replaced Apache statement with SPDX identifier and minor fixes

- Replaced long statements on the license with a single line. Fixes SyneRBI#175 - fix SPECT notebook JSON (related to cd_to_working_dir lines) - run nbstripout again on all files (DL and SPECT notebooks affected)
NicoleJurjew · Jan 19, 2023 · ab0a568 · ab0a568
1 parent e7d4057
commit ab0a568
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diff --git a/notebooks/Deep_Learning_PET/1_setup_fwd_model.ipynb b/notebooks/Deep_Learning_PET/1_setup_fwd_model.ipynb
@@ -17,7 +17,7 @@
     "\n",
     "This is software developed for the Collaborative Computational Project in Synergistic Reconstruction for Biomedical Imaging (http://www.ccpsynerbi.ac.uk/).\n",
     "\n",
-    "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.\n",
+    "SPDX-License-Identifier: Apache-2.0\n",
     "\n",
     "# Setting up the forward model\n",
     "\n",

diff --git a/notebooks/Deep_Learning_PET/2_setup_ellipses_dataset.ipynb b/notebooks/Deep_Learning_PET/2_setup_ellipses_dataset.ipynb
@@ -17,7 +17,7 @@
     "\n",
     "This is software developed for the Collaborative Computational Project in Synergistic Reconstruction for Biomedical Imaging (http://www.ccpsynerbi.ac.uk/).\n",
     "\n",
-    "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.\n",
+    "SPDX-License-Identifier: Apache-2.0\n",
     "\n",
     "# Setting up the Ellipses dataset\n",
     "\n",

diff --git a/notebooks/Deep_Learning_PET/3_setup_model.ipynb b/notebooks/Deep_Learning_PET/3_setup_model.ipynb
@@ -17,7 +17,7 @@
     "\n",
     "This is software developed for the Collaborative Computational Project in Synergistic Reconstruction for Biomedical Imaging (http://www.ccpsynerbi.ac.uk/).\n",
     "\n",
-    "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.\n",
+    "SPDX-License-Identifier: Apache-2.0\n",
     "\n",
     "# Setting up the model\n",
     "\n",

diff --git a/notebooks/Deep_Learning_PET/4_setup_training.ipynb b/notebooks/Deep_Learning_PET/4_setup_training.ipynb
@@ -17,7 +17,7 @@
     "\n",
     "This is software developed for the Collaborative Computational Project in Synergistic Reconstruction for Biomedical Imaging (http://www.ccpsynerbi.ac.uk/).\n",
     "\n",
-    "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.\n",
+    "SPDX-License-Identifier: Apache-2.0\n",
     "\n",
     "# Setting up the training\n",
     "\n",

diff --git a/notebooks/Geometry/a_geometry.ipynb b/notebooks/Geometry/a_geometry.ipynb
@@ -21,7 +21,7 @@
     "Copyright 2021 University College London.\n",
     "\n",
     "This is software developed for the Collaborative Computational Project in Synergistic Reconstruction for Biomedical Imaging (http://www.ccpsynerbi.ac.uk/).\n",
-    "Licensed under the Apache License, Version 2.0 (the \"License\"); you may not use this file except in compliance with the License. You may obtain a copy of the License at http://www.apache.org/licenses/LICENSE-2.0 Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an \"AS IS\" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License."
+    "SPDX-License-Identifier: Apache-2.0"
    ]
   },
   {

diff --git a/notebooks/Geometry/b_geom_resamp.ipynb b/notebooks/Geometry/b_geom_resamp.ipynb
@@ -21,7 +21,7 @@
     "Copyright 2021 University College London.\n",
     "\n",
     "This is software developed for the Collaborative Computational Project in Synergistic Reconstruction for Biomedical Imaging (http://www.ccpsynerbi.ac.uk/).\n",
-    "Licensed under the Apache License, Version 2.0 (the \"License\"); you may not use this file except in compliance with the License. You may obtain a copy of the License at http://www.apache.org/licenses/LICENSE-2.0 Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an \"AS IS\" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License."
+    "SPDX-License-Identifier: Apache-2.0"
    ]
   },
   {

diff --git a/notebooks/Geometry/c_fully3dgeom.ipynb b/notebooks/Geometry/c_fully3dgeom.ipynb
@@ -21,7 +21,7 @@
     "Copyright 2021 University College London.\n",
     "\n",
     "This is software developed for the Collaborative Computational Project in Synergistic Reconstruction for Biomedical Imaging (http://www.ccpsynerbi.ac.uk/).\n",
-    "Licensed under the Apache License, Version 2.0 (the \"License\"); you may not use this file except in compliance with the License. You may obtain a copy of the License at http://www.apache.org/licenses/LICENSE-2.0 Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an \"AS IS\" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License."
+    "SPDX-License-Identifier: Apache-2.0"
    ]
   },
   {

diff --git a/notebooks/Geometry/d_manipulation.ipynb b/notebooks/Geometry/d_manipulation.ipynb
@@ -21,7 +21,7 @@
     "Copyright 2021 University College London.\n",
     "\n",
     "This is software developed for the Collaborative Computational Project in Synergistic Reconstruction for Biomedical Imaging (http://www.ccpsynerbi.ac.uk/).\n",
-    "Licensed under the Apache License, Version 2.0 (the \"License\"); you may not use this file except in compliance with the License. You may obtain a copy of the License at http://www.apache.org/licenses/LICENSE-2.0 Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an \"AS IS\" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License."
+    "SPDX-License-Identifier: Apache-2.0"
    ]
   },
   {

diff --git a/notebooks/Introductory/acquisition_model_mr_pet_ct.ipynb b/notebooks/Introductory/acquisition_model_mr_pet_ct.ipynb
@@ -29,15 +29,7 @@
     "Project in Synergistic Reconstruction for Biomedical Imaging\n",
     "(http://www.ccpsynerbi.ac.uk/).\n",
     "\n",
-    "Licensed under the Apache License, Version 2.0 (the \"License\");\n",
-    "you may not use this file except in compliance with the License.\n",
-    "You may obtain a copy of the License at\n",
-    "    http://www.apache.org/licenses/LICENSE-2.0\n",
-    "Unless required by applicable law or agreed to in writing, software\n",
-    "distributed under the License is distributed on an \"AS IS\" BASIS,\n",
-    "WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.\n",
-    "See the License for the specific language governing permissions and\n",
-    "limitations under the License."
+    "SPDX-License-Identifier: Apache-2.0"
    ]
   },
   {

diff --git a/notebooks/Introductory/introduction.ipynb b/notebooks/Introductory/introduction.ipynb
@@ -29,15 +29,7 @@
     "Project in Synergistic Reconstruction for Biomedical Imaging\n",
     "(http://www.ccpsynerbi.ac.uk/).\n",
     "\n",
-    "Licensed under the Apache License, Version 2.0 (the \"License\");\n",
-    "you may not use this file except in compliance with the License.\n",
-    "You may obtain a copy of the License at\n",
-    "    http://www.apache.org/licenses/LICENSE-2.0\n",
-    "Unless required by applicable law or agreed to in writing, software\n",
-    "distributed under the License is distributed on an \"AS IS\" BASIS,\n",
-    "WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.\n",
-    "See the License for the specific language governing permissions and\n",
-    "limitations under the License."
+    "SPDX-License-Identifier: Apache-2.0"
    ]
   },
   {

diff --git a/notebooks/MR/Old_notebooks/Gadgetron/fully_sampled_recon_single_chain.ipynb b/notebooks/MR/Old_notebooks/Gadgetron/fully_sampled_recon_single_chain.ipynb
@@ -31,15 +31,7 @@
     "## Project in Positron Emission Tomography and Magnetic Resonance imaging\n",
     "## (http://www.ccppetmr.ac.uk/).\n",
     "##\n",
-    "## Licensed under the Apache License, Version 2.0 (the \"License\");\n",
-    "##   you may not use this file except in compliance with the License.\n",
-    "##   You may obtain a copy of the License at\n",
-    "##       http://www.apache.org/licenses/LICENSE-2.0\n",
-    "##   Unless required by applicable law or agreed to in writing, software\n",
-    "##   distributed under the License is distributed on an \"AS IS\" BASIS,\n",
-    "##   WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.\n",
-    "##   See the License for the specific language governing permissions and\n",
-    "##   limitations under the License.\n",
+    "## SPDX-License-Identifier: Apache-2.0\n",
     "\n",
     "__version__ = '0.1.0'\n",
     "from docopt import docopt\n",

diff --git a/notebooks/MR/Old_notebooks/Gadgetron/fully_sampled_recon_single_chain_short.ipynb b/notebooks/MR/Old_notebooks/Gadgetron/fully_sampled_recon_single_chain_short.ipynb
@@ -29,15 +29,7 @@
     "## Project in Positron Emission Tomography and Magnetic Resonance imaging\n",
     "## (http://www.ccppetmr.ac.uk/).\n",
     "##\n",
-    "## Licensed under the Apache License, Version 2.0 (the \"License\");\n",
-    "##   you may not use this file except in compliance with the License.\n",
-    "##   You may obtain a copy of the License at\n",
-    "##       http://www.apache.org/licenses/LICENSE-2.0\n",
-    "##   Unless required by applicable law or agreed to in writing, software\n",
-    "##   distributed under the License is distributed on an \"AS IS\" BASIS,\n",
-    "##   WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.\n",
-    "##   See the License for the specific language governing permissions and\n",
-    "##   limitations under the License.\n",
+    "## SPDX-License-Identifier: Apache-2.0\n",
     "\n",
     "__version__ = '0.1.0'\n",
     "from docopt import docopt\n",

diff --git a/notebooks/MR/Old_notebooks/Gadgetron/fully_sampled_recon_three_chains.ipynb b/notebooks/MR/Old_notebooks/Gadgetron/fully_sampled_recon_three_chains.ipynb
@@ -35,15 +35,7 @@
     "## Project in Positron Emission Tomography and Magnetic Resonance imaging\n",
     "## (http://www.ccppetmr.ac.uk/).\n",
     "##\n",
-    "## Licensed under the Apache License, Version 2.0 (the \"License\");\n",
-    "##   you may not use this file except in compliance with the License.\n",
-    "##   You may obtain a copy of the License at\n",
-    "##       http://www.apache.org/licenses/LICENSE-2.0\n",
-    "##   Unless required by applicable law or agreed to in writing, software\n",
-    "##   distributed under the License is distributed on an \"AS IS\" BASIS,\n",
-    "##   WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.\n",
-    "##   See the License for the specific language governing permissions and\n",
-    "##   limitations under the License.\n",
+    "## SPDX-License-Identifier: Apache-2.0\n",
     "\n",
     "__version__ = '0.1.0'\n",
     "from docopt import docopt\n",

diff --git a/notebooks/MR/Old_notebooks/Gadgetron/grappa_detail.ipynb b/notebooks/MR/Old_notebooks/Gadgetron/grappa_detail.ipynb
@@ -46,15 +46,7 @@
     "## Project in Positron Emission Tomography and Magnetic Resonance imaging\n",
     "## (http://www.ccppetmr.ac.uk/).\n",
     "##\n",
-    "## Licensed under the Apache License, Version 2.0 (the \"License\");\n",
-    "##   you may not use this file except in compliance with the License.\n",
-    "##   You may obtain a copy of the License at\n",
-    "##       http://www.apache.org/licenses/LICENSE-2.0\n",
-    "##   Unless required by applicable law or agreed to in writing, software\n",
-    "##   distributed under the License is distributed on an \"AS IS\" BASIS,\n",
-    "##   WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.\n",
-    "##   See the License for the specific language governing permissions and\n",
-    "##   limitations under the License.\n",
+    "## SPDX-License-Identifier: Apache-2.0\n",
     "\n",
     "__version__ = '0.1.0'\n",
     "from docopt import docopt\n",

diff --git a/notebooks/MR/Old_notebooks/acquisition_data.ipynb b/notebooks/MR/Old_notebooks/acquisition_data.ipynb
@@ -40,15 +40,7 @@
     "## Project in Positron Emission Tomography and Magnetic Resonance imaging\n",
     "## (http://www.ccppetmr.ac.uk/).\n",
     "##\n",
-    "## Licensed under the Apache License, Version 2.0 (the \"License\");\n",
-    "##   you may not use this file except in compliance with the License.\n",
-    "##   You may obtain a copy of the License at\n",
-    "##       http://www.apache.org/licenses/LICENSE-2.0\n",
-    "##   Unless required by applicable law or agreed to in writing, software\n",
-    "##   distributed under the License is distributed on an \"AS IS\" BASIS,\n",
-    "##   WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.\n",
-    "##   See the License for the specific language governing permissions and\n",
-    "##   limitations under the License.\n",
+    "## SPDX-License-Identifier: Apache-2.0\n",
     "\n",
     "__version__ = '0.1.0'\n",
     "from docopt import docopt\n",

diff --git a/notebooks/MR/Old_notebooks/acquisition_model.ipynb b/notebooks/MR/Old_notebooks/acquisition_model.ipynb
@@ -31,15 +31,7 @@
     "## Project in Positron Emission Tomography and Magnetic Resonance imaging\n",
     "## (http://www.ccppetmr.ac.uk/).\n",
     "##\n",
-    "## Licensed under the Apache License, Version 2.0 (the \"License\");\n",
-    "##   you may not use this file except in compliance with the License.\n",
-    "##   You may obtain a copy of the License at\n",
-    "##       http://www.apache.org/licenses/LICENSE-2.0\n",
-    "##   Unless required by applicable law or agreed to in writing, software\n",
-    "##   distributed under the License is distributed on an \"AS IS\" BASIS,\n",
-    "##   WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.\n",
-    "##   See the License for the specific language governing permissions and\n",
-    "##   limitations under the License.\n",
+    "## SPDX-License-Identifier: Apache-2.0\n",
     "\n",
     "__version__ = '0.1.0'\n",
     "from docopt import docopt\n",

diff --git a/notebooks/MR/Old_notebooks/fully_sampled_recon.ipynb b/notebooks/MR/Old_notebooks/fully_sampled_recon.ipynb
@@ -30,15 +30,7 @@
     "## Project in Positron Emission Tomography and Magnetic Resonance imaging\n",
     "## (http://www.ccppetmr.ac.uk/).\n",
     "##\n",
-    "## Licensed under the Apache License, Version 2.0 (the \"License\");\n",
-    "##   you may not use this file except in compliance with the License.\n",
-    "##   You may obtain a copy of the License at\n",
-    "##       http://www.apache.org/licenses/LICENSE-2.0\n",
-    "##   Unless required by applicable law or agreed to in writing, software\n",
-    "##   distributed under the License is distributed on an \"AS IS\" BASIS,\n",
-    "##   WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.\n",
-    "##   See the License for the specific language governing permissions and\n",
-    "##   limitations under the License.\n",
+    "## SPDX-License-Identifier: Apache-2.0\n",
     "\n",
     "__version__ = '0.1.0'\n",
     "from docopt import docopt\n",

diff --git a/notebooks/MR/Old_notebooks/grappa_and_steepest_descent.ipynb b/notebooks/MR/Old_notebooks/grappa_and_steepest_descent.ipynb
@@ -29,15 +29,7 @@
     "## Project in Positron Emission Tomography and Magnetic Resonance imaging\n",
     "## (http://www.ccppetmr.ac.uk/).\n",
     "##\n",
-    "## Licensed under the Apache License, Version 2.0 (the \"License\");\n",
-    "##   you may not use this file except in compliance with the License.\n",
-    "##   You may obtain a copy of the License at\n",
-    "##       http://www.apache.org/licenses/LICENSE-2.0\n",
-    "##   Unless required by applicable law or agreed to in writing, software\n",
-    "##   distributed under the License is distributed on an \"AS IS\" BASIS,\n",
-    "##   WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.\n",
-    "##   See the License for the specific language governing permissions and\n",
-    "##   limitations under the License.\n",
+    "## SPDX-License-Identifier: Apache-2.0\n",
     "\n",
     "__version__ = '0.1.0'\n",
     "from docopt import docopt\n",

diff --git a/notebooks/MR/Old_notebooks/grappa_basic.ipynb b/notebooks/MR/Old_notebooks/grappa_basic.ipynb
@@ -49,15 +49,7 @@
     "## Project in Positron Emission Tomography and Magnetic Resonance imaging\n",
     "## (http://www.ccppetmr.ac.uk/).\n",
     "##\n",
-    "## Licensed under the Apache License, Version 2.0 (the \"License\");\n",
-    "##   you may not use this file except in compliance with the License.\n",
-    "##   You may obtain a copy of the License at\n",
-    "##       http://www.apache.org/licenses/LICENSE-2.0\n",
-    "##   Unless required by applicable law or agreed to in writing, software\n",
-    "##   distributed under the License is distributed on an \"AS IS\" BASIS,\n",
-    "##   WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.\n",
-    "##   See the License for the specific language governing permissions and\n",
-    "##   limitations under the License.\n",
+    "## SPDX-License-Identifier: Apache-2.0\n",
     "\n",
     "#__version__ = '0.1.0'\n",
     "from docopt import docopt\n",

diff --git a/notebooks/MR/a_fully_sampled.ipynb b/notebooks/MR/a_fully_sampled.ipynb
@@ -32,15 +32,7 @@
     "Project in Positron Emission Tomography and Magnetic Resonance imaging\n",
     "(http://www.ccppetmr.ac.uk/).\n",
     "\n",
-    "Licensed under the Apache License, Version 2.0 (the \"License\");\n",
-    "you may not use this file except in compliance with the License.\n",
-    "You may obtain a copy of the License at\n",
-    "    http://www.apache.org/licenses/LICENSE-2.0\n",
-    "Unless required by applicable law or agreed to in writing, software\n",
-    "distributed under the License is distributed on an \"AS IS\" BASIS,\n",
-    "WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.\n",
-    "See the License for the specific language governing permissions and\n",
-    "limitations under the License."
+    "SPDX-License-Identifier: Apache-2.0"
    ]
   },
   {

diff --git a/notebooks/MR/b_kspace_filter.ipynb b/notebooks/MR/b_kspace_filter.ipynb
@@ -31,15 +31,7 @@
     "Project in Positron Emission Tomography and Magnetic Resonance imaging\n",
     "(http://www.ccppetmr.ac.uk/).\n",
     "\n",
-    "Licensed under the Apache License, Version 2.0 (the \"License\");\n",
-    "you may not use this file except in compliance with the License.\n",
-    "You may obtain a copy of the License at\n",
-    "    http://www.apache.org/licenses/LICENSE-2.0\n",
-    "Unless required by applicable law or agreed to in writing, software\n",
-    "distributed under the License is distributed on an \"AS IS\" BASIS,\n",
-    "WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.\n",
-    "See the License for the specific language governing permissions and\n",
-    "limitations under the License."
+    "SPDX-License-Identifier: Apache-2.0"
    ]
   },
   {

diff --git a/notebooks/MR/c_coil_combination.ipynb b/notebooks/MR/c_coil_combination.ipynb
@@ -31,15 +31,7 @@
     "Project in Positron Emission Tomography and Magnetic Resonance imaging\n",
     "(http://www.ccppetmr.ac.uk/).\n",
     "\n",
-    "Licensed under the Apache License, Version 2.0 (the \"License\");\n",
-    "you may not use this file except in compliance with the License.\n",
-    "You may obtain a copy of the License at\n",
-    "http://www.apache.org/licenses/LICENSE-2.0\n",
-    "Unless required by applicable law or agreed to in writing, software\n",
-    "distributed under the License is distributed on an \"AS IS\" BASIS,\n",
-    "WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.\n",
-    "See the License for the specific language governing permissions and\n",
-    "limitations under the License.\n"
+    "SPDX-License-Identifier: Apache-2.0"
    ]
   },
   {

diff --git a/notebooks/MR/d_undersampled_reconstructions.ipynb b/notebooks/MR/d_undersampled_reconstructions.ipynb
@@ -32,15 +32,7 @@
     "Project in Positron Emission Tomography and Magnetic Resonance imaging\n",
     "(http://www.ccppetmr.ac.uk/).\n",
     "\n",
-    "Licensed under the Apache License, Version 2.0 (the \"License\");\n",
-    "you may not use this file except in compliance with the License.\n",
-    "You may obtain a copy of the License at\n",
-    "    http://www.apache.org/licenses/LICENSE-2.0\n",
-    "Unless required by applicable law or agreed to in writing, software\n",
-    "distributed under the License is distributed on an \"AS IS\" BASIS,\n",
-    "WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.\n",
-    "See the License for the specific language governing permissions and\n",
-    "limitations under the License."
+    "SPDX-License-Identifier: Apache-2.0"
    ]
   },
   {