Mercurial > hg > orthanc

annotate Resources/Samples/ImportDicomFiles/ImportDicomFiles.py @ 733:29982cfc5009

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
improvements to ImportDicomFiles tx Karsten Hilbert
author Sebastien Jodogne <s.jodogne@gmail.com>
date Thu, 27 Feb 2014 09:45:15 +0100
parents 7000726bade7
children 44382c8bcd15
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
77e526e6fdf8 sample script to import DICOM files in Orthanc
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
3 import os
77e526e6fdf8 sample script to import DICOM files in Orthanc
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
4 import sys
77e526e6fdf8 sample script to import DICOM files in Orthanc
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
5 import os.path
77e526e6fdf8 sample script to import DICOM files in Orthanc
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
6 import httplib2
373
7000726bade7 fix ImportDicomFiles
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 370
diff changeset
7 import base64
280
77e526e6fdf8 sample script to import DICOM files in Orthanc
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
8
370
22bb88181e06 credentials
jodogne
parents: 280
diff changeset
9 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
10 print("""
77e526e6fdf8 sample script to import DICOM files in Orthanc
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
11 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
12 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
13 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
14 API.
77e526e6fdf8 sample script to import DICOM files in Orthanc
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
15
77e526e6fdf8 sample script to import DICOM files in Orthanc
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
16 Usage: %s [hostname] [HTTP port] [path]
370
22bb88181e06 credentials
jodogne
parents: 280
diff changeset
17 Usage: %s [hostname] [HTTP port] [path] [username] [password]
280
77e526e6fdf8 sample script to import DICOM files in Orthanc
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
18 For instance: %s localhost 8042 .
370
22bb88181e06 credentials
jodogne
parents: 280
diff changeset
19 """ % (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
20 exit(-1)
77e526e6fdf8 sample script to import DICOM files in Orthanc
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
21
77e526e6fdf8 sample script to import DICOM files in Orthanc
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
22 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
23
733
29982cfc5009 improvements to ImportDicomFiles tx Karsten Hilbert
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 373
diff changeset
24 success_count = 0
29982cfc5009 improvements to ImportDicomFiles tx Karsten Hilbert
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 373
diff changeset
25 total_file_count = 0
280
77e526e6fdf8 sample script to import DICOM files in Orthanc
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
26
77e526e6fdf8 sample script to import DICOM files in Orthanc
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
27
77e526e6fdf8 sample script to import DICOM files in Orthanc
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
28 # 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
29 def UploadFile(path):
733
29982cfc5009 improvements to ImportDicomFiles tx Karsten Hilbert
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 373
diff changeset
30 global success_count
29982cfc5009 improvements to ImportDicomFiles tx Karsten Hilbert
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 373
diff changeset
31 global total_file_count
280
77e526e6fdf8 sample script to import DICOM files in Orthanc
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
32
370
22bb88181e06 credentials
jodogne
parents: 280
diff changeset
33 f = open(path, "rb")
280
77e526e6fdf8 sample script to import DICOM files in Orthanc
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
34 content = f.read()
77e526e6fdf8 sample script to import DICOM files in Orthanc
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
35 f.close()
733
29982cfc5009 improvements to ImportDicomFiles tx Karsten Hilbert
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 373
diff changeset
36 total_file_count += 1
280
77e526e6fdf8 sample script to import DICOM files in Orthanc
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
37
77e526e6fdf8 sample script to import DICOM files in Orthanc
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
38 try:
77e526e6fdf8 sample script to import DICOM files in Orthanc
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
39 sys.stdout.write("Importing %s" % path)
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 h = httplib2.Http()
370
22bb88181e06 credentials
jodogne
parents: 280
diff changeset
42
373
7000726bade7 fix ImportDicomFiles
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 370
diff changeset
43 headers = { 'content-type' : 'application/dicom' }
7000726bade7 fix ImportDicomFiles
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 370
diff changeset
44
370
22bb88181e06 credentials
jodogne
parents: 280
diff changeset
45 if len(sys.argv) == 6:
373
7000726bade7 fix ImportDicomFiles
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 370
diff changeset
46 username = sys.argv[4]
7000726bade7 fix ImportDicomFiles
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 370
diff changeset
47 password = sys.argv[5]
7000726bade7 fix ImportDicomFiles
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 370
diff changeset
48
7000726bade7 fix ImportDicomFiles
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 370
diff changeset
49 # h.add_credentials(username, password)
7000726bade7 fix ImportDicomFiles
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 370
diff changeset
50
7000726bade7 fix ImportDicomFiles
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 370
diff changeset
51 # This is a custom reimplementation of the
7000726bade7 fix ImportDicomFiles
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 370
diff changeset
52 # "Http.add_credentials()" method for Basic HTTP Access
7000726bade7 fix ImportDicomFiles
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 370
diff changeset
53 # Authentication (for some weird reason, this method does
7000726bade7 fix ImportDicomFiles
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 370
diff changeset
54 # not always work)
7000726bade7 fix ImportDicomFiles
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 370
diff changeset
55 # http://en.wikipedia.org/wiki/Basic_access_authentication
7000726bade7 fix ImportDicomFiles
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 370
diff changeset
56 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
57
280
77e526e6fdf8 sample script to import DICOM files in Orthanc
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
58 resp, content = h.request(URL, 'POST',
77e526e6fdf8 sample script to import DICOM files in Orthanc
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
59 body = content,
373
7000726bade7 fix ImportDicomFiles
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 370
diff changeset
60 headers = headers)
280
77e526e6fdf8 sample script to import DICOM files in Orthanc
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
61
77e526e6fdf8 sample script to import DICOM files in Orthanc
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
62 if resp.status == 200:
77e526e6fdf8 sample script to import DICOM files in Orthanc
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
63 sys.stdout.write(" => success\n")
733
29982cfc5009 improvements to ImportDicomFiles tx Karsten Hilbert
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 373
diff changeset
64 success_count += 1
280
77e526e6fdf8 sample script to import DICOM files in Orthanc
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
65 else:
373
7000726bade7 fix ImportDicomFiles
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 370
diff changeset
66 sys.stdout.write(" => failure (Is it a DICOM file?)\n")
280
77e526e6fdf8 sample script to import DICOM files in Orthanc
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
67
77e526e6fdf8 sample script to import DICOM files in Orthanc
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
68 except:
373
7000726bade7 fix ImportDicomFiles
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 370
diff changeset
69 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
70
77e526e6fdf8 sample script to import DICOM files in Orthanc
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
71
77e526e6fdf8 sample script to import DICOM files in Orthanc
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
72 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
73 # Upload a single file
77e526e6fdf8 sample script to import DICOM files in Orthanc
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
74 UploadFile(sys.argv[3])
77e526e6fdf8 sample script to import DICOM files in Orthanc
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
75 else:
77e526e6fdf8 sample script to import DICOM files in Orthanc
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
76 # Recursively upload a directory
77e526e6fdf8 sample script to import DICOM files in Orthanc
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
77 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
78 for f in files:
77e526e6fdf8 sample script to import DICOM files in Orthanc
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
79 UploadFile(os.path.join(root, f))
77e526e6fdf8 sample script to import DICOM files in Orthanc
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
80
733
29982cfc5009 improvements to ImportDicomFiles tx Karsten Hilbert
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 373
diff changeset
81 if success_count == total_file_count:
29982cfc5009 improvements to ImportDicomFiles tx Karsten Hilbert
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 373
diff changeset
82 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
83 else:
29982cfc5009 improvements to ImportDicomFiles tx Karsten Hilbert
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 373
diff changeset
84 print("\nSummary: %d out of %d files have been imported successfully as DICOM instances" % (success_count, total_file_count))