Merge branch 'j_paper' into main

PyTomography · Nov 25, 2024 · 423b578 · 423b578
2 parents c9ed570 + 8f6f440
commit 423b578
Show file tree

Hide file tree

Showing 31 changed files with 4,664 additions and 4,379 deletions.
diff --git a/.github/workflows/draft-pdf.yml b/.github/workflows/draft-pdf.yml
@@ -0,0 +1,30 @@
+name: Draft PDF
+on:
+  push:
+    paths:
+      - paper/paper.md
+      - paper/paper.bib
+      - with_recon.png
+      - .github/workflows/draft-pdf.yml
+
+jobs:
+  paper:
+    runs-on: ubuntu-latest
+    name: Paper Draft
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+      - name: Build draft PDF
+        uses: openjournals/openjournals-draft-action@master
+        with:
+          journal: joss
+          # This should be the path to the paper within your repo.
+          paper-path: paper/paper.md
+      - name: Upload
+        uses: actions/upload-artifact@v4
+        with:
+          name: paper
+          # This is the output path where Pandoc will write the compiled
+          # PDF. Note, this should be the same directory as the input
+          # paper.md
+          path: paper/paper.pdf
diff --git a/.gitignore b/.gitignore
@@ -1,9 +1,9 @@
-*__pycache__*
-paper/jats
-paper/paper
-paper/*.png
-paper/*.pdf
-*code-workspace
-SlicerSPECTRecon/__pycache__/
-SlicerSPECTRecon/Logic/rough.ipynb
-.vscode
+*__pycache__*
+paper/jats
+paper/paper
+paper/*.png
+paper/*.pdf
+*code-workspace
+SlicerSPECTRecon/__pycache__/
+SlicerSPECTRecon/Logic/rough.ipynb
+.vscode
diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md
@@ -1,45 +1,45 @@
-# Contributing to SlicerSPECTRecon
-
-First off, thanks for your interest in contributing! There are many potential options for contributions to this library: most notably, implementation of conversion from alternative sources to dicom format, implementation of different prior functions, implementation of additional reconstruction algorithms, etc. If you wish to contribute:
-
-**Bugs**
-1. Open an issue. 
-2. Provide as much context as you can about what you're running into.
-3. Provide project and platform versions.
-
-**New Features**
-
-The recommended method of contributing is as follows:
-1. Create an issue on the [issues page](https://github.com/PyTomography/slicer_spect_recon/issues)
-2. Fork the repository to your own account
-3. Fix issue and push changes to your own fork on GitHub
-4. Create a pull request from your fork (whatever branch you worked on) to the development branch in the main repository.
-
-## Setup
-
-To activate and use this module please follow these steps:
-
-   1.  Either `unzip` the source code or `clone` it from GitHub.
-   2.  Add the respective path in `Slicer` by *Edit -> Application settings -> Modules -> Additional module paths -> Add -> OK*.
-   3.  `Restart` Slicer to apply the changes.
-   4.  `Choose` the module under *Modules -> Tomographic Reconstruction -> SlicerSPECTRecon*.
-
-## Testing
-
-The tests in `Logic/SlicerSPECTReconTest` can be run in `Slicer` itself. Therefore, the module has to be already imported and activated.
-
-Additionally, you have to enable the `developer mode` under *Edit -> Application settings -> Developer -> Enable developer mode -> OK*.
-
-After reloading Slicer, you should see a column `Reload and Test`. To run the tests and changes to the source code, just click this button. This reimports the module with the current changes and runs the code against the given tests.
-
-## Sample Data
-
-The links to the example data (sample patient and simind files) are in the sample_data.txt file in the `Resources` folder. 
-
-## Contribute
-
-If you'd like to contribute, you can find an orientation on the Slicer [documentation for developers](https://www.slicer.org/wiki/Documentation/Nightly/Developers).
-
-## License
-
-SlicerSPECTRecon is subject to the `MIT License`, which can be found in the project's root.
+# Contributing to SlicerSPECTRecon
+
+First off, thanks for your interest in contributing! There are many potential options for contributions to this library: most notably, implementation of conversion from alternative sources to dicom format, implementation of different prior functions, implementation of additional reconstruction algorithms, etc. If you wish to contribute:
+
+**Bugs**
+1. Open an issue. 
+2. Provide as much context as you can about what you're running into.
+3. Provide project and platform versions.
+
+**New Features**
+
+The recommended method of contributing is as follows:
+1. Create an issue on the [issues page](https://github.com/PyTomography/slicer_spect_recon/issues)
+2. Fork the repository to your own account
+3. Fix issue and push changes to your own fork on GitHub
+4. Create a pull request from your fork (whatever branch you worked on) to the development branch in the main repository.
+
+## Setup
+
+To activate and use this module please follow these steps:
+
+   1.  Either `unzip` the source code or `clone` it from GitHub.
+   2.  Add the respective path in `Slicer` by *Edit -> Application settings -> Modules -> Additional module paths -> Add -> OK*.
+   3.  `Restart` Slicer to apply the changes.
+   4.  `Choose` the module under *Modules -> Tomographic Reconstruction -> SlicerSPECTRecon*.
+
+## Testing
+
+The tests in `Logic/SlicerSPECTReconTest` can be run in `Slicer` itself. Therefore, the module has to be already imported and activated.
+
+Additionally, you have to enable the `developer mode` under *Edit -> Application settings -> Developer -> Enable developer mode -> OK*.
+
+After reloading Slicer, you should see a column `Reload and Test`. To run the tests and changes to the source code, just click this button. This reimports the module with the current changes and runs the code against the given tests.
+
+## Sample Data
+
+The links to the example data (sample patient and simind files) are in the sample_data.txt file in the `Resources` folder. 
+
+## Contribute
+
+If you'd like to contribute, you can find an orientation on the Slicer [documentation for developers](https://www.slicer.org/wiki/Documentation/Nightly/Developers).
+
+## License
+
+SlicerSPECTRecon is subject to the `MIT License`, which can be found in the project's root.
diff --git a/LICENSE.txt b/LICENSE.txt
@@ -1,21 +1,21 @@
-MIT License
-
-Copyright (c) [2024] [Obed Dzikunu]
-
-Permission is hereby granted, free of charge, to any person obtaining a copy
-of this software and associated documentation files (the "Software"), to deal
-in the Software without restriction, including without limitation the rights
-to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
-copies of the Software, and to permit persons to whom the Software is
-furnished to do so, subject to the following conditions:
-
-The above copyright notice and this permission notice shall be included in all
-copies or substantial portions of the Software.
-
-THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
-IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
-FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
-AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
-LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
-OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+MIT License
+
+Copyright (c) [2024] [Obed Dzikunu]
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
 SOFTWARE.
diff --git a/README.md b/README.md
@@ -1,50 +1,50 @@
-# SPECT Tomographic Reconstruction 3D Slicer Extension
-
-This is the official repository for the `Slicer` extension `SlicerSPECTRecon`.
-
-This module enables the reconstruction of raw SPECT projection data, providing customizable options for image modeling and image reconstruction. The module has a SIMIND to DICOM converter to permit reconstruction of SIMIND Monte Carlo data.
-
-The module is divided into the following sections:
-
-- Data Converters: Provides tools for converting data from various sources into the DICOM format.
-- Input Data: Users can select data from multiple bed positions after loading the projection data into the 3D Slicer DICOM database. 
-- System Modeling: Allows users to define transforms that are used to build the system matrix.
-- Likelihood: Allows users to choose their preferred likelihood function.
-- Reconstruction Algorithm: Provides the option of selecting a preferred reconstruction algorithm and their associated parameters
-
-Please refer to the `User_Manual.md` file for further information
-
-## User interface
-
-- Inputs
-  - Input volume: input SPECT/CT dicom files, simind file (convert to dicom using the data converter)
-- Outputs
-  - Reconstructed volume: The volume will be saved under the specified name (or as the dataset name appended with _reconstructed) and will be located within the Subject Hierarchy in the Data Module.
-
-## Resources
-
-The following link collection should facilitate understanding the code in this extension:
-
-- [Slicer Utils](https://github.com/Slicer/Slicer/blob/master/Base/Python/slicer/util.py)
-- [DICOM Introduction](https://www.slicer.org/wiki/Documentation/Nightly/FAQ/DICOM)
-- [DICOM Structure](https://www.slicer.org/wiki/Documentation/4.0/Modules/CreateDICOMSeries)
-- [DICOM Browser](https://dicom.innolitics.com/ciods)
-- [Subject Hierarchy](https://www.slicer.org/wiki/Documentation/4.5/Modules/SubjectHierarchy)
-
-## Sample Data
-
-The links to the example data (sample patient and simind files) are in the sample_data.txt file in the `Resources` folder. 
-
-## Contribute
-
-If you'd like to contribute, you can find an orientation on the Slicer [documentation for developers](https://www.slicer.org/wiki/Documentation/Nightly/Developers).
-
-Please read first the `CONTRIBUTING.md` file for further information on how to contribute. You can also check the Pytomography [readthedocs](https://pytomography.readthedocs.io/en/latest/) for an orientation on Pytomography.
-
-## License
-
-SlicerSPECTRecon is subject to the `MIT License`, which is in the project's root.
-
-## Contact
-
+# SPECT Tomographic Reconstruction 3D Slicer Extension
+
+This is the official repository for the `Slicer` extension `SlicerSPECTRecon`.
+
+This module enables the reconstruction of raw SPECT projection data, providing customizable options for image modeling and image reconstruction. The module has a SIMIND to DICOM converter to permit reconstruction of SIMIND Monte Carlo data.
+
+The module is divided into the following sections:
+
+- Data Converters: Provides tools for converting data from various sources into the DICOM format.
+- Input Data: Users can select data from multiple bed positions after loading the projection data into the 3D Slicer DICOM database. 
+- System Modeling: Allows users to define transforms that are used to build the system matrix.
+- Likelihood: Allows users to choose their preferred likelihood function.
+- Reconstruction Algorithm: Provides the option of selecting a preferred reconstruction algorithm and their associated parameters
+
+Please refer to the `User_Manual.md` file for further information
+
+## User interface
+
+- Inputs
+  - Input volume: input SPECT/CT dicom files, simind file (convert to dicom using the data converter)
+- Outputs
+  - Reconstructed volume: The volume will be saved under the specified name (or as the dataset name appended with _reconstructed) and will be located within the Subject Hierarchy in the Data Module.
+
+## Resources
+
+The following link collection should facilitate understanding the code in this extension:
+
+- [Slicer Utils](https://github.com/Slicer/Slicer/blob/master/Base/Python/slicer/util.py)
+- [DICOM Introduction](https://www.slicer.org/wiki/Documentation/Nightly/FAQ/DICOM)
+- [DICOM Structure](https://www.slicer.org/wiki/Documentation/4.0/Modules/CreateDICOMSeries)
+- [DICOM Browser](https://dicom.innolitics.com/ciods)
+- [Subject Hierarchy](https://www.slicer.org/wiki/Documentation/4.5/Modules/SubjectHierarchy)
+
+## Sample Data
+
+The links to the example data (sample patient and simind files) are in the sample_data.txt file in the `Resources` folder. 
+
+## Contribute
+
+If you'd like to contribute, you can find an orientation on the Slicer [documentation for developers](https://www.slicer.org/wiki/Documentation/Nightly/Developers).
+
+Please read first the `CONTRIBUTING.md` file for further information on how to contribute. You can also check the Pytomography [readthedocs](https://pytomography.readthedocs.io/en/latest/) for an orientation on Pytomography.
+
+## License
+
+SlicerSPECTRecon is subject to the `MIT License`, which is in the project's root.
+
+## Contact
+
 Please post any questions to the [Pytomography Discourse Forum](https://pytomography.discourse.group/).
diff --git a/SlicerSPECTRecon/CMakeLists.txt b/SlicerSPECTRecon/CMakeLists.txt
@@ -1,45 +1,45 @@
-#-----------------------------------------------------------------------------
-set(MODULE_NAME SlicerSPECTRecon)
-
-#-----------------------------------------------------------------------------
-set(MODULE_PYTHON_SCRIPTS
-  ${MODULE_NAME}.py
-  Logic/Algorithms.py
-  Logic/Callbacks.py
-  Logic/MetadataUtils.py
-  Logic/Priors.py
-  Logic/SimindToDicom.py
-  Logic/SlicerSPECTReconLogic.py
-  Logic/VolumeUtils.py
-  Logic/VtkkmrmlUtils.py
-  Testing/Python/reconstruction.py
-  Testing/Python/simind_to_dicom.py
-  Testing/Python/utils.py
-  )
-
-set(MODULE_PYTHON_RESOURCES
-  Resources/Icons/${MODULE_NAME}.png
-  Resources/UI/${MODULE_NAME}.ui
-  Resources/algorithmTestSettings.json
-  Resources/psfMeta.json
-  Resources/sampleDataMetaData.json
-  )
-
-#-----------------------------------------------------------------------------
-slicerMacroBuildScriptedModule(
-  NAME ${MODULE_NAME}
-  SCRIPTS ${MODULE_PYTHON_SCRIPTS}
-  RESOURCES ${MODULE_PYTHON_RESOURCES}
-  WITH_GENERIC_TESTS
-  )
-
-#-----------------------------------------------------------------------------
-if(BUILD_TESTING)
-
-  # Register the unittest subclass in the main script as a ctest.
-  # Note that the test will also be available at runtime.
-  # slicer_add_python_unittest(SCRIPT ${MODULE_NAME}.py)
-
-  # Additional build-time testing
-  add_subdirectory(Logic)
-endif()
+#-----------------------------------------------------------------------------
+set(MODULE_NAME SlicerSPECTRecon)
+
+#-----------------------------------------------------------------------------
+set(MODULE_PYTHON_SCRIPTS
+  ${MODULE_NAME}.py
+  Logic/Algorithms.py
+  Logic/Callbacks.py
+  Logic/MetadataUtils.py
+  Logic/Priors.py
+  Logic/SimindToDicom.py
+  Logic/SlicerSPECTReconLogic.py
+  Logic/VolumeUtils.py
+  Logic/VtkkmrmlUtils.py
+  Testing/Python/reconstruction.py
+  Testing/Python/simind_to_dicom.py
+  Testing/Python/utils.py
+  )
+
+set(MODULE_PYTHON_RESOURCES
+  Resources/Icons/${MODULE_NAME}.png
+  Resources/UI/${MODULE_NAME}.ui
+  Resources/algorithmTestSettings.json
+  Resources/psfMeta.json
+  Resources/sampleDataMetaData.json
+  )
+
+#-----------------------------------------------------------------------------
+slicerMacroBuildScriptedModule(
+  NAME ${MODULE_NAME}
+  SCRIPTS ${MODULE_PYTHON_SCRIPTS}
+  RESOURCES ${MODULE_PYTHON_RESOURCES}
+  WITH_GENERIC_TESTS
+  )
+
+#-----------------------------------------------------------------------------
+if(BUILD_TESTING)
+
+  # Register the unittest subclass in the main script as a ctest.
+  # Note that the test will also be available at runtime.
+  # slicer_add_python_unittest(SCRIPT ${MODULE_NAME}.py)
+
+  # Additional build-time testing
+  add_subdirectory(Logic)
+endif()