reduce amount of doxygen warnings

src/Doxyfile.in

@@ -853,7 +853,7 @@ EXAMPLE_RECURSIVE      = NO
 # that contain images that are to be included in the documentation (see the
 # \image command).
 
-IMAGE_PATH             = @PROJECT_SOURCE_DIR@/../doximages
+IMAGE_PATH             = @PROJECT_SOURCE_DIR@/doximages
 
 # The INPUT_FILTER tag can be used to specify a program that doxygen should
 # invoke to filter for each input file. Doxygen will invoke the filter program

src/experimental/utilities/list_TAC_ROI_values.cxx

@@ -23,7 +23,7 @@
   \param output_filename a text file sorted in list form of: | Frame_num | Start Time | End Time | Mean | StdDev | CV |
   \param data_filename should be in ECAT7 format.
   \param --CV is used to output the Coefficient of Variation as well.
-  \Note When ROI_filename.par is not given, the user will be asked for the parameters.
+  Note: When ROI_filename.par is not given, the user will be asked for the parameters.
 
   The .par file has the following format
   \verbatim

src/include/stir/DetectorCoordinateMap.h

@@ -47,7 +47,7 @@ class Succeeded;
 	ring,detector,(layer,)x,y,z
 	An empty line will terminate the reading at that line.
 
-    Optionally LOR end-points can be randomly displaced using a Gaussian distribution with standard deviation \sigma (in mm).
+    Optionally LOR end-points can be randomly displaced using a Gaussian distribution with standard deviation sigma (in mm).
 */
 class DetectorCoordinateMap
 {

src/include/stir/GeometryBlocksOnCylindrical.h

@@ -36,12 +36,12 @@ START_NAMESPACE_STIR
   \ingroup projdata
 	\brief A helper class to build the crystal map based on scanner info.
 
-	\This class builds two maps between cartesian coordinates (z, y, x)
-	\ and the corresponding detection position (tangential_num, axial_num, radial_num) for each crystal.
-	\The crystal map, then, is used in ProjDataInfoBlocksOnCylindrical, ProjDataInfoBlocksOnCylindricalNoArcCorr, and CListRecordSAFIR
+	This class builds two maps between cartesian coordinates (z, y, x)
+	and the corresponding detection position (tangential_num, axial_num, radial_num) for each crystal.
+	The crystal map, then, is used in ProjDataInfoBlocksOnCylindrical, ProjDataInfoBlocksOnCylindricalNoArcCorr, and CListRecordSAFIR
 
-	\The center of first ring is the center of coordinates.
-	\Distances are from center to center of crystals.
+	The center of first ring is the center of coordinates.
+	Distances are from center to center of crystals.
 
 */
 

src/include/stir/HighResWallClockTimer.h

@@ -17,7 +17,8 @@
  \author Alexey Zverovich
  \author PARAPET project
 
-
+*/
+/*
  Modification history:
 
   <TT>

src/include/stir/recon_buildblock/ForwardProjectorByBinUsingRayTracing.h

@@ -44,8 +44,8 @@ class ProjDataInfoCylindrical;
   \brief This class implements forward projection using Siddon's algorithm for
   ray tracing. That is, it computes length of intersection with the voxels.
 
-  Currently, the LOIs are divided by voxel_size.x(), unless NEWSCALE is
-  #defined during compilation time of ForwardProjectorByBinUsingRayTracing_Siddon.cxx. 
+  Currently, the LOIs are divided by voxel_size.x(), unless \c NEWSCALE is
+  \c \#defined during compilation time of ForwardProjectorByBinUsingRayTracing_Siddon.cxx.
 
   If the z voxel size is exactly twice the sampling in axial direction,
   multiple LORs are used, to avoid missing voxels. (TODOdoc describe how).

src/include/stir/recon_buildblock/PLSPrior.h

@@ -48,7 +48,7 @@ START_NAMESPACE_STIR
   \phi(f) = \sqrt{\alpha^2 + |\nabla f|^2 - {\langle\nabla f,\xi\rangle}^2}
   \f]
   where \f$ f \f$ is the PET image,
-  \f$\nabla \f$ is the finite difference operator (\textrm{not} taking voxel-sizes into account) and
+  \f$\nabla \f$ is the finite difference operator (\b not taking voxel-sizes into account) and
   \f$ \xi \f$ is the normalised gradient of the anatomical image calculated as follows:
 
   \f[

src/include/stir/recon_buildblock/ProjMatrixByBinPinholeSPECTUB.h

@@ -3,17 +3,7 @@
     Copyright (C) 2021, University College London
     This file is part of STIR.
 
-	Licensed under the Apache License, Version 2.0 (the "License");
-	you may not use this file except in compliance with the License.
-	You may obtain a copy of the License at
-
-		http://www.apache.org/licenses/LICENSE-2.0
-
-	Unless required by applicable law or agreed to in writing, software
-	distributed under the License is distributed on an "AS IS" BASIS,
-	WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
-	See the License for the specific language governing permissions and
-	limitations under the License.
+    SPDX-License-Identifier: Apache-2.0
 
     See STIR/LICENSE.txt for details
 */
@@ -53,7 +43,7 @@ class Bin;
 
   \warning this class currently only works with VoxelsOnCartesianGrid. 
 
-  \Sample parameter file
+  \par Sample parameter file
 
 \verbatim
     Projection Matrix By Bin Pinhole SPECT UB Parameters:=
@@ -83,7 +73,7 @@ class Bin;
     End Projection Matrix By Bin Pinhole SPECT UB Parameters:=
 \endverbatim
 
-  \Sample detector file
+  \par Sample detector file
   
 \verbatim
     Information of detector
@@ -104,7 +94,7 @@ class Bin;
     \#…………until here……………\#
 \endverbatim
 
-  \Sample collimator file
+  \par Sample collimator file
 \verbatim
     Information of collimator
     Comments are allowed here or anywhere in lines not containing parameters.

src/include/stir/recon_buildblock/ProjMatrixByBinUsingRayTracing.h

@@ -38,8 +38,8 @@ class ProjDataInfo;
   \brief Computes projection matrix elements for VoxelsOnCartesianGrid images
   by using a Length of Intersection (LOI) model. 
 
-  Currently, the LOIs are divided by voxel_size.x(), unless NEWSCALE is
-  #defined during compilation time of ProjMatrixByBinUsingRayTracing.cxx. 
+  Currently, the LOIs are divided by voxel_size.x(), unless \c NEWSCALE is
+  \c \#defined during compilation time of ProjMatrixByBinUsingRayTracing.cxx.
 
   It is possible to use multiple LORs in tangential direction. The result
   will then be the average of the various contributions. Currently all these

src/include/stir_experimental/modelling/BloodFrameData.inl

@@ -25,7 +25,8 @@ START_NAMESPACE_STIR
 BloodFrameData::BloodFrameData()
 { } 
 
-//! constructor giving a vector //ChT::ToDO: Better to use iterators
+//! constructor giving a vector
+//ChT::ToDO: Better to use iterators
 BloodFrameData::BloodFrameData(const std::vector<BloodFrame> & blood_plot)
 {this->_blood_plot=blood_plot;}
 

src/include/stir_experimental/motion/RigidObject3DTransformation.h

@@ -143,7 +143,7 @@ class RigidObject3DTransformation
   //! Transform bin from some projection data
   /*!  Finds 'closest' (in some sense) bin to the transformed LOR.
 
-     if NEW_ROT is not #defined at compilation time, 
+     if \c NEW_ROT is not \c \#defined at compilation time, 
     it will throw an exception when arc-corrected data is used.*/
   void transform_bin(Bin& bin,const ProjDataInfo& out_proj_data_info,
 	             const ProjDataInfo& in_proj_data_info) const;

src/include/stir_experimental/recon_buildblock/ProjMatrixByDenselOnCartesianGridUsingElement.h

@@ -32,8 +32,8 @@ template <int num_dimensions, typename elemT> class DiscretisedDensity;
   \brief Computes projection matrix elements for VoxelsOnCartesianGrid images
   by using a Length of Intersection (LOI) model. 
 
-  Currently, the LOIs are divided by voxel_size.x(), unless NEWSCALE is
-  #defined during compilation time of ProjMatrixByDenselOnCartesianGridUsingElement.cxx. 
+  Currently, the LOIs are divided by voxel_size.x(), unless \c NEWSCALE is
+  \c \#defined during compilation time of ProjMatrixByDenselOnCartesianGridUsingElement.cxx.
 
   If the z voxel size is exactly twice the sampling in axial direction,
   multiple LORs are used, to avoid missing voxels. (TODOdoc describe how).

src/include/stir_experimental/recon_buildblock/ProjMatrixByDenselUsingRayTracing.h

@@ -32,8 +32,8 @@ class DataSymmetriesForDensels_PET_CartesianGrid;
   \brief Computes projection matrix elements for VoxelsOnCartesianGrid images
   by using a Length of Intersection (LOI) model. 
 
-  Currently, the LOIs are divided by voxel_size.x(), unless NEWSCALE is
-  #defined during compilation time of ProjMatrixByDenselUsingRayTracing.cxx. 
+  Currently, the LOIs are divided by voxel_size.x(), unless \c NEWSCALE is
+  \c \#defined during compilation time of ProjMatrixByDenselUsingRayTracing.cxx.
 
   If the z voxel size is exactly twice the sampling in axial direction,
   multiple LORs are used, to avoid missing voxels. (TODOdoc describe how).

src/recon_buildblock/BackProjectorByBinUsingInterpolation_linear.cxx

@@ -9,7 +9,7 @@
   stir::BackProjectorByBinUsingInterpolation, for the case of piecewise 
   linear interpolation.
 
-  \warning This #includes BackProjectorByBinUsingInterpolation_3DCho.cxx 
+  \warning This \c \#includes BackProjectorByBinUsingInterpolation_3DCho.cxx
 
   This very ugly way of including a .cxx file is used to avoid replication of
   a lot of (difficult) code.

src/recon_buildblock/BackProjectorByBinUsingInterpolation_piecewise_linear.cxx

@@ -9,7 +9,7 @@
   stir::BackProjectorByBinUsingInterpolation, for the case of piecewise 
   linear interpolation.
 
-  \warning This #includes BackProjectorByBinUsingInterpolation_3DCho.cxx 
+  \warning This \c \#includes BackProjectorByBinUsingInterpolation_3DCho.cxx
 
   This very ugly way of including a .cxx file is used to avoid replication of
   a lot of (difficult) code.