Mercurial > hg > orthanc

annotate OrthancServer/Resources/Samples/ImportDicomFiles/OrthancImport.py @ 4748:4336642b8cff

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ignore JSON files in sample Python upload scripts
author Sebastien Jodogne <s.jodogne@gmail.com>
date Thu, 08 Jul 2021 14:42:20 +0200
parents 9bf2f9e0af47
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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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('')