Merge pull request #130 from jjjermiah/development

feat: add functionality to prepare filepaths from dicomtags

.github/workflows/main.yml

@@ -6,18 +6,17 @@ on:
     # push to any branch *
     branches: [ main ]
   pull_request:
-    branches: [ main , development]
+    branches: [ main , development ]
 
 jobs:
   Unit-Tests:
     runs-on: ${{ matrix.os }}
+    timeout-minutes: 15 # Consider increasing timeout
+
     strategy:
       matrix:
         os: [ubuntu-latest, macos-latest, macos-14]
         python-version: ["3.12", "3.11", "3.10"]
-        # include:
-        #   - os: ubuntu-latest
-        #     python-version: "3.9"
 
     steps:
       - uses: actions/checkout@v3
@@ -123,12 +122,6 @@ jobs:
       with:
         fetch-depth: 0
 
-   # This action uses Python Semantic Release v8
-   # What this action does:
-   # - Determines the next version number based on the commit history
-    # - Creates a new tag with the new version number
-    # - Pushes the new tag to GitHub
-    # - Creates a GitHub release with the new version number
     - name: Python Semantic Release
       id: release
       uses: python-semantic-release/python-semantic-release@master
@@ -140,8 +133,10 @@ jobs:
     if: needs.Continuous-Deployment.outputs.released == 'true'
     runs-on: ubuntu-latest
     steps:
-      - name: Checkout code
+      - name: Checkout the code with tag ${{ needs.Continuous-Deployment.outputs.tag }}
         uses: actions/checkout@v3
+        with:
+          ref: ${{ needs.Continuous-Deployment.outputs.tag }}
 
       - name: Set up Python 3.12
         uses: actions/setup-python@v4
@@ -170,24 +165,22 @@ jobs:
     steps:
       - name: Checkout code
         uses: actions/checkout@v3
+        with:
+          ref: ${{ needs.Continuous-Deployment.outputs.tag }}
 
       - 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
@@ -234,7 +227,7 @@ jobs:
 
       - name: Install using PyPi
         run: |
-          pip install  nbiatoolkit;
+          pip install nbiatoolkit==${{ needs.Continuous-Deployment.outputs.version }}
           NBIAToolkit
 
   Test-Docker-Image:
@@ -243,12 +236,12 @@ jobs:
     strategy:
       matrix:
         os: [ubuntu-latest, macos-latest]
-        docker_tag: ["latest", "${{ needs.Continuous-Deployment.outputs.tag }}"]
 
     steps:
-      - uses: actions/checkout@v3
+      - name: Setup Docker to pull images
+        uses: docker/setup-buildx-action@v3
 
       - name: Install using Docker
         run: |
-          docker pull ${{ secrets.DOCKERHUB_USERNAME }}/nbiatoolkit:${{ matrix.docker_tag }};
-          docker run --rm ${{ secrets.DOCKERHUB_USERNAME }}/nbiatoolkit:${{ matrix.docker_tag }} NBIAToolkit
+          docker pull ${{ secrets.DOCKERHUB_USERNAME }}/nbiatoolkit:${{ needs.Continuous-Deployment.outputs.tag }};
+          docker run --rm ${{ secrets.DOCKERHUB_USERNAME }}/nbiatoolkit:${{ needs.Continuous-Deployment.outputs.tag }} NBIAToolkit

docs/project_info/CHANGELOG.md

@@ -2,6 +2,29 @@
 
 
 
+## v1.2.0 (2024-04-01)
+
+### Build
+
+* build: Add development branch to CI/CD workflow ([`6ff1e96`](https://github.com/jjjermiah/nbia-toolkit/commit/6ff1e962c981f3a481728b2b0ba03c4d3d9edcc7))
+
+* build: Add timeout for Unit-Tests job and checkout code with tag in Continuous-Deployment job ([`2f85826`](https://github.com/jjjermiah/nbia-toolkit/commit/2f858265dd467267a0079919315280e62c34b173))
+
+### Feature
+
+* feat: release on development ([`b813e2a`](https://github.com/jjjermiah/nbia-toolkit/commit/b813e2a3e82d281f3cdfcb88415100ca451b43a2))
+
+* feat: release on development ([`71e68e0`](https://github.com/jjjermiah/nbia-toolkit/commit/71e68e02ce047331fe1adc7f5a658f9899c8d356))
+
+### Fix
+
+* fix: testing gha ([`272a9f5`](https://github.com/jjjermiah/nbia-toolkit/commit/272a9f52be5f6e1a5f2474c5cc433000a17fa4b6))
+
+### Unknown
+
+* Merge remote-tracking branch 'origin' into development ([`2ed6d37`](https://github.com/jjjermiah/nbia-toolkit/commit/2ed6d37f9d776992bb9bbe23239ce639083aae53))
+
+
 ## v1.1.0 (2024-04-01)
 
 ### Build
@@ -14,6 +37,8 @@
 
 ### Chore
 
+* chore(sem-ver): 1.1.0 ([`c41b230`](https://github.com/jjjermiah/nbia-toolkit/commit/c41b2304acd2fc0360ac26ef4736bf10e774871b))
+
 * chore: Update README: 1.0.1 ([`1b7508f`](https://github.com/jjjermiah/nbia-toolkit/commit/1b7508f515ce2820c5b232810fb26660448e66a4))
 
 ### Documentation
@@ -34,6 +59,8 @@
 
 ### Fix
 
+* fix: Fix string formatting in version function ([`dc4bbd7`](https://github.com/jjjermiah/nbia-toolkit/commit/dc4bbd749a2b281e81faf7a99a2903bef278beca))
+
 * fix: python 3.9 only on ubuntu ([`1adb7b8`](https://github.com/jjjermiah/nbia-toolkit/commit/1adb7b8c66a6d73fb27374b557eb3b76d9d0c01c))
 
 * fix: Update GitHub Actions workflow to include Ubuntu 3.9 only ([`8d376d3`](https://github.com/jjjermiah/nbia-toolkit/commit/8d376d35f8ef52386330dd8907f35a6ad4a15f4f))

pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "nbiatoolkit"
-version = "1.1.0"
+version = "1.2.0"
 description = "A python package to query the National Biomedical Imaging Archive (NBIA) database."
 authors = ["Jermiah Joseph"]
 license = "MIT"
@@ -64,7 +64,7 @@ changelog_file = "docs/project_info/CHANGELOG.md"
 exclude_commit_types = ["docs", "style", "refactor", "test", "chore"]
 
 [tool.semantic_release.branches.main]
-match = "(main|master)"
+match = "(main|master|development)"
 
 
 [tool.semantic_release.commit_parser_options]

src/nbiatoolkit/__init__.py

@@ -13,6 +13,7 @@
 from .auth import OAuth2
 from .logger.logger import setup_logger
 from .utils.nbia_endpoints import NBIA_ENDPOINTS
+from .dicomtags import *
 
 # define the __all__ variable
 __all__ = [

src/nbiatoolkit/dicomsort/__init__.py

@@ -8,12 +8,13 @@
 
 # ]
 
-from .dicomsort import DICOMSorter
+from .dicomsort import DICOMSorter, generateFilePathFromDICOMAttributes
 from .helper_functions import parseDICOMKeysFromFormat, sanitizeFileName, _truncateUID
 
 __all__ = [
     "parseDICOMKeysFromFormat",
     "sanitizeFileName",
     "_truncateUID",
     "DICOMSorter",
+    "generateFilePathFromDICOMAttributes",
 ]

src/nbiatoolkit/dicomsort/dicomsort.py

@@ -14,6 +14,7 @@
 import shutil
 from .helper_functions import parseDICOMKeysFromFormat, sanitizeFileName, _truncateUID
 from concurrent.futures import ThreadPoolExecutor, as_completed
+from typing import Union
 
 
 def get_dicom_files(sourceDir) -> list[str]:
@@ -39,7 +40,7 @@ def read_in_dicom_file(filePath: str) -> pydicom.FileDataset:
 
 
 def generateFilePathFromDICOMAttributes(
-    dataset: pydicom.FileDataset,
+    dataset: pydicom.Dataset,
     targetPattern: str,
     truncateUID: bool,
     sanitizeFilename: bool,
@@ -57,6 +58,10 @@ def generateFilePathFromDICOMAttributes(
         # Retrieve the attribute value if it exists or default to a placeholder string
         value = str(getattr(dataset, key, "Unknown" + key))
 
+        # if value is exactly "UnknownInstanceNumber", replace it with "1"
+        if value == "UnknownInstanceNumber":
+            value = "1"
+
         value = (
             _truncateUID(uid=value, lastDigits=5)
             if key.endswith("UID") and truncateUID

src/nbiatoolkit/dicomtags/__init__.py

@@ -10,6 +10,7 @@
     subsetSeriesTags,
     getReferencedFrameOfReferenceSequence,
     getReferencedSeriesUIDS,
+    extract_ROI_info,
 )
 
 __all__ = [
@@ -21,4 +22,5 @@
     "subsetSeriesTags",
     "getReferencedFrameOfReferenceSequence",
     "getReferencedSeriesUIDS",
+    "extract_ROI_info",
 ]

src/nbiatoolkit/dicomtags/tags.py

@@ -1,6 +1,6 @@
 from math import log
-from pydicom.datadict import dictionary_VR
-from pydicom.datadict import tag_for_keyword
+import pydicom
+from pydicom.datadict import dictionary_VR, tag_for_keyword
 import pandas as pd
 from typing import List
 
@@ -342,6 +342,32 @@ def extract_ROI_info(StructureSetROISequence) -> dict[str, dict[str, str]]:
     return ROISet
 
 
+def generateFileDatasetFromTags(tags_df: pd.DataFrame) -> pydicom.Dataset:
+    """
+    Generate a pydicom Dataset object from a DataFrame of DICOM tags.
+
+    Args:
+        tags_df (pd.DataFrame): DataFrame containing DICOM tags.
+
+    Returns:
+        pydicom.Dataset: A pydicom Dataset object containing the DICOM tags.
+    """
+
+    # Create a new FileDataset
+    ds = pydicom.Dataset()
+
+    for _, row in tags_df.iterrows():
+        tag = convert_element_to_int(row["element"])
+        value = row["data"]
+        if tag == -1:
+            continue
+        VR = element_VR_lookup(row["element"])[1]
+
+        ds.add_new(tag=tag, VR=VR, value=value)
+
+    return ds
+
+
 # def getRTSTRUCT_ROI_info(seriesUID: str) -> dict[str, dict[str, str]]:
 #     """
 #     Given a SeriesInstanceUID of an RTSTRUCT, retrieves the ROI information.

src/nbiatoolkit/nbia.py

@@ -4,7 +4,9 @@
 import re
 import zipfile
 from tempfile import TemporaryDirectory
-from .dicomsort import DICOMSorter
+
+from pydicom import Dataset, FileDataset
+from .dicomsort import DICOMSorter, generateFilePathFromDICOMAttributes
 
 import multiprocessing
 from .auth import OAuth2
@@ -26,6 +28,7 @@
     getReferencedSeriesUIDS,
     extract_ROI_info,
     getSequenceElement,
+    generateFileDatasetFromTags,
 )
 
 import pandas as pd
@@ -38,7 +41,7 @@
 from datetime import datetime
 
 # set __version__ variable
-__version__ = "1.1.0"
+__version__ = "1.2.0"
 
 
 def downloadSingleSeries(
@@ -637,6 +640,47 @@ def getRefSeriesUIDs(
 
         return getReferencedSeriesUIDS(series_tags_df=tags_df)
 
+    def generateFilePathFromDICOMTags(
+        self,
+        SeriesInstanceUID: str,
+        filePattern: str = "%PatientName/%Modality-%SeriesNumber-%SeriesInstanceUID/%InstanceNumber.dcm",
+    ) -> str:
+        """
+        Generates a file path from DICOM tags.
+
+        Args:
+            SeriesInstanceUID (str): The Series Instance UID of the DICOM series.
+            filePattern (str, optional): The file pattern to use for generating the file path. Defaults to "%PatientName/%Modality-%SeriesNumber-%SeriesInstanceUID/%InstanceNumber.dcm".
+
+        Returns:
+            str: The generated file path.
+
+        Note:
+            This only considers the first instance of the series.
+            Meant to be used to determine the dirname of the series files.
+        """
+        self.logger.debug("Getting DICOM tags for series %s", SeriesInstanceUID)
+        tags_df = self.getDICOMTags(
+            SeriesInstanceUID=SeriesInstanceUID,
+            return_type=ReturnType.DATAFRAME,
+        )
+
+        if type(tags_df) != pd.DataFrame:
+            raise ValueError("DICOM Tags not df or not found in the response.")
+
+        self.logger.debug("Generating file path from DICOM tags")
+        ds: Dataset = generateFileDatasetFromTags(tags_df=tags_df)
+        filePath: str = generateFilePathFromDICOMAttributes(
+            dataset=ds,
+            targetPattern=filePattern,
+            truncateUID=True,
+            sanitizeFilename=True,
+        )
+        self.logger.debug(
+            "Generated file path: %s for series %s", filePath, SeriesInstanceUID
+        )
+        return filePath
+
     def downloadSeries(
         self,
         SeriesInstanceUID: Union[str, list],

src/nbiatoolkit/nbia_cli.py

@@ -18,7 +18,7 @@
 
 
 def version():
-    f = """
+    f = r"""
         _   ______  _______  ______            ____   _ __
        / | / / __ )/  _/   |/_  __/___  ____  / / /__(_) /_
       /  |/ / __  |/ // /| | / / / __ \/ __ \/ / //_/ / __/