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annotate Resources/Samples/Python/AutoClassify.py @ 1182:d74ac5d0bcaf

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New sample: Automated classification of DICOM files
author Sebastien Jodogne <s.jodogne@gmail.com>
date Thu, 09 Oct 2014 17:11:00 +0200
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children 6ef2c81581cd
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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) 2012-2014 Medical Physics Department, CHU of Liege,
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6 # 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
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26 import RestToolbox
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27
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28 parser = argparse.ArgumentParser(
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29 description = 'Automated classification of DICOM files from Orthanc.',
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30 formatter_class = argparse.ArgumentDefaultsHelpFormatter)
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31
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32 parser.add_argument('--host', default = 'localhost',
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33 help = 'The host address that runs Orthanc')
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34 parser.add_argument('--port', type = int, default = '8042',
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35 help = 'The port number to which Orthanc is listening for the REST API')
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36 parser.add_argument('--target', default = 'OrthancFiles',
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37 help = 'The target directory where to store the DICOM files')
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38 parser.add_argument('--all', action = 'store_true',
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39 help = 'Replay the entire history on startup (disabled by default)')
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40 parser.set_defaults(all = False)
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41 parser.add_argument('--remove', action = 'store_true',
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42 help = 'Remove DICOM files from Orthanc once classified (disabled by default)')
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43 parser.set_defaults(remove = False)
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44
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45
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46 # Parse the arguments
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47 args = parser.parse_args()
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48 URL = 'http://%s:%d' % (args.host, args.port)
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49 print 'Connecting to Orthanc on address: %s' % URL
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50
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51 # Compute the starting point for the changes loop
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52 if args.all:
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53 current = 0
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54 else:
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55 current = RestToolbox.DoGet(URL + '/changes?last')['Last']
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56
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57 # Polling loop using the "changes" API of Orthanc, waiting for the
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58 # incoming of new DICOM files
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59 while True:
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60 r = RestToolbox.DoGet(URL + '/changes', {
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61 'since' : current,
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62 'limit' : 4 # Retrieve at most 4 changes at once
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63 })
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64
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65 for change in r['Changes']:
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66 # We are only interested interested in the arrival of new instances
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67 if change['ChangeType'] == 'NewInstance':
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68 # Extract the patient, study, series and instance information
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69 instance = RestToolbox.DoGet('%s/instances/%s' % (URL, change['ID']))
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70 series = RestToolbox.DoGet('%s/series/%s' % (URL, instance['ParentSeries']))
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71 study = RestToolbox.DoGet('%s/studies/%s' % (URL, series['ParentStudy']))
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72 patient = RestToolbox.DoGet('%s/patients/%s' % (URL, study['ParentPatient']))
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73
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74 # Construct a target path
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75 a = '%s - %s' % (patient['MainDicomTags']['PatientID'],
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76 patient['MainDicomTags']['PatientName'])
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77 b = study['MainDicomTags']['StudyDescription']
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78 c = '%s - %s' % (series['MainDicomTags']['Modality'],
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79 series['MainDicomTags']['SeriesDescription'])
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80 d = '%s.dcm' % instance['MainDicomTags']['SOPInstanceUID']
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81
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82 p = os.path.join(
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83 args.target,
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84 a.encode('ascii', 'ignore'),
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85 b.encode('ascii', 'ignore'),
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86 c.encode('ascii', 'ignore')
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87 )
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88
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89 f = os.path.join(p, d.encode('ascii', 'ignore'))
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90
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91
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92 # Copy the DICOM file to the target path
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93 print('Writing new DICOM file: %s' % f)
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94
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95 try:
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96 os.makedirs(p)
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97 except:
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98 # Already existing directory, ignore the error
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99 pass
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100
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101 dcm = RestToolbox.DoGet('%s/instances/%s/file' % (URL, change['ID']))
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102 with open(f, 'wb') as g:
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103 g.write(dcm)
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104
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105 # If requested, remove the instance once it has been copied
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106 if args.remove:
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107 RestToolbox.DoDelete('%s/instances/%s' % (URL, change['ID']))
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108
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109 current = r['Last']
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110
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111 if r['Done']:
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112 print "Everything has been processed: Waiting..."
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113 time.sleep(1)