annotate OrthancServer/Resources/Samples/ImportDicomFiles/OrthancImport.py @ 5469:514fd39f87a8

improved handling of X-Content-Type-Options
author Sebastien Jodogne <s.jodogne@gmail.com>
date Mon, 18 Dec 2023 21:06:41 +0100
parents 0ea402b4d901
children 48b8dae6dc77
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
5469
514fd39f87a8 improved handling of X-Content-Type-Options
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 5185
diff changeset
1 #!/usr/bin/env python3
4337
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
2
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
3 # Orthanc - A Lightweight, RESTful DICOM Store
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
4 # Copyright (C) 2012-2016 Sebastien Jodogne, Medical Physics
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
5 # Department, University Hospital of Liege, Belgium
5185
0ea402b4d901 upgrade to year 2023
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 4973
diff changeset
6 # Copyright (C) 2017-2023 Osimis S.A., Belgium
0ea402b4d901 upgrade to year 2023
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 4973
diff changeset
7 # Copyright (C) 2021-2023 Sebastien Jodogne, ICTEAM UCLouvain, Belgium
4337
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
8 #
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
9 # This program is free software: you can redistribute it and/or
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
10 # modify it under the terms of the GNU General Public License as
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
11 # published by the Free Software Foundation, either version 3 of the
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
12 # License, or (at your option) any later version.
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
13 #
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
14 # This program is distributed in the hope that it will be useful, but
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
15 # WITHOUT ANY WARRANTY; without even the implied warranty of
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
16 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
17 # General Public License for more details.
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
18 #
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
19 # You should have received a copy of the GNU General Public License
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
20 # along with this program. If not, see <http://www.gnu.org/licenses/>.
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
21
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
22
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
23 import argparse
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
24 import bz2
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
25 import gzip
4748
4336642b8cff ignore JSON files in sample Python upload scripts
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 4450
diff changeset
26 import json
4337
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
27 import os
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
28 import requests
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
29 import sys
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
30 import tarfile
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
31 import zipfile
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
32
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
33 from requests.auth import HTTPBasicAuth
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
34
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
35
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
36
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
37 parser = argparse.ArgumentParser(description = 'Command-line tool to import files or archives into Orthanc.')
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
38 parser.add_argument('--url',
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
39 default = 'http://localhost:8042',
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
40 help = 'URL to the REST API of the Orthanc server')
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
41 parser.add_argument('--username',
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
42 default = 'orthanc',
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
43 help = 'Username to the REST API')
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
44 parser.add_argument('--password',
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
45 default = 'orthanc',
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
46 help = 'Password to the REST API')
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
47 parser.add_argument('--force', help = 'Do not warn the user about deletion',
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
48 action = 'store_true')
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
49 parser.add_argument('--clear', help = 'Remove the content of the Orthanc database',
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
50 action = 'store_true')
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
51 parser.add_argument('--verbose', help = 'Be verbose',
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
52 action = 'store_true')
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
53 parser.add_argument('--ignore-errors', help = 'Do not stop if encountering non-DICOM files',
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
54 action = 'store_true')
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
55 parser.add_argument('files', metavar = 'N', nargs = '*',
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
56 help = 'Files to import')
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
57
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
58
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
59 args = parser.parse_args()
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
60
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
61 if args.clear and not args.force:
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
62 print("""
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
63 WARNING: This script will remove all the content of your
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
64 Orthanc instance running on %s!
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
65
4972
cde17b68d73e linor fix in OrthancImport.py
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 4870
diff changeset
66 Are you sure ["yes" to go on]?""" % args.url)
4337
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
67
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
68 if sys.stdin.readline().strip() != 'yes':
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
69 print('Aborting...')
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
70 exit(0)
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
71
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
72
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
73
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
74 IMPORTED_STUDIES = set()
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
75 COUNT_ERROR = 0
4748
4336642b8cff ignore JSON files in sample Python upload scripts
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 4450
diff changeset
76 COUNT_DICOM = 0
4336642b8cff ignore JSON files in sample Python upload scripts
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 4450
diff changeset
77 COUNT_JSON = 0
4336642b8cff ignore JSON files in sample Python upload scripts
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 4450
diff changeset
78
4336642b8cff ignore JSON files in sample Python upload scripts
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 4450
diff changeset
79
4336642b8cff ignore JSON files in sample Python upload scripts
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 4450
diff changeset
80 def IsJson(content):
4336642b8cff ignore JSON files in sample Python upload scripts
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 4450
diff changeset
81 try:
4336642b8cff ignore JSON files in sample Python upload scripts
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 4450
diff changeset
82 if (sys.version_info >= (3, 0)):
4336642b8cff ignore JSON files in sample Python upload scripts
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 4450
diff changeset
83 json.loads(content.decode())
4336642b8cff ignore JSON files in sample Python upload scripts
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 4450
diff changeset
84 return True
4336642b8cff ignore JSON files in sample Python upload scripts
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 4450
diff changeset
85 else:
4336642b8cff ignore JSON files in sample Python upload scripts
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 4450
diff changeset
86 json.loads(content)
4336642b8cff ignore JSON files in sample Python upload scripts
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 4450
diff changeset
87 return True
4336642b8cff ignore JSON files in sample Python upload scripts
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 4450
diff changeset
88 except:
4336642b8cff ignore JSON files in sample Python upload scripts
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 4450
diff changeset
89 return False
4336642b8cff ignore JSON files in sample Python upload scripts
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 4450
diff changeset
90
4336642b8cff ignore JSON files in sample Python upload scripts
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 4450
diff changeset
91
4337
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
92 def UploadBuffer(dicom):
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
93 global IMPORTED_STUDIES
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
94 global COUNT_ERROR
4748
4336642b8cff ignore JSON files in sample Python upload scripts
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 4450
diff changeset
95 global COUNT_DICOM
4336642b8cff ignore JSON files in sample Python upload scripts
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 4450
diff changeset
96 global COUNT_JSON
4336642b8cff ignore JSON files in sample Python upload scripts
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 4450
diff changeset
97
4336642b8cff ignore JSON files in sample Python upload scripts
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 4450
diff changeset
98 if IsJson(dicom):
4336642b8cff ignore JSON files in sample Python upload scripts
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 4450
diff changeset
99 COUNT_JSON += 1
4336642b8cff ignore JSON files in sample Python upload scripts
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 4450
diff changeset
100 return
4337
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
101
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
102 auth = HTTPBasicAuth(args.username, args.password)
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
103 r = requests.post('%s/instances' % args.url, auth = auth, data = dicom)
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
104
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
105 try:
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
106 r.raise_for_status()
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
107 except:
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
108 COUNT_ERROR += 1
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
109 if args.ignore_errors:
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
110 if args.verbose:
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
111 print(' not a valid DICOM file, ignoring it')
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
112 return
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
113 else:
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
114 raise
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
115
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
116 info = r.json()
4748
4336642b8cff ignore JSON files in sample Python upload scripts
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 4450
diff changeset
117 COUNT_DICOM += 1
4337
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
118
4973
17c91e054636 minor improvements
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 4972
diff changeset
119 if (isinstance(info, dict) and
17c91e054636 minor improvements
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 4972
diff changeset
120 not info['ParentStudy'] in IMPORTED_STUDIES):
4337
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
121 IMPORTED_STUDIES.add(info['ParentStudy'])
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
122
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
123 r2 = requests.get('%s/instances/%s/tags?short' % (args.url, info['ID']),
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
124 auth = auth)
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
125 r2.raise_for_status()
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
126 tags = r2.json()
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
127
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
128 print('')
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
129 print('New imported study:')
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
130 print(' Orthanc ID of the patient: %s' % info['ParentPatient'])
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
131 print(' Orthanc ID of the study: %s' % info['ParentStudy'])
4450
9bf2f9e0af47 support empty PatientID in OrthancImport.py
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 4437
diff changeset
132 print(' DICOM Patient ID: %s' % (
9bf2f9e0af47 support empty PatientID in OrthancImport.py
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 4437
diff changeset
133 tags['0010,0020'] if '0010,0020' in tags else '(empty)'))
9bf2f9e0af47 support empty PatientID in OrthancImport.py
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 4437
diff changeset
134 print(' DICOM Study Instance UID: %s' % (
9bf2f9e0af47 support empty PatientID in OrthancImport.py
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 4437
diff changeset
135 tags['0020,000d'] if '0020,000d' in tags else '(empty)'))
4337
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
136 print('')
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
137
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
138
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
139 def UploadFile(path):
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
140 with open(path, 'rb') as f:
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
141 dicom = f.read()
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
142 if args.verbose:
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
143 print('Uploading: %s (%dMB)' % (path, len(dicom) / (1024 * 1024)))
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
144
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
145 UploadBuffer(dicom)
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
146
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
147
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
148 def UploadBzip2(path):
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
149 with bz2.BZ2File(path, 'rb') as f:
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
150 dicom = f.read()
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
151 if args.verbose:
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
152 print('Uploading: %s (%dMB)' % (path, len(dicom) / (1024 * 1024)))
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
153
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
154 UploadBuffer(dicom)
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
155
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
156
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
157 def UploadGzip(path):
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
158 with gzip.open(path, 'rb') as f:
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
159 dicom = f.read()
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
160 if args.verbose:
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
161 print('Uploading: %s (%dMB)' % (path, len(dicom) / (1024 * 1024)))
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
162
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
163 UploadBuffer(dicom)
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
164
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
165
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
166 def UploadTar(path, decoder):
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
167 if args.verbose:
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
168 print('Uncompressing tar archive: %s' % path)
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
169 with tarfile.open(path, decoder) as tar:
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
170 for item in tar:
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
171 if item.isreg():
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
172 f = tar.extractfile(item)
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
173 dicom = f.read()
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
174 f.close()
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
175
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
176 if args.verbose:
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
177 print('Uploading: %s (%dMB)' % (item.name, len(dicom) / (1024 * 1024)))
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
178
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
179 UploadBuffer(dicom)
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
180
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
181
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
182 def UploadZip(path):
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
183 if args.verbose:
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
184 print('Uncompressing ZIP archive: %s' % path)
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
185 with zipfile.ZipFile(path, 'r') as zip:
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
186 for item in zip.infolist():
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
187 # WARNING - "item.is_dir()" would be better, but is not available in Python 2.7
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
188 if item.file_size > 0:
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
189 dicom = zip.read(item.filename)
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
190
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
191 if args.verbose:
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
192 print('Uploading: %s (%dMB)' % (item.filename, len(dicom) / (1024 * 1024)))
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
193
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
194 UploadBuffer(dicom)
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
195
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
196
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
197 def DecodeFile(path):
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
198 extension = os.path.splitext(path) [1]
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
199
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
200 if path.endswith('.tar.bz2'):
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
201 UploadTar(path, 'r:bz2')
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
202 elif path.endswith('.tar.gz'):
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
203 UploadTar(path, 'r:gz')
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
204 elif extension == '.zip':
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
205 UploadZip(path)
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
206 elif extension == '.tar':
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
207 UploadTar(path, 'r')
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
208 elif extension == '.bz2':
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
209 UploadBzip2(path)
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
210 elif extension == '.gz':
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
211 UploadGzip(path)
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
212 else:
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
213 UploadFile(path)
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
214
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
215
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
216 if args.clear:
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
217 print('Removing the content of Orthanc')
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
218
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
219 auth = HTTPBasicAuth(args.username, args.password)
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
220 r = requests.get('%s/studies' % args.url, auth = auth)
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
221 r.raise_for_status()
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
222
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
223 print(' %d studies are being removed...' % len(r.json()))
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
224
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
225 for study in r.json():
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
226 requests.delete('%s/studies/%s' % (args.url, study), auth = auth).raise_for_status()
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
227
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
228 print('Orthanc is now empty')
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
229 print('')
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
230
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
231
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
232 for path in args.files:
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
233 if os.path.isfile(path):
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
234 DecodeFile(path)
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
235 elif os.path.isdir(path):
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
236 for root, dirs, files in os.walk(path):
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
237 for name in files:
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
238 DecodeFile(os.path.join(root, name))
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
239 else:
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
240 raise Exception('Missing file or directory: %s' % path)
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
241
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
242
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
243 print('')
4748
4336642b8cff ignore JSON files in sample Python upload scripts
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 4450
diff changeset
244
4336642b8cff ignore JSON files in sample Python upload scripts
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 4450
diff changeset
245 if COUNT_ERROR == 0:
4336642b8cff ignore JSON files in sample Python upload scripts
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 4450
diff changeset
246 print('SUCCESS:')
4336642b8cff ignore JSON files in sample Python upload scripts
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 4450
diff changeset
247 else:
4336642b8cff ignore JSON files in sample Python upload scripts
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 4450
diff changeset
248 print('WARNING:')
4336642b8cff ignore JSON files in sample Python upload scripts
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 4450
diff changeset
249
4336642b8cff ignore JSON files in sample Python upload scripts
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 4450
diff changeset
250 print(' %d DICOM instances properly imported' % COUNT_DICOM)
4337
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
251 print(' %d DICOM studies properly imported' % len(IMPORTED_STUDIES))
4748
4336642b8cff ignore JSON files in sample Python upload scripts
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 4450
diff changeset
252 print(' %d JSON files ignored' % COUNT_JSON)
4337
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
253 print(' Error in %d files' % COUNT_ERROR)
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
254 print('')