Python/DicomSeriesReader2.py

#!/usr/bin/env python

#=========================================================================
#
#  Copyright Insight Software Consortium
#
#  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.
#
#=========================================================================


#
#  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.
#

from __future__ import print_function

import sys, getopt
import SimpleITK as sitk

target_series = ""
output_image = ""

def usage():
    print (  "\nUsage: %s [-s series_name] input_directory [output_image]\n" % (sys.argv[0]) )

# Parse command line options
try:
    opts, args = getopt.getopt(sys.argv[1:], "s:", [ "series" ] )
except getopt.GetoptError as err:
    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 == "" or target_series == serie):

                    print( "\nWriting", output_image )
                    sitk.WriteImage(image, output_image)
                    written = True
else:
    sys.exit(1)

print ()