Merge pull request #33 from tomaroberts/dunamai-production-fix

Fixes issue with pip install related to dunamai implementation

.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 +69,52 @@ 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
+
+ - 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
@@ -70,7 +70,7 @@ jobs:
 
  - name: Create dist/
  run: |
- python setup.py sdist bdist_wheel
+ python setup.py bdist_wheel
  twine check dist/*
 
  - name: Publish package to PyPI
@@ -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

@@ -12,10 +12,12 @@
 # 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
 
 on:
+ pull_request:
  push:
  branches:
  - main
@@ -67,7 +69,7 @@ jobs:
 
  - name: Create dist/
  run: |
- python setup.py sdist bdist_wheel
+ python setup.py bdist_wheel
  twine check dist/*
 
  - name: Publish package to TestPyPI
@@ -84,6 +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>
 
 
@@ -53,6 +57,7 @@ To install and run nii2dcm locally, you have two options:
 
 ### pip
 
+Create a new Python virtual environment, then:
 ```shell
 pip install nii2dcm
 ```
@@ -74,7 +79,6 @@ python -m pip install --upgrade pip
 
 Install dependencies and nii2dcm:
 ```sh
-pip install setuptools wheel
 pip install -r requirements.txt
 pip install .
 ```
@@ -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

@@ -23,7 +23,11 @@ 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", type=str, help="[string] type of DICOM. e.g. MR, CT, US, XR, etc.")
+ parser.add_argument(
+ "-d", "--dicom_type",
+ type=str,
+ help="[string] type of DICOM. Available types: MR, SVR."
+ )
  parser.add_argument("-r", "--ref_dicom", type=str, help="[.dcm] Reference DICOM file for Attribute transfer")
  parser.add_argument("-v", "--version", action="version", version=__version__)
 

nii2dcm/_version.py

@@ -1,2 +1,2 @@
-from dunamai import Version, Style
-__version__ = Version.from_git().serialize(metadata=False, style=Style.SemVer)
+import dunamai as _dunamai
+__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 @@ def __init__(self, filename=nii2dcm_temp_filename):
 
  """
  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

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

@@ -24,9 +24,9 @@ def __init__(self):
  # 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

requirements.txt

@@ -1,3 +1,5 @@
+setuptools
+wheel
 numpy==1.23.2
 matplotlib==3.6.2
 nibabel==5.0.0

setup.py

@@ -3,5 +3,5 @@
 
 setup(
  name="nii2dcm",
- version=Version.from_git().serialize(metadata=False, style=Style.SemVer),
+ version=Version.from_any_vcs().serialize(metadata=False, style=Style.SemVer),
 )