Merge pull request #65 from jjjermiah/development

Development

.github/workflows/main.yml

@@ -27,11 +27,12 @@ jobs:
       - name: Install poetry
         uses: snok/install-poetry@v1
 
+      - name: Install dependencies
+        run: poetry install
+
       - name: Test with pytest
         run: |
-          pip install -r requirements.txt
-          poetry install
-          pytest --cov --cov-report=xml:coverage-report/coverage.xml
+          poetry run pytest -n 2 --cov --cov-report xml:coverage-report/coverage.xml
 
       - name: Build documentation
         run: poetry run make html --directory docs/
@@ -58,7 +59,7 @@ jobs:
       - name: Use Codecov to track coverage
         uses: codecov/codecov-action@v3
         with:
-          CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
+          token: ${{ secrets.CODECOV_TOKEN }}
           files: ./coverage-report/coverage.xml
           fail_ci_if_error: true
           verbose: true
@@ -208,7 +209,7 @@ jobs:
           # test image with latest tag
           docker run --rm \
             ${{ secrets.DOCKERHUB_USERNAME }}/nbiatoolkit:${LATEST_TAG} \
-            python -c "import nbiatoolkit; print(nbiatoolkit.__version__)"
+            NBIAToolkit
 
 
   test_image_with_latest_tag:
@@ -222,4 +223,4 @@ jobs:
         run: |
           docker run --rm \
             ${{ secrets.DOCKERHUB_USERNAME }}/nbiatoolkit:latest \
-            python -c "import nbiatoolkit; print(nbiatoolkit.__version__)"
+            NBIAToolkit

Dockerfile

@@ -13,7 +13,7 @@ LABEL maintainer="Jermiah Joseph"
 # install the dependencies
 RUN python -m pip install nbiatoolkit
 
-RUN python -c 'import nbiatoolkit; print(nbiatoolkit.__version__)'
+RUN python -c 'import nbiatoolkit; print(nbiatoolkit.version())'
 
 # On run, open a bash shell
 CMD ["/bin/bash"]

docs/Tutorial.ipynb

@@ -54,7 +54,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 5,
+   "execution_count": 2,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -68,23 +68,23 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 6,
+   "execution_count": 3,
    "metadata": {},
    "outputs": [
     {
      "data": {
       "text/plain": [
-       "'0.10.9'"
+       "'NBIAToolkit version: 0.12.1'"
       ]
      },
-     "execution_count": 6,
+     "execution_count": 3,
      "metadata": {},
      "output_type": "execute_result"
     }
    ],
    "source": [
     "# import nbiatoolkit \n",
-    "nbiatoolkit.__version__"
+    "nbiatoolkit.version()"
    ]
   },
   {

docs/index.md

@@ -8,7 +8,6 @@
 wiki/NBIA.md
 Tutorial.ipynb
 CONTRIBUTING.md
-CONTRIBUTING.md
 CONDUCT.md
 autoapi/index
 ```

pyproject.toml

@@ -6,17 +6,22 @@ authors = ["Jermiah Joseph"]
 license = "MIT"
 readme = "README.md"
 
+[tool.poetry.scripts]
+DICOMSorter = "nbiatoolkit.dicomsort:DICOMSorter_cli"
+NBIAToolkit = "nbiatoolkit:version"
+
 [tool.poetry.dependencies]
 python = ">=3.11 || 3.12"
 requests = "2.31.0"
 pydicom = "^2.4.3"
 tqdm = "^4.66.1"
-
-[tool.poetry.dev-dependencies]
+pyfiglet = "^1.0"
 
 [tool.poetry.group.dev.dependencies]
 pytest = "^7.4.3"
 jupyter = "^1.0.0"
+pytest-cov = ">=4.0.0"
+pytest-xdist = ">=3.5.0"
 myst-nb = {version = "^1.0.0", python = "^3.9"}
 sphinx-autoapi = "^3.0.0"
 sphinx-rtd-theme = "^1.3.0"

requirements.txt

@@ -5,4 +5,5 @@ ruff==v0.0.260
 coverage-badge~=1.1.0
 requests==2.31.0
 pydicom==2.4.3
-tqdm==4.66.1
+tqdm==4.66.1
+pyfiglet~=1.0

src/nbiatoolkit/__init__.py

@@ -6,14 +6,12 @@
 # this file is used to import all the modules in the package
 # this file is used to define the __all__ variable
 
-# set __version__ variable
-__version__ = "0.12.1"
 
 # import the modules
-from .nbia import NBIAClient
+from .nbia import NBIAClient, version
 from .auth import OAuth2
 from .logger.logger import setup_logger
 from .utils.nbia_endpoints import NBIA_ENDPOINTS
 
 # define the __all__ variable
-__all__ = ["NBIAClient", "OAuth2", "setup_logger", "NBIA_ENDPOINTS", "__version__"]
+__all__ = ["NBIAClient", "OAuth2", "setup_logger", "NBIA_ENDPOINTS", "version"]

src/nbiatoolkit/dicomsort/__init__.py

@@ -7,7 +7,7 @@
 #     "validateMD5"
 # ]
 
-from .dicomsort import DICOMSorter
+from .dicomsort import DICOMSorter, DICOMSorter_cli
 from .helper_functions import parseDICOMKeysFromFormat, sanitizeFileName, truncateUID
 
-__all__ = ["DICOMSorter", "parseDICOMKeysFromFormat", "sanitizeFileName", "truncateUID"]
+__all__ = ["DICOMSorter", "parseDICOMKeysFromFormat", "sanitizeFileName", "truncateUID", "DICOMSorter_cli"]

src/nbiatoolkit/dicomsort/dicomsort.py

@@ -1,12 +1,15 @@
 import re, os, sys, shutil
 import pydicom
+import argparse
 
 from pydicom.errors import InvalidDicomError
 
 from .helper_functions import parseDICOMKeysFromFormat, sanitizeFileName, truncateUID
 
 from typing import Optional
 
+from concurrent.futures import ThreadPoolExecutor, as_completed
+from tqdm import tqdm
 
 class DICOMSorter:
     def __init__(
@@ -83,25 +86,29 @@ def sortSingleDICOMFile(
 
         os.makedirs(os.path.dirname(targetFilename), exist_ok=True)
 
-        match option:
-            case "copy":
-                shutil.copyfile(src=filePath, dst=targetFilename)
-            case "move":
-                shutil.move(src=filePath, dst=targetFilename)
+        if option == "copy":
+            shutil.copyfile(src=filePath, dst=targetFilename)
+        elif option == "move":
+            shutil.move(src=filePath, dst=targetFilename)
+        else:
+            raise ValueError(f"Invalid option: {option}")
 
         return True
 
-    def sortDICOMFiles(self, option: str = "copy", overwrite: bool = False) -> bool:
+    def sortDICOMFiles(self, option: str = "copy", overwrite: bool = False, nParallel: int = 1) -> bool:
         dicom_file_paths = self._get_dicom_files()
+        result = []
+        print("Running with {} parallel threads".format(nParallel))
 
-        results = [
-            self.sortSingleDICOMFile(file, option, overwrite)
-            for file in dicom_file_paths
-        ]
+        with ThreadPoolExecutor(max_workers=nParallel) as executor:
+            futures = [executor.submit(self.sortSingleDICOMFile, filePath, option, overwrite) for filePath in dicom_file_paths]
 
-        return all(results)
+            for future in tqdm(as_completed(futures), total=len(futures)):
+                result.append(future.result())
 
-    def _get_dicom_files(self) -> list[str]:
+        return all(result)
+
+    def _get_dicom_files(self) -> 'list[str]':
         dicom_file_paths = []
         # Iterate over all files in the source directory
         for root, dirs, files in os.walk(self.sourceDir):
@@ -112,17 +119,75 @@ def _get_dicom_files(self) -> list[str]:
 
         return dicom_file_paths
 
-
-# Test case
-# if __name__ == "__main__":
-
-# sorter = DICOMSorter(
-#     sourceDir = sourceDir,
-#     destinationDir=destinationDir,
-#     targetPattern=pattern,
-#     truncateUID=True,
-#     sanitizeFilename=True,
-#     overwrite=True
-#     )
-
-# sorter.sortDICOMFiles(option="move")
+# Create command line interface
+
+# Given a source directory, destination directory, and target pattern, sort DICOM files
+# into the destination directory according to the target pattern.
+# The target pattern is a string with placeholders matching '%<DICOMKey>'.
+
+def DICOMSorter_cli():
+    parser = argparse.ArgumentParser(
+        description="Sort DICOM files into destination directory according to target pattern."
+    )
+
+    parser.add_argument("sourceDir",
+        metavar="sourceDir",
+        type=str,
+        help="The source directory containing DICOM files.",
+    )
+
+    parser.add_argument("destinationDir",
+        metavar="destinationDir",
+        type=str,
+        help="The destination directory to sort DICOM files into.",
+    )
+
+    # Default is %%PatientName/%%SeriesNumber-%%SeriesInstanceUID/%%InstanceNumber.dcm
+    parser.add_argument("--targetPattern",
+        dest="targetPattern",
+        default="%PatientName/%SeriesNumber-%SeriesInstanceUID/%InstanceNumber.dcm",
+        type=str,
+        help='The target pattern for sorting DICOM files. Default is %%PatientName/%%SeriesNumber-%%SeriesInstanceUID/%%InstanceNumber.dcm.',
+    )
+
+    parser.add_argument("--truncateUID",
+        dest="truncateUID",
+        action="store_true",
+        default=True,
+        help="Truncate the UID to the last n characters (includes periods & underscores). Default is True.",
+    )
+
+    parser.add_argument("--sanitizeFilename",
+        dest="sanitizeFilename",
+        action="store_true",
+        help="Sanitize the file name by replacing potentially dangerous characters. Default is True.",
+    )
+
+    parser.add_argument("--overwrite",
+        dest="overwrite",
+        action="store_true",
+        help="Overwrite existing files. Default is False.",
+    )
+
+    parser.add_argument("--nParallel",
+        dest="nParallel",
+        action="store",
+        type=int,
+        help="Number of parallel threads. Default is 1.",)
+
+    parser.set_defaults(truncateUID=True)
+    parser.set_defaults(sanitizeFilename=True)
+    parser.set_defaults(overwrite=False)
+    parser.set_defaults(nParallel=1)
+
+    args = parser.parse_args()
+
+    sorter = DICOMSorter(
+        sourceDir=args.sourceDir,
+        destinationDir=args.destinationDir,
+        targetPattern=args.targetPattern,
+        truncateUID=args.truncateUID,
+        sanitizeFilename=args.sanitizeFilename,
+    )
+
+    sorter.sortDICOMFiles(option="copy", overwrite=args.overwrite, nParallel=int(args.nParallel))

src/nbiatoolkit/nbia.py

@@ -10,6 +10,18 @@
 import io
 import zipfile
 from tqdm import tqdm
+from pyfiglet import Figlet
+
+# set __version__ variable
+__version__ = "0.12.1"
+
+def version():
+
+    f = Figlet(font='slant')
+    print(f.renderText('NBIAToolkit'))
+    print("Version: {}".format(__version__))
+    return 
+
 
 
 class NBIAClient:
@@ -345,6 +357,7 @@ def parsePARAMS(self, params: dict) -> dict:
         return PARAMS
 
 
+
 # main
 if __name__ == "__main__":
     from pprint import pprint