Mercurial > hg > orthanc

annotate OrthancServer/Resources/Samples/ImportDicomFiles/OrthancImport.py @ 5640:f7adfb22e20e

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updated copyright, as Orthanc Team now replaces Osimis
author Sebastien Jodogne <s.jodogne@gmail.com>
date Thu, 30 May 2024 21:19:57 +0200
parents 48b8dae6dc77
children
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514fd39f87a8 improved handling of X-Content-Type-Options
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1 #!/usr/bin/env python3
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2
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3 # Orthanc - A Lightweight, RESTful DICOM Store
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4 # Copyright (C) 2012-2016 Sebastien Jodogne, Medical Physics
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5 # Department, University Hospital of Liege, Belgium
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6 # Copyright (C) 2017-2023 Osimis S.A., Belgium
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7 # Copyright (C) 2024-2024 Orthanc Team SRL, Belgium
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8 # Copyright (C) 2021-2024 Sebastien Jodogne, ICTEAM UCLouvain, Belgium
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9 #
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10 # This program is free software: you can redistribute it and/or
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11 # modify it under the terms of the GNU General Public License as
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12 # published by the Free Software Foundation, either version 3 of the
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13 # License, or (at your option) any later version.
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14 #
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15 # This program is distributed in the hope that it will be useful, but
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16 # WITHOUT ANY WARRANTY; without even the implied warranty of
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17 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
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18 # General Public License for more details.
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19 #
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20 # You should have received a copy of the GNU General Public License
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21 # along with this program. If not, see <http://www.gnu.org/licenses/>.
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22
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23
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24 import argparse
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25 import bz2
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26 import gzip
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27 import json
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28 import os
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29 import requests
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30 import sys
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31 import tarfile
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32 import zipfile
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33
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34 from requests.auth import HTTPBasicAuth
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36
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37
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38 parser = argparse.ArgumentParser(description = 'Command-line tool to import files or archives into Orthanc.')
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39 parser.add_argument('--url',
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40 default = 'http://localhost:8042',
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41 help = 'URL to the REST API of the Orthanc server')
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42 parser.add_argument('--username',
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43 default = 'orthanc',
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44 help = 'Username to the REST API')
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45 parser.add_argument('--password',
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46 default = 'orthanc',
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47 help = 'Password to the REST API')
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48 parser.add_argument('--force', help = 'Do not warn the user about deletion',
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49 action = 'store_true')
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50 parser.add_argument('--clear', help = 'Remove the content of the Orthanc database',
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51 action = 'store_true')
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52 parser.add_argument('--verbose', help = 'Be verbose',
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53 action = 'store_true')
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54 parser.add_argument('--ignore-errors', help = 'Do not stop if encountering non-DICOM files',
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55 action = 'store_true')
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56 parser.add_argument('files', metavar = 'N', nargs = '*',
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57 help = 'Files to import')
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58
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59
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60 args = parser.parse_args()
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61
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62 if args.clear and not args.force:
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63 print("""
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64 WARNING: This script will remove all the content of your
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65 Orthanc instance running on %s!
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66
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67 Are you sure ["yes" to go on]?""" % args.url)
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68
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69 if sys.stdin.readline().strip() != 'yes':
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70 print('Aborting...')
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71 exit(0)
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74
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75 IMPORTED_STUDIES = set()
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76 COUNT_ERROR = 0
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77 COUNT_DICOM = 0
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78 COUNT_JSON = 0
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80
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81 def IsJson(content):
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82 try:
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83 if (sys.version_info >= (3, 0)):
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84 json.loads(content.decode())
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85 return True
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86 else:
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87 json.loads(content)
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88 return True
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89 except:
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90 return False
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91
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92
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93 def UploadBuffer(dicom):
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94 global IMPORTED_STUDIES
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95 global COUNT_ERROR
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96 global COUNT_DICOM
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97 global COUNT_JSON
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98
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99 if IsJson(dicom):
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100 COUNT_JSON += 1
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101 return
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102
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103 auth = HTTPBasicAuth(args.username, args.password)
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104 r = requests.post('%s/instances' % args.url, auth = auth, data = dicom)
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105
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106 try:
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107 r.raise_for_status()
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108 except:
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109 COUNT_ERROR += 1
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110 if args.ignore_errors:
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111 if args.verbose:
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112 print(' not a valid DICOM file, ignoring it')
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113 return
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114 else:
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115 raise
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116
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117 info = r.json()
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118 COUNT_DICOM += 1
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119
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120 if (isinstance(info, dict) and
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121 not info['ParentStudy'] in IMPORTED_STUDIES):
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122 IMPORTED_STUDIES.add(info['ParentStudy'])
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123
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124 r2 = requests.get('%s/instances/%s/tags?short' % (args.url, info['ID']),
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125 auth = auth)
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126 r2.raise_for_status()
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127 tags = r2.json()
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128
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129 print('')
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130 print('New imported study:')
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131 print(' Orthanc ID of the patient: %s' % info['ParentPatient'])
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132 print(' Orthanc ID of the study: %s' % info['ParentStudy'])
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133 print(' DICOM Patient ID: %s' % (
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134 tags['0010,0020'] if '0010,0020' in tags else '(empty)'))
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135 print(' DICOM Study Instance UID: %s' % (
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136 tags['0020,000d'] if '0020,000d' in tags else '(empty)'))
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137 print('')
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138
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139
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140 def UploadFile(path):
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
141 with open(path, 'rb') as f:
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
142 dicom = f.read()
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
143 if args.verbose:
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
144 print('Uploading: %s (%dMB)' % (path, len(dicom) / (1024 * 1024)))
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
145
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
146 UploadBuffer(dicom)
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
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
149 def UploadBzip2(path):
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
150 with bz2.BZ2File(path, 'rb') as f:
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
151 dicom = f.read()
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
152 if args.verbose:
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
153 print('Uploading: %s (%dMB)' % (path, len(dicom) / (1024 * 1024)))
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
154
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
155 UploadBuffer(dicom)
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
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
158 def UploadGzip(path):
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
159 with gzip.open(path, 'rb') as f:
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
160 dicom = f.read()
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
161 if args.verbose:
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
162 print('Uploading: %s (%dMB)' % (path, len(dicom) / (1024 * 1024)))
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
163
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
164 UploadBuffer(dicom)
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
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
167 def UploadTar(path, decoder):
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
168 if args.verbose:
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
169 print('Uncompressing tar archive: %s' % path)
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
170 with tarfile.open(path, decoder) as tar:
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
171 for item in tar:
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
172 if item.isreg():
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
173 f = tar.extractfile(item)
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
174 dicom = f.read()
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
175 f.close()
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
176
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
177 if args.verbose:
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
178 print('Uploading: %s (%dMB)' % (item.name, len(dicom) / (1024 * 1024)))
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
179
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
180 UploadBuffer(dicom)
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
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
183 def UploadZip(path):
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
184 if args.verbose:
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
185 print('Uncompressing ZIP archive: %s' % path)
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
186 with zipfile.ZipFile(path, 'r') as zip:
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
187 for item in zip.infolist():
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
188 # 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
189 if item.file_size > 0:
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
190 dicom = zip.read(item.filename)
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
191
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
192 if args.verbose:
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
193 print('Uploading: %s (%dMB)' % (item.filename, len(dicom) / (1024 * 1024)))
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
194
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
195 UploadBuffer(dicom)
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
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
198 def DecodeFile(path):
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
199 extension = os.path.splitext(path) [1]
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
200
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
201 if path.endswith('.tar.bz2'):
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
202 UploadTar(path, 'r:bz2')
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
203 elif path.endswith('.tar.gz'):
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
204 UploadTar(path, 'r:gz')
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
205 elif extension == '.zip':
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
206 UploadZip(path)
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
207 elif extension == '.tar':
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
208 UploadTar(path, 'r')
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
209 elif extension == '.bz2':
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
210 UploadBzip2(path)
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
211 elif extension == '.gz':
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
212 UploadGzip(path)
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
213 else:
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
214 UploadFile(path)
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
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
217 if args.clear:
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
218 print('Removing the content of Orthanc')
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
219
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
220 auth = HTTPBasicAuth(args.username, args.password)
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
221 r = requests.get('%s/studies' % args.url, auth = auth)
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
222 r.raise_for_status()
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
223
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
224 print(' %d studies are being removed...' % len(r.json()))
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
225
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
226 for study in r.json():
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
227 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
228
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
229 print('Orthanc is now empty')
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
230 print('')
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
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
233 for path in args.files:
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
234 if os.path.isfile(path):
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
235 DecodeFile(path)
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
236 elif os.path.isdir(path):
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
237 for root, dirs, files in os.walk(path):
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
238 for name in files:
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
239 DecodeFile(os.path.join(root, name))
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
240 else:
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
241 raise Exception('Missing file or directory: %s' % path)
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
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
244 print('')
4748
4336642b8cff ignore JSON files in sample Python upload scripts
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 4450
diff changeset
245
4336642b8cff ignore JSON files in sample Python upload scripts
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 4450
diff changeset
246 if COUNT_ERROR == 0:
4336642b8cff ignore JSON files in sample Python upload scripts
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 4450
diff changeset
247 print('SUCCESS:')
4336642b8cff ignore JSON files in sample Python upload scripts
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 4450
diff changeset
248 else:
4336642b8cff ignore JSON files in sample Python upload scripts
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 4450
diff changeset
249 print('WARNING:')
4336642b8cff ignore JSON files in sample Python upload scripts
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 4450
diff changeset
250
4336642b8cff ignore JSON files in sample Python upload scripts
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 4450
diff changeset
251 print(' %d DICOM instances properly imported' % COUNT_DICOM)
4337
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
252 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
253 print(' %d JSON files ignored' % COUNT_JSON)
4337
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
254 print(' Error in %d files' % COUNT_ERROR)
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
255 print('')