Aide app

.dockerignore

@@ -0,0 +1,5 @@
+/tests/
+/documents/
+/.github/
+/venv/
+*.log*

.github/workflows/test_development_mrs.yml

@@ -8,75 +8,35 @@ on:
   # Allows you to run this workflow manually from the Actions tab
   workflow_dispatch:
 
-# A workflow run is made up of one or more jobs that can run sequentially or in parallel
 jobs:
-  # This workflow contains a single job called "build"
-  build:
-    # The type of runner that the job will run on
-    runs-on: ubuntu-latest
-
-    # Steps represent a sequence of tasks that will be executed as part of the job
-    steps:
-      # Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it
-      - uses: actions/checkout@v2
 
-      - name: Set up Python
-        uses: actions/setup-python@v2
-        with:
-          python-version: 3.6
+  build-and-test:
 
-      - name: setup virtual environment
-        run: |
-          python3.6 -m venv env
-          source ./env/bin/activate
-          echo "VIRTUAL ENV:" $VIRTUAL_ENV
-          python3.6 -m pip install --upgrade pip
-
-      - name: Install system requirements
-        run: |
-          source ./env/bin/activate
-          sudo apt-get update
-          sudo apt-get install default-libmysqlclient-dev poppler-utils wget dcmtk gnuplot libcairo2-dev libtiff5-dev libjpeg62 zlib1g-dev libfreetype6-dev liblcms2-dev libwebp-dev tcl8.6-dev tk8.6-dev python3-tk ghostscript -y
-          gs --version
-          sudo sed -i '/disable ghostscript format types/,+6d' /etc/ImageMagick-6/policy.xml
-#           https://stackoverflow.com/questions/52998331/imagemagick-security-policy-pdf-blocking-conversion
+    runs-on: ubuntu-latest
 
-      - name: install python packages
-        run: |
-          source ./env/bin/activate
-          python3.6 -m pip install -r requirements.txt
-          python3.6 -m pip install git+https://${{ secrets.dicomserver_uname }}:${{ secrets.dicomserver_pw }}@bitbucket.org/gsttmri/[email protected]
+    steps:
+      - name: checkout
+        uses: actions/checkout@v2
 
-      - name: GA fixes # https://github.com/actions/virtual-environments/issues/4799
-        run: |
-          sudo apt-get update
-          sudo apt-get remove mysql* && sudo apt-get install -y mysql-server libmysqlclient-dev
+      - name: Build and tag image
+        run: docker build -t mrs-tarquin:latest .
 
-      - name: Install Tarquin
-        run: |
-          source ./env/bin/activate
-          mkdir ../tarquin_folder && wget -O tarquin.tar.gz https://sourceforge.net/projects/tarquin/files/TARQUIN_4.3.11/TARQUIN_Linux_4.3.11.tar.gz/download && tar -xzf tarquin.tar.gz -C ../tarquin_folder && rm tarquin.tar.gz
-          mv ../tarquin_folder/TARQUIN_Linux_4.3.11_RC/tarquin /usr/local/bin/tarquin && ln -s /usr/bin/gnuplot /usr/local/bin/gnuplot
+      - name: Setup flake8 annotations
+        uses: rbialon/flake8-annotations@v1
 
-      - name: print env info
+      - name: Lint with flake8
         run: |
-          python3 -c "import sys; print('python3 sys.prefix: ' + sys.prefix)"
-          python3 -c "import sys; print('python3 sys.base_prefix: ' + sys.base_prefix)"
-          source ./env/bin/activate
-          python3 -c "import sys; print('post activate python3 sys.prefix' + sys.prefix)"
-          python3 -c "import sys; print('post activate python3 sys.base_prefix: ' + sys.base_prefix)"
+          # stop the build if there are Python syntax errors or undefined names
+          docker run --mount type=bind,source=$(pwd),target=/mrs mrs-tarquin flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
+          # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
+          docker run --mount type=bind,source=$(pwd),target=/mrs mrs-tarquin flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
 
-      - name: Run MRS tests
-        run: |
-          source ./env/bin/activate
-          pwd
-          python3.6 -m pytest --continue-on-collection-errors tests/
-          set -o pipefail
-          pytest --junitxml=pytest.xml --cov-report=term-missing:skip-covered tests/ | tee pytest-coverage.txt ; echo $?
+      - name: run tests
+        run: docker run --mount type=bind,source=$(pwd),target=/mrs mrs-tarquin pytest --junitxml=pytest.xml --cov-report=term-missing:skip-covered --cov=mrs --continue-on-collection-errors tests/ | tee pytest-coverage.txt ; echo $?
 
-      - name: Pytest coverage
+      - name: report coverage
         id: coverageComment
         uses: MishaKav/pytest-coverage-comment@main
         with:
-          pytest-coverage-path: ./pytest-coverage.txt
-          junitxml-path: ./pytest.xml
+          pytest-coverage-path: pytest-coverage.txt
+          junitxml-path: pytest.xml

.github/workflows/test_production_mrs.yml

@@ -8,84 +8,41 @@ on:
       - "main"
       - "release/*"
 
-
   # Allows you to run this workflow manually from the Actions tab
   workflow_dispatch:
 
-# A workflow run is made up of one or more jobs that can run sequentially or in parallel
 jobs:
-  # This workflow contains a single job called "build"
-  build:
-    # The type of runner that the job will run on
-    runs-on: ubuntu-latest
-
-    # Steps represent a sequence of tasks that will be executed as part of the job
-    steps:
-      # Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it
-      - uses: actions/checkout@v2
-
-      - name: Set up Python
-        uses: actions/setup-python@v2
-        with:
-          python-version: 3.6
 
-      - name: setup virtual environment
-        run: |
-          python3.6 -m venv env
-          source ./env/bin/activate
-          echo "VIRTUAL ENV:" $VIRTUAL_ENV
-          python3.6 -m pip install --upgrade pip
+  build-and-test:
 
-      - name: Install system requirements
-        run: |
-          source ./env/bin/activate
-          sudo apt-get update
-          sudo apt-get install default-libmysqlclient-dev poppler-utils wget dcmtk gnuplot libcairo2-dev libtiff5-dev libjpeg62 zlib1g-dev libfreetype6-dev liblcms2-dev libwebp-dev tcl8.6-dev tk8.6-dev python3-tk ghostscript -y
-          gs --version
-          sudo sed -i '/disable ghostscript format types/,+6d' /etc/ImageMagick-6/policy.xml
-#           https://stackoverflow.com/questions/52998331/imagemagick-security-policy-pdf-blocking-conversion
-
-      - name: install python packages
-        run: |
-          source ./env/bin/activate
-          python3.6 -m pip install -r requirements.txt
-          python3.6 -m pip install git+https://${{ secrets.dicomserver_uname }}:${{ secrets.dicomserver_pw }}@bitbucket.org/gsttmri/[email protected]
-
-      - name: GA fixes # https://github.com/actions/virtual-environments/issues/4799
-        run: |
-          sudo apt-get update
-          sudo apt-get remove mysql* && sudo apt-get install -y mysql-server libmysqlclient-dev
+    runs-on: ubuntu-latest
 
-      - name: Install Tarquin
-        run: |
-          source ./env/bin/activate
-          mkdir ../tarquin_folder && wget -O tarquin.tar.gz https://sourceforge.net/projects/tarquin/files/TARQUIN_4.3.11/TARQUIN_Linux_4.3.11.tar.gz/download && tar -xzf tarquin.tar.gz -C ../tarquin_folder && rm tarquin.tar.gz
-          mv ../tarquin_folder/TARQUIN_Linux_4.3.11_RC/tarquin /usr/local/bin/tarquin && ln -s /usr/bin/gnuplot /usr/local/bin/gnuplot
+    steps:
+      - name: checkout
+        uses: actions/checkout@v2
 
-      - name: print env info
-        run: |
-          python3 -c "import sys; print('python3 sys.prefix: ' + sys.prefix)"
-          python3 -c "import sys; print('python3 sys.base_prefix: ' + sys.base_prefix)"
-          source ./env/bin/activate
-          python3 -c "import sys; print('post activate python3 sys.prefix' + sys.prefix)"
-          python3 -c "import sys; print('post activate python3 sys.base_prefix: ' + sys.base_prefix)"
+      - name: Build and tag image
+        run: docker build -t mrs-tarquin:latest .
 
-      - name: Run MRS tests
-        run: |
-          source ./env/bin/activate
-          pwd
-          python3.6 -m pytest --continue-on-collection-errors tests/
+      - name: run tests
+        run: docker run --mount type=bind,source=$(pwd),target=/mrs mrs-tarquin pytest --junitxml=pytest.xml --cov-report=term-missing:skip-covered --cov=mrs --continue-on-collection-errors tests/ | tee pytest-coverage.txt ; echo $?
 
-#      - name: Update coverage Badge
-#        if: github.ref == 'refs/heads/main'  # only on main
-#        uses: schneegans/[email protected]
-#        with:
-#          auth: ${{ secrets.PYTEST_COVERAGE_COMMENT }}
-#          gistID: ba102d5f3e592fcd50451c2eff8a803d
-#          filename: mlops_pytest-coverage-comment.json
-#          label: Test coverage
-#          message: ${{ steps.coverageComment.outputs.coverage }}
-#          color: ${{ steps.coverageComment.outputs.color }}
-#          namedLogo: python
-#          logo: https://img.shields.io/badge/coverage-{{ steps.coverageComment.outputs.coverage }}-{{ steps.coverageComment.outputs.color }}.svg
+      - name: Pytest coverage comment
+        id: coverageComment
+        uses: MishaKav/pytest-coverage-comment@main
+        with:
+          pytest-coverage-path: ./pytest-coverage.txt
+          junitxml-path: ./pytest.xml
 
+      - name: Update coverage Badge
+        if: github.ref == 'refs/heads/main'  # only on main
+        uses: schneegans/[email protected]
+        with:
+          auth: ${{ secrets.PYTEST_COVERAGE_COMMENT }}
+          gistID: e1aa11345e5c62d9ea100a83a0f4bfc9
+          filename: MRS_cov_badge.json
+          label: Test coverage
+          message: ${{ steps.coverageComment.outputs.coverage }}
+          color: ${{ steps.coverageComment.outputs.color }}
+          namedLogo: python
+          logo: https://img.shields.io/badge/coverage-{{ steps.coverageComment.outputs.coverage }}-{{ steps.coverageComment.outputs.color }}.svg

.gitignore

@@ -127,4 +127,9 @@ dmypy.json
 
 # Pyre type checker
 .pyre/
-.idea
+.idea
+pytest-coverage.txt
+pytest.xml
+
+.idea/
+.pytest_cache/

Dockerfile

@@ -0,0 +1,25 @@
+FROM python:3.9-slim
+
+# Install tarquin
+RUN apt-get update -y && apt-get install -y gnuplot ghostscript git wget imagemagick
+RUN mkdir ../tarquin_folder
+RUN wget -O tarquin.tar.gz https://sourceforge.net/projects/tarquin/files/TARQUIN_4.3.11/TARQUIN_Linux_4.3.11.tar.gz/download
+RUN tar -xzf tarquin.tar.gz -C ../tarquin_folder
+RUN rm tarquin.tar.gz
+RUN mv ../tarquin_folder/TARQUIN_Linux_4.3.11_RC/tarquin /usr/local/bin/tarquin
+RUN ln -s /usr/bin/gnuplot /usr/local/bin/gnuplot
+
+COPY requirements.txt mrs/requirements.txt
+RUN pip install --upgrade pip
+RUN pip install -r mrs/requirements.txt
+
+RUN sed -i '/disable ghostscript format types/,+6d' /etc/ImageMagick-6/policy.xml
+COPY mrs/ mrs/mrs/
+COPY config/ mrs/config/
+COPY main.py mrs/main.py
+
+WORKDIR /mrs
+
+ENV MANIFEST_PATH=config/manifest.json
+
+CMD ["python", "main.py"]

README.md

@@ -1,3 +1,26 @@
+<!-- PROJECT HEADING -->
+<br />
+<p align="center">
+<a href="https://github.com/GSTT-CSC/0018-ds-mr-spectroscopy">
+    <img src="https://raw.githubusercontent.com/GSTT-CSC/gstt-csc.github.io/main/assets/transparent-CSC-logo-cropped.png" alt="Logo" width="50%">
+  </a>
+<h1 align="center">MR Spectroscopy</h1>
+<p align="center">
+<br />
+<a href="https://github.com/GSTT-CSC/0018-ds-mr-spectroscopy"><strong>Explore the docs »</strong></a>
+<br />
+<br />
+<a href="https://github.com/GSTT-CSC/0018-ds-mr-spectroscopy">View repo</a>
+·
+<a href="https://github.com/GSTT-CSC/0018-ds-mr-spectroscopy/issues">Report Bug</a>
+·
+<a href="https://github.com/GSTT-CSC/0018-ds-mr-spectroscopy/issues">Request Feature</a>
+</p>
+<p align="center">
+  <img src="https://github.com/GSTT-CSC/0018-ds-mr-spectroscopy/workflows/test_production_mrs.yml/badge.svg?branch=main">
+  <img src="https://img.shields.io/endpoint?url=https://gist.githubusercontent.com/laurencejackson/e1aa11345e5c62d9ea100a83a0f4bfc9/MRS_cov_badge.json">
+</p>
+
 # MR Spectroscopy
 
 Clinical MRS at the end of a standard MRI examination obtains functional information in addition to anatomical information. 

config/config.py

@@ -0,0 +1,22 @@
+import configparser
+import os
+import shutil
+import json
+
+manifest = json.load(open('config/manifest.json'))
+
+APP_DATA_DIR = '/mrs_app_data'
+CONFIG_DIR = os.path.dirname(os.path.realpath(__file__))  # same dir as this file
+VERSION = manifest['model_version']
+
+if os.path.exists(APP_DATA_DIR):
+    shutil.rmtree(APP_DATA_DIR)
+os.makedirs(APP_DATA_DIR, exist_ok=True)
+
+# Create configparser reader objects
+SETTINGS = configparser.ConfigParser()
+
+# This makes a list of config files for both server and local files
+config_files = list(os.path.join(CONFIG_DIR, x) for x in os.listdir(CONFIG_DIR) if x.endswith('cfg'))
+# Read config files
+SETTINGS.read(config_files)

config/manifest.json

@@ -0,0 +1,7 @@
+{
+  "model_description": "Magnetic Resonance Spectroscopy using Tarquin",
+  "predicate": "DICOM_Modality == 'MR' AND DICOM_Manufacturer == 'Philips Medical Systems' OR DICOM_Manufacturer == 'Siemens' OR DICOM_Manufacturer == 'SIEMENS' OR DICOM_Manufacturer == 'siemens'",
+  "mode": "QA",
+  "model_name": "mrs-tarquin",
+  "model_version": "0.1.2"
+}

config/mrs.cfg

@@ -0,0 +1,19 @@
+[mrs]
+qa_email_list = [email protected],[email protected],[email protected]
+clinical_email_list = [email protected]
+job_ref_acq_time_diff_thresh = 10
+stat_thresh = 1.5
+gnuplot = /usr/local/bin/gnuplot
+
+[philips_qa_tarquin_params]
+start_pnt = 10
+end_pnt = 1000
+ref = 4.85
+ref_signals = 1h_naa
+int_basis = braino
+w_conc = 55556
+w_att = 0.7
+
+[email]
+nhs_user=dsfsa
+nhs_pass=dsc

main.py

@@ -0,0 +1,5 @@
+from aide_sdk.application import AideApplication
+from mrs.MRSOperator import MRSOperator
+
+if __name__ == "__main__":
+    AideApplication.start(operator=MRSOperator())

mrs/MRSOperator.py

@@ -0,0 +1,33 @@
+from aide_sdk.inference.aideoperator import AideOperator
+from aide_sdk.model.operatorcontext import OperatorContext
+
+from mrs.dicom.study import Study
+from mrs.processing.MRSTask import MRSTask
+from mrs.tools.tools import check_valid_mrs
+from aide_sdk.logger.logger import LogManager
+logger = LogManager.get_logger()
+
+
+class MRSOperator(AideOperator):
+    """
+    MRSOperator class
+
+    This class is used to perform MRS processing, and then create a report and archive it to PACS.
+    """
+
+    def process(self, context: OperatorContext) -> OperatorContext:
+        """
+        Process the MRS task.
+        :param context:
+        :return: OperatorContext
+        """
+        mrs_study = Study(study_dir=context.origin.file_path)
+
+        if check_valid_mrs(mrs_study):
+            logger.info(f'Study {mrs_study} valid for MRS')
+            mrs_task = MRSTask(mrs_study, context)
+            context = mrs_task.process()
+        else:
+            context.set_failure("Data is not valid for MRS")
+
+        return context

mrs/__init__.py

@@ -0,0 +1 @@
+VERSION = '0.1.1'