From 691d3f63d221b2df4e192f9ca326cd6cc09a4d99 Mon Sep 17 00:00:00 2001
From: Kris Thielemans <k.thielemans@ucl.ac.uk>
Date: Tue, 6 Feb 2024 23:21:16 +0000
Subject: [PATCH 1/8] removed some unused variables

---
 src/recon_buildblock/LogcoshPrior.cxx            | 1 -
 src/recon_buildblock/QuadraticPrior.cxx          | 1 -
 src/recon_buildblock/RelativeDifferencePrior.cxx | 1 -
 3 files changed, 3 deletions(-)

diff --git a/src/recon_buildblock/LogcoshPrior.cxx b/src/recon_buildblock/LogcoshPrior.cxx
index d9b038fa6f..abccd71023 100644
--- a/src/recon_buildblock/LogcoshPrior.cxx
+++ b/src/recon_buildblock/LogcoshPrior.cxx
@@ -424,7 +424,6 @@ LogcoshPrior<elemT>::compute_Hessian(DiscretisedDensity<3, elemT>& prior_Hessian
   const int min_dx = max(weights[0][0].get_min_index(), prior_Hessian_for_single_densel[z][y].get_min_index() - x);
   const int max_dx = min(weights[0][0].get_max_index(), prior_Hessian_for_single_densel[z][y].get_max_index() - x);
 
-  elemT diagonal = 0;
   for (int dz = min_dz; dz <= max_dz; ++dz)
     for (int dy = min_dy; dy <= max_dy; ++dy)
       for (int dx = min_dx; dx <= max_dx; ++dx)
diff --git a/src/recon_buildblock/QuadraticPrior.cxx b/src/recon_buildblock/QuadraticPrior.cxx
index 1b2e7aeade..93c4db3fb0 100644
--- a/src/recon_buildblock/QuadraticPrior.cxx
+++ b/src/recon_buildblock/QuadraticPrior.cxx
@@ -467,7 +467,6 @@ QuadraticPrior<elemT>::compute_Hessian(DiscretisedDensity<3, elemT>& prior_Hessi
   const int min_dx = max(weights[0][0].get_min_index(), prior_Hessian_for_single_densel[z][y].get_min_index() - x);
   const int max_dx = min(weights[0][0].get_max_index(), prior_Hessian_for_single_densel[z][y].get_max_index() - x);
 
-  elemT diagonal = 0;
   for (int dz = min_dz; dz <= max_dz; ++dz)
     for (int dy = min_dy; dy <= max_dy; ++dy)
       for (int dx = min_dx; dx <= max_dx; ++dx)
diff --git a/src/recon_buildblock/RelativeDifferencePrior.cxx b/src/recon_buildblock/RelativeDifferencePrior.cxx
index d407f1d728..d23b9528a1 100644
--- a/src/recon_buildblock/RelativeDifferencePrior.cxx
+++ b/src/recon_buildblock/RelativeDifferencePrior.cxx
@@ -489,7 +489,6 @@ RelativeDifferencePrior<elemT>::compute_Hessian(DiscretisedDensity<3, elemT>& pr
   const int min_dx = max(weights[0][0].get_min_index(), prior_Hessian_for_single_densel[z][y].get_min_index() - x);
   const int max_dx = min(weights[0][0].get_max_index(), prior_Hessian_for_single_densel[z][y].get_max_index() - x);
 
-  elemT diagonal = 0;
   for (int dz = min_dz; dz <= max_dz; ++dz)
     for (int dy = min_dy; dy <= max_dy; ++dy)
       for (int dx = min_dx; dx <= max_dx; ++dx)

From 2df514472e411c9b207c5c75f1be3949e4744fd1 Mon Sep 17 00:00:00 2001
From: Kris Thielemans <k.thielemans@ucl.ac.uk>
Date: Tue, 6 Feb 2024 23:24:10 +0000
Subject: [PATCH 2/8] extra test for Array2D

---
 src/test/test_ArrayFilter.cxx | 10 ++++++----
 1 file changed, 6 insertions(+), 4 deletions(-)

diff --git a/src/test/test_ArrayFilter.cxx b/src/test/test_ArrayFilter.cxx
index 829cf06a23..36aa2fe44c 100644
--- a/src/test/test_ArrayFilter.cxx
+++ b/src/test/test_ArrayFilter.cxx
@@ -313,12 +313,14 @@ ArrayFilterTests::run_tests()
     Array<2, float> test_pos_offset(IndexRange2D(1, size1, 2, size2 + 1));
     // initialise to some arbitrary values
     {
-      Array<2, float>::full_iterator iter = test.begin_all();
-      /*for (int i=-100; iter != test.end_all(); ++i, ++iter)
-       *iter = 1;//i*i*2.F-i-100.F;*/
-      test[0][0] = 1;
+      auto iter = test.begin_all();
+      for (int i = -100; iter != test.end_all(); ++i, ++iter)
+        *iter = i * i * 2.F - i - 100.F;
+      test[0][0] = 1.F;
       std::copy(test.begin_all(), test.end_all(), test_neg_offset.begin_all());
       std::copy(test.begin_all(), test.end_all(), test_pos_offset.begin_all());
+      check_if_equal(test_neg_offset[-5][-10], 1.F);
+      check_if_equal(test_pos_offset[1][2], 1.F);
     }
     {
       const int kernel_half_length = 14;

From e0fcfc365c3dbe67eb2bdd2ed869fcdef65407a3 Mon Sep 17 00:00:00 2001
From: Kris Thielemans <k.thielemans@ucl.ac.uk>
Date: Tue, 6 Feb 2024 23:41:33 +0000
Subject: [PATCH 3/8] clean-up of release notes for 6.0.0

---
 documentation/release_6.0.htm | 66 +++++++++++++++++++----------------
 1 file changed, 36 insertions(+), 30 deletions(-)

diff --git a/documentation/release_6.0.htm b/documentation/release_6.0.htm
index 61ba0b89f6..8b13e1f21a 100644
--- a/documentation/release_6.0.htm
+++ b/documentation/release_6.0.htm
@@ -10,7 +10,7 @@ <h1>Summary of changes in STIR release 6.0</h1>
     <p>This version is 99% backwards compatible with STIR 5.x for the user (see below).
       Developers might need to make code changes as 
       detailed below. Note though that the <strong>locations of installed files have changed</strong>.
-      Developers of other software that uses STIR via CMake will need to adapt (see below).
+      Developers of other software that uses STIR via CMake will therefore need to adapt (see below).
     </p>
     <h2>Overall summary</h2>
     <p>
@@ -18,8 +18,8 @@ <h2>Overall summary</h2>
     </p>
 
 
-    <p>Of course, there is also the usual code-cleanup and 
-      improvements to the documentation.
+    <p>This version has a major code-cleanup related to removing old compiler work-arounds,
+      consistent use of <code>override</code> and white-space enforcement.
     </p>
 
     <p>Overall code management and assistance was Kris Thielemans (UCL and ASC). Other main contributors
@@ -33,7 +33,10 @@ <h2>Overall summary</h2>
 
     <h2>Patch release info</h2>
     <ul>
-      <li> 6.0.0 released ?/?/2024</li>
+      <li>
+        6.0.0 released 07/02/2024<br>
+        <a href="https://github.com/UCL/STIR/milestone/4">GitHub Milestone 6.0</a>
+      </li>
       <!--
       <li> 4.0.1 released 28/04/2020
         <ul>
@@ -72,6 +75,10 @@ <h3>Changes breaking backwards compatibility from a user-perspective</h3>
     <h3>Bug fixes</h3>
     <ul>
       <li>
+        Interfile parsing no longer gets confused by the use of <tt>:</tt> in a keyword (e.g., used by Siemens
+        for dates).
+        <br>
+        <a href=https://github.com/UCL/STIR/pull/1267>PR #1267</a>
       </li>
     </ul>
 
@@ -216,7 +223,7 @@ <h3>Changed functionality</h3>
         of non arc-corrected bins set for the scanner. If it is, an error is raised. You might therefore have to adapt your interfile header.
       </li>
       <li>
-        Write <code>STIR6.0</code> as Interfile key version to denote TOF changes.
+        Write <tt>STIR6.0</tt> as Interfile key <tt>version</tt> to denote TOF changes.
         This is currently ignored for parsing though.
       </li>
     </ul>
@@ -239,12 +246,6 @@ <h3>Build system</h3>
     <h3>Known problems</h3>
     <p>See <a href=https://github.com/UCL/STIR/labels/bug>our issue tracker</a>.</p>
 
-    <h3>Minor bug fixes</h3>
-    <ul>
-      <li>
-      </li>
-    </ul>
-
     <h3>Documentation changes</h3>
     <ul>
       <li>
@@ -259,30 +260,18 @@ <h3>Documentation changes</h3>
       </li>
     </ul>
 
-    <h3>Test changes</h3>
-    <h4>recon_test_pack changes</h4>
-    <ul>
-      <li>
-        additional tests for TOF, expansion of some existing tests for TOF
-      </li>
-      <li>
-        updated version number and added some clarification to the README.txt
-      </li>
-    </ul>
-
-    <h4>C++ tests</h4>
-    <ul>
-      <li>
-        additional tests for TOF, expansion of some existing tests for TOF
-      </li>
-    </ul>
-
     <h2>New deprecations for future versions</h2>
     <ul>
       <li>
         CMake option <code>STIR_USE_BOOST_SHARED_PTR</code> will be removed. It probably no longer
         works anyway. Therefore <code>stir::shared_ptr</code> will always be <code>std::shared_ptr</code>.
       </li>
+      <li>Direct X-windows display (corresponding to the CMake option `GRAPHICS=X`) will be removed. It is
+        very outdated and sometimes doesn't work.
+      </li>
+      <li>
+        remaining files for ECAT6 support will be removed.
+      </li>
     </ul>
 
     <H2>What's new for developers (aside from what should be obvious
@@ -407,7 +396,6 @@ <h4>TOF related</h4>
     </ul>
 
     <h3>Code clean-up</h3>
-
     <ul>
       <li>
         Clean-up of various work-arounds such as
@@ -418,6 +406,24 @@ <h3>Code clean-up</h3>
         Consistently use <code>override</code> in derived classes, via <tt>clang-tidy --modernize-use-override</tt>.
       </li>
     </ul>
+
+    <h3>Test changes</h3>
+    <h4>recon_test_pack changes</h4>
+    <ul>
+      <li>
+        additional tests for TOF, expansion of some existing tests for TOF
+      </li>
+      <li>
+        updated version number and added some clarification to the README.txt
+      </li>
+    </ul>
+
+    <h4>C++ tests</h4>
+    <ul>
+      <li>
+        additional tests for TOF, expansion of some existing tests for TOF
+      </li>
+    </ul>
 </body>
 
 </html>

From 89bb7008f56dcd1d44686b9fb134364b79cb8ac5 Mon Sep 17 00:00:00 2001
From: Kris Thielemans <k.thielemans@ucl.ac.uk>
Date: Wed, 7 Feb 2024 00:44:48 +0000
Subject: [PATCH 4/8] update .tex files for 6.0

---
 documentation/STIR-UsersGuide.tex          | 19 +++++++++++++------
 documentation/STIR-developers-overview.tex | 16 ++++++++--------
 documentation/STIR-general-overview.tex    | 11 ++++++-----
 3 files changed, 27 insertions(+), 19 deletions(-)

diff --git a/documentation/STIR-UsersGuide.tex b/documentation/STIR-UsersGuide.tex
index 74d30c42da..fd404074a3 100644
--- a/documentation/STIR-UsersGuide.tex
+++ b/documentation/STIR-UsersGuide.tex
@@ -44,7 +44,7 @@
 \\[3cm]
 
 \textbf{{\huge User's Guide\\
- Version 5.2}}
+ Version 6.0}}
 \end{center}
 
 \end{spacing}
@@ -1466,6 +1466,10 @@ \subsubsection{
 \texttt{boost::format} is used, so the pattern can be more flexible.} to allow
 constructing different filenames for each subset.
 
+\item[use time-of-flight sensitivities]
+Defaults to 0, i.e. off. By default, the sensitivity calculation will be non-TOF. However,
+this fails when using a TOF proj-data, as used by Siemens for the Vision 600 etc. In this case,
+you will need to set this parameter to 1.
 
 \item[Projector pair type]
 Specifies the back/forward projector pair to be used in the reconstruction. 
@@ -5714,25 +5718,28 @@ \section{Using STIR in an external C++ project
 \label{sec:ExternalProjectC++}}
 STIR exports its CMake settings. Therefore, an external project can do
 \begin{verbatim}
-find_package(STIR 5.2 CONFIG)
+find_package(STIR 6.0 REQUIRED CONFIG)
 add_library(my_lib file1.cxx file2.cxx)
 # my_lib uses STIR functionality
 target_link_libraries(my_lib PUBLIC ${STIR_LIBRARIES})
 add_executable(my_exe my_exe.cxx ${STIR_REGISTRIES})
-target_link_libraries(my_exe PUBLIC my_lib)
+target_link_libraries(my_exe PUBLIC my_lib))
 \end{verbatim}
 In addition, if your CMake is older than 3.12, you need to add
 \begin{verbatim}
 include_directories("${STIR_INCLUDE_DIRS}")
 \end{verbatim}
-to your CMake file to get the source code files listed in \texttt{STIR\_REGISTRIES} to compile.
-For more recent CMake, this should not be necessary (as \texttt{STIR\_REGISTRIES} is set to
+to your CMakeLists.txt file to get the source code files listed in \texttt{STIR\_REGISTRIES} to compile.
+(For more recent CMake, this should not be necessary (as \texttt{STIR\_REGISTRIES} is set to
 a list of compiled files).
 
+A fully working example is provided in the \texttt{examples/C++} folder, see also the
+\url{https://github.com/UCL/STIR/tree/master/examples/C\%2B\%2B/using_installed_STIR}{using\_installed\_STIR folder on GitHub}.
+
 Note that if CMake did not find the STIR files, you can point it to where they are installed.
 For example, if you installed STIR with
 \texttt{CMAKE\_INSTALL\_PREFIX=\$HOME/install}, set
-\texttt{STIR\_DIR=\$HOME/install/lib/cmake}.
+\texttt{CMAKE\_PREFIX\_PATH=\$HOME/install} or \texttt{STIR\_DIR=\$HOME/install/lib/cmake/STIR-6.0}.
 \footnote{This uses CMake Config mode for \texttt{find\_package}. There is no need for a \texttt{FindSTIR.cmake}}
 
 \section{
diff --git a/documentation/STIR-developers-overview.tex b/documentation/STIR-developers-overview.tex
index 5746a292f4..85e07a3cea 100644
--- a/documentation/STIR-developers-overview.tex
+++ b/documentation/STIR-developers-overview.tex
@@ -16,7 +16,7 @@
 \textbf{{\huge STIR \\
 Overview for developers}}\\
 \textbf{Kris Thielemans}\\
-\textbf{\textit{version 5.2}}
+\textbf{\textit{version 6.0}}
 
 \end{center}
 
@@ -274,7 +274,7 @@ \subsection{
 Pointers to an object called \textit{something\_ptr}. Currently there 
 is no naming distinction between shared pointers etc. This is 
 probably a bad idea. For new code, we recommend to use \textit{something\_sptr} 
-for shared pointers, and \textit{something\_aptr} for auto\_ptrs (see 
+for shared pointers, and \textit{something\_uptr} for unique\_ptrs (see 
 section \ref{sect:sharedptr}).
 \end{itemize}
 
@@ -314,7 +314,7 @@ \subsection{
 hence unnecessary rebuilds when modifying one \textit{.h} file), we 
 avoid including \textit{.h} files for 'supporting' classes as much 
 as possible. Instead, we only declare the classes needed, e.g. \textit{class 
-Bin;} instead of \textit{\#include stir/Bin.h.}
+Bin;} instead of \textit{\#include ``stir/Bin.h''.}
 
 
 
@@ -394,8 +394,8 @@ \subsection{
 \subsection{C++ conventions}
 STIR uses C++-14 and is compatible with C++-20 to the best of our knowledge.
 For legacy reasons, we have some preprocessor 
-macros (see \textit{stir/common.h}) that were used isolate work-arounds for older 
-compilers. Ideally, all these \#ifdefs should disappear at a 
+macros (see \textit{stir/common.h}) to define the stir namespace (see below).
+These should disappear at a 
 later development stage of the library.
 
 We use \texttt{override} for virtual functions in derived classes. This is clearer,
@@ -524,7 +524,7 @@ \subsubsection{
 generally use \texttt{shared\_ptr} instead. This is somewhat unfortunate 
 as these two smart pointers are generally quite different concepts. 
 
-\texttt{shared\_ptr} is a wrapper around the \texttt{std} (or boost\footnote{Boost smart pointer are probably no longer supported, and will no longer be from STIR 6.0.}) smart pointer class which 
+\texttt{shared\_ptr} is a wrapper around the \texttt{std} (or boost\footnote{Boost smart pointer are probably no longer supported, and will no longer be from STIR 6.1.}) smart pointer class which 
 is suitable when there are (potentially) more than one pointer 
 pointing to the same object. It keeps a reference count such 
 that the object is (only) deleted when the last shared pointer 
@@ -561,10 +561,10 @@ \subsubsection{
 
 We provide the convenience function \textit{stir::is\_null\_ptr()} 
 to test if a pointer is `null', i.e. does not point to anything. \textit{is\_null\_ptr} 
-works with ordinary pointers, shared\_ptrs and auto\_ptrs. Use 
+works with ordinary pointers, shared\_ptrs and unique\_ptrs. Use 
 it to avoid that your code depends on what type of (smart) pointer 
 you are using. Note however that since C++-11, it is more convenient to use the
-automatic converstion to \texttt{bool}.
+automatic conversion to \texttt{bool}.
 
 \subsection{Generic functionality of STIR classes}
 This is a (very incomplete) section describing some functionality that
diff --git a/documentation/STIR-general-overview.tex b/documentation/STIR-general-overview.tex
index 7a6a4ed5da..e7074cd4a6 100644
--- a/documentation/STIR-general-overview.tex
+++ b/documentation/STIR-general-overview.tex
@@ -17,7 +17,7 @@
 \textbf{{\huge STIR \\
 General Overview}}\\
 \textbf{Kris Thielemans}\\
-\textbf{\textit{version 5.2}}
+\textbf{\textit{version 6.0}}
 
 
 \end{spacing}
@@ -90,7 +90,7 @@ \section{
 processors, but also on massively parallel computers, or on clusters 
 of workstations. \\
 STIR is portable on all systems supporting the GNU C++ compiler, CLang++, Intel C++, 
-or MS Visual C++ (or hopefully any C++-11 compliant compiler). 
+or MS Visual C++ (or hopefully any C++-14 compliant compiler). 
 The library is fully documented.\\
 The object-oriented features make this library very modular and 
 flexible. This means that it is relatively easy to add new algorithms, 
@@ -273,8 +273,9 @@ \subsection{
 for small weights of the prior term, however becomes unstable 
 for larger values. 
 
-As prior we currently only distribute the ``quadratic penalty'', i.e. a
-Gibbs prior with a qudratic potential function, and a generalisation of the 
+As prior we currently distribute the ``quadratic penalty'', i.e. a
+Gibbs prior with a qudratic potential function, the more edge-preserving
+``log-cosh penalty'', the ``relative difference prior'' and a generalisation of the 
 Median Root prior (MRP) [Ale97]. In the MRP case, the assumption 
 is that the desired image is locally monotonic, and that the 
 most probable value of the pixel is close to the local median. 
@@ -310,7 +311,7 @@ \subsection{Other}
 With respect to dynamic and gated imaging
 techniques, we have direct estimation of Patlak
 parameters [Tso08] (using Parametric OSMAPOSL or OSSPS).
-We plan to release motion compensated image reconstruction [Thi06] as
+We include motion compensated image reconstruction as
 implemented by Tsoumpas et al [Tso11].
 
 \section{

From 31f82862ecbde9a84f3c0656c066c605e726eb2b Mon Sep 17 00:00:00 2001
From: Kris Thielemans <k.thielemans@ucl.ac.uk>
Date: Wed, 7 Feb 2024 00:46:26 +0000
Subject: [PATCH 5/8] remove more obsolete macros

removed *NAMESPACE_STD, STIR_SPEED_UP_STD_COPY and STIR_ASSERT

All were essentially unused anyway
---
 src/include/stir/common.h                 | 157 +---------------------
 src/recon_test/fwdtest.cxx                |   1 -
 src/test/IO/test_IO_ITKMulticomponent.cxx |   2 +-
 3 files changed, 3 insertions(+), 157 deletions(-)

diff --git a/src/include/stir/common.h b/src/include/stir/common.h
index dfe270b615..5a501a040a 100644
--- a/src/include/stir/common.h
+++ b/src/include/stir/common.h
@@ -46,21 +46,11 @@
    (If the attempts fail to determine the correct OS, you can pass
     the correct value as a preprocessor definition to the compiler)
  </LI>
- <LI> \c \#includes cstdio, cstdlib, cstring, cmath
+ <LI> \c \#includes cstdio, cstdlib, cstring, cmath, cassert
  </LI>
 
- <LI> \c \#ifdef \c STIR_ASSERT, then define our own assert, else include &lt;cassert&gt;
- </LI>
 </UL>
 
-<H3> Speeding up std::copy</H3>
-
- <UL>
- <LI> For old compilers (check the source!), overloads of std::copy for built-in
-      types to use memmove (so it's faster)
- </LI>
- </UL>
-
 <H3> stir namespace members declared here</H3>
 
  <UL>
@@ -81,6 +71,7 @@
 #include <cstdlib>
 #include <cstring>
 #include <cmath>
+#include <cassert>
 #include <boost/math/constants/constants.hpp>
 
 //*************** namespace macros
@@ -89,11 +80,6 @@
   {
 #define END_NAMESPACE_STIR }
 #define USING_NAMESPACE_STIR using namespace stir;
-#define START_NAMESPACE_STD                                                                                                      \
-  namespace std                                                                                                                  \
-  {
-#define END_NAMESPACE_STD }
-#define USING_NAMESPACE_STD using namespace std;
 
 //*************** define __OS_xxx__
 
@@ -139,145 +125,6 @@
 
 #endif // !defined(__OS_xxx_)
 
-//*************** overload std::copy for built-in types
-/* If you have an older compiler, chages are that std::copy is
-   implemented in the obvious way of iterating and copying along
-   the way. However, for simple types (such as floats), calling
-   memmove (not memcpy as the ranges could overlap) is faster.
-   So, we overload std::copy for some built-in types.
-
-   However, newer compilers (in particular gcc from version 2.8)
-   take care of this themselves. So, we only do this
-   conditionally.
-*/
-#ifdef STIR_SPEED_UP_STD_COPY
-#  include <algorithm>
-
-START_NAMESPACE_STD
-//! overloads std::copy for faster performance
-template <>
-inline double*
-copy(const double* first, const double* last, double* to)
-{
-  memmove(to, first, (last - first) * sizeof(double));
-  return to + (last - first);
-}
-
-template <>
-inline float*
-copy(const float* first, const float* last, float* to)
-{
-  memmove(to, first, (last - first) * sizeof(float));
-  return to + (last - first);
-}
-
-template <>
-inline unsigned long int*
-copy(const unsigned long int* first, const unsigned long int* last, unsigned long int* to)
-{
-  memmove(to, first, (last - first) * sizeof(unsigned long int));
-  return to + (last - first);
-}
-
-template <>
-inline signed long int*
-copy(const signed long int* first, const signed long int* last, signed long int* to)
-{
-  memmove(to, first, (last - first) * sizeof(signed long int));
-  return to + (last - first);
-}
-
-template <>
-inline unsigned int*
-copy(const unsigned int* first, const unsigned int* last, unsigned int* to)
-{
-  memmove(to, first, (last - first) * sizeof(unsigned int));
-  return to + (last - first);
-}
-
-template <>
-inline signed int*
-copy(const signed int* first, const signed int* last, signed int* to)
-{
-  memmove(to, first, (last - first) * sizeof(signed int));
-  return to + (last - first);
-}
-
-template <>
-inline unsigned short int*
-copy(const unsigned short int* first, const unsigned short int* last, unsigned short int* to)
-{
-  memmove(to, first, (last - first) * sizeof(unsigned short int));
-  return to + (last - first);
-}
-
-template <>
-inline signed short int*
-copy(const signed short int* first, const signed short int* last, signed short int* to)
-{
-  memmove(to, first, (last - first) * sizeof(signed short int));
-  return to + (last - first);
-}
-
-template <>
-inline unsigned char*
-copy(const unsigned char* first, const unsigned char* last, unsigned char* to)
-{
-  memmove(to, first, (last - first) * sizeof(unsigned char));
-  return to + (last - first);
-}
-
-template <>
-inline signed char*
-copy(const signed char* first, const signed char* last, signed char* to)
-{
-  memmove(to, first, (last - first) * sizeof(signed char));
-  return to + (last - first);
-}
-
-template <>
-inline char*
-copy(const char* first, const char* last, char* to)
-{
-  memmove(to, first, (last - first) * sizeof(char));
-  return to + (last - first);
-}
-
-template <>
-inline bool*
-copy(const bool* first, const bool* last, bool* to)
-{
-  memmove(to, first, (last - first) * sizeof(bool));
-  return to + (last - first);
-}
-
-END_NAMESPACE_STD
-
-#endif // #ifdef STIR_SPEED_UP_STD_COPY
-
-//*************** assert
-
-#ifndef STIR_ASSERT
-#  include <cassert>
-#else
-// use our own assert
-#  ifdef assert
-#    undef assert
-#  endif
-#  if !defined(NDEBUG)
-#    define assert(x)                                                                                                            \
-      {                                                                                                                          \
-        if (!(x))                                                                                                                \
-          {                                                                                                                      \
-            fprintf(stderr, "Assertion \"%s\" failed in file %s:%d\n", #x, __FILE__, __LINE__);                                  \
-            abort();                                                                                                             \
-          }                                                                                                                      \
-      }
-#  else
-#    define assert(x)
-#  endif
-#endif // STIR_ASSERT
-
 //***************
 START_NAMESPACE_STIR
 
diff --git a/src/recon_test/fwdtest.cxx b/src/recon_test/fwdtest.cxx
index d4e9bc708b..2f7cfe81ad 100644
--- a/src/recon_test/fwdtest.cxx
+++ b/src/recon_test/fwdtest.cxx
@@ -67,7 +67,6 @@ using std::cout;
 using std::endl;
 
 USING_NAMESPACE_STIR
-// USING_NAMESPACE_STD
 
 /******************* Declarations local functions *******************/
 
diff --git a/src/test/IO/test_IO_ITKMulticomponent.cxx b/src/test/IO/test_IO_ITKMulticomponent.cxx
index 8db3c6f0a2..e1dbd61c3b 100644
--- a/src/test/IO/test_IO_ITKMulticomponent.cxx
+++ b/src/test/IO/test_IO_ITKMulticomponent.cxx
@@ -75,7 +75,7 @@ IOTests_ITKMulticomponent::run_tests()
     }
 }
 
-END_NAMESPACE_STD
+END_NAMESPACE_STIR
 
 USING_NAMESPACE_STIR
 

From 8547dfd48281716ee9a697417f9c05f9f6020e26 Mon Sep 17 00:00:00 2001
From: Kris Thielemans <k.thielemans@ucl.ac.uk>
Date: Wed, 7 Feb 2024 01:05:24 +0000
Subject: [PATCH 6/8] fix some file permissions

---
 recon_test_pack/KOSMAPOSL_test_consistency.par |   0
 recon_test_pack/OSMAPOSL_test_lm.par           |   0
 recon_test_pack/OSMAPOSL_test_lmf.par          |   0
 recon_test_pack/OSMAPOSL_test_proj.par         |   0
 recon_test_pack/frame_single.fdef              |   0
 recon_test_pack/scatter_simulation.par         |   0
 recon_test_pack/small_listmode_file.l          | Bin
 7 files changed, 0 insertions(+), 0 deletions(-)
 mode change 100755 => 100644 recon_test_pack/KOSMAPOSL_test_consistency.par
 mode change 100755 => 100644 recon_test_pack/OSMAPOSL_test_lm.par
 mode change 100755 => 100644 recon_test_pack/OSMAPOSL_test_lmf.par
 mode change 100755 => 100644 recon_test_pack/OSMAPOSL_test_proj.par
 mode change 100755 => 100644 recon_test_pack/frame_single.fdef
 mode change 100755 => 100644 recon_test_pack/scatter_simulation.par
 mode change 100755 => 100644 recon_test_pack/small_listmode_file.l

diff --git a/recon_test_pack/KOSMAPOSL_test_consistency.par b/recon_test_pack/KOSMAPOSL_test_consistency.par
old mode 100755
new mode 100644
diff --git a/recon_test_pack/OSMAPOSL_test_lm.par b/recon_test_pack/OSMAPOSL_test_lm.par
old mode 100755
new mode 100644
diff --git a/recon_test_pack/OSMAPOSL_test_lmf.par b/recon_test_pack/OSMAPOSL_test_lmf.par
old mode 100755
new mode 100644
diff --git a/recon_test_pack/OSMAPOSL_test_proj.par b/recon_test_pack/OSMAPOSL_test_proj.par
old mode 100755
new mode 100644
diff --git a/recon_test_pack/frame_single.fdef b/recon_test_pack/frame_single.fdef
old mode 100755
new mode 100644
diff --git a/recon_test_pack/scatter_simulation.par b/recon_test_pack/scatter_simulation.par
old mode 100755
new mode 100644
diff --git a/recon_test_pack/small_listmode_file.l b/recon_test_pack/small_listmode_file.l
old mode 100755
new mode 100644

From 4a4a245f0ac57460798b45305eb294d3bc55094c Mon Sep 17 00:00:00 2001
From: Kris Thielemans <k.thielemans@ucl.ac.uk>
Date: Wed, 7 Feb 2024 01:52:27 +0000
Subject: [PATCH 7/8] update CITATION.cff

ran git-fame.sh again
---
 CITATION.cff | 95 +++++++++++++++++++++++++++-------------------------
 1 file changed, 49 insertions(+), 46 deletions(-)

diff --git a/CITATION.cff b/CITATION.cff
index 77d74b0396..2a473843da 100644
--- a/CITATION.cff
+++ b/CITATION.cff
@@ -8,12 +8,12 @@ message: >-
   metadata from this file.
 type: software
 authors:
-    - family-names: Mustafovic
-      given-names:  Sanida
-      affiliation:  Imperial College London (UK)
     - family-names: Efthimiou
       given-names:  Nikos
       orcid:        'https://orcid.org/0000-0003-1947-5033'
+    - family-names: Mustafovic
+      given-names:  Sanida
+      affiliation:  Imperial College London (UK)
     - family-names: Brown
       given-names:  Richard
       orcid:        'https://orcid.org/0000-0001-6989-9200'
@@ -21,31 +21,34 @@ authors:
     - family-names: Twyman Skelly
       given-names:  Robert
       affiliation:  University College London and Prescient Imaging
-    - family-names: Tsoumpas
-      given-names:  Charalampos
     - family-names: Deidda
       given-names:  Daniel
       orcid:        'https://orcid.org/0000-0002-2766-4339'
       affiliation:  National Physics Laboratory (UK)
+    - family-names: Tsoumpas
+      given-names:  Charalampos
     - family-names: Falcon
       given-names:  Carles
-    - family-names: Borgeaud
-      given-names:  Tim
-      affiliation:  Hammersmith Imanet Ltd
-    - family-names: Khateri
-      given-names:  Parisa
-      affiliation:  ETH Zuerich
     - family-names: Jehl
       given-names:  Markus
       affiliation:  Positrigo
-    - family-names: Wadhwa
-      given-names:  Palak
-      affiliation:  University of Leeds (UK)
     - family-names: Strugari
       given-names:  Matthew
       affiliation:  Dalhousie University (Canada)
+    - family-names: Khateri
+      given-names:  Parisa
+      affiliation:  ETH Zuerich
     - family-names: Beisel
       given-names:  Tobias
+    - family-names: Wadhwa
+      given-names:  Palak
+      affiliation:  University of Leeds (UK)
+    - family-names: Borgeaud
+      given-names:  Tim
+      affiliation:  Hammersmith Imanet Ltd
+    - family-names: Emond
+      given-names:  Elise
+      affiliation:  University College London
     - family-names: Jacobson
       given-names:  Matthew
     - family-names: Gillman
@@ -57,26 +60,24 @@ authors:
     - family-names: Zverovich
       given-names:  Alexey
       affiliation:  Brunel University (UK)
-    - family-names: Emond
-      given-names:  Elise
-      affiliation:  University College London
-    - family-names: Biguri
-      given-names:  Ander
-      orcid:        'https://orcid.org/0000-0002-2636-3032'
-      affiliation:  University College London
     - family-names: Fuster Marti
       given-names:  Berta
       affiliation:  University of Barcelona (Spain)
     - family-names: Labbe
       given-names:  Claire
+    - family-names: Biguri
+      given-names:  Ander
+      orcid:        'https://orcid.org/0000-0002-2636-3032'
+      affiliation:  University College London
     - family-names: Fischer
       given-names:  Jannis
       orcid:        'https://orcid.org/0000-0002-8329-0220'
     - family-names: Roethlisberger
       given-names:  Michael
       affiliation:  ETH Zuerich
-    - family-names: Aguiar
-      given-names:  Pablo
+    - family-names: Bertolli
+      given-names:  Ottavia
+      affiliation:  University College London
     - family-names: Brusaferri
       given-names:  Ludovica
       affiliation:  University College London
@@ -88,35 +89,34 @@ authors:
       given-names:  Benjamin
       orcid:        'https://orcid.org/0000-0002-9784-1177'
       affiliation:  University College London
-    - family-names: Bertolli
-      given-names:  Ottavia
-      affiliation:  University College London
+    - family-names: Aguiar
+      given-names:  Pablo
     - family-names: Niknejad
       given-names:  Tahereh
-    - family-names: Dikaios
-      given-names:  Nikos
     - family-names: Sadki
       given-names:  Mustapha
       affiliation:  Brunel University (UK)
-    - family-names: Fardell
-      given-names:  Gemma
-      orcid:        'https://orcid.org/0000-0003-2388-5211'
-      affiliation:  UK Research & Innovation
+    - family-names: Schmidtlein
+      given-names:  C Ross
     - family-names: Kerrouche
       given-names:  Nacer
       affiliation:  Hammersmith Imanet Ltd
-    - family-names: Ovtchinnikov
-      given-names:  Evgueni
-      orcid:        'https://orcid.org/0000-0002-9359-6514'
+    - family-names: Dikaios
+      given-names:  Nikos
+    - family-names: Fardell
+      given-names:  Gemma
+      orcid:        'https://orcid.org/0000-0003-2388-5211'
       affiliation:  UK Research & Innovation
     - family-names: Ehrhardt
       given-names:  Matthias J.
       orcid:        'https://orcid.org/0000-0001-8523-353X'
-    - family-names: Schmidtlein
-      given-names:  C Ross
     - family-names: Valente
       given-names:  Patrick
       affiliation:  Brunel University (UK)
+    - family-names: Ovtchinnikov
+      given-names:  Evgueni
+      orcid:        'https://orcid.org/0000-0002-9359-6514'
+      affiliation:  UK Research & Innovation
     - family-names: Schramm
       given-names:  Georg
       affiliation:  Katholieke Universiteit Leuven (Belgium)
@@ -127,6 +127,9 @@ authors:
     - family-names: Belluzzo
       given-names:  Damiano
       affiliation:  Hospedale San Raffaele Milano (Italy)
+    - family-names: Jurjew
+      given-names:  Nicole
+      affiliation:  University College London
     - family-names: Ching
       given-names:  Daniel
     - family-names: Hague
@@ -137,24 +140,24 @@ authors:
       affiliation:  University of Leeds (UK)
     - family-names: Chen
       given-names:  Gefei
-    - family-names: Dao
-      given-names:  Viet Anh
-      affiliation:  University of Leeds (UK)
-    - family-names: Mikhaylova
-      given-names:  Ekaterina
-      affiliation:  Positrigo
     - family-names: Porter
       given-names:  Sam David
       affiliation:  University College London, National Physics Laboratory (UK)
+    - family-names: Mikhaylova
+      given-names:  Ekaterina
+      affiliation:  Positrigo
+    - family-names: Dao
+      given-names:  Viet Anh
+      affiliation:  University of Leeds (UK)
     - family-names: da Costa-Luis
       given-names:  Casper O.
       orcid:        'https://orcid.org/0000-0002-7211-1557'
-    - family-names: Rashidnasab
-      given-names:  Alaleh
-      affiliation:  University College London
     - family-names: Whitehead
       given-names:  Alexander C.
       affiliation:  University College London
+    - family-names: Rashidnasab
+      given-names:  Alaleh
+      affiliation:  University College London
     - family-names: Gillen
       given-names:  Rebecca
       affiliation:  University College London

From fa06c2cfe178ec932a0aefbd263b2c912845e06c Mon Sep 17 00:00:00 2001
From: Kris Thielemans <k.thielemans@ucl.ac.uk>
Date: Wed, 7 Feb 2024 01:58:30 +0000
Subject: [PATCH 8/8] Interfile: mostly ignore "effective central bin size"
 keyword

This keyword only makes sense for arc-corrected data. Therefore, we now
only read/write it in that case.

Fixes #1034
---
 documentation/release_6.0.htm | 14 ++++++++++++--
 src/IO/InterfileHeader.cxx    | 24 ------------------------
 src/IO/interfile.cxx          | 14 +++++---------
 3 files changed, 17 insertions(+), 35 deletions(-)

diff --git a/documentation/release_6.0.htm b/documentation/release_6.0.htm
index 8b13e1f21a..ca7a983b46 100644
--- a/documentation/release_6.0.htm
+++ b/documentation/release_6.0.htm
@@ -223,9 +223,19 @@ <h3>Changed functionality</h3>
         of non arc-corrected bins set for the scanner. If it is, an error is raised. You might therefore have to adapt your interfile header.
       </li>
       <li>
-        Write <tt>STIR6.0</tt> as Interfile key <tt>version</tt> to denote TOF changes.
-        This is currently ignored for parsing though.
+        Interfile header changes:
+        <ul>
+          <li>
+            Write <tt>STIR6.0</tt> as Interfile key <tt>version</tt> to denote TOF changes.
+            This is currently ignored for parsing though.
+          </li>
+          <li>
+            (PET) The <tt>effective central bin size (cm)</tt> keyword for projection data is now only used for arc-corrected data.
+            It is no longer written to the header for non-arccorrected data.
+          </li>
+        </ul>
       </li>
+      <li>
     </ul>
 
     <h3>Build system</h3>
diff --git a/src/IO/InterfileHeader.cxx b/src/IO/InterfileHeader.cxx
index ab13846351..7e68cbbda2 100644
--- a/src/IO/InterfileHeader.cxx
+++ b/src/IO/InterfileHeader.cxx
@@ -1406,41 +1406,17 @@ InterfilePDFSHeader::post_processing()
                                                                     num_views,
                                                                     num_bins,
                                                                     tof_mash_factor));
-          if (effective_central_bin_size_in_cm > 0
-              && fabs(effective_central_bin_size_in_cm - data_info_sptr->get_sampling_in_s(Bin(0, 0, 0, 0)) / 10.) > .01)
-            {
-              warning(boost::format("Interfile warning: inconsistent effective_central_bin_size_in_cm\n"
-                                    "Value in header is %g while I expect %g from the inner ring radius etc\n"
-                                    "Ignoring value in header")
-                      % effective_central_bin_size_in_cm % (data_info_sptr->get_sampling_in_s(Bin(0, 0, 0, 0)) / 10.));
-            }
         }
     }
   else if (scanner_geometry == "BlocksOnCylindrical") // if block geometry
     {
       data_info_sptr.reset(new ProjDataInfoBlocksOnCylindricalNoArcCorr(
           scanner_sptr_from_file, sorted_num_rings_per_segment, sorted_min_ring_diff, sorted_max_ring_diff, num_views, num_bins));
-      if (effective_central_bin_size_in_cm > 0
-          && fabs(effective_central_bin_size_in_cm - data_info_sptr->get_sampling_in_s(Bin(0, 0, 0, 0)) / 10.) > .01)
-        {
-          warning(boost::format("Interfile warning: inconsistent effective_central_bin_size_in_cm\n"
-                                "Value in header is %g while I expect %g from the inner ring radius etc\n"
-                                "Ignoring value in header")
-                  % effective_central_bin_size_in_cm % (data_info_sptr->get_sampling_in_s(Bin(0, 0, 0, 0)) / 10.));
-        }
     }
   else // if generic geometry
     {
       data_info_sptr.reset(new ProjDataInfoGenericNoArcCorr(
           scanner_sptr_from_file, sorted_num_rings_per_segment, sorted_min_ring_diff, sorted_max_ring_diff, num_views, num_bins));
-      if (effective_central_bin_size_in_cm > 0
-          && fabs(effective_central_bin_size_in_cm - data_info_sptr->get_sampling_in_s(Bin(0, 0, 0, 0)) / 10.) > .01)
-        {
-          warning(boost::format("Interfile warning: inconsistent effective_central_bin_size_in_cm\n"
-                                "Value in header is %g while I expect %g from the inner ring radius etc\n"
-                                "Ignoring value in header")
-                  % effective_central_bin_size_in_cm % (data_info_sptr->get_sampling_in_s(Bin(0, 0, 0, 0)) / 10.));
-        }
     }
   if (data_info_sptr->get_num_tof_poss() != num_timing_poss)
     error(boost::format("Interfile header parsing with TOF: inconsistency between number of TOF bins in data (%d), "
diff --git a/src/IO/interfile.cxx b/src/IO/interfile.cxx
index c950ba561e..e7565fb549 100644
--- a/src/IO/interfile.cxx
+++ b/src/IO/interfile.cxx
@@ -1325,9 +1325,11 @@ write_basic_interfile_PDFS_header(const string& header_file_name, const string&
 
       output_header << scanner.parameter_info();
 
-      output_header << "effective central bin size (cm) := " << proj_data_info_sptr->get_sampling_in_s(Bin(0, 0, 0, 0)) / 10.
-                    << endl;
-
+      if (dynamic_pointer_cast<const ProjDataInfoCylindricalArcCorr>(pdfs.get_proj_data_info_sptr()))
+        {
+          output_header << "effective central bin size (cm) := " << proj_data_info_sptr->get_sampling_in_s(Bin(0, 0, 0, 0)) / 10.
+                        << "\n";
+        }
     } // end of cylindrical scanner
   else
     {
@@ -1377,9 +1379,6 @@ write_basic_interfile_PDFS_header(const string& header_file_name, const string&
 
           output_header << scanner.parameter_info();
 
-          output_header << "effective central bin size (cm) := " << proj_data_info_sptr->get_sampling_in_s(Bin(0, 0, 0, 0)) / 10.
-                        << endl;
-
         }  // end of BlocksOnCylindrical scanner
       else // generic scanner
         {
@@ -1410,9 +1409,6 @@ write_basic_interfile_PDFS_header(const string& header_file_name, const string&
 
               output_header << scanner.parameter_info();
 
-              output_header << "effective central bin size (cm) := "
-                            << proj_data_info_sptr->get_sampling_in_s(Bin(0, 0, 0, 0)) / 10. << endl;
-
             } // end generic scanner
           else if (!dynamic_pointer_cast<const ProjDataInfoSubsetByView>(pdfs.get_proj_data_info_sptr()))
             {