def datasetcontext(graph, ds, set_label=True):
ieuris = {}
iod = None
uid = getsinglevalue(ds, 0x00080018, 'UI') # SOP Instance UID
if uid is not None:
subject = uritools.urifromuid(uid)
label = str(uid)
else:
subject, label = generateuri()
if set_label:
graph.add((subject, RDFS.label, rdflib.Literal(label)))
sopuid = getsinglevalue(ds, 0x00080016, 'UI') # SOP Class UID
if sopuid is not None:
uidstring = uritools.uidasstring(sopuid)
if uidstring in sopclasses:
iod = sopclasses[uidstring]
for ie in iods[iod].keys():
ieuris[ie] = None
else:
print >> sys.stderr, "SOP Class", uidstring, "not found"
sopuiduri = uritools.urifromuid(sopuid)
graph.add((subject, RDF.type, sopuiduri))
return subject, ieuris, iod
def datasetcontext(graph,ds,set_label=True):
ieuris={}
iod=None
uid=getsinglevalue(ds,0x00080018,'UI') # SOP Instance UID
if uid is not None:
subject=uritools.urifromuid(uid)
label=str(uid)
else:
subject,label=generateuri()
if set_label:
graph.add((subject,RDFS.label,rdflib.Literal(label)))
sopuid=getsinglevalue(ds,0x00080016,'UI') # SOP Class UID
if sopuid is not None:
uidstring=uritools.uidasstring(sopuid)
if uidstring in sopclasses:
iod=sopclasses[uidstring]
for ie in iods[iod].keys():
ieuris[ie]=None
else:
print >> sys.stderr, "SOP Class",uidstring,"not found"
sopuiduri=uritools.urifromuid(sopuid)
graph.add((subject,RDF.type,sopuiduri))
return subject,ieuris,iod
def getieuri(graph,subject,ds,ie):
uidtag=None
if ie=='Study':
uidtag=0x0020000D
elif ie=='Series':
uidtag=0x0020000E
elif ie=='Frame of Reference':
uidtag=0x00200052
uri=None
if uidtag:
uid=getsinglevalue(ds,uidtag,'UI')
if uid is not None:
uri=uritools.urifromuid(uid)
label=str(uid)
if not uri:
uri,label=generateuri()
graph.add((uri,RDF.type,uritools.getieclass(ie)))
graph.add((uri,RDFS.label,rdflib.Literal(label)))
graph.add((subject,DCTERMS.subject,uri))
return uri
def getieuri(graph, subject, ds, ie):
uidtag = None
if ie == 'Study':
uidtag = 0x0020000D
elif ie == 'Series':
uidtag = 0x0020000E
elif ie == 'Frame of Reference':
uidtag = 0x00200052
uri = None
if uidtag:
uid = getsinglevalue(ds, uidtag, 'UI')
if uid is not None:
uri = uritools.urifromuid(uid)
label = str(uid)
if not uri:
uri, label = generateuri()
graph.add((uri, RDF.type, uritools.getieclass(ie)))
graph.add((uri, RDFS.label, rdflib.Literal(label)))
graph.add((subject, DCTERMS.subject, uri))
return uri
def tripleobject(vr,value):
if vr in ('AE','CS','LO','SH'):
value=unicode(value)
value=value.strip(' ') # leading and trailing spaces insignificant
value=cleantext(value)
if value=='': # will almost always mean unknown -> drop
return None
return rdflib.Literal(value)
elif vr in ('LT','ST','UT'):
value=unicode(value)
value=value.rstrip(' ') # trailing spaces insignificant
value=cleantext(value)
if value=='': # will almost always mean unknown -> drop
return None
return rdflib.Literal(value)
elif vr=='PN':
value=unicode(value)
value=value.strip(' ') # leading and trailing spaces insignificant
value=cleantext(value)
if value=='': # will almost always mean unknown -> drop
return None
return rdflib.Literal(value)
elif vr=='UI':
return uritools.urifromuid(value)
elif vr=='AS':
value=unicode(value)
value=cleantext(value)
if value=='': # will almost always mean unknown -> drop
return None
return parseduration(value)
elif vr=='IS':
value=str(value)
if value.strip()=='':
return None
value=int(value)
assert type(value)==int
return rdflib.Literal(long(value))
elif vr=='DS':
value=str(value)
if value.strip()=='':
return None
return rdflib.Literal(float(value),datatype=XSD.double)
elif vr in ('FL','OF'):
assert type(value)==float
return rdflib.Literal(value,datatype=XSD.double)
elif vr=='FD':
assert type(value)==float
return rdflib.Literal(value,datatype=XSD.double)
elif vr in ('SL','SS','UL','US','US or SS'):
# UL requires xsd:long!
assert type(value) in (int,long),type(value)
return rdflib.Literal(long(value))
elif vr=='AT':
return rdflib.Literal(long(value))
elif vr=='DA':
value=str(value)
if not value:
return None
return rdflib.Literal(parsedate(value))
elif vr=='TM':
value=str(value)
if not value:
return None
return rdflib.Literal(parsetime(value))
# rdf representation for missing seconds, hours ?
elif vr=='DT':
value=str(value)
if not value:
return None
return rdflib.Literal(parsedatetime(value))
# rdf representation for things missing after year ?
elif vr=='UN':
# represent UN as plain literal if possible
try:
value=unicode(value)
value=value.strip(' ') # leading and trailing spaces insignificant
value=cleantext(value)
except Exception:
return None
if value=='': # will almost always mean unknown -> drop
return None
return rdflib.Literal(value)
elif vr in ('OB','OW','OB or OW','OW or OB'):
return None
else:
assert False,vr
def tripleobject(vr, value):
if vr in ('AE', 'CS', 'LO', 'SH'):
value = unicode(value)
value = value.strip(' ') # leading and trailing spaces insignificant
value = cleantext(value)
if value == '': # will almost always mean unknown -> drop
return None
return rdflib.Literal(value)
elif vr in ('LT', 'ST', 'UT'):
value = unicode(value)
value = value.rstrip(' ') # trailing spaces insignificant
value = cleantext(value)
if value == '': # will almost always mean unknown -> drop
return None
return rdflib.Literal(value)
elif vr == 'PN':
value = unicode(value)
value = value.strip(' ') # leading and trailing spaces insignificant
value = cleantext(value)
if value == '': # will almost always mean unknown -> drop
return None
return rdflib.Literal(value)
elif vr == 'UI':
return uritools.urifromuid(value)
elif vr == 'AS':
value = unicode(value)
value = cleantext(value)
if value == '': # will almost always mean unknown -> drop
return None
return parseduration(value)
elif vr == 'IS':
value = str(value)
if value.strip() == '':
return None
value = int(value)
assert type(value) == int
return rdflib.Literal(long(value))
elif vr == 'DS':
value = str(value)
if value.strip() == '':
return None
return rdflib.Literal(float(value), datatype=XSD.double)
elif vr in ('FL', 'OF'):
assert type(value) == float
return rdflib.Literal(value, datatype=XSD.double)
elif vr == 'FD':
assert type(value) == float
return rdflib.Literal(value, datatype=XSD.double)
elif vr in ('SL', 'SS', 'UL', 'US', 'US or SS'):
# UL requires xsd:long!
assert type(value) in (int, long), type(value)
return rdflib.Literal(long(value))
elif vr == 'AT':
return rdflib.Literal(long(value))
elif vr == 'DA':
value = str(value)
if not value:
return None
return rdflib.Literal(parsedate(value))
elif vr == 'TM':
value = str(value)
if not value:
return None
return rdflib.Literal(parsetime(value))
# rdf representation for missing seconds, hours ?
elif vr == 'DT':
value = str(value)
if not value:
return None
return rdflib.Literal(parsedatetime(value))
# rdf representation for things missing after year ?
elif vr == 'UN':
# represent UN as plain literal if possible
try:
value = unicode(value)
value = value.strip(
' ') # leading and trailing spaces insignificant
value = cleantext(value)
except Exception:
return None
if value == '': # will almost always mean unknown -> drop
return None
return rdflib.Literal(value)
elif vr in ('OB', 'OW', 'OB or OW', 'OW or OB'):
return None
else:
assert False, vr
#!/usr/bin/python
import sys
import dicom, rdflib
sys.path.append('..')
import uritools
from sopclasses import *
from namespaces import *
graph = uritools.newgraph()
for uid, value in dicom._UID_dict.UID_dictionary.items():
name = value[0]
if not uid or not name:
continue
uid = uid.strip()
subject = uritools.urifromuid(uid)
graph.add((subject, RDFS.label, rdflib.Literal(name)))
if uid in sopclasses:
graph.add((subject, RDF.type, OWL.Class))
graph = graph.serialize(sys.stdout, format="pretty-xml")
#!/usr/bin/python
import sys
import dicom,rdflib
sys.path.append('..')
import uritools
from sopclasses import *
from namespaces import *
graph=uritools.newgraph()
for uid,value in dicom._UID_dict.UID_dictionary.items():
name=value[0]
if not uid or not name:
continue
uid=uid.strip()
subject=uritools.urifromuid(uid)
graph.add((subject,RDFS.label,rdflib.Literal(name)))
if uid in sopclasses:
graph.add((subject,RDF.type,OWL.Class))
graph=graph.serialize(sys.stdout,format="pretty-xml")
