update dicom/interfile utils

mu_map/file/dicom.py

+from datetime import datetime, timedelta
 from typing import Tuple
 
 import numpy as np
@@ -15,6 +16,12 @@ DCM_TAG_PIXEL_SCALE_FACTOR = 0x00331038
 Maximum value that can be stored in an unsigned integer with 16 bist.
 """
 UINT16_MAX = 2**16 - 1
+"""
+DICOM images always contain UIDs to indicate their uniqueness.
+Thus, when a DICOM image is updated, UIDs have to be changed for
+which the following prefix is used.
+"""
+UID_PREFIX = "1.2.826.0.1.3680043.2.521."
 
 
 def load_dcm(filename: str) -> Tuple[pydicom.dataset.FileDataset, np.ndarray]:
@@ -89,3 +96,21 @@ def update_dcm(
     dcm.LargestImagePixelValue = image.max()
     dcm[DCM_TAG_PIXEL_SCALE_FACTOR].value = scale
     return dcm
+
+def change_uid(dcm: pydicom.dataset.FileDataset) -> pydicom.dataset.FileDataset:
+    """
+    Change the UIDs (SeriesInstance and SOPInstance) in a DICOM header so that
+    it becomes its own unique file. Note that this method does not guarantee
+    that the UIDs are fully unique. Since the creation of UIDs is time dependent,
+    this function should not be used to rapidly change many UIDs.
+
+    :param dcm: the DICOM file to be udpated
+    :return: the DICOM file with updated UIDs
+    """
+
+    now = datetime.now()
+    soon = now + timedelta(seconds=1)
+
+    dcm.SeriesInstanceUID = UID_PREFIX + now.strftime("%Y%m%d%H%M%S")
+    dcm.SOPInstanceUID = UID_PREFIX + soon.strftime("%Y%m%d%H%M%S")
+    return dcm

mu_map/file/interfile2dicom.py

@@ -4,8 +4,8 @@ import os
 import numpy as np
 import pydicom
 
-from mu_map.file.dicom import update_dcm
-from mu_map.file.interfile import read_interfile
+from mu_map.file.dicom import update_dcm, change_uid
+from mu_map.file.interfile import load_interfile_img
 
 parser = argparse.ArgumentParser(
     description="convert an INTERFILE image to a DICOM image",
@@ -25,13 +25,21 @@ parser.add_argument(
     type=str,
     help="the output file - defaults to the INTERFILE input with a dcm extension",
 )
+parser.add_argument(
+    "--description",
+    type=str,
+    help="if provided the series description will be updated",
+)
 args = parser.parse_args()
 
 if args.out is None:
     args.out = os.path.splitext(args.inter)[0] + ".dcm"
 
-image, header = read_interfile(args.inter)
+image = load_interfile_img(args.inter)
 
 dcm = pydicom.dcmread(args.dcm)
 dcm = update_dcm(dcm.copy(), image)
+dcm = change_uid(dcm)
+if args.description:
+    dcm.SeriesDescription = args.description
 pydicom.dcmwrite(args.out, dcm)