Mercurial > hg > orthanc
annotate Resources/Samples/Python/AutoClassify.py @ 3786:3801435e34a1 SylvainRouquette/fix-issue169-95b752c
integration Orthanc-1.6.0->SylvainRouquette
author | Sebastien Jodogne <s.jodogne@gmail.com> |
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date | Thu, 19 Mar 2020 11:48:30 +0100 |
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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 |
1900 | 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) 2017-2020 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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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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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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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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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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126 |
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127 if r['Done']: |
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128 print('Everything has been processed: Waiting...') |
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129 time.sleep(1) |