Mercurial > hg > orthanc

annotate OrthancServer/Resources/Samples/ImportDicomFiles/OrthancImport.py @ 4789:51ec061516c9

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Fix handling of option "DeidentifyLogs", notably for tags (0010,0010) and (0010,0020)
author Sebastien Jodogne <s.jodogne@gmail.com>
date Thu, 09 Sep 2021 13:02:33 +0200
parents 4336642b8cff
children 7053502fbf97
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1 #!/usr/bin/env python
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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) 2017-2021 Osimis S.A., Belgium
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7 #
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8 # This program is free software: you can redistribute it and/or
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9 # modify it under the terms of the GNU General Public License as
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10 # published by the Free Software Foundation, either version 3 of the
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11 # License, or (at your option) any later version.
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12 #
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13 # This program is distributed in the hope that it will be useful, but
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14 # WITHOUT ANY WARRANTY; without even the implied warranty of
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15 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
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16 # General Public License for more details.
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17 #
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18 # You should have received a copy of the GNU General Public License
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19 # along with this program. If not, see <http://www.gnu.org/licenses/>.
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20
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21
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22 import argparse
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23 import bz2
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24 import gzip
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25 import json
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26 import os
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27 import requests
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28 import sys
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29 import tarfile
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30 import zipfile
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31
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32 from requests.auth import HTTPBasicAuth
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33
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34
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35
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36 parser = argparse.ArgumentParser(description = 'Command-line tool to import files or archives into Orthanc.')
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37 parser.add_argument('--url',
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38 default = 'http://localhost:8042',
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39 help = 'URL to the REST API of the Orthanc server')
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40 parser.add_argument('--username',
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41 default = 'orthanc',
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42 help = 'Username to the REST API')
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43 parser.add_argument('--password',
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44 default = 'orthanc',
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45 help = 'Password to the REST API')
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46 parser.add_argument('--force', help = 'Do not warn the user about deletion',
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47 action = 'store_true')
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48 parser.add_argument('--clear', help = 'Remove the content of the Orthanc database',
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49 action = 'store_true')
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50 parser.add_argument('--verbose', help = 'Be verbose',
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51 action = 'store_true')
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52 parser.add_argument('--ignore-errors', help = 'Do not stop if encountering non-DICOM files',
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53 action = 'store_true')
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54 parser.add_argument('files', metavar = 'N', nargs = '*',
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55 help = 'Files to import')
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56
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57
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58 args = parser.parse_args()
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59
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60 if args.clear and not args.force:
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61 print("""
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62 WARNING: This script will remove all the content of your
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63 Orthanc instance running on %s!
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64
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65 Are you sure ["yes" to go on]?""" % args.server)
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66
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67 if sys.stdin.readline().strip() != 'yes':
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68 print('Aborting...')
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69 exit(0)
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72
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73 IMPORTED_STUDIES = set()
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74 COUNT_ERROR = 0
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75 COUNT_DICOM = 0
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76 COUNT_JSON = 0
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77
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78
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79 def IsJson(content):
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80 try:
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81 if (sys.version_info >= (3, 0)):
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82 json.loads(content.decode())
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83 return True
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84 else:
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85 json.loads(content)
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86 return True
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87 except:
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88 return False
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89
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90
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91 def UploadBuffer(dicom):
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92 global IMPORTED_STUDIES
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93 global COUNT_ERROR
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94 global COUNT_DICOM
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95 global COUNT_JSON
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96
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97 if IsJson(dicom):
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98 COUNT_JSON += 1
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99 return
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100
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101 auth = HTTPBasicAuth(args.username, args.password)
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102 r = requests.post('%s/instances' % args.url, auth = auth, data = dicom)
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103
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104 try:
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105 r.raise_for_status()
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106 except:
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107 COUNT_ERROR += 1
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108 if args.ignore_errors:
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109 if args.verbose:
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110 print(' not a valid DICOM file, ignoring it')
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111 return
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112 else:
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113 raise
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114
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115 info = r.json()
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116 COUNT_DICOM += 1
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117
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118 if not info['ParentStudy'] in IMPORTED_STUDIES:
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119 IMPORTED_STUDIES.add(info['ParentStudy'])
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120
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121 r2 = requests.get('%s/instances/%s/tags?short' % (args.url, info['ID']),
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122 auth = auth)
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123 r2.raise_for_status()
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124 tags = r2.json()
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125
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126 print('')
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127 print('New imported study:')
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128 print(' Orthanc ID of the patient: %s' % info['ParentPatient'])
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129 print(' Orthanc ID of the study: %s' % info['ParentStudy'])
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130 print(' DICOM Patient ID: %s' % (
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131 tags['0010,0020'] if '0010,0020' in tags else '(empty)'))
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132 print(' DICOM Study Instance UID: %s' % (
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133 tags['0020,000d'] if '0020,000d' in tags else '(empty)'))
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134 print('')
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135
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136
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137 def UploadFile(path):
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138 with open(path, 'rb') as f:
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139 dicom = f.read()
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140 if args.verbose:
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141 print('Uploading: %s (%dMB)' % (path, len(dicom) / (1024 * 1024)))
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
142
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
143 UploadBuffer(dicom)
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
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
146 def UploadBzip2(path):
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
147 with bz2.BZ2File(path, 'rb') as f:
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
148 dicom = f.read()
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
149 if args.verbose:
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
150 print('Uploading: %s (%dMB)' % (path, len(dicom) / (1024 * 1024)))
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
151
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
152 UploadBuffer(dicom)
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
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
155 def UploadGzip(path):
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
156 with gzip.open(path, 'rb') as f:
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
157 dicom = f.read()
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
158 if args.verbose:
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
159 print('Uploading: %s (%dMB)' % (path, len(dicom) / (1024 * 1024)))
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
160
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
161 UploadBuffer(dicom)
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
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
164 def UploadTar(path, decoder):
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
165 if args.verbose:
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
166 print('Uncompressing tar archive: %s' % path)
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
167 with tarfile.open(path, decoder) as tar:
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
168 for item in tar:
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
169 if item.isreg():
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
170 f = tar.extractfile(item)
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
171 dicom = f.read()
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
172 f.close()
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
173
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
174 if args.verbose:
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
175 print('Uploading: %s (%dMB)' % (item.name, len(dicom) / (1024 * 1024)))
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 UploadBuffer(dicom)
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
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
180 def UploadZip(path):
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
181 if args.verbose:
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
182 print('Uncompressing ZIP archive: %s' % path)
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
183 with zipfile.ZipFile(path, 'r') as zip:
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
184 for item in zip.infolist():
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
185 # 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
186 if item.file_size > 0:
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
187 dicom = zip.read(item.filename)
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
188
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
189 if args.verbose:
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
190 print('Uploading: %s (%dMB)' % (item.filename, len(dicom) / (1024 * 1024)))
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 UploadBuffer(dicom)
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
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
195 def DecodeFile(path):
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
196 extension = os.path.splitext(path) [1]
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 if path.endswith('.tar.bz2'):
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
199 UploadTar(path, 'r:bz2')
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
200 elif path.endswith('.tar.gz'):
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
201 UploadTar(path, 'r:gz')
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
202 elif extension == '.zip':
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
203 UploadZip(path)
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
204 elif extension == '.tar':
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
205 UploadTar(path, 'r')
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
206 elif extension == '.bz2':
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
207 UploadBzip2(path)
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
208 elif extension == '.gz':
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
209 UploadGzip(path)
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
210 else:
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
211 UploadFile(path)
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
212
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
213
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
214 if args.clear:
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
215 print('Removing the content of Orthanc')
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 auth = HTTPBasicAuth(args.username, args.password)
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
218 r = requests.get('%s/studies' % args.url, auth = auth)
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
219 r.raise_for_status()
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
220
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
221 print(' %d studies are being removed...' % len(r.json()))
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 for study in r.json():
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
224 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
225
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
226 print('Orthanc is now empty')
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
227 print('')
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
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
230 for path in args.files:
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
231 if os.path.isfile(path):
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
232 DecodeFile(path)
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
233 elif os.path.isdir(path):
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
234 for root, dirs, files in os.walk(path):
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
235 for name in files:
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
236 DecodeFile(os.path.join(root, name))
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
237 else:
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
238 raise Exception('Missing file or directory: %s' % path)
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
239
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
240
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
241 print('')
4748
4336642b8cff ignore JSON files in sample Python upload scripts
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 4450
diff changeset
242
4336642b8cff ignore JSON files in sample Python upload scripts
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 4450
diff changeset
243 if COUNT_ERROR == 0:
4336642b8cff ignore JSON files in sample Python upload scripts
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 4450
diff changeset
244 print('SUCCESS:')
4336642b8cff ignore JSON files in sample Python upload scripts
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 4450
diff changeset
245 else:
4336642b8cff ignore JSON files in sample Python upload scripts
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 4450
diff changeset
246 print('WARNING:')
4336642b8cff ignore JSON files in sample Python upload scripts
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 4450
diff changeset
247
4336642b8cff ignore JSON files in sample Python upload scripts
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 4450
diff changeset
248 print(' %d DICOM instances properly imported' % COUNT_DICOM)
4337
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
249 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
250 print(' %d JSON files ignored' % COUNT_JSON)
4337
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
251 print(' Error in %d files' % COUNT_ERROR)
7707fa761b71 OrthancImport.py sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
252 print('')