Mercurial > hg > orthanc
comparison Resources/Samples/Python/AutoClassify.py @ 1183:6ef2c81581cd
more fault-tolerant sample
author | Sebastien Jodogne <s.jodogne@gmail.com> |
---|---|
date | Fri, 10 Oct 2014 08:52:56 +0200 |
parents | d74ac5d0bcaf |
children | 4e9d517503ae |
comparison
equal
deleted
inserted
replaced
1182:d74ac5d0bcaf | 1183:6ef2c81581cd |
---|---|
41 parser.add_argument('--remove', action = 'store_true', | 41 parser.add_argument('--remove', action = 'store_true', |
42 help = 'Remove DICOM files from Orthanc once classified (disabled by default)') | 42 help = 'Remove DICOM files from Orthanc once classified (disabled by default)') |
43 parser.set_defaults(remove = False) | 43 parser.set_defaults(remove = False) |
44 | 44 |
45 | 45 |
46 def FixPath(p): | |
47 return p.encode('ascii', 'ignore').strip() | |
48 | |
49 def GetTag(resource, tag): | |
50 if ('MainDicomTags' in resource and | |
51 tag in resource['MainDicomTags']): | |
52 return resource['MainDicomTags'][tag] | |
53 else: | |
54 return 'No' + tag | |
55 | |
56 def ClassifyInstance(instanceId): | |
57 # Extract the patient, study, series and instance information | |
58 instance = RestToolbox.DoGet('%s/instances/%s' % (URL, instanceId)) | |
59 series = RestToolbox.DoGet('%s/series/%s' % (URL, instance['ParentSeries'])) | |
60 study = RestToolbox.DoGet('%s/studies/%s' % (URL, series['ParentStudy'])) | |
61 patient = RestToolbox.DoGet('%s/patients/%s' % (URL, study['ParentPatient'])) | |
62 | |
63 # Construct a target path | |
64 a = '%s - %s' % (GetTag(patient, 'PatientID'), | |
65 GetTag(patient, 'PatientName')) | |
66 b = GetTag(study, 'StudyDescription') | |
67 c = '%s - %s' % (GetTag(series, 'Modality'), | |
68 GetTag(series, 'SeriesDescription')) | |
69 d = '%s.dcm' % GetTag(instance, 'SOPInstanceUID') | |
70 | |
71 p = os.path.join(args.target, FixPath(a), FixPath(b), FixPath(c)) | |
72 f = os.path.join(p, FixPath(d)) | |
73 | |
74 # Copy the DICOM file to the target path | |
75 print('Writing new DICOM file: %s' % f) | |
76 | |
77 try: | |
78 os.makedirs(p) | |
79 except: | |
80 # Already existing directory, ignore the error | |
81 pass | |
82 | |
83 dcm = RestToolbox.DoGet('%s/instances/%s/file' % (URL, instanceId)) | |
84 with open(f, 'wb') as g: | |
85 g.write(dcm) | |
86 | |
87 | |
46 # Parse the arguments | 88 # Parse the arguments |
47 args = parser.parse_args() | 89 args = parser.parse_args() |
48 URL = 'http://%s:%d' % (args.host, args.port) | 90 URL = 'http://%s:%d' % (args.host, args.port) |
49 print 'Connecting to Orthanc on address: %s' % URL | 91 print('Connecting to Orthanc on address: %s' % URL) |
50 | 92 |
51 # Compute the starting point for the changes loop | 93 # Compute the starting point for the changes loop |
52 if args.all: | 94 if args.all: |
53 current = 0 | 95 current = 0 |
54 else: | 96 else: |
55 current = RestToolbox.DoGet(URL + '/changes?last')['Last'] | 97 current = RestToolbox.DoGet(URL + '/changes?last')['Last'] |
56 | 98 |
57 # Polling loop using the "changes" API of Orthanc, waiting for the | 99 # Polling loop using the 'changes' API of Orthanc, waiting for the |
58 # incoming of new DICOM files | 100 # incoming of new DICOM files |
59 while True: | 101 while True: |
60 r = RestToolbox.DoGet(URL + '/changes', { | 102 r = RestToolbox.DoGet(URL + '/changes', { |
61 'since' : current, | 103 'since' : current, |
62 'limit' : 4 # Retrieve at most 4 changes at once | 104 'limit' : 4 # Retrieve at most 4 changes at once |
63 }) | 105 }) |
64 | 106 |
65 for change in r['Changes']: | 107 for change in r['Changes']: |
66 # We are only interested interested in the arrival of new instances | 108 # We are only interested interested in the arrival of new instances |
67 if change['ChangeType'] == 'NewInstance': | 109 if change['ChangeType'] == 'NewInstance': |
68 # Extract the patient, study, series and instance information | 110 try: |
69 instance = RestToolbox.DoGet('%s/instances/%s' % (URL, change['ID'])) | 111 ClassifyInstance(change['ID']) |
70 series = RestToolbox.DoGet('%s/series/%s' % (URL, instance['ParentSeries'])) | 112 except: |
71 study = RestToolbox.DoGet('%s/studies/%s' % (URL, series['ParentStudy'])) | 113 print('Unable to write instance %s to the disk' % change['ID']) |
72 patient = RestToolbox.DoGet('%s/patients/%s' % (URL, study['ParentPatient'])) | |
73 | 114 |
74 # Construct a target path | |
75 a = '%s - %s' % (patient['MainDicomTags']['PatientID'], | |
76 patient['MainDicomTags']['PatientName']) | |
77 b = study['MainDicomTags']['StudyDescription'] | |
78 c = '%s - %s' % (series['MainDicomTags']['Modality'], | |
79 series['MainDicomTags']['SeriesDescription']) | |
80 d = '%s.dcm' % instance['MainDicomTags']['SOPInstanceUID'] | |
81 | |
82 p = os.path.join( | |
83 args.target, | |
84 a.encode('ascii', 'ignore'), | |
85 b.encode('ascii', 'ignore'), | |
86 c.encode('ascii', 'ignore') | |
87 ) | |
88 | |
89 f = os.path.join(p, d.encode('ascii', 'ignore')) | |
90 | |
91 | |
92 # Copy the DICOM file to the target path | |
93 print('Writing new DICOM file: %s' % f) | |
94 | |
95 try: | |
96 os.makedirs(p) | |
97 except: | |
98 # Already existing directory, ignore the error | |
99 pass | |
100 | |
101 dcm = RestToolbox.DoGet('%s/instances/%s/file' % (URL, change['ID'])) | |
102 with open(f, 'wb') as g: | |
103 g.write(dcm) | |
104 | |
105 # If requested, remove the instance once it has been copied | 115 # If requested, remove the instance once it has been copied |
106 if args.remove: | 116 if args.remove: |
107 RestToolbox.DoDelete('%s/instances/%s' % (URL, change['ID'])) | 117 RestToolbox.DoDelete('%s/instances/%s' % (URL, change['ID'])) |
108 | 118 |
109 current = r['Last'] | 119 current = r['Last'] |
110 | 120 |
111 if r['Done']: | 121 if r['Done']: |
112 print "Everything has been processed: Waiting..." | 122 print('Everything has been processed: Waiting...') |
113 time.sleep(1) | 123 time.sleep(1) |