update to 6.1 and minor doc improvements

CMakeLists.txt

@@ -54,9 +54,9 @@ endif()
 
 ####### Set Version number etc
 set(VERSION_MAJOR   6)
-set(VERSION_MINOR   0)
+set(VERSION_MINOR   1)
 set(VERSION_PATCH   0)
-set(VERSION   060000) # only used in STIRConfig.h.in and swig/CMakeLists.txt
+set(VERSION   060100) # only used in STIRConfig.h.in and swig/CMakeLists.txt
 
 set(STIR_VERSION
   ${VERSION_MAJOR}.${VERSION_MINOR}.${VERSION_PATCH})

VERSION.txt

@@ -1 +1 @@
-6.0.0
+6.1.0

documentation/STIR-UsersGuide.tex

@@ -44,7 +44,7 @@
 \\[3cm]
 
 \textbf{{\huge User's Guide\\
- Version 6.0}}
+ Version 6.1}}
 \end{center}
 
 \end{spacing}
@@ -444,7 +444,8 @@ \subsubsection{
 
 { \subsubsubsection{Cygwin on Windows}
 }
-\textit{Cygwin support has not been tested since about 2018 but likely still works. Instructions below might be out-of-date though.}
+\textit{Cygwin support has not been tested since about 2018 but likely still works. Instructions below are likely out-of-date though.
+We highly recommend to use WSL instead.}
 
 If you are using Windows but would like 
 to have nearly everything that Linux/Unix has to offer, Cygwin could help. Check out http://cygwin.com.

documentation/STIR-developers-overview.tex

@@ -60,8 +60,8 @@ \section{
 doxygen on the source files that come in the STIR distribution). 
 
 \subsection{Language support}
-STIR is written in C++ and currently requires C++-11, but it is compatible with newer versions of the C++ standard.
-We will enforce C++-14 from STIR 6.0.
+STIR is written in C++ and currently requires C++-14, but it is compatible with newer versions of the C++ standard.
+We will enforce C++-16 from STIR 6.2.
 
 Python and MATLAB support is provided via \R2Lurl{http://www.swig.org/}{SWIG}. This means that Python/MATLAB interfaces follow
 the C++ classes closely, although some differences are required as these languages do not support templates for instance.
@@ -170,8 +170,8 @@ \subsection{
 view.
 \end{itemize} 
 
-Note that in STIR version 6.0, Time-of-Flight (TOF) will be supported. This introduces another
-index. However, \texttt{Sinogram} and \texttt{Viewgram} will remain 2D objects, and \texttt{Segment*} 3D.
+Note that since STIR version 6.0, Time-of-Flight (TOF) is supported. This introduces another
+index. However, \texttt{Sinogram} and \texttt{Viewgram} remain 2D objects, and \texttt{Segment*} 3D.
 This will also be the case once we have layers and energy windows.
 In STIR 5.2, we have therefore introduced new classes
 \texttt{SinogramIndices}, \texttt{ViewgramIndices}\footnote{Replacing \texttt{ViewSegmentNumbers} in previous versions of STIR.}
@@ -897,7 +897,7 @@ \subsubsection{
 \end{itemize}
 
 
-At the moment, we have three derived classes:
+At the moment, we have the following derived classes:
 \begin{itemize}
 \item 
 \texttt{ProjMatrixByBinUsingRayTracing} uses essentially the same 
@@ -916,6 +916,10 @@ \subsubsection{
 part of the projection matrix needs to be stored. Our current 
 implementation does not yet provide a very compact format for 
 storing the elements (although they are of course stored sparsely).
+\item
+\texttt{ProjMatrixByBinSPECTUB} is for parallel hole SPECT
+\item
+\texttt{ProjMatrixByBinPinholeSPECTUB} is for multi-pinhole SPECT
 \end{itemize}
 
 \begin{figure}[htbp]
@@ -956,8 +960,10 @@ \subsection{Objective functions}
 that is computed is generally not the gradient of the
 log-likelihood that corresponds to the forward projector.
 However, one hopes that it still points towards the optimum.
-The corresponding objective function is implemented in the class\\
-\texttt{PoissonLogLikelihoodWithLinearModelForMeanAndProjData}.
+The corresponding objective function is implemented in the classes\\
+\texttt{PoissonLogLikelihoodWithLinearModelForMeanAndProjData} for
+projection data and \texttt{PoissonLogLikelihoodWithLinearModelForMeanAndListModeDataWithProjMatrixByBin}
+for list-mode data. There are classes for dynamic and gated data as well.
 
 There can be different objective function that use common operations.
 For instance, the objective function could implement a least squares