Merge branch 'main' into Fix_website

Author: oliverchampion

.github/workflows/analysis.yml

@@ -29,8 +29,9 @@ jobs:
 
       - name: Install dependencies
         run: |
+          pip install torch --extra-index-url https://download.pytorch.org/whl/cpu
           pip install -r requirements.txt
-
+          
       - name: Read algorithms
         id: algorithms
         run: |
@@ -79,7 +80,7 @@ jobs:
               test_output_${{ matrix.algorithm }}_${{ matrix.SNR }}.csv
               test_duration_${{ matrix.algorithm }}_${{ matrix.SNR }}.csv
             overwrite: true
-  
+
   merge:
     runs-on: ubuntu-latest
     needs: build

.github/workflows/docker-build-and-run.yml

@@ -23,6 +23,7 @@ jobs:
       - name: Install Python dependencies
         run: |
           python -m pip install --upgrade pip
+          pip install torch --extra-index-url https://download.pytorch.org/whl/cpu
           pip install -r requirements.txt
 
       - name: Generate input files

.github/workflows/unit_test.yml

@@ -29,9 +29,11 @@ jobs:
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip
+          pip install torch --extra-index-url https://download.pytorch.org/whl/cpu
           pip install -r requirements.txt
       - name: Test with pytest
         run: |
           pip install pytest pytest-cov
           python -m pytest --doctest-modules --junitxml=junit/test-results.xml --cov=. --cov-report=xml --cov-report=html -r w
+          python -m pytest --doctest-modules --junitxml=junit/test-results-brain.xml --cov=. --cov-report=xml --cov-report=html --dataFile tests/IVIMmodels/unit_tests/generic_brain.json -r w -k test_ivim_fit_saved
 

.github/workflows/website.yml

@@ -41,10 +41,12 @@ jobs:
 
       - name: Install dependencies
         run: |
+          pip install torch --extra-index-url https://download.pytorch.org/whl/cpu
           pip install -r requirements.txt
 
       # Download Figures artifact
       - name: Download Figures artifact
+
         if: ${{ github.event.workflow_run.conclusion == 'success' }}
         uses: actions/download-artifact@v4
         with:

.gitignore

@@ -5,6 +5,8 @@
 __pycache__/
 *.nii.gz
 *.nii
+*.bval
+*.bvec
 *.npy
 *.dcm
 *.npy
@@ -37,3 +39,5 @@ coverage.xml
 phantoms/MR_XCAT_qMRI/*.json
 phantoms/MR_XCAT_qMRI/*.txt
 tests/IVIMmodels/unit_tests/models
+models
+test_output.csv

README.md

@@ -4,7 +4,7 @@ The ISMRM Open Science Initiative for Perfusion Imaging (OSIPI) is an initiative
 
 >“promote the sharing of perfusion imaging software in order to eliminate the practice of duplicate development, improve the reproducibility of perfusion imaging research, and speed up the translation into tools for discovery science, drug development, and clinical practice”
 
-This **IVIM code collection** code library is maintained by OSIPI [Taskforce 2.4](https://www.osipi.org/task-force-2-4/) (*currently not available*) and aims to collect, test and share open-source code related to intravoxel incoherent motion (IVIM) analysis of diffusion encoded MRI data to be used in research and software development. Code contributions can include any code related IVIM analysis (denoising, motion correction, model fitting, etc.), but at an initial phase, development of tests and other features of the repository will predominantly focus on fitting algorithms. A goal of the IVIM OSIPI task force is to develop a fully tested and harmonized code library, building upon the contributions obtained through this initiative. Documentation and analysis are available on the [OSIPI TF2.4](https://osipi.github.io/TF2.4_IVIM-MRI_CodeCollection/).
+This **IVIM code collection** code library is maintained by OSIPI [Taskforce 2.4](https://osipi.ismrm.org/task-forces/task-force-2-4/) and aims to collect, test and share open-source code related to intravoxel incoherent motion (IVIM) analysis of diffusion encoded MRI data to be used in research and software development. Code contributions can include any code related IVIM analysis (denoising, motion correction, model fitting, etc.), but at an initial phase, development of tests and other features of the repository will predominantly focus on fitting algorithms. A goal of the IVIM OSIPI task force is to develop a fully tested and harmonized code library, building upon the contributions obtained through this initiative. Documentation and analysis are available on the [OSIPI TF2.4](https://osipi.github.io/TF2.4_IVIM-MRI_CodeCollection/).
 
 We have some useful tools and further documentation on https://osipi.github.io/TF2.4_IVIM-MRI_CodeCollection/.
 
@@ -22,6 +22,9 @@ If you would like to contribute with code, please follow the instructions below:
 If you would like to use code from the repository and/or are new to Github or IVIM, please see the jupyter notebook below:
 *   [Introduction to TF2.4_IVIM-MRI_CodeCollection github and IVIM Analysis using Python](doc/Introduction_to_TF24_IVIM-MRI_CodeCollection_github_and_IVIM_Analysis_using_Python.ipynb)
 
+If you would like to use MATLAB-based algorithms or apply the testing framework to one of these algorithms, please have a look at these instructions:
+* [MATLAB-related instructions](doc/matlab_instructions.md)
+
 ## Repository Organization
 
 The repository is organized in four main folders along with configuration files for automated testing. 

conftest.py

@@ -267,8 +267,7 @@ def algorithmlist(algorithms):
     for algorithm in algorithms["algorithms"]:
         algorithm_dict = algorithms.get(algorithm, {})
         requires_matlab = algorithm_dict.get("requires_matlab", False)
-        if not algorithm_dict.get('deep_learning', False):
-            yield algorithm, requires_matlab
+        yield algorithm, requires_matlab, algorithm_dict.get('deep_learning', False)
 
 
 def bound_input(datafile, algorithms):

doc/matlab_instructions.md

@@ -0,0 +1,7 @@
+## MATLAB-related instructions
+
+A large portion of IVIM-related code has historically been written in the MATLAB programming language. For this reason, we have included the possibility to call and test MATLAB-based code from the Python-based code developed here. This requires a few additional steps to get going
+
+- In addition to the Python packages listed requirements.txt, one also need to install matlab.engine, for example with pip: `python -m pip install matlabengine`. This requires a corresponding version of MATLAB to be installed.
+- To be able to call the MATLAB code in this repository, the src/original folder must be added to the MATLAB path
+- Testing of MATLAB-based code only runs offline (not on Github). This is done by running `python -m pytest --withmatlab`

phantoms/brain/data/diffusive_snr2000.bval

@@ -0,0 +1 @@
+0 10 20 30 40 80 110 140 170 200 300 400 500 600 700 800 900

requirements.txt

@@ -17,4 +17,5 @@ sphinx
 sphinx_rtd_theme
 pytest-json-report
 statsmodels
-ivimnet
+ivimnet
+nlopt