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annotate Resources/Samples/Python/AutoClassify.py @ 3493:c465c6ee2bfb

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author Benjamin Golinvaux <bgo@osimis.io>
date Mon, 19 Aug 2019 10:18:04 +0200
parents d00db444a3a3
children 94f4a18a79cc
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1 #!/usr/bin/python
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2 # -*- coding: utf-8 -*-
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3
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4 # Orthanc - A Lightweight, RESTful DICOM Store
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5 # Copyright (C) 2012-2016 Sebastien Jodogne, Medical Physics
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6 # Department, University Hospital of Liege, Belgium
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7 # Copyright (C) 2017-2019 Osimis S.A., 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 time
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25 import os
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26 import os.path
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27 import sys
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28 import RestToolbox
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29
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30 parser = argparse.ArgumentParser(
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31 description = 'Automated classification of DICOM files from Orthanc.',
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32 formatter_class = argparse.ArgumentDefaultsHelpFormatter)
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33
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34 parser.add_argument('--host', default = '127.0.0.1',
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35 help = 'The host address that runs Orthanc')
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36 parser.add_argument('--port', type = int, default = '8042',
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37 help = 'The port number to which Orthanc is listening for the REST API')
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38 parser.add_argument('--target', default = 'OrthancFiles',
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39 help = 'The target directory where to store the DICOM files')
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40 parser.add_argument('--all', action = 'store_true',
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41 help = 'Replay the entire history on startup (disabled by default)')
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42 parser.set_defaults(all = False)
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43 parser.add_argument('--remove', action = 'store_true',
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44 help = 'Remove DICOM files from Orthanc once classified (disabled by default)')
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45 parser.set_defaults(remove = False)
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46
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47
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48 def FixPath(p):
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49 return p.encode('ascii', errors = 'replace').translate(None, r"'\/:*?\"<>|!=").strip()
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50
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51 def GetTag(resource, tag):
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52 if ('MainDicomTags' in resource and
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53 tag in resource['MainDicomTags']):
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54 return resource['MainDicomTags'][tag]
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55 else:
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56 return 'No' + tag
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57
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58 def ClassifyInstance(instanceId):
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59 # Extract the patient, study, series and instance information
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60 instance = RestToolbox.DoGet('%s/instances/%s' % (URL, instanceId))
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61 series = RestToolbox.DoGet('%s/series/%s' % (URL, instance['ParentSeries']))
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62 study = RestToolbox.DoGet('%s/studies/%s' % (URL, series['ParentStudy']))
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63 patient = RestToolbox.DoGet('%s/patients/%s' % (URL, study['ParentPatient']))
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64
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65 # Construct a target path
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66 a = '%s - %s' % (GetTag(patient, 'PatientID'),
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67 GetTag(patient, 'PatientName'))
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68 b = GetTag(study, 'StudyDescription')
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69 c = '%s - %s' % (GetTag(series, 'Modality'),
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70 GetTag(series, 'SeriesDescription'))
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71 d = '%s.dcm' % GetTag(instance, 'SOPInstanceUID')
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72
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73 p = os.path.join(args.target, FixPath(a), FixPath(b), FixPath(c))
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74 f = os.path.join(p, FixPath(d))
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75
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76 # Copy the DICOM file to the target path
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77 print('Writing new DICOM file: %s' % f)
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78
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79 try:
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80 os.makedirs(p)
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81 except:
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82 # Already existing directory, ignore the error
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83 pass
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84
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85 dcm = RestToolbox.DoGet('%s/instances/%s/file' % (URL, instanceId))
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86 with open(f, 'wb') as g:
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87 g.write(dcm)
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88
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89
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90 # Parse the arguments
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91 args = parser.parse_args()
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92 URL = 'http://%s:%d' % (args.host, args.port)
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93 print('Connecting to Orthanc on address: %s' % URL)
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94
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95 # Compute the starting point for the changes loop
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96 if args.all:
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97 current = 0
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98 else:
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99 current = RestToolbox.DoGet(URL + '/changes?last')['Last']
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100
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101 # Polling loop using the 'changes' API of Orthanc, waiting for the
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102 # incoming of new DICOM files
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103 while True:
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104 r = RestToolbox.DoGet(URL + '/changes', {
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105 'since' : current,
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106 'limit' : 4 # Retrieve at most 4 changes at once
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107 })
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108
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109 for change in r['Changes']:
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110 # We are only interested in the arrival of new instances
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111 if change['ChangeType'] == 'NewInstance':
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112 try:
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113 ClassifyInstance(change['ID'])
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114
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115 # If requested, remove the instance once it has been
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116 # properly handled by "ClassifyInstance()". Thanks to
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117 # the "try/except" block, the instance is not removed
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118 # if the "ClassifyInstance()" function fails.
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119 if args.remove:
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120 RestToolbox.DoDelete('%s/instances/%s' % (URL, change['ID']))
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121
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122 except:
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123 print('Unable to write instance %s to the disk' % change['ID'])
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124
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125 current = r['Last']
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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126
d74ac5d0bcaf New sample: Automated classification of DICOM files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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127 if r['Done']:
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6ef2c81581cd more fault-tolerant sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1182
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128 print('Everything has been processed: Waiting...')
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d74ac5d0bcaf New sample: Automated classification of DICOM files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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129 time.sleep(1)