Mercurial > hg > orthanc

annotate Resources/Samples/ImportDicomFiles/ImportDicomFiles.py @ 2253:441352e7a9d1

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
fix
author Sebastien Jodogne <s.jodogne@gmail.com>
date Wed, 25 Jan 2017 14:16:46 +0100
parents a3a65de1840f
children b85f68a98474
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
280
77e526e6fdf8 sample script to import DICOM files in Orthanc
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1 #!/usr/bin/python
77e526e6fdf8 sample script to import DICOM files in Orthanc
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
2
747
44382c8bcd15 added explicit licensing terms for samples
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 733
diff changeset
3 # Orthanc - A Lightweight, RESTful DICOM Store
1900
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1766
diff changeset
4 # Copyright (C) 2012-2016 Sebastien Jodogne, Medical Physics
1288
6e7e5ed91c2d upgrade to year 2015
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 747
diff changeset
5 # Department, University Hospital of Liege, Belgium
2244
a3a65de1840f shared copyright with osimis
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2032
diff changeset
6 # Copyright (C) 2017 Osimis, Belgium
747
44382c8bcd15 added explicit licensing terms for samples
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 733
diff changeset
7 #
44382c8bcd15 added explicit licensing terms for samples
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 733
diff changeset
8 # This program is free software: you can redistribute it and/or
44382c8bcd15 added explicit licensing terms for samples
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 733
diff changeset
9 # modify it under the terms of the GNU General Public License as
44382c8bcd15 added explicit licensing terms for samples
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 733
diff changeset
10 # published by the Free Software Foundation, either version 3 of the
44382c8bcd15 added explicit licensing terms for samples
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 733
diff changeset
11 # License, or (at your option) any later version.
44382c8bcd15 added explicit licensing terms for samples
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 733
diff changeset
12 #
44382c8bcd15 added explicit licensing terms for samples
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 733
diff changeset
13 # This program is distributed in the hope that it will be useful, but
44382c8bcd15 added explicit licensing terms for samples
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 733
diff changeset
14 # WITHOUT ANY WARRANTY; without even the implied warranty of
44382c8bcd15 added explicit licensing terms for samples
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 733
diff changeset
15 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
44382c8bcd15 added explicit licensing terms for samples
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 733
diff changeset
16 # General Public License for more details.
44382c8bcd15 added explicit licensing terms for samples
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 733
diff changeset
17 #
44382c8bcd15 added explicit licensing terms for samples
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 733
diff changeset
18 # You should have received a copy of the GNU General Public License
44382c8bcd15 added explicit licensing terms for samples
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 733
diff changeset
19 # along with this program. If not, see <http://www.gnu.org/licenses/>.
44382c8bcd15 added explicit licensing terms for samples
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 733
diff changeset
20
44382c8bcd15 added explicit licensing terms for samples
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 733
diff changeset
21
280
77e526e6fdf8 sample script to import DICOM files in Orthanc
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
22 import os
77e526e6fdf8 sample script to import DICOM files in Orthanc
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
23 import sys
77e526e6fdf8 sample script to import DICOM files in Orthanc
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
24 import os.path
77e526e6fdf8 sample script to import DICOM files in Orthanc
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
25 import httplib2
373
7000726bade7 fix ImportDicomFiles
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 370
diff changeset
26 import base64
280
77e526e6fdf8 sample script to import DICOM files in Orthanc
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
27
370
22bb88181e06 credentials
jodogne
parents: 280
diff changeset
28 if len(sys.argv) != 4 and len(sys.argv) != 6:
280
77e526e6fdf8 sample script to import DICOM files in Orthanc
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
29 print("""
77e526e6fdf8 sample script to import DICOM files in Orthanc
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
30 Sample script to recursively import in Orthanc all the DICOM files
77e526e6fdf8 sample script to import DICOM files in Orthanc
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
31 that are stored in some path. Please make sure that Orthanc is running
77e526e6fdf8 sample script to import DICOM files in Orthanc
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
32 before starting this script. The files are uploaded through the REST
77e526e6fdf8 sample script to import DICOM files in Orthanc
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
33 API.
77e526e6fdf8 sample script to import DICOM files in Orthanc
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
34
77e526e6fdf8 sample script to import DICOM files in Orthanc
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
35 Usage: %s [hostname] [HTTP port] [path]
370
22bb88181e06 credentials
jodogne
parents: 280
diff changeset
36 Usage: %s [hostname] [HTTP port] [path] [username] [password]
2032
65b1ce7cb84f Replaced "localhost" by "127.0.0.1", as it might impact performance on Windows
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1900
diff changeset
37 For instance: %s 127.0.0.1 8042 .
370
22bb88181e06 credentials
jodogne
parents: 280
diff changeset
38 """ % (sys.argv[0], sys.argv[0], sys.argv[0]))
280
77e526e6fdf8 sample script to import DICOM files in Orthanc
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
39 exit(-1)
77e526e6fdf8 sample script to import DICOM files in Orthanc
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
40
77e526e6fdf8 sample script to import DICOM files in Orthanc
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
41 URL = 'http://%s:%d/instances' % (sys.argv[1], int(sys.argv[2]))
77e526e6fdf8 sample script to import DICOM files in Orthanc
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
42
733
29982cfc5009 improvements to ImportDicomFiles tx Karsten Hilbert
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 373
diff changeset
43 success_count = 0
29982cfc5009 improvements to ImportDicomFiles tx Karsten Hilbert
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 373
diff changeset
44 total_file_count = 0
280
77e526e6fdf8 sample script to import DICOM files in Orthanc
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
45
77e526e6fdf8 sample script to import DICOM files in Orthanc
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
46
77e526e6fdf8 sample script to import DICOM files in Orthanc
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
47 # This function will upload a single file to Orthanc through the REST API
77e526e6fdf8 sample script to import DICOM files in Orthanc
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
48 def UploadFile(path):
733
29982cfc5009 improvements to ImportDicomFiles tx Karsten Hilbert
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 373
diff changeset
49 global success_count
29982cfc5009 improvements to ImportDicomFiles tx Karsten Hilbert
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 373
diff changeset
50 global total_file_count
280
77e526e6fdf8 sample script to import DICOM files in Orthanc
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
51
370
22bb88181e06 credentials
jodogne
parents: 280
diff changeset
52 f = open(path, "rb")
280
77e526e6fdf8 sample script to import DICOM files in Orthanc
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
53 content = f.read()
77e526e6fdf8 sample script to import DICOM files in Orthanc
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
54 f.close()
733
29982cfc5009 improvements to ImportDicomFiles tx Karsten Hilbert
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 373
diff changeset
55 total_file_count += 1
280
77e526e6fdf8 sample script to import DICOM files in Orthanc
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
56
77e526e6fdf8 sample script to import DICOM files in Orthanc
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
57 try:
77e526e6fdf8 sample script to import DICOM files in Orthanc
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
58 sys.stdout.write("Importing %s" % path)
77e526e6fdf8 sample script to import DICOM files in Orthanc
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
59
77e526e6fdf8 sample script to import DICOM files in Orthanc
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
60 h = httplib2.Http()
370
22bb88181e06 credentials
jodogne
parents: 280
diff changeset
61
373
7000726bade7 fix ImportDicomFiles
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 370
diff changeset
62 headers = { 'content-type' : 'application/dicom' }
7000726bade7 fix ImportDicomFiles
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 370
diff changeset
63
370
22bb88181e06 credentials
jodogne
parents: 280
diff changeset
64 if len(sys.argv) == 6:
373
7000726bade7 fix ImportDicomFiles
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 370
diff changeset
65 username = sys.argv[4]
7000726bade7 fix ImportDicomFiles
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 370
diff changeset
66 password = sys.argv[5]
7000726bade7 fix ImportDicomFiles
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 370
diff changeset
67
7000726bade7 fix ImportDicomFiles
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 370
diff changeset
68 # h.add_credentials(username, password)
7000726bade7 fix ImportDicomFiles
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 370
diff changeset
69
7000726bade7 fix ImportDicomFiles
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 370
diff changeset
70 # This is a custom reimplementation of the
7000726bade7 fix ImportDicomFiles
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 370
diff changeset
71 # "Http.add_credentials()" method for Basic HTTP Access
7000726bade7 fix ImportDicomFiles
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 370
diff changeset
72 # Authentication (for some weird reason, this method does
7000726bade7 fix ImportDicomFiles
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 370
diff changeset
73 # not always work)
7000726bade7 fix ImportDicomFiles
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 370
diff changeset
74 # http://en.wikipedia.org/wiki/Basic_access_authentication
7000726bade7 fix ImportDicomFiles
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 370
diff changeset
75 headers['authorization'] = 'Basic ' + base64.b64encode(username + ':' + password)
733
29982cfc5009 improvements to ImportDicomFiles tx Karsten Hilbert
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 373
diff changeset
76
280
77e526e6fdf8 sample script to import DICOM files in Orthanc
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
77 resp, content = h.request(URL, 'POST',
77e526e6fdf8 sample script to import DICOM files in Orthanc
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
78 body = content,
373
7000726bade7 fix ImportDicomFiles
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 370
diff changeset
79 headers = headers)
280
77e526e6fdf8 sample script to import DICOM files in Orthanc
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
80
77e526e6fdf8 sample script to import DICOM files in Orthanc
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
81 if resp.status == 200:
77e526e6fdf8 sample script to import DICOM files in Orthanc
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
82 sys.stdout.write(" => success\n")
733
29982cfc5009 improvements to ImportDicomFiles tx Karsten Hilbert
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 373
diff changeset
83 success_count += 1
280
77e526e6fdf8 sample script to import DICOM files in Orthanc
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
84 else:
1766
d178fab186dd reminder of password
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1288
diff changeset
85 sys.stdout.write(" => failure (Is it a DICOM file? Is there a password?)\n")
280
77e526e6fdf8 sample script to import DICOM files in Orthanc
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
86
77e526e6fdf8 sample script to import DICOM files in Orthanc
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
87 except:
373
7000726bade7 fix ImportDicomFiles
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 370
diff changeset
88 sys.stdout.write(" => unable to connect (Is Orthanc running? Is there a password?)\n")
280
77e526e6fdf8 sample script to import DICOM files in Orthanc
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
89
77e526e6fdf8 sample script to import DICOM files in Orthanc
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
90
77e526e6fdf8 sample script to import DICOM files in Orthanc
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
91 if os.path.isfile(sys.argv[3]):
77e526e6fdf8 sample script to import DICOM files in Orthanc
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
92 # Upload a single file
77e526e6fdf8 sample script to import DICOM files in Orthanc
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
93 UploadFile(sys.argv[3])
77e526e6fdf8 sample script to import DICOM files in Orthanc
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
94 else:
77e526e6fdf8 sample script to import DICOM files in Orthanc
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
95 # Recursively upload a directory
77e526e6fdf8 sample script to import DICOM files in Orthanc
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
96 for root, dirs, files in os.walk(sys.argv[3]):
77e526e6fdf8 sample script to import DICOM files in Orthanc
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
97 for f in files:
77e526e6fdf8 sample script to import DICOM files in Orthanc
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
98 UploadFile(os.path.join(root, f))
77e526e6fdf8 sample script to import DICOM files in Orthanc
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
99
733
29982cfc5009 improvements to ImportDicomFiles tx Karsten Hilbert
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 373
diff changeset
100 if success_count == total_file_count:
29982cfc5009 improvements to ImportDicomFiles tx Karsten Hilbert
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 373
diff changeset
101 print("\nSummary: all %d DICOM file(s) have been imported successfully" % success_count)
29982cfc5009 improvements to ImportDicomFiles tx Karsten Hilbert
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 373
diff changeset
102 else:
29982cfc5009 improvements to ImportDicomFiles tx Karsten Hilbert
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 373
diff changeset
103 print("\nSummary: %d out of %d files have been imported successfully as DICOM instances" % (success_count, total_file_count))