Python/DicomModifyTags.py

# =========================================================================
#
#  Copyright NumFOCUS
#
#  Licensed under the Apache License, Version 2.0 (the "License");
#  you may not use this file except in compliance with the License.
#  You may obtain a copy of the License at
#
#         http://www.apache.org/licenses/LICENSE-2.0.txt
#
#  Unless required by applicable law or agreed to in writing, software
#  distributed under the License is distributed on an "AS IS" BASIS,
#  WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
#  See the License for the specific language governing permissions and
#  limitations under the License.
#
# =========================================================================
 
 
import SimpleITK as sitk
 
import sys
import time
 
if len(sys.argv) < 3:
    print("Usage: python " + __file__ + " <input_image> <output_image>")
    sys.exit(1)
 
# Read the image, single 3D DICOM slice
image = sitk.ReadImage(sys.argv[1])
 
# Modify the image (mean)
mean_image = sitk.BoxMean(image, [3, 3, 1])
 
# Save the modified image:
# We do not provide a method that copies all keys blindly. Our intent is
# to force us to remember that we always need to modify the meta-data
# dictionary keys when we save processed images in DICOM format.
# In case of the DICOM format, amongst other keys we need to set the Image Type
# (0008,0008), the Series Date (0008,0021), and Series Time (0008,0021).
# Obviously we need to set a different series number (0020,0011), series
# instance UID (0020,000E), etc. - we don't do that here.
# Please see the DICOM standard (http://dicom.nema.org/standard.html) for
# complete details on how to create valid DICOM images.
 
all_keys = image.GetMetaDataKeys()
for key in all_keys:
    mean_image.SetMetaData(key, image.GetMetaData(key))
mean_image.SetMetaData("0008|0008", "DERIVED\\SECONDARY")
modification_time = time.strftime("%H%M%S")
modification_date = time.strftime("%Y%m%d")
mean_image.SetMetaData("0008|0031", modification_time)
mean_image.SetMetaData("0008|0021", modification_date)
 
sitk.WriteImage(mean_image, sys.argv[2])
 
# Finally, read the image back and see that changes were made.
# Note that the image type (0008|0008) can contain additional spaces. The
# requirement is that the string have an even length
# (ftp://dicom.nema.org/medical/DICOM/2013/output/chtml/part05/sect_6.2.html).
# Where spaces are added is not specified and thus may vary
# ("DERIVED\SECONDARY ", "DERIVED\ SECONDARY" are equivalent).
modified_image = sitk.ReadImage(sys.argv[2])
if (
    modified_image.GetMetaData("0008|0008").replace(" ", "")
    != "DERIVED\\SECONDARY"
    or modified_image.GetMetaData("0008|0031") != modification_time
    or modified_image.GetMetaData("0008|0021") != modification_date
):
    sys.exit(1)
 
sys.exit(0)