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comparison Resources/Samples/Python/AutoClassify.py @ 1182:d74ac5d0bcaf

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New sample: Automated classification of DICOM files
author Sebastien Jodogne <s.jodogne@gmail.com>
date Thu, 09 Oct 2014 17:11:00 +0200
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children 6ef2c81581cd
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1181:17302d83abfd 1182:d74ac5d0bcaf
1 #!/usr/bin/python
2 # -*- coding: utf-8 -*-
3
4 # Orthanc - A Lightweight, RESTful DICOM Store
5 # Copyright (C) 2012-2014 Medical Physics Department, CHU of Liege,
6 # Belgium
7 #
8 # This program is free software: you can redistribute it and/or
9 # modify it under the terms of the GNU General Public License as
10 # published by the Free Software Foundation, either version 3 of the
11 # License, or (at your option) any later version.
12 #
13 # This program is distributed in the hope that it will be useful, but
14 # WITHOUT ANY WARRANTY; without even the implied warranty of
15 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
16 # General Public License for more details.
17 #
18 # You should have received a copy of the GNU General Public License
19 # along with this program. If not, see <http://www.gnu.org/licenses/>.
20
21
22 import argparse
23 import time
24 import os
25 import os.path
26 import RestToolbox
27
28 parser = argparse.ArgumentParser(
29 description = 'Automated classification of DICOM files from Orthanc.',
30 formatter_class = argparse.ArgumentDefaultsHelpFormatter)
31
32 parser.add_argument('--host', default = 'localhost',
33 help = 'The host address that runs Orthanc')
34 parser.add_argument('--port', type = int, default = '8042',
35 help = 'The port number to which Orthanc is listening for the REST API')
36 parser.add_argument('--target', default = 'OrthancFiles',
37 help = 'The target directory where to store the DICOM files')
38 parser.add_argument('--all', action = 'store_true',
39 help = 'Replay the entire history on startup (disabled by default)')
40 parser.set_defaults(all = False)
41 parser.add_argument('--remove', action = 'store_true',
42 help = 'Remove DICOM files from Orthanc once classified (disabled by default)')
43 parser.set_defaults(remove = False)
44
45
46 # Parse the arguments
47 args = parser.parse_args()
48 URL = 'http://%s:%d' % (args.host, args.port)
49 print 'Connecting to Orthanc on address: %s' % URL
50
51 # Compute the starting point for the changes loop
52 if args.all:
53 current = 0
54 else:
55 current = RestToolbox.DoGet(URL + '/changes?last')['Last']
56
57 # Polling loop using the "changes" API of Orthanc, waiting for the
58 # incoming of new DICOM files
59 while True:
60 r = RestToolbox.DoGet(URL + '/changes', {
61 'since' : current,
62 'limit' : 4 # Retrieve at most 4 changes at once
63 })
64
65 for change in r['Changes']:
66 # We are only interested interested in the arrival of new instances
67 if change['ChangeType'] == 'NewInstance':
68 # Extract the patient, study, series and instance information
69 instance = RestToolbox.DoGet('%s/instances/%s' % (URL, change['ID']))
70 series = RestToolbox.DoGet('%s/series/%s' % (URL, instance['ParentSeries']))
71 study = RestToolbox.DoGet('%s/studies/%s' % (URL, series['ParentStudy']))
72 patient = RestToolbox.DoGet('%s/patients/%s' % (URL, study['ParentPatient']))
73
74 # Construct a target path
75 a = '%s - %s' % (patient['MainDicomTags']['PatientID'],
76 patient['MainDicomTags']['PatientName'])
77 b = study['MainDicomTags']['StudyDescription']
78 c = '%s - %s' % (series['MainDicomTags']['Modality'],
79 series['MainDicomTags']['SeriesDescription'])
80 d = '%s.dcm' % instance['MainDicomTags']['SOPInstanceUID']
81
82 p = os.path.join(
83 args.target,
84 a.encode('ascii', 'ignore'),
85 b.encode('ascii', 'ignore'),
86 c.encode('ascii', 'ignore')
87 )
88
89 f = os.path.join(p, d.encode('ascii', 'ignore'))
90
91
92 # Copy the DICOM file to the target path
93 print('Writing new DICOM file: %s' % f)
94
95 try:
96 os.makedirs(p)
97 except:
98 # Already existing directory, ignore the error
99 pass
100
101 dcm = RestToolbox.DoGet('%s/instances/%s/file' % (URL, change['ID']))
102 with open(f, 'wb') as g:
103 g.write(dcm)
104
105 # If requested, remove the instance once it has been copied
106 if args.remove:
107 RestToolbox.DoDelete('%s/instances/%s' % (URL, change['ID']))
108
109 current = r['Last']
110
111 if r['Done']:
112 print "Everything has been processed: Waiting..."
113 time.sleep(1)