def getAnnotation ( self, ch, annid ):
"""Return a RAMON object by identifier"""
kvdict = self.annodb.getAnnotationKV ( ch, annid )
annotype = int(kvdict['ann_type'])
# switch on the type of annotation
if annotype is None:
return None
elif annotype == annotation.ANNO_SYNAPSE:
anno = annotation.AnnSynapse(self.annodb,ch)
elif annotype == annotation.ANNO_SEED:
anno = annotation.AnnSeed(self.annodb,ch)
elif annotype == annotation.ANNO_SEGMENT:
anno = annotation.AnnSegment(self.annodb,ch)
elif annotype == annotation.ANNO_NEURON:
anno = annotation.AnnNeuron(self.annodb,ch)
elif annotype == annotation.ANNO_ORGANELLE:
anno = annotation.AnnOrganelle(self.annodb,ch)
elif annotype == annotation.ANNO_NODE:
anno = annotation.AnnNode(self.annodb,ch)
elif annotype == annotation.ANNO_SKELETON:
anno = annotation.AnnSkeleton(self.annodb,ch)
elif annotype == annotation.ANNO_ROI:
anno = annotation.AnnROI(self.annodb,ch)
elif annotype == annotation.ANNO_ANNOTATION:
anno = annotation.Annotation(self.annodb,ch)
else:
raise NDWSError ( "Unrecognized annotation type {}".format(type) )
# load the annotation
anno.fromDict ( kvdict )
return anno
def _readOrganelle(self, id):
# create a new organelle
anno = annotation.AnnOrganelle(self.annodb, self.ch)
# set the organelle ID
anno.setField('annid', id)
# fill in the fields
# basic metadata first
[confidence, status] = self._readAnnoMetadata(id)
anno.setField('status', status)
anno.setField('confidence', confidence)
# segment related metadata
with closing(
MySQLdb.connect(
host=self.proj.getDBHost(),
user=settings.DATABASES['default']['USER'],
passwd=settings.DATABASES['default']['PASSWORD'],
db=self.proj.getDBName(),
connect_timeout=1)) as conn:
with closing(conn.cursor()) as cursor:
orgTableName = "{}_organelles".format(self.ch.channel_name)
sql = "SELECT organelleclass, parentseed, centroidx, centroidy, centroidz FROM {} WHERE annoid={}".format(
orgTableName, id)
try:
cursor.execute(sql)
res = cursor.fetchall()[0]
except MySQLdb.Error, e:
print "Error: Failed to get annotation type for RAMON object with ID {}: {}".format(
id, e)
sys.exit(1)
def H5toAnnotation(key, idgrp, annodb, ch):
"""Return an annotation constructed from the contents of this HDF5 file"""
# get the annotation type
# if idgrp.get('ANNOTATION_TYPE'):
if 'ANNOTATION_TYPE' in idgrp:
annotype = idgrp['ANNOTATION_TYPE'][0]
else:
annotype = annotation.ANNO_ANNOTATION
# And get the metadata group
mdgrp = idgrp.get('METADATA')
if annotype == annotation.ANNO_SEED:
# Create the appropriate annotation type
anno = annotation.AnnSeed(annodb, ch)
# Load metadata if it exists
if mdgrp:
# load the seed specific metadata
if 'PARENT' in mdgrp:
anno.parent = mdgrp['PARENT'][0]
if 'POSITION' in mdgrp:
anno.position = mdgrp['POSITION'][:]
if 'CUBE_LOCATION' in mdgrp:
anno.cubelocation = mdgrp['CUBE_LOCATION'][0]
if 'SOURCE' in mdgrp:
anno.source = mdgrp['SOURCE'][0]
elif annotype == annotation.ANNO_SYNAPSE:
# Create the appropriate annotation type
anno = annotation.AnnSynapse(annodb, ch)
# Load metadata if it exists
if mdgrp:
# load the synapse specific metadata
if 'SYNAPSE_TYPE' in mdgrp:
anno.synapse_type = mdgrp['SYNAPSE_TYPE'][0]
if 'WEIGHT' in mdgrp:
anno.weight = mdgrp['WEIGHT'][0]
if 'SEEDS' in mdgrp:
anno.seeds = mdgrp['SEEDS'][:]
if 'SEGMENTS' in mdgrp:
anno.segments = mdgrp['SEGMENTS'][:]
if 'PRESEGMENTS' in mdgrp:
anno.presegments = mdgrp['PRESEGMENTS'][:]
if 'POSTSEGMENTS' in mdgrp:
anno.postsegments = mdgrp['POSTSEGMENTS'][:]
elif annotype == annotation.ANNO_SEGMENT:
# Create the appropriate annotation type
anno = annotation.AnnSegment(annodb, ch)
# Load metadata if it exists
if mdgrp:
# load the synapse specific metadata
if mdgrp.get('PARENTSEED'):
anno.parentseed = mdgrp['PARENTSEED'][0]
if mdgrp.get('SEGMENTCLASS'):
anno.segmentclass = mdgrp['SEGMENTCLASS'][0]
if mdgrp.get('NEURON'):
anno.neuron = mdgrp['NEURON'][0]
if mdgrp.get('SYNAPSES') and len(mdgrp['SYNAPSES']) != 0:
anno.synapses = mdgrp['SYNAPSES'][:]
if mdgrp.get('ORGANELLES') and len(mdgrp['ORGANELLES']) != 0:
anno.organelles = mdgrp['ORGANELLES'][:]
elif annotype == annotation.ANNO_NEURON:
# Create the appropriate annotation type
anno = annotation.AnnNeuron(annodb, ch)
# Load metadata if it exists
if mdgrp:
# load the synapse specific metadata
if mdgrp.get('SEGMENTS') and len(mdgrp['SEGMENTS']) != 0:
anno.segments = mdgrp['SEGMENTS'][:]
elif annotype == annotation.ANNO_ORGANELLE:
# Create the appropriate annotation type
anno = annotation.AnnOrganelle(annodb, ch)
# Load metadata if it exists
if mdgrp:
# load the synapse specific metadata
if mdgrp.get('PARENTSEED'):
anno.parentseed = mdgrp['PARENTSEED'][0]
if mdgrp.get('ORGANELLECLASS'):
anno.organelleclass = mdgrp['ORGANELLECLASS'][0]
if mdgrp.get('SEEDS') and len(mdgrp['SEEDS']) != 0:
anno.seeds = mdgrp['SEEDS'][:]
if mdgrp.get('CENTROID'):
anno.centroid = mdgrp['CENTROID'][:]
elif annotype == annotation.ANNO_NODE:
# Create the appropriate annotation type
anno = annotation.AnnNode(annodb, ch)
# Load metadata if it exists
if mdgrp:
# load the synapse specific metadata
if 'NODETYPE' in mdgrp:
anno.nodetype = mdgrp['NODETYPE'][0]
if 'PARENTID' in mdgrp:
anno.parentid = mdgrp['PARENTID'][0]
if 'SKELETONID' in mdgrp:
anno.skeletonid = mdgrp['SKELETONID'][0]
if 'RADIUS' in mdgrp:
anno.radius = mdgrp['RADIUS'][0]
if mdgrp.get('CHILDREN') and len(mdgrp['CHILDREN']) != 0:
anno.children = mdgrp['CHILDREN'][:]
if mdgrp.get('LOCATION'):
anno.location = mdgrp['LOCATION'][:]
elif annotype == annotation.ANNO_SKELETON:
# Create the appropriate annotation type
anno = annotation.AnnSkeleton(annodb, ch)
# Load metadata if it exists
if mdgrp:
# load the synapse specific metadata
if 'SKELETONTYPE' in mdgrp:
anno.skeletontype = mdgrp['SKELETONTYPE'][0]
if 'ROOTNODE' in mdgrp:
anno.rootnode = mdgrp['ROOTNODE'][0]
elif annotype == annotation.ANNO_ROI:
# Create the appropriate annotation type
anno = annotation.AnnROI(annodb, ch)
# Load metadata if it exists
if mdgrp:
# load the synapse specific metadata
if 'PARENT' in mdgrp:
anno.parent = mdgrp['PARENT'][0]
# No special action if it's a no type
elif annotype == annotation.ANNO_ANNOTATION:
# Just create a generic annotation object
anno = annotation.Annotation(annodb, ch)
else:
logger.warning("Do not support this annotation type yet. Type = %s" %
annotype)
raise NDWSError("Do n0t support this annotation type yet. Type = %s" %
annotype)
# now load the annotation common fields
if re.match("^\d+$", key):
anno.annid = int(key)
else:
anno.annid = 0
if mdgrp:
# now load the metadata common fields
if mdgrp.get('STATUS'):
anno.status = mdgrp['STATUS'][0]
if mdgrp.get('CONFIDENCE'):
anno.confidence = mdgrp['CONFIDENCE'][0]
if mdgrp.get('AUTHOR'):
anno.author = mdgrp['AUTHOR'][0]
# and the key/value pairs
if mdgrp.get('KVPAIRS'):
fstring = cStringIO.StringIO(mdgrp['KVPAIRS'][0])
csvr = csv.reader(fstring, delimiter=',')
for r in csvr:
anno.kvpairs[r[0]] = r[1]
return anno