feat: Update DICOMSorter command line interface

jjjermiah · Feb 3, 2024 · 6b6a2a8 · 6b6a2a8
1 parent 9552b6c
commit 6b6a2a8
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Showing 4 changed files with 88 additions and 86 deletions.
diff --git a/pyproject.toml b/pyproject.toml
@@ -7,7 +7,7 @@ license = "MIT"
 readme = "README.md"
 
 [tool.poetry.scripts]
-DICOMSorter = "nbiatoolkit.dicomsort:DICOMSorter_cli"
+dicomsort = "nbiatoolkit.nbia_cli:DICOMSorter_cli"
 NBIAToolkit = "nbiatoolkit:version"
 getCollections = "nbiatoolkit.nbia_cli:getCollections_cli"
 getPatients = "nbiatoolkit.nbia_cli:getPatients_cli"

diff --git a/src/nbiatoolkit/dicomsort/__init__.py b/src/nbiatoolkit/dicomsort/__init__.py
@@ -7,7 +7,7 @@
 #     "validateMD5"
 # ]
 
-from .dicomsort import DICOMSorter, DICOMSorter_cli
+from .dicomsort import DICOMSorter
 from .helper_functions import parseDICOMKeysFromFormat, sanitizeFileName, truncateUID
 
 __all__ = [

diff --git a/src/nbiatoolkit/dicomsort/dicomsort.py b/src/nbiatoolkit/dicomsort/dicomsort.py
@@ -126,86 +126,3 @@ def _get_dicom_files(self) -> "list[str]":
         return dicom_file_paths
 
 
-# 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)
-    )
diff --git a/src/nbiatoolkit/nbia_cli.py b/src/nbiatoolkit/nbia_cli.py
@@ -1,6 +1,6 @@
 import io
 from .nbia import NBIAClient, __version__
-
+from .dicomsort import DICOMSorter
 
 import argparse
 import sys
@@ -32,6 +32,7 @@ def version():
         "getBodyPartCounts",
         "getSeries",
         "downloadSingleSeries",
+        "dicomsort"
     ]
     for command in commands:
         result = subprocess.run([command, "-h"], capture_output=True, text=True)
@@ -369,3 +370,87 @@ def downloadSingleSeries_cli() -> None:
         filePattern=args.filePattern,
         overwrite=args.overwrite,
     )
+
+# 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="NBIAToolkit: 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 5 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)
+    )