diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
index 44b2d6d..e8a7020 100644
--- a/.github/workflows/main.yml
+++ b/.github/workflows/main.yml
@@ -13,10 +13,11 @@ jobs:
runs-on: ${{ matrix.os }}
strategy:
matrix:
- # os: [ubuntu-latest]
- # python-version: ["3.12"]
os: [ubuntu-latest, macos-latest, macos-14]
- python-version: ["3.12", "3.11"]
+ python-version: ["3.12", "3.11", "3.10"]
+ # include:
+ # - os: ubuntu-latest
+ # python-version: "3.9"
steps:
- uses: actions/checkout@v3
@@ -122,12 +123,6 @@ jobs:
with:
fetch-depth: 0
- - name: Install poetry
- uses: snok/install-poetry@v1
-
- - name: Install package
- run: poetry install
-
# This action uses Python Semantic Release v8
# What this action does:
# - Determines the next version number based on the commit history
@@ -140,154 +135,97 @@ jobs:
with:
github_token: ${{ secrets.GITHUB_TOKEN }}
- - name: Test Outputs of semantic release step
- run: |
- echo "${{ steps.release.outputs.released }}"
- echo "${{ steps.release.outputs.version }}"
- echo "${{ steps.release.outputs.tag }}"
-
- - name: Install packaging-related tool
- run:
- python3 -m pip install build twine
-
- # Build Package step:
- # After semantic release, we should have a new tag if the commit history
- # has been updated. If there isnt a new tag, then we dont need to build
- # a new package. If there is a new tag, then we need to build a new package
- # and publish it to PyPI
- - name: Build package
- if: steps.release.outputs.released == 'true'
- run: |
- poetry version ${{ steps.release.outputs.version }}
- python -m build --sdist --wheel --outdir dist/ .
-
- - name: Publish package distributions to PyPI
- if: steps.release.outputs.released == 'true'
- uses: pypa/gh-action-pypi-publish@release/v1
- with:
- verbose: true
- user: __token__
- password: ${{ secrets.PYPI_API_TOKEN }}
-
- - name: Set up QEMU
- if: steps.release.outputs.released == 'true'
- uses: docker/setup-qemu-action@v3
-
- - name: Set up Docker Buildx
- if: steps.release.outputs.released == 'true'
- uses: docker/setup-buildx-action@v3
-
- - name: Login to Docker Hub
- if: steps.release.outputs.released == 'true'
- uses: docker/login-action@v3
- with:
- username: ${{ secrets.DOCKERHUB_USERNAME }}
- password: ${{ secrets.DOCKERHUB_TOKEN }}
-
- - name: Login to the GitHub Container Registry
- if: steps.release.outputs.released == 'true'
- uses: docker/login-action@v3
- with:
- registry: ghcr.io
- username: ${{ github.actor }}
- password: ${{ secrets.GITHUB_TOKEN }}
-
- - name: Extract metadata (tags, labels) for Docker
- id: meta
- uses: docker/metadata-action@v3
- with:
- images: |
- ${{ secrets.DOCKERHUB_USERNAME }}/nbiatoolkit:${{ steps.release.outputs.tag }}
- ghcr.io/${{ github.repository }}/nbiatoolkit:${{ steps.release.outputs.tag }}
-
- - name: Build
- if: steps.release.outputs.released == 'true'
- uses: docker/build-push-action@v5
- with:
- context: .
- platforms: linux/amd64,linux/arm64
- file: ./Dockerfile
- push: true
- tags: |
- ${{ secrets.DOCKERHUB_USERNAME }}/nbiatoolkit:${{ steps.release.outputs.tag }}
- ${{ secrets.DOCKERHUB_USERNAME }}/nbiatoolkit:latest
- ghcr.io/${{ github.repository }}/nbiatoolkit:${{ steps.release.outputs.tag }}
- ghcr.io/${{ github.repository }}/nbiatoolkit:latest
- labels: ${{ steps.meta.outputs.labels }}
-
- test_install_withPyPi:
+ Publish-To-PyPi:
needs: Continuous-Deployment
- runs-on: ${{ matrix.os }}
- strategy:
- matrix:
- os: [ubuntu-latest, macos-latest, macos-14]
- python-version: ["3.12", "3.11", "3.10"]
-
+ if: needs.Continuous-Deployment.outputs.released == 'true'
+ runs-on: ubuntu-latest
steps:
- - uses: actions/checkout@v3
+ - name: Checkout code
+ uses: actions/checkout@v3
- - name: Set up Python ${{ matrix.python-version }}
+ - name: Set up Python 3.12
uses: actions/setup-python@v4
with:
- python-version: ${{ matrix.python-version }}
+ python-version: 3.12
- - name: Install using PyPi
- run: |
- pip install nbiatoolkit;
- NBIAToolkit
+ - name: Install Package-Building Tool
+ run:
+ python3 -m pip install build twine
+ - name: Build package
+ run:
+ python3 -m build --sdist --wheel --outdir dist/
- test_image_with_new_tag:
+ - name: Publish to PyPI
+ uses: pypa/gh-action-pypi-publish@release/v1
+ with:
+ verbose: true
+ user: __token__
+ password: ${{ secrets.PYPI_API_TOKEN }}
+
+ Build-Docker-Images:
needs: Continuous-Deployment
+ if: needs.Continuous-Deployment.outputs.released == 'true'
runs-on: ubuntu-latest
steps:
- name: Checkout code
uses: actions/checkout@v3
- - name: Test Image With new Tag
- run: |
- # test image with latest tag
- docker run --rm \
- ${{ secrets.DOCKERHUB_USERNAME }}/nbiatoolkit:${{ needs.Continuous-Deployment.outputs.tag }} \
- NBIAToolkit
+ - name: Set up QEMU
+ if: steps.release.outputs.released == 'true'
+ uses: docker/setup-qemu-action@v3
+ - name: Set up Docker Buildx
+ if: steps.release.outputs.released == 'true'
+ uses: docker/setup-buildx-action@v3
- test_image_with_latest_tag:
- needs: Continuous-Deployment
- runs-on: ubuntu-latest
- steps:
- - name: Checkout code
- uses: actions/checkout@v2
-
- - name: Test Image with "latest" Tag
- run: |
- docker run --rm \
- ${{ secrets.DOCKERHUB_USERNAME }}/nbiatoolkit:latest \
- NBIAToolkit
+ - name: Login to Docker Hub
+ if: steps.release.outputs.released == 'true'
+ uses: docker/login-action@v3
+ with:
+ username: ${{ secrets.DOCKERHUB_USERNAME }}
+ password: ${{ secrets.DOCKERHUB_TOKEN }}
- Update-README:
- needs: Continuous-Deployment
- runs-on: ubuntu-latest
- # if: jobs.Continuous-Deployment.outputs.released == 'true'
- steps:
- - name: Checkout code
- uses: actions/checkout@v3
+ - name: Login to the GitHub Container Registry
+ if: steps.release.outputs.released == 'true'
+ uses: docker/login-action@v3
+ with:
+ registry: ghcr.io
+ username: ${{ github.actor }}
+ password: ${{ secrets.GITHUB_TOKEN }}
- - name: Get Current branch
- run: |
- echo "Current branch is: ${{ github.ref }}"
- echo "Current branch is: ${{ github.head_ref }}"
- echo "Current branch is: ${{ github.base_ref }}"
- echo "Current branch is: ${{ github.event_name }}"
+ - name: Extract metadata (tags, labels) for Docker
+ id: meta
+ uses: docker/metadata-action@v3
+ with:
+ images: |
+ ${{ secrets.DOCKERHUB_USERNAME }}/nbiatoolkit:${{ needs.Continuous-Deployment.outputs.tag }}
+ ghcr.io/${{ github.repository }}/nbiatoolkit:${{ needs.Continuous-Deployment.outputs.tag }}
- # if main, then git pull main
- if [ "${{ github.ref }}" == "refs/heads/main" ]; then
- git pull origin main
- fi
+ - name: Build and push Docker images
+ uses: docker/build-push-action@v5
+ with:
+ context: .
+ platforms: linux/amd64,linux/arm64
+ file: ./Dockerfile
+ push: true
+ tags: |
+ ${{ secrets.DOCKERHUB_USERNAME }}/nbiatoolkit:${{ needs.Continuous-Deployment.outputs.tag }}
+ ${{ secrets.DOCKERHUB_USERNAME }}/nbiatoolkit:latest
+ ghcr.io/${{ github.repository }}/nbiatoolkit:${{ needs.Continuous-Deployment.outputs.tag }}
+ ghcr.io/${{ github.repository }}/nbiatoolkit:latest
+ labels: ${{ steps.meta.outputs.labels }}
+
+ Test-PyPi-Install:
+ needs: Publish-To-PyPi
+ runs-on: ${{ matrix.os }}
+ strategy:
+ matrix:
+ os: [ubuntu-latest, macos-latest, macos-14]
+ python-version: ["3.12", "3.11", "3.10"]
- # fix diverged branch
- git fetch origin ${{ github.head_ref }}
- git checkout ${{ github.head_ref }}
+ steps:
+ - uses: actions/checkout@v3
- name: Set up Python ${{ matrix.python-version }}
uses: actions/setup-python@v4
@@ -296,57 +234,21 @@ jobs:
- name: Install using PyPi
run: |
- # update pip
- pip install .
+ pip install nbiatoolkit;
NBIAToolkit
- - name: Update README code block
- run: |
- awk '/``` bash NBIAToolkit-Output/ {
- print "``` bash NBIAToolkit-Output";
- print "> NBIAToolkit --version";
- system("NBIAToolkit --version");
- f=1;
- next
- } f && /```/ {
- print "```";
- f=0;
- next
- } !f' README.md > temp && mv temp README.md
-
- - name: Commit and push changes
+ Test-Docker-Image:
+ needs: Build-Docker-Images
+ runs-on: ${{ matrix.os }}
+ strategy:
+ matrix:
+ os: [ubuntu-latest, macos-latest]
+ docker_tag: ["latest", "${{ needs.Continuous-Deployment.outputs.tag }}"]
+
+ steps:
+ - uses: actions/checkout@v3
+
+ - name: Install using Docker
run: |
- LATEST_TAG=$(curl -s \
- "https://api.github.com/repos/${{ github.repository }}/releases/latest" \
- | jq -r .tag_name | sed 's/^v//')
- echo "LATEST_TAG=${LATEST_TAG}"
- # Check for changes
- if [[ $(git status --porcelain) ]]; then
- # Changes are present
- echo "Changes found. Committing and pushing..."
-
- git config --global user.name 'jjjermiah'
- git config --global user.email 'jjjermiah@users.noreply.github.com'
-
- # Add all changes
- git add .
-
- # Commit with a timestamp
- git commit -m "chore: Update README: $LATEST_TAG"
-
- # Push changes to the remote repository
- # if github.head_ref is not null
- # then push to the branch
- # else push to the base branch
- if [ -n "${{ github.head_ref }}" ]; then
- git push origin HEAD:${{ github.head_ref }}
- else
- git push origin HEAD:${{ github.ref }}
- fi
-
-
- echo "Changes committed and pushed successfully."
- else
- # No changes
- echo "No changes found. Nothing to commit or push."
- fi
+ docker pull ${{ secrets.DOCKERHUB_USERNAME }}/nbiatoolkit:${{ matrix.docker_tag }};
+ docker run --rm ${{ secrets.DOCKERHUB_USERNAME }}/nbiatoolkit:${{ matrix.docker_tag }} NBIAToolkit
diff --git a/README.md b/README.md
index b38b701..d4a2c73 100644
--- a/README.md
+++ b/README.md
@@ -16,11 +16,11 @@
[](https://hub.docker.com/r/jjjermiah/nbiatoolkit)
-
[](https://github.com/jjjermiah/nbia-toolkit/issues)
## Table of Contents
+
- [Features](#features)
- [Installation](#installation)
- [Python Usage](#python-usage)
@@ -43,7 +43,7 @@
- ***Validate doownloads with MD5 checksums*** for downloaded images
- **Auto-sort** DICOM files using a user-defined pattern of DICOM tags with specialized ***DICOMSorter class***
-
+See [Developer Notes](devnotes/README.md) for more details on the features and the development process.
## Installation
@@ -93,10 +93,10 @@ For quick access to the NBIA, the toolkit also provides a command line interface
/ |/ / __ |/ // /| | / / / __ \/ __ \/ / //_/ / __/
/ /| / /_/ // // ___ |/ / / /_/ / /_/ / / ,< / / /_
/_/ |_/_____/___/_/ |_/_/ \____/\____/_/_/|_/_/\__/
-
+
Version: 1.0.1
-Available CLI tools:
+Available CLI tools:
getCollections [-h] [-u USERNAME] [-pw PASSWORD] [-p PREFIX]
[-o OUTPUTFILE] [--version]
diff --git a/devnotes/CI-CD_2024-03-17.md b/devnotes/CI-CD_2024-03-17.md
new file mode 100644
index 0000000..c9ee4ce
--- /dev/null
+++ b/devnotes/CI-CD_2024-03-17.md
@@ -0,0 +1,14 @@
+# Continuous Integration and Continuous Deployment Diagram
+
+```mermaid
+graph LR
+ A[Push or Pull Request\nto main] --> B[Unit-Tests]
+ B --> C[Codecov]
+ B --> D[Continuous-Deployment]
+ D --> E[Publish-To-PyPi]
+ D --> F[Build-Docker-Images]
+ E --> G[Test-PyPi-Install]
+ F --> H[Test-Docker-Image]
+ A --> I[Build-Documentation]
+
+```
diff --git a/devnotes/README.md b/devnotes/README.md
new file mode 100644
index 0000000..8bf1b16
--- /dev/null
+++ b/devnotes/README.md
@@ -0,0 +1,4 @@
+# Developer Notes
+
+[CI-CD](CI-CD_2024-03-17.md)
+[Sequence Diagram](Sequence-diagram_2024-03-17.md)
diff --git a/devnotes/class.svg b/devnotes/class.svg
new file mode 100644
index 0000000..205beca
--- /dev/null
+++ b/devnotes/class.svg
@@ -0,0 +1,151 @@
+
+
+
+
+
diff --git a/devnotes/classes_nbiatoolkit.dot b/devnotes/classes_nbiatoolkit.dot
new file mode 100644
index 0000000..36e8385
--- /dev/null
+++ b/devnotes/classes_nbiatoolkit.dot
@@ -0,0 +1,12 @@
+digraph "classes_nbiatoolkit" {
+rankdir=BT
+charset="utf-8"
+"nbiatoolkit.nbia.NBIAClient" [color="#77AADD", fontcolor="black", label=<{NBIAClient|OAuth_client
base_url
headers
logger
return_type
|downloadSeries(SeriesInstanceUID: Union[str, list], downloadDir: str, filePattern: str, overwrite: bool, nParallel: int, Progressbar: bool): bool
getBodyPartCounts(Collection: str, Modality: str, return_type: Optional[Union[ReturnType, str]]): List[dict[Any, Any]] \| pd.DataFrame
getCollectionDescriptions(collectionName: str, return_type: Optional[Union[ReturnType, str]]): List[dict[Any, Any]] \| pd.DataFrame
getCollectionPatientCount(prefix: str, return_type: Optional[Union[ReturnType, str]]): List[dict[Any, Any]] \| pd.DataFrame
getCollections(prefix: str, return_type: Optional[Union[ReturnType, str]]): List[dict[Any, Any]] \| pd.DataFrame
getDICOMTags(SeriesInstanceUID: str, return_type: Optional[Union[ReturnType, str]]): List[dict[Any, Any]] \| pd.DataFrame
getModalityValues(Collection: str, BodyPartExamined: str, Counts: bool, return_type: Optional[Union[ReturnType, str]]): List[dict[Any, Any]] \| pd.DataFrame
getNewPatients(Collection: str, Date: Union[str, datetime], return_type: Optional[Union[ReturnType, str]]): List[dict[Any, Any]] \| pd.DataFrame
getNewSeries(Date: Union[str, datetime], return_type: Optional[Union[ReturnType, str]]): List[dict[Any, Any]] \| pd.DataFrame
getPatients(Collection: str, return_type: Optional[Union[ReturnType, str]]): List[dict[Any, Any]] \| pd.DataFrame
getPatientsByCollectionAndModality(Collection: str, Modality: str, return_type: Optional[Union[ReturnType, str]]): List[dict[Any, Any]] \| pd.DataFrame
getSeries(Collection: str, PatientID: str, StudyInstanceUID: str, Modality: str, SeriesInstanceUID: str, BodyPartExamined: str, ManufacturerModelName: str, Manufacturer: str, return_type: Optional[Union[ReturnType, str]]): List[dict[Any, Any]] \| pd.DataFrame
getSeriesMetadata(SeriesInstanceUID: Union[str, list[str]], return_type: Optional[Union[ReturnType, str]]): List[dict[Any, Any]] \| pd.DataFrame
getStudies(Collection: str, PatientID: str, StudyInstanceUID: str, return_type: Optional[Union[ReturnType, str]]): List[dict[Any, Any]] \| pd.DataFrame
parsePARAMS(params: dict): dict
query_api(endpoint: NBIA_ENDPOINTS, params: dict): List[dict[Any, Any]]
}>, shape="record", style="filled"];
+"nbiatoolkit.utils.nbia_endpoints.NBIA_BASE_URLS" [color="#BBCC33", fontcolor="black", label=<{NBIA_BASE_URLS|name
|}>, shape="record", style="filled"];
+"nbiatoolkit.auth.OAuth2" [color="#77AADD", fontcolor="black", label=<{OAuth2|access_token
api_headers
base_url : NBIA, str
client_id : str
expiry_time : NoneType
fernet_key
password : str
refresh_expiration_time
refresh_expiry : NoneType
refresh_token : str
scope : NoneType
token_expiration_time
token_scope
username : str
|is_logged_out(): bool
is_token_expired(): bool
logout(): None
refresh_token_or_request_new(): None
request_new_access_token()
set_token_data(token_data: dict)
}>, shape="record", style="filled"];
+"nbiatoolkit.utils.nbia_endpoints.ReturnType" [color="#BBCC33", fontcolor="black", label=<{ReturnType|name
|}>, shape="record", style="filled"];
+"nbiatoolkit.auth.OAuth2" -> "nbiatoolkit.nbia.NBIAClient" [arrowhead="diamond", arrowtail="none", fontcolor="green", label="_oauth2_client", style="solid"];
+"nbiatoolkit.utils.nbia_endpoints.NBIA_BASE_URLS" -> "nbiatoolkit.nbia.NBIAClient" [arrowhead="diamond", arrowtail="none", fontcolor="green", label="_base_url", style="solid"];
+"nbiatoolkit.utils.nbia_endpoints.ReturnType" -> "nbiatoolkit.nbia.NBIAClient" [arrowhead="diamond", arrowtail="none", fontcolor="green", label="_return_type", style="solid"];
+"nbiatoolkit.utils.nbia_endpoints.ReturnType" -> "nbiatoolkit.nbia.NBIAClient" [arrowhead="diamond", arrowtail="none", fontcolor="green", label="_return_type", style="solid"];
+}
diff --git a/devnotes/packages.svg b/devnotes/packages.svg
new file mode 100644
index 0000000..776fef9
--- /dev/null
+++ b/devnotes/packages.svg
@@ -0,0 +1,229 @@
+
+
+
+
+
diff --git a/devnotes/packages_nbiatoolkit.dot b/devnotes/packages_nbiatoolkit.dot
new file mode 100644
index 0000000..f358676
--- /dev/null
+++ b/devnotes/packages_nbiatoolkit.dot
@@ -0,0 +1,40 @@
+digraph "packages_nbiatoolkit" {
+rankdir=BT
+charset="utf-8"
+"nbiatoolkit" [color="#77AADD", label=, shape="box", style="filled"];
+"nbiatoolkit.auth" [color="#77AADD", label=, shape="box", style="filled"];
+"nbiatoolkit.dicomsort" [color="#99DDFF", label=, shape="box", style="filled"];
+"nbiatoolkit.dicomsort.dicomsort" [color="#99DDFF", label=, shape="box", style="filled"];
+"nbiatoolkit.dicomsort.helper_functions" [color="#99DDFF", label=, shape="box", style="filled"];
+"nbiatoolkit.logger" [color="#44BB99", label=, shape="box", style="filled"];
+"nbiatoolkit.logger.logger" [color="#44BB99", label=, shape="box", style="filled"];
+"nbiatoolkit.nbia" [color="#77AADD", label=, shape="box", style="filled"];
+"nbiatoolkit.nbia_cli" [color="#77AADD", label=, shape="box", style="filled"];
+"nbiatoolkit.utils" [color="#BBCC33", label=, shape="box", style="filled"];
+"nbiatoolkit.utils.conv_response_list" [color="#BBCC33", label=, shape="box", style="filled"];
+"nbiatoolkit.utils.md5" [color="#BBCC33", label=, shape="box", style="filled"];
+"nbiatoolkit.utils.nbia_endpoints" [color="#BBCC33", label=, shape="box", style="filled"];
+"nbiatoolkit.utils.parsers" [color="#BBCC33", label=, shape="box", style="filled"];
+"nbiatoolkit" -> "nbiatoolkit.auth" [arrowhead="open", arrowtail="none"];
+"nbiatoolkit" -> "nbiatoolkit.logger.logger" [arrowhead="open", arrowtail="none"];
+"nbiatoolkit" -> "nbiatoolkit.nbia" [arrowhead="open", arrowtail="none"];
+"nbiatoolkit" -> "nbiatoolkit.nbia_cli" [arrowhead="open", arrowtail="none"];
+"nbiatoolkit" -> "nbiatoolkit.utils.nbia_endpoints" [arrowhead="open", arrowtail="none"];
+"nbiatoolkit.auth" -> "nbiatoolkit.utils" [arrowhead="open", arrowtail="none"];
+"nbiatoolkit.dicomsort" -> "nbiatoolkit.dicomsort" [arrowhead="open", arrowtail="none"];
+"nbiatoolkit.dicomsort" -> "nbiatoolkit.dicomsort.helper_functions" [arrowhead="open", arrowtail="none"];
+"nbiatoolkit.dicomsort.dicomsort" -> "nbiatoolkit.dicomsort.helper_functions" [arrowhead="open", arrowtail="none"];
+"nbiatoolkit.logger" -> "nbiatoolkit.logger" [arrowhead="open", arrowtail="none"];
+"nbiatoolkit.nbia" -> "nbiatoolkit.auth" [arrowhead="open", arrowtail="none"];
+"nbiatoolkit.nbia" -> "nbiatoolkit.dicomsort" [arrowhead="open", arrowtail="none"];
+"nbiatoolkit.nbia" -> "nbiatoolkit.logger.logger" [arrowhead="open", arrowtail="none"];
+"nbiatoolkit.nbia" -> "nbiatoolkit.utils" [arrowhead="open", arrowtail="none"];
+"nbiatoolkit.nbia" -> "nbiatoolkit.utils.conv_response_list" [arrowhead="open", arrowtail="none"];
+"nbiatoolkit.nbia_cli" -> "nbiatoolkit.dicomsort" [arrowhead="open", arrowtail="none"];
+"nbiatoolkit.nbia_cli" -> "nbiatoolkit.nbia" [arrowhead="open", arrowtail="none"];
+"nbiatoolkit.utils" -> "nbiatoolkit.utils.conv_response_list" [arrowhead="open", arrowtail="none"];
+"nbiatoolkit.utils" -> "nbiatoolkit.utils.md5" [arrowhead="open", arrowtail="none"];
+"nbiatoolkit.utils" -> "nbiatoolkit.utils.nbia_endpoints" [arrowhead="open", arrowtail="none"];
+"nbiatoolkit.utils" -> "nbiatoolkit.utils.parsers" [arrowhead="open", arrowtail="none"];
+"nbiatoolkit.utils.conv_response_list" -> "nbiatoolkit.utils.nbia_endpoints" [arrowhead="open", arrowtail="none"];
+}
diff --git a/devnotes/sequence-diagram_2024-03-17.md b/devnotes/sequence-diagram_2024-03-17.md
new file mode 100644
index 0000000..c284411
--- /dev/null
+++ b/devnotes/sequence-diagram_2024-03-17.md
@@ -0,0 +1,26 @@
+# Sequence Diagram
+## Date: 2024-03-17
+
+```mermaid
+sequenceDiagram
+ participant User
+ participant NBIAClient
+ participant OAuth2
+ participant NBIA_API
+ User->>NBIAClient: Initialize NBIAClient(username, password)
+ NBIAClient->>OAuth2: Initialize OAuth2Client(username, password, client_id, base_url)
+ OAuth2->>NBIA_API: POST request to TOKEN_URL
+ NBIA_API-->>OAuth2: Return access_token, refresh_token, expires_in
+ OAuth2-->>NBIAClient: Return OAuth2 instance
+ User->>NBIAClient: getCollections()
+ NBIAClient->>OAuth2: Access access_token
+ OAuth2->>OAuth2: Check if token is expired
+ OAuth2-->>NBIAClient: Return access_token
+ NBIAClient->>NBIA_API: GET request to COLLECTIONS_URL with access_token in headers
+ NBIA_API-->>NBIAClient: Return collections data
+ User->>NBIAClient: logout()
+ NBIAClient->>OAuth2: logout()
+ OAuth2->>NBIA_API: GET request to LOGOUT_URL
+ NBIA_API-->>OAuth2: Response
+ OAuth2->>OAuth2: Clear all properties
+```
diff --git a/devnotes/updateREADME.sh b/devnotes/updateREADME.sh
new file mode 100644
index 0000000..a71b493
--- /dev/null
+++ b/devnotes/updateREADME.sh
@@ -0,0 +1,17 @@
+# This script updates the version information in the README.md file.
+# It uses awk to search for a code block starting with "```bash" in the README.md file.
+# When it finds the code block, it prints "```bash" and executes the command "NBIAToolkit --version" using the system function.
+# After executing the command, it prints "```" to close the code block.
+# The script then redirects the modified content to a temporary file named "temp" and renames it back to README.md.
+# This ensures that the version information is updated in the README.md file.
+awk '/``` bash NBIAToolkit-Output/ {
+ print "``` bash NBIAToolkit-Output";
+ print "> NBIAToolkit --version";
+ system("NBIAToolkit --version");
+ f=1;
+ next
+} f && /```/ {
+ print "```";
+ f=0;
+ next
+} !f' README.md > temp && mv temp README.md
diff --git a/poetry.lock b/poetry.lock
index 43fa731..245b1d7 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -964,6 +964,9 @@ files = [
{file = "importlib_resources-6.1.1.tar.gz", hash = "sha256:3893a00122eafde6894c59914446a512f728a0c1a45f9bb9b63721b6bacf0b4a"},
]
+[package.dependencies]
+zipp = {version = ">=3.1.0", markers = "python_version < \"3.10\""}
+
[package.extras]
docs = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (<7.2.5)", "sphinx (>=3.5)", "sphinx-lint"]
testing = ["pytest (>=6)", "pytest-black (>=0.3.7)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=2.2)", "pytest-mypy (>=0.9.1)", "pytest-ruff", "zipp (>=3.17)"]
@@ -1014,13 +1017,13 @@ test = ["flaky", "ipyparallel", "pre-commit", "pytest (>=7.0)", "pytest-asyncio
[[package]]
name = "ipython"
-version = "8.21.0"
+version = "8.18.1"
description = "IPython: Productive Interactive Computing"
optional = false
-python-versions = ">=3.10"
+python-versions = ">=3.9"
files = [
- {file = "ipython-8.21.0-py3-none-any.whl", hash = "sha256:1050a3ab8473488d7eee163796b02e511d0735cf43a04ba2a8348bd0f2eaf8a5"},
- {file = "ipython-8.21.0.tar.gz", hash = "sha256:48fbc236fbe0e138b88773fa0437751f14c3645fb483f1d4c5dee58b37e5ce73"},
+ {file = "ipython-8.18.1-py3-none-any.whl", hash = "sha256:e8267419d72d81955ec1177f8a29aaa90ac80ad647499201119e2f05e99aa397"},
+ {file = "ipython-8.18.1.tar.gz", hash = "sha256:ca6f079bb33457c66e233e4580ebfc4128855b4cf6370dddd73842a9563e8a27"},
]
[package.dependencies]
@@ -1034,19 +1037,20 @@ prompt-toolkit = ">=3.0.41,<3.1.0"
pygments = ">=2.4.0"
stack-data = "*"
traitlets = ">=5"
+typing-extensions = {version = "*", markers = "python_version < \"3.10\""}
[package.extras]
-all = ["black", "curio", "docrepr", "exceptiongroup", "ipykernel", "ipyparallel", "ipywidgets", "matplotlib", "matplotlib (!=3.2.0)", "nbconvert", "nbformat", "notebook", "numpy (>=1.23)", "pandas", "pickleshare", "pytest (<8)", "pytest-asyncio (<0.22)", "qtconsole", "setuptools (>=18.5)", "sphinx (>=1.3)", "sphinx-rtd-theme", "stack-data", "testpath", "trio", "typing-extensions"]
+all = ["black", "curio", "docrepr", "exceptiongroup", "ipykernel", "ipyparallel", "ipywidgets", "matplotlib", "matplotlib (!=3.2.0)", "nbconvert", "nbformat", "notebook", "numpy (>=1.22)", "pandas", "pickleshare", "pytest (<7)", "pytest (<7.1)", "pytest-asyncio (<0.22)", "qtconsole", "setuptools (>=18.5)", "sphinx (>=1.3)", "sphinx-rtd-theme", "stack-data", "testpath", "trio", "typing-extensions"]
black = ["black"]
-doc = ["docrepr", "exceptiongroup", "ipykernel", "matplotlib", "pickleshare", "pytest (<8)", "pytest-asyncio (<0.22)", "setuptools (>=18.5)", "sphinx (>=1.3)", "sphinx-rtd-theme", "stack-data", "testpath", "typing-extensions"]
+doc = ["docrepr", "exceptiongroup", "ipykernel", "matplotlib", "pickleshare", "pytest (<7)", "pytest (<7.1)", "pytest-asyncio (<0.22)", "setuptools (>=18.5)", "sphinx (>=1.3)", "sphinx-rtd-theme", "stack-data", "testpath", "typing-extensions"]
kernel = ["ipykernel"]
nbconvert = ["nbconvert"]
nbformat = ["nbformat"]
notebook = ["ipywidgets", "notebook"]
parallel = ["ipyparallel"]
qtconsole = ["qtconsole"]
-test = ["pickleshare", "pytest (<8)", "pytest-asyncio (<0.22)", "testpath"]
-test-extra = ["curio", "matplotlib (!=3.2.0)", "nbformat", "numpy (>=1.23)", "pandas", "pickleshare", "pytest (<8)", "pytest-asyncio (<0.22)", "testpath", "trio"]
+test = ["pickleshare", "pytest (<7.1)", "pytest-asyncio (<0.22)", "testpath"]
+test-extra = ["curio", "matplotlib (!=3.2.0)", "nbformat", "numpy (>=1.22)", "pandas", "pickleshare", "pytest (<7.1)", "pytest-asyncio (<0.22)", "testpath", "trio"]
[[package]]
name = "ipywidgets"
@@ -1246,6 +1250,7 @@ files = [
]
[package.dependencies]
+importlib-metadata = {version = ">=4.8.3", markers = "python_version < \"3.10\""}
jupyter-core = ">=4.12,<5.0.dev0 || >=5.1.dev0"
python-dateutil = ">=2.8.2"
pyzmq = ">=23.0"
@@ -1337,6 +1342,7 @@ files = [
]
[package.dependencies]
+importlib-metadata = {version = ">=4.8.3", markers = "python_version < \"3.10\""}
jupyter-server = ">=1.1.2"
[[package]]
@@ -1407,6 +1413,7 @@ files = [
[package.dependencies]
async-lru = ">=1.0.0"
+importlib-metadata = {version = ">=4.8.3", markers = "python_version < \"3.10\""}
ipykernel = "*"
jinja2 = ">=3.0.3"
jupyter-core = "*"
@@ -1449,6 +1456,7 @@ files = [
[package.dependencies]
babel = ">=2.10"
+importlib-metadata = {version = ">=4.8.3", markers = "python_version < \"3.10\""}
jinja2 = ">=3.0.3"
json5 = ">=0.9.0"
jsonschema = ">=4.18.0"
@@ -1483,6 +1491,9 @@ files = [
{file = "Markdown-3.5.2.tar.gz", hash = "sha256:e1ac7b3dc550ee80e602e71c1d168002f062e49f1b11e26a36264dafd4df2ef8"},
]
+[package.dependencies]
+importlib-metadata = {version = ">=4.4", markers = "python_version < \"3.10\""}
+
[package.extras]
docs = ["mdx-gh-links (>=0.2)", "mkdocs (>=1.5)", "mkdocs-gen-files", "mkdocs-literate-nav", "mkdocs-nature (>=0.6)", "mkdocs-section-index", "mkdocstrings[python]"]
testing = ["coverage", "pyyaml"]
@@ -1661,6 +1672,7 @@ files = [
click = ">=7.0"
colorama = {version = ">=0.4", markers = "platform_system == \"Windows\""}
ghp-import = ">=1.0"
+importlib-metadata = {version = ">=4.3", markers = "python_version < \"3.10\""}
jinja2 = ">=2.11.1"
markdown = ">=3.2.1"
markupsafe = ">=2.0.1"
@@ -1767,6 +1779,7 @@ files = [
beautifulsoup4 = "*"
bleach = "!=5.0.0"
defusedxml = "*"
+importlib-metadata = {version = ">=3.6", markers = "python_version < \"3.10\""}
jinja2 = ">=3.0"
jupyter-core = ">=4.7"
jupyterlab-pygments = "*"
@@ -3134,6 +3147,7 @@ babel = ">=2.9"
colorama = {version = ">=0.4.5", markers = "sys_platform == \"win32\""}
docutils = ">=0.18.1,<0.21"
imagesize = ">=1.3"
+importlib-metadata = {version = ">=4.8", markers = "python_version < \"3.10\""}
Jinja2 = ">=3.0"
packaging = ">=21.0"
Pygments = ">=2.14"
@@ -3755,5 +3769,5 @@ testing = ["big-O", "jaraco.functools", "jaraco.itertools", "more-itertools", "p
[metadata]
lock-version = "2.0"
-python-versions = ">=3.10 || 3.12"
-content-hash = "08a55ea078d191fe9148c91630c8792ddf3b032223713050ac6c06d5b342e40f"
+python-versions = ">=3.09 || 3.12"
+content-hash = "d53786b72809319147f84cd80957abcc0235c847ba90cfe64bf1cf847115088b"
diff --git a/pyproject.toml b/pyproject.toml
index baf670c..3304de1 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -19,7 +19,7 @@ getNewSeries = "nbiatoolkit.nbia_cli:getNewSeries_cli"
[tool.poetry.dependencies]
-python = ">=3.10 || 3.12"
+python = ">=3.09 || 3.12"
requests = "2.31.0"
pydicom = "^2.4.0"
tqdm = "^4.66.1"
diff --git a/src/nbiatoolkit/dicomtags/tags.py b/src/nbiatoolkit/dicomtags/tags.py
new file mode 100644
index 0000000..41adb5d
--- /dev/null
+++ b/src/nbiatoolkit/dicomtags/tags.py
@@ -0,0 +1,222 @@
+from pydicom.datadict import dictionary_VR
+from pydicom.datadict import tag_for_keyword
+from pydicom._dicom_dict import DicomDictionary
+import pandas as pd
+from typing import Any, Union, List
+
+
+def convert_element_to_int(element_str: str) -> int:
+ """
+ Converts a DICOM element string representation to an integer.
+
+ Args:
+ element_str (str): The DICOM element string representation.
+
+ Returns:
+ int: The converted integer value.
+
+ Examples:
+ >>> convert_element_to_int('(0028,0010)')
+ 2621456
+
+ Raises:
+ ValueError: If the element format is invalid.
+
+ """
+ if element_str.startswith(">"):
+ return -1
+
+ elements: list[str] = element_str.strip("()'").split(",")
+
+ # Check if the element has the correct structure
+ if len(elements) != 2:
+ raise ValueError(
+ f"Invalid element format. Element must have the structure '(,)': {element_str}"
+ )
+
+ # Convert each element from string to integer
+ elements_int: list[int]
+ elements_int = [int(elem, base=16) for elem in elements]
+
+ # Combine the integers into a single integer
+ combined_int: int = (elements_int[0] << 16) + elements_int[1]
+
+ return combined_int
+
+
+def convert_int_to_element(combined_int: int) -> str:
+ """
+ Converts a combined integer into a DICOM element string representation.
+
+ Args:
+ combined_int (int): The combined integer to be converted.
+
+ Returns:
+ str: The DICOM element string representation of the combined integer.
+
+ Examples:
+ >>> convert_int_to_element(0x00080060)
+ (0008,0060)
+ >>> convert_int_to_element(524384)
+ (0008,0060)
+ """
+ assert isinstance(combined_int, int), "combined_int must be an integer."
+
+ if combined_int == -1:
+ return "Unknown"
+
+ # Split the integer into two parts
+ # i.e 131073 should become (2,1)
+ part1: int = combined_int >> 16 # shift right by 16 bits
+ part2: int = combined_int & 0xFFFF # bitwise AND with 0xFFFF (16 bits)
+
+ # Convert the integers to hex strings
+ part1_str: str = hex(part1)[2:]
+ part2_str: str = hex(part2)[2:]
+
+ # (2,1) should become (0002,0001)
+ part1_str = part1_str.zfill(4)
+ part2_str = part2_str.zfill(4)
+
+ # capitalize any lowercase letters
+ part1_str = part1_str.upper()
+ part2_str = part2_str.upper()
+
+ # Combine the hex strings into a single string
+ combined_str: str = f"({part1_str},{part2_str})"
+
+ return combined_str
+
+
+def LOOKUP_TAG(keyword: str) -> int:
+ """
+ Looks up a DICOM tag based on the keyword. A wrapper around the pydicom's `tag_for_keyword` function.
+ """
+ tag: int | None = tag_for_keyword(keyword=keyword)
+ if tag is None:
+ raise (ValueError(f"Tag not found for keyword: {keyword}"))
+ return tag
+
+
+def element_VR_lookup(element_str: str) -> tuple[int, str]:
+ """
+ Looks up the VR (Value Representation) for a given DICOM element.
+
+ Args:
+ element_str (str): The DICOM element as a string.
+
+ Returns:
+ tuple[int, str]: A tuple containing the combined integer representation of the element and its VR.
+ """
+
+ combined_int: int = convert_element_to_int(element_str=element_str)
+ if combined_int == -1:
+ return (-1, "Unknown")
+
+ VR: str
+ try:
+ VR = dictionary_VR(tag=combined_int)
+ except KeyError:
+ VR = "Unknown,KeyError"
+
+ return (combined_int, VR)
+
+
+def getSeriesModality(series_tags_df: pd.DataFrame) -> str:
+ """
+ Retrieves the modality of a DICOM series.
+
+ Args:
+ series_tags_df (pd.DataFrame): A DataFrame containing DICOM series tags.
+
+ Returns:
+ str: The modality of the DICOM series.
+
+ Raises:
+ ValueError: If the modality tag is not found in the DICOM dictionary.
+ """
+ modality_tag: int | None
+ modality_tag = LOOKUP_TAG(keyword="Modality")
+
+ if modality_tag is None:
+ raise ValueError("Modality tag not found in the DICOM dictionary.")
+
+ modality_tag_element: str = convert_int_to_element(combined_int=modality_tag)
+
+ modality_row: pd.DataFrame = series_tags_df[
+ series_tags_df["element"] == modality_tag_element
+ ]
+ modality: str = modality_row["data"].values[0]
+
+ return modality
+
+
+def subsetSeriesTags(series_tags_df: pd.DataFrame, element: str) -> pd.DataFrame:
+ """
+ Subsets a DataFrame containing DICOM series tags based on the start and end elements.
+ """
+
+ locs: pd.DataFrame
+ locs = series_tags_df[series_tags_df["element"].str.contains(element)]
+
+ if len(locs) == 0:
+ raise ValueError("Element not found in the series tags.")
+
+ if len(locs) > 2:
+ raise ValueError("More than two elements found in the series tags.")
+
+ return series_tags_df.iloc[locs.index[0] : locs.index[1]]
+
+
+def getReferencedFrameOfReferenceSequence(series_tags_df: pd.DataFrame) -> pd.DataFrame:
+ modality = getSeriesModality(series_tags_df=series_tags_df)
+ if modality != "RTSTRUCT":
+ raise ValueError("Series is not an RTSTRUCT.")
+
+ tag: int = LOOKUP_TAG(keyword="ReferencedFrameOfReferenceSequence")
+
+ ReferencedFrameOfReferenceSequence_element: str = convert_int_to_element(
+ combined_int=tag
+ )
+
+ df: pd.DataFrame = subsetSeriesTags(
+ series_tags_df=series_tags_df,
+ element=ReferencedFrameOfReferenceSequence_element,
+ )
+
+ return df
+
+
+def getReferencedSeriesUIDS(series_tags_df: pd.DataFrame) -> List[str]:
+ """
+ Given a DataFrame containing DICOM series tags, retrieves the SeriesInstanceUIDs of the referenced series.
+ Useful for RTSTRUCT DICOM files to find the series that the RTSTRUCT references.
+ TODO:: implement SEG and RTDOSE
+
+ Args:
+ series_tags_df (pd.DataFrame): A DataFrame containing DICOM series tags.
+
+ Returns:
+ List[str]: A list of SeriesInstanceUIDs of the referenced series.
+
+ Raises:
+ ValueError: If the series is not an RTSTRUCT.
+ """
+
+ # "SeriesInstanceUID" ---LOOKUP_TAG--> 2097166 ---convert_int_to_element--> (0020,000E)
+ SeriesInstanceUIDtag: int = LOOKUP_TAG(keyword="SeriesInstanceUID")
+ SeriesInstanceUID_element: str = convert_int_to_element(
+ combined_int=SeriesInstanceUIDtag
+ )
+
+ search_space: pd.DataFrame = getReferencedFrameOfReferenceSequence(
+ series_tags_df=series_tags_df
+ )
+
+ value: pd.DataFrame = search_space[
+ search_space["element"].str.contains(SeriesInstanceUID_element)
+ ]
+
+ UIDS: list[str] = value["data"].to_list()
+
+ return UIDS
diff --git a/src/nbiatoolkit/nbia.py b/src/nbiatoolkit/nbia.py
index 324a77a..7da54ed 100644
--- a/src/nbiatoolkit/nbia.py
+++ b/src/nbiatoolkit/nbia.py
@@ -146,11 +146,6 @@ def __init__(
self._log.debug("Setting up OAuth2 client... with username %s", username)
self._oauth2_client = OAuth2(username=username, password=password)
- self._api_headers: dict[str, str] = {
- "Authorization": f"Bearer {self._oauth2_client.access_token}",
- "Content-Type": "application/json",
- }
-
self._base_url: NBIA_BASE_URLS = NBIA_BASE_URLS.NBIA
self._return_type: ReturnType = (
return_type
@@ -170,7 +165,13 @@ def OAuth_client(self) -> OAuth2:
@property
def headers(self):
- return self._api_headers
+
+ API_HEADERS: dict[str, str] = {
+ "Authorization": f"Bearer {self.OAuth_client.access_token}",
+ "Content-Type": "application/json",
+ }
+
+ return API_HEADERS
# create a setter for the base_url in case user want to use NLST
@property
@@ -639,7 +640,7 @@ def downloadSeries(
downloadDir,
filePattern,
overwrite,
- self._api_headers,
+ self.headers,
self._base_url,
self._log,
Progressbar,
diff --git a/tests/test_tags.py b/tests/test_tags.py
new file mode 100644
index 0000000..b0c6be8
--- /dev/null
+++ b/tests/test_tags.py
@@ -0,0 +1,156 @@
+import pytest
+from src.nbiatoolkit import NBIAClient
+from src.nbiatoolkit.dicomtags.tags import convert_int_to_element
+from src.nbiatoolkit.dicomtags.tags import convert_element_to_int
+from src.nbiatoolkit.dicomtags.tags import LOOKUP_TAG
+from src.nbiatoolkit.dicomtags.tags import *
+
+
+def test_convert_int_to_element():
+ # Test case 1: combined_int = 0x00080060
+ result = convert_int_to_element(0x00080060)
+ assert result == "(0008,0060)", f"Expected (0008,0060), but got {result}"
+
+ # Test case 2: combined_int = 524384
+ result = convert_int_to_element(524384)
+ assert result == "(0008,0060)", f"Expected (0008,0060), but got {result}"
+
+ # Test case 3: combined_int = -1
+ result = convert_int_to_element(-1)
+ assert result == "Unknown", f"Expected Unknown, but got {result}"
+
+ # Test case 4: combined_int = 0
+ result = convert_int_to_element(0)
+ assert result == "(0000,0000)", f"Expected (0000,0000), but got {result}"
+
+ # Test case 5: combined_int = 65535
+ result = convert_int_to_element(65535)
+ assert result == "(0000,FFFF)", f"Expected (0000,FFFF), but got {result}"
+
+ with pytest.raises(ValueError) as e:
+ convert_element_to_int("(1,1,1)")
+
+ print("All test cases passed!")
+
+
+def test_convert_element_to_int():
+ # Test case 1: element_str = '(0028,0010)'
+ result = convert_element_to_int("(0028,0010)")
+ assert result == 2621456, f"Expected 2621456, but got {result}"
+
+ # Test case 2: element_str = '(0008,0060)'
+ result = convert_element_to_int("(0008,0060)")
+ assert result == 524384, f"Expected 524384, but got {result}"
+
+ # Test case 3: element_str = '(0000,0000)'
+ result = convert_element_to_int("(0000,0000)")
+ assert result == 0, f"Expected 0, but got {result}"
+
+ # Test case 4: element_str = '(0000,FFFF)'
+ result = convert_element_to_int("(0000,FFFF)")
+ assert result == 65535, f"Expected 65535, but got {result}"
+
+ # Test case 5: element_str = '>Unknown'
+ result = convert_element_to_int(">Unknown")
+ assert result == -1, f"Expected -1, but got {result}"
+
+ print("All test cases passed!")
+
+
+def test_LOOKUP_TAG():
+ # Test case 1: keyword = "PatientName"
+ result = LOOKUP_TAG("PatientName")
+ assert result == 0x00100010, f"Expected 0x00100010, but got {result}"
+
+ # Test case 2: keyword = "StudyDate"
+ result = LOOKUP_TAG("StudyDate")
+ assert result == 0x00080020, f"Expected 0x00080020, but got {result}"
+
+ # Test case 3: keyword = "UnknownKeyword"
+ try:
+ LOOKUP_TAG("UnknownKeyword")
+ except ValueError as e:
+ assert (
+ str(e) == "Tag not found for keyword: UnknownKeyword"
+ ), f"Expected 'Tag not found for keyword: UnknownKeyword', but got {str(e)}"
+ else:
+ assert False, "Expected ValueError to be raised for unknown keyword"
+
+ print("All test cases passed!")
+
+
+def test_element_VR_lookup():
+ # Test case 1: element_str = '(0028,0010)'
+ result = element_VR_lookup("(0028,0010)")
+ assert result == (2621456, "US"), f"Expected (2621456, 'US'), but got {result}"
+
+ # Test case 2: element_str = '(0008,0060)'
+ result = element_VR_lookup("(0008,0060)")
+ assert result == (524384, "CS"), f"Expected (524384, 'CS'), but got {result}"
+
+ # Test case 3: element_str = '(0000,0000)'
+ result = element_VR_lookup("(0000,0000)")
+ assert result == (0, "UL"), f"Expected (0, 'UL'), but got {result}"
+
+ # Test case 4: element_str = '(0000,FFFF)'
+ result = element_VR_lookup("(0000,FFFF)")
+ assert result == (
+ 65535,
+ "Unknown,KeyError",
+ ), f"Expected (65535, 'Unknown,KeyError'), but got {result}"
+
+ # Test case 5: element_str = '>Unknown'
+ result = element_VR_lookup(">Unknown")
+ assert result == (-1, "Unknown"), f"Expected (-1, 'Unknown'), but got {result}"
+
+ print("All test cases passed!")
+
+
+@pytest.fixture(scope="session")
+def client():
+ return NBIAClient(return_type="dataframe")
+
+
+@pytest.fixture(scope="session")
+def series(client):
+ return client.getSeries(Collection="Pediatric-CT-SEG", Modality="RTSTRUCT")
+
+
+@pytest.fixture(scope="session")
+def RTSTRUCT_Series(series):
+ return series[series["Modality"] == "RTSTRUCT"]
+
+
+@pytest.fixture(scope="session")
+def RTSTRUCT_Tags(client, RTSTRUCT_Series):
+ seriesUID = RTSTRUCT_Series["SeriesInstanceUID"].values[0]
+ assert seriesUID is not None, "Expected seriesUID to be returned, but got None"
+
+ tags_df = client.getDICOMTags(seriesUID)
+ assert tags_df is not None, "Expected tags to be returned, but got None"
+
+ return tags_df
+
+
+def test_getDICOMTags(RTSTRUCT_Tags):
+ seriesUIDS = getReferencedSeriesUIDS(RTSTRUCT_Tags)
+ expected = ["1.3.6.1.4.1.14519.5.2.1.133742245714270925254982946723351496764"]
+ assert seriesUIDS == expected, f"Expected {expected}, but got {seriesUIDS}"
+
+
+def test_getSeriesModality(RTSTRUCT_Tags):
+ modality = getSeriesModality(RTSTRUCT_Tags)
+ assert modality == "RTSTRUCT", f"Expected 'RTSTRUCT', but got {modality}"
+
+ # Test case 2: modality tag not found
+ RTSTRUCT_Tags.drop(
+ RTSTRUCT_Tags[RTSTRUCT_Tags["element"] == "(0008,0060)"].index, inplace=True
+ )
+
+ with pytest.raises(IndexError) as e:
+ getSeriesModality(RTSTRUCT_Tags)
+
+
+def test_failsubsetSeriesTags(RTSTRUCT_Series):
+ with pytest.raises(KeyError) as e:
+ subsetSeriesTags(RTSTRUCT_Series, "(0008,0060)")