DicomSeriesReadModifyWrite/DicomSeriesReadModifySeriesWrite.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
import os
 
if len(sys.argv) < 3:
    print(
        "Usage: python "
        + __file__
        + " <input_directory_with_DICOM_series> <output_directory>"
    )
    sys.exit(1)
 
# Read the original series. First obtain the series file names using the
# image series reader.
data_directory = sys.argv[1]
series_IDs = sitk.ImageSeriesReader.GetGDCMSeriesIDs(data_directory)
if not series_IDs:
    print(
        'ERROR: given directory "'
        + data_directory
        + '" does not contain a DICOM series.'
    )
    sys.exit(1)
series_file_names = sitk.ImageSeriesReader.GetGDCMSeriesFileNames(
    data_directory, series_IDs[0]
)
 
series_reader = sitk.ImageSeriesReader()
series_reader.SetFileNames(series_file_names)
 
# Configure the reader to load all of the DICOM tags (public+private):
# By default tags are not loaded (saves time).
# By default if tags are loaded, the private tags are not loaded.
# We explicitly configure the reader to load tags, including the
# private ones.
series_reader.MetaDataDictionaryArrayUpdateOn()
series_reader.LoadPrivateTagsOn()
image3D = series_reader.Execute()
 
# Modify the image (blurring)
filtered_image = sitk.DiscreteGaussian(image3D)
 
# Write the 3D image as a series
# IMPORTANT: There are many DICOM tags that need to be updated when you modify
#            an original image. This is a delicate operation and requires
#            knowledge of the DICOM standard. This example only modifies some.
#            For a more complete list of tags that need to be modified see:
#                http://gdcm.sourceforge.net/wiki/index.php/Writing_DICOM
 
writer = sitk.ImageFileWriter()
# Use the study/series/frame of reference information given in the meta-data
# dictionary and not the automatically generated information from the file IO
writer.KeepOriginalImageUIDOn()
 
# Copy relevant tags from the original meta-data dictionary (private tags are
# also accessible).
tags_to_copy = [
    "0010|0010",  # Patient Name
    "0010|0020",  # Patient ID
    "0010|0030",  # Patient Birth Date
    "0020|000D",  # Study Instance UID, for machine consumption
    "0020|0010",  # Study ID, for human consumption
    "0008|0020",  # Study Date
    "0008|0030",  # Study Time
    "0008|0050",  # Accession Number
    "0008|0060",  # Modality
]
 
modification_time = time.strftime("%H%M%S")
modification_date = time.strftime("%Y%m%d")
 
# Copy some of the tags and add the relevant tags indicating the change.
# For the series instance UID (0020|000e), each of the components is a number,
# cannot start with zero, and separated by a '.' We create a unique series ID
# using the date and time.
# NOTE: DICOM tags represent hexadecimal numbers, so 0020|000D and 0020|000d
#       are equivalent. The ITK/SimpleITK dictionary is string based, so these
#       are two different keys, case sensitive. When read from a DICOM file the
#       hexadecimal string representations are in lower case, so we check for
#       existence and get the value after converting to lower case.
# Tags of interest:
direction = filtered_image.GetDirection()
series_tag_values = [
    (k, series_reader.GetMetaData(0, k.lower()))
    for k in tags_to_copy
    if series_reader.HasMetaDataKey(0, k.lower())
] + [
    ("0008|0031", modification_time),  # Series Time
    ("0008|0021", modification_date),  # Series Date
    ("0008|0008", "DERIVED\\SECONDARY"),  # Image Type
    (
        "0020|000e",
        "1.2.826.0.1.3680043.2.1125." + modification_date + ".1" + modification_time,
    ),
    # Series Instance UID
    (
        "0020|0037",
        "\\".join(
            map(
                str,
                (
                    direction[0],
                    direction[3],
                    direction[6],
                    direction[1],
                    direction[4],
                    direction[7],
                ),  # Image Orientation (Patient)
            )
        ),
    ),
    (
        "0008|103e",
        series_reader.GetMetaData(0, "0008|103e")
        if series_reader.HasMetaDataKey(0, "0008|103e")
        else "" + " Processed-SimpleITK",
    ),  # Series Description is an optional tag, so may not exist
]
 
for i in range(filtered_image.GetDepth()):
    image_slice = filtered_image[:, :, i]
    # Tags shared by the series.
    for tag, value in series_tag_values:
        image_slice.SetMetaData(tag, value)
    # Slice specific tags.
    #   Instance Creation Date
    image_slice.SetMetaData("0008|0012", time.strftime("%Y%m%d"))
    #   Instance Creation Time
    image_slice.SetMetaData("0008|0013", time.strftime("%H%M%S"))
    #   Image Position (Patient)
    image_slice.SetMetaData(
        "0020|0032",
        "\\".join(map(str, filtered_image.TransformIndexToPhysicalPoint((0, 0, i)))),
    )
    #   Instance Number
    image_slice.SetMetaData("0020|0013", str(i))
 
    # Write to the output directory and add the extension dcm, to force writing
    # in DICOM format.
    writer.SetFileName(os.path.join(sys.argv[2], str(i) + ".dcm"))
    writer.Execute(image_slice)
sys.exit(0)