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#!/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 ()
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