Merge pull request #707 from KrisThielemans/updateCopyright

updated copyright statements and PETMR->SyneRBI

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
 

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.

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.
 

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). 

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.

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.

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.

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
+end

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.

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
+end

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.

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.

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')
+subplot(1,2,2), imshow(angle(image_array(:,:,sl)),[-pi pi]), title('Phase')

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
+end

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);
+%AcquisitionData.set_storage_scheme(scheme);

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
+end

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
+end

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
+end