def listIds(imageargs, dbcfg, proj):
"""Return the list of annotation identifiers in a region"""
# Perform argument processing
try:
args = restargs.BrainRestArgs()
args.cutoutArgs(imageargs, dbcfg)
except restargs.RESTArgsError, e:
logger.warning("REST Arguments failed: %s" % (e))
raise ANNError(e)
def cutout(imageargs, dbcfg, proj, channel=None):
"""Build the returned cube of data. This method is called by all
of the more basic services to build the data.
They then format and refine the output."""
# Perform argument processing
try:
args = restargs.BrainRestArgs()
args.cutoutArgs(imageargs, dbcfg)
except restargs.RESTArgsError, e:
logger.warning("REST Arguments failed: %s" % (e))
raise ANNError(e)
def yzAnno(imageargs, dbcfg, proj):
"""Return an yz plane fileobj.read()"""
[annoidstr, sym, imageargs] = imageargs.partition('/')
annoid = int(annoidstr)
# Perform argument processing
try:
args = restargs.BrainRestArgs()
args.yzArgs(imageargs, dbcfg)
except restargs.RESTArgsError, e:
logger.warning("REST Arguments failed: %s" % (e))
raise ANNError(e)
def __init__(self, token, cutout):
"""Load the annotation database and project"""
projdb = ocpcaproj.OCPCAProjectsDB()
self.proj = projdb.loadProject(token)
# Bind the annotation database
self.annoDB = ocpcadb.OCPCADB(self.proj)
# Perform argument processing
try:
args = restargs.BrainRestArgs()
args.cutoutArgs(cutout + "/", self.proj.datasetcfg)
except restargs.RESTArgsError, e:
raise OCPCAError(e.value)
def yzSlice(imageargs, dbcfg, proj):
"""Return an yz plane as a cube"""
if proj.getDBType() == emcaproj.CHANNELS:
[channel, sym, imageargs] = imageargs.partition('/')
else:
channel = None
# Perform argument processing
try:
args = restargs.BrainRestArgs()
args.yzArgs(imageargs, dbcfg)
except restargs.RESTArgsError, e:
logger.warning("REST Arguments failed: %s" % (e))
raise ANNError(e)
def getAnnotations(webargs, postdata):
"""Get multiple annotations. Takes an HDF5 that lists ids in the post."""
[token, objectsliteral, otherargs] = webargs.split('/', 2)
# Get the annotation database
projdb = emcaproj.EMCAProjectsDB()
proj = projdb.getProj(token)
dbcfg = dbconfig.switchDataset(proj.getDataset())
db = emcadb.EMCADB(dbcfg, proj)
# Read the post data HDF5 and get a list of identifiers
tmpinfile = tempfile.NamedTemporaryFile()
tmpinfile.write(postdata)
tmpinfile.seek(0)
h5in = h5py.File(tmpinfile.name)
# IDENTIFIERS
if not h5in.get('ANNOIDS'):
logger.warning(
"Requesting multiple annotations. But no HDF5 \'ANNOIDS\' field specified."
)
raise ANNError(
"Requesting multiple annotations. But no HDF5 \'ANNOIDS\' field specified."
)
# GET the data out of the HDF5 file. Never operate on the data in place.
annoids = h5in['ANNOIDS'][:]
# set variables to None: need them in call to getAnnoByID, but not all paths set all
corner = None
dim = None
resolution = None
dataarg = ''
# process options
# Split the URL and get the args
if otherargs != '':
(dataarg, cutout) = otherargs.split('/', 1)
if dataarg == '' or dataarg == 'nodata':
dataoption = AR_NODATA
elif dataarg == 'voxels':
dataoption = AR_VOXELS
# only arg to voxels is resolution
[resstr, sym, rest] = cutout.partition('/')
resolution = int(resstr) if resstr != '' else proj.getResolution()
elif dataarg == 'cutout':
# if blank of just resolution then a tightcutout
if cutout == '' or re.match('^\d+[\/]*$', cutout):
dataoption = AR_TIGHTCUTOUT
[resstr, sym, rest] = cutout.partition('/')
resolution = int(resstr) if resstr != '' else proj.getResolution()
else:
dataoption = AR_CUTOUT
# Perform argument processing
brargs = restargs.BrainRestArgs()
brargs.cutoutArgs(cutout, dbcfg)
# Extract the relevant values
corner = brargs.getCorner()
dim = brargs.getDim()
resolution = brargs.getResolution()
# RBTODO test this interface
elif dataarg == 'boundingbox':
# if blank of just resolution then a tightcutout
if cutout == '' or re.match('^\d+[\/]*$', cutout):
dataoption = AR_BOUNDINGBOX
[resstr, sym, rest] = cutout.partition('/')
resolution = int(resstr) if resstr != '' else proj.getResolution()
else:
logger.warning("In getAnnotations: Error: no such data option %s " %
(dataarg))
raise ANNError("In getAnnotations: Error: no such data option %s " %
(dataarg))
# Make the HDF5 output file
# Create an in-memory HDF5 file
tmpoutfile = tempfile.NamedTemporaryFile()
h5fout = h5py.File(tmpoutfile.name)
# get annotations for each identifier
for annoid in annoids:
# the int here is to prevent using a numpy value in an inner loop. This is a 10x performance gain.
getAnnoById(int(annoid), h5fout, db, dbcfg, dataoption, resolution,
corner, dim)
# close temporary file
h5in.close()
tmpinfile.close()
# Transmit back the populated HDF5 file
h5fout.flush()
tmpoutfile.seek(0)
return tmpoutfile.read()
def getAnnotation(webargs):
"""Fetch a RAMON object as HDF5 by object identifier"""
[token, sym, otherargs] = webargs.partition('/')
# Get the annotation database
projdb = emcaproj.EMCAProjectsDB()
proj = projdb.getProj(token)
dbcfg = dbconfig.switchDataset(proj.getDataset())
db = emcadb.EMCADB(dbcfg, proj)
# Split the URL and get the args
args = otherargs.split('/', 2)
# Make the HDF5 file
# Create an in-memory HDF5 file
tmpfile = tempfile.NamedTemporaryFile()
h5f = h5py.File(tmpfile.name)
# if the first argument is numeric. it is an annoid
if re.match('^[\d,]+$', args[0]):
annoids = map(int, args[0].split(','))
for annoid in annoids:
# default is no data
if args[1] == '' or args[1] == 'nodata':
dataoption = AR_NODATA
getAnnoById(annoid, h5f, db, dbcfg, dataoption)
# if you want voxels you either requested the resolution id/voxels/resolution
# or you get data from the default resolution
elif args[1] == 'voxels':
dataoption = AR_VOXELS
[resstr, sym, rest] = args[2].partition('/')
resolution = int(
resstr) if resstr != '' else proj.getResolution()
getAnnoById(annoid, h5f, db, dbcfg, dataoption, resolution)
elif args[1] == 'cutout':
# if there are no args or only resolution, it's a tight cutout request
if args[2] == '' or re.match('^\d+[\/]*$', args[2]):
dataoption = AR_TIGHTCUTOUT
[resstr, sym, rest] = args[2].partition('/')
resolution = int(
resstr) if resstr != '' else proj.getResolution()
getAnnoById(annoid, h5f, db, dbcfg, dataoption, resolution)
else:
dataoption = AR_CUTOUT
# Perform argument processing
brargs = restargs.BrainRestArgs()
brargs.cutoutArgs(args[2], dbcfg)
# Extract the relevant values
corner = brargs.getCorner()
dim = brargs.getDim()
resolution = brargs.getResolution()
getAnnoById(annoid, h5f, db, dbcfg, dataoption, resolution,
corner, dim)
elif args[1] == 'boundingbox':
dataoption = AR_BOUNDINGBOX
[resstr, sym, rest] = args[2].partition('/')
resolution = int(
resstr) if resstr != '' else proj.getResolution()
getAnnoById(annoid, h5f, db, dbcfg, dataoption, resolution)
else:
logger.warning(
"Fetch identifier %s. Error: no such data option %s " %
(annoid, args[1]))
raise ANNError(
"Fetch identifier %s. Error: no such data option %s " %
(annoid, args[1]))
# the first argument is not numeric. it is a service other than getAnnotation
else:
logger.warning(
"Get interface %s requested. Illegal or not implemented. Args: %s"
% (args[0], webargs))
raise ANNError(
"Get interface %s requested. Illegal or not implemented" %
(args[0]))
h5f.flush()
tmpfile.seek(0)
return tmpfile.read()
def selectPost(webargs, dbcfg, proj, postdata):
"""Parse the first arg and call the right post service"""
[service, sym, postargs] = webargs.partition('/')
# Don't write to readonly projects
if proj.getReadOnly() == 1:
logger.warning("Attempt to write to read only project. %s: %s" %
(proj.getDBName(), webargs))
raise ANNError("Attempt to write to read only project. %s: %s" %
(proj.getDBName(), webargs))
# choose to overwrite (default), preserve, or make exception lists
# when voxels conflict
# Perform argument processing
# Bind the annotation database
db = emcadb.EMCADB(dbcfg, proj)
db.startTxn()
tries = 0
done = False
while not done and tries < 5:
try:
if service == 'npvoxels':
# get the resolution
[entity, resolution, conflictargs] = postargs.split('/', 2)
# Grab the voxel list
fileobj = cStringIO.StringIO(postdata)
voxlist = np.load(fileobj)
conflictopt = restargs.conflictOption(conflictargs)
entityid = db.annotate(int(entity), int(resolution), voxlist,
conflictopt)
elif service == 'npdense':
# Process the arguments
try:
args = restargs.BrainRestArgs()
args.cutoutArgs(postargs, dbcfg)
except restargs.RESTArgsError, e:
logger.warning("REST Arguments failed: %s" % (e))
raise ANNError(e)
corner = args.getCorner()
resolution = args.getResolution()
# This is used for ingest only now. So, overwrite conflict option.
conflictopt = restargs.conflictOption("")
# get the data out of the compressed blob
rawdata = zlib.decompress(postdata)
fileobj = cStringIO.StringIO(rawdata)
voxarray = np.load(fileobj)
# Get the annotation database
db = emcadb.EMCADB(dbcfg, proj)
if proj.getDBType() == emcaproj.IMAGES:
db.writeImageCuboid(corner, resolution, voxarray)
# this is just a status
entityid = 0
# Choose the verb, get the entity (as needed), and annotate
# Translates the values directly
else:
entityid = db.annotateDense(corner, resolution, voxarray,
conflictopt)
db.conn.commit()
else:
logger.warning(
"An illegal Web POST service was requested: %s. Args %s" %
(service, webargs))
raise ANNError("No such Web service: %s" % service)
db.commit()
done = True
