Merge pull request #1372 from KrisThielemans/6.0.0-final-prep

6.0.0 final preparation
UCL · Feb 7, 2024 · 41cf3d9 · 41cf3d9
2 parents 1fec2bf + fa06c2c
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diff --git a/CITATION.cff b/CITATION.cff
@@ -8,44 +8,47 @@ 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'
       affiliation:  University College London
     - 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

diff --git 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
@@ -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
@@ -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{