Adds Docker build and GHA test of container

.github/workflows/build_and_test_cli.yml

@@ -1,13 +1,13 @@
-# Workflow to build nii2dcm and test different command line interface (CLI) options
+# Workflow to build nii2dcm, run unit tests and then execute command line interface (CLI) end-to-end
 
-name: Build nii2dcm
+name: Build & Test nii2dcm
 
 on:
   pull_request:
 
 jobs:
-  build-and-test:
-    name: Build
+  venv-build-and-test:
+    name: venv + E2E
 
     runs-on: ${{ matrix.os }}
 
@@ -57,6 +57,10 @@ jobs:
         nii2dcm -h
         nii2dcm -v
 
+    - name: Run unit tests
+      run: |
+        pytest tests/
+
     - name: Test DicomMRISVR creation
       run: |
         # run nii2dcm
@@ -65,3 +69,53 @@ jobs:
         ls ./output
         # assert DICOM files exist
         [ -f "./output/IM_0001.dcm" ] && echo "Output DICOM file exists" || exit 1
+
+    - name: Build pytest coverage file
+      run: |
+        pytest --junitxml=pytest.xml --cov-report=term-missing:skip-covered --cov=nii2dcm tests/ | tee pytest-coverage.txt ; echo $?
+
+    - name: Pytest coverage comment
+      id: coverageComment
+      uses: MishaKav/pytest-coverage-comment@main
+      with:
+        pytest-coverage-path: ./pytest-coverage.txt
+        junitxml-path: ./pytest.xml
+        default-branch: unit-tests
+
+    - name: Update Coverage Badge
+      uses: schneegans/dynamic-badges-action@v1.7.0
+      with:
+        auth: ${{ secrets.PYTEST_COVERAGE_COMMENT }}
+        gistID: 57ef8057d04f67dbe6e64df410b83079
+        filename: nii2dcm-pytest-coverage-comment.json
+        label: Coverage Report
+        message: ${{ steps.coverageComment.outputs.coverage }}
+        color: ${{ steps.coverageComment.outputs.color }}
+        namedLogo: python
+
+  container-build-and-test:
+    name: Container
+
+    runs-on: ${{ matrix.os }}
+
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ ubuntu-latest ]
+        python-version: [ '3.9' ]
+
+    steps:
+      - uses: actions/checkout@v3
+        with:
+          fetch-depth: 0
+
+      - name: Build container
+        run: |
+          docker build -t nii2dcm --progress=plain --no-cache .
+          docker ps
+
+      - name: Test nii2dcm container
+        run: |
+          docker run nii2dcm -h
+          echo "nii2dcm version:"
+          docker run nii2dcm -v

.github/workflows/publish_pypi.yml

@@ -27,7 +27,7 @@ permissions:
   actions: write
 
 jobs:
-  testpypi-publish:
+  pypi-publish:
 
     name: Publish to PyPI
     runs-on: ubuntu-latest
@@ -86,6 +86,7 @@ jobs:
         time: '150'  # seconds
 
     - name: Install latest PyPI version in fresh venv
+      id: attempt1
       run: |
         NII2DCM_VERSION=`echo "$(nii2dcm -v)"`
         echo $NII2DCM_VERSION
@@ -97,3 +98,58 @@ jobs:
         nii2dcm -h
         echo "nii2dcm version:"
         nii2dcm -v
+      continue-on-error: true
+
+    - name: Wait longer
+      if: steps.attempt1.outcome != 'success'
+      uses: GuillaumeFalourd/wait-sleep-action@v1
+      with:
+        time: '150'  # seconds
+
+    - name: Re-attempt PyPI install
+      if: steps.attempt1.outcome != 'success'
+      run: |
+        NII2DCM_VERSION=`echo "$(nii2dcm -v)"`
+        echo $NII2DCM_VERSION
+        python -m venv nii2dcm-temp
+        source nii2dcm-temp/bin/activate
+        pip install --upgrade pip
+        pip install setuptools wheel
+        pip install nii2dcm==$NII2DCM_VERSION
+        nii2dcm -h
+        echo "nii2dcm version:"
+        nii2dcm -v
+
+  ghcr-publish:
+    needs: pypi-publish
+    runs-on: ubuntu-latest
+
+    permissions:
+      contents: read
+      packages: write
+
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v4
+
+      - name: Log in to GHCR
+        uses: docker/login-action@v3
+        with:
+          registry: ghcr.io
+          username: ${{ secrets.GHCR_USERNAME }}
+          password: ${{ secrets.GHCR_TOKEN }}
+
+      - name: Extract metadata (tags, labels) for Docker
+        id: meta
+        uses: docker/metadata-action@v5
+        with:
+          images: |
+            ghcr.io/tomaroberts/nii2dcm
+
+      - name: Build and push Docker image
+        uses: docker/build-push-action@v5
+        with:
+          context: .
+          push: true
+          tags: ${{ steps.meta.outputs.tags }}
+          labels: ${{ steps.meta.outputs.labels }}

.github/workflows/publish_testpypi.yml

@@ -12,6 +12,7 @@
 # They are provided by a third-party and are governed by
 # separate terms of service, privacy policy, and support
 # documentation.
+#
 
 name: Publish package to TestPyPI
 
@@ -85,6 +86,28 @@ jobs:
         time: '150'  # seconds
 
     - name: Install latest TestPyPI version in fresh venv
+      id: attempt1
+      run: |
+        NII2DCM_VERSION=`echo "$(nii2dcm -v)"`
+        echo $NII2DCM_VERSION
+        python -m venv nii2dcm-temp
+        source nii2dcm-temp/bin/activate
+        pip install --upgrade pip
+        pip install setuptools wheel
+        pip install --index-url https://test.pypi.org/simple/ --extra-index-url https://pypi.org/simple/ nii2dcm==$NII2DCM_VERSION
+        nii2dcm -h
+        echo "nii2dcm version:"
+        nii2dcm -v
+      continue-on-error: true
+
+    - name: Wait longer
+      if: steps.attempt1.outcome != 'success'
+      uses: GuillaumeFalourd/wait-sleep-action@v1
+      with:
+        time: '150'  # seconds
+
+    - name: Re-attempt TestPyPI install
+      if: steps.attempt1.outcome != 'success'
       run: |
         NII2DCM_VERSION=`echo "$(nii2dcm -v)"`
         echo $NII2DCM_VERSION

.gitignore

@@ -48,6 +48,8 @@ coverage.xml
 .hypothesis/
 .pytest_cache/
 cover/
+pytest-coverage.txt
+pytest.xml
 
 # Sphinx documentation
 docs/_build/

Dockerfile

@@ -0,0 +1,29 @@
+# Use the official Python image as the base image
+FROM python:3.9-slim
+
+LABEL org.opencontainers.image.source https://github.com/tomaroberts/nii2dcm
+
+# Setup
+COPY . /home/nii2dcm
+WORKDIR /home/nii2dcm
+
+# Install system dependencies
+RUN apt-get update && apt-get install -y \
+    bash git \
+    && apt-get clean
+
+# Update base packages
+RUN pip install --upgrade pip && \
+    pip install setuptools wheel
+
+# Install nii2dcm requirements
+RUN pip install -r requirements.txt
+
+# Build package from source
+RUN pip install .
+
+# Test nii2dcm install
+# To see output locally during build process: docker build -t nii2dcm --progress=plain .
+RUN nii2dcm -h
+
+ENTRYPOINT ["nii2dcm"]

README.md

@@ -20,6 +20,10 @@
     ·
     <a href="https://github.com/tomaroberts/nii2dcm/issues">Request Feature</a>
   </p>
+  <p align="center">
+    <img src="https://github.com/tomaroberts/nii2dcm/actions/workflows/build_and_test_cli.yml/badge.svg?branch=unit-tests">
+    <img src="https://img.shields.io/endpoint?url=https://gist.githubusercontent.com/tomaroberts/57ef8057d04f67dbe6e64df410b83079/raw/nii2dcm-pytest-coverage-comment.json"> 
+</p>
 </div>
 
 
@@ -138,6 +142,26 @@ Currently, attributes to transfer are [listed here in the DicomMRI class](https:
 <p align="right">(<a href="#readme-top">back to top</a>)</p>
 
 
+<!-- Docker -->
+## Docker
+nii2dcm is also available as a Docker container. 
+
+Pull the latest container with:
+```shell
+docker pull ghcr.io/tomaroberts/nii2dcm/nii2dcm:latest
+```
+
+Run the containerised nii2dcm:
+```shell
+# display nii2dcm version
+docker run nii2dcm -v
+
+# perform nii2dcm conversion
+docker run nii2dcm nifti-file.nii.gz dicom-output-directory/ -d MR
+```
+
+<p align="right">(<a href="#readme-top">back to top</a>)</p>
+
 <!-- ROADMAP -->
 ## Roadmap
 

nii2dcm/__main__.py

@@ -24,7 +24,7 @@ def cli(args=None):
     parser.add_argument("input_file", type=str, help="[.nii/.nii.gz] input NIfTI file")
     parser.add_argument("output_dir", type=str, help="[directory] output DICOM path")
     parser.add_argument(
-        "-d","--dicom_type",
+        "-d", "--dicom_type",
         type=str,
         help="[string] type of DICOM. Available types: MR, SVR."
     )

nii2dcm/_version.py

@@ -1,2 +1,2 @@
 import dunamai as _dunamai
-__version__ = _dunamai.get_version("nii2dcm", third_choice=_dunamai.Version.from_any_vcs).serialize()
+__version__ = _dunamai.get_version("nii2dcm", third_choice=_dunamai.Version.from_any_vcs).serialize()

nii2dcm/dcm.py

@@ -11,7 +11,6 @@
 import pydicom as pyd
 from pydicom.dataset import FileDataset, FileMetaDataset
 
-from nii2dcm.utils import dcm_dictionary_update
 from nii2dcm.modules.patient import Patient
 from nii2dcm.modules.general_study import GeneralStudy
 from nii2dcm.modules.patient_study import PatientStudy
@@ -67,7 +66,7 @@
 
         """
         Set Dicom Date/Time
-        Important: doing this once sets all Instances/Series/Study creation dates and times to the same values. Whereas, 
+        Important: doing this once sets all Instances/Series/Study creation dates and times to the same values. Whereas,
         doing this within the Modules would every so slightly offset the times
         """
         # TODO shift to utils.py and propagate to Modules, or, create method within this Dicom class
@@ -209,7 +208,7 @@
         super().__init__(filename)
 
         """
         Set DICOM attributes which are located outside of the MR Image Module to MR-specific values 
         """
         self.ds.Modality = 'MR'
 
@@ -302,4 +301,4 @@
             'RequestingService',
         ]
 
 

nii2dcm/dcm_writer.py

@@ -6,19 +6,19 @@
 import pydicom as pyd
 
 
-def write_slice(dcm, img_data, instance_index, output_dir):
+def write_slice(dcm, img_data, slice_index, output_dir):
     """
     write a single DICOM slice
 
     dcm – nii2dcm DICOM object
     img_data - [nX, nY, nSlice] image pixel data, such as from NIfTI file
-    instance_index – instance index (important: counts from 0)
+    slice_index – slice index in nibabel img_data array (important: counts from 0, whereas DICOM instances count from 1)
     output_dir – output DICOM file save location
     """
 
-    output_filename = r'IM_%04d.dcm' % (instance_index + 1)  # begin filename from 1, e.g. IM_0001.dcm
+    output_filename = r'IM_%04d.dcm' % (slice_index + 1)  # begin filename from 1, e.g. IM_0001.dcm
 
-    img_slice = img_data[:, :, instance_index]
+    img_slice = img_data[:, :, slice_index]
 
     # Instance UID – unique to current slice
     dcm.ds.SOPInstanceUID = pyd.uid.generate_uid(None)

nii2dcm/modules/mr_image.py

@@ -24,28 +24,28 @@
         # https://dicom.nema.org/medical/Dicom/current/output/chtml/part03/sect_C.8.3.html#sect_C.8.3.1.1.1
         # For now, will omit thereby inheriting parent value
         # self.ds.ImageType = ''
-    
+
         self.ds.SamplesPerPixel = 1
-    
+
         # PhotometricInterpretation
         # TODO: decide MONOCHROME1 or MONOCHROME2 as default
         # https://dicom.nema.org/medical/Dicom/current/output/chtml/part03/sect_C.7.6.3.html#sect_C.7.6.3.1.2
         self.ds.PhotometricInterpretation = 'MONOCHROME2'
 
         # PresentationLUTShape
         # depends on PhotometricInterpretation: https://dicom.innolitics.com/ciods/mr-image/general-image/20500020
         if self.ds.PhotometricInterpretation == 'MONOCHROME2':
             self.ds.PresentationLUTShape = 'IDENTITY'
         elif self.ds.PhotometricInterpretation == 'MONOCHROME1':
             self.ds.PresentationLUTShape = 'INVERSE'
 
         # Bits Allocated
         # defined to equal 16 for MR Image Module
         # https://dicom.nema.org/medical/Dicom/current/output/chtml/part03/sect_C.8.3.html#sect_C.8.3.1.1.4
         self.ds.BitsAllocated = 16
         self.ds.BitsStored = 12
         self.ds.HighBit = self.ds.BitsStored - 1
 
         self.ds.ScanningSequence = 'RM'  # :missing:, 'RM' = Research Mode
         self.ds.SequenceVariant = ''  # :missing:
         self.ds.ScanOptions = ''  # :missing:
@@ -89,10 +89,10 @@
         self.ds.TemporalPositionIdentifier = ''  # :missing:
         self.ds.NumberOfTemporalPositions = ''
         self.ds.TemporalResolution = ''  # :missing:
 
         # Currently omitting, but part of NEMA MR Image module:
         # NEMA Table 10-7 “General Anatomy Optional Macro Attributes”
 
         # Currently omitting, but part of NEMA MR Image module:
         # NEMA Table 10-25 “Optional View and Slice Progression Direction Macro Attributes”