the scanner based on the
@@ -241,9 +250,12 @@ <h3>Backward incompatibities</h3>
         <code>virtual ListModeData::get_scanner_ptr()</code> is replaced by <code>ListModeData::get_scanner()</code>.
       </li>
       <li>
-        <code>ProjDataInfo*NoArcCorr::get_bin_for_det_pair</code> is now private.
+       <code>ProjDataInfo*NoArcCorr::get_bin_for_det_pair</code> is now private.
         Use <code>get_bin_for_det_pos_pair</code> instead.
       </li>
+      <li><code>BinNormalisatoonWithCalibration::get/set_branching_ratio</code> members have
+        been removed, as they shouldn't really be part of the normalisation object.
+      </li>
     </ul>
 
     <h3>New functionality</h3>
diff --git a/src/include/stir/recon_buildblock/BinNormalisationWithCalibration.h b/src/include/stir/recon_buildblock/BinNormalisationWithCalibration.h
index 6a0e571384..f338ef7035 100644
--- a/src/include/stir/recon_buildblock/BinNormalisationWithCalibration.h
+++ b/src/include/stir/recon_buildblock/BinNormalisationWithCalibration.h
@@ -1,7 +1,7 @@
 //
 //
 /*
-    Copyright (C) 2020-2021, University College London
+    Copyright (C) 2020-2021, 2024, University College London
     Copyright (C) 2020, National Physical Laboratory
     This file is part of STIR.
 
@@ -34,11 +34,16 @@ START_NAMESPACE_STIR
 
 /*!
   \ingroup normalisation
-This class provides the facility to use a calibration factor and (isotope) branching ratio when normalising data.
+  This class provides the facility to use a calibration factor and (isotope) branching ratio when normalising data.
   Therefore, if they are set correctly, the reconstructed image will be calibrated as well.
   
   Note that it is the responsibility of the derived classes to set the calibration factor.
   The branching ratio is obtained from the radionuclide set in \c ExamInfo (passed by set_up()).
+
+  Efficiency is computed as
+  <pre>
+  calibration_factor * branching_ratio * uncalibrated_efficiency
+  </pre>
   */
 class BinNormalisationWithCalibration : 
         public  BinNormalisation
@@ -55,10 +60,8 @@ class BinNormalisationWithCalibration :
   //! product of calibration factor etc
   float get_calib_decay_branching_ratio_factor(const Bin&) const; // TODO find a better name
   float get_calibration_factor() const override;
-  float get_branching_ratio() const;
   
   void set_calibration_factor(const float);
-  void set_radionuclide(const Radionuclide&);
   
   // needs to be implemented by derived class
   virtual float get_uncalibrated_bin_efficiency(const Bin&) const  = 0;
@@ -81,7 +84,6 @@ class BinNormalisationWithCalibration :
   //  need to be added to the parsing keywords
 //  bool use_calibration_factor; // default to true
   float calibration_factor;
-  Radionuclide radionuclide;
   //! product of various factors
   /*! computed by set_up() */
   float _calib_decay_branching_ratio;
diff --git a/src/recon_buildblock/BinNormalisationWithCalibration.cxx b/src/recon_buildblock/BinNormalisationWithCalibration.cxx
index 7e9163ae13..3895696b29 100644
--- a/src/recon_buildblock/BinNormalisationWithCalibration.cxx
+++ b/src/recon_buildblock/BinNormalisationWithCalibration.cxx
@@ -22,6 +22,8 @@
 
 #include "stir/recon_buildblock/BinNormalisationWithCalibration.h"
 #include "stir/Succeeded.h"
+#include "stir/ExamInfo.h"
+#include "stir/Radionuclide.h"
 #include "stir/warning.h"
 #include "stir/error.h"
 
@@ -39,9 +41,8 @@ void
 BinNormalisationWithCalibration::
 initialise_keymap()
 {
-  base_type::initialise_keymap();/*
-  this->parser.add_key("calibration_factor", &this->calibration_factor);
-  this->parser.add_key("branching_ratio", &this->branching_ratio);*/
+  base_type::initialise_keymap();
+  // this->parser.add_key("calibration_factor", &this->calibration_factor);
 }
 
 bool 
@@ -65,7 +66,15 @@ BinNormalisationWithCalibration::set_up(const shared_ptr<const ExamInfo>& exam_i
   if (this->calibration_factor == 1.F)
     warning("BinNormalisationWithCalibration:: calibration factor not set. I will use 1, but your data will not be calibrated.");
 
-  this->_calib_decay_branching_ratio = this->calibration_factor* this->get_branching_ratio(); //TODO: multiply by decay
+  
+  float branching_ratio = exam_info_sptr->get_radionuclide().get_branching_ratio(false); // get value without check
+  if (branching_ratio <= 0.F)
+    {
+      warning("BinNormalisationWithCalibration: radionuclide branching_ratio not known. I will use 1.");
+      branching_ratio = 1.F;
+    }
+ 
+  this->_calib_decay_branching_ratio = this->calibration_factor * branching_ratio; //TODO: multiply by decay
   return base_type::set_up(exam_info_sptr, proj_data_info_sptr);
 }
 
@@ -93,25 +102,4 @@ set_calibration_factor(const float calib)
   this->calibration_factor=calib;
 }
 
-float
-BinNormalisationWithCalibration::
-get_branching_ratio() const
-{
-  float branching_ratio = this->radionuclide.get_branching_ratio(false); // get value without check
-  if (branching_ratio <=0)
-    {
-      warning("BinNormalisationWithCalibration: radionuclide branching_ratio not known. I will use 1.");
-      return 1.F;
-    }
-   return branching_ratio;
-}
-
-
-void
-BinNormalisationWithCalibration::
-set_radionuclide(const Radionuclide &rnuclide){
-    this->radionuclide=rnuclide;
-}
-
-
 END_NAMESPACE_STIR