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comparison OrthancServer/Resources/Samples/Python/AutoClassify.py @ 4044:d25f4c0fa160 framework

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splitting code into OrthancFramework and OrthancServer
author Sebastien Jodogne <s.jodogne@gmail.com>
date Wed, 10 Jun 2020 20:30:34 +0200
parents Resources/Samples/Python/AutoClassify.py@94f4a18a79cc
children d9473bd5ed43
comparison
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4043:6c6239aec462 4044:d25f4c0fa160
1 #!/usr/bin/python
2 # -*- coding: utf-8 -*-
3
4 # Orthanc - A Lightweight, RESTful DICOM Store
5 # Copyright (C) 2012-2016 Sebastien Jodogne, Medical Physics
6 # Department, University Hospital of Liege, Belgium
7 # Copyright (C) 2017-2020 Osimis S.A., Belgium
8 #
9 # This program is free software: you can redistribute it and/or
10 # modify it under the terms of the GNU General Public License as
11 # published by the Free Software Foundation, either version 3 of the
12 # License, or (at your option) any later version.
13 #
14 # This program is distributed in the hope that it will be useful, but
15 # WITHOUT ANY WARRANTY; without even the implied warranty of
16 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
17 # General Public License for more details.
18 #
19 # You should have received a copy of the GNU General Public License
20 # along with this program. If not, see <http://www.gnu.org/licenses/>.
21
22
23 import argparse
24 import time
25 import os
26 import os.path
27 import sys
28 import RestToolbox
29
30 parser = argparse.ArgumentParser(
31 description = 'Automated classification of DICOM files from Orthanc.',
32 formatter_class = argparse.ArgumentDefaultsHelpFormatter)
33
34 parser.add_argument('--host', default = '127.0.0.1',
35 help = 'The host address that runs Orthanc')
36 parser.add_argument('--port', type = int, default = '8042',
37 help = 'The port number to which Orthanc is listening for the REST API')
38 parser.add_argument('--target', default = 'OrthancFiles',
39 help = 'The target directory where to store the DICOM files')
40 parser.add_argument('--all', action = 'store_true',
41 help = 'Replay the entire history on startup (disabled by default)')
42 parser.set_defaults(all = False)
43 parser.add_argument('--remove', action = 'store_true',
44 help = 'Remove DICOM files from Orthanc once classified (disabled by default)')
45 parser.set_defaults(remove = False)
46
47
48 def FixPath(p):
49 return p.encode('ascii', errors = 'replace').translate(None, r"'\/:*?\"<>|!=").strip()
50
51 def GetTag(resource, tag):
52 if ('MainDicomTags' in resource and
53 tag in resource['MainDicomTags']):
54 return resource['MainDicomTags'][tag]
55 else:
56 return 'No' + tag
57
58 def ClassifyInstance(instanceId):
59 # Extract the patient, study, series and instance information
60 instance = RestToolbox.DoGet('%s/instances/%s' % (URL, instanceId))
61 series = RestToolbox.DoGet('%s/series/%s' % (URL, instance['ParentSeries']))
62 study = RestToolbox.DoGet('%s/studies/%s' % (URL, series['ParentStudy']))
63 patient = RestToolbox.DoGet('%s/patients/%s' % (URL, study['ParentPatient']))
64
65 # Construct a target path
66 a = '%s - %s' % (GetTag(patient, 'PatientID'),
67 GetTag(patient, 'PatientName'))
68 b = GetTag(study, 'StudyDescription')
69 c = '%s - %s' % (GetTag(series, 'Modality'),
70 GetTag(series, 'SeriesDescription'))
71 d = '%s.dcm' % GetTag(instance, 'SOPInstanceUID')
72
73 p = os.path.join(args.target, FixPath(a), FixPath(b), FixPath(c))
74 f = os.path.join(p, FixPath(d))
75
76 # Copy the DICOM file to the target path
77 print('Writing new DICOM file: %s' % f)
78
79 try:
80 os.makedirs(p)
81 except:
82 # Already existing directory, ignore the error
83 pass
84
85 dcm = RestToolbox.DoGet('%s/instances/%s/file' % (URL, instanceId))
86 with open(f, 'wb') as g:
87 g.write(dcm)
88
89
90 # Parse the arguments
91 args = parser.parse_args()
92 URL = 'http://%s:%d' % (args.host, args.port)
93 print('Connecting to Orthanc on address: %s' % URL)
94
95 # Compute the starting point for the changes loop
96 if args.all:
97 current = 0
98 else:
99 current = RestToolbox.DoGet(URL + '/changes?last')['Last']
100
101 # Polling loop using the 'changes' API of Orthanc, waiting for the
102 # incoming of new DICOM files
103 while True:
104 r = RestToolbox.DoGet(URL + '/changes', {
105 'since' : current,
106 'limit' : 4 # Retrieve at most 4 changes at once
107 })
108
109 for change in r['Changes']:
110 # We are only interested in the arrival of new instances
111 if change['ChangeType'] == 'NewInstance':
112 try:
113 ClassifyInstance(change['ID'])
114
115 # If requested, remove the instance once it has been
116 # properly handled by "ClassifyInstance()". Thanks to
117 # the "try/except" block, the instance is not removed
118 # if the "ClassifyInstance()" function fails.
119 if args.remove:
120 RestToolbox.DoDelete('%s/instances/%s' % (URL, change['ID']))
121
122 except:
123 print('Unable to write instance %s to the disk' % change['ID'])
124
125 current = r['Last']
126
127 if r['Done']:
128 print('Everything has been processed: Waiting...')
129 time.sleep(1)