SIRFReg

.gitignore

@@ -266,3 +266,7 @@ coverage.xml
 *_out.txt
 # submodules which should be explicitly force-pushed
 /data
+
+# Dont track NiftyAladinSym.cpp/NiftyF3dSym.cpp as they are generated with CMake's configure_file
+NiftyAladinSym.cpp
+NiftyF3dSym.cpp

CMakeLists.txt

@@ -138,3 +138,17 @@ ADD_SUBDIRECTORY(src/common)
 ADD_SUBDIRECTORY(src/xSTIR)
 ADD_SUBDIRECTORY(src/xGadgetron)
 include("${CMAKE_CURRENT_SOURCE_DIR}/cmake/setup.py.cmake")
+
+# Optional registration
+option(REG_ENABLE "Build the SIRF registration package" ON)
+if (REG_ENABLE)
+  ADD_SUBDIRECTORY(src/Registration)
+endif()
+
+# Synergistic code currently only works if STIR (with ITK), Gadgetron and Registration are built
+if (REG_ENABLE AND STIR_REGISTRIES AND cGadgetron_LIBRARY_DIRS AND "${STIR_BUILT_WITH_ITK}")
+  MESSAGE(STATUS "Registration, Gadgetron and STIR (with ITK) have been built. Building synergistic code.")
+  ADD_SUBDIRECTORY(src/Synergistic)
+else()
+  MESSAGE(STATUS "One or more of the following components are missing: Registration, Gadgetron and STIR (with ITK). Synergistic code will not be built.")
+endif()

cmake/FindNiftyReg.cmake

@@ -0,0 +1,86 @@
+#========================================================================
+# Author: Richard Brown
+# Copyright 2016, 2017 University College London
+#
+#  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.txt
+#
+#  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.
+#
+#=========================================================================
+
+set(NiftyReg_FOUND 0)
+
+SET(NiftyReg_Binary_DIR CACHE PATH "NiftyReg binary directory" )
+
+# Ask for the binary and check
+IF (NOT IS_DIRECTORY ${NiftyReg_Binary_DIR})
+	MESSAGE(FATAL_ERROR "Enter the binary directory of NiftyReg.")
+ENDIF()
+
+IF(EXISTS "${NiftyReg_Binary_DIR}/CMakeCache.txt")
+  LOAD_CACHE("${NiftyReg_Binary_DIR}" READ_WITH_PREFIX "nifty" "NiftyReg_SOURCE_DIR" "CMAKE_INSTALL_PREFIX" "USE_OPENMP")
+endif()
+
+SET(NiftyReg_Source_DIR ${niftyNiftyReg_SOURCE_DIR})
+SET(NiftyReg_Install_DIR ${niftyCMAKE_INSTALL_PREFIX})
+SET(NiftyReg_built_with_openmp ${niftyUSE_OPENMP})
+
+# Include
+INCLUDE_DIRECTORIES(${NiftyReg_Source_DIR}/reg-io/nrrd/NrrdIO) # ugly, but required for nrrdIO.h
+INCLUDE_DIRECTORIES(${NiftyReg_Binary_DIR})                    # ugly, but required for NrrdConfigure.h
+INCLUDE_DIRECTORIES(${NiftyReg_Install_DIR}/include)
+
+# Get the NiftyReg versions from its CMakeLists.txt
+# This for older versions of NiftyReg
+FILE(READ ${NiftyReg_Source_DIR}/CMakeLists.txt NiftyReg_CMakeLists)
+STRING(REGEX MATCH "NiftyReg_VERSION_MAJOR ([0-9]*)" _ ${NiftyReg_CMakeLists} )
+SET(NiftyReg_VERSION_MAJOR ${CMAKE_MATCH_1})
+STRING(REGEX MATCH "NiftyReg_VERSION_MINOR ([0-9]*)" _ ${NiftyReg_CMakeLists} )
+SET(NiftyReg_VERSION_MINOR ${CMAKE_MATCH_1})
+STRING(REGEX MATCH "NiftyReg_VERSION_PATCH ([0-9]*)" _ ${NiftyReg_CMakeLists} )
+SET(NiftyReg_VERSION_PATCH ${CMAKE_MATCH_1})
+# This for more recent versions of NiftyReg
+IF (NOT DEFINED NiftyReg_VERSION_MAJOR)
+	STRING(REGEX MATCH "NR_VERSION_MAJOR ([0-9]*)" _ ${NiftyReg_CMakeLists} )
+	SET(NiftyReg_VERSION_MAJOR ${CMAKE_MATCH_1})
+	STRING(REGEX MATCH "NR_VERSION_MINOR ([0-9]*)" _ ${NiftyReg_CMakeLists} )
+	SET(NiftyReg_VERSION_MINOR ${CMAKE_MATCH_1})
+	FILE(READ ${NiftyReg_Source_DIR}/niftyreg_build_version.txt NiftyReg_VERSION_PATCH)
+ENDIF()
+SET(NR_VERSION "${NiftyReg_VERSION_MAJOR}.${NiftyReg_VERSION_MINOR}.${NiftyReg_VERSION_PATCH}")
+string(REGEX REPLACE "\n$" "" NR_VERSION "${NR_VERSION}")
+
+SET(NiftyReg_requiredLibs
+    _reg_aladin
+    _reg_blockMatching
+    _reg_f3d
+    _reg_maths
+    _reg_ReadWriteImage
+    _reg_resampling
+    _reg_tools
+    reg_nifti
+    reg_png
+    _reg_femTrans
+    _reg_globalTrans
+    _reg_localTrans
+    _reg_measure
+    )
+
+# Loop over each library, find it and add it. 
+# Do it twice to resolve linking errors depending on order
+FOREACH(elem ${NiftyReg_requiredLibs} ${NiftyReg_requiredLibs})
+    FIND_LIBRARY(NiftyReg_${elem} ${elem} HINTS ${NiftyReg_Install_DIR}/lib)
+    MARK_AS_ADVANCED(NiftyReg_${elem})
+    SET(NiftyReg_Libs ${NiftyReg_Libs} ${NiftyReg_${elem}} )
+ENDFOREACH(elem ${NiftyReg_requiredLibs})
+
+# Success!
+set(NiftyReg_FOUND 1)

cmake/setup.py.cmake

@@ -18,6 +18,8 @@ if(BUILD_PYTHON)
   python_pkg_alias(pygadgetron "sirf.pygadgetron")
   python_pkg_alias(pystir "sirf.pystir")
   python_pkg_alias(pyiutilities "sirf.pyiutilities")
+  python_pkg_alias(pReg "sirf.Reg")
+  python_pkg_alias(pyreg "sirf.pyreg")
   # convert to python CSV tuple for setup.py configure_file
   string(REPLACE ";" "', '" PYTHON_SETUP_PKGS_CSV "${PYTHON_SETUP_PKGS}")
   set(PYTHON_SETUP_PKGS_CSV "'${PYTHON_SETUP_PKGS_CSV}'")

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.
+*/

examples/Matlab/Registration/sirf_registration.m

@@ -0,0 +1,173 @@
+function registration(varargin)
+% Registration of SIRF images. 
+%   --eng_ref <eng>              engine for reference image [default: Reg]
+%   --eng_flo <eng>              engine for floating image [default: Reg]
+%   --ref <file>                 reference image (default: test.nii.gz)
+%   --flo <file>                 floating image (default: test2.nii.gz)
+%   --par <file>                 parameter file (default: niftyreg_aladin.par)
+%   --algo <algo>                registration algorithm [default: NiftyAladinSym]
+%   --rmask                      mask of reference image
+%   --fmask                      mask of floating image
+%   --warped <file>              warped image filename [default: warped]
+%   --TM_forward                 forward transformation matrix (if rigid/affine)
+%   --TM_inverse                 inverse transformation matrix (if rigid/affine)
+%   --disp_fwd_4D                4D forward displacement field image
+%   --def_fwd_4D                 4D forward deformation field image
+%   --disp_inv_4D                4D inverse displacement field image
+%   --def_inv_4D                 4D inverse deformation field image
+
+% CCP PETMR Synergistic Image Reconstruction Framework (SIRF).
+% Copyright 2018 - 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.
+
+%% Parse the input
+i=1;
+while i <= length(varargin)
+    if     strcmp(varargin{i},'eng_ref')
+        eng_ref = get_arg(varargin,i,1);
+        i=i+2;
+    elseif strcmp(varargin{i},'eng_flo')
+        eng_flo = get_arg(varargin,i,1);
+        i=i+2;
+    elseif strcmp(varargin{i},'ref')
+        ref_file = get_arg(varargin,i,1);
+        i=i+2;
+    elseif strcmp(varargin{i},'flo')
+        flo_file = get_arg(varargin,i,1);
+        i=i+2;
+   elseif strcmp(varargin{i},'algo')
+        algo = get_arg(varargin,i,1);
+        i=i+2;
+   elseif strcmp(varargin{i},'warped')
+        warped = get_arg(varargin,i,1);
+        i=i+2;
+    elseif strcmp(varargin{i},'par')
+        par_file = get_arg(varargin,i,1);
+        i=i+2;
+
+    elseif strcmp(varargin{i},'rmask')
+        rmask = get_arg(varargin,i,1);
+        i=i+2;        
+    elseif strcmp(varargin{i},'fmask')
+        fmask = get_arg(varargin,i,1);
+        i=i+2;        
+
+    elseif strcmp(varargin{i},'TM_forward')
+        TM_forward = get_arg(varargin,i,1);
+        i=i+2;        
+    elseif strcmp(varargin{i},'TM_inverse')
+        TM_inverse = get_arg(varargin,i,1);
+        i=i+2;        
+    elseif strcmp(varargin{i},'disp_fwd_4D')
+        disp_fwd_4D = get_arg(varargin,i,1);
+        i=i+2;        
+    elseif strcmp(varargin{i},'disp_inv_4D')
+        disp_inv_4D = get_arg(varargin,i,1);
+        i=i+2;        
+    elseif strcmp(varargin{i},'def_fwd_4D')
+        def_fwd_4D = get_arg(varargin,i,1);
+        i=i+2;        
+    elseif strcmp(varargin{i},'def_inv_4D')
+        def_inv_4D = get_arg(varargin,i,1);
+        i=i+2;
+    else
+        error(['Unknown argument: ' varargin{i} '. Use help(function) for help.']);  
+    end    
+end
+
+%% Default values
+% If using default ref or flo images, need SIRF data
+if ~exist('ref_file','var') || ~exist('flo_file','var')
+    SIRF_PATH     = getenv('SIRF_PATH');
+    examples_path = fullfile(SIRF_PATH, '/data/examples/Registration');
+end
+
+if ~exist('eng_ref','var')  eng_ref  = 'Reg'; end
+if ~exist('eng_flo','var')  eng_flo  = 'Reg'; end
+if ~exist('ref_file','var') ref_file = fullfile(examples_path, 'test.nii.gz');  end
+if ~exist('flo_file','var') flo_file = fullfile(examples_path, 'test2.nii.gz'); end
+if ~exist('algo','var')     algo     = 'NiftyAladinSym'; end
+if ~exist('warped','var')   warped   = 'warped'; end
+if ~exist('par_file','var') par_file = fullfile(examples_path, 'paramFiles/niftyreg_aladin.par'); end
+
+%% Registration
+% Open reference and floating images
+disp(['Engine for reference image: ', eng_ref])
+disp(['Engine for floating image: ', eng_flo])
+disp(['Reference image: ', ref_file])
+disp(['Floating image: ', flo_file])
+
+% Dynamically set up the engines required
+set_up_Reg();
+eng_ref = set_up_engine(eng_ref);
+eng_flo = set_up_engine(eng_flo);
+
+ref = eng_ref.ImageData(ref_file);
+flo = eng_flo.ImageData(flo_file);
+
+% Dynamically create resample algorithm
+reg = eval(['mReg.' algo]);
+reg.set_reference_image(ref)
+reg.set_floating_image(flo)
+if exist('par_file','var')
+    reg.set_parameter_file(par_file);
+end
+if exist('rmask_file','var')
+    rmask = eng_ref.ImageData(rmask_file);
+    reg.set_reference_mask(rmask)
+end
+if exist('fmask_file','var')
+    fmask = eng_ref.ImageData(fmask_file);
+    reg.set_floating_mask(fmask)
+end
+
+reg.process();
+
+%% Output 
+reg.get_output().write(warped);
+
+% TMs
+if exist('TM_forward','var')
+    reg.get_transformation_matrix_forward().write(TM_forward)
+end
+if exist('TM_inverse','var')
+    reg.get_transformation_matrix_forward().write(TM_inverse)
+end
+
+% Disp fields
+if exist('disp_fwd_4D','var')
+    reg.get_displacement_field_forward().write(disp_fwd_4D)
+end
+if exist('disp_inv_4D','var')
+    reg.get_displacement_field_inverse().write(disp_inv_4D)
+end
+
+% Def fields
+if exist('def_fwd_4D','var')
+    reg.get_deformation_field_forward().write(def_fwd_4D)
+end
+if exist('disp_inv_4D','var')
+    reg.get_deformation_field_inverse().write(def_inv_4D)
+end
+
+end
+
+function arg = get_arg(list,index,increment)
+    if (index+increment > length(list))
+        error(['Not sufficient arguments following: ' list{index}])
+    end
+    arg = list{index+increment};
+end