Python/DicomSeriesReader2.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
#
#         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.
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# =========================================================================
 
 
""" This example shows how to read a specific series from a Dicom directory that
may contain more than one series.  The script scans for all series.  If an
output name is given, it writes out the requested series.  If no specific
series name is given, the first series found is written.
"""
 
 
import sys
import getopt
import SimpleITK as sitk
 
target_series = ""
output_image = ""
 
 
def usage():
    """ Print usage information. """
    print(
        f"\nUsage: {sys.argv[0]} [-s series_name] input_directory [output_image]\n"
    )
 
 
# Parse command line options
try:
    opts, args = getopt.getopt(sys.argv[1:], "s:", ["series"])
except getopt.GetoptError:
    usage()
    sys.exit(1)
 
for o, a in opts:
    if o in ("-s", "--series"):
        target_series = a
    else:
        assert False, "unhandled options"
 
# Get input/output names
if len(args) < 1:
    print(args)
    usage()
    sys.exit(1)
 
input_directory = args[0]
if len(args) > 1:
    output_image = args[1]
 
# Find the Dicom series
reader = sitk.ImageSeriesReader()
written = False
 
series_found = reader.GetGDCMSeriesIDs(input_directory)
 
# Process each Dicom series
if len(series_found):
 
    for serie in series_found:
 
        print("\nSeries:", serie)
 
        # Get the Dicom filename corresponding to the current series
        dicom_names = reader.GetGDCMSeriesFileNames(input_directory, serie)
 
        print("\nFiles in series: ", dicom_names)
 
        if len(dicom_names):
            reader.SetFileNames(dicom_names)
            image = reader.Execute()
            print("\nImage size: ", image.GetSize())
 
            if (output_image != "") and not written:
                if target_series in ('', serie):
                    print("\nWriting", output_image)
                    sitk.WriteImage(image, output_image)
                    written = True
else:
    sys.exit(1)
 
print()