Mercurial > hg > orthanc
annotate OrthancServer/Resources/Samples/ImportDicomFiles/OrthancImport.py @ 4437:d9473bd5ed43
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author | Sebastien Jodogne <s.jodogne@gmail.com> |
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date | Wed, 06 Jan 2021 17:27:28 +0100 |
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OrthancImport.py sample
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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 os |
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26 import requests |
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27 import sys |
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28 import tarfile |
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29 import zipfile |
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30 |
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31 from requests.auth import HTTPBasicAuth |
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32 |
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33 |
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34 |
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35 parser = argparse.ArgumentParser(description = 'Command-line tool to import files or archives into Orthanc.') |
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36 parser.add_argument('--url', |
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37 default = 'http://localhost:8042', |
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38 help = 'URL to the REST API of the Orthanc server') |
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39 parser.add_argument('--username', |
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40 default = 'orthanc', |
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41 help = 'Username to the REST API') |
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42 parser.add_argument('--password', |
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43 default = 'orthanc', |
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44 help = 'Password to the REST API') |
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45 parser.add_argument('--force', help = 'Do not warn the user about deletion', |
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46 action = 'store_true') |
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47 parser.add_argument('--clear', help = 'Remove the content of the Orthanc database', |
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48 action = 'store_true') |
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49 parser.add_argument('--verbose', help = 'Be verbose', |
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50 action = 'store_true') |
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51 parser.add_argument('--ignore-errors', help = 'Do not stop if encountering non-DICOM files', |
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52 action = 'store_true') |
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53 parser.add_argument('files', metavar = 'N', nargs = '*', |
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54 help = 'Files to import') |
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55 |
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56 |
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57 args = parser.parse_args() |
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58 |
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59 if args.clear and not args.force: |
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60 print(""" |
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61 WARNING: This script will remove all the content of your |
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62 Orthanc instance running on %s! |
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63 |
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64 Are you sure ["yes" to go on]?""" % args.server) |
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65 |
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66 if sys.stdin.readline().strip() != 'yes': |
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67 print('Aborting...') |
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68 exit(0) |
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69 |
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70 |
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71 |
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72 IMPORTED_STUDIES = set() |
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73 COUNT_ERROR = 0 |
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74 COUNT_SUCCESS = 0 |
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75 |
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76 def UploadBuffer(dicom): |
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77 global IMPORTED_STUDIES |
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78 global COUNT_ERROR |
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79 global COUNT_SUCCESS |
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80 |
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81 auth = HTTPBasicAuth(args.username, args.password) |
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82 r = requests.post('%s/instances' % args.url, auth = auth, data = dicom) |
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83 |
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84 try: |
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85 r.raise_for_status() |
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86 except: |
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87 COUNT_ERROR += 1 |
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88 if args.ignore_errors: |
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89 if args.verbose: |
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90 print(' not a valid DICOM file, ignoring it') |
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91 return |
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92 else: |
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93 raise |
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94 |
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95 info = r.json() |
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96 COUNT_SUCCESS += 1 |
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97 |
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98 if not info['ParentStudy'] in IMPORTED_STUDIES: |
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99 IMPORTED_STUDIES.add(info['ParentStudy']) |
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100 |
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101 r2 = requests.get('%s/instances/%s/tags?short' % (args.url, info['ID']), |
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102 auth = auth) |
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103 r2.raise_for_status() |
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104 tags = r2.json() |
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105 |
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106 print('') |
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107 print('New imported study:') |
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108 print(' Orthanc ID of the patient: %s' % info['ParentPatient']) |
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109 print(' Orthanc ID of the study: %s' % info['ParentStudy']) |
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110 print(' DICOM Patient ID: %s' % tags['0010,0020']) |
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111 print(' DICOM Study Instance UID: %s' % tags['0020,000d']) |
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112 print('') |
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113 |
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114 |
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115 def UploadFile(path): |
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116 with open(path, 'rb') as f: |
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117 dicom = f.read() |
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118 if args.verbose: |
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119 print('Uploading: %s (%dMB)' % (path, len(dicom) / (1024 * 1024))) |
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120 |
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121 UploadBuffer(dicom) |
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122 |
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123 |
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124 def UploadBzip2(path): |
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125 with bz2.BZ2File(path, 'rb') as f: |
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126 dicom = f.read() |
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127 if args.verbose: |
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128 print('Uploading: %s (%dMB)' % (path, len(dicom) / (1024 * 1024))) |
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129 |
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130 UploadBuffer(dicom) |
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131 |
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132 |
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133 def UploadGzip(path): |
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134 with gzip.open(path, 'rb') as f: |
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135 dicom = f.read() |
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136 if args.verbose: |
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137 print('Uploading: %s (%dMB)' % (path, len(dicom) / (1024 * 1024))) |
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138 |
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139 UploadBuffer(dicom) |
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140 |
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141 |
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142 def UploadTar(path, decoder): |
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143 if args.verbose: |
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144 print('Uncompressing tar archive: %s' % path) |
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145 with tarfile.open(path, decoder) as tar: |
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146 for item in tar: |
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147 if item.isreg(): |
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148 f = tar.extractfile(item) |
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149 dicom = f.read() |
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150 f.close() |
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151 |
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152 if args.verbose: |
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153 print('Uploading: %s (%dMB)' % (item.name, len(dicom) / (1024 * 1024))) |
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154 |
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155 UploadBuffer(dicom) |
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156 |
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157 |
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158 def UploadZip(path): |
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159 if args.verbose: |
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160 print('Uncompressing ZIP archive: %s' % path) |
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161 with zipfile.ZipFile(path, 'r') as zip: |
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162 for item in zip.infolist(): |
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163 # WARNING - "item.is_dir()" would be better, but is not available in Python 2.7 |
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164 if item.file_size > 0: |
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165 dicom = zip.read(item.filename) |
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166 |
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167 if args.verbose: |
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168 print('Uploading: %s (%dMB)' % (item.filename, len(dicom) / (1024 * 1024))) |
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169 |
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170 UploadBuffer(dicom) |
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171 |
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172 |
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173 def DecodeFile(path): |
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174 extension = os.path.splitext(path) [1] |
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175 |
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176 if path.endswith('.tar.bz2'): |
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177 UploadTar(path, 'r:bz2') |
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178 elif path.endswith('.tar.gz'): |
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179 UploadTar(path, 'r:gz') |
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180 elif extension == '.zip': |
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181 UploadZip(path) |
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182 elif extension == '.tar': |
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183 UploadTar(path, 'r') |
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184 elif extension == '.bz2': |
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185 UploadBzip2(path) |
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186 elif extension == '.gz': |
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187 UploadGzip(path) |
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188 else: |
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189 UploadFile(path) |
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190 |
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191 |
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192 if args.clear: |
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193 print('Removing the content of Orthanc') |
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194 |
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195 auth = HTTPBasicAuth(args.username, args.password) |
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196 r = requests.get('%s/studies' % args.url, auth = auth) |
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197 r.raise_for_status() |
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198 |
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199 print(' %d studies are being removed...' % len(r.json())) |
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200 |
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201 for study in r.json(): |
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202 requests.delete('%s/studies/%s' % (args.url, study), auth = auth).raise_for_status() |
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203 |
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204 print('Orthanc is now empty') |
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205 print('') |
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206 |
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207 |
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208 for path in args.files: |
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209 if os.path.isfile(path): |
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210 DecodeFile(path) |
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211 elif os.path.isdir(path): |
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212 for root, dirs, files in os.walk(path): |
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213 for name in files: |
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214 DecodeFile(os.path.join(root, name)) |
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215 else: |
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216 raise Exception('Missing file or directory: %s' % path) |
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217 |
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218 |
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219 print('') |
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220 print('Status:') |
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221 print(' %d DICOM instances properly imported' % COUNT_SUCCESS) |
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222 print(' %d DICOM studies properly imported' % len(IMPORTED_STUDIES)) |
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223 print(' Error in %d files' % COUNT_ERROR) |
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224 print('') |