diff --git a/CHANGES.md b/CHANGES.md index 451727b94..7aab0b19d 100644 --- a/CHANGES.md +++ b/CHANGES.md @@ -105,7 +105,7 @@ * Build with OpenMP delivers stable and substantially accelerated performance * More documentation * Developer's Guide - * Doxygen inline documentation (available on CCP PETMR website) + * Doxygen inline documentation (available on SyneRBI website) * More tests (now run via CTest), for Python, Matlab and C++. * Coverage reporting for Python tests done by ctest diff --git a/CMakeLists.txt b/CMakeLists.txt index 5ba09b236..38544b949 100644 --- a/CMakeLists.txt +++ b/CMakeLists.txt @@ -1,8 +1,8 @@ #======================================================================== # Author: Kris Thielemans -# Copyright 2016 - 2019 University College London -# Copyright 2016 - 2018 Science Technology Facilities Council +# Copyright 2016 - 2020 University College London +# Copyright 2016 - 2020 Science Technology Facilities Council # # Licensed under the Apache License, Version 2.0 (the "License"); # you may not use this file except in compliance with the License. diff --git a/NOTICE.txt b/NOTICE.txt index fc67a52b5..954979f0d 100644 --- a/NOTICE.txt +++ b/NOTICE.txt @@ -1,11 +1,11 @@ CCP SyneRBI (formerly PETMR) Synergistic Image Reconstruction Framework (SIRF). Copyright 2015-2020 Rutherford Appleton Laboratory STFC Copyright 2015-2020 University College London (UCL) -Copyright 2017-2019 Physikalisch-Technische Bundesanstalt (PTB) +Copyright 2017-2020 Physikalisch-Technische Bundesanstalt (PTB) This software product is developed for the Collaborative Computational Project in Synergistic Reconstruction for Biomedical Imaging, -formerly CCP PETMR, (http://www.ccpsynerbi.ac.uk/) +formerly SyneRBI, (http://www.ccpsynerbi.ac.uk/) at RAL STFC (http://www.stfc.ac.uk), UCL (http://www.ucl.ac.uk/) and other contributing institutions. diff --git a/README.md b/README.md index d8e2b3cbe..22b26df55 100644 --- a/README.md +++ b/README.md @@ -3,8 +3,8 @@ [![travis-badge]][travis] [![coveralls-badge]][coveralls] [![codecov-badge]][codecov] -This software is the main output of [CCP PETMR](https://www.ccppetmr.ac.uk), the Collaborative Computational -Platform for Synergistic Reconstruction for PET/MR. +This software is the main output of [SyneRBI](https://www.ccpsynerbi.ac.uk), the Collaborative Computational +Platform for Synergistic Reconstruction for Biomedical Imaging (formerly CCP PETMR). Please start with our latest [User's Guide](doc/UserGuide.md). See [our Wiki page for installation instructions](https://github.com/CCPPETMR/SIRF/wiki/Installation-instructions). diff --git a/doxygen/doxygengroups.h b/doxygen/doxygengroups.h index ece254fed..39c415c51 100644 --- a/doxygen/doxygengroups.h +++ b/doxygen/doxygengroups.h @@ -1,10 +1,10 @@ /* -CCP PETMR Synergistic Image Reconstruction Framework (SIRF) +SyneRBI 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/). +Project in Synergistic Reconstruction for Biomedical Imaging (formerly CCP PETMR) +(http://www.ccpsynerbi.ac.uk/). Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. diff --git a/examples/Matlab/MR/Gadgetron/fully_sampled_recon_single_chain.m b/examples/Matlab/MR/Gadgetron/fully_sampled_recon_single_chain.m index 77dfc58e9..5e8ff97a6 100644 --- a/examples/Matlab/MR/Gadgetron/fully_sampled_recon_single_chain.m +++ b/examples/Matlab/MR/Gadgetron/fully_sampled_recon_single_chain.m @@ -3,13 +3,13 @@ function fully_sampled_recon_single_chain(engine) % % See FULLY_SAMPLED_RECON for example data files. -% CCP PETMR Synergistic Image Reconstruction Framework (SIRF). -% Copyright 2015 - 2017 Rutherford Appleton Laboratory STFC. -% Copyright 2015 - 2017 University College London. +% SyneRBI Synergistic Image Reconstruction Framework (SIRF). +% Copyright 2015 - 2019 Rutherford Appleton Laboratory STFC. +% Copyright 2015 - 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/). +% Project in Synergistic Reconstruction for Biomedical Imaging (formerly CCP PETMR) +% (http://www.ccpsynerbi.ac.uk/). % % Licensed under the Apache License, Version 2.0 (the "License"); % you may not use this file except in compliance with the License. diff --git a/examples/Matlab/MR/Gadgetron/fully_sampled_recon_three_chains.m b/examples/Matlab/MR/Gadgetron/fully_sampled_recon_three_chains.m index 5d2b88ef3..cdddd19b6 100644 --- a/examples/Matlab/MR/Gadgetron/fully_sampled_recon_three_chains.m +++ b/examples/Matlab/MR/Gadgetron/fully_sampled_recon_three_chains.m @@ -8,13 +8,13 @@ function fully_sampled_recon_three_chains(engine) % % See also FULLY_SAMPLED_RECON -% CCP PETMR Synergistic Image Reconstruction Framework (SIRF). -% Copyright 2015 - 2017 Rutherford Appleton Laboratory STFC. -% Copyright 2015 - 2017 University College London. +% SyneRBI Synergistic Image Reconstruction Framework (SIRF). +% Copyright 2015 - 2020 Rutherford Appleton Laboratory STFC. +% Copyright 2015 - 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/). +% Project in Synergistic Reconstruction for Biomedical Imaging (formerly CCP PETMR) +% (http://www.ccpsynerbi.ac.uk/). % % Licensed under the Apache License, Version 2.0 (the "License"); % you may not use this file except in compliance with the License. diff --git a/examples/Matlab/MR/Gadgetron/grappa_detail.m b/examples/Matlab/MR/Gadgetron/grappa_detail.m index 34e155bb2..8f63fdb4c 100644 --- a/examples/Matlab/MR/Gadgetron/grappa_detail.m +++ b/examples/Matlab/MR/Gadgetron/grappa_detail.m @@ -14,7 +14,7 @@ % 2) An input data file from a GRAPPA MRI acquisition in the ISMRMRD format. % Example GRAPPA datasets: % a) 'meas_MID00108_FID57249_test_2D_2x.dat' is -% available from https://www.ccppetmr.ac.uk/downloads +% available from https://www.ccpsynerbi.ac.uk/downloads % This is in the manufacturer's raw data format and needs to be % converted to ISMRMRD format using 'siemens_to_ismrmrd'. % This executable is installed on the Virtual Machine. @@ -28,13 +28,13 @@ % % See also GRAPPA_BASIC GEN_US_DATA -% CCP PETMR Synergistic Image Reconstruction Framework (SIRF). -% Copyright 2015 - 2017 Rutherford Appleton Laboratory STFC. -% Copyright 2015 - 2017 University College London. +% SyneRBI Synergistic Image Reconstruction Framework (SIRF). +% Copyright 2015 - 2019 Rutherford Appleton Laboratory STFC. +% Copyright 2015 - 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/). +% Project in Synergistic Reconstruction for Biomedical Imaging (formerly CCP PETMR) +% (http://www.ccpsynerbi.ac.uk/). % % Licensed under the Apache License, Version 2.0 (the "License"); % you may not use this file except in compliance with the License. @@ -183,4 +183,4 @@ sirf.Utilities.show_3D_array(image_array, title, 'samples', 'readouts', 'slice'); title = 'G-factor data (magnitude)'; sirf.Utilities.show_3D_array(gfact_array, title, 'samples', 'readouts', 'slice'); -end \ No newline at end of file +end diff --git a/examples/Matlab/MR/acquisition_data.m b/examples/Matlab/MR/acquisition_data.m index 78215fb0e..3d0415867 100644 --- a/examples/Matlab/MR/acquisition_data.m +++ b/examples/Matlab/MR/acquisition_data.m @@ -5,13 +5,13 @@ function acquisition_data(engine) % In MATLAB, there are also ISMRMRD tools available for examining % data before processing. % -% CCP PETMR Synergistic Image Reconstruction Framework (SIRF). -% Copyright 2015 - 2017 Rutherford Appleton Laboratory STFC. -% Copyright 2015 - 2017 University College London. +% SyneRBI Synergistic Image Reconstruction Framework (SIRF). +% Copyright 2015 - 2020 Rutherford Appleton Laboratory STFC. +% Copyright 2015 - 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/). +% Project in Synergistic Reconstruction for Biomedical Imaging (formerly CCP PETMR) +% (http://www.ccpsynerbi.ac.uk/). % % Licensed under the Apache License, Version 2.0 (the "License"); % you may not use this file except in compliance with the License. diff --git a/examples/Matlab/MR/acquisition_model.m b/examples/Matlab/MR/acquisition_model.m index c4e8c0c22..97e020369 100644 --- a/examples/Matlab/MR/acquisition_model.m +++ b/examples/Matlab/MR/acquisition_model.m @@ -6,13 +6,13 @@ function acquisition_model(engine) % In MATLAB, there are also ISMRMRD tools available for examining % data before processing. % -% CCP PETMR Synergistic Image Reconstruction Framework (SIRF). -% Copyright 2015 - 2017 Rutherford Appleton Laboratory STFC. -% Copyright 2015 - 2017 University College London. +% SyneRBI Synergistic Image Reconstruction Framework (SIRF). +% Copyright 2015 - 2020 Rutherford Appleton Laboratory STFC. +% Copyright 2015 - 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/). +% Project in Synergistic Reconstruction for Biomedical Imaging (formerly CCP PETMR) +% (http://www.ccpsynerbi.ac.uk/). % % Licensed under the Apache License, Version 2.0 (the "License"); % you may not use this file except in compliance with the License. @@ -122,4 +122,4 @@ function acquisition_model(engine) sirf.Utilities.show_3D_array... (abs(backprojected_array), title, 'samples', 'readouts', 'slice'); -end \ No newline at end of file +end diff --git a/examples/Matlab/MR/fully_sampled_recon.m b/examples/Matlab/MR/fully_sampled_recon.m index 67653d337..1ce1dd4ac 100644 --- a/examples/Matlab/MR/fully_sampled_recon.m +++ b/examples/Matlab/MR/fully_sampled_recon.m @@ -11,7 +11,7 @@ function fully_sampled_recon(engine) % 2) An input data file in the ISMRMRD format. % Example datasets: % a) 'meas_MID00103_FID57244_test.dat' is -% available from https://www.ccppetmr.ac.uk/downloads +% available from https://www.ccpsynerbi.ac.uk/downloads % This is in the manufacturer's raw data format and needs to be % converted to ISMRMRD format using 'siemens_to_ismrmrd'. % This executable is installed on the Virtual Machine. @@ -29,13 +29,13 @@ function fully_sampled_recon(engine) % See also FULLY_SAMPLED_RECON_SINGLE_CHAIN % FULLY_SAMPLED_RECON_THREE_CHAINS -% CCP PETMR Synergistic Image Reconstruction Framework (SIRF). -% Copyright 2015 - 2017 Rutherford Appleton Laboratory STFC. -% Copyright 2015 - 2017 University College London. +% SyneRBI Synergistic Image Reconstruction Framework (SIRF). +% Copyright 2015 - 2019 Rutherford Appleton Laboratory STFC. +% Copyright 2015 - 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/). +% Project in Synergistic Reconstruction for Biomedical Imaging (formerly CCP PETMR) +% (http://www.ccpsynerbi.ac.uk/). % % Licensed under the Apache License, Version 2.0 (the "License"); % you may not use this file except in compliance with the License. diff --git a/examples/Matlab/MR/grappa_and_steepest_descent.m b/examples/Matlab/MR/grappa_and_steepest_descent.m index a78419e0b..34ac72e1e 100644 --- a/examples/Matlab/MR/grappa_and_steepest_descent.m +++ b/examples/Matlab/MR/grappa_and_steepest_descent.m @@ -2,13 +2,13 @@ function grappa_and_steepest_descent(engine) % GRAPPA reconstruction with the steepest descent step % to illustrate the use of Acquisition Model projections. -% CCP PETMR Synergistic Image Reconstruction Framework (SIRF). -% Copyright 2015 - 2017 Rutherford Appleton Laboratory STFC. -% Copyright 2015 - 2017 University College London. +% SyneRBI Synergistic Image Reconstruction Framework (SIRF). +% Copyright 2015 - 2019 Rutherford Appleton Laboratory STFC. +% Copyright 2015 - 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/). +% Project in Synergistic Reconstruction for Biomedical Imaging (formerly CCP PETMR) +% (http://www.ccpsynerbi.ac.uk/). % % Licensed under the Apache License, Version 2.0 (the "License"); % you may not use this file except in compliance with the License. diff --git a/examples/Matlab/MR/grappa_basic.m b/examples/Matlab/MR/grappa_basic.m index e6e64ba89..b6fd21954 100644 --- a/examples/Matlab/MR/grappa_basic.m +++ b/examples/Matlab/MR/grappa_basic.m @@ -16,7 +16,7 @@ function grappa_basic(engine) % 2) An input data file from a GRAPPA MRI acquisition in the ISMRMRD format. % Example GRAPPA datasets: % a) 'meas_MID00108_FID57249_test_2D_2x.dat' is -% available from https://www.ccppetmr.ac.uk/downloads +% available from https://www.ccpsynerbi.ac.uk/downloads % This is in the manufacturer's raw data format and needs to be % converted to ISMRMRD format using 'siemens_to_ismrmrd'. % This executable is installed on the Virtual Machine. @@ -35,13 +35,13 @@ function grappa_basic(engine) % % See also GRAPPA_DETAIL GEN_US_DATA -% CCP PETMR Synergistic Image Reconstruction Framework (SIRF). -% Copyright 2015 - 2017 Rutherford Appleton Laboratory STFC. -% Copyright 2015 - 2017 University College London. +% SyneRBI Synergistic Image Reconstruction Framework (SIRF). +% Copyright 2015 - 2019 Rutherford Appleton Laboratory STFC. +% Copyright 2015 - 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/). +% Project in Synergistic Reconstruction for Biomedical Imaging (formerly CCP PETMR) +% (http://www.ccpsynerbi.ac.uk/). % % Licensed under the Apache License, Version 2.0 (the "License"); % you may not use this file except in compliance with the License. @@ -97,4 +97,4 @@ function grappa_basic(engine) % Display the modulus and phase for this reconstructed slice. figure('Name',['idata, slice: ',num2str(sl)]) subplot(1,2,1), imshow(abs(image_array(:,:,sl)),[]), title('Abs') -subplot(1,2,2), imshow(angle(image_array(:,:,sl)),[-pi pi]), title('Phase') \ No newline at end of file +subplot(1,2,2), imshow(angle(image_array(:,:,sl)),[-pi pi]), title('Phase') diff --git a/examples/Matlab/PET/acquisition_data.m b/examples/Matlab/PET/acquisition_data.m index b9a55ca55..16b92c930 100644 --- a/examples/Matlab/PET/acquisition_data.m +++ b/examples/Matlab/PET/acquisition_data.m @@ -1,13 +1,13 @@ function acquisition_data(engine) % A demo showing basics of PET acquisition data handling. -% CCP PETMR Synergistic Image Reconstruction Framework (SIRF). -% Copyright 2015 - 2017 Rutherford Appleton Laboratory STFC. -% Copyright 2015 - 2017 University College London. +% SyneRBI Synergistic Image Reconstruction Framework (SIRF). +% Copyright 2015 - 2019 Rutherford Appleton Laboratory STFC. +% Copyright 2015 - 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/). +% Project in Synergistic Reconstruction for Biomedical Imaging (formerly CCP PETMR) +% (http://www.ccpsynerbi.ac.uk/). % % Licensed under the Apache License, Version 2.0 (the "License"); % you may not use this file except in compliance with the License. @@ -99,4 +99,4 @@ function acquisition_data(engine) % Restore previous storage scheme AD.set_storage_scheme(scheme); %AcquisitionData.set_storage_scheme(scheme); -end \ No newline at end of file +end diff --git a/examples/Matlab/PET/acquisition_data_from_scanner_info.m b/examples/Matlab/PET/acquisition_data_from_scanner_info.m index fbd16e322..6f4bc5bf2 100644 --- a/examples/Matlab/PET/acquisition_data_from_scanner_info.m +++ b/examples/Matlab/PET/acquisition_data_from_scanner_info.m @@ -1,13 +1,13 @@ function acquisition_data_from_scanner_info(engine) % A demo showing basics of PET acquisition data handling. -% CCP PETMR Synergistic Image Reconstruction Framework (SIRF). -% Copyright 2018 Rutherford Appleton Laboratory STFC. +% SyneRBI Synergistic Image Reconstruction Framework (SIRF). +% Copyright 2018 - 2019 Rutherford Appleton Laboratory STFC. % Copyright 2018 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/). +% Project in Synergistic Reconstruction for Biomedical Imaging (formerly CCP PETMR) +% (http://www.ccpsynerbi.ac.uk/). % % Licensed under the Apache License, Version 2.0 (the "License"); % you may not use this file except in compliance with the License. @@ -74,4 +74,4 @@ function acquisition_data_from_scanner_info(engine) fprintf('error id is %s\n', err.identifier) end AD.set_storage_scheme(scheme); -%AcquisitionData.set_storage_scheme(scheme); \ No newline at end of file +%AcquisitionData.set_storage_scheme(scheme); diff --git a/examples/Matlab/PET/acquisition_model.m b/examples/Matlab/PET/acquisition_model.m index e0dcf08c3..397c7a2fb 100644 --- a/examples/Matlab/PET/acquisition_model.m +++ b/examples/Matlab/PET/acquisition_model.m @@ -5,13 +5,13 @@ function acquisition_model(engine) % Uncomment the next line to get more information on PET acquisition model % doc AcquisitionModel -% CCP PETMR Synergistic Image Reconstruction Framework (SIRF). -% Copyright 2015 - 2018 Rutherford Appleton Laboratory STFC. -% Copyright 2015 - 2018 University College London. +% SyneRBI Synergistic Image Reconstruction Framework (SIRF). +% Copyright 2015 - 2019 Rutherford Appleton Laboratory STFC. +% Copyright 2015 - 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/). +% Project in Synergistic Reconstruction for Biomedical Imaging (formerly CCP PETMR) +% (http://www.ccpsynerbi.ac.uk/). % % Licensed under the Apache License, Version 2.0 (the "License"); % you may not use this file except in compliance with the License. @@ -139,4 +139,4 @@ function acquisition_model(engine) fprintf('??? %s\n', err.message) fprintf('error id is %s\n', err.identifier) end -end \ No newline at end of file +end diff --git a/examples/Matlab/PET/acquisition_sensitivity_from_attenuation.m b/examples/Matlab/PET/acquisition_sensitivity_from_attenuation.m index 0a8fa3477..b14c708cc 100644 --- a/examples/Matlab/PET/acquisition_sensitivity_from_attenuation.m +++ b/examples/Matlab/PET/acquisition_sensitivity_from_attenuation.m @@ -1,13 +1,13 @@ function acquisition_sensitivity_from_attenuation(engine) % Acquisition sensitivity model using attenuation image. -% CCP PETMR Synergistic Image Reconstruction Framework (SIRF). -% Copyright 2015 - 2018 Rutherford Appleton Laboratory STFC. -% Copyright 2015 - 2018 University College London. +% SyneRBI Synergistic Image Reconstruction Framework (SIRF). +% Copyright 2015 - 2019 Rutherford Appleton Laboratory STFC. +% Copyright 2015 - 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/). +% Project in Synergistic Reconstruction for Biomedical Imaging (formerly CCP PETMR) +% (http://www.ccpsynerbi.ac.uk/). % % Licensed under the Apache License, Version 2.0 (the "License"); % you may not use this file except in compliance with the License. @@ -78,4 +78,4 @@ function acquisition_sensitivity_from_attenuation(engine) fprintf('??? %s\n', err.message) fprintf('error id is %s\n', err.identifier) end -end \ No newline at end of file +end diff --git a/examples/Matlab/PET/acquisition_sensitivity_from_ecat8.m b/examples/Matlab/PET/acquisition_sensitivity_from_ecat8.m index b9e0ebff2..bc665bdf4 100644 --- a/examples/Matlab/PET/acquisition_sensitivity_from_ecat8.m +++ b/examples/Matlab/PET/acquisition_sensitivity_from_ecat8.m @@ -1,13 +1,13 @@ function acquisition_sensitivity_from_ecat8(engine) % Acquisition sensitivity model using ECAT8 bin normalization. -% CCP PETMR Synergistic Image Reconstruction Framework (SIRF). -% Copyright 2015 - 2018 Rutherford Appleton Laboratory STFC. -% Copyright 2015 - 2018 University College London. +% SyneRBI Synergistic Image Reconstruction Framework (SIRF). +% Copyright 2015 - 2019 Rutherford Appleton Laboratory STFC. +% Copyright 2015 - 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/). +% Project in Synergistic Reconstruction for Biomedical Imaging (formerly CCP PETMR) +% (http://www.ccpsynerbi.ac.uk/). % % Licensed under the Apache License, Version 2.0 (the "License"); % you may not use this file except in compliance with the License. @@ -63,4 +63,4 @@ function acquisition_sensitivity_from_ecat8(engine) fprintf('??? %s\n', err.message) fprintf('error id is %s\n', err.identifier) end -end \ No newline at end of file +end diff --git a/examples/Matlab/PET/fbp2d_reconstruction.m b/examples/Matlab/PET/fbp2d_reconstruction.m index 8da12b3a1..d32dd90e5 100644 --- a/examples/Matlab/PET/fbp2d_reconstruction.m +++ b/examples/Matlab/PET/fbp2d_reconstruction.m @@ -1,13 +1,13 @@ function fbp2d_reconstruction(engine) % FBP2D reconstruction demo. -% CCP PETMR Synergistic Image Reconstruction Framework (SIRF). -% Copyright 2015 - 2017 Rutherford Appleton Laboratory STFC. -% Copyright 2015 - 2017 University College London. +% SyneRBI Synergistic Image Reconstruction Framework (SIRF). +% Copyright 2015 - 2020 Rutherford Appleton Laboratory STFC. +% Copyright 2015 - 2020 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/). +% Project in Synergistic Reconstruction for Biomedical Imaging (formerly CCP PETMR) +% (http://www.ccpsynerbi.ac.uk/). % % Licensed under the Apache License, Version 2.0 (the "License"); % you may not use this file except in compliance with the License. @@ -89,4 +89,4 @@ function fbp2d_reconstruction(engine) fprintf('%s\n', err.message) fprintf('error id is %s\n', err.identifier) end -end \ No newline at end of file +end diff --git a/examples/Matlab/PET/input_output.m b/examples/Matlab/PET/input_output.m index f3d558f43..5f99caaf0 100644 --- a/examples/Matlab/PET/input_output.m +++ b/examples/Matlab/PET/input_output.m @@ -5,13 +5,13 @@ function input_output(engine) % Uncomment the next line to get more information on PET acquisition model % doc AcquisitionModel -% CCP PETMR Synergistic Image Reconstruction Framework (SIRF). -% Copyright 2015 - 2017 Rutherford Appleton Laboratory STFC. -% Copyright 2015 - 2017 University College London. +% SyneRBI Synergistic Image Reconstruction Framework (SIRF). +% Copyright 2015 - 2019 Rutherford Appleton Laboratory STFC. +% Copyright 2015 - 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/). +% Project in Synergistic Reconstruction for Biomedical Imaging (formerly CCP PETMR) +% (http://www.ccpsynerbi.ac.uk/). % % Licensed under the Apache License, Version 2.0 (the "License"); % you may not use this file except in compliance with the License. @@ -85,4 +85,4 @@ function input_output(engine) fprintf('??? %s\n', err.message) fprintf('error id is %s\n', err.identifier) end -end \ No newline at end of file +end diff --git a/examples/Matlab/PET/listmode_to_sinograms.m b/examples/Matlab/PET/listmode_to_sinograms.m index 0d09627aa..4ce56273e 100644 --- a/examples/Matlab/PET/listmode_to_sinograms.m +++ b/examples/Matlab/PET/listmode_to_sinograms.m @@ -4,13 +4,13 @@ function listmode_to_sinograms(engine) % output will be in the current working directory. % input defaults to the mMR subfolder of pet_data_path -% CCP PETMR Synergistic Image Reconstruction Framework (SIRF). -% Copyright 2018 Rutherford Appleton Laboratory STFC. -% Copyright 2018 University College London. +% SyneRBI Synergistic Image Reconstruction Framework (SIRF). +% Copyright 2018 - 2019 Rutherford Appleton Laboratory STFC. +% 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/). +% Project in Synergistic Reconstruction for Biomedical Imaging (formerly CCP PETMR) +% (http://www.ccpsynerbi.ac.uk/). % % Licensed under the Apache License, Version 2.0 (the "License"); % you may not use this file except in compliance with the License. diff --git a/examples/Matlab/PET/my_osmaposl.m b/examples/Matlab/PET/my_osmaposl.m index fc2246d56..d29853d08 100644 --- a/examples/Matlab/PET/my_osmaposl.m +++ b/examples/Matlab/PET/my_osmaposl.m @@ -4,13 +4,13 @@ % Step Late algorithm (OSL) from Green et al for Maximum a Posteriori (MAP) % maximisation. -% CCP PETMR Synergistic Image Reconstruction Framework (SIRF). -% Copyright 2015 - 2017 Rutherford Appleton Laboratory STFC. +% SyneRBI Synergistic Image Reconstruction Framework (SIRF). +% Copyright 2015 - 2018 Rutherford Appleton Laboratory STFC. % Copyright 2015 - 2017 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/). +% Project in Synergistic Reconstruction for Biomedical Imaging (formerly CCP PETMR) +% (http://www.ccpsynerbi.ac.uk/). % % Licensed under the Apache License, Version 2.0 (the "License"); % you may not use this file except in compliance with the License. @@ -54,4 +54,4 @@ filter.apply(image); end -end \ No newline at end of file +end diff --git a/examples/Matlab/PET/osem_reconstruction.m b/examples/Matlab/PET/osem_reconstruction.m index bf97c89e1..46f420706 100644 --- a/examples/Matlab/PET/osem_reconstruction.m +++ b/examples/Matlab/PET/osem_reconstruction.m @@ -5,13 +5,13 @@ function osem_reconstruction(engine) % from Green et al for Maximum a Posteriori (MAP) maximisation. Here we use it % for Maximum Likelihood (ML) in which case it is equivalent to OSEM. -% CCP PETMR Synergistic Image Reconstruction Framework (SIRF). -% Copyright 2015 - 2017 Rutherford Appleton Laboratory STFC. -% Copyright 2015 - 2017 University College London. +% SyneRBI Synergistic Image Reconstruction Framework (SIRF). +% Copyright 2015 - 2020 Rutherford Appleton Laboratory STFC. +% Copyright 2015 - 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/). +% Project in Synergistic Reconstruction for Biomedical Imaging (formerly CCP PETMR) +% (http://www.ccpsynerbi.ac.uk/). % % Licensed under the Apache License, Version 2.0 (the "License"); % you may not use this file except in compliance with the License. @@ -106,4 +106,4 @@ function osem_reconstruction(engine) fprintf('%s\n', err.message) fprintf('error id is %s\n', err.identifier) end -end \ No newline at end of file +end diff --git a/examples/Matlab/PET/reconstruct_from_listmode.m b/examples/Matlab/PET/reconstruct_from_listmode.m index dadb460c0..7e333df96 100644 --- a/examples/Matlab/PET/reconstruct_from_listmode.m +++ b/examples/Matlab/PET/reconstruct_from_listmode.m @@ -4,13 +4,13 @@ function reconstruct_from_listmode(engine) % output will be in the current working directory. % input defaults to the mMR subfolder of pet_data_path -% CCP PETMR Synergistic Image Reconstruction Framework (SIRF). -% Copyright 2018 Rutherford Appleton Laboratory STFC. -% Copyright 2018 University College London. +% SyneRBI Synergistic Image Reconstruction Framework (SIRF). +% Copyright 2018 - 2019 Rutherford Appleton Laboratory STFC. +% 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/). +% Project in Synergistic Reconstruction for Biomedical Imaging (formerly CCP PETMR) +% (http://www.ccpsynerbi.ac.uk/). % % Licensed under the Apache License, Version 2.0 (the "License"); % you may not use this file except in compliance with the License. @@ -173,4 +173,4 @@ function reconstruct_from_listmode(engine) % display error information fprintf('??? %s\n', err.message) fprintf('error id is %s\n', err.identifier) -end \ No newline at end of file +end diff --git a/examples/Matlab/PET/steepest_ascent.m b/examples/Matlab/PET/steepest_ascent.m index ab99cc5b6..28b66cb46 100644 --- a/examples/Matlab/PET/steepest_ascent.m +++ b/examples/Matlab/PET/steepest_ascent.m @@ -3,13 +3,13 @@ function steepest_ascent(engine) % Applies few steps of steepest ascent for the minimization of Poisson % logarithmic likelihood objective function using gradient for subset 0. -% CCP PETMR Synergistic Image Reconstruction Framework (SIRF). -% Copyright 2015 - 2017 Rutherford Appleton Laboratory STFC. -% Copyright 2015 - 2017 University College London. +% SyneRBI Synergistic Image Reconstruction Framework (SIRF). +% Copyright 2015 - 2019 Rutherford Appleton Laboratory STFC. +% Copyright 2015 - 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/). +% Project in Synergistic Reconstruction for Biomedical Imaging (formerly CCP PETMR) +% (http://www.ccpsynerbi.ac.uk/). % % Licensed under the Apache License, Version 2.0 (the "License"); % you may not use this file except in compliance with the License. @@ -146,4 +146,4 @@ function steepest_ascent(engine) fprintf('??? %s\n', err.message) fprintf('error id is %s\n', err.identifier) end -end \ No newline at end of file +end diff --git a/examples/Matlab/PET/user_osmaposl.m b/examples/Matlab/PET/user_osmaposl.m index f825508ba..eeee061fb 100644 --- a/examples/Matlab/PET/user_osmaposl.m +++ b/examples/Matlab/PET/user_osmaposl.m @@ -5,13 +5,13 @@ function user_osmaposl(engine) % from Green et al for Maximum a Posteriori (MAP) maximisation. Here we use it % for Maximum Likelihood (ML) in which case it is equivalent to OSEM. -% CCP PETMR Synergistic Image Reconstruction Framework (SIRF). -% Copyright 2015 - 2017 Rutherford Appleton Laboratory STFC. -% Copyright 2015 - 2017 University College London. +% SyneRBI Synergistic Image Reconstruction Framework (SIRF). +% Copyright 2015 - 2019 Rutherford Appleton Laboratory STFC. +% Copyright 2015 - 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/). +% Project in Synergistic Reconstruction for Biomedical Imaging (formerly CCP PETMR) +% (http://www.ccpsynerbi.ac.uk/). % % Licensed under the Apache License, Version 2.0 (the "License"); % you may not use this file except in compliance with the License. @@ -81,4 +81,4 @@ function user_osmaposl(engine) fprintf('%s\n', err.message) fprintf('error id is %s\n', err.identifier) end -end \ No newline at end of file +end diff --git a/examples/Matlab/PETMR/simplistic_petmr.m b/examples/Matlab/PETMR/simplistic_petmr.m index 0fbfafe45..d408f864a 100644 --- a/examples/Matlab/PETMR/simplistic_petmr.m +++ b/examples/Matlab/PETMR/simplistic_petmr.m @@ -10,13 +10,13 @@ function simplistic_petmr(mr_engine, pet_engine) % % 2) An input data file in the ISMRMRD format. -% CCP PETMR Synergistic Image Reconstruction Framework (SIRF). -% Copyright 2015 - 2017 Rutherford Appleton Laboratory STFC. -% Copyright 2015 - 2017 University College London. +% SyneRBI Synergistic Image Reconstruction Framework (SIRF). +% Copyright 2015 - 2019 Rutherford Appleton Laboratory STFC. +% Copyright 2015 - 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/). +% Project in Synergistic Reconstruction for Biomedical Imaging (formerly CCP PETMR) +% (http://www.ccpsynerbi.ac.uk/). % % Licensed under the Apache License, Version 2.0 (the "License"); % you may not use this file except in compliance with the License. @@ -92,4 +92,4 @@ function simplistic_petmr(mr_engine, pet_engine) % display filtered PET image sirf.Utilities.show_3D_array(pet_image.as_array(), 'PET image data', 'x', 'y', 'slice'); -end \ No newline at end of file +end diff --git a/examples/Matlab/Registration/sirf_registration.m b/examples/Matlab/Registration/sirf_registration.m index b25686a29..3e7d6b0a0 100644 --- a/examples/Matlab/Registration/sirf_registration.m +++ b/examples/Matlab/Registration/sirf_registration.m @@ -53,12 +53,12 @@ function sirf_registration(varargin) % --flo test2.nii.gz Reg % --algo aladin -% CCP PETMR Synergistic Image Reconstruction Framework (SIRF). +% SyneRBI Synergistic Image Reconstruction Framework (SIRF). % Copyright 2018 - 2020 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/). +% Project in Synergistic Reconstruction for Biomedical Imaging (formerly CCP PETMR) +% (http://www.ccpsynerbi.ac.uk/). % % Licensed under the Apache License, Version 2.0 (the "License"); % you may not use this file except in compliance with the License. diff --git a/examples/Matlab/Registration/sirf_resample.m b/examples/Matlab/Registration/sirf_resample.m index 4cc2a8d68..2022d1c04 100644 --- a/examples/Matlab/Registration/sirf_resample.m +++ b/examples/Matlab/Registration/sirf_resample.m @@ -11,12 +11,12 @@ function resample(varargin) % --trans_types ... transformation types, e.g. (with quotations): "AffineTransformation,NiftiImageData3DDeformation,NiftiImageData3DDisplacement" % --pad Padding value -% CCP PETMR Synergistic Image Reconstruction Framework (SIRF). +% SyneRBI 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/). +% Project in Synergistic Reconstruction for Biomedical Imaging (formerly CCP PETMR) +% (http://www.ccpsynerbi.ac.uk/). % % Licensed under the Apache License, Version 2.0 (the "License"); % you may not use this file except in compliance with the License. diff --git a/examples/Python/MR/Gadgetron/GPU/golden_radial_mode2_gpusense_cg.py b/examples/Python/MR/Gadgetron/GPU/golden_radial_mode2_gpusense_cg.py index 560d33e9e..57d2c038c 100644 --- a/examples/Python/MR/Gadgetron/GPU/golden_radial_mode2_gpusense_cg.py +++ b/examples/Python/MR/Gadgetron/GPU/golden_radial_mode2_gpusense_cg.py @@ -12,14 +12,12 @@ subfolder of SIRF root folder ''' -## CCP PETMR Synergistic Image Reconstruction Framework (SIRF). -## Copyright 2015 - 2017 Rutherford Appleton Laboratory STFC. -## Copyright 2015 - 2017 University College London. -## Copyright 2015 - 2017 Physikalisch-Technische Bundesanstalt. +## SyneRBI Synergistic Image Reconstruction Framework (SIRF). +## Copyright 2019 - 2020 Rutherford Appleton Laboratory STFC. ## ## This is software developed for the Collaborative Computational -## Project in Positron Emission Tomography and Magnetic Resonance imaging -## (http://www.ccppetmr.ac.uk/). +## Project in Synergistic Reconstruction for Biomedical Imaging (formerly CCP PETMR) +## (http://www.ccpsynerbi.ac.uk/). ## ## Licensed under the Apache License, Version 2.0 (the "License"); ## you may not use this file except in compliance with the License. diff --git a/examples/Python/MR/Gadgetron/fully_sampled_recon_single_chain.py b/examples/Python/MR/Gadgetron/fully_sampled_recon_single_chain.py index 8091728e2..9c6857677 100755 --- a/examples/Python/MR/Gadgetron/fully_sampled_recon_single_chain.py +++ b/examples/Python/MR/Gadgetron/fully_sampled_recon_single_chain.py @@ -17,14 +17,14 @@ --show show plots ''' -## CCP PETMR Synergistic Image Reconstruction Framework (SIRF). -## Copyright 2015 - 2017 Rutherford Appleton Laboratory STFC. -## Copyright 2015 - 2017 University College London. +## SyneRBI Synergistic Image Reconstruction Framework (SIRF). +## Copyright 2015 - 2020 Rutherford Appleton Laboratory STFC. +## Copyright 2015 - 2019 University College London. ## Copyright 2015 - 2017 Physikalisch-Technische Bundesanstalt. ## ## This is software developed for the Collaborative Computational -## Project in Positron Emission Tomography and Magnetic Resonance imaging -## (http://www.ccppetmr.ac.uk/). +## Project in Synergistic Reconstruction for Biomedical Imaging (formerly CCP PETMR) +## (http://www.ccpsynerbi.ac.uk/). ## ## Licensed under the Apache License, Version 2.0 (the "License"); ## you may not use this file except in compliance with the License. diff --git a/examples/Python/MR/Gadgetron/fully_sampled_recon_single_chain_short.py b/examples/Python/MR/Gadgetron/fully_sampled_recon_single_chain_short.py index 105915188..ecfd1f257 100755 --- a/examples/Python/MR/Gadgetron/fully_sampled_recon_single_chain_short.py +++ b/examples/Python/MR/Gadgetron/fully_sampled_recon_single_chain_short.py @@ -13,13 +13,13 @@ -o , --output= images output file ''' -## CCP PETMR Synergistic Image Reconstruction Framework (SIRF) -## Copyright 2015 - 2017 Rutherford Appleton Laboratory STFC -## Copyright 2015 - 2017 University College London. +## SyneRBI Synergistic Image Reconstruction Framework (SIRF) +## Copyright 2015 - 2020 Rutherford Appleton Laboratory STFC +## Copyright 2015 - 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/). +## Project in Synergistic Reconstruction for Biomedical Imaging (formerly CCP PETMR) +## (http://www.ccpsynerbi.ac.uk/). ## ## Licensed under the Apache License, Version 2.0 (the "License"); ## you may not use this file except in compliance with the License. diff --git a/examples/Python/MR/Gadgetron/fully_sampled_recon_three_chains.py b/examples/Python/MR/Gadgetron/fully_sampled_recon_three_chains.py index a4ce4ac25..e579895bc 100644 --- a/examples/Python/MR/Gadgetron/fully_sampled_recon_three_chains.py +++ b/examples/Python/MR/Gadgetron/fully_sampled_recon_three_chains.py @@ -18,14 +18,14 @@ -s=, --sigma= gaussian sigma [default: 20] ''' -## CCP PETMR Synergistic Image Reconstruction Framework (SIRF). -## Copyright 2015 - 2017 Rutherford Appleton Laboratory STFC. +## SyneRBI Synergistic Image Reconstruction Framework (SIRF). +## Copyright 2015 - 2019 Rutherford Appleton Laboratory STFC. ## Copyright 2015 - 2017 University College London. ## Copyright 2015 - 2017 Physikalisch-Technische Bundesanstalt. ## ## This is software developed for the Collaborative Computational -## Project in Positron Emission Tomography and Magnetic Resonance imaging -## (http://www.ccppetmr.ac.uk/). +## Project in Synergistic Reconstruction for Biomedical Imaging (formerly CCP PETMR) +## (http://www.ccpsynerbi.ac.uk/). ## ## Licensed under the Apache License, Version 2.0 (the "License"); ## you may not use this file except in compliance with the License. diff --git a/examples/Python/MR/Gadgetron/grappa_detail.py b/examples/Python/MR/Gadgetron/grappa_detail.py index d59edb2c1..adab52402 100644 --- a/examples/Python/MR/Gadgetron/grappa_detail.py +++ b/examples/Python/MR/Gadgetron/grappa_detail.py @@ -12,7 +12,7 @@ 2) An input data file from a GRAPPA MRI acquisition in the ISMRMRD format. Example GRAPPA datasets: a) 'meas_MID00108_FID57249_test_2D_2x.dat' is - available from https://www.ccppetmr.ac.uk/downloads + available from https://www.ccpsynerbi.ac.uk/downloads This is in the manufacturer's raw data format and needs to be converted to ISMRMRD format using 'siemens_to_ismrmrd'. This executable is installed on the Virtual Machine. @@ -29,14 +29,14 @@ subfolder of SIRF root folder ''' -## CCP PETMR Synergistic Image Reconstruction Framework (SIRF). -## Copyright 2015 - 2017 Rutherford Appleton Laboratory STFC. +## SyneRBI Synergistic Image Reconstruction Framework (SIRF). +## Copyright 2015 - 2020 Rutherford Appleton Laboratory STFC. ## Copyright 2015 - 2017 University College London. ## Copyright 2015 - 2017 Physikalisch-Technische Bundesanstalt. ## ## This is software developed for the Collaborative Computational -## Project in Positron Emission Tomography and Magnetic Resonance imaging -## (http://www.ccppetmr.ac.uk/). +## Project in Synergistic Reconstruction for Biomedical Imaging (formerly CCP PETMR) +## (http://www.ccpsynerbi.ac.uk/). ## ## Licensed under the Apache License, Version 2.0 (the "License"); ## you may not use this file except in compliance with the License. diff --git a/examples/Python/MR/Gadgetron/run_all.py b/examples/Python/MR/Gadgetron/run_all.py index 2c0d02bda..d9e5f8e7f 100644 --- a/examples/Python/MR/Gadgetron/run_all.py +++ b/examples/Python/MR/Gadgetron/run_all.py @@ -1,12 +1,12 @@ #!/usr/bin/env python -## CCP PETMR Synergistic Image Reconstruction Framework (SIRF) +## SyneRBI Synergistic Image Reconstruction Framework (SIRF) ## Copyright 2015 - 2017 Rutherford Appleton Laboratory STFC ## Copyright 2015 - 2017 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/). +## Project in Synergistic Reconstruction for Biomedical Imaging (formerly CCP PETMR) +## (http://www.ccpsynerbi.ac.uk/). ## ## Licensed under the Apache License, Version 2.0 (the "License"); ## you may not use this file except in compliance with the License. diff --git a/examples/Python/MR/acquisition_data.py b/examples/Python/MR/acquisition_data.py index 099666aaa..652eafedb 100644 --- a/examples/Python/MR/acquisition_data.py +++ b/examples/Python/MR/acquisition_data.py @@ -14,14 +14,14 @@ -e , --engine= reconstruction engine [default: Gadgetron] ''' -## CCP PETMR Synergistic Image Reconstruction Framework (SIRF). -## Copyright 2015 - 2017 Rutherford Appleton Laboratory STFC. +## SyneRBI Synergistic Image Reconstruction Framework (SIRF). +## Copyright 2015 - 2020 Rutherford Appleton Laboratory STFC. ## Copyright 2015 - 2017 University College London. ## Copyright 2015 - 2017 Physikalisch-Technische Bundesanstalt. ## ## This is software developed for the Collaborative Computational -## Project in Positron Emission Tomography and Magnetic Resonance imaging -## (http://www.ccppetmr.ac.uk/). +## Project in Synergistic Reconstruction for Biomedical Imaging (formerly CCP PETMR) +## (http://www.ccpsynerbi.ac.uk/). ## ## Licensed under the Apache License, Version 2.0 (the "License"); ## you may not use this file except in compliance with the License. diff --git a/examples/Python/MR/acquisition_model.py b/examples/Python/MR/acquisition_model.py index 56edeaf21..eb3dce591 100644 --- a/examples/Python/MR/acquisition_model.py +++ b/examples/Python/MR/acquisition_model.py @@ -15,13 +15,13 @@ -e , --engine= reconstruction engine [default: Gadgetron] ''' -## CCP PETMR Synergistic Image Reconstruction Framework (SIRF) -## Copyright 2015 - 2017 Rutherford Appleton Laboratory STFC +## SyneRBI Synergistic Image Reconstruction Framework (SIRF) +## Copyright 2015 - 2020 Rutherford Appleton Laboratory STFC ## Copyright 2015 - 2017 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/). +## Project in Synergistic Reconstruction for Biomedical Imaging (formerly CCP PETMR) +## (http://www.ccpsynerbi.ac.uk/). ## ## Licensed under the Apache License, Version 2.0 (the "License"); ## you may not use this file except in compliance with the License. diff --git a/examples/Python/MR/coil_sensitivity_maps.py b/examples/Python/MR/coil_sensitivity_maps.py index 40b33cfab..5f92da6b8 100644 --- a/examples/Python/MR/coil_sensitivity_maps.py +++ b/examples/Python/MR/coil_sensitivity_maps.py @@ -14,14 +14,14 @@ -e , --engine= reconstruction engine [default: Gadgetron] ''' -## CCP PETMR Synergistic Image Reconstruction Framework (SIRF). -## Copyright 2015 - 2017 Rutherford Appleton Laboratory STFC. +## SyneRBI Synergistic Image Reconstruction Framework (SIRF). +## Copyright 2015 - 2020 Rutherford Appleton Laboratory STFC. ## Copyright 2015 - 2017 University College London. ## Copyright 2015 - 2017 Physikalisch-Technische Bundesanstalt. ## ## This is software developed for the Collaborative Computational -## Project in Positron Emission Tomography and Magnetic Resonance imaging -## (http://www.ccppetmr.ac.uk/). +## Project in Synergistic Reconstruction for Biomedical Imaging (formerly CCP PETMR) +## (http://www.ccpsynerbi.ac.uk/). ## ## Licensed under the Apache License, Version 2.0 (the "License"); ## you may not use this file except in compliance with the License. diff --git a/examples/Python/MR/fully_sampled_recon.py b/examples/Python/MR/fully_sampled_recon.py index 7f0771c8c..8ad029681 100644 --- a/examples/Python/MR/fully_sampled_recon.py +++ b/examples/Python/MR/fully_sampled_recon.py @@ -14,14 +14,14 @@ -o , --output= output file name [default: output.h5] ''' -## CCP PETMR Synergistic Image Reconstruction Framework (SIRF). -## Copyright 2015 - 2017 Rutherford Appleton Laboratory STFC. -## Copyright 2015 - 2017 University College London. +## SyneRBI Synergistic Image Reconstruction Framework (SIRF). +## Copyright 2015 - 2020 Rutherford Appleton Laboratory STFC. +## Copyright 2015 - 2019 University College London. ## Copyright 2015 - 2017 Physikalisch-Technische Bundesanstalt. ## ## This is software developed for the Collaborative Computational -## Project in Positron Emission Tomography and Magnetic Resonance imaging -## (http://www.ccppetmr.ac.uk/). +## Project in Synergistic Reconstruction for Biomedical Imaging (formerly CCP PETMR) +## (http://www.ccpsynerbi.ac.uk/). ## ## Licensed under the Apache License, Version 2.0 (the "License"); ## you may not use this file except in compliance with the License. diff --git a/examples/Python/MR/grappa_and_steepest_descent.py b/examples/Python/MR/grappa_and_steepest_descent.py index fd80d6ae7..2236ad339 100644 --- a/examples/Python/MR/grappa_and_steepest_descent.py +++ b/examples/Python/MR/grappa_and_steepest_descent.py @@ -19,13 +19,13 @@ -o , --output= images output file ''' -## CCP PETMR Synergistic Image Reconstruction Framework (SIRF) -## Copyright 2015 - 2017 Rutherford Appleton Laboratory STFC. -## Copyright 2015 - 2017 University College London. +## SyneRBI Synergistic Image Reconstruction Framework (SIRF) +## Copyright 2015 - 2019 Rutherford Appleton Laboratory STFC. +## Copyright 2015 - 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/). +## Project in Synergistic Reconstruction for Biomedical Imaging (formerly CCP PETMR) +## (http://www.ccpsynerbi.ac.uk/). ## ## Licensed under the Apache License, Version 2.0 (the "License"); ## you may not use this file except in compliance with the License. diff --git a/examples/Python/MR/grappa_basic.py b/examples/Python/MR/grappa_basic.py index 8f3f7bf7a..33a387d08 100644 --- a/examples/Python/MR/grappa_basic.py +++ b/examples/Python/MR/grappa_basic.py @@ -14,7 +14,7 @@ 2) An input data file from a GRAPPA MRI acquisition in the ISMRMRD format. Example GRAPPA datasets: a) 'meas_MID00108_FID57249_test_2D_2x.dat' is - available from https://www.ccppetmr.ac.uk/downloads + available from https://www.ccpsynerbi.ac.uk/downloads This is in the manufacturer's raw data format and needs to be converted to ISMRMRD format using 'siemens_to_ismrmrd'. This executable is installed on the Virtual Machine. @@ -34,14 +34,14 @@ --show show plots ''' -## CCP PETMR Synergistic Image Reconstruction Framework (SIRF) -## Copyright 2015 - 2017 Rutherford Appleton Laboratory STFC. -## Copyright 2015 - 2017 University College London. +## SyneRBI Synergistic Image Reconstruction Framework (SIRF) +## Copyright 2015 - 2020 Rutherford Appleton Laboratory STFC. +## Copyright 2015 - 2019 University College London. ## Copyright 2015 - 2017 Physikalisch-Technische Bundesanstalt. ## ## This is software developed for the Collaborative Computational -## Project in Positron Emission Tomography and Magnetic Resonance imaging -## (http://www.ccppetmr.ac.uk/). +## Project in Synergistic Reconstruction for Biomedical Imaging (formerly CCP PETMR) +## (http://www.ccpsynerbi.ac.uk/). ## ## Licensed under the Apache License, Version 2.0 (the "License"); ## you may not use this file except in compliance with the License. diff --git a/examples/Python/MR/interactive/coil_combination.py b/examples/Python/MR/interactive/coil_combination.py index f7dbec53f..b4fe320ae 100644 --- a/examples/Python/MR/interactive/coil_combination.py +++ b/examples/Python/MR/interactive/coil_combination.py @@ -13,14 +13,14 @@ # Author: Christoph Kolbitsch # -# CCP PETMR Synergistic Image Reconstruction Framework (SIRF). -# Copyright 2015 - 2017 Rutherford Appleton Laboratory STFC. +# SyneRBI Synergistic Image Reconstruction Framework (SIRF). +# Copyright 2015 - 2020 Rutherford Appleton Laboratory STFC. # Copyright 2015 - 2017 University College London. # Copyright 2015 - 2017 Physikalisch-Technische Bundesanstalt. # # This is software developed for the Collaborative Computational -# Project in Positron Emission Tomography and Magnetic Resonance imaging -# (http://www.ccppetmr.ac.uk/). +# Project in Synergistic Reconstruction for Biomedical Imaging (formerly CCP PETMR) +# (http://www.ccpsynerbi.ac.uk/). # # Licensed under the Apache License, Version 2.0 (the "License"); # you may not use this file except in compliance with the License. diff --git a/examples/Python/MR/interactive/fully_sampled.py b/examples/Python/MR/interactive/fully_sampled.py index bf0080bb1..633fa4a2e 100644 --- a/examples/Python/MR/interactive/fully_sampled.py +++ b/examples/Python/MR/interactive/fully_sampled.py @@ -13,14 +13,14 @@ # Author: Christoph Kolbitsch # -## CCP PETMR Synergistic Image Reconstruction Framework (SIRF). -## Copyright 2015 - 2017 Rutherford Appleton Laboratory STFC. +## SyneRBI Synergistic Image Reconstruction Framework (SIRF). +## Copyright 2015 - 2019 Rutherford Appleton Laboratory STFC. ## Copyright 2015 - 2017 University College London. ## Copyright 2015 - 2017 Physikalisch-Technische Bundesanstalt. ## ## This is software developed for the Collaborative Computational -## Project in Positron Emission Tomography and Magnetic Resonance imaging -## (http://www.ccppetmr.ac.uk/). +## Project in Synergistic Reconstruction for Biomedical Imaging (formerly CCP PETMR) +## (http://www.ccpsynerbi.ac.uk/). ## ## Licensed under the Apache License, Version 2.0 (the "License"); ## you may not use this file except in compliance with the License. diff --git a/examples/Python/MR/interactive/kspace_filter.py b/examples/Python/MR/interactive/kspace_filter.py index f2fc25105..d32e65751 100644 --- a/examples/Python/MR/interactive/kspace_filter.py +++ b/examples/Python/MR/interactive/kspace_filter.py @@ -13,14 +13,14 @@ # Author: Christoph Kolbitsch # -## CCP PETMR Synergistic Image Reconstruction Framework (SIRF). -## Copyright 2015 - 2017 Rutherford Appleton Laboratory STFC. +## SyneRBI Synergistic Image Reconstruction Framework (SIRF). +## Copyright 2015 - 2019 Rutherford Appleton Laboratory STFC. ## Copyright 2015 - 2017 University College London. ## Copyright 2015 - 2017 Physikalisch-Technische Bundesanstalt. ## ## This is software developed for the Collaborative Computational -## Project in Positron Emission Tomography and Magnetic Resonance imaging -## (http://www.ccppetmr.ac.uk/). +## Project in Synergistic Reconstruction for Biomedical Imaging (formerly CCP PETMR) +## (http://www.ccpsynerbi.ac.uk/). ## ## Licensed under the Apache License, Version 2.0 (the "License"); ## you may not use this file except in compliance with the License. diff --git a/examples/Python/MR/run_all.py b/examples/Python/MR/run_all.py index 2c0d02bda..d9e5f8e7f 100644 --- a/examples/Python/MR/run_all.py +++ b/examples/Python/MR/run_all.py @@ -1,12 +1,12 @@ #!/usr/bin/env python -## CCP PETMR Synergistic Image Reconstruction Framework (SIRF) +## SyneRBI Synergistic Image Reconstruction Framework (SIRF) ## Copyright 2015 - 2017 Rutherford Appleton Laboratory STFC ## Copyright 2015 - 2017 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/). +## Project in Synergistic Reconstruction for Biomedical Imaging (formerly CCP PETMR) +## (http://www.ccpsynerbi.ac.uk/). ## ## Licensed under the Apache License, Version 2.0 (the "License"); ## you may not use this file except in compliance with the License. diff --git a/examples/Python/PET/acquisition_data.py b/examples/Python/PET/acquisition_data.py index 4b2e8302c..00da8ec50 100644 --- a/examples/Python/PET/acquisition_data.py +++ b/examples/Python/PET/acquisition_data.py @@ -11,13 +11,13 @@ -s , --storage= acquisition data storage scheme [default: file] ''' -## CCP PETMR Synergistic Image Reconstruction Framework (SIRF) -## Copyright 2015 - 2017 Rutherford Appleton Laboratory STFC +## SyneRBI Synergistic Image Reconstruction Framework (SIRF) +## Copyright 2015 - 2020 Rutherford Appleton Laboratory STFC ## Copyright 2015 - 2017 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/). +## Project in Synergistic Reconstruction for Biomedical Imaging (formerly CCP PETMR) +## (http://www.ccpsynerbi.ac.uk/). ## ## Licensed under the Apache License, Version 2.0 (the "License"); ## you may not use this file except in compliance with the License. diff --git a/examples/Python/PET/acquisition_data_from_scanner_info.py b/examples/Python/PET/acquisition_data_from_scanner_info.py index 9a2f7c5f9..fc2835dc2 100644 --- a/examples/Python/PET/acquisition_data_from_scanner_info.py +++ b/examples/Python/PET/acquisition_data_from_scanner_info.py @@ -8,13 +8,13 @@ -s , --storage= acquisition data storage scheme [default: file] ''' -## CCP PETMR Synergistic Image Reconstruction Framework (SIRF) -## Copyright 2018 Rutherford Appleton Laboratory STFC -## Copyright 2018 University College London. +## SyneRBI Synergistic Image Reconstruction Framework (SIRF) +## Copyright 2018 - 2020 Rutherford Appleton Laboratory STFC +## Copyright 2018 - 2020 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/). +## Project in Synergistic Reconstruction for Biomedical Imaging (formerly CCP PETMR) +## (http://www.ccpsynerbi.ac.uk/). ## ## Licensed under the Apache License, Version 2.0 (the "License"); ## you may not use this file except in compliance with the License. diff --git a/examples/Python/PET/acquisition_model.py b/examples/Python/PET/acquisition_model.py index 81ca3dff9..63adc2912 100644 --- a/examples/Python/PET/acquisition_model.py +++ b/examples/Python/PET/acquisition_model.py @@ -18,13 +18,13 @@ You probably want to check that instead. ''' -## CCP PETMR Synergistic Image Reconstruction Framework (SIRF) -## Copyright 2015 - 2017 Rutherford Appleton Laboratory STFC -## Copyright 2015 - 2018 University College London. +## SyneRBI Synergistic Image Reconstruction Framework (SIRF) +## Copyright 2015 - 2019 Rutherford Appleton Laboratory STFC +## Copyright 2015 - 2020 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/). +## Project in Synergistic Reconstruction for Biomedical Imaging (formerly CCP PETMR) +## (http://www.ccpsynerbi.ac.uk/). ## ## Licensed under the Apache License, Version 2.0 (the "License"); ## you may not use this file except in compliance with the License. diff --git a/examples/Python/PET/acquisition_sensitivity_from_attenuation.py b/examples/Python/PET/acquisition_sensitivity_from_attenuation.py index 82d47c960..be11e0bbc 100644 --- a/examples/Python/PET/acquisition_sensitivity_from_attenuation.py +++ b/examples/Python/PET/acquisition_sensitivity_from_attenuation.py @@ -12,13 +12,13 @@ -s , --storage= acquisition data storage scheme [default: file] ''' -## CCP PETMR Synergistic Image Reconstruction Framework (SIRF) -## Copyright 2015 - 2017 Rutherford Appleton Laboratory STFC +## SyneRBI Synergistic Image Reconstruction Framework (SIRF) +## Copyright 2015 - 2019 Rutherford Appleton Laboratory STFC ## Copyright 2015 - 2017 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/). +## Project in Synergistic Reconstruction for Biomedical Imaging (formerly CCP PETMR) +## (http://www.ccpsynerbi.ac.uk/). ## ## Licensed under the Apache License, Version 2.0 (the "License"); ## you may not use this file except in compliance with the License. diff --git a/examples/Python/PET/acquisition_sensitivity_from_bin_efficiencies.py b/examples/Python/PET/acquisition_sensitivity_from_bin_efficiencies.py index 9c0673d54..b918dca73 100644 --- a/examples/Python/PET/acquisition_sensitivity_from_bin_efficiencies.py +++ b/examples/Python/PET/acquisition_sensitivity_from_bin_efficiencies.py @@ -11,13 +11,13 @@ -s , --storage= acquisition data storage scheme [default: file] ''' -## CCP PETMR Synergistic Image Reconstruction Framework (SIRF) -## Copyright 2015 - 2017 Rutherford Appleton Laboratory STFC +## SyneRBI Synergistic Image Reconstruction Framework (SIRF) +## Copyright 2015 - 2019 Rutherford Appleton Laboratory STFC ## Copyright 2015 - 2017 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/). +## Project in Synergistic Reconstruction for Biomedical Imaging (formerly CCP PETMR) +## (http://www.ccpsynerbi.ac.uk/). ## ## Licensed under the Apache License, Version 2.0 (the "License"); ## you may not use this file except in compliance with the License. diff --git a/examples/Python/PET/acquisition_sensitivity_from_ecat8.py b/examples/Python/PET/acquisition_sensitivity_from_ecat8.py index 6903da711..ef9896384 100644 --- a/examples/Python/PET/acquisition_sensitivity_from_ecat8.py +++ b/examples/Python/PET/acquisition_sensitivity_from_ecat8.py @@ -12,13 +12,13 @@ -s , --storage= acquisition data storage scheme [default: file] ''' -## CCP PETMR Synergistic Image Reconstruction Framework (SIRF) -## Copyright 2015 - 2017 Rutherford Appleton Laboratory STFC +## SyneRBI Synergistic Image Reconstruction Framework (SIRF) +## Copyright 2015 - 2019 Rutherford Appleton Laboratory STFC ## Copyright 2015 - 2017 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/). +## Project in Synergistic Reconstruction for Biomedical Imaging (formerly CCP PETMR) +## (http://www.ccpsynerbi.ac.uk/). ## ## Licensed under the Apache License, Version 2.0 (the "License"); ## you may not use this file except in compliance with the License. diff --git a/examples/Python/PET/fbp2d_reconstruction.py b/examples/Python/PET/fbp2d_reconstruction.py index c1c28e507..ef12e7a67 100644 --- a/examples/Python/PET/fbp2d_reconstruction.py +++ b/examples/Python/PET/fbp2d_reconstruction.py @@ -11,13 +11,13 @@ -e , --engine= reconstruction engine [default: STIR] ''' -## CCP PETMR Synergistic Image Reconstruction Framework (SIRF) -## Copyright 2018 Rutherford Appleton Laboratory STFC +## SyneRBI Synergistic Image Reconstruction Framework (SIRF) +## Copyright 2018 - 2020 Rutherford Appleton Laboratory STFC ## Copyright 2018 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/). +## Project in Synergistic Reconstruction for Biomedical Imaging (formerly CCP PETMR) +## (http://www.ccpsynerbi.ac.uk/). ## ## Licensed under the Apache License, Version 2.0 (the "License"); ## you may not use this file except in compliance with the License. diff --git a/examples/Python/PET/hkem_reconstruction.py b/examples/Python/PET/hkem_reconstruction.py index 1e84d95d6..c5c1257a1 100644 --- a/examples/Python/PET/hkem_reconstruction.py +++ b/examples/Python/PET/hkem_reconstruction.py @@ -15,13 +15,13 @@ -e , --engine= reconstruction engine [default: STIR] ''' -## CCP PETMR Synergistic Image Reconstruction Framework (SIRF) -## Copyright 2015 - 2018 Rutherford Appleton Laboratory STFC +## SyneRBI Synergistic Image Reconstruction Framework (SIRF) +## Copyright 2015 - 2020 Rutherford Appleton Laboratory STFC ## Copyright 2015 - 2018 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/). +## Project in Synergistic Reconstruction for Biomedical Imaging (formerly CCP PETMR) +## (http://www.ccpsynerbi.ac.uk/). ## ## Licensed under the Apache License, Version 2.0 (the "License"); ## you may not use this file except in compliance with the License. diff --git a/examples/Python/PET/input_output.py b/examples/Python/PET/input_output.py index f95834fc2..02e87b139 100644 --- a/examples/Python/PET/input_output.py +++ b/examples/Python/PET/input_output.py @@ -13,13 +13,13 @@ -e , --engine= reconstruction engine [default: STIR] ''' -## CCP PETMR Synergistic Image Reconstruction Framework (SIRF) -## Copyright 2015 - 2017 Rutherford Appleton Laboratory STFC +## SyneRBI Synergistic Image Reconstruction Framework (SIRF) +## Copyright 2015 - 2019 Rutherford Appleton Laboratory STFC ## Copyright 2015 - 2017 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/). +## Project in Synergistic Reconstruction for Biomedical Imaging (formerly CCP PETMR) +## (http://www.ccpsynerbi.ac.uk/). ## ## Licensed under the Apache License, Version 2.0 (the "License"); ## you may not use this file except in compliance with the License. diff --git a/examples/Python/PET/interactive/01-display_and_projection.py b/examples/Python/PET/interactive/01-display_and_projection.py index 74e9c47b4..dac5c8726 100644 --- a/examples/Python/PET/interactive/01-display_and_projection.py +++ b/examples/Python/PET/interactive/01-display_and_projection.py @@ -19,13 +19,13 @@ # First version: 8th of September 2016 # -## CCP PETMR Synergistic Image Reconstruction Framework (SIRF) +## SyneRBI Synergistic Image Reconstruction Framework (SIRF) ## Copyright 2015 - 2017 Rutherford Appleton Laboratory STFC ## Copyright 2015 - 2017 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/). +## Project in Synergistic Reconstruction for Biomedical Imaging (formerly CCP PETMR) +## (http://www.ccpsynerbi.ac.uk/). ## ## Licensed under the Apache License, Version 2.0 (the "License"); ## you may not use this file except in compliance with the License. diff --git a/examples/Python/PET/interactive/02-image_creation_and_projection.py b/examples/Python/PET/interactive/02-image_creation_and_projection.py index faaf2ce22..11bdd0c14 100644 --- a/examples/Python/PET/interactive/02-image_creation_and_projection.py +++ b/examples/Python/PET/interactive/02-image_creation_and_projection.py @@ -12,13 +12,13 @@ # Author: Kris Thielemans # Author: Evgueni Ovtchinnikov # -## CCP PETMR Synergistic Image Reconstruction Framework (SIRF) +## SyneRBI Synergistic Image Reconstruction Framework (SIRF) ## Copyright 2015 - 2017 Rutherford Appleton Laboratory STFC ## Copyright 2015 - 2017 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/). +## Project in Synergistic Reconstruction for Biomedical Imaging (formerly CCP PETMR) +## (http://www.ccpsynerbi.ac.uk/). ## ## Licensed under the Apache License, Version 2.0 (the "License"); ## you may not use this file except in compliance with the License. diff --git a/examples/Python/PET/interactive/03-basic_reconstruction.py b/examples/Python/PET/interactive/03-basic_reconstruction.py index 7657ff411..40115e2ca 100644 --- a/examples/Python/PET/interactive/03-basic_reconstruction.py +++ b/examples/Python/PET/interactive/03-basic_reconstruction.py @@ -12,13 +12,13 @@ # Author: Kris Thielemans # Author: Evgueni Ovtchinnikov # -## CCP PETMR Synergistic Image Reconstruction Framework (SIRF) +## SyneRBI Synergistic Image Reconstruction Framework (SIRF) ## Copyright 2015 - 2017 Rutherford Appleton Laboratory STFC ## Copyright 2015 - 2017 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/). +## Project in Synergistic Reconstruction for Biomedical Imaging (formerly CCP PETMR) +## (http://www.ccpsynerbi.ac.uk/). ## ## Licensed under the Apache License, Version 2.0 (the "License"); ## you may not use this file except in compliance with the License. diff --git a/examples/Python/PET/interactive/reconstruction.py b/examples/Python/PET/interactive/reconstruction.py index abc0f8f85..07d3d9876 100644 --- a/examples/Python/PET/interactive/reconstruction.py +++ b/examples/Python/PET/interactive/reconstruction.py @@ -13,13 +13,13 @@ # Author: Kris Thielemans # -## CCP PETMR Synergistic Image Reconstruction Framework (SIRF) -## Copyright 2015 - 2017 Rutherford Appleton Laboratory STFC +## SyneRBI Synergistic Image Reconstruction Framework (SIRF) +## Copyright 2015 - 2019 Rutherford Appleton Laboratory STFC ## Copyright 2015 - 2017 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/). +## Project in Synergistic Reconstruction for Biomedical Imaging (formerly CCP PETMR) +## (http://www.ccpsynerbi.ac.uk/). ## ## Licensed under the Apache License, Version 2.0 (the "License"); ## you may not use this file except in compliance with the License. diff --git a/examples/Python/PET/listmode_to_sinograms.py b/examples/Python/PET/listmode_to_sinograms.py index 4dae8b03b..cbd2e3562 100644 --- a/examples/Python/PET/listmode_to_sinograms.py +++ b/examples/Python/PET/listmode_to_sinograms.py @@ -15,13 +15,13 @@ -s , --storage= acquisition data storage scheme [default: memory] ''' -## CCP PETMR Synergistic Image Reconstruction Framework (SIRF) -## Copyright 2018 Rutherford Appleton Laboratory STFC +## SyneRBI Synergistic Image Reconstruction Framework (SIRF) +## Copyright 2018 - 2019 Rutherford Appleton Laboratory STFC ## Copyright 2018 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/). +## Project in Synergistic Reconstruction for Biomedical Imaging (formerly CCP PETMR) +## (http://www.ccpsynerbi.ac.uk/). ## ## Licensed under the Apache License, Version 2.0 (the "License"); ## you may not use this file except in compliance with the License. diff --git a/examples/Python/PET/osem_reconstruction.py b/examples/Python/PET/osem_reconstruction.py index 155af1e1a..b76dd17c5 100644 --- a/examples/Python/PET/osem_reconstruction.py +++ b/examples/Python/PET/osem_reconstruction.py @@ -17,13 +17,13 @@ -e , --engine= reconstruction engine [default: STIR] ''' -## CCP PETMR Synergistic Image Reconstruction Framework (SIRF) -## Copyright 2015 - 2018 Rutherford Appleton Laboratory STFC +## SyneRBI Synergistic Image Reconstruction Framework (SIRF) +## Copyright 2015 - 2020 Rutherford Appleton Laboratory STFC ## Copyright 2015 - 2018 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/). +## Project in Synergistic Reconstruction for Biomedical Imaging (formerly CCP PETMR) +## (http://www.ccpsynerbi.ac.uk/). ## ## Licensed under the Apache License, Version 2.0 (the "License"); ## you may not use this file except in compliance with the License. diff --git a/examples/Python/PET/osem_reconstruction_gpu.py b/examples/Python/PET/osem_reconstruction_gpu.py index 7bebdcaa2..091dc5a90 100644 --- a/examples/Python/PET/osem_reconstruction_gpu.py +++ b/examples/Python/PET/osem_reconstruction_gpu.py @@ -25,13 +25,13 @@ --gpu use gpu ''' -## CCP PETMR Synergistic Image Reconstruction Framework (SIRF) +## SyneRBI Synergistic Image Reconstruction Framework (SIRF) ## Copyright 2015 - 2018 Rutherford Appleton Laboratory STFC -## Copyright 2015 - 2018 University College London. +## Copyright 2015 - 2020 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/). +## Project in Synergistic Reconstruction for Biomedical Imaging (formerly CCP PETMR) +## (http://www.ccpsynerbi.ac.uk/). ## ## Licensed under the Apache License, Version 2.0 (the "License"); ## you may not use this file except in compliance with the License. diff --git a/examples/Python/PET/osl_reconstruction.py b/examples/Python/PET/osl_reconstruction.py index a102041c4..9798c3854 100644 --- a/examples/Python/PET/osl_reconstruction.py +++ b/examples/Python/PET/osl_reconstruction.py @@ -24,13 +24,13 @@ -e , --engine= reconstruction engine [default: STIR] ''' -## CCP PETMR Synergistic Image Reconstruction Framework (SIRF) -## Copyright 2015 - 2018 Rutherford Appleton Laboratory STFC +## SyneRBI Synergistic Image Reconstruction Framework (SIRF) +## Copyright 2015 - 2019 Rutherford Appleton Laboratory STFC ## Copyright 2015 - 2018 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/). +## Project in Synergistic Reconstruction for Biomedical Imaging (formerly CCP PETMR) +## (http://www.ccpsynerbi.ac.uk/). ## ## Licensed under the Apache License, Version 2.0 (the "License"); ## you may not use this file except in compliance with the License. diff --git a/examples/Python/PET/ossps_reconstruction.py b/examples/Python/PET/ossps_reconstruction.py index ff78609c9..d88c33e9b 100644 --- a/examples/Python/PET/ossps_reconstruction.py +++ b/examples/Python/PET/ossps_reconstruction.py @@ -16,13 +16,13 @@ -e , --engine= reconstruction engine [default: STIR] ''' -## CCP PETMR Synergistic Image Reconstruction Framework (SIRF) -## Copyright 2015 - 2017 Rutherford Appleton Laboratory STFC +## SyneRBI Synergistic Image Reconstruction Framework (SIRF) +## Copyright 2015 - 2019 Rutherford Appleton Laboratory STFC ## Copyright 2015 - 2017 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/). +## Project in Synergistic Reconstruction for Biomedical Imaging (formerly CCP PETMR) +## (http://www.ccpsynerbi.ac.uk/). ## ## Licensed under the Apache License, Version 2.0 (the "License"); ## you may not use this file except in compliance with the License. diff --git a/examples/Python/PET/randoms_from_listmode.py b/examples/Python/PET/randoms_from_listmode.py index 12e43f615..ca0fe41fa 100644 --- a/examples/Python/PET/randoms_from_listmode.py +++ b/examples/Python/PET/randoms_from_listmode.py @@ -20,13 +20,13 @@ -s , --storage= acquisition data storage scheme [default: file] ''' -## CCP PETMR Synergistic Image Reconstruction Framework (SIRF) -## Copyright 2018 Rutherford Appleton Laboratory STFC +## SyneRBI Synergistic Image Reconstruction Framework (SIRF) +## Copyright 2018 - 2019 Rutherford Appleton Laboratory STFC ## Copyright 2018 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/). +## Project in Synergistic Reconstruction for Biomedical Imaging (formerly CCP PETMR) +## (http://www.ccpsynerbi.ac.uk/). ## ## Licensed under the Apache License, Version 2.0 (the "License"); ## you may not use this file except in compliance with the License. diff --git a/examples/Python/PET/reconstruct_from_listmode.py b/examples/Python/PET/reconstruct_from_listmode.py index 0e753c460..2262fe412 100644 --- a/examples/Python/PET/reconstruct_from_listmode.py +++ b/examples/Python/PET/reconstruct_from_listmode.py @@ -26,13 +26,13 @@ --gpu use gpu ''' -## CCP PETMR Synergistic Image Reconstruction Framework (SIRF) -## Copyright 2018 Rutherford Appleton Laboratory STFC -## Copyright 2018 University College London. +## SyneRBI Synergistic Image Reconstruction Framework (SIRF) +## Copyright 2018 - 2019 Rutherford Appleton Laboratory STFC +## Copyright 2018 - 2020 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/). +## Project in Synergistic Reconstruction for Biomedical Imaging (formerly CCP PETMR) +## (http://www.ccpsynerbi.ac.uk/). ## ## Licensed under the Apache License, Version 2.0 (the "License"); ## you may not use this file except in compliance with the License. diff --git a/examples/Python/PET/run_all.py b/examples/Python/PET/run_all.py index 2c0d02bda..d9e5f8e7f 100644 --- a/examples/Python/PET/run_all.py +++ b/examples/Python/PET/run_all.py @@ -1,12 +1,12 @@ #!/usr/bin/env python -## CCP PETMR Synergistic Image Reconstruction Framework (SIRF) +## SyneRBI Synergistic Image Reconstruction Framework (SIRF) ## Copyright 2015 - 2017 Rutherford Appleton Laboratory STFC ## Copyright 2015 - 2017 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/). +## Project in Synergistic Reconstruction for Biomedical Imaging (formerly CCP PETMR) +## (http://www.ccpsynerbi.ac.uk/). ## ## Licensed under the Apache License, Version 2.0 (the "License"); ## you may not use this file except in compliance with the License. diff --git a/examples/Python/PET/steepest_ascent.py b/examples/Python/PET/steepest_ascent.py index a465908ec..18586e4e4 100644 --- a/examples/Python/PET/steepest_ascent.py +++ b/examples/Python/PET/steepest_ascent.py @@ -16,13 +16,13 @@ -v, --verbose verbose ''' -## CCP PETMR Synergistic Image Reconstruction Framework (SIRF) +## SyneRBI Synergistic Image Reconstruction Framework (SIRF) ## Copyright 2015 - 2020 Rutherford Appleton Laboratory STFC ## Copyright 2015 - 2020 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/). +## Project in Synergistic Reconstruction for Biomedical Imaging (formerly CCP PETMR) +## (http://www.ccpsynerbi.ac.uk/). ## ## Licensed under the Apache License, Version 2.0 (the "License"); ## you may not use this file except in compliance with the License. diff --git a/examples/Python/PET/user_osmaposl.py b/examples/Python/PET/user_osmaposl.py index 207a9b003..4ee5002f9 100644 --- a/examples/Python/PET/user_osmaposl.py +++ b/examples/Python/PET/user_osmaposl.py @@ -13,13 +13,13 @@ -e , --engine= reconstruction engine [default: STIR] ''' -## CCP PETMR Synergistic Image Reconstruction Framework (SIRF) -## Copyright 2015 - 2017 Rutherford Appleton Laboratory STFC +## SyneRBI Synergistic Image Reconstruction Framework (SIRF) +## Copyright 2015 - 2019 Rutherford Appleton Laboratory STFC ## Copyright 2015 - 2017 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/). +## Project in Synergistic Reconstruction for Biomedical Imaging (formerly CCP PETMR) +## (http://www.ccpsynerbi.ac.uk/). ## ## Licensed under the Apache License, Version 2.0 (the "License"); ## you may not use this file except in compliance with the License. diff --git a/examples/Python/PETMR/PET_MCIR.py b/examples/Python/PETMR/PET_MCIR.py index d3cd641cb..0bd6e1d2b 100644 --- a/examples/Python/PETMR/PET_MCIR.py +++ b/examples/Python/PETMR/PET_MCIR.py @@ -21,12 +21,12 @@ -s , --save_interval= save every x iterations [default: 10] """ -## CCP PETMR Synergistic Image Reconstruction Framework (SIRF) +## SyneRBI Synergistic Image Reconstruction Framework (SIRF) ## Copyright 2020 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/). +## Project in Synergistic Reconstruction for Biomedical Imaging (formerly CCP PETMR) +## (http://www.ccpsynerbi.ac.uk/). ## ## Licensed under the Apache License, Version 2.0 (the "License"); ## you may not use this file except in compliance with the License. diff --git a/examples/Python/PETMR/generate_MCIR_data.py b/examples/Python/PETMR/generate_MCIR_data.py index a2fab9b17..5284b11f7 100644 --- a/examples/Python/PETMR/generate_MCIR_data.py +++ b/examples/Python/PETMR/generate_MCIR_data.py @@ -10,12 +10,12 @@ -n , --num_ms= number of motion states [default: 4] """ -## CCP PETMR Synergistic Image Reconstruction Framework (SIRF) +## SyneRBI Synergistic Image Reconstruction Framework (SIRF) ## Copyright 2020 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/). +## Project in Synergistic Reconstruction for Biomedical Imaging (formerly CCP PETMR) +## (http://www.ccpsynerbi.ac.uk/). ## ## Licensed under the Apache License, Version 2.0 (the "License"); ## you may not use this file except in compliance with the License. diff --git a/examples/Python/PETMR/simplistic_petmr.py b/examples/Python/PETMR/simplistic_petmr.py index 74166fc7b..acc20732e 100644 --- a/examples/Python/PETMR/simplistic_petmr.py +++ b/examples/Python/PETMR/simplistic_petmr.py @@ -12,13 +12,13 @@ --pet_engine= PET reconstruction engine [default: STIR] ''' -## CCP PETMR Synergistic Image Reconstruction Framework (SIRF) -## Copyright 2015 - 2017 Rutherford Appleton Laboratory STFC +## SyneRBI Synergistic Image Reconstruction Framework (SIRF) +## Copyright 2015 - 2019 Rutherford Appleton Laboratory STFC ## Copyright 2015 - 2017 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/). +## Project in Synergistic Reconstruction for Biomedical Imaging (formerly CCP PETMR) +## (http://www.ccpsynerbi.ac.uk/). ## ## Licensed under the Apache License, Version 2.0 (the "License"); ## you may not use this file except in compliance with the License. diff --git a/examples/Python/Registration/sirf_registration.py b/examples/Python/Registration/sirf_registration.py index 641a39554..3d8c60616 100644 --- a/examples/Python/Registration/sirf_registration.py +++ b/examples/Python/Registration/sirf_registration.py @@ -32,12 +32,12 @@ --delete should I delete temporary files? (SPM only) (default: True) ''' -## CCP PETMR Synergistic Image Reconstruction Framework (SIRF) +## SyneRBI Synergistic Image Reconstruction Framework (SIRF) ## Copyright 2018 - 2020 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/). +## Project in Synergistic Reconstruction for Biomedical Imaging (formerly CCP PETMR) +## (http://www.ccpsynerbi.ac.uk/). ## ## Licensed under the Apache License, Version 2.0 (the "License"); ## you may not use this file except in compliance with the License. diff --git a/examples/Python/Registration/sirf_resample.py b/examples/Python/Registration/sirf_resample.py index d11482ffd..8a0715d04 100644 --- a/examples/Python/Registration/sirf_resample.py +++ b/examples/Python/Registration/sirf_resample.py @@ -16,12 +16,12 @@ --pad Padding value ''' -## CCP PETMR Synergistic Image Reconstruction Framework (SIRF) +## SyneRBI 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/). +## Project in Synergistic Reconstruction for Biomedical Imaging (formerly CCP PETMR) +## (http://www.ccpsynerbi.ac.uk/). ## ## Licensed under the Apache License, Version 2.0 (the "License"); ## you may not use this file except in compliance with the License. diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt index eab862a05..bb162df38 100644 --- a/src/CMakeLists.txt +++ b/src/CMakeLists.txt @@ -1,8 +1,8 @@ #======================================================================== # Author: Richard Brown, Kris Thielemans -# Copyright 2016 - 2019 University College London -# Copyright 2016 - 2018 Science Technology Facilities Council +# Copyright 2016 - 2020 University College London +# Copyright 2016 - 2020 Science Technology Facilities Council # # Licensed under the Apache License, Version 2.0 (the "License"); # you may not use this file except in compliance with the License. @@ -122,4 +122,4 @@ else() endif() endif() -ADD_SUBDIRECTORY(common) \ No newline at end of file +ADD_SUBDIRECTORY(common) diff --git a/src/Registration/NiftyMoMo/CMakeLists.txt b/src/Registration/NiftyMoMo/CMakeLists.txt index cd821ceae..12cfe9fdf 100644 --- a/src/Registration/NiftyMoMo/CMakeLists.txt +++ b/src/Registration/NiftyMoMo/CMakeLists.txt @@ -1,6 +1,6 @@ #======================================================================== # Author: Richard Brown -# Copyright 2018 - 2019 University College London +# Copyright 2018 - 2020 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. diff --git a/src/Registration/cReg/AffineTransformation.cpp b/src/Registration/cReg/AffineTransformation.cpp index d82f1748a..c96506735 100644 --- a/src/Registration/cReg/AffineTransformation.cpp +++ b/src/Registration/cReg/AffineTransformation.cpp @@ -1,10 +1,10 @@ /* -CCP PETMR Synergistic Image Reconstruction Framework (SIRF) +SyneRBI Synergistic Image Reconstruction Framework (SIRF) Copyright 2017 - 2020 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/). +Project in Synergistic Reconstruction for Biomedical Imaging (formerly CCP PETMR) +(http://www.ccpsynerbi.ac.uk/). Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. @@ -24,7 +24,7 @@ limitations under the License. \brief Class for affine transformations. \author Richard Brown -\author CCP PETMR +\author SyneRBI */ #include "sirf/Reg/AffineTransformation.h" diff --git a/src/Registration/cReg/ImageWeightedMean.cpp b/src/Registration/cReg/ImageWeightedMean.cpp index 5f5db4d9f..0700e03fb 100644 --- a/src/Registration/cReg/ImageWeightedMean.cpp +++ b/src/Registration/cReg/ImageWeightedMean.cpp @@ -1,10 +1,10 @@ /* -CCP PETMR Synergistic Image Reconstruction Framework (SIRF) -Copyright 2017 - 2019 University College London +SyneRBI Synergistic Image Reconstruction Framework (SIRF) +Copyright 2017 - 2020 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/). +Project in Synergistic Reconstruction for Biomedical Imaging (formerly CCP PETMR) +(http://www.ccpsynerbi.ac.uk/). Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. @@ -24,7 +24,7 @@ limitations under the License. \brief Perform weighted mean of multiple images. \author Richard Brown -\author CCP PETMR +\author SyneRBI */ #include "sirf/Reg/ImageWeightedMean.h" diff --git a/src/Registration/cReg/NiftiBasedRegistration.cpp b/src/Registration/cReg/NiftiBasedRegistration.cpp index 3d4aba3f1..9990072f6 100644 --- a/src/Registration/cReg/NiftiBasedRegistration.cpp +++ b/src/Registration/cReg/NiftiBasedRegistration.cpp @@ -1,10 +1,10 @@ /* -CCP PETMR Synergistic Image Reconstruction Framework (SIRF) +SyneRBI Synergistic Image Reconstruction Framework (SIRF) Copyright 2017 - 2020 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/). +Project in Synergistic Reconstruction for Biomedical Imaging (formerly CCP PETMR) +(http://www.ccpsynerbi.ac.uk/). Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. @@ -24,7 +24,7 @@ limitations under the License. \brief Base class for all NIfTI-based registration algorithms. \author Richard Brown -\author CCP PETMR +\author SyneRBI */ #include "sirf/Reg/NiftiBasedRegistration.h" diff --git a/src/Registration/cReg/NiftiImageData.cpp b/src/Registration/cReg/NiftiImageData.cpp index 7964b8ca3..b0814d535 100644 --- a/src/Registration/cReg/NiftiImageData.cpp +++ b/src/Registration/cReg/NiftiImageData.cpp @@ -1,10 +1,11 @@ /* -CCP PETMR Synergistic Image Reconstruction Framework (SIRF) -Copyright 2017 - 2019 University College London +SyneRBI Synergistic Image Reconstruction Framework (SIRF) +Copyright 2017 - 2020 University College London +Copyright 2019 - 2020 Rutherford Appleton Laboratory STFC This is software developed for the Collaborative Computational -Project in Positron Emission Tomography and Magnetic Resonance imaging -(http://www.ccppetmr.ac.uk/). +Project in Synergistic Reconstruction for Biomedical Imaging (formerly CCP PETMR) +(http://www.ccpsynerbi.ac.uk/). Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. @@ -24,7 +25,7 @@ limitations under the License. \brief Base class for SIRF image data. \author Richard Brown -\author CCP PETMR +\author SyneRBI */ #include "sirf/Reg/NiftiImageData.h" diff --git a/src/Registration/cReg/NiftiImageData3D.cpp b/src/Registration/cReg/NiftiImageData3D.cpp index 6acc2e162..cb794222d 100644 --- a/src/Registration/cReg/NiftiImageData3D.cpp +++ b/src/Registration/cReg/NiftiImageData3D.cpp @@ -1,10 +1,10 @@ /* -CCP PETMR Synergistic Image Reconstruction Framework (SIRF) +SyneRBI Synergistic Image Reconstruction Framework (SIRF) Copyright 2017 - 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/). +Project in Synergistic Reconstruction for Biomedical Imaging (formerly CCP PETMR) +(http://www.ccpsynerbi.ac.uk/). Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. @@ -24,7 +24,7 @@ limitations under the License. \brief Base class for 3D SIRF image data. \author Richard Brown -\author CCP PETMR +\author SyneRBI */ #include "sirf/Reg/NiftiImageData3D.h" diff --git a/src/Registration/cReg/NiftiImageData3DDeformation.cpp b/src/Registration/cReg/NiftiImageData3DDeformation.cpp index d8fb35ce7..1dbe9eec9 100644 --- a/src/Registration/cReg/NiftiImageData3DDeformation.cpp +++ b/src/Registration/cReg/NiftiImageData3DDeformation.cpp @@ -1,10 +1,10 @@ /* -CCP PETMR Synergistic Image Reconstruction Framework (SIRF) -Copyright 2017 - 2019 University College London +SyneRBI Synergistic Image Reconstruction Framework (SIRF) +Copyright 2017 - 2020 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/). +Project in Synergistic Reconstruction for Biomedical Imaging (formerly CCP PETMR) +(http://www.ccpsynerbi.ac.uk/). Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. @@ -24,7 +24,7 @@ limitations under the License. \brief Class for deformation field transformations. \author Richard Brown -\author CCP PETMR +\author SyneRBI */ #include "sirf/Reg/NiftiImageData3DDeformation.h" diff --git a/src/Registration/cReg/NiftiImageData3DDisplacement.cpp b/src/Registration/cReg/NiftiImageData3DDisplacement.cpp index 170633ee3..5811ce560 100644 --- a/src/Registration/cReg/NiftiImageData3DDisplacement.cpp +++ b/src/Registration/cReg/NiftiImageData3DDisplacement.cpp @@ -1,10 +1,10 @@ /* -CCP PETMR Synergistic Image Reconstruction Framework (SIRF) -Copyright 2017 - 2019 University College London +SyneRBI Synergistic Image Reconstruction Framework (SIRF) +Copyright 2017 - 2020 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/). +Project in Synergistic Reconstruction for Biomedical Imaging (formerly CCP PETMR) +(http://www.ccpsynerbi.ac.uk/). Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. @@ -24,7 +24,7 @@ limitations under the License. \brief Class for displacement field transformations. \author Richard Brown -\author CCP PETMR +\author SyneRBI */ #include "sirf/Reg/NiftiImageData3DDisplacement.h" diff --git a/src/Registration/cReg/NiftiImageData3DTensor.cpp b/src/Registration/cReg/NiftiImageData3DTensor.cpp index d870075d8..aec54adb1 100644 --- a/src/Registration/cReg/NiftiImageData3DTensor.cpp +++ b/src/Registration/cReg/NiftiImageData3DTensor.cpp @@ -1,10 +1,10 @@ /* -CCP PETMR Synergistic Image Reconstruction Framework (SIRF) -Copyright 2017 - 2019 University College London +SyneRBI Synergistic Image Reconstruction Framework (SIRF) +Copyright 2017 - 2020 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/). +Project in Synergistic Reconstruction for Biomedical Imaging (formerly CCP PETMR) +(http://www.ccpsynerbi.ac.uk/). Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. @@ -24,7 +24,7 @@ limitations under the License. \brief Class for tensor SIRF image data. \author Richard Brown -\author CCP PETMR +\author SyneRBI */ #include "sirf/Reg/NiftiImageData3DTensor.h" diff --git a/src/Registration/cReg/NiftyAladinSym.cpp.in b/src/Registration/cReg/NiftyAladinSym.cpp.in index 1ea7d6ddb..742a82789 100644 --- a/src/Registration/cReg/NiftyAladinSym.cpp.in +++ b/src/Registration/cReg/NiftyAladinSym.cpp.in @@ -1,10 +1,10 @@ /* -CCP PETMR Synergistic Image Reconstruction Framework (SIRF) +SyneRBI Synergistic Image Reconstruction Framework (SIRF) Copyright 2017 - 2020 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/). +Project in Synergistic Reconstruction for Biomedical Imaging (formerly CCP PETMR) +(http://www.ccpsynerbi.ac.uk/). Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. @@ -24,7 +24,7 @@ limitations under the License. \brief NiftyReg's aladin class for rigid and affine registrations. \author Richard Brown -\author CCP PETMR +\author SyneRBI */ #include "sirf/Reg/NiftyAladinSym.h" diff --git a/src/Registration/cReg/NiftyF3dSym.cpp.in b/src/Registration/cReg/NiftyF3dSym.cpp.in index ce477e4b1..c4f00ffff 100644 --- a/src/Registration/cReg/NiftyF3dSym.cpp.in +++ b/src/Registration/cReg/NiftyF3dSym.cpp.in @@ -1,10 +1,10 @@ /* -CCP PETMR Synergistic Image Reconstruction Framework (SIRF) +SyneRBI Synergistic Image Reconstruction Framework (SIRF) Copyright 2017 - 2020 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/). +Project in Synergistic Reconstruction for Biomedical Imaging (formerly CCP PETMR) +(http://www.ccpsynerbi.ac.uk/). Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. @@ -24,7 +24,7 @@ limitations under the License. \brief NiftyReg's f3d class for non-rigid registrations. \author Richard Brown -\author CCP PETMR +\author SyneRBI */ #include "sirf/Reg/NiftyF3dSym.h" diff --git a/src/Registration/cReg/NiftyRegistration.cpp b/src/Registration/cReg/NiftyRegistration.cpp index 1f161c462..39fbcad26 100644 --- a/src/Registration/cReg/NiftyRegistration.cpp +++ b/src/Registration/cReg/NiftyRegistration.cpp @@ -1,10 +1,10 @@ /* -CCP PETMR Synergistic Image Reconstruction Framework (SIRF) +SyneRBI Synergistic Image Reconstruction Framework (SIRF) Copyright 2017 - 2020 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/). +Project in Synergistic Reconstruction for Biomedical Imaging (formerly CCP PETMR) +(http://www.ccpsynerbi.ac.uk/). Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. @@ -24,7 +24,7 @@ limitations under the License. \brief Base class for all NiftyReg registration algorithms. \author Richard Brown -\author CCP PETMR +\author SyneRBI */ #include "sirf/Reg/NiftyRegistration.h" diff --git a/src/Registration/cReg/NiftyResample.cpp b/src/Registration/cReg/NiftyResample.cpp index ff840043c..fbfe3ef51 100644 --- a/src/Registration/cReg/NiftyResample.cpp +++ b/src/Registration/cReg/NiftyResample.cpp @@ -1,10 +1,10 @@ /* -CCP PETMR Synergistic Image Reconstruction Framework (SIRF) -Copyright 2017 - 2019 University College London +SyneRBI Synergistic Image Reconstruction Framework (SIRF) +Copyright 2017 - 2020 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/). +Project in Synergistic Reconstruction for Biomedical Imaging (formerly CCP PETMR) +(http://www.ccpsynerbi.ac.uk/). Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. @@ -24,7 +24,7 @@ limitations under the License. \brief Resampling class based on nifty resample \author Richard Brown -\author CCP PETMR +\author SyneRBI */ #include "sirf/Reg/NiftyResample.h" diff --git a/src/Registration/cReg/Quaternion.cpp b/src/Registration/cReg/Quaternion.cpp index e6f8a6717..0b0d963b2 100644 --- a/src/Registration/cReg/Quaternion.cpp +++ b/src/Registration/cReg/Quaternion.cpp @@ -1,10 +1,10 @@ /* -CCP PETMR Synergistic Image Reconstruction Framework (SIRF) +SyneRBI Synergistic Image Reconstruction Framework (SIRF) Copyright 2017 - 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/). +Project in Synergistic Reconstruction for Biomedical Imaging (formerly CCP PETMR) +(http://www.ccpsynerbi.ac.uk/). Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. @@ -24,7 +24,7 @@ limitations under the License. \brief Class for affine transformations. \author Richard Brown -\author CCP PETMR +\author SyneRBI */ #include "sirf/Reg/Quaternion.h" diff --git a/src/Registration/cReg/Registration.cpp b/src/Registration/cReg/Registration.cpp index 5a9cd9367..4e5212690 100644 --- a/src/Registration/cReg/Registration.cpp +++ b/src/Registration/cReg/Registration.cpp @@ -1,10 +1,10 @@ /* -CCP PETMR Synergistic Image Reconstruction Framework (SIRF) +SyneRBI Synergistic Image Reconstruction Framework (SIRF) Copyright 2017 - 2020 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/). +Project in Synergistic Reconstruction for Biomedical Imaging (formerly CCP PETMR) +(http://www.ccpsynerbi.ac.uk/). Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. @@ -24,7 +24,7 @@ limitations under the License. \brief Base class for all SIRF registration. \author Richard Brown -\author CCP PETMR +\author SyneRBI */ #include "sirf/Reg/Registration.h" diff --git a/src/Registration/cReg/Resample.cpp b/src/Registration/cReg/Resample.cpp index b3bd6e779..25edcb09f 100644 --- a/src/Registration/cReg/Resample.cpp +++ b/src/Registration/cReg/Resample.cpp @@ -1,10 +1,10 @@ /* -CCP PETMR Synergistic Image Reconstruction Framework (SIRF) +SyneRBI Synergistic Image Reconstruction Framework (SIRF) Copyright 2017 - 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/). +Project in Synergistic Reconstruction for Biomedical Imaging (formerly CCP PETMR) +(http://www.ccpsynerbi.ac.uk/). Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. @@ -24,7 +24,7 @@ limitations under the License. \brief Abstract resampling base class \author Richard Brown -\author CCP PETMR +\author SyneRBI */ #include "sirf/Reg/Resample.h" diff --git a/src/Registration/cReg/SPMRegistration.cpp b/src/Registration/cReg/SPMRegistration.cpp index 0417986ae..864908756 100644 --- a/src/Registration/cReg/SPMRegistration.cpp +++ b/src/Registration/cReg/SPMRegistration.cpp @@ -1,10 +1,10 @@ /* -CCP PETMR Synergistic Image Reconstruction Framework (SIRF) +SyneRBI Synergistic Image Reconstruction Framework (SIRF) Copyright 2017 - 2020 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/). +Project in Synergistic Reconstruction for Biomedical Imaging (formerly CCP PETMR) +(http://www.ccpsynerbi.ac.uk/). Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. @@ -24,7 +24,7 @@ limitations under the License. \brief NiftyReg's aladin class for rigid and affine registrations. \author Richard Brown -\author CCP PETMR +\author SyneRBI */ #include "sirf/Reg/SPMRegistration.h" diff --git a/src/Registration/cReg/Transformation.cpp b/src/Registration/cReg/Transformation.cpp index d24d3c5c0..d4e68a664 100644 --- a/src/Registration/cReg/Transformation.cpp +++ b/src/Registration/cReg/Transformation.cpp @@ -1,10 +1,10 @@ /* -CCP PETMR Synergistic Image Reconstruction Framework (SIRF) +SyneRBI Synergistic Image Reconstruction Framework (SIRF) Copyright 2017 - 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/). +Project in Synergistic Reconstruction for Biomedical Imaging (formerly CCP PETMR) +(http://www.ccpsynerbi.ac.uk/). Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. @@ -24,7 +24,7 @@ limitations under the License. \brief Base class for transformations. \author Richard Brown -\author CCP PETMR +\author SyneRBI */ #include "sirf/Reg/Transformation.h" diff --git a/src/Registration/cReg/cReg.cpp b/src/Registration/cReg/cReg.cpp index 7658ff0c7..a06fff828 100644 --- a/src/Registration/cReg/cReg.cpp +++ b/src/Registration/cReg/cReg.cpp @@ -1,11 +1,11 @@ /* -CCP PETMR Synergistic Image Reconstruction Framework (SIRF) +SyneRBI Synergistic Image Reconstruction Framework (SIRF) Copyright 2015 - 2017 Rutherford Appleton Laboratory STFC Copyright 2017 - 2020 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/). +Project in Synergistic Reconstruction for Biomedical Imaging (formerly CCP PETMR) +(http://www.ccpsynerbi.ac.uk/). Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. diff --git a/src/Registration/cReg/cReg_p.cpp b/src/Registration/cReg/cReg_p.cpp index f2dfdf6bc..d814ef176 100644 --- a/src/Registration/cReg/cReg_p.cpp +++ b/src/Registration/cReg/cReg_p.cpp @@ -1,11 +1,11 @@ /* -CCP PETMR Synergistic Image Reconstruction Framework (SIRF) +SyneRBI Synergistic Image Reconstruction Framework (SIRF) Copyright 2015 - 2017 Rutherford Appleton Laboratory STFC Copyright 2017 - 2020 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/). +Project in Synergistic Reconstruction for Biomedical Imaging (formerly CCP PETMR) +(http://www.ccpsynerbi.ac.uk/). Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. diff --git a/src/Registration/cReg/include/sirf/Reg/AffineTransformation.h b/src/Registration/cReg/include/sirf/Reg/AffineTransformation.h index 54440fa21..aedfd4235 100644 --- a/src/Registration/cReg/include/sirf/Reg/AffineTransformation.h +++ b/src/Registration/cReg/include/sirf/Reg/AffineTransformation.h @@ -1,10 +1,10 @@ /* -CCP PETMR Synergistic Image Reconstruction Framework (SIRF) +SyneRBI Synergistic Image Reconstruction Framework (SIRF) Copyright 2017 - 2020 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/). +Project in Synergistic Reconstruction for Biomedical Imaging (formerly CCP PETMR) +(http://www.ccpsynerbi.ac.uk/). Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. @@ -23,7 +23,7 @@ limitations under the License. \ingroup Registration \brief Class for affine transformations. \author Richard Brown -\author CCP PETMR +\author SyneRBI */ #pragma once @@ -42,7 +42,7 @@ template class Quaternion; \ingroup Registration \brief Class for affine transformations. \author Richard Brown -\author CCP PETMR +\author SyneRBI */ template class AffineTransformation : public Transformation diff --git a/src/Registration/cReg/include/sirf/Reg/ImageWeightedMean.h b/src/Registration/cReg/include/sirf/Reg/ImageWeightedMean.h index 439147465..c26a517de 100644 --- a/src/Registration/cReg/include/sirf/Reg/ImageWeightedMean.h +++ b/src/Registration/cReg/include/sirf/Reg/ImageWeightedMean.h @@ -1,10 +1,10 @@ /* -CCP PETMR Synergistic Image Reconstruction Framework (SIRF) +SyneRBI Synergistic Image Reconstruction Framework (SIRF) Copyright 2017 - 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/). +Project in Synergistic Reconstruction for Biomedical Imaging (formerly CCP PETMR) +(http://www.ccpsynerbi.ac.uk/). Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. @@ -24,7 +24,7 @@ limitations under the License. \brief Perform weighted mean of multiple images. \author Richard Brown -\author CCP PETMR +\author SyneRBI */ #pragma once @@ -45,7 +45,7 @@ template class NiftiImageData; TODO - would be simple for this to work in terms of ImageData instead of NiftiImageData. \author Richard Brown -\author CCP PETMR +\author SyneRBI */ template class ImageWeightedMean diff --git a/src/Registration/cReg/include/sirf/Reg/NiftiBasedRegistration.h b/src/Registration/cReg/include/sirf/Reg/NiftiBasedRegistration.h index 94c385f02..642299ec9 100644 --- a/src/Registration/cReg/include/sirf/Reg/NiftiBasedRegistration.h +++ b/src/Registration/cReg/include/sirf/Reg/NiftiBasedRegistration.h @@ -1,10 +1,10 @@ /* -CCP PETMR Synergistic Image Reconstruction Framework (SIRF) +SyneRBI Synergistic Image Reconstruction Framework (SIRF) Copyright 2017 - 2020 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/). +Project in Synergistic Reconstruction for Biomedical Imaging (formerly CCP PETMR) +(http://www.ccpsynerbi.ac.uk/). Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. @@ -24,7 +24,7 @@ limitations under the License. \brief Base class for all NIfTI-based registrations. \author Richard Brown -\author CCP PETMR +\author SyneRBI */ #pragma once @@ -41,7 +41,7 @@ template class NiftiImageData3D; \brief Base class for all NIfTI-based registrations. \author Richard Brown -\author CCP PETMR +\author SyneRBI */ template class NiftiBasedRegistration : public Registration diff --git a/src/Registration/cReg/include/sirf/Reg/NiftiImageData.h b/src/Registration/cReg/include/sirf/Reg/NiftiImageData.h index 8ea1c4d21..6edd52bcb 100644 --- a/src/Registration/cReg/include/sirf/Reg/NiftiImageData.h +++ b/src/Registration/cReg/include/sirf/Reg/NiftiImageData.h @@ -1,10 +1,10 @@ /* -CCP PETMR Synergistic Image Reconstruction Framework (SIRF) -Copyright 2017 - 2019 University College London +SyneRBI Synergistic Image Reconstruction Framework (SIRF) +Copyright 2017 - 2020 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/). +Project in Synergistic Reconstruction for Biomedical Imaging (formerly CCP PETMR) +(http://www.ccpsynerbi.ac.uk/). Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. @@ -24,7 +24,7 @@ limitations under the License. \brief Base class for SIRF nifti image data. \author Richard Brown -\author CCP PETMR +\author SyneRBI */ #pragma once @@ -70,7 +70,7 @@ of sform_code; for example, for the Talairach coordinate system, (0,0,0) corresponds to the Anterior Commissure. \author Richard Brown -\author CCP PETMR +\author SyneRBI */ template diff --git a/src/Registration/cReg/include/sirf/Reg/NiftiImageData3D.h b/src/Registration/cReg/include/sirf/Reg/NiftiImageData3D.h index e7ae888d8..55ef6fb1c 100644 --- a/src/Registration/cReg/include/sirf/Reg/NiftiImageData3D.h +++ b/src/Registration/cReg/include/sirf/Reg/NiftiImageData3D.h @@ -1,10 +1,10 @@ /* -CCP PETMR Synergistic Image Reconstruction Framework (SIRF) +SyneRBI Synergistic Image Reconstruction Framework (SIRF) Copyright 2017 - 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/). +Project in Synergistic Reconstruction for Biomedical Imaging (formerly CCP PETMR) +(http://www.ccpsynerbi.ac.uk/). Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. @@ -24,7 +24,7 @@ limitations under the License. \brief 3D Nifti image. \author Richard Brown -\author CCP PETMR +\author SyneRBI */ #pragma once @@ -40,7 +40,7 @@ namespace sirf { Here, we require that the number of dimensions == 3. \author Richard Brown -\author CCP PETMR +\author SyneRBI */ template class NiftiImageData3D : public NiftiImageData diff --git a/src/Registration/cReg/include/sirf/Reg/NiftiImageData3DDeformation.h b/src/Registration/cReg/include/sirf/Reg/NiftiImageData3DDeformation.h index b7d6d7d48..874baa451 100644 --- a/src/Registration/cReg/include/sirf/Reg/NiftiImageData3DDeformation.h +++ b/src/Registration/cReg/include/sirf/Reg/NiftiImageData3DDeformation.h @@ -1,10 +1,10 @@ /* -CCP PETMR Synergistic Image Reconstruction Framework (SIRF) -Copyright 2017 - 2019 University College London +SyneRBI Synergistic Image Reconstruction Framework (SIRF) +Copyright 2017 - 2020 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/). +Project in Synergistic Reconstruction for Biomedical Imaging (formerly CCP PETMR) +(http://www.ccpsynerbi.ac.uk/). Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. @@ -24,7 +24,7 @@ limitations under the License. \brief Class for deformation SIRF image data. \author Richard Brown -\author CCP PETMR +\author SyneRBI */ #pragma once @@ -48,7 +48,7 @@ Here, we require ndim == 5, nt == 1 (so contains x,y,z dimensions as well as u== Also require intent_p1 == DEF_FIELD. \author Richard Brown -\author CCP PETMR +\author SyneRBI */ template class NiftiImageData3DDeformation : public NiftiImageData3DTensor, public NonRigidTransformation diff --git a/src/Registration/cReg/include/sirf/Reg/NiftiImageData3DDisplacement.h b/src/Registration/cReg/include/sirf/Reg/NiftiImageData3DDisplacement.h index 99cd9949d..cb23eed3f 100644 --- a/src/Registration/cReg/include/sirf/Reg/NiftiImageData3DDisplacement.h +++ b/src/Registration/cReg/include/sirf/Reg/NiftiImageData3DDisplacement.h @@ -1,10 +1,10 @@ /* -CCP PETMR Synergistic Image Reconstruction Framework (SIRF) -Copyright 2017 - 2019 University College London +SyneRBI Synergistic Image Reconstruction Framework (SIRF) +Copyright 2017 - 2020 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/). +Project in Synergistic Reconstruction for Biomedical Imaging (formerly CCP PETMR) +(http://www.ccpsynerbi.ac.uk/). Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. @@ -24,7 +24,7 @@ limitations under the License. \brief Class for displacement SIRF image data. \author Richard Brown -\author CCP PETMR +\author SyneRBI */ #pragma once @@ -46,7 +46,7 @@ Here, we require ndim == 5, nt == 1 (so contains x,y,z dimensions as well as u== Also require intent_p1 == DISP_FIELD. \author Richard Brown -\author CCP PETMR +\author SyneRBI */ template class NiftiImageData3DDisplacement : public NiftiImageData3DTensor, public NonRigidTransformation diff --git a/src/Registration/cReg/include/sirf/Reg/NiftiImageData3DTensor.h b/src/Registration/cReg/include/sirf/Reg/NiftiImageData3DTensor.h index 4cb41c4d6..46b8a0dfd 100644 --- a/src/Registration/cReg/include/sirf/Reg/NiftiImageData3DTensor.h +++ b/src/Registration/cReg/include/sirf/Reg/NiftiImageData3DTensor.h @@ -1,10 +1,10 @@ /* -CCP PETMR Synergistic Image Reconstruction Framework (SIRF) -Copyright 2017 - 2019 University College London +SyneRBI Synergistic Image Reconstruction Framework (SIRF) +Copyright 2017 - 2020 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/). +Project in Synergistic Reconstruction for Biomedical Imaging (formerly CCP PETMR) +(http://www.ccpsynerbi.ac.uk/). Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. @@ -24,7 +24,7 @@ limitations under the License. \brief Class for tensor SIRF image data. \author Richard Brown -\author CCP PETMR +\author SyneRBI */ #pragma once @@ -45,7 +45,7 @@ This is the general tensor class, so we do not care if the image is a deformatio Hence, any value of intent_p1 is fine. \author Richard Brown -\author CCP PETMR +\author SyneRBI */ template class NiftiImageData3DTensor : public NiftiImageData diff --git a/src/Registration/cReg/include/sirf/Reg/NiftyAladinSym.h b/src/Registration/cReg/include/sirf/Reg/NiftyAladinSym.h index e2296e30e..78a778ca5 100644 --- a/src/Registration/cReg/include/sirf/Reg/NiftyAladinSym.h +++ b/src/Registration/cReg/include/sirf/Reg/NiftyAladinSym.h @@ -1,10 +1,10 @@ /* -CCP PETMR Synergistic Image Reconstruction Framework (SIRF) +SyneRBI Synergistic Image Reconstruction Framework (SIRF) Copyright 2017 - 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/). +Project in Synergistic Reconstruction for Biomedical Imaging (formerly CCP PETMR) +(http://www.ccpsynerbi.ac.uk/). Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. @@ -24,7 +24,7 @@ limitations under the License. \brief NiftyReg's aladin class for rigid and affine registrations. \author Richard Brown -\author CCP PETMR +\author SyneRBI */ #pragma once @@ -45,7 +45,7 @@ template class AffineTransformation; Since this algorithm is affine/rigid, it can also return a transformation matrix if desired. \author Richard Brown -\author CCP PETMR +\author SyneRBI */ template class NiftyAladinSym : public NiftyRegistration { diff --git a/src/Registration/cReg/include/sirf/Reg/NiftyF3dSym.h b/src/Registration/cReg/include/sirf/Reg/NiftyF3dSym.h index 4ae2fbb86..1a7b72958 100644 --- a/src/Registration/cReg/include/sirf/Reg/NiftyF3dSym.h +++ b/src/Registration/cReg/include/sirf/Reg/NiftyF3dSym.h @@ -1,10 +1,10 @@ /* -CCP PETMR Synergistic Image Reconstruction Framework (SIRF) -Copyright 2017 - 2019 University College London +SyneRBI Synergistic Image Reconstruction Framework (SIRF) +Copyright 2017 - 2020 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/). +Project in Synergistic Reconstruction for Biomedical Imaging (formerly CCP PETMR) +(http://www.ccpsynerbi.ac.uk/). Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. @@ -28,7 +28,7 @@ We believe there to be an upstream bug (https://github.com/KCL-BMEIS/niftyreg/is in the symmetric version, and therefore do not recommend using it until that issue is closed. \author Richard Brown -\author CCP PETMR +\author SyneRBI */ #pragma once @@ -52,7 +52,7 @@ In theory, multiple time points can be used, but thus far has only been tested f t == 1 for both reference and floating images. \author Richard Brown -\author CCP PETMR +\author SyneRBI */ template class NiftyF3dSym : public NiftyRegistration { diff --git a/src/Registration/cReg/include/sirf/Reg/NiftyRegistration.h b/src/Registration/cReg/include/sirf/Reg/NiftyRegistration.h index b0ac863be..129852693 100644 --- a/src/Registration/cReg/include/sirf/Reg/NiftyRegistration.h +++ b/src/Registration/cReg/include/sirf/Reg/NiftyRegistration.h @@ -1,10 +1,10 @@ /* -CCP PETMR Synergistic Image Reconstruction Framework (SIRF) +SyneRBI Synergistic Image Reconstruction Framework (SIRF) Copyright 2017 - 2020 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/). +Project in Synergistic Reconstruction for Biomedical Imaging (formerly CCP PETMR) +(http://www.ccpsynerbi.ac.uk/). Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. @@ -24,7 +24,7 @@ limitations under the License. \brief Base class for all NiftyReg registrations. \author Richard Brown -\author CCP PETMR +\author SyneRBI */ #pragma once @@ -41,7 +41,7 @@ template class NiftiImageData3D; \brief Base class for all NiftyReg registrations. \author Richard Brown -\author CCP PETMR +\author SyneRBI */ template class NiftyRegistration : public NiftiBasedRegistration diff --git a/src/Registration/cReg/include/sirf/Reg/NiftyResample.h b/src/Registration/cReg/include/sirf/Reg/NiftyResample.h index b169d97b6..c79043d43 100644 --- a/src/Registration/cReg/include/sirf/Reg/NiftyResample.h +++ b/src/Registration/cReg/include/sirf/Reg/NiftyResample.h @@ -1,10 +1,10 @@ /* -CCP PETMR Synergistic Image Reconstruction Framework (SIRF) -Copyright 2017 - 2019 University College London +SyneRBI Synergistic Image Reconstruction Framework (SIRF) +Copyright 2017 - 2020 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/). +Project in Synergistic Reconstruction for Biomedical Imaging (formerly CCP PETMR) +(http://www.ccpsynerbi.ac.uk/). Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. @@ -24,7 +24,7 @@ limitations under the License. \brief Resampling class based on nifty resample \author Richard Brown -\author CCP PETMR +\author SyneRBI */ #pragma once @@ -95,7 +95,7 @@ class ComplexNiftiImageData The reference image and floating image can have nt and/or nu != 1. \author Richard Brown -\author CCP PETMR +\author SyneRBI */ template class NiftyResample : public Resample diff --git a/src/Registration/cReg/include/sirf/Reg/NonRigidTransformation.h b/src/Registration/cReg/include/sirf/Reg/NonRigidTransformation.h index c6b80fc8a..b06dbcb16 100644 --- a/src/Registration/cReg/include/sirf/Reg/NonRigidTransformation.h +++ b/src/Registration/cReg/include/sirf/Reg/NonRigidTransformation.h @@ -1,10 +1,10 @@ /* -CCP PETMR Synergistic Image Reconstruction Framework (SIRF) +SyneRBI Synergistic Image Reconstruction Framework (SIRF) Copyright 2020 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/). +Project in Synergistic Reconstruction for Biomedical Imaging (formerly CCP PETMR) +(http://www.ccpsynerbi.ac.uk/). Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. @@ -23,7 +23,7 @@ limitations under the License. \ingroup Registration \brief Base class for transformations. \author Richard Brown -\author CCP PETMR +\author SyneRBI */ #pragma once @@ -37,7 +37,7 @@ namespace sirf { \brief Base class for non-rigid transformations. \author Richard Brown -\author CCP PETMR +\author SyneRBI */template class NonRigidTransformation : public Transformation { diff --git a/src/Registration/cReg/include/sirf/Reg/Parser.h b/src/Registration/cReg/include/sirf/Reg/Parser.h index 02e77b87e..712a60a7d 100644 --- a/src/Registration/cReg/include/sirf/Reg/Parser.h +++ b/src/Registration/cReg/include/sirf/Reg/Parser.h @@ -1,10 +1,10 @@ /* -CCP PETMR Synergistic Image Reconstruction Framework (SIRF) +SyneRBI Synergistic Image Reconstruction Framework (SIRF) Copyright 2017 - 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/). +Project in Synergistic Reconstruction for Biomedical Imaging (formerly CCP PETMR) +(http://www.ccpsynerbi.ac.uk/). Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. @@ -24,7 +24,7 @@ limitations under the License. \brief Small class to parse parameter files. \author Richard Brown -\author CCP PETMR +\author SyneRBI */ #pragma once @@ -43,7 +43,7 @@ namespace sirf { \brief Small class to parse parameter files. \author Richard Brown -\author CCP PETMR +\author SyneRBI */ template class Parser diff --git a/src/Registration/cReg/include/sirf/Reg/ParserKey.h b/src/Registration/cReg/include/sirf/Reg/ParserKey.h index c1e68a460..a29b0e219 100644 --- a/src/Registration/cReg/include/sirf/Reg/ParserKey.h +++ b/src/Registration/cReg/include/sirf/Reg/ParserKey.h @@ -1,10 +1,10 @@ /* -CCP PETMR Synergistic Image Reconstruction Framework (SIRF) +SyneRBI Synergistic Image Reconstruction Framework (SIRF) Copyright 2017 - 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/). +Project in Synergistic Reconstruction for Biomedical Imaging (formerly CCP PETMR) +(http://www.ccpsynerbi.ac.uk/). Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. @@ -24,7 +24,7 @@ limitations under the License. \brief Parser keys for 0, 1 and 2 arguments \author Richard Brown -\author CCP PETMR +\author SyneRBI */ #pragma once @@ -52,7 +52,7 @@ std::string get_typename(A) \brief Base for parser keys \author Richard Brown -\author CCP PETMR +\author SyneRBI */ template class ParserKeyBase @@ -161,7 +161,7 @@ class ParserKeyBase \brief Class for parser keys with 0 arguments \author Richard Brown -\author CCP PETMR +\author SyneRBI */ template class ParserKey0Arg : public ParserKeyBase @@ -206,7 +206,7 @@ class ParserKey0Arg : public ParserKeyBase \brief Class for parser keys with 1 argument \author Richard Brown -\author CCP PETMR +\author SyneRBI */ template class ParserKey1Arg : public ParserKeyBase @@ -258,7 +258,7 @@ class ParserKey1Arg : public ParserKeyBase \brief Class for parser keys with 2 arguments \author Richard Brown -\author CCP PETMR +\author SyneRBI */ template class ParserKey2Arg : public ParserKeyBase diff --git a/src/Registration/cReg/include/sirf/Reg/Quaternion.h b/src/Registration/cReg/include/sirf/Reg/Quaternion.h index 0111f5b30..d24ca68e0 100644 --- a/src/Registration/cReg/include/sirf/Reg/Quaternion.h +++ b/src/Registration/cReg/include/sirf/Reg/Quaternion.h @@ -1,10 +1,10 @@ /* -CCP PETMR Synergistic Image Reconstruction Framework (SIRF) +SyneRBI Synergistic Image Reconstruction Framework (SIRF) Copyright 2017 - 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/). +Project in Synergistic Reconstruction for Biomedical Imaging (formerly CCP PETMR) +(http://www.ccpsynerbi.ac.uk/). Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. @@ -23,7 +23,7 @@ limitations under the License. \ingroup Registration \brief Class for quaternions. \author Richard Brown -\author CCP PETMR +\author SyneRBI */ #pragma once @@ -40,7 +40,7 @@ template class AffineTransformation; \ingroup Registration \brief Class for quaternions. \author Richard Brown -\author CCP PETMR +\author SyneRBI */ template class Quaternion diff --git a/src/Registration/cReg/include/sirf/Reg/Registration.h b/src/Registration/cReg/include/sirf/Reg/Registration.h index b6732f726..ef211d3d2 100644 --- a/src/Registration/cReg/include/sirf/Reg/Registration.h +++ b/src/Registration/cReg/include/sirf/Reg/Registration.h @@ -1,10 +1,10 @@ /* -CCP PETMR Synergistic Image Reconstruction Framework (SIRF) +SyneRBI Synergistic Image Reconstruction Framework (SIRF) Copyright 2017 - 2020 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/). +Project in Synergistic Reconstruction for Biomedical Imaging (formerly CCP PETMR) +(http://www.ccpsynerbi.ac.uk/). Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. @@ -24,7 +24,7 @@ limitations under the License. \brief Base class for all SIRF registration. \author Richard Brown -\author CCP PETMR +\author SyneRBI */ #pragma once @@ -65,7 +65,7 @@ An example is given below: More examples can be found in data/examples/Registration/paramFiles \author Richard Brown -\author CCP PETMR +\author SyneRBI */ template class Registration diff --git a/src/Registration/cReg/include/sirf/Reg/Resample.h b/src/Registration/cReg/include/sirf/Reg/Resample.h index def8cd6dc..b85b28e3c 100644 --- a/src/Registration/cReg/include/sirf/Reg/Resample.h +++ b/src/Registration/cReg/include/sirf/Reg/Resample.h @@ -1,10 +1,10 @@ /* -CCP PETMR Synergistic Image Reconstruction Framework (SIRF) -Copyright 2017 - 2019 University College London +SyneRBI Synergistic Image Reconstruction Framework (SIRF) +Copyright 2017 - 2020 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/). +Project in Synergistic Reconstruction for Biomedical Imaging (formerly CCP PETMR) +(http://www.ccpsynerbi.ac.uk/). Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. @@ -24,7 +24,7 @@ limitations under the License. \brief Abstract resampling base class \author Richard Brown -\author CCP PETMR +\author SyneRBI */ #pragma once @@ -49,7 +49,7 @@ If multiple transformations are set, they will be used in the order that they ha i.e., Trans3(Trans2(Trans1(x))). \author Richard Brown -\author CCP PETMR +\author SyneRBI */ template class Resample diff --git a/src/Registration/cReg/include/sirf/Reg/SPMRegistration.h b/src/Registration/cReg/include/sirf/Reg/SPMRegistration.h index 1f2677e08..4989edbba 100644 --- a/src/Registration/cReg/include/sirf/Reg/SPMRegistration.h +++ b/src/Registration/cReg/include/sirf/Reg/SPMRegistration.h @@ -1,10 +1,10 @@ /* -CCP PETMR Synergistic Image Reconstruction Framework (SIRF) +SyneRBI Synergistic Image Reconstruction Framework (SIRF) Copyright 2017 - 2020 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/). +Project in Synergistic Reconstruction for Biomedical Imaging (formerly CCP PETMR) +(http://www.ccpsynerbi.ac.uk/). Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. @@ -24,7 +24,7 @@ limitations under the License. \brief Wrapper around SPM's registration class. \author Richard Brown -\author CCP PETMR +\author SyneRBI */ #pragma once @@ -42,7 +42,7 @@ template class AffineTransformation; \brief Wrapper around SPM's registration class. \author Richard Brown -\author CCP PETMR +\author SyneRBI */ template class SPMRegistration : public NiftiBasedRegistration { diff --git a/src/Registration/cReg/include/sirf/Reg/Transformation.h b/src/Registration/cReg/include/sirf/Reg/Transformation.h index 66120a8de..1782d9dac 100644 --- a/src/Registration/cReg/include/sirf/Reg/Transformation.h +++ b/src/Registration/cReg/include/sirf/Reg/Transformation.h @@ -1,10 +1,10 @@ /* -CCP PETMR Synergistic Image Reconstruction Framework (SIRF) +SyneRBI Synergistic Image Reconstruction Framework (SIRF) Copyright 2017 - 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/). +Project in Synergistic Reconstruction for Biomedical Imaging (formerly CCP PETMR) +(http://www.ccpsynerbi.ac.uk/). Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. @@ -23,7 +23,7 @@ limitations under the License. \ingroup Registration \brief Base class for transformations. \author Richard Brown -\author CCP PETMR +\author SyneRBI */ #pragma once @@ -46,7 +46,7 @@ to a deformation field. In this fashion, they can be composed into a single transformation. \author Richard Brown -\author CCP PETMR +\author SyneRBI */template class Transformation { diff --git a/src/Registration/cReg/include/sirf/Reg/cReg.h b/src/Registration/cReg/include/sirf/Reg/cReg.h index edcef7ac4..2172ff5d0 100644 --- a/src/Registration/cReg/include/sirf/Reg/cReg.h +++ b/src/Registration/cReg/include/sirf/Reg/cReg.h @@ -1,11 +1,11 @@ /* -CCP PETMR Synergistic Image Reconstruction Framework (SIRF) +SyneRBI Synergistic Image Reconstruction Framework (SIRF) Copyright 2015 - 2017 Rutherford Appleton Laboratory STFC Copyright 2017 - 2020 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/). +Project in Synergistic Reconstruction for Biomedical Imaging (formerly CCP PETMR) +(http://www.ccpsynerbi.ac.uk/). Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. diff --git a/src/Registration/cReg/include/sirf/Reg/cReg_p.h b/src/Registration/cReg/include/sirf/Reg/cReg_p.h index eec940aef..f7337b4ca 100644 --- a/src/Registration/cReg/include/sirf/Reg/cReg_p.h +++ b/src/Registration/cReg/include/sirf/Reg/cReg_p.h @@ -1,11 +1,11 @@ /* -CCP PETMR Synergistic Image Reconstruction Framework (SIRF) +SyneRBI Synergistic Image Reconstruction Framework (SIRF) Copyright 2015 - 2017 Rutherford Appleton Laboratory STFC Copyright 2017 - 2020 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/). +Project in Synergistic Reconstruction for Biomedical Imaging (formerly CCP PETMR) +(http://www.ccpsynerbi.ac.uk/). Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. diff --git a/src/Registration/cReg/sirf_affine_to_disp.cpp b/src/Registration/cReg/sirf_affine_to_disp.cpp index 6308a5097..a2a54c4bf 100644 --- a/src/Registration/cReg/sirf_affine_to_disp.cpp +++ b/src/Registration/cReg/sirf_affine_to_disp.cpp @@ -1,10 +1,10 @@ /* -CCP PETMR Synergistic Image Reconstruction Framework (SIRF) +SyneRBI Synergistic Image Reconstruction Framework (SIRF) Copyright 2017 - 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/). +Project in Synergistic Reconstruction for Biomedical Imaging (formerly CCP PETMR) +(http://www.ccpsynerbi.ac.uk/). Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. @@ -24,7 +24,7 @@ limitations under the License. \brief Convert affine transformation matrix to displacement or deformation field image(s) \author Richard Brown -\author CCP PETMR +\author SyneRBI */ #include diff --git a/src/Registration/cReg/sirf_change_datatype.cpp b/src/Registration/cReg/sirf_change_datatype.cpp index a0a4cd485..077e2fefa 100644 --- a/src/Registration/cReg/sirf_change_datatype.cpp +++ b/src/Registration/cReg/sirf_change_datatype.cpp @@ -1,10 +1,10 @@ /* -CCP PETMR Synergistic Image Reconstruction Framework (SIRF) -Copyright 2017 - 2019 University College London +SyneRBI Synergistic Image Reconstruction Framework (SIRF) +Copyright 2017 - 2020 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/). +Project in Synergistic Reconstruction for Biomedical Imaging (formerly CCP PETMR) +(http://www.ccpsynerbi.ac.uk/). Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. @@ -24,7 +24,7 @@ limitations under the License. \brief Change the datatype of a nifti image (e.g., int->float) \author Richard Brown -\author CCP PETMR +\author SyneRBI */ #include diff --git a/src/Registration/cReg/sirf_crop_image.cpp b/src/Registration/cReg/sirf_crop_image.cpp index 53b59403b..716bc071c 100644 --- a/src/Registration/cReg/sirf_crop_image.cpp +++ b/src/Registration/cReg/sirf_crop_image.cpp @@ -1,10 +1,10 @@ /* -CCP PETMR Synergistic Image Reconstruction Framework (SIRF) +SyneRBI Synergistic Image Reconstruction Framework (SIRF) Copyright 2017 - 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/). +Project in Synergistic Reconstruction for Biomedical Imaging (formerly CCP PETMR) +(http://www.ccpsynerbi.ac.uk/). Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. @@ -24,7 +24,7 @@ limitations under the License. \brief Crop a nifti image \author Richard Brown -\author CCP PETMR +\author SyneRBI */ #include diff --git a/src/Registration/cReg/sirf_flip_or_mirror_image.cpp b/src/Registration/cReg/sirf_flip_or_mirror_image.cpp index 7048a18f1..2e992db1e 100644 --- a/src/Registration/cReg/sirf_flip_or_mirror_image.cpp +++ b/src/Registration/cReg/sirf_flip_or_mirror_image.cpp @@ -1,10 +1,10 @@ /* -CCP PETMR Synergistic Image Reconstruction Framework (SIRF) +SyneRBI Synergistic Image Reconstruction Framework (SIRF) Copyright 2017 - 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/). +Project in Synergistic Reconstruction for Biomedical Imaging (formerly CCP PETMR) +(http://www.ccpsynerbi.ac.uk/). Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. @@ -24,7 +24,7 @@ limitations under the License. \brief Flip or mirror image \author Richard Brown -\author CCP PETMR +\author SyneRBI */ #include diff --git a/src/Registration/cReg/sirf_inverse_transform.cpp b/src/Registration/cReg/sirf_inverse_transform.cpp index 0563749a8..cdf623cc3 100644 --- a/src/Registration/cReg/sirf_inverse_transform.cpp +++ b/src/Registration/cReg/sirf_inverse_transform.cpp @@ -1,10 +1,10 @@ /* -CCP PETMR Synergistic Image Reconstruction Framework (SIRF) -Copyright 2017 - 2019 University College London +SyneRBI Synergistic Image Reconstruction Framework (SIRF) +Copyright 2017 - 2020 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/). +Project in Synergistic Reconstruction for Biomedical Imaging (formerly CCP PETMR) +(http://www.ccpsynerbi.ac.uk/). Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. @@ -24,7 +24,7 @@ limitations under the License. \brief Crop a nifti image \author Richard Brown -\author CCP PETMR +\author SyneRBI */ #include diff --git a/src/Registration/cReg/sirf_nifti_maths.cpp b/src/Registration/cReg/sirf_nifti_maths.cpp index 830f350b4..e79212ac8 100644 --- a/src/Registration/cReg/sirf_nifti_maths.cpp +++ b/src/Registration/cReg/sirf_nifti_maths.cpp @@ -1,10 +1,10 @@ /* -CCP PETMR Synergistic Image Reconstruction Framework (SIRF) -Copyright 2017 - 2019 University College London +SyneRBI Synergistic Image Reconstruction Framework (SIRF) +Copyright 2017 - 2020 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/). +Project in Synergistic Reconstruction for Biomedical Imaging (formerly CCP PETMR) +(http://www.ccpsynerbi.ac.uk/). Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. @@ -24,7 +24,7 @@ limitations under the License. \brief Crop a nifti image \author Richard Brown -\author CCP PETMR +\author SyneRBI */ #include diff --git a/src/Registration/cReg/sirf_print_nifti_info.cpp b/src/Registration/cReg/sirf_print_nifti_info.cpp index b8d54c834..980fe60d4 100644 --- a/src/Registration/cReg/sirf_print_nifti_info.cpp +++ b/src/Registration/cReg/sirf_print_nifti_info.cpp @@ -1,10 +1,10 @@ /* -CCP PETMR Synergistic Image Reconstruction Framework (SIRF) +SyneRBI Synergistic Image Reconstruction Framework (SIRF) Copyright 2017 - 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/). +Project in Synergistic Reconstruction for Biomedical Imaging (formerly CCP PETMR) +(http://www.ccpsynerbi.ac.uk/). Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. @@ -24,7 +24,7 @@ limitations under the License. \brief Dump info of one or more nifti images \author Richard Brown -\author CCP PETMR +\author SyneRBI */ #include "sirf/Reg/NiftiImageData.h" diff --git a/src/Registration/cReg/sirf_tensor_split_join.cpp b/src/Registration/cReg/sirf_tensor_split_join.cpp index 08bf929e4..a40216429 100644 --- a/src/Registration/cReg/sirf_tensor_split_join.cpp +++ b/src/Registration/cReg/sirf_tensor_split_join.cpp @@ -1,10 +1,10 @@ /* -CCP PETMR Synergistic Image Reconstruction Framework (SIRF) +SyneRBI Synergistic Image Reconstruction Framework (SIRF) Copyright 2017 - 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/). +Project in Synergistic Reconstruction for Biomedical Imaging (formerly CCP PETMR) +(http://www.ccpsynerbi.ac.uk/). Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. @@ -24,7 +24,7 @@ limitations under the License. \brief Split or join tensor images (i.e., deformation or displacement fields) \author Richard Brown -\author CCP PETMR +\author SyneRBI */ #include diff --git a/src/Registration/cReg/tests/CMakeLists.txt b/src/Registration/cReg/tests/CMakeLists.txt index f97ecd64a..0100a1407 100644 --- a/src/Registration/cReg/tests/CMakeLists.txt +++ b/src/Registration/cReg/tests/CMakeLists.txt @@ -1,6 +1,6 @@ #======================================================================== # Author: Richard Brown -# Copyright 2016, 2017 University College London +# Copyright 2016 - 2019 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. diff --git a/src/Registration/cReg/tests/test_cReg.cpp b/src/Registration/cReg/tests/test_cReg.cpp index 6fcff1df3..e68e53ace 100644 --- a/src/Registration/cReg/tests/test_cReg.cpp +++ b/src/Registration/cReg/tests/test_cReg.cpp @@ -1,10 +1,11 @@ /* -CCP PETMR Synergistic Image Reconstruction Framework (SIRF) +SyneRBI Synergistic Image Reconstruction Framework (SIRF) Copyright 2017 - 2020 University College London +Copyright 2020 Rutherford Appleton Laboratory STFC This is software developed for the Collaborative Computational -Project in Positron Emission Tomography and Magnetic Resonance imaging -(http://www.ccppetmr.ac.uk/). +Project in Synergistic Reconstruction for Biomedical Imaging (formerly CCP PETMR) +(http://www.ccpsynerbi.ac.uk/). Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. @@ -24,7 +25,7 @@ limitations under the License. \brief Test for creation of a weighted-mean image \author Richard Brown -\author CCP PETMR +\author SyneRBI */ #include diff --git a/src/Registration/mReg/+sirf/+Reg/AffineTransformation.m b/src/Registration/mReg/+sirf/+Reg/AffineTransformation.m index a0435c820..11c8849df 100644 --- a/src/Registration/mReg/+sirf/+Reg/AffineTransformation.m +++ b/src/Registration/mReg/+sirf/+Reg/AffineTransformation.m @@ -1,12 +1,12 @@ classdef AffineTransformation < sirf.Reg.Transformation % Class for affine transformations. -% CCP PETMR Synergistic Image Reconstruction Framework (SIRF). +% SyneRBI Synergistic Image Reconstruction Framework (SIRF). % Copyright 2018-2020 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/). +% Project in Synergistic Reconstruction for Biomedical Imaging (formerly CCP PETMR) +% (http://www.ccpsynerbi.ac.uk/). % % Licensed under the Apache License, Version 2.0 (the "License"); % you may not use this file except in compliance with the License. diff --git a/src/Registration/mReg/+sirf/+Reg/ImageData.m b/src/Registration/mReg/+sirf/+Reg/ImageData.m index ae3d89cad..00e4fe0f6 100644 --- a/src/Registration/mReg/+sirf/+Reg/ImageData.m +++ b/src/Registration/mReg/+sirf/+Reg/ImageData.m @@ -1,12 +1,12 @@ classdef ImageData < sirf.Reg.NiftiImageData3D % Alias class for nifti image data. -% CCP PETMR Synergistic Image Reconstruction Framework (SIRF). +% SyneRBI 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/). +% Project in Synergistic Reconstruction for Biomedical Imaging (formerly CCP PETMR) +% (http://www.ccpsynerbi.ac.uk/). % % Licensed under the Apache License, Version 2.0 (the "License"); % you may not use this file except in compliance with the License. diff --git a/src/Registration/mReg/+sirf/+Reg/ImageWeightedMean.m b/src/Registration/mReg/+sirf/+Reg/ImageWeightedMean.m index b0b9b56d4..3d2530524 100644 --- a/src/Registration/mReg/+sirf/+Reg/ImageWeightedMean.m +++ b/src/Registration/mReg/+sirf/+Reg/ImageWeightedMean.m @@ -1,12 +1,12 @@ classdef ImageWeightedMean < handle % Class for performing weighted mean of images. -% CCP PETMR Synergistic Image Reconstruction Framework (SIRF). +% SyneRBI 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/). +% Project in Synergistic Reconstruction for Biomedical Imaging (formerly CCP PETMR) +% (http://www.ccpsynerbi.ac.uk/). % % Licensed under the Apache License, Version 2.0 (the "License"); % you may not use this file except in compliance with the License. diff --git a/src/Registration/mReg/+sirf/+Reg/NiftiImageData.m b/src/Registration/mReg/+sirf/+Reg/NiftiImageData.m index 63ab03bca..50eb2a260 100644 --- a/src/Registration/mReg/+sirf/+Reg/NiftiImageData.m +++ b/src/Registration/mReg/+sirf/+Reg/NiftiImageData.m @@ -1,12 +1,12 @@ classdef NiftiImageData < sirf.SIRF.ImageData % Class for image data. -% CCP PETMR Synergistic Image Reconstruction Framework (SIRF). -% Copyright 2018-2019 University College London +% SyneRBI Synergistic Image Reconstruction Framework (SIRF). +% Copyright 2018-2020 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/). +% Project in Synergistic Reconstruction for Biomedical Imaging (formerly CCP PETMR) +% (http://www.ccpsynerbi.ac.uk/). % % Licensed under the Apache License, Version 2.0 (the "License"); % you may not use this file except in compliance with the License. @@ -279,4 +279,4 @@ function print_headers(to_print) % dim = dim(2:dim(1)+1); % end % end -end \ No newline at end of file +end diff --git a/src/Registration/mReg/+sirf/+Reg/NiftiImageData3D.m b/src/Registration/mReg/+sirf/+Reg/NiftiImageData3D.m index d59de1e42..9ce9590db 100644 --- a/src/Registration/mReg/+sirf/+Reg/NiftiImageData3D.m +++ b/src/Registration/mReg/+sirf/+Reg/NiftiImageData3D.m @@ -1,12 +1,12 @@ classdef NiftiImageData3D < sirf.Reg.NiftiImageData % Class for 3D image data. -% CCP PETMR Synergistic Image Reconstruction Framework (SIRF). +% SyneRBI 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/). +% Project in Synergistic Reconstruction for Biomedical Imaging (formerly CCP PETMR) +% (http://www.ccpsynerbi.ac.uk/). % % Licensed under the Apache License, Version 2.0 (the "License"); % you may not use this file except in compliance with the License. diff --git a/src/Registration/mReg/+sirf/+Reg/NiftiImageData3DDeformation.m b/src/Registration/mReg/+sirf/+Reg/NiftiImageData3DDeformation.m index d363ee228..860d1ce86 100644 --- a/src/Registration/mReg/+sirf/+Reg/NiftiImageData3DDeformation.m +++ b/src/Registration/mReg/+sirf/+Reg/NiftiImageData3DDeformation.m @@ -4,12 +4,12 @@ % Deformation fields (as opposed to Displacement fields) describe the absolute position (in real world units) of the pixel locations on the reference image. % A deformation field of an identity transformation will contain the location of each of the pixels centroids in the world coordinates. -% CCP PETMR Synergistic Image Reconstruction Framework (SIRF). -% Copyright 2018-2019 University College London +% SyneRBI Synergistic Image Reconstruction Framework (SIRF). +% Copyright 2018-2020 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/). +% Project in Synergistic Reconstruction for Biomedical Imaging (formerly CCP PETMR) +% (http://www.ccpsynerbi.ac.uk/). % % Licensed under the Apache License, Version 2.0 (the "License"); % you may not use this file except in compliance with the License. @@ -99,4 +99,4 @@ function delete(self) z.handle_ = calllib('mreg', 'mReg_NiftiImageData3DDeformation_compose_single_deformation',ref.handle_, types, vec.handle_); end end -end \ No newline at end of file +end diff --git a/src/Registration/mReg/+sirf/+Reg/NiftiImageData3DDisplacement.m b/src/Registration/mReg/+sirf/+Reg/NiftiImageData3DDisplacement.m index 433e18a50..6223b088f 100644 --- a/src/Registration/mReg/+sirf/+Reg/NiftiImageData3DDisplacement.m +++ b/src/Registration/mReg/+sirf/+Reg/NiftiImageData3DDisplacement.m @@ -4,12 +4,12 @@ % Displacement fields (as opposed to Deformation fields) describe the change (in real world units) of the pixel locations between images % A displacement field of an identity transformation will be of zero value. -% CCP PETMR Synergistic Image Reconstruction Framework (SIRF). +% SyneRBI 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/). +% Project in Synergistic Reconstruction for Biomedical Imaging (formerly CCP PETMR) +% (http://www.ccpsynerbi.ac.uk/). % % Licensed under the Apache License, Version 2.0 (the "License"); % you may not use this file except in compliance with the License. diff --git a/src/Registration/mReg/+sirf/+Reg/NiftiImageData3DTensor.m b/src/Registration/mReg/+sirf/+Reg/NiftiImageData3DTensor.m index 8154c9683..380890af0 100644 --- a/src/Registration/mReg/+sirf/+Reg/NiftiImageData3DTensor.m +++ b/src/Registration/mReg/+sirf/+Reg/NiftiImageData3DTensor.m @@ -1,12 +1,12 @@ classdef NiftiImageData3DTensor < sirf.Reg.NiftiImageData % Class for tensor image data. -% CCP PETMR Synergistic Image Reconstruction Framework (SIRF). +% SyneRBI 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/). +% Project in Synergistic Reconstruction for Biomedical Imaging (formerly CCP PETMR) +% (http://www.ccpsynerbi.ac.uk/). % % Licensed under the Apache License, Version 2.0 (the "License"); % you may not use this file except in compliance with the License. diff --git a/src/Registration/mReg/+sirf/+Reg/NiftyAladinSym.m b/src/Registration/mReg/+sirf/+Reg/NiftyAladinSym.m index 3fb5ab26b..8fdd10745 100644 --- a/src/Registration/mReg/+sirf/+Reg/NiftyAladinSym.m +++ b/src/Registration/mReg/+sirf/+Reg/NiftyAladinSym.m @@ -1,12 +1,12 @@ classdef NiftyAladinSym < sirf.Reg.NiftyRegistration % Registration class using NiftyReg's symmetric aladin. -% CCP PETMR Synergistic Image Reconstruction Framework (SIRF). +% SyneRBI Synergistic Image Reconstruction Framework (SIRF). % Copyright 2018-2020 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/). +% Project in Synergistic Reconstruction for Biomedical Imaging (formerly CCP PETMR) +% (http://www.ccpsynerbi.ac.uk/). % % Licensed under the Apache License, Version 2.0 (the "License"); % you may not use this file except in compliance with the License. diff --git a/src/Registration/mReg/+sirf/+Reg/NiftyF3dSym.m b/src/Registration/mReg/+sirf/+Reg/NiftyF3dSym.m index 1c1b96407..f8e6c9891 100644 --- a/src/Registration/mReg/+sirf/+Reg/NiftyF3dSym.m +++ b/src/Registration/mReg/+sirf/+Reg/NiftyF3dSym.m @@ -1,12 +1,12 @@ classdef NiftyF3dSym < sirf.Reg.NiftyRegistration % Registration class using NiftyReg's symmetric f3d. -% CCP PETMR Synergistic Image Reconstruction Framework (SIRF). +% SyneRBI Synergistic Image Reconstruction Framework (SIRF). % Copyright 2018-2020 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/). +% Project in Synergistic Reconstruction for Biomedical Imaging (formerly CCP PETMR) +% (http://www.ccpsynerbi.ac.uk/). % % Licensed under the Apache License, Version 2.0 (the "License"); % you may not use this file except in compliance with the License. diff --git a/src/Registration/mReg/+sirf/+Reg/NiftyRegistration.m b/src/Registration/mReg/+sirf/+Reg/NiftyRegistration.m index bdc82eb0c..7ae021c4a 100644 --- a/src/Registration/mReg/+sirf/+Reg/NiftyRegistration.m +++ b/src/Registration/mReg/+sirf/+Reg/NiftyRegistration.m @@ -1,12 +1,12 @@ classdef (Abstract = true) NiftyRegistration < sirf.Reg.Registration % Abstract class for NiftyReg registration classes. -% CCP PETMR Synergistic Image Reconstruction Framework (SIRF). +% SyneRBI Synergistic Image Reconstruction Framework (SIRF). % Copyright 2018-2020 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/). +% Project in Synergistic Reconstruction for Biomedical Imaging (formerly CCP PETMR) +% (http://www.ccpsynerbi.ac.uk/). % % Licensed under the Apache License, Version 2.0 (the "License"); % you may not use this file except in compliance with the License. diff --git a/src/Registration/mReg/+sirf/+Reg/NiftyResample.m b/src/Registration/mReg/+sirf/+Reg/NiftyResample.m index 48e291b0d..f6042a123 100644 --- a/src/Registration/mReg/+sirf/+Reg/NiftyResample.m +++ b/src/Registration/mReg/+sirf/+Reg/NiftyResample.m @@ -1,12 +1,12 @@ classdef NiftyResample < handle % Class for resampling using NiftyReg. -% CCP PETMR Synergistic Image Reconstruction Framework (SIRF). -% Copyright 2018-2019 University College London +% SyneRBI Synergistic Image Reconstruction Framework (SIRF). +% Copyright 2018-2020 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/). +% Project in Synergistic Reconstruction for Biomedical Imaging (formerly CCP PETMR) +% (http://www.ccpsynerbi.ac.uk/). % % Licensed under the Apache License, Version 2.0 (the "License"); % you may not use this file except in compliance with the License. diff --git a/src/Registration/mReg/+sirf/+Reg/Quaternion.m b/src/Registration/mReg/+sirf/+Reg/Quaternion.m index b480d4087..9c5025c09 100644 --- a/src/Registration/mReg/+sirf/+Reg/Quaternion.m +++ b/src/Registration/mReg/+sirf/+Reg/Quaternion.m @@ -1,12 +1,12 @@ classdef Quaternion < handle % Class for quaternions. -% CCP PETMR Synergistic Image Reconstruction Framework (SIRF). +% SyneRBI 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/). +% Project in Synergistic Reconstruction for Biomedical Imaging (formerly CCP PETMR) +% (http://www.ccpsynerbi.ac.uk/). % % Licensed under the Apache License, Version 2.0 (the "License"); % you may not use this file except in compliance with the License. diff --git a/src/Registration/mReg/+sirf/+Reg/Registration.m b/src/Registration/mReg/+sirf/+Reg/Registration.m index 341f5aa61..4814ecf22 100644 --- a/src/Registration/mReg/+sirf/+Reg/Registration.m +++ b/src/Registration/mReg/+sirf/+Reg/Registration.m @@ -1,12 +1,12 @@ classdef (Abstract = true) Registration < handle % Abstract class for registration classes. -% CCP PETMR Synergistic Image Reconstruction Framework (SIRF). +% SyneRBI Synergistic Image Reconstruction Framework (SIRF). % Copyright 2018-2020 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/). +% Project in Synergistic Reconstruction for Biomedical Imaging (formerly CCP PETMR) +% (http://www.ccpsynerbi.ac.uk/). % % Licensed under the Apache License, Version 2.0 (the "License"); % you may not use this file except in compliance with the License. diff --git a/src/Registration/mReg/+sirf/+Reg/SPMRegistration.m b/src/Registration/mReg/+sirf/+Reg/SPMRegistration.m index 61d53b6d1..9a19869aa 100644 --- a/src/Registration/mReg/+sirf/+Reg/SPMRegistration.m +++ b/src/Registration/mReg/+sirf/+Reg/SPMRegistration.m @@ -1,12 +1,12 @@ classdef SPMRegistration < sirf.Reg.NiftyRegistration % Registration class using SPM. -% CCP PETMR Synergistic Image Reconstruction Framework (SIRF). +% SyneRBI Synergistic Image Reconstruction Framework (SIRF). % Copyright 2018-2020 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/). +% Project in Synergistic Reconstruction for Biomedical Imaging (formerly CCP PETMR) +% (http://www.ccpsynerbi.ac.uk/). % % Licensed under the Apache License, Version 2.0 (the "License"); % you may not use this file except in compliance with the License. diff --git a/src/Registration/mReg/+sirf/+Reg/Transformation.m b/src/Registration/mReg/+sirf/+Reg/Transformation.m index ac9c9dcec..6c29822bf 100644 --- a/src/Registration/mReg/+sirf/+Reg/Transformation.m +++ b/src/Registration/mReg/+sirf/+Reg/Transformation.m @@ -1,12 +1,12 @@ classdef (Abstract = true) Transformation < handle & matlab.mixin.Heterogeneous % Abstract class for transformations. -% CCP PETMR Synergistic Image Reconstruction Framework (SIRF). +% SyneRBI Synergistic Image Reconstruction Framework (SIRF). % Copyright 2015 - 2017 Rutherford Appleton Laboratory STFC. % % This is software developed for the Collaborative Computational -% Project in Positron Emission Tomography and Magnetic Resonance imaging -% (http://www.ccppetmr.ac.uk/). +% Project in Synergistic Reconstruction for Biomedical Imaging (formerly CCP PETMR) +% (http://www.ccpsynerbi.ac.uk/). % % Licensed under the Apache License, Version 2.0 (the "License"); % you may not use this file except in compliance with the License. diff --git a/src/Registration/mReg/gmi/gmi_xreg.cpp b/src/Registration/mReg/gmi/gmi_xreg.cpp index 3ab6bcc61..7a7e65ef3 100644 --- a/src/Registration/mReg/gmi/gmi_xreg.cpp +++ b/src/Registration/mReg/gmi/gmi_xreg.cpp @@ -1,11 +1,11 @@ /* -CCP PETMR Synergistic Image Reconstruction Framework (SIRF) +SyneRBI Synergistic Image Reconstruction Framework (SIRF) Copyright 2015 - 2017 Rutherford Appleton Laboratory STFC -Copyright 2017 - 2019 University College London +Copyright 2017 - 2020 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/). +Project in Synergistic Reconstruction for Biomedical Imaging (formerly CCP PETMR) +(http://www.ccpsynerbi.ac.uk/). Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. @@ -25,7 +25,7 @@ limitations under the License. \brief The executable for generating Matlab interface for cstir library. \author Evgueni Ovtchinnikov -\author CCP PETMR +\author SyneRBI */ #include @@ -72,4 +72,4 @@ int main(int argc, char *argv[]) cout << "wrong input file format" << endl; return 1; } -} \ No newline at end of file +} diff --git a/src/Registration/mReg/printer.cpp b/src/Registration/mReg/printer.cpp index 00fd4de63..95bcba35d 100644 --- a/src/Registration/mReg/printer.cpp +++ b/src/Registration/mReg/printer.cpp @@ -1,11 +1,11 @@ /* -CCP PETMR Synergistic Image Reconstruction Framework (SIRF) +SyneRBI Synergistic Image Reconstruction Framework (SIRF) Copyright 2015 - 2017 Rutherford Appleton Laboratory STFC Copyright 2017 - 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/). +Project in Synergistic Reconstruction for Biomedical Imaging (formerly CCP PETMR) +(http://www.ccpsynerbi.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 diff --git a/src/Registration/mReg/printer.h b/src/Registration/mReg/printer.h index 0d6722691..fbbea0183 100644 --- a/src/Registration/mReg/printer.h +++ b/src/Registration/mReg/printer.h @@ -1,11 +1,11 @@ /* -CCP PETMR Synergistic Image Reconstruction Framework (SIRF) +SyneRBI Synergistic Image Reconstruction Framework (SIRF) Copyright 2015 - 2017 Rutherford Appleton Laboratory STFC Copyright 2017 - 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/). +Project in Synergistic Reconstruction for Biomedical Imaging (formerly CCP PETMR) +(http://www.ccpsynerbi.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 diff --git a/src/Registration/mReg/tests/test_mReg.m b/src/Registration/mReg/tests/test_mReg.m index 23eda44cc..f190a33a2 100644 --- a/src/Registration/mReg/tests/test_mReg.m +++ b/src/Registration/mReg/tests/test_mReg.m @@ -1,9 +1,9 @@ -% CCP PETMR Synergistic Image Reconstruction Framework (SIRF). +% SyneRBI Synergistic Image Reconstruction Framework (SIRF). % Copyright 2018 - 2020 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/). +% Project in Synergistic Reconstruction for Biomedical Imaging (formerly CCP PETMR) +% (http://www.ccpsynerbi.ac.uk/). % % Licensed under the Apache License, Version 2.0 (the "License"); % you may not use this file except in compliance with the License. diff --git a/src/Registration/mReg/tests/test_mReg_spm.m b/src/Registration/mReg/tests/test_mReg_spm.m index b2f352e74..3f9803df8 100644 --- a/src/Registration/mReg/tests/test_mReg_spm.m +++ b/src/Registration/mReg/tests/test_mReg_spm.m @@ -1,9 +1,9 @@ -% CCP PETMR Synergistic Image Reconstruction Framework (SIRF). +% SyneRBI Synergistic Image Reconstruction Framework (SIRF). % Copyright 2018 - 2020 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/). +% Project in Synergistic Reconstruction for Biomedical Imaging (formerly CCP PETMR) +% (http://www.ccpsynerbi.ac.uk/). % % Licensed under the Apache License, Version 2.0 (the "License"); % you may not use this file except in compliance with the License. diff --git a/src/Registration/pReg/Reg.py.in b/src/Registration/pReg/Reg.py.in index f8f94c297..14d9dc65a 100644 --- a/src/Registration/pReg/Reg.py.in +++ b/src/Registration/pReg/Reg.py.in @@ -2,12 +2,12 @@ Object-Oriented wrap for the cReg-to-Python interface pyreg.py """ -# CCP PETMR Synergistic Image Reconstruction Framework (SIRF) +# SyneRBI Synergistic Image Reconstruction Framework (SIRF) # Copyright 2018 - 2020 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/). +# Project in Synergistic Reconstruction for Biomedical Imaging (formerly CCP PETMR) +# (http://www.ccpsynerbi.ac.uk/). # # Licensed under the Apache License, Version 2.0 (the "License"); # you may not use this file except in compliance with the License. diff --git a/src/Registration/pReg/tests/test_pReg.py b/src/Registration/pReg/tests/test_pReg.py index 49fb4b4b4..8c954fa03 100644 --- a/src/Registration/pReg/tests/test_pReg.py +++ b/src/Registration/pReg/tests/test_pReg.py @@ -1,9 +1,9 @@ -# CCP PETMR Synergistic Image Reconstruction Framework (SIRF) +# SyneRBI Synergistic Image Reconstruction Framework (SIRF) # Copyright 2018 - 2020 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/). +# Project in Synergistic Reconstruction for Biomedical Imaging (formerly CCP PETMR) +# (http://www.ccpsynerbi.ac.uk/). # # Licensed under the Apache License, Version 2.0 (the "License"); # you may not use this file except in compliance with the License. diff --git a/src/Registration/pReg/tests/test_pReg_spm.py b/src/Registration/pReg/tests/test_pReg_spm.py index a276f5918..b2d532b0a 100644 --- a/src/Registration/pReg/tests/test_pReg_spm.py +++ b/src/Registration/pReg/tests/test_pReg_spm.py @@ -7,12 +7,12 @@ --spm test spm functionality ''' -# CCP PETMR Synergistic Image Reconstruction Framework (SIRF) +# SyneRBI Synergistic Image Reconstruction Framework (SIRF) # Copyright 2018 - 2020 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/). +# Project in Synergistic Reconstruction for Biomedical Imaging (formerly CCP PETMR) +# (http://www.ccpsynerbi.ac.uk/). # # Licensed under the Apache License, Version 2.0 (the "License"); # you may not use this file except in compliance with the License. diff --git a/src/Synergistic/CMakeLists.txt b/src/Synergistic/CMakeLists.txt index 325310ebd..8ec4a46df 100644 --- a/src/Synergistic/CMakeLists.txt +++ b/src/Synergistic/CMakeLists.txt @@ -1,6 +1,6 @@ #======================================================================== # Author: Richard Brown -# Copyright 2018 - 2019 University College London +# Copyright 2018 - 2020 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. @@ -37,4 +37,4 @@ ADD_SUBDIRECTORY(mSyn) ADD_SUBDIRECTORY(pSyn) # Tests -ADD_SUBDIRECTORY(tests) \ No newline at end of file +ADD_SUBDIRECTORY(tests) diff --git a/src/Synergistic/cSyn/CMakeLists.txt b/src/Synergistic/cSyn/CMakeLists.txt index f59c67539..251a45e6a 100644 --- a/src/Synergistic/cSyn/CMakeLists.txt +++ b/src/Synergistic/cSyn/CMakeLists.txt @@ -1,7 +1,7 @@ #======================================================================== # Author: Richard Brown # Author: Evgueni Ovtchinnikov -# Copyright 2018 - 2019 University College London +# Copyright 2018 - 2020 University College London # Copyright 2020 UKRI-STFC # # Licensed under the Apache License, Version 2.0 (the "License"); @@ -31,4 +31,4 @@ target_include_directories(csyn PUBLIC target_link_libraries(csyn PUBLIC cgadgetron cstir Reg) INSTALL(TARGETS csyn DESTINATION ${CMAKE_INSTALL_PREFIX}/lib) -ADD_SUBDIRECTORY(tests) \ No newline at end of file +ADD_SUBDIRECTORY(tests) diff --git a/src/Synergistic/cSyn/include/sirf/Syn/utilities.h b/src/Synergistic/cSyn/include/sirf/Syn/utilities.h index 837ecb6b4..58a520712 100644 --- a/src/Synergistic/cSyn/include/sirf/Syn/utilities.h +++ b/src/Synergistic/cSyn/include/sirf/Syn/utilities.h @@ -1,11 +1,11 @@ /* -CCP PETMR Synergistic Image Reconstruction Framework (SIRF) +SyneRBI Synergistic Image Reconstruction Framework (SIRF) Copyright 2020 Rutherford Appleton Laboratory STFC Copyright 2020 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/). +Project in Synergistic Reconstruction for Biomedical Imaging (formerly CCP PETMR) +(http://www.ccpsynerbi.ac.uk/). Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. @@ -25,7 +25,7 @@ limitations under the License. \brief C++ synergistic utilities. \author Evgueni Ovtchinnikov -\author CCP PETMR +\author SyneRBI */ #pragma once diff --git a/src/Synergistic/cSyn/tests/CMakeLists.txt b/src/Synergistic/cSyn/tests/CMakeLists.txt index 58206543a..d52864aae 100644 --- a/src/Synergistic/cSyn/tests/CMakeLists.txt +++ b/src/Synergistic/cSyn/tests/CMakeLists.txt @@ -1,6 +1,6 @@ #======================================================================== # Author: Richard Brown -# Copyright 2018 - 2019 University College London +# Copyright 2018 - 2020 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. diff --git a/src/Synergistic/cSyn/tests/test_conv_img.cpp b/src/Synergistic/cSyn/tests/test_conv_img.cpp index bf5e9673b..5183f1f6c 100644 --- a/src/Synergistic/cSyn/tests/test_conv_img.cpp +++ b/src/Synergistic/cSyn/tests/test_conv_img.cpp @@ -1,11 +1,11 @@ /* -CCP PETMR Synergistic Image Reconstruction Framework (SIRF) +SyneRBI Synergistic Image Reconstruction Framework (SIRF) Copyright 2020 Rutherford Appleton Laboratory STFC Copyright 2020 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/). +Project in Synergistic Reconstruction for Biomedical Imaging (formerly CCP PETMR) +(http://www.ccpsynerbi.ac.uk/). Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. diff --git a/src/Synergistic/cSyn/utilities.cpp b/src/Synergistic/cSyn/utilities.cpp index 0650f8b46..7a446e116 100644 --- a/src/Synergistic/cSyn/utilities.cpp +++ b/src/Synergistic/cSyn/utilities.cpp @@ -1,11 +1,11 @@ /* -CCP PETMR Synergistic Image Reconstruction Framework (SIRF) +SyneRBI Synergistic Image Reconstruction Framework (SIRF) Copyright 2020 Rutherford Appleton Laboratory STFC Copyright 2020 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/). +Project in Synergistic Reconstruction for Biomedical Imaging (formerly CCP PETMR) +(http://www.ccpsynerbi.ac.uk/). Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. @@ -26,7 +26,7 @@ limitations under the License. \author Richard Brown \author Evgueni Ovtchinnikov -\author CCP PETMR +\author SyneRBI */ #include "sirf/Gadgetron/gadgetron_data_containers.h" diff --git a/src/Synergistic/mSyn/tests/CMakeLists.txt b/src/Synergistic/mSyn/tests/CMakeLists.txt index 3c081ce83..a339df64d 100644 --- a/src/Synergistic/mSyn/tests/CMakeLists.txt +++ b/src/Synergistic/mSyn/tests/CMakeLists.txt @@ -1,9 +1,9 @@ #======================================================================== # Author: Evgueni Ovtchinnikov -# Copyright 2017 University College London +# Copyright 2017 - 2020 University College London # Copyright 2017 Science Technology Facilities Council # -# This file is part of the CCP PETMR Synergistic Image Reconstruction Framework (SIRF) SuperBuild. +# This file is part of the SyneRBI Synergistic Image Reconstruction Framework (SIRF) SuperBuild. # # Licensed under the Apache License, Version 2.0 (the "License"); # you may not use this file except in compliance with the License. diff --git a/src/Synergistic/mSyn/tests/gadgetron_to_nifti.m b/src/Synergistic/mSyn/tests/gadgetron_to_nifti.m index 5d7e65a5f..d37a69c10 100644 --- a/src/Synergistic/mSyn/tests/gadgetron_to_nifti.m +++ b/src/Synergistic/mSyn/tests/gadgetron_to_nifti.m @@ -1,10 +1,10 @@ -% CCP PETMR Synergistic Image Reconstruction Framework (SIRF). +% SyneRBI Synergistic Image Reconstruction Framework (SIRF). % Copyright 2020 Rutherford Appleton Laboratory STFC. % Copyright 2020 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/). +% Project in Synergistic Reconstruction for Biomedical Imaging (formerly CCP PETMR) +% (http://www.ccpsynerbi.ac.uk/). % % Licensed under the Apache License, Version 2.0 (the "License"); % you may not use this file except in compliance with the License. diff --git a/src/Synergistic/mSyn/tests/stir_to_nifti.m b/src/Synergistic/mSyn/tests/stir_to_nifti.m index 633cfa8f8..9bda68975 100644 --- a/src/Synergistic/mSyn/tests/stir_to_nifti.m +++ b/src/Synergistic/mSyn/tests/stir_to_nifti.m @@ -1,10 +1,10 @@ -% CCP PETMR Synergistic Image Reconstruction Framework (SIRF). +% SyneRBI Synergistic Image Reconstruction Framework (SIRF). % Copyright 2020 Rutherford Appleton Laboratory STFC. % Copyright 2020 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/). +% Project in Synergistic Reconstruction for Biomedical Imaging (formerly CCP PETMR) +% (http://www.ccpsynerbi.ac.uk/). % % Licensed under the Apache License, Version 2.0 (the "License"); % you may not use this file except in compliance with the License. diff --git a/src/Synergistic/pSyn/tests/CMakeLists.txt b/src/Synergistic/pSyn/tests/CMakeLists.txt index e5cf44c44..21a506773 100644 --- a/src/Synergistic/pSyn/tests/CMakeLists.txt +++ b/src/Synergistic/pSyn/tests/CMakeLists.txt @@ -1,6 +1,6 @@ #======================================================================== # Author: Richard Brown -# Copyright 2018 - 2019 University College London +# Copyright 2018 - 2020 University College London # Author: Evgueni Ovtchinnikov # Copyright 2020 UKRI-STFC # diff --git a/src/Synergistic/sirf_convert_image_type.cpp b/src/Synergistic/sirf_convert_image_type.cpp index a27036d98..b4e61d582 100644 --- a/src/Synergistic/sirf_convert_image_type.cpp +++ b/src/Synergistic/sirf_convert_image_type.cpp @@ -1,10 +1,10 @@ /* -CCP PETMR Synergistic Image Reconstruction Framework (SIRF) +SyneRBI 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/). +Project in Synergistic Reconstruction for Biomedical Imaging (formerly CCP PETMR) +(http://www.ccpsynerbi.ac.uk/). Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. @@ -24,7 +24,7 @@ limitations under the License. \brief Convert any SIRF image type into any other. \author Richard Brown -\author CCP PETMR +\author SyneRBI */ #include "sirf/Reg/NiftiImageData3D.h" diff --git a/src/Synergistic/sirf_do_images_match.cpp b/src/Synergistic/sirf_do_images_match.cpp index 0ef3602aa..081115ce9 100644 --- a/src/Synergistic/sirf_do_images_match.cpp +++ b/src/Synergistic/sirf_do_images_match.cpp @@ -1,10 +1,10 @@ /* -CCP PETMR Synergistic Image Reconstruction Framework (SIRF) +SyneRBI 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/). +Project in Synergistic Reconstruction for Biomedical Imaging (formerly CCP PETMR) +(http://www.ccpsynerbi.ac.uk/). Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. @@ -24,7 +24,7 @@ limitations under the License. \brief Check if two SIRF images match to a given precision. \author Richard Brown -\author CCP PETMR +\author SyneRBI */ #include "sirf/Reg/NiftiImageData3D.h" diff --git a/src/Synergistic/sirf_registration.cpp b/src/Synergistic/sirf_registration.cpp index 5d19a8db5..1d38312b4 100644 --- a/src/Synergistic/sirf_registration.cpp +++ b/src/Synergistic/sirf_registration.cpp @@ -1,10 +1,10 @@ /* -CCP PETMR Synergistic Image Reconstruction Framework (SIRF) +SyneRBI Synergistic Image Reconstruction Framework (SIRF) Copyright 2018-2020 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/). +Project in Synergistic Reconstruction for Biomedical Imaging (formerly CCP PETMR) +(http://www.ccpsynerbi.ac.uk/). Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. @@ -24,7 +24,7 @@ limitations under the License. \brief Perform registration with any types of SIRF image and any SIRF registration algorithm. \author Richard Brown -\author CCP PETMR +\author SyneRBI */ #include "sirf/Reg/NiftyAladinSym.h" diff --git a/src/Synergistic/sirf_resample.cpp b/src/Synergistic/sirf_resample.cpp index 24ca0593f..849de7024 100644 --- a/src/Synergistic/sirf_resample.cpp +++ b/src/Synergistic/sirf_resample.cpp @@ -1,10 +1,10 @@ /* -CCP PETMR Synergistic Image Reconstruction Framework (SIRF) +SyneRBI 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/). +Project in Synergistic Reconstruction for Biomedical Imaging (formerly CCP PETMR) +(http://www.ccpsynerbi.ac.uk/). Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. @@ -27,7 +27,7 @@ If no transformations are given, identity will be used. If multiple transformations are given, they will be applied in the order they were given. \author Richard Brown -\author CCP PETMR +\author SyneRBI */ #include "sirf/Reg/NiftyResample.h" diff --git a/src/Synergistic/tests/CMakeLists.txt b/src/Synergistic/tests/CMakeLists.txt index 90ac9eff9..a9fb52aa6 100644 --- a/src/Synergistic/tests/CMakeLists.txt +++ b/src/Synergistic/tests/CMakeLists.txt @@ -1,6 +1,6 @@ #======================================================================== # Author: Richard Brown -# Copyright 2018 - 2019 University College London +# Copyright 2018 - 2020 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. @@ -71,4 +71,4 @@ if (BUILD_MATLAB) ADDITIONAL_PATH ${CMAKE_CURRENT_SOURCE_DIR} NO_UNITTEST_FRAMEWORK WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}) -endif() \ No newline at end of file +endif() diff --git a/src/Synergistic/tests/test_cSynergistic.cpp b/src/Synergistic/tests/test_cSynergistic.cpp index e4bfedc3a..82dfe288d 100644 --- a/src/Synergistic/tests/test_cSynergistic.cpp +++ b/src/Synergistic/tests/test_cSynergistic.cpp @@ -1,10 +1,10 @@ /* -CCP PETMR Synergistic Image Reconstruction Framework (SIRF) -Copyright 2017 - 2019 University College London +SyneRBI Synergistic Image Reconstruction Framework (SIRF) +Copyright 2017 - 2020 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/). +Project in Synergistic Reconstruction for Biomedical Imaging (formerly CCP PETMR) +(http://www.ccpsynerbi.ac.uk/). Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. @@ -24,7 +24,7 @@ limitations under the License. \brief Synergistic tests \author Richard Brown -\author CCP PETMR +\author SyneRBI */ #include "sirf/Gadgetron/gadgetron_data_containers.h" diff --git a/src/Synergistic/tests/test_mSynergistic.m b/src/Synergistic/tests/test_mSynergistic.m index 19d94a4ff..06299a040 100644 --- a/src/Synergistic/tests/test_mSynergistic.m +++ b/src/Synergistic/tests/test_mSynergistic.m @@ -1,9 +1,9 @@ -% CCP PETMR Synergistic Image Reconstruction Framework (SIRF). +% SyneRBI 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/). +% Project in Synergistic Reconstruction for Biomedical Imaging (formerly CCP PETMR) +% (http://www.ccpsynerbi.ac.uk/). % % Licensed under the Apache License, Version 2.0 (the "License"); % you may not use this file except in compliance with the License. diff --git a/src/Synergistic/tests/test_pSynergistic.py b/src/Synergistic/tests/test_pSynergistic.py index 35f99cc06..0b33d8197 100644 --- a/src/Synergistic/tests/test_pSynergistic.py +++ b/src/Synergistic/tests/test_pSynergistic.py @@ -1,9 +1,9 @@ -# CCP PETMR Synergistic Image Reconstruction Framework (SIRF) -# Copyright 2018 - 2019 University College London +# SyneRBI Synergistic Image Reconstruction Framework (SIRF) +# Copyright 2018 - 2020 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/). +# Project in Synergistic Reconstruction for Biomedical Imaging (formerly CCP PETMR) +# (http://www.ccpsynerbi.ac.uk/). # # Licensed under the Apache License, Version 2.0 (the "License"); # you may not use this file except in compliance with the License. diff --git a/src/common/+sirf/+SIRF/DataContainer.m b/src/common/+sirf/+SIRF/DataContainer.m index ea3b3aec6..1af435234 100644 --- a/src/common/+sirf/+SIRF/DataContainer.m +++ b/src/common/+sirf/+SIRF/DataContainer.m @@ -2,12 +2,13 @@ % INTERNAL USE ONLY. % Class for an abstract data container. -% CCP PETMR Synergistic Image Reconstruction Framework (SIRF). -% Copyright 2015 - 2017 Rutherford Appleton Laboratory STFC. +% SyneRBI Synergistic Image Reconstruction Framework (SIRF). +% Copyright 2015 - 2020 Rutherford Appleton Laboratory STFC. +% Copyright 2020 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/). +% Project in Synergistic Reconstruction for Biomedical Imaging (formerly CCP PETMR) +% (http://www.ccpsynerbi.ac.uk/). % % Licensed under the Apache License, Version 2.0 (the "License"); % you may not use this file except in compliance with the License. @@ -161,4 +162,4 @@ function write(self, filename) sirf.Utilities.check_status('DataContainer:axpby', z.handle_); end end -end \ No newline at end of file +end diff --git a/src/common/+sirf/+SIRF/DataHandleVector.m b/src/common/+sirf/+SIRF/DataHandleVector.m index 64cee6a33..5386a8e0b 100644 --- a/src/common/+sirf/+SIRF/DataHandleVector.m +++ b/src/common/+sirf/+SIRF/DataHandleVector.m @@ -2,12 +2,12 @@ % INTERNAL USE ONLY. % Class for an abstract data container. -% CCP PETMR Synergistic Image Reconstruction Framework (SIRF). +% SyneRBI 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/). +% Project in Synergistic Reconstruction for Biomedical Imaging (formerly CCP PETMR) +% (http://www.ccpsynerbi.ac.uk/). % % Licensed under the Apache License, Version 2.0 (the "License"); % you may not use this file except in compliance with the License. diff --git a/src/common/+sirf/+SIRF/GeometricalInfo.m b/src/common/+sirf/+SIRF/GeometricalInfo.m index b5cf08223..8efb0f553 100644 --- a/src/common/+sirf/+SIRF/GeometricalInfo.m +++ b/src/common/+sirf/+SIRF/GeometricalInfo.m @@ -2,12 +2,12 @@ % INTERNAL USE ONLY. % Class for image geometrical info. -% CCP PETMR Synergistic Image Reconstruction Framework (SIRF). -% Copyright 2015 - 2017 Rutherford Appleton Laboratory STFC. +% SyneRBI Synergistic Image Reconstruction Framework (SIRF). +% Copyright 2020 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/). +% Project in Synergistic Reconstruction for Biomedical Imaging (formerly CCP PETMR) +% (http://www.ccpsynerbi.ac.uk/). % % Licensed under the Apache License, Version 2.0 (the "License"); % you may not use this file except in compliance with the License. @@ -72,4 +72,4 @@ function print_info(self) value = ptr_i.Value; end end -end \ No newline at end of file +end diff --git a/src/common/+sirf/+SIRF/ImageData.m b/src/common/+sirf/+SIRF/ImageData.m index 75328bc95..a1e583645 100644 --- a/src/common/+sirf/+SIRF/ImageData.m +++ b/src/common/+sirf/+SIRF/ImageData.m @@ -2,12 +2,13 @@ % INTERNAL USE ONLY. % Class for an abstract data container. -% CCP PETMR Synergistic Image Reconstruction Framework (SIRF). -% Copyright 2015 - 2017 Rutherford Appleton Laboratory STFC. -% +% SyneRBI Synergistic Image Reconstruction Framework (SIRF). +% Copyright 2015 - 2020 Rutherford Appleton Laboratory STFC. +% Copyright 2018 - 2020 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/). +% Project in Synergistic Reconstruction for Biomedical Imaging (formerly CCP PETMR) +% (http://www.ccpsynerbi.ac.uk/). % % Licensed under the Apache License, Version 2.0 (the "License"); % you may not use this file except in compliance with the License. @@ -53,4 +54,4 @@ function reorient(self, geom_info) sirf.Utilities.delete(h) end end -end \ No newline at end of file +end diff --git a/src/common/+sirf/+Utilities/assert_validities.m b/src/common/+sirf/+Utilities/assert_validities.m index 1177b2bc5..62f7ec5e0 100644 --- a/src/common/+sirf/+Utilities/assert_validities.m +++ b/src/common/+sirf/+Utilities/assert_validities.m @@ -1,12 +1,12 @@ function assert_validities(x, y) % Ensures x and y are of the same type and not empty. -% CCP PETMR Synergistic Image Reconstruction Framework (SIRF). +% SyneRBI Synergistic Image Reconstruction Framework (SIRF). % Copyright 2015 - 2017 Rutherford Appleton Laboratory STFC. % % This is software developed for the Collaborative Computational -% Project in Positron Emission Tomography and Magnetic Resonance imaging -% (http://www.ccppetmr.ac.uk/). +% Project in Synergistic Reconstruction for Biomedical Imaging (formerly CCP PETMR) +% (http://www.ccpsynerbi.ac.uk/). % % Licensed under the Apache License, Version 2.0 (the "License"); % you may not use this file except in compliance with the License. diff --git a/src/common/+sirf/+Utilities/assert_validity.m b/src/common/+sirf/+Utilities/assert_validity.m index 212213625..d1136a2a1 100644 --- a/src/common/+sirf/+Utilities/assert_validity.m +++ b/src/common/+sirf/+Utilities/assert_validity.m @@ -1,12 +1,12 @@ function assert_validity(object, type) % Ensures the object is of a correct type and is not empty. -% CCP PETMR Synergistic Image Reconstruction Framework (SIRF). +% SyneRBI Synergistic Image Reconstruction Framework (SIRF). % Copyright 2015 - 2017 Rutherford Appleton Laboratory STFC. % % This is software developed for the Collaborative Computational -% Project in Positron Emission Tomography and Magnetic Resonance imaging -% (http://www.ccppetmr.ac.uk/). +% Project in Synergistic Reconstruction for Biomedical Imaging (formerly CCP PETMR) +% (http://www.ccpsynerbi.ac.uk/). % % Licensed under the Apache License, Version 2.0 (the "License"); % you may not use this file except in compliance with the License. diff --git a/src/common/+sirf/+Utilities/check_status.m b/src/common/+sirf/+Utilities/check_status.m index 948117c2e..27a0d2e7f 100644 --- a/src/common/+sirf/+Utilities/check_status.m +++ b/src/common/+sirf/+Utilities/check_status.m @@ -1,12 +1,12 @@ function check_status(f, handle) % Checks the execution status recorded in handle. -% CCP PETMR Synergistic Image Reconstruction Framework (SIRF). +% SyneRBI Synergistic Image Reconstruction Framework (SIRF). % Copyright 2015 - 2017 Rutherford Appleton Laboratory STFC. % % This is software developed for the Collaborative Computational -% Project in Positron Emission Tomography and Magnetic Resonance imaging -% (http://www.ccppetmr.ac.uk/). +% Project in Synergistic Reconstruction for Biomedical Imaging (formerly CCP PETMR) +% (http://www.ccpsynerbi.ac.uk/). % % Licensed under the Apache License, Version 2.0 (the "License"); % you may not use this file except in compliance with the License. diff --git a/src/common/+sirf/+Utilities/delete.m b/src/common/+sirf/+Utilities/delete.m index 23c363951..c710c2bbd 100644 --- a/src/common/+sirf/+Utilities/delete.m +++ b/src/common/+sirf/+Utilities/delete.m @@ -1,12 +1,12 @@ function delete(handle) % Deletes the object referred to by handle. -% CCP PETMR Synergistic Image Reconstruction Framework (SIRF). +% SyneRBI Synergistic Image Reconstruction Framework (SIRF). % Copyright 2015 - 2017 Rutherford Appleton Laboratory STFC. % % This is software developed for the Collaborative Computational -% Project in Positron Emission Tomography and Magnetic Resonance imaging -% (http://www.ccppetmr.ac.uk/). +% Project in Synergistic Reconstruction for Biomedical Imaging (formerly CCP PETMR) +% (http://www.ccpsynerbi.ac.uk/). % % Licensed under the Apache License, Version 2.0 (the "License"); % you may not use this file except in compliance with the License. diff --git a/src/common/+sirf/+Utilities/examples_data_path.m b/src/common/+sirf/+Utilities/examples_data_path.m index 562dfc1a3..024f0d320 100644 --- a/src/common/+sirf/+Utilities/examples_data_path.m +++ b/src/common/+sirf/+Utilities/examples_data_path.m @@ -2,12 +2,12 @@ % If SIRF_PATH is defined, returns path to PET or MR examples raw data. % Otherwise, defaults to current folder. -% CCP PETMR Synergistic Image Reconstruction Framework (SIRF). +% SyneRBI Synergistic Image Reconstruction Framework (SIRF). % Copyright 2015 - 2017 Rutherford Appleton Laboratory STFC. % % This is software developed for the Collaborative Computational -% Project in Positron Emission Tomography and Magnetic Resonance imaging -% (http://www.ccppetmr.ac.uk/). +% Project in Synergistic Reconstruction for Biomedical Imaging (formerly CCP PETMR) +% (http://www.ccpsynerbi.ac.uk/). % % Licensed under the Apache License, Version 2.0 (the "License"); % you may not use this file except in compliance with the License. diff --git a/src/common/+sirf/+Utilities/label_and_name.m b/src/common/+sirf/+Utilities/label_and_name.m index fe1ec54c1..d7a6b9d6b 100644 --- a/src/common/+sirf/+Utilities/label_and_name.m +++ b/src/common/+sirf/+Utilities/label_and_name.m @@ -1,12 +1,12 @@ function [label, name] = label_and_name(input) % Parses the input of the form [label:]name. -% CCP PETMR Synergistic Image Reconstruction Framework (SIRF). +% SyneRBI Synergistic Image Reconstruction Framework (SIRF). % Copyright 2015 - 2017 Rutherford Appleton Laboratory STFC. % % This is software developed for the Collaborative Computational -% Project in Positron Emission Tomography and Magnetic Resonance imaging -% (http://www.ccppetmr.ac.uk/). +% Project in Synergistic Reconstruction for Biomedical Imaging (formerly CCP PETMR) +% (http://www.ccpsynerbi.ac.uk/). % % Licensed under the Apache License, Version 2.0 (the "License"); % you may not use this file except in compliance with the License. diff --git a/src/common/+sirf/+Utilities/mTest.m b/src/common/+sirf/+Utilities/mTest.m index 97337767c..a9031fd0e 100644 --- a/src/common/+sirf/+Utilities/mTest.m +++ b/src/common/+sirf/+Utilities/mTest.m @@ -1,12 +1,12 @@ classdef mTest < handle % Convenience class for writing test scripts. -% CCP PETMR Synergistic Image Reconstruction Framework (SIRF). +% SyneRBI Synergistic Image Reconstruction Framework (SIRF). % Copyright 2015 - 2017 Rutherford Appleton Laboratory STFC. % % This is software developed for the Collaborative Computational -% Project in Positron Emission Tomography and Magnetic Resonance imaging -% (http://www.ccppetmr.ac.uk/). +% Project in Synergistic Reconstruction for Biomedical Imaging (formerly CCP PETMR) +% (http://www.ccpsynerbi.ac.uk/). % % Licensed under the Apache License, Version 2.0 (the "License"); % you may not use this file except in compliance with the License. diff --git a/src/common/+sirf/+Utilities/name_and_parameters.m b/src/common/+sirf/+Utilities/name_and_parameters.m index 0c036a67d..056a19e20 100644 --- a/src/common/+sirf/+Utilities/name_and_parameters.m +++ b/src/common/+sirf/+Utilities/name_and_parameters.m @@ -1,12 +1,12 @@ function [name, par] = name_and_parameters(input) % Parses the input of the form name(parameters). -% CCP PETMR Synergistic Image Reconstruction Framework (SIRF). +% SyneRBI Synergistic Image Reconstruction Framework (SIRF). % Copyright 2015 - 2017 Rutherford Appleton Laboratory STFC. % % This is software developed for the Collaborative Computational -% Project in Positron Emission Tomography and Magnetic Resonance imaging -% (http://www.ccppetmr.ac.uk/). +% Project in Synergistic Reconstruction for Biomedical Imaging (formerly CCP PETMR) +% (http://www.ccpsynerbi.ac.uk/). % % Licensed under the Apache License, Version 2.0 (the "License"); % you may not use this file except in compliance with the License. diff --git a/src/common/+sirf/+Utilities/run_all_scripts.m b/src/common/+sirf/+Utilities/run_all_scripts.m index 5ca4f964c..64bf8a12e 100644 --- a/src/common/+sirf/+Utilities/run_all_scripts.m +++ b/src/common/+sirf/+Utilities/run_all_scripts.m @@ -2,12 +2,12 @@ function run_all_scripts(path) % This script contains common part of all run_all.m scripts % to reduce duplication. -% CCP PETMR Synergistic Image Reconstruction Framework (SIRF). +% SyneRBI Synergistic Image Reconstruction Framework (SIRF). % Copyright 2015 - 2017 Rutherford Appleton Laboratory STFC. % % This is software developed for the Collaborative Computational -% Project in Positron Emission Tomography and Magnetic Resonance imaging -% (http://www.ccppetmr.ac.uk/). +% Project in Synergistic Reconstruction for Biomedical Imaging (formerly CCP PETMR) +% (http://www.ccpsynerbi.ac.uk/). % % Licensed under the Apache License, Version 2.0 (the "License"); % you may not use this file except in compliance with the License. diff --git a/src/common/+sirf/+Utilities/set_window.m b/src/common/+sirf/+Utilities/set_window.m index 0d128d7a6..c2a0d3606 100644 --- a/src/common/+sirf/+Utilities/set_window.m +++ b/src/common/+sirf/+Utilities/set_window.m @@ -1,12 +1,12 @@ function set_window(left, bottom, width, height) % Sets window for displaying current figure. -% CCP PETMR Synergistic Image Reconstruction Framework (SIRF). +% SyneRBI Synergistic Image Reconstruction Framework (SIRF). % Copyright 2015 - 2017 Rutherford Appleton Laboratory STFC. % % This is software developed for the Collaborative Computational -% Project in Positron Emission Tomography and Magnetic Resonance imaging -% (http://www.ccppetmr.ac.uk/). +% Project in Synergistic Reconstruction for Biomedical Imaging (formerly CCP PETMR) +% (http://www.ccpsynerbi.ac.uk/). % % Licensed under the Apache License, Version 2.0 (the "License"); % you may not use this file except in compliance with the License. diff --git a/src/common/+sirf/+Utilities/show_2D_array.m b/src/common/+sirf/+Utilities/show_2D_array.m index 6d1b763ad..11a77873d 100644 --- a/src/common/+sirf/+Utilities/show_2D_array.m +++ b/src/common/+sirf/+Utilities/show_2D_array.m @@ -1,12 +1,12 @@ function show_2D_array(array, the_title, x_label, y_label, scale) %, window) % Displays a 2D array. -% CCP PETMR Synergistic Image Reconstruction Framework (SIRF). +% SyneRBI Synergistic Image Reconstruction Framework (SIRF). % Copyright 2015 - 2017 Rutherford Appleton Laboratory STFC. % % This is software developed for the Collaborative Computational -% Project in Positron Emission Tomography and Magnetic Resonance imaging -% (http://www.ccppetmr.ac.uk/). +% Project in Synergistic Reconstruction for Biomedical Imaging (formerly CCP PETMR) +% (http://www.ccpsynerbi.ac.uk/). % % Licensed under the Apache License, Version 2.0 (the "License"); % you may not use this file except in compliance with the License. diff --git a/src/common/+sirf/+Utilities/show_3D_array.m b/src/common/+sirf/+Utilities/show_3D_array.m index f9b6b1f89..76e3be55f 100644 --- a/src/common/+sirf/+Utilities/show_3D_array.m +++ b/src/common/+sirf/+Utilities/show_3D_array.m @@ -9,12 +9,12 @@ % : 'a, b-c, ...', where 'b-c' is decoded as 'b, b+1, ..., c'; % : out-of-range index value causes error (non-zero) return -% CCP PETMR Synergistic Image Reconstruction Framework (SIRF). +% SyneRBI Synergistic Image Reconstruction Framework (SIRF). % Copyright 2015 - 2017 Rutherford Appleton Laboratory STFC. % % This is software developed for the Collaborative Computational -% Project in Positron Emission Tomography and Magnetic Resonance imaging -% (http://www.ccppetmr.ac.uk/). +% Project in Synergistic Reconstruction for Biomedical Imaging (formerly CCP PETMR) +% (http://www.ccpsynerbi.ac.uk/). % % Licensed under the Apache License, Version 2.0 (the "License"); % you may not use this file except in compliance with the License. diff --git a/src/common/+sirf/+Utilities/str_to_int_list.m b/src/common/+sirf/+Utilities/str_to_int_list.m index b58bbbddb..cef652ee1 100644 --- a/src/common/+sirf/+Utilities/str_to_int_list.m +++ b/src/common/+sirf/+Utilities/str_to_int_list.m @@ -2,12 +2,12 @@ % Converts the string str_list of the form n1{-n2] [, n2[-n3]] [, ...] % into a list of numbers n1[, n1 + 1, ..., n2] etc. -% CCP PETMR Synergistic Image Reconstruction Framework (SIRF). +% SyneRBI Synergistic Image Reconstruction Framework (SIRF). % Copyright 2015 - 2017 Rutherford Appleton Laboratory STFC. % % This is software developed for the Collaborative Computational -% Project in Positron Emission Tomography and Magnetic Resonance imaging -% (http://www.ccppetmr.ac.uk/). +% Project in Synergistic Reconstruction for Biomedical Imaging (formerly CCP PETMR) +% (http://www.ccpsynerbi.ac.uk/). % % Licensed under the Apache License, Version 2.0 (the "License"); % you may not use this file except in compliance with the License. diff --git a/src/common/CMakeLists.txt b/src/common/CMakeLists.txt index 51eff269c..228a96fe8 100644 --- a/src/common/CMakeLists.txt +++ b/src/common/CMakeLists.txt @@ -1,6 +1,6 @@ #======================================================================== # Author: Evgueni Ovtchinnikov -# Copyright 2017 University College London +# Copyright 2020 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. diff --git a/src/common/GeometricalInfo.cpp b/src/common/GeometricalInfo.cpp index 0d6a2dfcb..f657415bd 100644 --- a/src/common/GeometricalInfo.cpp +++ b/src/common/GeometricalInfo.cpp @@ -1,10 +1,10 @@ /* -CCP PETMR Synergistic Image Reconstruction Framework (SIRF) +SyneRBI 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/). +Project in Synergistic Reconstruction for Biomedical Imaging (formerly CCP PETMR) +(http://www.ccpsynerbi.ac.uk/). Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. diff --git a/src/common/ImageData.cpp b/src/common/ImageData.cpp index e4f2f0437..d49b217b6 100644 --- a/src/common/ImageData.cpp +++ b/src/common/ImageData.cpp @@ -1,10 +1,10 @@ /* -CCP PETMR Synergistic Image Reconstruction Framework (SIRF) +SyneRBI Synergistic Image Reconstruction Framework (SIRF) Copyright 2020 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/). +Project in Synergistic Reconstruction for Biomedical Imaging (formerly CCP PETMR) +(http://www.ccpsynerbi.ac.uk/). Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. diff --git a/src/common/SIRF.py b/src/common/SIRF.py index b8f4a2713..d26330a98 100644 --- a/src/common/SIRF.py +++ b/src/common/SIRF.py @@ -2,13 +2,13 @@ Object-Oriented wrap for the cSIRF-to-Python interface pysirf.py ''' -## CCP PETMR Synergistic Image Reconstruction Framework (SIRF) -## Copyright 2015 - 2017 Rutherford Appleton Laboratory STFC -## Copyright 2015 - 2019 University College London +## SyneRBI Synergistic Image Reconstruction Framework (SIRF) +## Copyright 2015 - 2020 Rutherford Appleton Laboratory STFC +## Copyright 2015 - 2020 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/). +## Project in Synergistic Reconstruction for Biomedical Imaging (formerly CCP PETMR) +## (http://www.ccpsynerbi.ac.uk/). ## ## Licensed under the Apache License, Version 2.0 (the "License"); ## you may not use this file except in compliance with the License. diff --git a/src/common/Utilities.py b/src/common/Utilities.py index 4bb52c891..1388907f4 100644 --- a/src/common/Utilities.py +++ b/src/common/Utilities.py @@ -8,13 +8,13 @@ import sirf.pyiutilities as pyiutil import re -__licence__ = """CCP PETMR Synergistic Image Reconstruction Framework (SIRF) +__licence__ = """SyneRBI Synergistic Image Reconstruction Framework (SIRF) Copyright 2015 - 2019 Rutherford Appleton Laboratory STFC -Copyright 2015 - 2019 University College London +Copyright 2015 - 2020 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/). +Project in Synergistic Reconstruction for Biomedical Imaging (formerly CCP PETMR) +(http://www.ccpsynerbi.ac.uk/). Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. diff --git a/src/common/csirf.cpp b/src/common/csirf.cpp index 70651a816..05bfb8136 100644 --- a/src/common/csirf.cpp +++ b/src/common/csirf.cpp @@ -1,11 +1,11 @@ /* -CCP PETMR Synergistic Image Reconstruction Framework (SIRF) -Copyright 2015 - 2017 Rutherford Appleton Laboratory STFC -Copyright 2015 - 2017 University College London. +SyneRBI Synergistic Image Reconstruction Framework (SIRF) +Copyright 2015 - 2020 Rutherford Appleton Laboratory STFC +Copyright 2020 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/). +Project in Synergistic Reconstruction for Biomedical Imaging (formerly CCP PETMR) +(http://www.ccpsynerbi.ac.uk/). Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. @@ -385,4 +385,4 @@ cSIRF_GeomInfo_get_index_to_physical_point_matrix(const void* ptr_geom, void* pt for (unsigned j=0; j<4; ++j) data[i*3+j] = tm[i][j]; return new DataHandle; -} \ No newline at end of file +} diff --git a/src/common/gmi/gmi_csirf.cpp b/src/common/gmi/gmi_csirf.cpp index 939b8011e..a0d8b0820 100644 --- a/src/common/gmi/gmi_csirf.cpp +++ b/src/common/gmi/gmi_csirf.cpp @@ -1,10 +1,10 @@ /* -CCP PETMR Synergistic Image Reconstruction Framework (SIRF) -Copyright 2015 - 2017 Rutherford Appleton Laboratory STFC +SyneRBI Synergistic Image Reconstruction Framework (SIRF) +Copyright 2015 - 2019 Rutherford Appleton Laboratory STFC This is software developed for the Collaborative Computational -Project in Positron Emission Tomography and Magnetic Resonance imaging -(http://www.ccppetmr.ac.uk/). +Project in Synergistic Reconstruction for Biomedical Imaging (formerly CCP PETMR) +(http://www.ccpsynerbi.ac.uk/). Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. @@ -24,7 +24,7 @@ limitations under the License. \brief The executable for generating Matlab interface for cgadgetron library. \author Evgueni Ovtchinnikov -\author CCP PETMR +\author SyneRBI */ #include @@ -70,4 +70,4 @@ int main(int argc, char *argv[]) cout << "wrong input file format" << endl; return 1; } -} \ No newline at end of file +} diff --git a/src/common/include/sirf/Syn/utilities.h b/src/common/include/sirf/Syn/utilities.h index 837ecb6b4..58a520712 100644 --- a/src/common/include/sirf/Syn/utilities.h +++ b/src/common/include/sirf/Syn/utilities.h @@ -1,11 +1,11 @@ /* -CCP PETMR Synergistic Image Reconstruction Framework (SIRF) +SyneRBI Synergistic Image Reconstruction Framework (SIRF) Copyright 2020 Rutherford Appleton Laboratory STFC Copyright 2020 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/). +Project in Synergistic Reconstruction for Biomedical Imaging (formerly CCP PETMR) +(http://www.ccpsynerbi.ac.uk/). Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. @@ -25,7 +25,7 @@ limitations under the License. \brief C++ synergistic utilities. \author Evgueni Ovtchinnikov -\author CCP PETMR +\author SyneRBI */ #pragma once diff --git a/src/common/include/sirf/common/ANumRef.h b/src/common/include/sirf/common/ANumRef.h index a6dac2f29..da9b10dfb 100644 --- a/src/common/include/sirf/common/ANumRef.h +++ b/src/common/include/sirf/common/ANumRef.h @@ -1,10 +1,11 @@ /* -CCP PETMR Synergistic Image Reconstruction Framework (SIRF) -Copyright 2015 - 2017 Rutherford Appleton Laboratory STFC +SyneRBI Synergistic Image Reconstruction Framework (SIRF) +Copyright 2018 Rutherford Appleton Laboratory STFC +Copyright 2020 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/). +Project in Synergistic Reconstruction for Biomedical Imaging (formerly CCP PETMR) +(http://www.ccpsynerbi.ac.uk/). Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. @@ -359,4 +360,4 @@ namespace sirf { } // namespace sirf -#endif \ No newline at end of file +#endif diff --git a/src/common/include/sirf/common/DataContainer.h b/src/common/include/sirf/common/DataContainer.h index 5866e11bc..70e1a28de 100644 --- a/src/common/include/sirf/common/DataContainer.h +++ b/src/common/include/sirf/common/DataContainer.h @@ -1,10 +1,10 @@ /* -CCP PETMR Synergistic Image Reconstruction Framework (SIRF) -Copyright 2015 - 2017 Rutherford Appleton Laboratory STFC +SyneRBI Synergistic Image Reconstruction Framework (SIRF) +Copyright 2015 - 2019 Rutherford Appleton Laboratory STFC This is software developed for the Collaborative Computational -Project in Positron Emission Tomography and Magnetic Resonance imaging -(http://www.ccppetmr.ac.uk/). +Project in Synergistic Reconstruction for Biomedical Imaging (formerly CCP PETMR) +(http://www.ccpsynerbi.ac.uk/). Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. @@ -63,4 +63,4 @@ namespace sirf { }; } -#endif \ No newline at end of file +#endif diff --git a/src/common/include/sirf/common/GeometricalInfo.h b/src/common/include/sirf/common/GeometricalInfo.h index a211ce461..f6054984e 100644 --- a/src/common/include/sirf/common/GeometricalInfo.h +++ b/src/common/include/sirf/common/GeometricalInfo.h @@ -1,11 +1,13 @@ /* - CCP PETMR Synergistic Image Reconstruction Framework (SIRF) + SyneRBI Synergistic Image Reconstruction Framework (SIRF) Copyright 2018 Commonwealth Scientific and Industrial Research Organisation's Australian eHealth Research Organisation + Copyright 2020 Rutherford Appleton Laboratory STFC + Copyright 2019 - 2020 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/). + Project in Synergistic Reconstruction for Biomedical Imaging (formerly CCP PETMR) + (http://www.ccpsynerbi.ac.uk/). Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. diff --git a/src/common/include/sirf/common/ImageData.h b/src/common/include/sirf/common/ImageData.h index d51c6eb44..be6a7c8dc 100644 --- a/src/common/include/sirf/common/ImageData.h +++ b/src/common/include/sirf/common/ImageData.h @@ -1,11 +1,11 @@ /* -CCP PETMR Synergistic Image Reconstruction Framework (SIRF) -Copyright 2018 Rutherford Appleton Laboratory STFC -Copyright 2018 University College London +SyneRBI Synergistic Image Reconstruction Framework (SIRF) +Copyright 2018 - 2020 Rutherford Appleton Laboratory STFC +Copyright 2018 - 2020 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/). +Project in Synergistic Reconstruction for Biomedical Imaging (formerly CCP PETMR) +(http://www.ccpsynerbi.ac.uk/). Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. @@ -145,4 +145,4 @@ namespace sirf { }; } -#endif \ No newline at end of file +#endif diff --git a/src/common/include/sirf/common/csirf.h b/src/common/include/sirf/common/csirf.h index b7b0502f8..36a596797 100644 --- a/src/common/include/sirf/common/csirf.h +++ b/src/common/include/sirf/common/csirf.h @@ -1,11 +1,11 @@ /* -CCP PETMR Synergistic Image Reconstruction Framework (SIRF) -Copyright 2015 - 2017 Rutherford Appleton Laboratory STFC -Copyright 2015 - 2017 University College London. +SyneRBI Synergistic Image Reconstruction Framework (SIRF) +Copyright 2015 - 2020 Rutherford Appleton Laboratory STFC +Copyright 2018 - 2020 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/). +Project in Synergistic Reconstruction for Biomedical Imaging (formerly CCP PETMR) +(http://www.ccpsynerbi.ac.uk/). Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. diff --git a/src/common/mig.cpp b/src/common/mig.cpp index 14a820588..811413ef7 100644 --- a/src/common/mig.cpp +++ b/src/common/mig.cpp @@ -1,10 +1,11 @@ /* -CCP PETMR Synergistic Image Reconstruction Framework (SIRF) +SyneRBI Synergistic Image Reconstruction Framework (SIRF) Copyright 2015 - 2017 Rutherford Appleton Laboratory STFC +Copyright 2020 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/). +Project in Synergistic Reconstruction for Biomedical Imaging (formerly CCP PETMR) +(http://www.ccpsynerbi.ac.uk/). Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. diff --git a/src/common/set_up_MR.m b/src/common/set_up_MR.m index 19a3289cb..cd4539676 100644 --- a/src/common/set_up_MR.m +++ b/src/common/set_up_MR.m @@ -5,13 +5,13 @@ % Caveat: help(eng.ImageData) etc. will work, but help(eng) will not (because eng is just a struct). % See also set_up_engine and set_up_PET and set_up_Reg -% CCP PETMR Synergistic Image Reconstruction Framework (SIRF). -% Copyright 2015 - 2017 Rutherford Appleton Laboratory STFC. +% SyneRBI Synergistic Image Reconstruction Framework (SIRF). +% Copyright 2015 - 2019 Rutherford Appleton Laboratory STFC. % 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/). +% Project in Synergistic Reconstruction for Biomedical Imaging (formerly CCP PETMR) +% (http://www.ccpsynerbi.ac.uk/). % % Licensed under the Apache License, Version 2.0 (the "License"); % you may not use this file except in compliance with the License. @@ -31,4 +31,4 @@ else alias = set_up_engine(engine); end -end \ No newline at end of file +end diff --git a/src/common/set_up_PET.m b/src/common/set_up_PET.m index e5b579026..76508a7ee 100644 --- a/src/common/set_up_PET.m +++ b/src/common/set_up_PET.m @@ -5,13 +5,13 @@ % Caveat: help(eng.ImageData) etc. will work, but help(eng) will not (because eng is just a struct). % See also set_up_engine and set_up_MR and set_up_Reg -% CCP PETMR Synergistic Image Reconstruction Framework (SIRF). -% Copyright 2015 - 2017 Rutherford Appleton Laboratory STFC. +% SyneRBI Synergistic Image Reconstruction Framework (SIRF). +% Copyright 2015 - 2019 Rutherford Appleton Laboratory STFC. % 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/). +% Project in Synergistic Reconstruction for Biomedical Imaging (formerly CCP PETMR) +% (http://www.ccpsynerbi.ac.uk/). % % Licensed under the Apache License, Version 2.0 (the "License"); % you may not use this file except in compliance with the License. @@ -31,4 +31,4 @@ else alias = set_up_engine(engine); end -end \ No newline at end of file +end diff --git a/src/common/set_up_Reg.m b/src/common/set_up_Reg.m index f2c7f3110..2c03a3b75 100644 --- a/src/common/set_up_Reg.m +++ b/src/common/set_up_Reg.m @@ -5,13 +5,13 @@ % Caveat: help(eng.ImageData) etc. will work, but help(eng) will not (because eng is just a struct). % See also set_up_engine and set_up_PET and set_up_Reg -% CCP PETMR Synergistic Image Reconstruction Framework (SIRF). +% SyneRBI Synergistic Image Reconstruction Framework (SIRF). % Copyright 2015 - 2017 Rutherford Appleton Laboratory STFC. -% Copyright 2019 University College London. +% 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/). +% Project in Synergistic Reconstruction for Biomedical Imaging (formerly CCP PETMR) +% (http://www.ccpsynerbi.ac.uk/). % % Licensed under the Apache License, Version 2.0 (the "License"); % you may not use this file except in compliance with the License. @@ -31,4 +31,4 @@ else alias = set_up_engine(engine); end -end \ No newline at end of file +end diff --git a/src/common/set_up_engine.m b/src/common/set_up_engine.m index b9232413b..99db38bb1 100644 --- a/src/common/set_up_engine.m +++ b/src/common/set_up_engine.m @@ -5,13 +5,13 @@ % Caveat: help(eng.ImageData) etc. will work, but help(eng) will not (because eng is just a struct). % See also set_up_PET and set_up_MR and set_up_Reg -% CCP PETMR Synergistic Image Reconstruction Framework (SIRF). -% Copyright 2015 - 2017 Rutherford Appleton Laboratory STFC. +% SyneRBI Synergistic Image Reconstruction Framework (SIRF). +% Copyright 2015 - 2019 Rutherford Appleton Laboratory STFC. % 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/). +% Project in Synergistic Reconstruction for Biomedical Imaging (formerly CCP PETMR) +% (http://www.ccpsynerbi.ac.uk/). % % Licensed under the Apache License, Version 2.0 (the "License"); % you may not use this file except in compliance with the License. @@ -48,4 +48,4 @@ [~,file,~] = fileparts(files(i).name); alias.(file) = eval(['@sirf.' engine '.' file]); end -end \ No newline at end of file +end diff --git a/src/common/show_image.py b/src/common/show_image.py index 848da1d0f..d372f0f0f 100644 --- a/src/common/show_image.py +++ b/src/common/show_image.py @@ -3,12 +3,12 @@ show_image.py ''' -## CCP PETMR Synergistic Image Reconstruction Framework (SIRF) +## SyneRBI Synergistic Image Reconstruction Framework (SIRF) ## Copyright 2020 Rutherford Appleton Laboratory STFC ## ## This is software developed for the Collaborative Computational -## Project in Positron Emission Tomography and Magnetic Resonance imaging -## (http://www.ccppetmr.ac.uk/). +## Project in Synergistic Reconstruction for Biomedical Imaging (formerly CCP PETMR) +## (http://www.ccpsynerbi.ac.uk/). ## ## Licensed under the Apache License, Version 2.0 (the "License"); ## you may not use this file except in compliance with the License. diff --git a/src/common/syn_utilities.cpp b/src/common/syn_utilities.cpp index 0650f8b46..7a446e116 100644 --- a/src/common/syn_utilities.cpp +++ b/src/common/syn_utilities.cpp @@ -1,11 +1,11 @@ /* -CCP PETMR Synergistic Image Reconstruction Framework (SIRF) +SyneRBI Synergistic Image Reconstruction Framework (SIRF) Copyright 2020 Rutherford Appleton Laboratory STFC Copyright 2020 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/). +Project in Synergistic Reconstruction for Biomedical Imaging (formerly CCP PETMR) +(http://www.ccpsynerbi.ac.uk/). Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. @@ -26,7 +26,7 @@ limitations under the License. \author Richard Brown \author Evgueni Ovtchinnikov -\author CCP PETMR +\author SyneRBI */ #include "sirf/Gadgetron/gadgetron_data_containers.h" diff --git a/src/doxymain.h b/src/doxymain.h index 6856b991c..84094635f 100644 --- a/src/doxymain.h +++ b/src/doxymain.h @@ -3,12 +3,12 @@ // // This file is for doxygen only. It does not contain any code. /* -CCP PETMR Synergistic Image Reconstruction Framework (SIRF) -Copyright 2015 - 2017 Rutherford Appleton Laboratory STFC +SyneRBI Synergistic Image Reconstruction Framework (SIRF) +Copyright 2015 - 2020 Rutherford Appleton Laboratory STFC This is software developed for the Collaborative Computational -Project in Positron Emission Tomography and Magnetic Resonance imaging -(http://www.ccppetmr.ac.uk/). +Project in Synergistic Reconstruction for Biomedical Imaging (formerly CCP PETMR) +(http://www.ccpsynerbi.ac.uk/). Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. @@ -37,4 +37,4 @@ into the documentation presented here. The current pages are automatically generated by doxygen from text comments in the files. -*/ \ No newline at end of file +*/ diff --git a/src/iUtilities/CMakeLists.txt b/src/iUtilities/CMakeLists.txt index bddf2fd67..ca1ab8440 100644 --- a/src/iUtilities/CMakeLists.txt +++ b/src/iUtilities/CMakeLists.txt @@ -1,6 +1,6 @@ #======================================================================== -# Author: Kris Thielemans -# Copyright 2016, 2017 University College London +# Author: Kris Thielemans, Richard Brown +# Copyright 2016, 2018, 2020 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. diff --git a/src/iUtilities/gmi/gmi.cpp b/src/iUtilities/gmi/gmi.cpp index 72ce60d5a..217a19fcd 100644 --- a/src/iUtilities/gmi/gmi.cpp +++ b/src/iUtilities/gmi/gmi.cpp @@ -1,10 +1,11 @@ /* -CCP PETMR Synergistic Image Reconstruction Framework (SIRF) -Copyright 2015 - 2017 Rutherford Appleton Laboratory STFC +SyneRBI Synergistic Image Reconstruction Framework (SIRF) +Copyright 2015 - 2018 Rutherford Appleton Laboratory STFC +Copyright 2019 - 2020 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/). +Project in Synergistic Reconstruction for Biomedical Imaging (formerly CCP PETMR) +(http://www.ccpsynerbi.ac.uk/). Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. @@ -24,7 +25,7 @@ limitations under the License. \brief The executable for generating Matlab interface for iutilities library. \author Evgueni Ovtchinnikov -\author CCP PETMR +\author SyneRBI */ #include @@ -70,4 +71,4 @@ int main(int argc, char *argv[]) cout << "wrong input file format" << endl; return 1; } -} \ No newline at end of file +} diff --git a/src/iUtilities/include/sirf/iUtilities/DataHandle.h b/src/iUtilities/include/sirf/iUtilities/DataHandle.h index a23dff36a..5f37b0882 100644 --- a/src/iUtilities/include/sirf/iUtilities/DataHandle.h +++ b/src/iUtilities/include/sirf/iUtilities/DataHandle.h @@ -1,10 +1,10 @@ /* -CCP PETMR Synergistic Image Reconstruction Framework (SIRF) -Copyright 2015 - 2017 Rutherford Appleton Laboratory STFC - +SyneRBI Synergistic Image Reconstruction Framework (SIRF) +Copyright 2015 - 2020 Rutherford Appleton Laboratory STFC +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/). +Project in Synergistic Reconstruction for Biomedical Imaging (formerly CCP PETMR) +(http://www.ccpsynerbi.ac.uk/). Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. @@ -24,7 +24,7 @@ limitations under the License. \brief Execution status type and basic wrapper for C++ objects. \author Evgueni Ovtchinnikov -\author CCP PETMR +\author SyneRBI */ #ifndef DATA_HANDLE_TYPES diff --git a/src/iUtilities/include/sirf/iUtilities/LocalisedException.h b/src/iUtilities/include/sirf/iUtilities/LocalisedException.h index a1d502dc5..115410a52 100644 --- a/src/iUtilities/include/sirf/iUtilities/LocalisedException.h +++ b/src/iUtilities/include/sirf/iUtilities/LocalisedException.h @@ -1,10 +1,10 @@ /* -CCP PETMR Synergistic Image Reconstruction Framework (SIRF) -Copyright 2015 - 2017 Rutherford Appleton Laboratory STFC +SyneRBI Synergistic Image Reconstruction Framework (SIRF) +Copyright 2015 - 2020 Rutherford Appleton Laboratory STFC This is software developed for the Collaborative Computational -Project in Positron Emission Tomography and Magnetic Resonance imaging -(http://www.ccppetmr.ac.uk/). +Project in Synergistic Reconstruction for Biomedical Imaging (formerly CCP PETMR) +(http://www.ccpsynerbi.ac.uk/). Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. @@ -61,4 +61,4 @@ class LocalisedException : public std::exception { int line_; }; -#endif \ No newline at end of file +#endif diff --git a/src/iUtilities/include/sirf/iUtilities/iutilities.h b/src/iUtilities/include/sirf/iUtilities/iutilities.h index d9ce110af..21ab51943 100644 --- a/src/iUtilities/include/sirf/iUtilities/iutilities.h +++ b/src/iUtilities/include/sirf/iUtilities/iutilities.h @@ -1,10 +1,11 @@ /* -CCP PETMR Synergistic Image Reconstruction Framework (SIRF) +SyneRBI Synergistic Image Reconstruction Framework (SIRF) Copyright 2015 - 2017 Rutherford Appleton Laboratory STFC +Copyright 2020 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/). +Project in Synergistic Reconstruction for Biomedical Imaging (formerly CCP PETMR) +(http://www.ccpsynerbi.ac.uk/). Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. @@ -61,4 +62,4 @@ extern "C" { } #endif -#endif \ No newline at end of file +#endif diff --git a/src/iUtilities/iutilities.cpp b/src/iUtilities/iutilities.cpp index 1dafbe67b..fea170096 100644 --- a/src/iUtilities/iutilities.cpp +++ b/src/iUtilities/iutilities.cpp @@ -1,10 +1,11 @@ /* -CCP PETMR Synergistic Image Reconstruction Framework (SIRF) -Copyright 2015 - 2017 Rutherford Appleton Laboratory STFC +SyneRBI Synergistic Image Reconstruction Framework (SIRF) +Copyright 2015 - 2018 Rutherford Appleton Laboratory STFC +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/). +Project in Synergistic Reconstruction for Biomedical Imaging (formerly CCP PETMR) +(http://www.ccpsynerbi.ac.uk/). Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. @@ -25,7 +26,7 @@ limitations under the License. Defines C functions handling DataHandle objects. \author Evgueni Ovtchinnikov -\author CCP PETMR +\author SyneRBI */ #include diff --git a/src/xGadgetron/cGadgetron/CMakeLists.txt b/src/xGadgetron/cGadgetron/CMakeLists.txt index 68f2f168b..e4b13cfc4 100644 --- a/src/xGadgetron/cGadgetron/CMakeLists.txt +++ b/src/xGadgetron/cGadgetron/CMakeLists.txt @@ -1,6 +1,6 @@ #======================================================================== # Author: Kris Thielemans -# Copyright 2016, 2017, 2019 University College London +# Copyright 2016, 2017, 2019, 2020 University College London # Copyright 2018 Science Technology Facilities Council # # Licensed under the Apache License, Version 2.0 (the "License"); diff --git a/src/xGadgetron/cGadgetron/cgadgetron.cpp b/src/xGadgetron/cGadgetron/cgadgetron.cpp index cf5b2bb39..464a64b66 100644 --- a/src/xGadgetron/cGadgetron/cgadgetron.cpp +++ b/src/xGadgetron/cGadgetron/cgadgetron.cpp @@ -1,10 +1,12 @@ /* -CCP PETMR Synergistic Image Reconstruction Framework (SIRF) -Copyright 2015 - 2017 Rutherford Appleton Laboratory STFC +SyneRBI Synergistic Image Reconstruction Framework (SIRF) +Copyright 2015 - 2020 Rutherford Appleton Laboratory STFC +Copyright 2019 - 2020 University College London +Copyright 2020 Physikalisch-Technische Bundesanstalt (PTB) This is software developed for the Collaborative Computational -Project in Positron Emission Tomography and Magnetic Resonance imaging -(http://www.ccppetmr.ac.uk/). +Project in Synergistic Reconstruction for Biomedical Imaging (formerly CCP PETMR) +(http://www.ccpsynerbi.ac.uk/). Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. diff --git a/src/xGadgetron/cGadgetron/gadgetron_client.cpp b/src/xGadgetron/cGadgetron/gadgetron_client.cpp index a2d19dc5d..8c568348b 100644 --- a/src/xGadgetron/cGadgetron/gadgetron_client.cpp +++ b/src/xGadgetron/cGadgetron/gadgetron_client.cpp @@ -1,10 +1,10 @@ /* -CCP PETMR Synergistic Image Reconstruction Framework (SIRF) -Copyright 2015 - 2017 Rutherford Appleton Laboratory STFC +SyneRBI Synergistic Image Reconstruction Framework (SIRF) +Copyright 2015 - 2019 Rutherford Appleton Laboratory STFC This is software developed for the Collaborative Computational -Project in Positron Emission Tomography and Magnetic Resonance imaging -(http://www.ccppetmr.ac.uk/). +Project in Synergistic Reconstruction for Biomedical Imaging (formerly CCP PETMR) +(http://www.ccpsynerbi.ac.uk/). Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. @@ -57,7 +57,7 @@ IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. \brief Implementation file for SIRF Gadgetron client. \author Evgueni Ovtchinnikov -\author CCP PETMR +\author SyneRBI */ #include diff --git a/src/xGadgetron/cGadgetron/gadgetron_data_containers.cpp b/src/xGadgetron/cGadgetron/gadgetron_data_containers.cpp index b03fc048d..97461b130 100644 --- a/src/xGadgetron/cGadgetron/gadgetron_data_containers.cpp +++ b/src/xGadgetron/cGadgetron/gadgetron_data_containers.cpp @@ -1,11 +1,12 @@ /* -CCP PETMR Synergistic Image Reconstruction Framework (SIRF) -Copyright 2015 - 2017 Rutherford Appleton Laboratory STFC -Copyright 2018 University College London +SyneRBI Synergistic Image Reconstruction Framework (SIRF) +Copyright 2015 - 2020 Rutherford Appleton Laboratory STFC +Copyright 2018 - 2020 University College London +Copyright 2020 Physikalisch-Technische Bundesanstalt (PTB) This is software developed for the Collaborative Computational -Project in Positron Emission Tomography and Magnetic Resonance imaging -(http://www.ccppetmr.ac.uk/). +Project in Synergistic Reconstruction for Biomedical Imaging (formerly CCP PETMR) +(http://www.ccpsynerbi.ac.uk/). Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. @@ -25,7 +26,7 @@ limitations under the License. \brief Implementation file for SIRF data container classes for Gadgetron data. \author Evgueni Ovtchinnikov -\author CCP PETMR +\author SyneRBI */ #include #include diff --git a/src/xGadgetron/cGadgetron/gadgetron_x.cpp b/src/xGadgetron/cGadgetron/gadgetron_x.cpp index 6c6df2af4..6e4d04f45 100644 --- a/src/xGadgetron/cGadgetron/gadgetron_x.cpp +++ b/src/xGadgetron/cGadgetron/gadgetron_x.cpp @@ -1,10 +1,11 @@ /* -CCP PETMR Synergistic Image Reconstruction Framework (SIRF) -Copyright 2015 - 2017 Rutherford Appleton Laboratory STFC +SyneRBI Synergistic Image Reconstruction Framework (SIRF) +Copyright 2015 - 2020 Rutherford Appleton Laboratory STFC +Copyright 2019 - 2020 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/). +Project in Synergistic Reconstruction for Biomedical Imaging (formerly CCP PETMR) +(http://www.ccpsynerbi.ac.uk/). Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. @@ -24,7 +25,7 @@ limitations under the License. \brief Implementation file for extended Gadgetron functionality classes. \author Evgueni Ovtchinnikov -\author CCP PETMR +\author SyneRBI */ #include "sirf/iUtilities/DataHandle.h" diff --git a/src/xGadgetron/cGadgetron/include/sirf/Gadgetron/cgadgetron.h b/src/xGadgetron/cGadgetron/include/sirf/Gadgetron/cgadgetron.h index 688002616..31ae773ab 100644 --- a/src/xGadgetron/cGadgetron/include/sirf/Gadgetron/cgadgetron.h +++ b/src/xGadgetron/cGadgetron/include/sirf/Gadgetron/cgadgetron.h @@ -1,10 +1,11 @@ /* -CCP PETMR Synergistic Image Reconstruction Framework (SIRF) -Copyright 2015 - 2017 Rutherford Appleton Laboratory STFC +SyneRBI Synergistic Image Reconstruction Framework (SIRF) +Copyright 2015 - 2020 Rutherford Appleton Laboratory STFC +Copyright 2020 Physikalisch-Technische Bundesanstalt (PTB) This is software developed for the Collaborative Computational -Project in Positron Emission Tomography and Magnetic Resonance imaging -(http://www.ccppetmr.ac.uk/). +Project in Synergistic Reconstruction for Biomedical Imaging (formerly CCP PETMR) +(http://www.ccpsynerbi.ac.uk/). Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. diff --git a/src/xGadgetron/cGadgetron/include/sirf/Gadgetron/cgadgetron_p.h b/src/xGadgetron/cGadgetron/include/sirf/Gadgetron/cgadgetron_p.h index f6477bfff..eec8f5af2 100644 --- a/src/xGadgetron/cGadgetron/include/sirf/Gadgetron/cgadgetron_p.h +++ b/src/xGadgetron/cGadgetron/include/sirf/Gadgetron/cgadgetron_p.h @@ -1,10 +1,10 @@ /* -CCP PETMR Synergistic Image Reconstruction Framework (SIRF) -Copyright 2015 - 2017 Rutherford Appleton Laboratory STFC +SyneRBI Synergistic Image Reconstruction Framework (SIRF) +Copyright 2015 - 2019 Rutherford Appleton Laboratory STFC This is software developed for the Collaborative Computational -Project in Positron Emission Tomography and Magnetic Resonance imaging -(http://www.ccppetmr.ac.uk/). +Project in Synergistic Reconstruction for Biomedical Imaging (formerly CCP PETMR) +(http://www.ccpsynerbi.ac.uk/). Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. diff --git a/src/xGadgetron/cGadgetron/include/sirf/Gadgetron/cgadgetron_shared_ptr.h b/src/xGadgetron/cGadgetron/include/sirf/Gadgetron/cgadgetron_shared_ptr.h index 849501813..dd91e46ef 100644 --- a/src/xGadgetron/cGadgetron/include/sirf/Gadgetron/cgadgetron_shared_ptr.h +++ b/src/xGadgetron/cGadgetron/include/sirf/Gadgetron/cgadgetron_shared_ptr.h @@ -1,10 +1,10 @@ /* -CCP PETMR Synergistic Image Reconstruction Framework (SIRF) -Copyright 2015 - 2017 Rutherford Appleton Laboratory STFC +SyneRBI Synergistic Image Reconstruction Framework (SIRF) +Copyright 2015 - 2019 Rutherford Appleton Laboratory STFC This is software developed for the Collaborative Computational -Project in Positron Emission Tomography and Magnetic Resonance imaging -(http://www.ccppetmr.ac.uk/). +Project in Synergistic Reconstruction for Biomedical Imaging (formerly CCP PETMR) +(http://www.ccpsynerbi.ac.uk/). Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. diff --git a/src/xGadgetron/cGadgetron/include/sirf/Gadgetron/chain_lib.h b/src/xGadgetron/cGadgetron/include/sirf/Gadgetron/chain_lib.h index 774e5be8a..c98e17bd0 100644 --- a/src/xGadgetron/cGadgetron/include/sirf/Gadgetron/chain_lib.h +++ b/src/xGadgetron/cGadgetron/include/sirf/Gadgetron/chain_lib.h @@ -1,10 +1,10 @@ /* -CCP PETMR Synergistic Image Reconstruction Framework (SIRF) -Copyright 2015 - 2017 Rutherford Appleton Laboratory STFC +SyneRBI Synergistic Image Reconstruction Framework (SIRF) +Copyright 2015 - 2019 Rutherford Appleton Laboratory STFC This is software developed for the Collaborative Computational -Project in Positron Emission Tomography and Magnetic Resonance imaging -(http://www.ccppetmr.ac.uk/). +Project in Synergistic Reconstruction for Biomedical Imaging (formerly CCP PETMR) +(http://www.ccpsynerbi.ac.uk/). Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. @@ -25,7 +25,7 @@ limitations under the License. of Gadgetron gadget chains. \author Evgueni Ovtchinnikov -\author CCP PETMR +\author SyneRBI */ #ifndef PROCESSOR_CHAINS_LIBRARY @@ -121,4 +121,4 @@ namespace sirf { } -#endif \ No newline at end of file +#endif diff --git a/src/xGadgetron/cGadgetron/include/sirf/Gadgetron/gadget_lib.h b/src/xGadgetron/cGadgetron/include/sirf/Gadgetron/gadget_lib.h index 218817cc9..351f41702 100644 --- a/src/xGadgetron/cGadgetron/include/sirf/Gadgetron/gadget_lib.h +++ b/src/xGadgetron/cGadgetron/include/sirf/Gadgetron/gadget_lib.h @@ -1,10 +1,11 @@ /* -CCP PETMR Synergistic Image Reconstruction Framework (SIRF) -Copyright 2015 - 2017 Rutherford Appleton Laboratory STFC +SyneRBI Synergistic Image Reconstruction Framework (SIRF) +Copyright 2015 - 2019 Rutherford Appleton Laboratory STFC +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/). +Project in Synergistic Reconstruction for Biomedical Imaging (formerly CCP PETMR) +(http://www.ccpsynerbi.ac.uk/). Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. @@ -25,7 +26,7 @@ limitations under the License. of Gadgetron gadgets. \author Evgueni Ovtchinnikov -\author CCP PETMR +\author SyneRBI */ #ifndef GADGETS_LIBRARY diff --git a/src/xGadgetron/cGadgetron/include/sirf/Gadgetron/gadgetron_client.h b/src/xGadgetron/cGadgetron/include/sirf/Gadgetron/gadgetron_client.h index 568ee2277..2982cbd4f 100644 --- a/src/xGadgetron/cGadgetron/include/sirf/Gadgetron/gadgetron_client.h +++ b/src/xGadgetron/cGadgetron/include/sirf/Gadgetron/gadgetron_client.h @@ -1,10 +1,10 @@ /* -CCP PETMR Synergistic Image Reconstruction Framework (SIRF) -Copyright 2015 - 2017 Rutherford Appleton Laboratory STFC +SyneRBI Synergistic Image Reconstruction Framework (SIRF) +Copyright 2015 - 2019 Rutherford Appleton Laboratory STFC This is software developed for the Collaborative Computational -Project in Positron Emission Tomography and Magnetic Resonance imaging -(http://www.ccppetmr.ac.uk/). +Project in Synergistic Reconstruction for Biomedical Imaging (formerly CCP PETMR) +(http://www.ccpsynerbi.ac.uk/). Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. @@ -57,7 +57,7 @@ IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. \brief Utilities for data exchange between SIRF and Gadgetron server. \author Evgueni Ovtchinnikov -\author CCP PETMR +\author SyneRBI */ #ifndef GADGETRON_CLIENT diff --git a/src/xGadgetron/cGadgetron/include/sirf/Gadgetron/gadgetron_data_containers.h b/src/xGadgetron/cGadgetron/include/sirf/Gadgetron/gadgetron_data_containers.h index b7194cd8a..3a75db028 100644 --- a/src/xGadgetron/cGadgetron/include/sirf/Gadgetron/gadgetron_data_containers.h +++ b/src/xGadgetron/cGadgetron/include/sirf/Gadgetron/gadgetron_data_containers.h @@ -1,10 +1,12 @@ /* -CCP PETMR Synergistic Image Reconstruction Framework (SIRF) -Copyright 2015 - 2017 Rutherford Appleton Laboratory STFC +SyneRBI Synergistic Image Reconstruction Framework (SIRF) +Copyright 2015 - 2020 Rutherford Appleton Laboratory STFC +Copyright 2020 University College London +Copyright 2020 Physikalisch-Technische Bundesanstalt (PTB) This is software developed for the Collaborative Computational -Project in Positron Emission Tomography and Magnetic Resonance imaging -(http://www.ccppetmr.ac.uk/). +Project in Synergistic Reconstruction for Biomedical Imaging (formerly CCP PETMR) +(http://www.ccpsynerbi.ac.uk/). Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. @@ -24,7 +26,7 @@ limitations under the License. \brief Specification file for data container classes for Gadgetron data. \author Evgueni Ovtchinnikov -\author CCP PETMR +\author SyneRBI */ #ifndef GADGETRON_DATA_CONTAINERS diff --git a/src/xGadgetron/cGadgetron/include/sirf/Gadgetron/gadgetron_image_wrap.h b/src/xGadgetron/cGadgetron/include/sirf/Gadgetron/gadgetron_image_wrap.h index 182e5537c..23f9c226d 100644 --- a/src/xGadgetron/cGadgetron/include/sirf/Gadgetron/gadgetron_image_wrap.h +++ b/src/xGadgetron/cGadgetron/include/sirf/Gadgetron/gadgetron_image_wrap.h @@ -1,10 +1,11 @@ /* -CCP PETMR Synergistic Image Reconstruction Framework (SIRF) -Copyright 2015 - 2017 Rutherford Appleton Laboratory STFC +SyneRBI Synergistic Image Reconstruction Framework (SIRF) +Copyright 2015 - 2020 Rutherford Appleton Laboratory STFC +Copyright 2020 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/). +Project in Synergistic Reconstruction for Biomedical Imaging (formerly CCP PETMR) +(http://www.ccpsynerbi.ac.uk/). Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. @@ -24,7 +25,7 @@ limitations under the License. \brief Specification file for a wrapper class for ISMRMRD::Image. \author Evgueni Ovtchinnikov -\author CCP PETMR +\author SyneRBI */ #ifndef GADGETRON_IMAGE_WRAP_TYPE @@ -789,4 +790,4 @@ namespace sirf { }; } -#endif \ No newline at end of file +#endif diff --git a/src/xGadgetron/cGadgetron/include/sirf/Gadgetron/gadgetron_x.h b/src/xGadgetron/cGadgetron/include/sirf/Gadgetron/gadgetron_x.h index c05a7c069..97c396e27 100644 --- a/src/xGadgetron/cGadgetron/include/sirf/Gadgetron/gadgetron_x.h +++ b/src/xGadgetron/cGadgetron/include/sirf/Gadgetron/gadgetron_x.h @@ -1,10 +1,10 @@ /* -CCP PETMR Synergistic Image Reconstruction Framework (SIRF) -Copyright 2015 - 2017 Rutherford Appleton Laboratory STFC +SyneRBI Synergistic Image Reconstruction Framework (SIRF) +Copyright 2015 - 2020 Rutherford Appleton Laboratory STFC This is software developed for the Collaborative Computational -Project in Positron Emission Tomography and Magnetic Resonance imaging -(http://www.ccppetmr.ac.uk/). +Project in Synergistic Reconstruction for Biomedical Imaging (formerly CCP PETMR) +(http://www.ccpsynerbi.ac.uk/). Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. @@ -24,7 +24,7 @@ limitations under the License. \brief Specification file for extended Gadgetron functionality classes. \author Evgueni Ovtchinnikov -\author CCP PETMR +\author SyneRBI */ #ifndef GADGETRON_EXTENSIONS diff --git a/src/xGadgetron/cGadgetron/include/sirf/Gadgetron/xgadgetron_utilities.h b/src/xGadgetron/cGadgetron/include/sirf/Gadgetron/xgadgetron_utilities.h index 452a86d6c..495cc1331 100644 --- a/src/xGadgetron/cGadgetron/include/sirf/Gadgetron/xgadgetron_utilities.h +++ b/src/xGadgetron/cGadgetron/include/sirf/Gadgetron/xgadgetron_utilities.h @@ -1,10 +1,10 @@ /* -CCP PETMR Synergistic Image Reconstruction Framework (SIRF) -Copyright 2015 - 2017 Rutherford Appleton Laboratory STFC +SyneRBI Synergistic Image Reconstruction Framework (SIRF) +Copyright 2015 - 2019 Rutherford Appleton Laboratory STFC This is software developed for the Collaborative Computational -Project in Positron Emission Tomography and Magnetic Resonance imaging -(http://www.ccppetmr.ac.uk/). +Project in Synergistic Reconstruction for Biomedical Imaging (formerly CCP PETMR) +(http://www.ccpsynerbi.ac.uk/). Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. @@ -24,7 +24,7 @@ limitations under the License. \brief Various utilities used by SIRF Gadgetron extensions. \author Evgueni Ovtchinnikov -\author CCP PETMR +\author SyneRBI */ #ifndef XGADGETRON_UTILITIES @@ -136,4 +136,4 @@ namespace sirf { } -#endif \ No newline at end of file +#endif diff --git a/src/xGadgetron/cGadgetron/shepp_logan_phantom.cpp b/src/xGadgetron/cGadgetron/shepp_logan_phantom.cpp index 4723e6522..88e0a67f5 100644 --- a/src/xGadgetron/cGadgetron/shepp_logan_phantom.cpp +++ b/src/xGadgetron/cGadgetron/shepp_logan_phantom.cpp @@ -1,10 +1,10 @@ /* -CCP PETMR Synergistic Image Reconstruction Framework (SIRF) -Copyright 2015 - 2017 Rutherford Appleton Laboratory STFC +SyneRBI Synergistic Image Reconstruction Framework (SIRF) +Copyright 2015 - 2019 Rutherford Appleton Laboratory STFC This is software developed for the Collaborative Computational -Project in Positron Emission Tomography and Magnetic Resonance imaging -(http://www.ccppetmr.ac.uk/). +Project in Synergistic Reconstruction for Biomedical Imaging (formerly CCP PETMR) +(http://www.ccpsynerbi.ac.uk/). Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. @@ -93,4 +93,4 @@ void generate_cartesian_shepp_logan(unsigned int matrix_size, unsigned int ncoil acq.available_channels() = ncoils; acq.center_sample() = (readout >> 1); -} \ No newline at end of file +} diff --git a/src/xGadgetron/cGadgetron/tests/CMakeLists.txt b/src/xGadgetron/cGadgetron/tests/CMakeLists.txt index ff24f0d52..d672b99dd 100644 --- a/src/xGadgetron/cGadgetron/tests/CMakeLists.txt +++ b/src/xGadgetron/cGadgetron/tests/CMakeLists.txt @@ -1,6 +1,6 @@ #======================================================================== # Author: Johannes Mayer -# Copyright 2016 University College London +# Copyright 2016 - 2020 University College London # Copyright 2020 Physikalisch-Technische Bundesanstalt Berlin # # Licensed under the Apache License, Version 2.0 (the "License"); diff --git a/src/xGadgetron/cGadgetron/tests/mrtests.cpp b/src/xGadgetron/cGadgetron/tests/mrtests.cpp index 2205ae9b7..4e8d985fa 100644 --- a/src/xGadgetron/cGadgetron/tests/mrtests.cpp +++ b/src/xGadgetron/cGadgetron/tests/mrtests.cpp @@ -1,3 +1,33 @@ +/* +SyneRBI Synergistic Image Reconstruction Framework (SIRF) +Copyright 2019 - 2020 Rutherford Appleton Laboratory STFC +Copyright 2019 - 2020 University College London + +This is software developed for the Collaborative Computational +Project in Synergistic Reconstruction for Biomedical Imaging (formerly CCP PETMR) +(http://www.ccpsynerbi.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. + +*/ + +/*! +\file +\ingroup Gadgetron Tests + +\author Evgueni Ovtchinnikov +\author Richard Brown +\author SyneRBI +*/ + #include #include diff --git a/src/xGadgetron/mGadgetron/+sirf/+Gadgetron/Acquisition.m b/src/xGadgetron/mGadgetron/+sirf/+Gadgetron/Acquisition.m index 23cab4ca7..3daa1d185 100644 --- a/src/xGadgetron/mGadgetron/+sirf/+Gadgetron/Acquisition.m +++ b/src/xGadgetron/mGadgetron/+sirf/+Gadgetron/Acquisition.m @@ -2,12 +2,12 @@ % INTERNAL USE ONLY. % Class for the ISMRMRD acquisition object. -% CCP PETMR Synergistic Image Reconstruction Framework (SIRF). +% SyneRBI Synergistic Image Reconstruction Framework (SIRF). % Copyright 2015 - 2017 Rutherford Appleton Laboratory STFC. % % This is software developed for the Collaborative Computational -% Project in Positron Emission Tomography and Magnetic Resonance imaging -% (http://www.ccppetmr.ac.uk/). +% Project in Synergistic Reconstruction for Biomedical Imaging (formerly CCP PETMR) +% (http://www.ccpsynerbi.ac.uk/). % % Licensed under the Apache License, Version 2.0 (the "License"); % you may not use this file except in compliance with the License. diff --git a/src/xGadgetron/mGadgetron/+sirf/+Gadgetron/AcquisitionData.m b/src/xGadgetron/mGadgetron/+sirf/+Gadgetron/AcquisitionData.m index a0e7813b1..24fce6e53 100644 --- a/src/xGadgetron/mGadgetron/+sirf/+Gadgetron/AcquisitionData.m +++ b/src/xGadgetron/mGadgetron/+sirf/+Gadgetron/AcquisitionData.m @@ -3,12 +3,12 @@ % Each item in the container is a complex array of acquisition % samples for each coil. -% CCP PETMR Synergistic Image Reconstruction Framework (SIRF). -% Copyright 2015 - 2017 Rutherford Appleton Laboratory STFC. +% SyneRBI Synergistic Image Reconstruction Framework (SIRF). +% Copyright 2015 - 2020 Rutherford Appleton Laboratory STFC. % % This is software developed for the Collaborative Computational -% Project in Positron Emission Tomography and Magnetic Resonance imaging -% (http://www.ccppetmr.ac.uk/). +% Project in Synergistic Reconstruction for Biomedical Imaging (formerly CCP PETMR) +% (http://www.ccpsynerbi.ac.uk/). % % Licensed under the Apache License, Version 2.0 (the "License"); % you may not use this file except in compliance with the License. diff --git a/src/xGadgetron/mGadgetron/+sirf/+Gadgetron/AcquisitionDataProcessor.m b/src/xGadgetron/mGadgetron/+sirf/+Gadgetron/AcquisitionDataProcessor.m index 0f48e110a..e156441b0 100644 --- a/src/xGadgetron/mGadgetron/+sirf/+Gadgetron/AcquisitionDataProcessor.m +++ b/src/xGadgetron/mGadgetron/+sirf/+Gadgetron/AcquisitionDataProcessor.m @@ -1,12 +1,12 @@ classdef AcquisitionDataProcessor < sirf.Gadgetron.GadgetChain % Class for a chain of gadgets that has AcquisitionData on input and output. -% CCP PETMR Synergistic Image Reconstruction Framework (SIRF). +% SyneRBI Synergistic Image Reconstruction Framework (SIRF). % Copyright 2015 - 2017 Rutherford Appleton Laboratory STFC. % % This is software developed for the Collaborative Computational -% Project in Positron Emission Tomography and Magnetic Resonance imaging -% (http://www.ccppetmr.ac.uk/). +% Project in Synergistic Reconstruction for Biomedical Imaging (formerly CCP PETMR) +% (http://www.ccpsynerbi.ac.uk/). % % Licensed under the Apache License, Version 2.0 (the "License"); % you may not use this file except in compliance with the License. diff --git a/src/xGadgetron/mGadgetron/+sirf/+Gadgetron/AcquisitionModel.m b/src/xGadgetron/mGadgetron/+sirf/+Gadgetron/AcquisitionModel.m index 1cea7a394..f8abe3608 100644 --- a/src/xGadgetron/mGadgetron/+sirf/+Gadgetron/AcquisitionModel.m +++ b/src/xGadgetron/mGadgetron/+sirf/+Gadgetron/AcquisitionModel.m @@ -3,12 +3,12 @@ % The MR acquisition model describes the transformation (encoding) % of image data into MR acquisitions -% CCP PETMR Synergistic Image Reconstruction Framework (SIRF). +% SyneRBI Synergistic Image Reconstruction Framework (SIRF). % Copyright 2015 - 2017 Rutherford Appleton Laboratory STFC. % % This is software developed for the Collaborative Computational -% Project in Positron Emission Tomography and Magnetic Resonance imaging -% (http://www.ccppetmr.ac.uk/). +% Project in Synergistic Reconstruction for Biomedical Imaging (formerly CCP PETMR) +% (http://www.ccpsynerbi.ac.uk/). % % Licensed under the Apache License, Version 2.0 (the "License"); % you may not use this file except in compliance with the License. diff --git a/src/xGadgetron/mGadgetron/+sirf/+Gadgetron/CartesianGRAPPAReconstructor.m b/src/xGadgetron/mGadgetron/+sirf/+Gadgetron/CartesianGRAPPAReconstructor.m index 409850f79..2f54af72d 100644 --- a/src/xGadgetron/mGadgetron/+sirf/+Gadgetron/CartesianGRAPPAReconstructor.m +++ b/src/xGadgetron/mGadgetron/+sirf/+Gadgetron/CartesianGRAPPAReconstructor.m @@ -1,12 +1,12 @@ classdef CartesianGRAPPAReconstructor < sirf.Gadgetron.Reconstructor % Class for the GRAPPA reconstructor from undersampled Cartesian raw data. -% CCP PETMR Synergistic Image Reconstruction Framework (SIRF). +% SyneRBI Synergistic Image Reconstruction Framework (SIRF). % Copyright 2015 - 2017 Rutherford Appleton Laboratory STFC. % % This is software developed for the Collaborative Computational -% Project in Positron Emission Tomography and Magnetic Resonance imaging -% (http://www.ccppetmr.ac.uk/). +% Project in Synergistic Reconstruction for Biomedical Imaging (formerly CCP PETMR) +% (http://www.ccpsynerbi.ac.uk/). % % Licensed under the Apache License, Version 2.0 (the "License"); % you may not use this file except in compliance with the License. diff --git a/src/xGadgetron/mGadgetron/+sirf/+Gadgetron/ClientConnector.m b/src/xGadgetron/mGadgetron/+sirf/+Gadgetron/ClientConnector.m index 17a75ca3e..6c7ba03e0 100644 --- a/src/xGadgetron/mGadgetron/+sirf/+Gadgetron/ClientConnector.m +++ b/src/xGadgetron/mGadgetron/+sirf/+Gadgetron/ClientConnector.m @@ -2,12 +2,12 @@ % ADVANCED USERS ONLY. % Class for Gadgetron client connector. -% CCP PETMR Synergistic Image Reconstruction Framework (SIRF). +% SyneRBI Synergistic Image Reconstruction Framework (SIRF). % Copyright 2015 - 2017 Rutherford Appleton Laboratory STFC. % % This is software developed for the Collaborative Computational -% Project in Positron Emission Tomography and Magnetic Resonance imaging -% (http://www.ccppetmr.ac.uk/). +% Project in Synergistic Reconstruction for Biomedical Imaging (formerly CCP PETMR) +% (http://www.ccpsynerbi.ac.uk/). % % Licensed under the Apache License, Version 2.0 (the "License"); % you may not use this file except in compliance with the License. diff --git a/src/xGadgetron/mGadgetron/+sirf/+Gadgetron/CoilSensitivityData.m b/src/xGadgetron/mGadgetron/+sirf/+Gadgetron/CoilSensitivityData.m index f38f01d2a..76d4d1fde 100644 --- a/src/xGadgetron/mGadgetron/+sirf/+Gadgetron/CoilSensitivityData.m +++ b/src/xGadgetron/mGadgetron/+sirf/+Gadgetron/CoilSensitivityData.m @@ -3,12 +3,12 @@ % Each item in the container is a 4D (x-y-z-coil) complex array of csm % values. -% CCP PETMR Synergistic Image Reconstruction Framework (SIRF). -% Copyright 2015 - 2017 Rutherford Appleton Laboratory STFC. +% SyneRBI Synergistic Image Reconstruction Framework (SIRF). +% Copyright 2015 - 2020 Rutherford Appleton Laboratory STFC. % % This is software developed for the Collaborative Computational -% Project in Positron Emission Tomography and Magnetic Resonance imaging -% (http://www.ccppetmr.ac.uk/). +% Project in Synergistic Reconstruction for Biomedical Imaging (formerly CCP PETMR) +% (http://www.ccpsynerbi.ac.uk/). % % Licensed under the Apache License, Version 2.0 (the "License"); % you may not use this file except in compliance with the License. diff --git a/src/xGadgetron/mGadgetron/+sirf/+Gadgetron/FullySampledCartesianReconstructor.m b/src/xGadgetron/mGadgetron/+sirf/+Gadgetron/FullySampledCartesianReconstructor.m index 72a71a4f5..47d8f527c 100644 --- a/src/xGadgetron/mGadgetron/+sirf/+Gadgetron/FullySampledCartesianReconstructor.m +++ b/src/xGadgetron/mGadgetron/+sirf/+Gadgetron/FullySampledCartesianReconstructor.m @@ -1,12 +1,12 @@ classdef FullySampledCartesianReconstructor < sirf.Gadgetron.Reconstructor % Class for a fully sampled Cartesian MR data reconstructor. -% CCP PETMR Synergistic Image Reconstruction Framework (SIRF). +% SyneRBI Synergistic Image Reconstruction Framework (SIRF). % Copyright 2015 - 2017 Rutherford Appleton Laboratory STFC. % % This is software developed for the Collaborative Computational -% Project in Positron Emission Tomography and Magnetic Resonance imaging -% (http://www.ccppetmr.ac.uk/). +% Project in Synergistic Reconstruction for Biomedical Imaging (formerly CCP PETMR) +% (http://www.ccpsynerbi.ac.uk/). % % Licensed under the Apache License, Version 2.0 (the "License"); % you may not use this file except in compliance with the License. diff --git a/src/xGadgetron/mGadgetron/+sirf/+Gadgetron/Gadget.m b/src/xGadgetron/mGadgetron/+sirf/+Gadgetron/Gadget.m index 1e5ec8d11..7c50e35f3 100644 --- a/src/xGadgetron/mGadgetron/+sirf/+Gadgetron/Gadget.m +++ b/src/xGadgetron/mGadgetron/+sirf/+Gadgetron/Gadget.m @@ -2,12 +2,12 @@ % ADVANCED USERS ONLY. % Class for Gadgetron gadgets. -% CCP PETMR Synergistic Image Reconstruction Framework (SIRF). +% SyneRBI Synergistic Image Reconstruction Framework (SIRF). % Copyright 2015 - 2017 Rutherford Appleton Laboratory STFC. % % This is software developed for the Collaborative Computational -% Project in Positron Emission Tomography and Magnetic Resonance imaging -% (http://www.ccppetmr.ac.uk/). +% Project in Synergistic Reconstruction for Biomedical Imaging (formerly CCP PETMR) +% (http://www.ccpsynerbi.ac.uk/). % % Licensed under the Apache License, Version 2.0 (the "License"); % you may not use this file except in compliance with the License. diff --git a/src/xGadgetron/mGadgetron/+sirf/+Gadgetron/GadgetChain.m b/src/xGadgetron/mGadgetron/+sirf/+Gadgetron/GadgetChain.m index c1af57543..446192380 100644 --- a/src/xGadgetron/mGadgetron/+sirf/+Gadgetron/GadgetChain.m +++ b/src/xGadgetron/mGadgetron/+sirf/+Gadgetron/GadgetChain.m @@ -2,12 +2,12 @@ % ADVANCED USERS ONLY. % Class for Gadgetron gadget chains. -% CCP PETMR Synergistic Image Reconstruction Framework (SIRF). -% Copyright 2015 - 2017 Rutherford Appleton Laboratory STFC. +% SyneRBI Synergistic Image Reconstruction Framework (SIRF). +% Copyright 2015 - 2020 Rutherford Appleton Laboratory STFC. % % This is software developed for the Collaborative Computational -% Project in Positron Emission Tomography and Magnetic Resonance imaging -% (http://www.ccppetmr.ac.uk/). +% Project in Synergistic Reconstruction for Biomedical Imaging (formerly CCP PETMR) +% (http://www.ccpsynerbi.ac.uk/). % % Licensed under the Apache License, Version 2.0 (the "License"); % you may not use this file except in compliance with the License. @@ -116,4 +116,4 @@ function set_gadget_property(self, id, property, value) sirf.Utilities.delete(hv) end end -end \ No newline at end of file +end diff --git a/src/xGadgetron/mGadgetron/+sirf/+Gadgetron/Image.m b/src/xGadgetron/mGadgetron/+sirf/+Gadgetron/Image.m index 7b16d4dcb..71d7514e2 100644 --- a/src/xGadgetron/mGadgetron/+sirf/+Gadgetron/Image.m +++ b/src/xGadgetron/mGadgetron/+sirf/+Gadgetron/Image.m @@ -2,12 +2,12 @@ % INTERNAL USE ONLY. % Class for the ISMRMRD image object. -% CCP PETMR Synergistic Image Reconstruction Framework (SIRF). +% SyneRBI Synergistic Image Reconstruction Framework (SIRF). % Copyright 2015 - 2017 Rutherford Appleton Laboratory STFC. % % This is software developed for the Collaborative Computational -% Project in Positron Emission Tomography and Magnetic Resonance imaging -% (http://www.ccppetmr.ac.uk/). +% Project in Synergistic Reconstruction for Biomedical Imaging (formerly CCP PETMR) +% (http://www.ccpsynerbi.ac.uk/). % % Licensed under the Apache License, Version 2.0 (the "License"); % you may not use this file except in compliance with the License. diff --git a/src/xGadgetron/mGadgetron/+sirf/+Gadgetron/ImageData.m b/src/xGadgetron/mGadgetron/+sirf/+Gadgetron/ImageData.m index 0aabd6aca..b0cca4491 100644 --- a/src/xGadgetron/mGadgetron/+sirf/+Gadgetron/ImageData.m +++ b/src/xGadgetron/mGadgetron/+sirf/+Gadgetron/ImageData.m @@ -1,12 +1,13 @@ classdef ImageData < sirf.SIRF.ImageData % Class for MR image data objects. -% CCP PETMR Synergistic Image Reconstruction Framework (SIRF). -% Copyright 2015 - 2017 Rutherford Appleton Laboratory STFC. -% +% SyneRBI Synergistic Image Reconstruction Framework (SIRF). +% Copyright 2015 - 2020 Rutherford Appleton Laboratory STFC. +% 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/). +% Project in Synergistic Reconstruction for Biomedical Imaging (formerly CCP PETMR) +% (http://www.ccpsynerbi.ac.uk/). % % Licensed under the Apache License, Version 2.0 (the "License"); % you may not use this file except in compliance with the License. diff --git a/src/xGadgetron/mGadgetron/+sirf/+Gadgetron/ImageDataProcessor.m b/src/xGadgetron/mGadgetron/+sirf/+Gadgetron/ImageDataProcessor.m index 8640d911d..f092eb228 100644 --- a/src/xGadgetron/mGadgetron/+sirf/+Gadgetron/ImageDataProcessor.m +++ b/src/xGadgetron/mGadgetron/+sirf/+Gadgetron/ImageDataProcessor.m @@ -1,12 +1,12 @@ classdef ImageDataProcessor < sirf.Gadgetron.GadgetChain % Class for a chain of gadgets that has ImageData on input and output. -% CCP PETMR Synergistic Image Reconstruction Framework (SIRF). +% SyneRBI Synergistic Image Reconstruction Framework (SIRF). % Copyright 2015 - 2017 Rutherford Appleton Laboratory STFC. % % This is software developed for the Collaborative Computational -% Project in Positron Emission Tomography and Magnetic Resonance imaging -% (http://www.ccppetmr.ac.uk/). +% Project in Synergistic Reconstruction for Biomedical Imaging (formerly CCP PETMR) +% (http://www.ccpsynerbi.ac.uk/). % % Licensed under the Apache License, Version 2.0 (the "License"); % you may not use this file except in compliance with the License. diff --git a/src/xGadgetron/mGadgetron/+sirf/+Gadgetron/Reconstructor.m b/src/xGadgetron/mGadgetron/+sirf/+Gadgetron/Reconstructor.m index 936a7f994..098d3d704 100644 --- a/src/xGadgetron/mGadgetron/+sirf/+Gadgetron/Reconstructor.m +++ b/src/xGadgetron/mGadgetron/+sirf/+Gadgetron/Reconstructor.m @@ -7,13 +7,13 @@ % process - performs the call to gadgetron % get_output - returns output -% CCP PETMR Synergistic Image Reconstruction Framework (SIRF). +% SyneRBI Synergistic Image Reconstruction Framework (SIRF). % Copyright 2015 - 2017 Rutherford Appleton Laboratory STFC. % Copyright 2015 - 2017 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/). +% Project in Synergistic Reconstruction for Biomedical Imaging (formerly CCP PETMR) +% (http://www.ccpsynerbi.ac.uk/). % % Licensed under the Apache License, Version 2.0 (the "License"); % you may not use this file except in compliance with the License. diff --git a/src/xGadgetron/mGadgetron/+sirf/+Gadgetron/preprocess_acquisition_data.m b/src/xGadgetron/mGadgetron/+sirf/+Gadgetron/preprocess_acquisition_data.m index 979e7e869..7afc469df 100644 --- a/src/xGadgetron/mGadgetron/+sirf/+Gadgetron/preprocess_acquisition_data.m +++ b/src/xGadgetron/mGadgetron/+sirf/+Gadgetron/preprocess_acquisition_data.m @@ -6,13 +6,13 @@ % - Remove oversampling along acquisition direction (RemoveROOversamplingGadget) -% CCP PETMR Synergistic Image Reconstruction Framework (SIRF). +% SyneRBI Synergistic Image Reconstruction Framework (SIRF). % Copyright 2015 - 2017 Rutherford Appleton Laboratory STFC. % Copyright 2015 - 2017 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/). +% Project in Synergistic Reconstruction for Biomedical Imaging (formerly CCP PETMR) +% (http://www.ccpsynerbi.ac.uk/). % % Licensed under the Apache License, Version 2.0 (the "License"); % you may not use this file except in compliance with the License. diff --git a/src/xGadgetron/mGadgetron/CMakeLists.txt b/src/xGadgetron/mGadgetron/CMakeLists.txt index e6995140d..e8f53e25d 100644 --- a/src/xGadgetron/mGadgetron/CMakeLists.txt +++ b/src/xGadgetron/mGadgetron/CMakeLists.txt @@ -1,6 +1,6 @@ #======================================================================== # Author: Kris Thielemans -# Copyright 2017 University College London +# Copyright 2017 - 2020 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. diff --git a/src/xGadgetron/mGadgetron/gmi/gmi_xgadgetron.cpp b/src/xGadgetron/mGadgetron/gmi/gmi_xgadgetron.cpp index 155839684..cd0ddd95d 100644 --- a/src/xGadgetron/mGadgetron/gmi/gmi_xgadgetron.cpp +++ b/src/xGadgetron/mGadgetron/gmi/gmi_xgadgetron.cpp @@ -1,10 +1,11 @@ /* -CCP PETMR Synergistic Image Reconstruction Framework (SIRF) -Copyright 2015 - 2017 Rutherford Appleton Laboratory STFC +SyneRBI Synergistic Image Reconstruction Framework (SIRF) +Copyright 2015 - 2018 Rutherford Appleton Laboratory STFC +Copyright 2020 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/). +Project in Synergistic Reconstruction for Biomedical Imaging (formerly CCP PETMR) +(http://www.ccpsynerbi.ac.uk/). Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. @@ -24,7 +25,7 @@ limitations under the License. \brief The executable for generating Matlab interface for cgadgetron library. \author Evgueni Ovtchinnikov -\author CCP PETMR +\author SyneRBI */ #include @@ -70,4 +71,4 @@ int main(int argc, char *argv[]) cout << "wrong input file format" << endl; return 1; } -} \ No newline at end of file +} diff --git a/src/xGadgetron/mGadgetron/tests/CMakeLists.txt b/src/xGadgetron/mGadgetron/tests/CMakeLists.txt index 322d0f6ae..ee5181d6e 100644 --- a/src/xGadgetron/mGadgetron/tests/CMakeLists.txt +++ b/src/xGadgetron/mGadgetron/tests/CMakeLists.txt @@ -1,9 +1,9 @@ #======================================================================== # Author: Evgueni Ovtchinnikov # Copyright 2017 University College London -# Copyright 2017 Science Technology Facilities Council +# Copyright 2017 - 2018 Science Technology Facilities Council # -# This file is part of the CCP PETMR Synergistic Image Reconstruction Framework (SIRF) SuperBuild. +# This file is part of the SyneRBI Synergistic Image Reconstruction Framework (SIRF) SuperBuild. # # Licensed under the Apache License, Version 2.0 (the "License"); # you may not use this file except in compliance with the License. diff --git a/src/xGadgetron/mGadgetron/tests/test1.m b/src/xGadgetron/mGadgetron/tests/test1.m index b4b6b1e1f..44f153e8b 100644 --- a/src/xGadgetron/mGadgetron/tests/test1.m +++ b/src/xGadgetron/mGadgetron/tests/test1.m @@ -4,13 +4,13 @@ % Fully sampled reconstruction and the illustration of the use of % Acquisition Model projections. -% CCP PETMR Synergistic Image Reconstruction Framework (SIRF). -% Copyright 2015 - 2017 Rutherford Appleton Laboratory STFC. -% Copyright 2015 - 2017 University College London. +% SyneRBI Synergistic Image Reconstruction Framework (SIRF). +% Copyright 2015 - 2019 Rutherford Appleton Laboratory STFC. +% Copyright 2015 - 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/). +% Project in Synergistic Reconstruction for Biomedical Imaging (formerly CCP PETMR) +% (http://www.ccpsynerbi.ac.uk/). % % Licensed under the Apache License, Version 2.0 (the "License"); % you may not use this file except in compliance with the License. diff --git a/src/xGadgetron/mGadgetron/tests/test2.m b/src/xGadgetron/mGadgetron/tests/test2.m index 0ca074109..455bfb417 100644 --- a/src/xGadgetron/mGadgetron/tests/test2.m +++ b/src/xGadgetron/mGadgetron/tests/test2.m @@ -4,13 +4,13 @@ % GRAPPA reconstruction and the illustration of the use of % Acquisition Model projections. -% CCP PETMR Synergistic Image Reconstruction Framework (SIRF). -% Copyright 2015 - 2017 Rutherford Appleton Laboratory STFC. +% SyneRBI Synergistic Image Reconstruction Framework (SIRF). +% Copyright 2015 - 2019 Rutherford Appleton Laboratory STFC. % Copyright 2015 - 2017 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/). +% Project in Synergistic Reconstruction for Biomedical Imaging (formerly CCP PETMR) +% (http://www.ccpsynerbi.ac.uk/). % % Licensed under the Apache License, Version 2.0 (the "License"); % you may not use this file except in compliance with the License. @@ -85,4 +85,4 @@ else fprintf('%d out of %d tests failed\n', failed, ntests); end -end \ No newline at end of file +end diff --git a/src/xGadgetron/pGadgetron/CMakeLists.txt b/src/xGadgetron/pGadgetron/CMakeLists.txt index c7f07f4f2..ef7f57fab 100644 --- a/src/xGadgetron/pGadgetron/CMakeLists.txt +++ b/src/xGadgetron/pGadgetron/CMakeLists.txt @@ -1,6 +1,6 @@ #======================================================================== # Author: Kris Thielemans -# Copyright 2016 University College London +# Copyright 2016 - 2019 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. diff --git a/src/xGadgetron/pGadgetron/Gadgetron.py b/src/xGadgetron/pGadgetron/Gadgetron.py index 85e6d1375..f356de73b 100644 --- a/src/xGadgetron/pGadgetron/Gadgetron.py +++ b/src/xGadgetron/pGadgetron/Gadgetron.py @@ -2,12 +2,13 @@ Object-Oriented wrap for the cGadgetron-to-Python interface pygadgetron.py ''' -# CCP PETMR Synergistic Image Reconstruction Framework (SIRF) -# Copyright 2015 - 2017 Rutherford Appleton Laboratory STFC +# SyneRBI Synergistic Image Reconstruction Framework (SIRF) +# Copyright 2015 - 2020 Rutherford Appleton Laboratory STFC +# Copyright 2018 - 2020 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/). +# Project in Synergistic Reconstruction for Biomedical Imaging (formerly CCP PETMR) +# (http://www.ccpsynerbi.ac.uk/). # # Licensed under the Apache License, Version 2.0 (the "License"); # you may not use this file except in compliance with the License. diff --git a/src/xGadgetron/pGadgetron/tests/CMakeLists.txt b/src/xGadgetron/pGadgetron/tests/CMakeLists.txt index 7f11df513..db2b47877 100644 --- a/src/xGadgetron/pGadgetron/tests/CMakeLists.txt +++ b/src/xGadgetron/pGadgetron/tests/CMakeLists.txt @@ -5,7 +5,7 @@ # Author: Casper da Costa-Luis # Copyright 2017 # -# This file is part of the CCP PETMR Synergistic Image Reconstruction Framework (SIRF) SuperBuild. +# This file is part of the SyneRBI Synergistic Image Reconstruction Framework (SIRF) SuperBuild. # # Licensed under the Apache License, Version 2.0 (the "License"); # you may not use this file except in compliance with the License. diff --git a/src/xSTIR/cSTIR/CMakeLists.txt b/src/xSTIR/cSTIR/CMakeLists.txt index 764793994..fd513bf00 100644 --- a/src/xSTIR/cSTIR/CMakeLists.txt +++ b/src/xSTIR/cSTIR/CMakeLists.txt @@ -1,6 +1,6 @@ #======================================================================== -# Author: Kris Thielemans -# Copyright 2016 - 2018 University College London +# Author: Kris Thielemans, Richard Brown +# Copyright 2016 - 2020 University College London # Copyright 2017, 2018 Science Technology Facilities Council # # Licensed under the Apache License, Version 2.0 (the "License"); diff --git a/src/xSTIR/cSTIR/cstir.cpp b/src/xSTIR/cSTIR/cstir.cpp index 99f6d2044..ae523e9a5 100644 --- a/src/xSTIR/cSTIR/cstir.cpp +++ b/src/xSTIR/cSTIR/cstir.cpp @@ -1,11 +1,11 @@ /* -CCP PETMR Synergistic Image Reconstruction Framework (SIRF) -Copyright 2015 - 2017 Rutherford Appleton Laboratory STFC -Copyright 2015 - 2017 University College London. +SyneRBI Synergistic Image Reconstruction Framework (SIRF) +Copyright 2017 - 2020 Rutherford Appleton Laboratory STFC +Copyright 2018 - 2020 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/). +Project in Synergistic Reconstruction for Biomedical Imaging (formerly CCP PETMR) +(http://www.ccpsynerbi.ac.uk/). Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. diff --git a/src/xSTIR/cSTIR/cstir_p.cpp b/src/xSTIR/cSTIR/cstir_p.cpp index 3ab3e27ed..4f783e96c 100644 --- a/src/xSTIR/cSTIR/cstir_p.cpp +++ b/src/xSTIR/cSTIR/cstir_p.cpp @@ -1,11 +1,11 @@ /* -CCP PETMR Synergistic Image Reconstruction Framework (SIRF) +SyneRBI Synergistic Image Reconstruction Framework (SIRF) Copyright 2015 - 2020 Rutherford Appleton Laboratory STFC Copyright 2019 - 2020 UCL This is software developed for the Collaborative Computational -Project in Positron Emission Tomography and Magnetic Resonance imaging -(http://www.ccppetmr.ac.uk/). +Project in Synergistic Reconstruction for Biomedical Imaging (formerly CCP PETMR) +(http://www.ccpsynerbi.ac.uk/). Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. diff --git a/src/xSTIR/cSTIR/cstir_tw.cpp b/src/xSTIR/cSTIR/cstir_tw.cpp index b8e4bc14a..3a48c2386 100644 --- a/src/xSTIR/cSTIR/cstir_tw.cpp +++ b/src/xSTIR/cSTIR/cstir_tw.cpp @@ -1,10 +1,10 @@ /* -CCP PETMR Synergistic Image Reconstruction Framework (SIRF) -Copyright 2015 - 2017 Rutherford Appleton Laboratory STFC +SyneRBI Synergistic Image Reconstruction Framework (SIRF) +Copyright 2015 - 2018 Rutherford Appleton Laboratory STFC This is software developed for the Collaborative Computational -Project in Positron Emission Tomography and Magnetic Resonance imaging -(http://www.ccppetmr.ac.uk/). +Project in Synergistic Reconstruction for Biomedical Imaging (formerly CCP PETMR) +(http://www.ccpsynerbi.ac.uk/). Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. diff --git a/src/xSTIR/cSTIR/include/sirf/STIR/cstir.h b/src/xSTIR/cSTIR/include/sirf/STIR/cstir.h index aa42d020d..5969ca83d 100644 --- a/src/xSTIR/cSTIR/include/sirf/STIR/cstir.h +++ b/src/xSTIR/cSTIR/include/sirf/STIR/cstir.h @@ -1,11 +1,11 @@ /* -CCP PETMR Synergistic Image Reconstruction Framework (SIRF) +SyneRBI Synergistic Image Reconstruction Framework (SIRF) Copyright 2015 - 2017 Rutherford Appleton Laboratory STFC Copyright 2015 - 2017 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/). +Project in Synergistic Reconstruction for Biomedical Imaging (formerly CCP PETMR) +(http://www.ccpsynerbi.ac.uk/). Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. diff --git a/src/xSTIR/cSTIR/include/sirf/STIR/cstir_p.h b/src/xSTIR/cSTIR/include/sirf/STIR/cstir_p.h index b51c7dba8..e9b98a069 100644 --- a/src/xSTIR/cSTIR/include/sirf/STIR/cstir_p.h +++ b/src/xSTIR/cSTIR/include/sirf/STIR/cstir_p.h @@ -1,10 +1,11 @@ /* -CCP PETMR Synergistic Image Reconstruction Framework (SIRF) -Copyright 2015 - 2017 Rutherford Appleton Laboratory STFC +SyneRBI Synergistic Image Reconstruction Framework (SIRF) +Copyright 2015 - 2019 Rutherford Appleton Laboratory STFC +Copyright 2017 - 2020 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/). +Project in Synergistic Reconstruction for Biomedical Imaging (formerly CCP PETMR) +(http://www.ccpsynerbi.ac.uk/). Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. @@ -151,4 +152,4 @@ namespace sirf { } -#endif \ No newline at end of file +#endif diff --git a/src/xSTIR/cSTIR/include/sirf/STIR/stir_data_containers.h b/src/xSTIR/cSTIR/include/sirf/STIR/stir_data_containers.h index 0fd55dd50..566054335 100644 --- a/src/xSTIR/cSTIR/include/sirf/STIR/stir_data_containers.h +++ b/src/xSTIR/cSTIR/include/sirf/STIR/stir_data_containers.h @@ -1,11 +1,11 @@ /* -CCP PETMR Synergistic Image Reconstruction Framework (SIRF) +SyneRBI Synergistic Image Reconstruction Framework (SIRF) Copyright 2015 - 2019 Rutherford Appleton Laboratory STFC -Copyright (C) 2018 - 2020 University College London +Copyright 2018 - 2020 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/). +Project in Synergistic Reconstruction for Biomedical Imaging (formerly CCP PETMR) +(http://www.ccpsynerbi.ac.uk/). Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. @@ -26,7 +26,7 @@ limitations under the License. \author Evgueni Ovtchinnikov \author Richard Brown -\author CCP PETMR +\author SyneRBI */ #ifndef STIR_DATA_CONTAINER_TYPES diff --git a/src/xSTIR/cSTIR/include/sirf/STIR/stir_types.h b/src/xSTIR/cSTIR/include/sirf/STIR/stir_types.h index 69819a1b1..885606221 100644 --- a/src/xSTIR/cSTIR/include/sirf/STIR/stir_types.h +++ b/src/xSTIR/cSTIR/include/sirf/STIR/stir_types.h @@ -1,10 +1,11 @@ /* -CCP PETMR Synergistic Image Reconstruction Framework (SIRF) -Copyright 2015 - 2017 Rutherford Appleton Laboratory STFC +SyneRBI Synergistic Image Reconstruction Framework (SIRF) +Copyright 2015 - 2019 Rutherford Appleton Laboratory STFC +Copyright 2019 - 2020 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/). +Project in Synergistic Reconstruction for Biomedical Imaging (formerly CCP PETMR) +(http://www.ccpsynerbi.ac.uk/). Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. @@ -100,4 +101,4 @@ namespace sirf { } -#endif \ No newline at end of file +#endif diff --git a/src/xSTIR/cSTIR/include/sirf/STIR/stir_x.h b/src/xSTIR/cSTIR/include/sirf/STIR/stir_x.h index 1f35b9347..7d69d61a9 100644 --- a/src/xSTIR/cSTIR/include/sirf/STIR/stir_x.h +++ b/src/xSTIR/cSTIR/include/sirf/STIR/stir_x.h @@ -1,10 +1,11 @@ /* -CCP PETMR Synergistic Image Reconstruction Framework (SIRF) -Copyright 2015 - 2017 Rutherford Appleton Laboratory STFC +SyneRBI Synergistic Image Reconstruction Framework (SIRF) +Copyright 2015 - 2020 Rutherford Appleton Laboratory STFC +Copyright 2019 - 2020 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/). +Project in Synergistic Reconstruction for Biomedical Imaging (formerly CCP PETMR) +(http://www.ccpsynerbi.ac.uk/). Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. @@ -29,7 +30,7 @@ limitations under the License. \brief Specification file for extended STIR functionality classes. \author Evgueni Ovtchinnikov -\author CCP PETMR +\author SyneRBI */ #include diff --git a/src/xSTIR/cSTIR/stir_data_containers.cpp b/src/xSTIR/cSTIR/stir_data_containers.cpp index e94e5511e..472746339 100644 --- a/src/xSTIR/cSTIR/stir_data_containers.cpp +++ b/src/xSTIR/cSTIR/stir_data_containers.cpp @@ -1,11 +1,11 @@ /* -CCP PETMR Synergistic Image Reconstruction Framework (SIRF) -Copyright 2015 - 2017 Rutherford Appleton Laboratory STFC -Copyright 2018 University College London +SyneRBI Synergistic Image Reconstruction Framework (SIRF) +Copyright 2017 - 2019 Rutherford Appleton Laboratory STFC +Copyright 2018 - 2020 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/). +Project in Synergistic Reconstruction for Biomedical Imaging (formerly CCP PETMR) +(http://www.ccpsynerbi.ac.uk/). Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. diff --git a/src/xSTIR/cSTIR/stir_x.cpp b/src/xSTIR/cSTIR/stir_x.cpp index b17082167..0c2554c6b 100644 --- a/src/xSTIR/cSTIR/stir_x.cpp +++ b/src/xSTIR/cSTIR/stir_x.cpp @@ -1,11 +1,11 @@ /* -CCP PETMR Synergistic Image Reconstruction Framework (SIRF) -Copyright 2015 - 2017 Rutherford Appleton Laboratory STFC -Copyright 2015 - 2017 University College London. +SyneRBI Synergistic Image Reconstruction Framework (SIRF) +Copyright 2015 - 2020 Rutherford Appleton Laboratory STFC +Copyright 2015 - 2020 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/). +Project in Synergistic Reconstruction for Biomedical Imaging (formerly CCP PETMR) +(http://www.ccpsynerbi.ac.uk/). Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. diff --git a/src/xSTIR/cSTIR/tests/CMakeLists.txt b/src/xSTIR/cSTIR/tests/CMakeLists.txt index 0680bd17b..4818ba19d 100644 --- a/src/xSTIR/cSTIR/tests/CMakeLists.txt +++ b/src/xSTIR/cSTIR/tests/CMakeLists.txt @@ -1,6 +1,6 @@ #======================================================================== # Author: Kris Thielemans -# Copyright 2016 University College London +# Copyright 2016, 2018 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. diff --git a/src/xSTIR/cSTIR/tests/envar.h b/src/xSTIR/cSTIR/tests/envar.h index c60648977..5afa1f0fd 100644 --- a/src/xSTIR/cSTIR/tests/envar.h +++ b/src/xSTIR/cSTIR/tests/envar.h @@ -1,10 +1,10 @@ /* -CCP PETMR Synergistic Image Reconstruction Framework (SIRF) +SyneRBI Synergistic Image Reconstruction Framework (SIRF) Copyright 2015 - 2017 Rutherford Appleton Laboratory STFC This is software developed for the Collaborative Computational -Project in Positron Emission Tomography and Magnetic Resonance imaging -(http://www.ccppetmr.ac.uk/). +Project in Synergistic Reconstruction for Biomedical Imaging (formerly CCP PETMR) +(http://www.ccpsynerbi.ac.uk/). Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. diff --git a/src/xSTIR/cSTIR/tests/test1.cpp b/src/xSTIR/cSTIR/tests/test1.cpp index 89cb63df4..0e9c9f213 100644 --- a/src/xSTIR/cSTIR/tests/test1.cpp +++ b/src/xSTIR/cSTIR/tests/test1.cpp @@ -1,3 +1,32 @@ +/* +SyneRBI Synergistic Image Reconstruction Framework (SIRF) +Copyright 2018 Rutherford Appleton Laboratory STFC +Copyright 2018 - 2020 University College London + +This is software developed for the Collaborative Computational +Project in Synergistic Reconstruction for Biomedical Imaging (formerly CCP PETMR) +(http://www.ccpsynerbi.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. + +*/ + +/*! +\file +\ingroup STIR Tests + +\author Evgueni Ovtchinnikov +\author Richard Brown +\author SyneRBI +*/ #include #include diff --git a/src/xSTIR/cSTIR/tests/test2.cpp b/src/xSTIR/cSTIR/tests/test2.cpp index 9a2faa9b1..a53cd9bc6 100644 --- a/src/xSTIR/cSTIR/tests/test2.cpp +++ b/src/xSTIR/cSTIR/tests/test2.cpp @@ -1,3 +1,30 @@ +/* +SyneRBI Synergistic Image Reconstruction Framework (SIRF) +Copyright 2017 - 2018 Rutherford Appleton Laboratory STFC + +This is software developed for the Collaborative Computational +Project in Synergistic Reconstruction for Biomedical Imaging (formerly CCP PETMR) +(http://www.ccpsynerbi.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. + +*/ + +/*! +\file +\ingroup STIR Tests + +\author Evgueni Ovtchinnikov +\author SyneRBI +*/ #include #include "stir/common.h" diff --git a/src/xSTIR/cSTIR/tests/test3.cpp b/src/xSTIR/cSTIR/tests/test3.cpp index 7eeb1197c..00244813b 100644 --- a/src/xSTIR/cSTIR/tests/test3.cpp +++ b/src/xSTIR/cSTIR/tests/test3.cpp @@ -1,3 +1,30 @@ +/* +SyneRBI Synergistic Image Reconstruction Framework (SIRF) +Copyright 2018 Rutherford Appleton Laboratory STFC + +This is software developed for the Collaborative Computational +Project in Synergistic Reconstruction for Biomedical Imaging (formerly CCP PETMR) +(http://www.ccpsynerbi.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. + +*/ + +/*! +\file +\ingroup STIR Tests + +\author Evgueni Ovtchinnikov +\author SyneRBI +*/ #include #include @@ -178,4 +205,4 @@ int test3d() { } return 0; -} \ No newline at end of file +} diff --git a/src/xSTIR/cSTIR/tests/test4.cpp b/src/xSTIR/cSTIR/tests/test4.cpp index a0fb9811e..682f79293 100644 --- a/src/xSTIR/cSTIR/tests/test4.cpp +++ b/src/xSTIR/cSTIR/tests/test4.cpp @@ -1,3 +1,32 @@ +/* +SyneRBI Synergistic Image Reconstruction Framework (SIRF) +Copyright 2018 - 2020 Rutherford Appleton Laboratory STFC +Copyright 2018 - 2020 University College London + +This is software developed for the Collaborative Computational +Project in Synergistic Reconstruction for Biomedical Imaging (formerly CCP PETMR) +(http://www.ccpsynerbi.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. + +*/ + +/*! +\file +\ingroup STIR Tests + +\author Evgueni Ovtchinnikov +\author Richard Brown +\author SyneRBI +*/ #include #include @@ -118,4 +147,4 @@ int main() { return test4(); //return test5(); -} \ No newline at end of file +} diff --git a/src/xSTIR/cSTIR/tests/test5.cpp b/src/xSTIR/cSTIR/tests/test5.cpp index bdf7eca48..196fca04c 100644 --- a/src/xSTIR/cSTIR/tests/test5.cpp +++ b/src/xSTIR/cSTIR/tests/test5.cpp @@ -1,3 +1,30 @@ +/* +SyneRBI Synergistic Image Reconstruction Framework (SIRF) +Copyright 2018 Rutherford Appleton Laboratory STFC + +This is software developed for the Collaborative Computational +Project in Synergistic Reconstruction for Biomedical Imaging (formerly CCP PETMR) +(http://www.ccpsynerbi.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. + +*/ + +/*! +\file +\ingroup STIR Tests + +\author Evgueni Ovtchinnikov +\author SyneRBI +*/ #include //#include "stir/common.h" diff --git a/src/xSTIR/mSTIR/+sirf/+STIR/AcquisitionData.m b/src/xSTIR/mSTIR/+sirf/+STIR/AcquisitionData.m index eb6861b57..ecdb1a6c8 100644 --- a/src/xSTIR/mSTIR/+sirf/+STIR/AcquisitionData.m +++ b/src/xSTIR/mSTIR/+sirf/+STIR/AcquisitionData.m @@ -1,12 +1,13 @@ classdef AcquisitionData < sirf.SIRF.DataContainer % Class for PET acquisition data objects. -% CCP PETMR Synergistic Image Reconstruction Framework (SIRF). -% Copyright 2015 - 2017 Rutherford Appleton Laboratory STFC. +% SyneRBI Synergistic Image Reconstruction Framework (SIRF). +% Copyright 2015 - 2019 Rutherford Appleton Laboratory STFC. +% Copyright 2018 - 2020 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/). +% Project in Synergistic Reconstruction for Biomedical Imaging (formerly CCP PETMR) +% (http://www.ccpsynerbi.ac.uk/). % % Licensed under the Apache License, Version 2.0 (the "License"); % you may not use this file except in compliance with the License. diff --git a/src/xSTIR/mSTIR/+sirf/+STIR/AcquisitionModel.m b/src/xSTIR/mSTIR/+sirf/+STIR/AcquisitionModel.m index b9222e0fb..a02a39063 100644 --- a/src/xSTIR/mSTIR/+sirf/+STIR/AcquisitionModel.m +++ b/src/xSTIR/mSTIR/+sirf/+STIR/AcquisitionModel.m @@ -16,12 +16,12 @@ % (B) z = G' [1/n] y % where G' is the transpose of G, is referred to as backprojection. -% CCP PETMR Synergistic Image Reconstruction Framework (SIRF). +% SyneRBI Synergistic Image Reconstruction Framework (SIRF). % Copyright 2015 - 2017 Rutherford Appleton Laboratory STFC. % % This is software developed for the Collaborative Computational -% Project in Positron Emission Tomography and Magnetic Resonance imaging -% (http://www.ccppetmr.ac.uk/). +% Project in Synergistic Reconstruction for Biomedical Imaging (formerly CCP PETMR) +% (http://www.ccpsynerbi.ac.uk/). % % Licensed under the Apache License, Version 2.0 (the "License"); % you may not use this file except in compliance with the License. diff --git a/src/xSTIR/mSTIR/+sirf/+STIR/AcquisitionModelUsingMatrix.m b/src/xSTIR/mSTIR/+sirf/+STIR/AcquisitionModelUsingMatrix.m index eafb61ac8..beb19fdc7 100644 --- a/src/xSTIR/mSTIR/+sirf/+STIR/AcquisitionModelUsingMatrix.m +++ b/src/xSTIR/mSTIR/+sirf/+STIR/AcquisitionModelUsingMatrix.m @@ -3,12 +3,12 @@ % Class for PET acquisition model with the geometric projection G % represented by a sparse matrix - see AcquisitionModel. -% CCP PETMR Synergistic Image Reconstruction Framework (SIRF). +% SyneRBI Synergistic Image Reconstruction Framework (SIRF). % Copyright 2015 - 2017 Rutherford Appleton Laboratory STFC. % % This is software developed for the Collaborative Computational -% Project in Positron Emission Tomography and Magnetic Resonance imaging -% (http://www.ccppetmr.ac.uk/). +% Project in Synergistic Reconstruction for Biomedical Imaging (formerly CCP PETMR) +% (http://www.ccpsynerbi.ac.uk/). % % Licensed under the Apache License, Version 2.0 (the "License"); % you may not use this file except in compliance with the License. diff --git a/src/xSTIR/mSTIR/+sirf/+STIR/AcquisitionModelUsingRayTracingMatrix.m b/src/xSTIR/mSTIR/+sirf/+STIR/AcquisitionModelUsingRayTracingMatrix.m index 4799ce1f0..c71c4e887 100644 --- a/src/xSTIR/mSTIR/+sirf/+STIR/AcquisitionModelUsingRayTracingMatrix.m +++ b/src/xSTIR/mSTIR/+sirf/+STIR/AcquisitionModelUsingRayTracingMatrix.m @@ -2,12 +2,12 @@ sirf.STIR.AcquisitionModelUsingMatrix % Class for PET acquisition model using the ray tracing projection matrix. -% CCP PETMR Synergistic Image Reconstruction Framework (SIRF). +% SyneRBI Synergistic Image Reconstruction Framework (SIRF). % Copyright 2015 - 2017 Rutherford Appleton Laboratory STFC. % % This is software developed for the Collaborative Computational -% Project in Positron Emission Tomography and Magnetic Resonance imaging -% (http://www.ccppetmr.ac.uk/). +% Project in Synergistic Reconstruction for Biomedical Imaging (formerly CCP PETMR) +% (http://www.ccpsynerbi.ac.uk/). % % Licensed under the Apache License, Version 2.0 (the "License"); % you may not use this file except in compliance with the License. diff --git a/src/xSTIR/mSTIR/+sirf/+STIR/AcquisitionSensitivityModel.m b/src/xSTIR/mSTIR/+sirf/+STIR/AcquisitionSensitivityModel.m index ad4fb12cc..71708a887 100644 --- a/src/xSTIR/mSTIR/+sirf/+STIR/AcquisitionSensitivityModel.m +++ b/src/xSTIR/mSTIR/+sirf/+STIR/AcquisitionSensitivityModel.m @@ -1,12 +1,12 @@ classdef AcquisitionSensitivityModel < handle % Class for PET acquisition sensitivity model objects. -% CCP PETMR Synergistic Image Reconstruction Framework (SIRF). +% SyneRBI Synergistic Image Reconstruction Framework (SIRF). % Copyright 2015 - 2017 Rutherford Appleton Laboratory STFC. % % This is software developed for the Collaborative Computational -% Project in Positron Emission Tomography and Magnetic Resonance imaging -% (http://www.ccppetmr.ac.uk/). +% Project in Synergistic Reconstruction for Biomedical Imaging (formerly CCP PETMR) +% (http://www.ccpsynerbi.ac.uk/). % % Licensed under the Apache License, Version 2.0 (the "License"); % you may not use this file except in compliance with the License. diff --git a/src/xSTIR/mSTIR/+sirf/+STIR/EllipticCylinder.m b/src/xSTIR/mSTIR/+sirf/+STIR/EllipticCylinder.m index 5ffd5e231..54df604fb 100644 --- a/src/xSTIR/mSTIR/+sirf/+STIR/EllipticCylinder.m +++ b/src/xSTIR/mSTIR/+sirf/+STIR/EllipticCylinder.m @@ -1,12 +1,12 @@ classdef EllipticCylinder < sirf.STIR.Shape % Class for elliptic cylinder shape. -% CCP PETMR Synergistic Image Reconstruction Framework (SIRF). +% SyneRBI Synergistic Image Reconstruction Framework (SIRF). % Copyright 2015 - 2017 Rutherford Appleton Laboratory STFC. % % This is software developed for the Collaborative Computational -% Project in Positron Emission Tomography and Magnetic Resonance imaging -% (http://www.ccppetmr.ac.uk/). +% Project in Synergistic Reconstruction for Biomedical Imaging (formerly CCP PETMR) +% (http://www.ccpsynerbi.ac.uk/). % % Licensed under the Apache License, Version 2.0 (the "License"); % you may not use this file except in compliance with the License. diff --git a/src/xSTIR/mSTIR/+sirf/+STIR/FBP2DReconstructor.m b/src/xSTIR/mSTIR/+sirf/+STIR/FBP2DReconstructor.m index 60d58b42e..d67020aad 100644 --- a/src/xSTIR/mSTIR/+sirf/+STIR/FBP2DReconstructor.m +++ b/src/xSTIR/mSTIR/+sirf/+STIR/FBP2DReconstructor.m @@ -13,12 +13,12 @@ % % (alpha + (1 - alpha) * cos(pi * f / fc)) -% CCP PETMR Synergistic Image Reconstruction Framework (SIRF). +% SyneRBI Synergistic Image Reconstruction Framework (SIRF). % Copyright 2015 - 2017 Rutherford Appleton Laboratory STFC. % % This is software developed for the Collaborative Computational -% Project in Positron Emission Tomography and Magnetic Resonance imaging -% (http://www.ccppetmr.ac.uk/). +% Project in Synergistic Reconstruction for Biomedical Imaging (formerly CCP PETMR) +% (http://www.ccpsynerbi.ac.uk/). % % Licensed under the Apache License, Version 2.0 (the "License"); % you may not use this file except in compliance with the License. diff --git a/src/xSTIR/mSTIR/+sirf/+STIR/ImageData.m b/src/xSTIR/mSTIR/+sirf/+STIR/ImageData.m index b0b3ea331..25e517d0b 100644 --- a/src/xSTIR/mSTIR/+sirf/+STIR/ImageData.m +++ b/src/xSTIR/mSTIR/+sirf/+STIR/ImageData.m @@ -1,12 +1,13 @@ classdef ImageData < sirf.SIRF.ImageData % Class for PET image data objects. -% CCP PETMR Synergistic Image Reconstruction Framework (SIRF). -% Copyright 2015 - 2017 Rutherford Appleton Laboratory STFC. -% +% SyneRBI Synergistic Image Reconstruction Framework (SIRF). +% Copyright 2015 - 2020 Rutherford Appleton Laboratory STFC. +% Copyright 2015 - 2020 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/). +% Project in Synergistic Reconstruction for Biomedical Imaging (formerly CCP PETMR) +% (http://www.ccpsynerbi.ac.uk/). % % Licensed under the Apache License, Version 2.0 (the "License"); % you may not use this file except in compliance with the License. @@ -224,4 +225,4 @@ function show(self, z) end end end -end \ No newline at end of file +end diff --git a/src/xSTIR/mSTIR/+sirf/+STIR/ImageDataProcessor.m b/src/xSTIR/mSTIR/+sirf/+STIR/ImageDataProcessor.m index 57f95694e..aede4053a 100644 --- a/src/xSTIR/mSTIR/+sirf/+STIR/ImageDataProcessor.m +++ b/src/xSTIR/mSTIR/+sirf/+STIR/ImageDataProcessor.m @@ -1,12 +1,12 @@ classdef ImageDataProcessor < handle % Class for image processor objects (filters). -% CCP PETMR Synergistic Image Reconstruction Framework (SIRF). +% SyneRBI Synergistic Image Reconstruction Framework (SIRF). % Copyright 2015 - 2017 Rutherford Appleton Laboratory STFC. % % This is software developed for the Collaborative Computational -% Project in Positron Emission Tomography and Magnetic Resonance imaging -% (http://www.ccppetmr.ac.uk/). +% Project in Synergistic Reconstruction for Biomedical Imaging (formerly CCP PETMR) +% (http://www.ccpsynerbi.ac.uk/). % % Licensed under the Apache License, Version 2.0 (the "License"); % you may not use this file except in compliance with the License. diff --git a/src/xSTIR/mSTIR/+sirf/+STIR/IterativeReconstructor.m b/src/xSTIR/mSTIR/+sirf/+STIR/IterativeReconstructor.m index b10cc2198..b6a8ba706 100644 --- a/src/xSTIR/mSTIR/+sirf/+STIR/IterativeReconstructor.m +++ b/src/xSTIR/mSTIR/+sirf/+STIR/IterativeReconstructor.m @@ -4,12 +4,12 @@ % that is formed by components corresponding to subsets of the acquisition % data. -% CCP PETMR Synergistic Image Reconstruction Framework (SIRF). +% SyneRBI Synergistic Image Reconstruction Framework (SIRF). % Copyright 2015 - 2017 Rutherford Appleton Laboratory STFC. % % This is software developed for the Collaborative Computational -% Project in Positron Emission Tomography and Magnetic Resonance imaging -% (http://www.ccppetmr.ac.uk/). +% Project in Synergistic Reconstruction for Biomedical Imaging (formerly CCP PETMR) +% (http://www.ccpsynerbi.ac.uk/). % % Licensed under the Apache License, Version 2.0 (the "License"); % you may not use this file except in compliance with the License. diff --git a/src/xSTIR/mSTIR/+sirf/+STIR/ListmodeToSinograms.m b/src/xSTIR/mSTIR/+sirf/+STIR/ListmodeToSinograms.m index 42f9b84e7..2a5a326c1 100644 --- a/src/xSTIR/mSTIR/+sirf/+STIR/ListmodeToSinograms.m +++ b/src/xSTIR/mSTIR/+sirf/+STIR/ListmodeToSinograms.m @@ -28,12 +28,12 @@ % in 2002 IEEE Nuclear Science Symposium Conference Record, vol. 3. IEEE, % Nov. 2002, pp. 1519-1523 (http://dx.doi.org/10.1109/nssmic.2002.1239610). -% CCP PETMR Synergistic Image Reconstruction Framework (SIRF). +% SyneRBI Synergistic Image Reconstruction Framework (SIRF). % Copyright 2015 - 2017 Rutherford Appleton Laboratory STFC. % % This is software developed for the Collaborative Computational -% Project in Positron Emission Tomography and Magnetic Resonance imaging -% (http://www.ccppetmr.ac.uk/). +% Project in Synergistic Reconstruction for Biomedical Imaging (formerly CCP PETMR) +% (http://www.ccpsynerbi.ac.uk/). % % Licensed under the Apache License, Version 2.0 (the "License"); % you may not use this file except in compliance with the License. diff --git a/src/xSTIR/mSTIR/+sirf/+STIR/OSMAPOSLReconstructor.m b/src/xSTIR/mSTIR/+sirf/+STIR/OSMAPOSLReconstructor.m index 920345df5..cb7f6b8ec 100644 --- a/src/xSTIR/mSTIR/+sirf/+STIR/OSMAPOSLReconstructor.m +++ b/src/xSTIR/mSTIR/+sirf/+STIR/OSMAPOSLReconstructor.m @@ -3,12 +3,12 @@ % OSMAPOSL stands for Ordered Subsets Maximum A Posteriori One Step Late, see % http://stir.sourceforge.net/documentation/doxy/html/classstir_1_1OSMAPOSLReconstruction.html -% CCP PETMR Synergistic Image Reconstruction Framework (SIRF). +% SyneRBI Synergistic Image Reconstruction Framework (SIRF). % Copyright 2015 - 2017 Rutherford Appleton Laboratory STFC. % % This is software developed for the Collaborative Computational -% Project in Positron Emission Tomography and Magnetic Resonance imaging -% (http://www.ccppetmr.ac.uk/). +% Project in Synergistic Reconstruction for Biomedical Imaging (formerly CCP PETMR) +% (http://www.ccpsynerbi.ac.uk/). % % Licensed under the Apache License, Version 2.0 (the "License"); % you may not use this file except in compliance with the License. diff --git a/src/xSTIR/mSTIR/+sirf/+STIR/ObjectiveFunction.m b/src/xSTIR/mSTIR/+sirf/+STIR/ObjectiveFunction.m index 3d83ed19d..6c599fa5b 100644 --- a/src/xSTIR/mSTIR/+sirf/+STIR/ObjectiveFunction.m +++ b/src/xSTIR/mSTIR/+sirf/+STIR/ObjectiveFunction.m @@ -1,12 +1,12 @@ classdef ObjectiveFunction < handle % Class for the iterative reconstruction algorithms objective function. -% CCP PETMR Synergistic Image Reconstruction Framework (SIRF). +% SyneRBI Synergistic Image Reconstruction Framework (SIRF). % Copyright 2015 - 2017 Rutherford Appleton Laboratory STFC. % % This is software developed for the Collaborative Computational -% Project in Positron Emission Tomography and Magnetic Resonance imaging -% (http://www.ccppetmr.ac.uk/). +% Project in Synergistic Reconstruction for Biomedical Imaging (formerly CCP PETMR) +% (http://www.ccpsynerbi.ac.uk/). % % Licensed under the Apache License, Version 2.0 (the "License"); % you may not use this file except in compliance with the License. diff --git a/src/xSTIR/mSTIR/+sirf/+STIR/PoissonLogLikelihoodWithLinearModelForMean.m b/src/xSTIR/mSTIR/+sirf/+STIR/PoissonLogLikelihoodWithLinearModelForMean.m index a0e510423..9fb715835 100644 --- a/src/xSTIR/mSTIR/+sirf/+STIR/PoissonLogLikelihoodWithLinearModelForMean.m +++ b/src/xSTIR/mSTIR/+sirf/+STIR/PoissonLogLikelihoodWithLinearModelForMean.m @@ -3,12 +3,12 @@ % Class for STIR PoissonLogLikelihoodWithLinearModelForMean object, see % http://stir.sourceforge.net/documentation/doxy/html/classstir_1_1PoissonLogLikelihoodWithLinearModelForMean.html -% CCP PETMR Synergistic Image Reconstruction Framework (SIRF). +% SyneRBI Synergistic Image Reconstruction Framework (SIRF). % Copyright 2015 - 2017 Rutherford Appleton Laboratory STFC. % % This is software developed for the Collaborative Computational -% Project in Positron Emission Tomography and Magnetic Resonance imaging -% (http://www.ccppetmr.ac.uk/). +% Project in Synergistic Reconstruction for Biomedical Imaging (formerly CCP PETMR) +% (http://www.ccpsynerbi.ac.uk/). % % Licensed under the Apache License, Version 2.0 (the "License"); % you may not use this file except in compliance with the License. diff --git a/src/xSTIR/mSTIR/+sirf/+STIR/PoissonLogLikelihoodWithLinearModelForMeanAndProjData.m b/src/xSTIR/mSTIR/+sirf/+STIR/PoissonLogLikelihoodWithLinearModelForMeanAndProjData.m index d78d43912..ae22370ca 100644 --- a/src/xSTIR/mSTIR/+sirf/+STIR/PoissonLogLikelihoodWithLinearModelForMeanAndProjData.m +++ b/src/xSTIR/mSTIR/+sirf/+STIR/PoissonLogLikelihoodWithLinearModelForMeanAndProjData.m @@ -5,12 +5,12 @@ % see % http://stir.sourceforge.net/documentation/doxy/html/classstir_1_1PoissonLogLikelihoodWithLinearModelForMeanAndProjData.html -% CCP PETMR Synergistic Image Reconstruction Framework (SIRF). +% SyneRBI Synergistic Image Reconstruction Framework (SIRF). % Copyright 2015 - 2017 Rutherford Appleton Laboratory STFC. % % This is software developed for the Collaborative Computational -% Project in Positron Emission Tomography and Magnetic Resonance imaging -% (http://www.ccppetmr.ac.uk/). +% Project in Synergistic Reconstruction for Biomedical Imaging (formerly CCP PETMR) +% (http://www.ccpsynerbi.ac.uk/). % % Licensed under the Apache License, Version 2.0 (the "License"); % you may not use this file except in compliance with the License. diff --git a/src/xSTIR/mSTIR/+sirf/+STIR/Prior.m b/src/xSTIR/mSTIR/+sirf/+STIR/Prior.m index 4e48bfdb9..2ca830819 100644 --- a/src/xSTIR/mSTIR/+sirf/+STIR/Prior.m +++ b/src/xSTIR/mSTIR/+sirf/+STIR/Prior.m @@ -3,12 +3,12 @@ % The prior is a penalty term added to the objective function maximized % by iterative reconstruction algorithms. -% CCP PETMR Synergistic Image Reconstruction Framework (SIRF). +% SyneRBI Synergistic Image Reconstruction Framework (SIRF). % Copyright 2015 - 2017 Rutherford Appleton Laboratory STFC. % % This is software developed for the Collaborative Computational -% Project in Positron Emission Tomography and Magnetic Resonance imaging -% (http://www.ccppetmr.ac.uk/). +% Project in Synergistic Reconstruction for Biomedical Imaging (formerly CCP PETMR) +% (http://www.ccpsynerbi.ac.uk/). % % Licensed under the Apache License, Version 2.0 (the "License"); % you may not use this file except in compliance with the License. diff --git a/src/xSTIR/mSTIR/+sirf/+STIR/QuadraticPrior.m b/src/xSTIR/mSTIR/+sirf/+STIR/QuadraticPrior.m index 4629e371d..c53e972dd 100644 --- a/src/xSTIR/mSTIR/+sirf/+STIR/QuadraticPrior.m +++ b/src/xSTIR/mSTIR/+sirf/+STIR/QuadraticPrior.m @@ -1,12 +1,12 @@ classdef QuadraticPrior < sirf.STIR.Prior % Class for the prior that is a quadratic function of the image values. -% CCP PETMR Synergistic Image Reconstruction Framework (SIRF). +% SyneRBI Synergistic Image Reconstruction Framework (SIRF). % Copyright 2015 - 2017 Rutherford Appleton Laboratory STFC. % % This is software developed for the Collaborative Computational -% Project in Positron Emission Tomography and Magnetic Resonance imaging -% (http://www.ccppetmr.ac.uk/). +% Project in Synergistic Reconstruction for Biomedical Imaging (formerly CCP PETMR) +% (http://www.ccpsynerbi.ac.uk/). % % Licensed under the Apache License, Version 2.0 (the "License"); % you may not use this file except in compliance with the License. diff --git a/src/xSTIR/mSTIR/+sirf/+STIR/RayTracingMatrix.m b/src/xSTIR/mSTIR/+sirf/+STIR/RayTracingMatrix.m index 14e81d789..b6892827e 100644 --- a/src/xSTIR/mSTIR/+sirf/+STIR/RayTracingMatrix.m +++ b/src/xSTIR/mSTIR/+sirf/+STIR/RayTracingMatrix.m @@ -3,12 +3,12 @@ % holding sparse matrix representation of the ray % tracing projector G (see AcquisitionModel class). -% CCP PETMR Synergistic Image Reconstruction Framework (SIRF). +% SyneRBI Synergistic Image Reconstruction Framework (SIRF). % Copyright 2015 - 2017 Rutherford Appleton Laboratory STFC. % % This is software developed for the Collaborative Computational -% Project in Positron Emission Tomography and Magnetic Resonance imaging -% (http://www.ccppetmr.ac.uk/). +% Project in Synergistic Reconstruction for Biomedical Imaging (formerly CCP PETMR) +% (http://www.ccpsynerbi.ac.uk/). % % Licensed under the Apache License, Version 2.0 (the "License"); % you may not use this file except in compliance with the License. diff --git a/src/xSTIR/mSTIR/+sirf/+STIR/Reconstructor.m b/src/xSTIR/mSTIR/+sirf/+STIR/Reconstructor.m index 1ad8cea81..abb1f5c73 100644 --- a/src/xSTIR/mSTIR/+sirf/+STIR/Reconstructor.m +++ b/src/xSTIR/mSTIR/+sirf/+STIR/Reconstructor.m @@ -1,12 +1,12 @@ classdef Reconstructor < handle % Class for a generic PET reconstructor object. -% CCP PETMR Synergistic Image Reconstruction Framework (SIRF). +% SyneRBI Synergistic Image Reconstruction Framework (SIRF). % Copyright 2015 - 2017 Rutherford Appleton Laboratory STFC. % % This is software developed for the Collaborative Computational -% Project in Positron Emission Tomography and Magnetic Resonance imaging -% (http://www.ccppetmr.ac.uk/). +% Project in Synergistic Reconstruction for Biomedical Imaging (formerly CCP PETMR) +% (http://www.ccpsynerbi.ac.uk/). % % Licensed under the Apache License, Version 2.0 (the "License"); % you may not use this file except in compliance with the License. diff --git a/src/xSTIR/mSTIR/+sirf/+STIR/Shape.m b/src/xSTIR/mSTIR/+sirf/+STIR/Shape.m index 03b5dac1a..c2fdeeef5 100644 --- a/src/xSTIR/mSTIR/+sirf/+STIR/Shape.m +++ b/src/xSTIR/mSTIR/+sirf/+STIR/Shape.m @@ -2,12 +2,12 @@ % Class for an abstract geometric shape. % Objects of this class are used as building blocks for creating phantom images. -% CCP PETMR Synergistic Image Reconstruction Framework (SIRF). +% SyneRBI Synergistic Image Reconstruction Framework (SIRF). % Copyright 2015 - 2017 Rutherford Appleton Laboratory STFC. % % This is software developed for the Collaborative Computational -% Project in Positron Emission Tomography and Magnetic Resonance imaging -% (http://www.ccppetmr.ac.uk/). +% Project in Synergistic Reconstruction for Biomedical Imaging (formerly CCP PETMR) +% (http://www.ccpsynerbi.ac.uk/). % % Licensed under the Apache License, Version 2.0 (the "License"); % you may not use this file except in compliance with the License. diff --git a/src/xSTIR/mSTIR/+sirf/+STIR/TruncateToCylinderProcessor.m b/src/xSTIR/mSTIR/+sirf/+STIR/TruncateToCylinderProcessor.m index 7394130e4..fa59f8aa4 100644 --- a/src/xSTIR/mSTIR/+sirf/+STIR/TruncateToCylinderProcessor.m +++ b/src/xSTIR/mSTIR/+sirf/+STIR/TruncateToCylinderProcessor.m @@ -1,12 +1,12 @@ classdef TruncateToCylinderProcessor < sirf.STIR.ImageDataProcessor % Class for the image filter that zeroes the image outside a cylinder. -% CCP PETMR Synergistic Image Reconstruction Framework (SIRF). +% SyneRBI Synergistic Image Reconstruction Framework (SIRF). % Copyright 2015 - 2017 Rutherford Appleton Laboratory STFC. % % This is software developed for the Collaborative Computational -% Project in Positron Emission Tomography and Magnetic Resonance imaging -% (http://www.ccppetmr.ac.uk/). +% Project in Synergistic Reconstruction for Biomedical Imaging (formerly CCP PETMR) +% (http://www.ccpsynerbi.ac.uk/). % % Licensed under the Apache License, Version 2.0 (the "License"); % you may not use this file except in compliance with the License. diff --git a/src/xSTIR/mSTIR/+sirf/+STIR/make_Poisson_loglikelihood.m b/src/xSTIR/mSTIR/+sirf/+STIR/make_Poisson_loglikelihood.m index b63958e92..b0c37a8bb 100644 --- a/src/xSTIR/mSTIR/+sirf/+STIR/make_Poisson_loglikelihood.m +++ b/src/xSTIR/mSTIR/+sirf/+STIR/make_Poisson_loglikelihood.m @@ -6,12 +6,12 @@ % returns an objective function appropriate for the % specified acquisition data. -% CCP PETMR Synergistic Image Reconstruction Framework (SIRF). +% SyneRBI Synergistic Image Reconstruction Framework (SIRF). % Copyright 2015 - 2017 Rutherford Appleton Laboratory STFC. % % This is software developed for the Collaborative Computational -% Project in Positron Emission Tomography and Magnetic Resonance imaging -% (http://www.ccppetmr.ac.uk/). +% Project in Synergistic Reconstruction for Biomedical Imaging (formerly CCP PETMR) +% (http://www.ccpsynerbi.ac.uk/). % % Licensed under the Apache License, Version 2.0 (the "License"); % you may not use this file except in compliance with the License. diff --git a/src/xSTIR/mSTIR/CMakeLists.txt b/src/xSTIR/mSTIR/CMakeLists.txt index db7ed19f0..2b81777e3 100644 --- a/src/xSTIR/mSTIR/CMakeLists.txt +++ b/src/xSTIR/mSTIR/CMakeLists.txt @@ -1,6 +1,6 @@ #======================================================================== -# Author: Kris Thielemans -# Copyright 2017 University College London +# Author: Kris Thielemans, Richard Brown +# Copyright 2017 - 2020 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. diff --git a/src/xSTIR/mSTIR/gmi/gmi_xstir.cpp b/src/xSTIR/mSTIR/gmi/gmi_xstir.cpp index 40cc98562..af3700e3d 100644 --- a/src/xSTIR/mSTIR/gmi/gmi_xstir.cpp +++ b/src/xSTIR/mSTIR/gmi/gmi_xstir.cpp @@ -1,10 +1,11 @@ /* -CCP PETMR Synergistic Image Reconstruction Framework (SIRF) -Copyright 2015 - 2017 Rutherford Appleton Laboratory STFC +SyneRBI Synergistic Image Reconstruction Framework (SIRF) +Copyright 2015 - 2019 Rutherford Appleton Laboratory STFC +Copyright 2020 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/). +Project in Synergistic Reconstruction for Biomedical Imaging (formerly CCP PETMR) +(http://www.ccpsynerbi.ac.uk/). Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. @@ -24,7 +25,7 @@ limitations under the License. \brief The executable for generating Matlab interface for cstir library. \author Evgueni Ovtchinnikov -\author CCP PETMR +\author SyneRBI */ #include @@ -70,4 +71,4 @@ int main(int argc, char *argv[]) cout << "wrong input file format" << endl; return 1; } -} \ No newline at end of file +} diff --git a/src/xSTIR/mSTIR/printer.cpp b/src/xSTIR/mSTIR/printer.cpp index b19b89395..d61fbd32d 100644 --- a/src/xSTIR/mSTIR/printer.cpp +++ b/src/xSTIR/mSTIR/printer.cpp @@ -1,9 +1,9 @@ /* -CCP PETMR Synergistic Image Reconstruction Framework (SIRF) -Copyright 2015 - 2017 Rutherford Appleton Laboratory STFC +SyneRBI Synergistic Image Reconstruction Framework (SIRF) +Copyright 2015 - 2018 Rutherford Appleton Laboratory STFC This is software developed for the Collaborative Computational -Project in Positron Emission Tomography and Magnetic Resonance imaging -(http://www.ccppetmr.ac.uk/). +Project in Synergistic Reconstruction for Biomedical Imaging (formerly CCP PETMR) +(http://www.ccpsynerbi.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 diff --git a/src/xSTIR/mSTIR/printer.h b/src/xSTIR/mSTIR/printer.h index 7539bc823..78151832e 100644 --- a/src/xSTIR/mSTIR/printer.h +++ b/src/xSTIR/mSTIR/printer.h @@ -1,9 +1,9 @@ /* -CCP PETMR Synergistic Image Reconstruction Framework (SIRF) -Copyright 2015 - 2017 Rutherford Appleton Laboratory STFC +SyneRBI Synergistic Image Reconstruction Framework (SIRF) +Copyright 2015 - 2018 Rutherford Appleton Laboratory STFC This is software developed for the Collaborative Computational -Project in Positron Emission Tomography and Magnetic Resonance imaging -(http://www.ccppetmr.ac.uk/). +Project in Synergistic Reconstruction for Biomedical Imaging (formerly CCP PETMR) +(http://www.ccpsynerbi.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 diff --git a/src/xSTIR/mSTIR/tests/CMakeLists.txt b/src/xSTIR/mSTIR/tests/CMakeLists.txt index af25d5c12..198f24013 100644 --- a/src/xSTIR/mSTIR/tests/CMakeLists.txt +++ b/src/xSTIR/mSTIR/tests/CMakeLists.txt @@ -2,7 +2,7 @@ # Author: Kris Thielemans # Copyright 2017 University College London # -# This file is part of the CCP PETMR Synergistic Image Reconstruction Framework (SIRF) SuperBuild. +# This file is part of the SyneRBI Synergistic Image Reconstruction Framework (SIRF) SuperBuild. # # Licensed under the Apache License, Version 2.0 (the "License"); # you may not use this file except in compliance with the License. diff --git a/src/xSTIR/mSTIR/tests/test1.m b/src/xSTIR/mSTIR/tests/test1.m index 2024f7d43..376600855 100644 --- a/src/xSTIR/mSTIR/tests/test1.m +++ b/src/xSTIR/mSTIR/tests/test1.m @@ -1,13 +1,13 @@ function [failed, ntests] = test1(record, engine) % PET test set 1. -% CCP PETMR Synergistic Image Reconstruction Framework (SIRF). -% Copyright 2015 - 2017 Rutherford Appleton Laboratory STFC. -% Copyright 2015 - 2017 University College London. +% SyneRBI Synergistic Image Reconstruction Framework (SIRF). +% Copyright 2015 - 2019 Rutherford Appleton Laboratory STFC. +% Copyright 2015 - 2020 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/). +% Project in Synergistic Reconstruction for Biomedical Imaging (formerly CCP PETMR) +% (http://www.ccpsynerbi.ac.uk/). % % Licensed under the Apache License, Version 2.0 (the "License"); % you may not use this file except in compliance with the License. diff --git a/src/xSTIR/mSTIR/tests/test_listmode.m b/src/xSTIR/mSTIR/tests/test_listmode.m index 33df5bb1d..335f82392 100644 --- a/src/xSTIR/mSTIR/tests/test_listmode.m +++ b/src/xSTIR/mSTIR/tests/test_listmode.m @@ -1,13 +1,13 @@ function [failed, ntests] = test_listmode(record, engine) % PET test set 1. -% CCP PETMR Synergistic Image Reconstruction Framework (SIRF). +% SyneRBI Synergistic Image Reconstruction Framework (SIRF). % Copyright 2015 - 2017 Rutherford Appleton Laboratory STFC. -% Copyright 2015 - 2017 University College London. +% Copyright 2015 - 2020 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/). +% Project in Synergistic Reconstruction for Biomedical Imaging (formerly CCP PETMR) +% (http://www.ccpsynerbi.ac.uk/). % % Licensed under the Apache License, Version 2.0 (the "License"); % you may not use this file except in compliance with the License. diff --git a/src/xSTIR/pSTIR/CMakeLists.txt b/src/xSTIR/pSTIR/CMakeLists.txt index e5911c7fe..f403728f1 100644 --- a/src/xSTIR/pSTIR/CMakeLists.txt +++ b/src/xSTIR/pSTIR/CMakeLists.txt @@ -1,6 +1,6 @@ #======================================================================== -# Author: Kris Thielemans -# Copyright 2016 University College London +# Author: Kris Thielemans, Richard Brown +# Copyright 2016 - 2020 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. diff --git a/src/xSTIR/pSTIR/STIR.py.in b/src/xSTIR/pSTIR/STIR.py.in index a7b74ff0d..9ffcffdba 100644 --- a/src/xSTIR/pSTIR/STIR.py.in +++ b/src/xSTIR/pSTIR/STIR.py.in @@ -2,13 +2,13 @@ Object-Oriented wrap for the cSTIR-to-Python interface pystir.py ''' -# CCP PETMR Synergistic Image Reconstruction Framework (SIRF) -# Copyright 2015 - 2017 Rutherford Appleton Laboratory STFC -# Copyright 2015 - 2017 University College London +# SyneRBI Synergistic Image Reconstruction Framework (SIRF) +# Copyright 2015 - 2020 Rutherford Appleton Laboratory STFC +# Copyright 2015 - 2020 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/). +# Project in Synergistic Reconstruction for Biomedical Imaging (formerly CCP PETMR) +# (http://www.ccpsynerbi.ac.uk/). # # Licensed under the Apache License, Version 2.0 (the "License"); # you may not use this file except in compliance with the License. diff --git a/src/xSTIR/pSTIR/tests/CMakeLists.txt b/src/xSTIR/pSTIR/tests/CMakeLists.txt index 892edb94a..7978ff485 100644 --- a/src/xSTIR/pSTIR/tests/CMakeLists.txt +++ b/src/xSTIR/pSTIR/tests/CMakeLists.txt @@ -1,11 +1,11 @@ #======================================================================== # Author: Edoardo Pasca -# Copyright 2017 University College London +# Copyright 2017 - 2020 University College London # Copyright 2017 Science Technology Facilities Council # Author: Casper da Costa-Luis # Copyright 2017 # -# This file is part of the CCP PETMR Synergistic Image Reconstruction Framework (SIRF) SuperBuild. +# This file is part of the SyneRBI Synergistic Image Reconstruction Framework (SIRF) SuperBuild. # # Licensed under the Apache License, Version 2.0 (the "License"); # you may not use this file except in compliance with the License. diff --git a/tests/NiftyPET_test.sh b/tests/NiftyPET_test.sh index c639db2e3..ed4dd6708 100755 --- a/tests/NiftyPET_test.sh +++ b/tests/NiftyPET_test.sh @@ -1,5 +1,21 @@ #!/bin/bash +# Copyright 2020 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. +# +#========================================================================= + function print_usage() { echo "Usage: $0 [-h|--help] RAW_DATA_FOLDER TSTART TSTOP" } @@ -558,4 +574,4 @@ if [ $fail_count -eq 0 ]; then else echo -e "\nFinished with $fail_count errors..." exit 1 -fi \ No newline at end of file +fi