Mercurial > hg > orthanc

annotate OrthancServer/Resources/Samples/ImportDicomFiles/OrthancImport.py @ 4973:17c91e054636

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minor improvements
author Sebastien Jodogne <s.jodogne@gmail.com>
date Thu, 07 Apr 2022 12:04:48 +0200
parents cde17b68d73e
children 0ea402b4d901
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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) 2017-2022 Osimis S.A., Belgium
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7 # Copyright (C) 2021-2022 Sebastien Jodogne, ICTEAM UCLouvain, Belgium
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8 #
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9 # This program is free software: you can redistribute it and/or
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10 # modify it under the terms of the GNU General Public License as
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11 # published by the Free Software Foundation, either version 3 of the
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12 # License, or (at your option) any later version.
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13 #
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14 # This program is distributed in the hope that it will be useful, but
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15 # WITHOUT ANY WARRANTY; without even the implied warranty of
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16 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
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17 # General Public License for more details.
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18 #
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19 # You should have received a copy of the GNU General Public License
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20 # along with this program. If not, see <http://www.gnu.org/licenses/>.
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21
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22
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23 import argparse
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24 import bz2
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25 import gzip
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26 import json
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27 import os
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28 import requests
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29 import sys
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30 import tarfile
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31 import zipfile
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32
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33 from requests.auth import HTTPBasicAuth
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34
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35
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36
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37 parser = argparse.ArgumentParser(description = 'Command-line tool to import files or archives into Orthanc.')
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38 parser.add_argument('--url',
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39 default = 'http://localhost:8042',
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40 help = 'URL to the REST API of the Orthanc server')
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41 parser.add_argument('--username',
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42 default = 'orthanc',
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43 help = 'Username to the REST API')
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44 parser.add_argument('--password',
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45 default = 'orthanc',
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46 help = 'Password to the REST API')
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47 parser.add_argument('--force', help = 'Do not warn the user about deletion',
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48 action = 'store_true')
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49 parser.add_argument('--clear', help = 'Remove the content of the Orthanc database',
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50 action = 'store_true')
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51 parser.add_argument('--verbose', help = 'Be verbose',
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52 action = 'store_true')
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53 parser.add_argument('--ignore-errors', help = 'Do not stop if encountering non-DICOM files',
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54 action = 'store_true')
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55 parser.add_argument('files', metavar = 'N', nargs = '*',
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56 help = 'Files to import')
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57
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58
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59 args = parser.parse_args()
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60
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61 if args.clear and not args.force:
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62 print("""
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63 WARNING: This script will remove all the content of your
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64 Orthanc instance running on %s!
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65
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66 Are you sure ["yes" to go on]?""" % args.url)
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67
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68 if sys.stdin.readline().strip() != 'yes':
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69 print('Aborting...')
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70 exit(0)
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73
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74 IMPORTED_STUDIES = set()
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75 COUNT_ERROR = 0
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76 COUNT_DICOM = 0
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77 COUNT_JSON = 0
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79
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80 def IsJson(content):
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81 try:
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82 if (sys.version_info >= (3, 0)):
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83 json.loads(content.decode())
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84 return True
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85 else:
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86 json.loads(content)
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87 return True
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88 except:
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89 return False
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90
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91
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92 def UploadBuffer(dicom):
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93 global IMPORTED_STUDIES
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94 global COUNT_ERROR
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95 global COUNT_DICOM
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96 global COUNT_JSON
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97
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98 if IsJson(dicom):
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99 COUNT_JSON += 1
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100 return
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101
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102 auth = HTTPBasicAuth(args.username, args.password)
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103 r = requests.post('%s/instances' % args.url, auth = auth, data = dicom)
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104
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105 try:
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106 r.raise_for_status()
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107 except:
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108 COUNT_ERROR += 1
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109 if args.ignore_errors:
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110 if args.verbose:
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111 print(' not a valid DICOM file, ignoring it')
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112 return
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113 else:
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114 raise
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115
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116 info = r.json()
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117 COUNT_DICOM += 1
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118
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119 if (isinstance(info, dict) and
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120 not info['ParentStudy'] in IMPORTED_STUDIES):
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121 IMPORTED_STUDIES.add(info['ParentStudy'])
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122
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123 r2 = requests.get('%s/instances/%s/tags?short' % (args.url, info['ID']),
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124 auth = auth)
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125 r2.raise_for_status()
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126 tags = r2.json()
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127
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128 print('')
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129 print('New imported study:')
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130 print(' Orthanc ID of the patient: %s' % info['ParentPatient'])
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131 print(' Orthanc ID of the study: %s' % info['ParentStudy'])
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132 print(' DICOM Patient ID: %s' % (
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133 tags['0010,0020'] if '0010,0020' in tags else '(empty)'))
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134 print(' DICOM Study Instance UID: %s' % (
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135 tags['0020,000d'] if '0020,000d' in tags else '(empty)'))
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136 print('')
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137
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138
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139 def UploadFile(path):
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140 with open(path, 'rb') as f:
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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('')