Merge branch 'master' into blockoperator-norms

Signed-off-by: Margaret Duff <[email protected]>

.github/workflows/conda_and_docs_build.yml

@@ -1,29 +1,27 @@
 #  -*- 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:
   release:
     types: [published]
   push:
-    branches: [ master ]
+    branches: [master]
     tags:
       - '**'
     paths-ignore:
@@ -33,92 +31,77 @@ on:
     - 'scripts/**'
     - 'NOTICE.txt'
     - 'README.md'
-
   pull_request:
-    branches: [ master ]
+    branches: [master]
     paths-ignore:
     - 'CHANGELOG.md'
     - 'CITATION.cff'
     - 'LICENSE'
     - 'scripts/**'
     - 'NOTICE.txt'
     - 'README.md'
-
 jobs:
   conda_build:
     runs-on: ubuntu-20.04
     steps:
-    - uses: actions/checkout@v3.1.0
+    - uses: actions/checkout@v4
       with:
         fetch-depth: 0
     - name: conda-build
       uses: paskino/[email protected]
       with:
-        subDir: 'recipe'
-        channels: '-c conda-forge -c intel -c astra-toolbox -c ccpi'
+        subDir: recipe
+        channels: -c conda-forge -c intel -c ccpi
         convert_win: false
         convert_osx: false
         test_pyver: 3.9
         test_npver: 1.22
     - name: Upload artifact of the conda package.
-      uses: actions/upload-artifact@v3.1.1
+      uses: actions/upload-artifact@v3
       with:
         name: cil-package
         path: recipe/linux-64/cil*
   docs_build:
     needs: conda_build
     runs-on: ubuntu-20.04
     steps:
-    - uses: actions/checkout@v3.1.0
+    - uses: actions/checkout@v4
       with:
         fetch-depth: 0
-    - name: change directory
-      run: |
-        ls
+    - run: ls
     - name: Download artifact of the conda package.
-      uses: actions/download-artifact@v3.0.1
+      uses: actions/download-artifact@v3
       with:
-        name: 'cil-package'
+        name: cil-package
         path: 'conda_package'
     - uses: conda-incubator/setup-miniconda@v2
       with:
         python-version: 3.9
     - uses: lauramurgatroyd/[email protected]
       with:
-        DOCS_PATH: 'docs'
-        CONDA_BUILD_ENV_FILEPATH: 'docs/docs_environment.yml'
-        ARTIFACT_NAME: 'DocumentationHTML'
-        PACKAGE_FOLDER_PATH: 'conda_package'
-        PACKAGE_NAME: 'cil'
-        PACKAGE_CONDA_CHANNELS: 'conda-forge -c intel -c astra-toolbox -c ccpi'
-        BUILD_SUBDIR_NAME: 'nightly'
+        DOCS_PATH: docs
+        CONDA_BUILD_ENV_FILEPATH: docs/docs_environment.yml
+        ARTIFACT_NAME: DocumentationHTML
+        PACKAGE_FOLDER_PATH: conda_package
+        PACKAGE_NAME: cil
+        PACKAGE_CONDA_CHANNELS: conda-forge -c intel -c ccpi
+        BUILD_SUBDIR_NAME: nightly
         python_version: 3.9
   docs_publish:
     needs: docs_build
-    runs-on: ubuntu-latest
     if: github.ref == 'refs/heads/master'
+    runs-on: ubuntu-latest
     steps:
+    - uses: actions/checkout@v4
     - name: Download artifact of the html output.
-      uses: actions/download-artifact@v3.0.1
+      uses: actions/download-artifact@v3
       with:
         name: DocumentationHTML
         path: docs/build
-    - name: Commit documentation changes
-      run: |
-        git clone https://github.com/TomographicImaging/CIL.git --branch gh-pages --single-branch gh-pages
-        cp -r docs/build/* gh-pages/
-        cd gh-pages
-        touch .nojekyll
-        git config --local user.email "[email protected]"
-        git config --local user.name "GitHub Action"
-        git add .
-        git commit -m "Update documentation" -a || true
-        # The above command will fail if no changes were present, so we ignore
-        # that.
     - name: Push changes
-      uses: ad-m/github-push-[email protected]
+      uses: casperdcl/push-dir@v1
       with:
+        message: Update documentation
         branch: gh-pages
-        directory: gh-pages
-        github_token: ${{ secrets.GITHUB_TOKEN }}
-
+        dir: docs/build
+        nojekyll: true

CHANGELOG.md

@@ -1,17 +1,18 @@
 
-* x.x.x
+* 23.1.0
   - Fix bug in IndicatorBox proximal_conjugate
   - Allow CCPi Regulariser functions for non CIL object
   - Add norm for CompositionOperator
   - Refactor SIRT algorithm to make it more computationally and memory efficient
   - Optimisation in L2NormSquared
   - Added support for partitioner, when partitions have size 1
   - Fix for show_geometry bug for 2D data
+  - FBP split processing bug fix - now respects panel origin set in geometry
+  - Binner/Padder/Slicer bug fix - now respects panel origin set in geometry
   - Added warmstart capability to proximal evaluation of the CIL TotalVariation function.
-  - FBP split processing bug fix - now respects panel origin
+  - Bug fix in the LinearOperator norm with an additional flag for the algorithm linearOperator.PowerMethod
   - Tidied up documentation in the framework folder
 
-
 * 23.0.1
   - Fix bug with NikonReader requiring ROI to be set in constructor.
 

README.md

@@ -16,16 +16,23 @@ The documentation for CIL can be accessed [here](https://tomographicimaging.gith
 
 # Installation of CIL
 
-Binary installation of CIL can be done with `conda`. Install a new environment using:
+Binary installation of CIL can be achieved with `conda` or `mamba`. `mamba`'s environment solver (`libmamba`) provides faster environment resolution so we recommend this route, although in many cases the default `conda` will still work but may be very slow.
+
+`miniconda` is a minimal installer for `conda`. Installation instructions can be found [here](https://docs.conda.io/projects/miniconda/en/latest/).
+You can then force your `conda` installation to use `libmamba` instructions are [here](https://www.anaconda.com/blog/a-faster-conda-for-a-growing-community).
+
+Alternatively, `mamba` can be installed via [`miniforge`](https://github.com/conda-forge/miniforge) which is another minimal installer for `conda` with optional support for `mamba`. In this case replace `conda` with `mamba` in the below commands.
+
+Install a new environment using:
 
 ```bash
-conda create --name cil -c conda-forge -c intel -c ccpi cil=23.0.1
+conda create --name cil -c conda-forge -c intel -c ccpi cil=23.1.0
 ```
 
 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 ccpi cil=23.0.1 astra-toolbox tigre ccpi-regulariser tomophantom "ipywidgets<8"
+conda create --name cil -c conda-forge -c intel -c ccpi cil=23.1.0 astra-toolbox tigre ccpi-regulariser tomophantom "ipywidgets<8"
 ```
 where,
 

Wrappers/Python/cil/framework/framework.py

@@ -521,7 +521,7 @@ def __init__ (self, dof):
     @staticmethod  
     def create_vector(val):
         try:
-            vec = numpy.asarray(val, dtype=numpy.float64).reshape(len(val))
+            vec = numpy.array(val, dtype=numpy.float64).reshape(len(val))
         except:
             raise ValueError("Can't convert to numpy array")
 
@@ -1984,6 +1984,48 @@ def configured(self):
             configured = False
         return configured
 
+    def shift_detector_in_plane(self,
+                                          pixel_offset,
+                                          direction='horizontal'):
+        """
+        Adjusts the position of the detector in a specified direction within the imaging plane.
+
+        Parameters:
+        -----------
+        pixel_offset : float
+            The number of pixels to adjust the detector's position by.
+        direction : {'horizontal', 'vertical'}, optional
+            The direction in which to adjust the detector's position. Defaults to 'horizontal'.
+
+        Notes:
+        ------
+        - If `direction` is 'horizontal':
+            - If the panel's origin is 'left', positive offsets translate the detector to the right.
+            - If the panel's origin is 'right', positive offsets translate the detector to the left.
+
+        - If `direction` is 'vertical':
+            - If the panel's origin is 'bottom', positive offsets translate the detector upward.
+            - If the panel's origin is 'top', positive offsets translate the detector downward.
+
+        Returns:
+        --------
+        None
+        """
+
+        if direction == 'horizontal':
+            pixel_size = self.panel.pixel_size[0]
+            pixel_direction = self.system.detector.direction_x
+
+        elif direction == 'vertical':
+            pixel_size = self.panel.pixel_size[1]
+            pixel_direction = self.system.detector.direction_y
+
+        if 'bottom' in self.panel.origin or 'left' in self.panel.origin:
+            self.system.detector.position -= pixel_offset * pixel_direction * pixel_size
+        else:
+            self.system.detector.position += pixel_offset * pixel_direction * pixel_size
+
+
     def __str__(self):
         repres = ""
         if self.configured: