SphinxExamples/src/IO/GDCM/ReadDICOMSeriesAndWrite3DImage/Code.py

#!/usr/bin/env python
 
# 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
#
#        https://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 sys
import os
import itk
import argparse
 
parser = argparse.ArgumentParser(description="Read DICOM Series And Write 3D Image.")
parser.add_argument(
    "dicom_directory",
    nargs="?",
    help="If DicomDirectory is not specified, current directory is used",
)
parser.add_argument("output_image", nargs="?")
parser.add_argument("series_name", nargs="?")
args = parser.parse_args()
 
# current directory by default
dirName = "."
if args.dicom_directory:
    dirName = args.dicom_directory
 
PixelType = itk.ctype("signed short")
Dimension = 3
 
ImageType = itk.Image[PixelType, Dimension]
 
namesGenerator = itk.GDCMSeriesFileNames.New()
namesGenerator.SetUseSeriesDetails(True)
namesGenerator.AddSeriesRestriction("0008|0021")
namesGenerator.SetGlobalWarningDisplay(False)
namesGenerator.SetDirectory(dirName)
 
seriesUID = namesGenerator.GetSeriesUIDs()
 
if len(seriesUID) < 1:
    print("No DICOMs in: " + dirName)
    sys.exit(1)
 
print("The directory: " + dirName)
print("Contains the following DICOM Series: ")
for uid in seriesUID:
    print(uid)
 
seriesFound = False
for uid in seriesUID:
    seriesIdentifier = uid
    if args.series_name:
        seriesIdentifier = args.series_name
        seriesFound = True
    print("Reading: " + seriesIdentifier)
    fileNames = namesGenerator.GetFileNames(seriesIdentifier)
 
    reader = itk.ImageSeriesReader[ImageType].New()
    dicomIO = itk.GDCMImageIO.New()
    reader.SetImageIO(dicomIO)
    reader.SetFileNames(fileNames)
    reader.ForceOrthogonalDirectionOff()
 
    writer = itk.ImageFileWriter[ImageType].New()
    outFileName = os.path.join(dirName, seriesIdentifier + ".nrrd")
    if args.output_image:
        outFileName = args.output_image
    writer.SetFileName(outFileName)
    writer.UseCompressionOn()
    writer.SetInput(reader.GetOutput())
    print("Writing: " + outFileName)
    writer.Update()
 
    if seriesFound:
        break