Merge branch 'sirt_memory_efficiency' of github.com:paskino/CIL into …

…sirt_memory_efficiency_changes

.github/workflows/conda_and_docs_build.yml

@@ -1,3 +1,22 @@
+#  -*- coding: utf-8 -*-
+# Copyright 2021 United Kingdom Research and Innovation
+# Copyright 2021 The University of Manchester
+
+# 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.
+
+# Authors:
+# CIL Developers, listed at: https://github.com/TomographicImaging/CIL/blob/master/NOTICE.txt
+
 name: conda_and_docs_build
 
 on:

CHANGELOG.md

@@ -1,7 +1,18 @@
 * x.x.x
   - Refactor SIRT algorithm to make it more computationally and memory efficient
+
+* 23.0.1
+  - Fix bug with NikonReader requiring ROI to be set in constructor.
+
+* 23.0.0
   - Partitioner is now able to create batches even if angle is not the outer dimension
   - Renamed `max_iteration_stop_cryterion` method in the Algorithm class to `max_iteration_stop_criterion`
+  - Removed (previously deprecated) `very_verbose` parameter in `Algorithm`'s run method.
+  - Removed (previously deprecated) `axpby` method in DataContainer.
+  - Deprecate use of integer compression in NEXUSDataWriter.
+  - Improved and tidied up documentation for all readers and writers, including hiding special members.
+  - Use arguments instead of kwargs in all readers and writers with multiple kwargs, making documentation easier.
+  - Update Apache2 License Headers.
 
 * 22.2.0
   - BlockGeometry is iterable

CMakeLists.txt

@@ -1,3 +1,22 @@
+#  Copyright 2020 United Kingdom Research and Innovation
+#  Copyright 2020 The University of Manchester
+#
+#  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.
+#
+# Authors:
+# CIL Developers, listed at: https://github.com/TomographicImaging/CIL/blob/master/NOTICE.txt
+# Richard Brown (University College London)
+
 if(APPLE)
   cmake_minimum_required(VERSION 3.16)
 else()

NOTICE.txt

@@ -1,28 +1,62 @@
 CCPi Core Imaging Library (CIL).
-Copyright 2017-2022 United Kingdom Research and Innovation
-Copyright 2017-2022 University of Manchester
+Copyright 2017 United Kingdom Research and Innovation
+Copyright 2017 The University of Manchester
+
+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.
+
 
 This software product is developed for the Collaborative Computational 
 Project in Tomographic Imaging CCPi (http://www.ccpi.ac.uk/) with
 substantial contributions by UKRI-STFC and The University of Manchester.
 and other contributing institutions.
 
-Main contributors in alphabetical order:
-Evelina Ametova (UoM)
-Gemma Fardell (STFC)
-Jakob Jorgensen (DTU)
-Laura Murgatroyd (STFC)
-Evangelos Papoutsellis (STFC)
-Edoardo Pasca (STFC)
-Kyle Pidgeon (STFC)
-
-Other contributors:
-Claire Delplancke (UoB)
-Daniil Kazantsev (Diamond Light Source)
-Tomas Kulhanek (STFC)
-Srikanth Nagella (STFC)
-Andrew Sharits (UES Inc.)
-Kris Thielemans (UCL)
-Sam Tygier (STFC)
-Ryan Warr (UoM)
+Institutions Key:
+1 - United Kingdom Research and Innovation - Science & Technology Facilities Council (UKRI-STFC)
+2 - Technical University of Denmark (DTU)
+3 - The University of Manchester
+4 - Finden
+5 - University College London (UCL)
+6 - Karlsruhe Institute of Technology (KIT)
+7 - University of Bath
+8 - UES Inc.
+9 - Swansea University
+10 - University of Warwick
+
+CIL Developers in date order:
+Edoardo Pasca (2017 – present) - 1 
+Jakob Sauer Jørgensen (2017 - present) - 2, 3
+Evangelos Papoutsellis (2018 – 2020) - 3, (2020-2022) - 1, (2022-present) - 4
+Gemma Fardell (2019 - present) - 1
+Kris Thielemans (2020 - present) - 5
+Laura Murgatroyd (2021 - present) - 1
+Evelina Ametova (2018-2020) - 3, (2020-2021) - 6 
+
+CIL Contributors:
+Srikanth Nagella (2017-2018) - 1
+Daniil Kazantsev (2018) - 3
+Ryan Warr (2019) - 3
+Tomas Kulhanek (2019) - 1
+Claire Delplancke (2019 - 2022) - 7
+Matthias Ehrhardt (2019 - 2023) - 7
+Richard Brown (2020-2021) - 5
+Sam Tygier (2022) - 1
+Andrew Sharits (2022) - 8
+Kyle Pidgeon (2023) - 1
 
+CIL Advisory Board:
+Llion Evans - 9
+William Lionheart - 3
+Kris Thielemans - 5
+Martin Turner - 3
+Jay Warnett - 10
+Philip Withers - 3

README.md

@@ -19,15 +19,14 @@ The documentation for CIL can be accessed [here](https://tomographicimaging.gith
 Binary installation of CIL can be done with `conda`. Install a new environment using:
 
 ```bash
-conda create --name cil -c conda-forge -c intel -c ccpi cil=22.2.0
+conda create --name cil -c conda-forge -c intel -c ccpi cil=23.0.1
 ```
 
 To install CIL and the additional packages and plugins needed to run the [CIL demos](https://github.com/TomographicImaging/CIL-Demos) install the environment with:
 
 ```bash
-conda create --name cil -c conda-forge -c intel -c astra-toolbox -c ccpi cil=22.2.0 astra-toolbox tigre ccpi-regulariser tomophantom "ipywidgets<8"
+conda create --name cil -c conda-forge -c intel -c ccpi cil=23.0.1 astra-toolbox tigre ccpi-regulariser tomophantom "ipywidgets<8"
 ```
-
 where,
 
 ```astra-toolbox``` will allow you to use CIL with the [ASTRA toolbox](http://www.astra-toolbox.com/) projectors (GPLv3 license).
@@ -38,7 +37,7 @@ where,
 
 ```tomophantom``` [Tomophantom](https://github.com/dkazanc/TomoPhantom) will allow you to generate phantoms to use as test data.
 
-```cudatoolkit``` If you have GPU drivers compatible with more recent CUDA versions you can modify this package selector (installing tigre via conda requires 9.2).
+```cudatoolkit``` If you have GPU drivers compatible with more recent CUDA versions you can modify this package selector (installing tigre via conda requires 10.2).
 
 
 ## Dependency

Wrappers/Python/CMake/parse_git_describe.py

@@ -1,3 +1,22 @@
+# -*- coding: utf-8 -*-
+#  Copyright 2022 United Kingdom Research and Innovation
+#  Copyright 2022 The University of Manchester
+#
+#  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.
+#
+# Authors:
+# CIL Developers, listed at: https://github.com/TomographicImaging/CIL/blob/master/NOTICE.txt
+
 import re, subprocess, sys, os
 
 git_executable = os.path.abspath(sys.argv[1])

Wrappers/Python/CMake/setup.py.in

@@ -1,19 +1,21 @@
 # -*- coding: utf-8 -*-
-#   This work is part of the Core Imaging Library (CIL) developed by CCPi 
-#   (Collaborative Computational Project in Tomographic Imaging), with 
-#   substantial contributions by UKRI-STFC and University of Manchester.
-
-#   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.
+#  Copyright 2018 United Kingdom Research and Innovation
+#  Copyright 2018 The University of Manchester
+#
+#  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.
+#
+# Authors:
+# CIL Developers, listed at: https://github.com/TomographicImaging/CIL/blob/master/NOTICE.txt
 
 from setuptools import setup
 import os

Wrappers/Python/CMake/sp_dir.py

@@ -1,2 +1,21 @@
+# -*- coding: utf-8 -*-
+#  Copyright 2020 United Kingdom Research and Innovation
+#  Copyright 2020 The University of Manchester
+#
+#  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.
+#
+# Authors:
+# CIL Developers, listed at: https://github.com/TomographicImaging/CIL/blob/master/NOTICE.txt
+
 import os
 print (os.path.dirname(os.__file__))

Wrappers/Python/CMake/version.py.in

@@ -1,3 +1,22 @@
+# -*- coding: utf-8 -*-
+#  Copyright 2021 United Kingdom Research and Innovation
+#  Copyright 2021 The University of Manchester
+#
+#  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.
+#
+# Authors:
+# CIL Developers, listed at: https://github.com/TomographicImaging/CIL/blob/master/NOTICE.txt
+
 version = '@CIL_VERSION_MAJOR@.@CIL_VERSION_MINOR@.@CIL_VERSION_PATCH@'
 major = '@CIL_VERSION_MAJOR@'
 minor = '@CIL_VERSION_MINOR@'

Wrappers/Python/CMakeLists.txt

@@ -1,3 +1,22 @@
+# -*- coding: utf-8 -*-
+#  Copyright 2019 United Kingdom Research and Innovation
+#  Copyright 2019 The University of Manchester
+#
+#  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.
+#
+# Authors:
+# CIL Developers, listed at: https://github.com/TomographicImaging/CIL/blob/master/NOTICE.txt
+
 option (BUILD_PYTHON_WRAPPER "Build Python Wrapper" ON)
 
 if (BUILD_PYTHON_WRAPPER)

Wrappers/Python/cil/__init__.py

@@ -1,18 +1,20 @@
 # -*- coding: utf-8 -*-
-#   This work is part of the Core Imaging Library (CIL) developed by CCPi 
-#   (Collaborative Computational Project in Tomographic Imaging), with 
-#   substantial contributions by UKRI-STFC and University of Manchester.
-
-#   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.
+#  Copyright 2018 United Kingdom Research and Innovation
+#  Copyright 2018 The University of Manchester
+#
+#  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.
+#
+# Authors:
+# CIL Developers, listed at: https://github.com/TomographicImaging/CIL/blob/master/NOTICE.txt
 
 from .version import version as __version__

Wrappers/Python/cil/framework/BlockDataContainer.py

@@ -1,19 +1,22 @@
 # -*- coding: utf-8 -*-
-#   This work is part of the Core Imaging Library (CIL) developed by CCPi 
-#   (Collaborative Computational Project in Tomographic Imaging), with 
-#   substantial contributions by UKRI-STFC and University of Manchester.
+#  Copyright 2019 United Kingdom Research and Innovation
+#  Copyright 2019 The University of Manchester
+#
+#  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.
+#
+# Authors:
+# CIL Developers, listed at: https://github.com/TomographicImaging/CIL/blob/master/NOTICE.txt
 
-#   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.
 import numpy
 from numbers import Number
 import functools