Mercurial > hg > orthanc

annotate OrthancServer/Resources/GenerateAnonymizationProfile.py @ 4675:7e4d1f2b3a8f

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GenerateAnonymizationProfile.py can read from URL
author Sebastien Jodogne <s.jodogne@gmail.com>
date Thu, 03 Jun 2021 19:41:11 +0200
parents d9473bd5ed43
children caf963ee3de9
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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 # In addition, as a special exception, the copyright holders of this
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14 # program give permission to link the code of its release with the
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15 # OpenSSL project's "OpenSSL" library (or with modified versions of it
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16 # that use the same license as the "OpenSSL" library), and distribute
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17 # the linked executables. You must obey the GNU General Public License
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18 # in all respects for all of the code used other than "OpenSSL". If you
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19 # modify file(s) with this exception, you may extend this exception to
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20 # your version of the file(s), but you are not obligated to do so. If
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21 # you do not wish to do so, delete this exception statement from your
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22 # version. If you delete this exception statement from all source files
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23 # in the program, then also delete it here.
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24 #
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25 # This program is distributed in the hope that it will be useful, but
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26 # WITHOUT ANY WARRANTY; without even the implied warranty of
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27 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
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28 # General Public License for more details.
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29 #
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30 # You should have received a copy of the GNU General Public License
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31 # along with this program. If not, see <http://www.gnu.org/licenses/>.
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33
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34 import re
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35 import requests
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36 import sys
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37 import xml.etree.ElementTree as ET
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38
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39 # Usage:
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40 # ./GenerateAnonymizationProfile.py https://raw.githubusercontent.com/jodogne/dicom-specification/master/2021b/part15.xml
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41
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42 if len(sys.argv) != 2:
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43 raise Exception('Please provide the path or the URL to the part15.xml file from the DICOM standard')
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44
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45 source = sys.argv[1]
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46
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47 if (source.startswith('http://') or
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48 source.startswith('https://')):
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49 part15 = requests.get(source).content
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50 else:
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51 with open(source, 'r') as f:
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52 part15 = f.read()
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53
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54 root = ET.fromstring(part15)
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55
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56 br = '{http://docbook.org/ns/docbook}' # Shorthand variable
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57
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58
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59 LINES = []
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60
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61 def FormatLine(command, name):
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62 indentation = 65
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63
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64 if len(command) > indentation:
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65 raise Exception('Too long command')
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66
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67 line = ' ' + command + (' ' * (indentation - len(command))) + '// ' + name
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68 LINES.append(line)
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69
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70 def FormatUnknown(rawTag, name, profile):
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71 FormatLine('// TODO: %s with rule %s' % (rawTag, profile), name)
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73
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74 RAW_TAG_RE = re.compile(r'^\(\s*([0-9A-F]{4})\s*,\s*([0-9A-F]{4})\s*\)$')
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77 for table in root.iter('%stable' % br):
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78 if table.attrib['label'] == 'E.1-1':
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79 for row in table.find('%stbody' % br).iter('%str' % br):
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80 rawTag = row.find('%std[2]/%spara' % (br, br)).text
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81 name = row.find('%std[1]/%spara' % (br, br)).text
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82 profile = row.find('%std[5]/%spara' % (br, br)).text
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83
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84 if len(name.strip()) == 0:
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85 continue
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86
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87 match = RAW_TAG_RE.match(rawTag)
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88 if match == None:
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89 FormatUnknown(rawTag, name, profile)
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90 else:
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91 tag = '0x%s, 0x%s' % (match.group(1).lower(), match.group(2).lower())
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92
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93 if name in [
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94 'SOP Instance UID',
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95 'Series Instance UID',
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96 'Study Instance UID',
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97 ]:
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98 FormatLine('// Tag (%s) is set in Apply() /* %s */' % (tag, profile), name)
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99 elif name in [
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100 'Referenced Image Sequence',
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101 'Source Image Sequence',
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102 'Referenced SOP Instance UID',
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103 'Frame of Reference UID',
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104 'Referenced Frame of Reference UID',
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105 'Related Frame of Reference UID',
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106 ]:
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107 FormatLine('// Tag (%s) => RelationshipsVisitor /* %s */' % (tag, profile), name)
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108 elif name in [
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109 'Patient\'s Name',
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110 'Patient ID',
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111 ]:
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112 FormatLine('// Tag (%s) is set below (*) /* %s */' % (tag, profile), name)
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113 elif profile == 'X':
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114 FormatLine('removals_.insert(DicomTag(%s));' % tag, name)
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115 elif profile.startswith('X/'):
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116 FormatLine('removals_.insert(DicomTag(%s)); /* %s */' % (tag, profile), name)
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117 elif profile == 'Z':
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118 FormatLine('clearings_.insert(DicomTag(%s));' % tag, name)
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119 elif profile == 'D' or profile.startswith('Z/'):
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120 FormatLine('clearings_.insert(DicomTag(%s)); /* %s */' % (tag, profile), name)
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121 elif profile == 'U':
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122 FormatLine('removals_.insert(DicomTag(%s)); /* TODO UID */' % (tag), name)
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123 else:
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124 FormatUnknown(rawTag, name, profile)
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125
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126 for line in sorted(LINES):
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127 print(line.encode('ascii', 'ignore').decode('ascii'))
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128
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129
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Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2312
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130 # D - replace with a non-zero length value that may be a dummy value and consistent with the VR
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Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2312
diff changeset
131 # Z - replace with a zero length value, or a non-zero length value that may be a dummy value and consistent with the VR
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Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2312
diff changeset
132 # X - remove
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Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2312
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133 # K - keep (unchanged for non-sequence attributes, cleaned for sequences)
d19e716b79fa switch to anonymization according to DICOM 2017c
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2312
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134 # C - clean, that is replace with values of similar meaning known not to contain identifying information and consistent with the VR
d19e716b79fa switch to anonymization according to DICOM 2017c
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2312
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135 # U - replace with a non-zero length UID that is internally consistent within a set of Instances
d19e716b79fa switch to anonymization according to DICOM 2017c
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2312
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136 # Z/D - Z unless D is required to maintain IOD conformance (Type 2 versus Type 1)
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Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2312
diff changeset
137 # X/Z - X unless Z is required to maintain IOD conformance (Type 3 versus Type 2)
d19e716b79fa switch to anonymization according to DICOM 2017c
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2312
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138 # X/D - X unless D is required to maintain IOD conformance (Type 3 versus Type 1)
d19e716b79fa switch to anonymization according to DICOM 2017c
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2312
diff changeset
139 # X/Z/D - X unless Z or D is required to maintain IOD conformance (Type 3 versus Type 2 versus Type 1)
d19e716b79fa switch to anonymization according to DICOM 2017c
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2312
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140 # X/Z/U* - X unless Z or replacement of contained instance UIDs (U) is required to maintain IOD conformance (Type 3 versus Type 2 versus Type 1 sequences containing UID references)