Update doxygen

doxygen/doxygengroups.h

@@ -0,0 +1,55 @@
+/*
+CCP PETMR Synergistic Image Reconstruction Framework (SIRF)
+Copyright 2019 University College London
+
+This is software developed for the Collaborative Computational
+Project in Positron Emission Tomography and Magnetic Resonance imaging
+(http://www.ccppetmr.ac.uk/).
+
+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.
+
+*/
+
+// define some doxygen groups and namespace
+// This file does not contain any code
+
+/*! \namespace sirf
+  \brief Namespace for the SIRF library (and some/most of its applications)
+
+  This namespace encompasses the whole
+  library. All classes, functions and symbols are in this namespace.
+  This has the effect that conflicts with any other library is
+  impossible (except if that library uses the same namespace...).
+*/
+
+/*!
+\defgroup PET SIRF PET
+\ingroup SIRF
+All PET functionality of SIRF.
+*/
+
+/*!
+\defgroup MR SIRF MR
+\ingroup SIRF
+All MR functionality of SIRF.
+*/
+
+/*!
+\defgroup Registration SIRF registration
+\ingroup SIRF
+All registration/resampling functionality of SIRF.
+*/
+
+/*!
+\defgroup Synergistic SIRF synergistic
+\ingroup SIRF
+All synergistic functionality of SIRF.
+*/

src/Registration/cReg/NiftiImageData3D.cpp

@@ -21,7 +21,7 @@ limitations under the License.
 /*!
 \file
 \ingroup Registration
-\brief Base class for SIRF image data.
+\brief Base class for 3D SIRF image data.
 
 \author Richard Brown
 \author CCP PETMR

src/Registration/cReg/NiftiImageData3DTensor.cpp

@@ -21,7 +21,7 @@ limitations under the License.
 /*!
 \file
 \ingroup Registration
-\brief Class for deformation and displacement SIRF image data.
+\brief Class for tensor SIRF image data.
 
 \author Richard Brown
 \author CCP PETMR

src/Registration/cReg/NiftyRegistration.cpp

@@ -21,7 +21,7 @@ limitations under the License.
 /*!
 \file
 \ingroup Registration
-\brief Base class for all SIRF registration.
+\brief Base class for all NiftyReg registration algorithms.
 
 \author Richard Brown
 \author CCP PETMR

src/Registration/cReg/Resample.cpp

@@ -21,7 +21,7 @@ limitations under the License.
 /*!
 \file
 \ingroup Registration
-\brief bstract resampling base class
+\brief Abstract resampling base class
 
 \author Richard Brown
 \author CCP PETMR

src/Registration/cReg/include/sirf/cReg/AffineTransformation.h

@@ -33,7 +33,12 @@ limitations under the License.
 #include "sirf/cReg/Transformation.h"
 
 namespace sirf {
-///Class for affine transformations
+/*!
+\ingroup Registration
+\brief Class for affine transformations.
+\author Richard Brown
+\author CCP PETMR
+*/
 template<class dataType>
 class AffineTransformation : public Transformation<dataType>
 {

src/Registration/cReg/include/sirf/cReg/ImageWeightedMean.h

@@ -37,7 +37,16 @@ namespace sirf {
 // Forward delcarations
 template<class dataType> class NiftiImageData;
 
-/// Calculate the weighted mean of a set of images
+/*!
+\file
+\ingroup Registration
+\brief Perform weighted mean of multiple images.
+
+TODO - would be simple for this to work in terms of ImageData instead of NiftiImageData.
+
+\author Richard Brown
+\author CCP PETMR
+*/
 template<class dataType>
 class ImageWeightedMean
 {

src/Registration/cReg/include/sirf/cReg/NiftiImageData.h

@@ -23,22 +23,6 @@ limitations under the License.
 \ingroup Registration
 \brief Base class for SIRF nifti image data.
 
-Generally SIRF (not necessarily NiftyReg) will preferentially use
-the qform over the sform code. This is the same for ITK and ANTs, but
-is not the case for SPM/MRIcroGL/FSLeyes/Mango.
-
-qform/sform
-The qform code describes "scanner-anatomical" coordinates, whereas the
-sform code describes the location of the voxels in some standard space.
-
-For qform > 0, the origin of coordinates would generally be whatever
-the scanner origin is; for example, in MRI, (0,0,0) is the center
-of the gradient coil.
-
-For sform > 0, the origin of coordinates would depend on the value
-of sform_code; for example, for the Talairach coordinate system,
-(0,0,0) corresponds to the Anterior Commissure.
-
 \author Richard Brown
 \author CCP PETMR
 */
@@ -57,7 +41,37 @@ of sform_code; for example, for the Talairach coordinate system,
 
 namespace sirf {
 
-/// SIRF image data
+/*!
+\file
+\ingroup Registration
+\brief Base class for SIRF's nifti image data.
+
+This is a wrapper around the basic nifti_image (stored as a sptr),
+with extra functionality.
+
+This is the general form, and any number of dimensions are allowed. 
+This is contrary to the derived classes, which have specific requirements
+(e.g., NiftiImageData3DDeformation requires 5 dimensions, of which the 4th (time) == 1).
+
+To move between different images types (e.g., STIRImageData and MRImageData), 
+we need to know the patient's position relative to the scanner. For this, only
+qform_code == 1 will suffice.
+
+qform/sform
+The qform code describes "scanner-anatomical" coordinates, whereas the
+sform code describes the location of the voxels in some standard space.
+
+For qform > 0, the origin of coordinates would generally be whatever
+the scanner origin is; for example, in MRI, (0,0,0) is the center
+of the gradient coil.
+
+For sform > 0, the origin of coordinates would depend on the value
+of sform_code; for example, for the Talairach coordinate system,
+(0,0,0) corresponds to the Anterior Commissure.
+
+\author Richard Brown
+\author CCP PETMR
+*/
 template<class dataType>
 class NiftiImageData : public ImageData
 {

src/Registration/cReg/include/sirf/cReg/NiftiImageData3D.h

@@ -21,7 +21,7 @@ limitations under the License.
 /*!
 \file
 \ingroup Registration
-\brief Base class for SIRF image data.
+\brief 3D Nifti image.
 
 \author Richard Brown
 \author CCP PETMR
@@ -33,7 +33,15 @@ limitations under the License.
 
 namespace sirf {
 
-/// SIRF image data
+/*!
+\ingroup Registration
+\brief 3D Nifti image.
+
+Here, we require that the number of dimensions == 3.
+
+\author Richard Brown
+\author CCP PETMR
+*/
 template<class dataType>
 class NiftiImageData3D : public NiftiImageData<dataType>
 {

src/Registration/cReg/include/sirf/cReg/NiftiImageData3DDeformation.h

@@ -21,7 +21,7 @@ limitations under the License.
 /*!
 \file
 \ingroup Registration
-\brief Class for deformation/displacement SIRF image data.
+\brief Class for deformation SIRF image data.
 
 \author Richard Brown
 \author CCP PETMR
@@ -38,7 +38,16 @@ namespace sirf {
 template<class dataType> class NiftiImageData3D;
 template<class dataType> class NiftiImageData3DDisplacement;
 
-/// SIRF nifti image data deformation field image
+/*!
+\ingroup Registration
+\brief Class for deformation SIRF image data.
+
+Here, we require ndim == 5, nt == 1 (so contains x,y,z dimensions as well as u==3 for the tensor component).
+Also require intent_p1 == DEF_FIELD.
+
+\author Richard Brown
+\author CCP PETMR
+*/
 template<class dataType>
 class NiftiImageData3DDeformation : public NiftiImageData3DTensor<dataType>, public Transformation<dataType>
 {
@@ -68,7 +77,7 @@ class NiftiImageData3DDeformation : public NiftiImageData3DTensor<dataType>, pub
     /// Create from 3D image
     void create_from_3D_image(const NiftiImageData3D<dataType> &image);
 
-    /// Create from CPP image
+    /// Create from control point grid image
     void create_from_cpp(NiftiImageData3DTensor<dataType> &cpp, const NiftiImageData3D<dataType> &ref);
 
     /// Get as deformation field

src/Registration/cReg/include/sirf/cReg/NiftiImageData3DDisplacement.h

@@ -21,7 +21,7 @@ limitations under the License.
 /*!
 \file
 \ingroup Registration
-\brief Class for deformation/displacement SIRF image data.
+\brief Class for displacement SIRF image data.
 
 \author Richard Brown
 \author CCP PETMR
@@ -36,7 +36,16 @@ limitations under the License.
 namespace sirf {
 template<class dataType> class NiftiImageData3D;
 
-/// SIRF nifti image data displacement field image
+/*!
+\ingroup Registration
+\brief Class for displacement SIRF image data.
+
+Here, we require ndim == 5, nt == 1 (so contains x,y,z dimensions as well as u==3 for the tensor component).
+Also require intent_p1 == DISP_FIELD.
+
+\author Richard Brown
+\author CCP PETMR
+*/
 template<class dataType>
 class NiftiImageData3DDisplacement : public NiftiImageData3DTensor<dataType>, public Transformation<dataType>
 {

src/Registration/cReg/include/sirf/cReg/NiftiImageData3DTensor.h

@@ -21,7 +21,7 @@ limitations under the License.
 /*!
 \file
 \ingroup Registration
-\brief Class for deformation/displacement SIRF image data.
+\brief Class for tensor SIRF image data.
 
 \author Richard Brown
 \author CCP PETMR
@@ -36,7 +36,17 @@ namespace sirf {
 // Forward declarations
 template<class dataType> class NiftiImageData3D;
 
-/// SIRF image data
+/*!
+\ingroup Registration
+\brief Class for tensor SIRF image data.
+
+Here, we require ndim == 5, nt == 1 (so contains x,y,z dimensions as well as u==3 for the tensor component).
+This is the general tensor class, so we do not care if the image is a deformation or displacement field (or any other type).
+Hence, any value of intent_p1 is fine.
+
+\author Richard Brown
+\author CCP PETMR
+*/
 template<class dataType>
 class NiftiImageData3DTensor : public NiftiImageData<dataType>
 {

src/Registration/cReg/include/sirf/cReg/NiftyAladinSym.h

@@ -38,7 +38,15 @@ namespace sirf {
 /// Forward declarations
 template<class dataType> class AffineTransformation;
 
-/// Wrapper around NiftyReg's aladin class for rigid and affine transformations
+/*!
+\ingroup Registration
+\brief NiftyReg's aladin class for rigid and affine registrations.
+
+Since this algorithm is affine/rigid, it can also return a transformation matrix if desired.
+
+\author Richard Brown
+\author CCP PETMR
+*/
 template<class dataType> class NiftyAladinSym : public NiftyRegistration<dataType>
 {
 public:

src/Registration/cReg/include/sirf/cReg/NiftyF3dSym.h

@@ -38,7 +38,18 @@ namespace sirf {
 /// Forward declarations
 template<class dataType> class AffineTransformation;
 
-/// Wrapper around NiftyReg's f3d class for non-rigid transformations
+/*!
+\ingroup Registration
+\brief NiftyReg's f3d class for non-rigid registrations.
+
+User can set an initial affine transformation if desired. 
+
+In theory, multiple time points can be used, but thus far has only been tested for
+t == 1 for both reference and floating images.
+
+\author Richard Brown
+\author CCP PETMR
+*/
 template<class dataType> class NiftyF3dSym : public NiftyRegistration<dataType>
 {
 public:

src/Registration/cReg/include/sirf/cReg/NiftyRegistration.h

@@ -21,24 +21,7 @@ limitations under the License.
 /*!
 \file
 \ingroup Registration
-\brief Base class for all SIRF registration.
-
-The parameter file should have interfile-like syntax.
-The variables will be stored as a vector of floats and converted into the required type (int, unsigned int, etc) if necessary.
-Multiple variables for a given parameter should be comma separated.
-Spaces and tabs will be ignored.
-For the title, it doesn't matter what is written as it will be ignored, but something has to be there (otherwise the first parameter will be ignored).
-Possible parameters are all the Set<something> methods for each class (e.g., nifty_aladin::SetPerformRigid) and should be written in the parameter file without the "Set" (e.g., PerformRigid).
-
-An example is given below:
-    SomeTitle :=
-        ReferenceTimePoint := 1
-        FloatingTimePoint := 2
-        LinearEnergyWeights := 1.5,1
-        AdditiveMC :=
-    end :=
-
-More examples can be found in data/examples/Registration/paramFiles
+\brief Base class for all NiftyReg registrations.
 
 \author Richard Brown
 \author CCP PETMR
@@ -53,7 +36,13 @@ namespace sirf {
 /// Forward declarations
 template<class dataType> class NiftiImageData3D;
 
-/// Base class for wrapped NiftyReg registration algorithms
+/*!
+\ingroup Registration
+\brief Base class for all NiftyReg registrations.
+
+\author Richard Brown
+\author CCP PETMR
+*/
 template<class dataType>
 class NiftyRegistration : public Registration<dataType>
 {