Mercurial > hg > orthanc
annotate Resources/Samples/Python/AutoClassify.py @ 1687:4d80fc990dae
refactoring
author | Sebastien Jodogne <s.jodogne@gmail.com> |
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date | Wed, 07 Oct 2015 14:29:09 +0200 |
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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) 2012-2015 Sebastien Jodogne, Medical Physics |
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6 # Department, University Hospital of Liege, 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 time |
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24 import os |
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25 import os.path |
1184 | 26 import sys |
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27 import RestToolbox |
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28 |
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29 parser = argparse.ArgumentParser( |
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30 description = 'Automated classification of DICOM files from Orthanc.', |
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31 formatter_class = argparse.ArgumentDefaultsHelpFormatter) |
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32 |
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33 parser.add_argument('--host', default = 'localhost', |
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34 help = 'The host address that runs Orthanc') |
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35 parser.add_argument('--port', type = int, default = '8042', |
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36 help = 'The port number to which Orthanc is listening for the REST API') |
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37 parser.add_argument('--target', default = 'OrthancFiles', |
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38 help = 'The target directory where to store the DICOM files') |
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39 parser.add_argument('--all', action = 'store_true', |
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40 help = 'Replay the entire history on startup (disabled by default)') |
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41 parser.set_defaults(all = False) |
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42 parser.add_argument('--remove', action = 'store_true', |
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43 help = 'Remove DICOM files from Orthanc once classified (disabled by default)') |
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44 parser.set_defaults(remove = False) |
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45 |
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46 |
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47 def FixPath(p): |
1184 | 48 return p.encode('ascii', 'ignore').strip().decode() |
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49 |
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50 def GetTag(resource, tag): |
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51 if ('MainDicomTags' in resource and |
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52 tag in resource['MainDicomTags']): |
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53 return resource['MainDicomTags'][tag] |
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54 else: |
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55 return 'No' + tag |
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56 |
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57 def ClassifyInstance(instanceId): |
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58 # Extract the patient, study, series and instance information |
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59 instance = RestToolbox.DoGet('%s/instances/%s' % (URL, instanceId)) |
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60 series = RestToolbox.DoGet('%s/series/%s' % (URL, instance['ParentSeries'])) |
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61 study = RestToolbox.DoGet('%s/studies/%s' % (URL, series['ParentStudy'])) |
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62 patient = RestToolbox.DoGet('%s/patients/%s' % (URL, study['ParentPatient'])) |
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63 |
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64 # Construct a target path |
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65 a = '%s - %s' % (GetTag(patient, 'PatientID'), |
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66 GetTag(patient, 'PatientName')) |
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67 b = GetTag(study, 'StudyDescription') |
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68 c = '%s - %s' % (GetTag(series, 'Modality'), |
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69 GetTag(series, 'SeriesDescription')) |
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70 d = '%s.dcm' % GetTag(instance, 'SOPInstanceUID') |
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71 |
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72 p = os.path.join(args.target, FixPath(a), FixPath(b), FixPath(c)) |
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73 f = os.path.join(p, FixPath(d)) |
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75 # Copy the DICOM file to the target path |
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76 print('Writing new DICOM file: %s' % f) |
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77 |
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78 try: |
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79 os.makedirs(p) |
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80 except: |
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81 # Already existing directory, ignore the error |
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82 pass |
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83 |
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84 dcm = RestToolbox.DoGet('%s/instances/%s/file' % (URL, instanceId)) |
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85 with open(f, 'wb') as g: |
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86 g.write(dcm) |
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87 |
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88 |
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89 # Parse the arguments |
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90 args = parser.parse_args() |
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91 URL = 'http://%s:%d' % (args.host, args.port) |
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92 print('Connecting to Orthanc on address: %s' % URL) |
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93 |
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94 # Compute the starting point for the changes loop |
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95 if args.all: |
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96 current = 0 |
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97 else: |
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98 current = RestToolbox.DoGet(URL + '/changes?last')['Last'] |
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99 |
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100 # Polling loop using the 'changes' API of Orthanc, waiting for the |
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101 # incoming of new DICOM files |
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102 while True: |
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103 r = RestToolbox.DoGet(URL + '/changes', { |
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104 'since' : current, |
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105 'limit' : 4 # Retrieve at most 4 changes at once |
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106 }) |
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107 |
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108 for change in r['Changes']: |
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109 # We are only interested interested in the arrival of new instances |
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110 if change['ChangeType'] == 'NewInstance': |
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111 try: |
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112 ClassifyInstance(change['ID']) |
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113 except: |
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1182
diff
changeset
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114 print('Unable to write instance %s to the disk' % change['ID']) |
1182
d74ac5d0bcaf
New sample: Automated classification of DICOM files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
115 |
d74ac5d0bcaf
New sample: Automated classification of DICOM files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
116 # If requested, remove the instance once it has been copied |
d74ac5d0bcaf
New sample: Automated classification of DICOM files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
117 if args.remove: |
d74ac5d0bcaf
New sample: Automated classification of DICOM files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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118 RestToolbox.DoDelete('%s/instances/%s' % (URL, change['ID'])) |
d74ac5d0bcaf
New sample: Automated classification of DICOM files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
119 |
d74ac5d0bcaf
New sample: Automated classification of DICOM files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
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120 current = r['Last'] |
d74ac5d0bcaf
New sample: Automated classification of DICOM files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
|
121 |
d74ac5d0bcaf
New sample: Automated classification of DICOM files
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff
changeset
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122 if r['Done']: |
1183
6ef2c81581cd
more fault-tolerant sample
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1182
diff
changeset
|
123 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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124 time.sleep(1) |