def _attemptOpenAsDvidVolume(self, filePath):
"""
Two ways to specify a dvid volume.
1) via a file that contains the hostname, uuid, and dataset name (1 per line)
2) as a url, e.g. http://localhost:8000/api/node/uuid/dataname
"""
if os.path.splitext(filePath)[1] == '.dvidvol':
with open(filePath) as f:
filetext = f.read()
hostname, uuid, dataname = filetext.splitlines()
opDvidVolume = OpDvidVolume( hostname, uuid, dataname, transpose_axes=True, parent=self )
return [opDvidVolume], opDvidVolume.Output
if '://' in filePath:
url_format = "^protocol://hostname/api/node/uuid/dataname(\\?query_string)?"
for field in ['protocol', 'hostname', 'uuid', 'dataname', 'query_string']:
url_format = url_format.replace( field, '(?P<' + field + '>[^?]+)' )
match = re.match( url_format, filePath )
if match:
fields = match.groupdict()
try:
query_string = fields['query_string']
query_args = {}
if query_string:
query_args = dict( map(lambda s: s.split('='), query_string.split('&')) )
opDvidVolume = OpDvidVolume( fields['hostname'], fields['uuid'], fields['dataname'], query_args,
transpose_axes=True, parent=self )
return [opDvidVolume], opDvidVolume.Output
except OpDvidVolume.DatasetReadError as e:
raise OpInputDataReader.DatasetReadError( *e.args )
return ([], None)
def _test_volume(self, hostname, uuid, dataname, start, stop):
"""
hostname: The dvid server host
uuid: The node we can test with
dataname: The data instance to test with
start, stop: The bounds of the cutout volume to retrieve from the server. C ORDER FOR THIS TEST BECAUSE we use transpose_axes=True
"""
# Retrieve from server
graph = Graph()
opDvidVolume = OpDvidVolume(hostname,
uuid,
dataname, {},
transpose_axes=True,
graph=graph)
subvol = opDvidVolume.Output(start, stop).wait()
# Retrieve from file (which uses fortran order)
slicing = tuple(slice(x, y) for x, y in zip(start, stop))
slicing = tuple(reversed(slicing))
expected_data = self.original_data[slicing]
# Compare.
assert ( subvol.view(numpy.ndarray) == expected_data.transpose() ).all(),\
"Data from server didn't match data from file!"
def _test_volume(self, hostname, h5filename, uuid, dataname, start, stop):
"""
hostname: The dvid server host
h5filename: The h5 file to compare against
h5group: The hdf5 group, also used as the uuid of the dvid dataset
h5dataset: The dataset name, also used as the name of the dvid dataset
start, stop: The bounds of the cutout volume to retrieve from the server. C ORDER FOR THIS TEST BECAUSE we use transpose_axes=True
"""
# Retrieve from server
graph = Graph()
opDvidVolume = OpDvidVolume(hostname,
uuid,
dataname, {},
transpose_axes=True,
graph=graph)
subvol = opDvidVolume.Output(start, stop).wait()
# Retrieve from file (which uses fortran order)
slicing = tuple(slice(x, y) for x, y in zip(start, stop))
slicing = tuple(reversed(slicing))
with h5py.File(h5filename, 'r') as f:
expected_data = f['all_nodes'][uuid][dataname][slicing]
# Compare.
assert ( subvol.view(numpy.ndarray) == expected_data.transpose() ).all(),\
"Data from server didn't match data from file!"
def _attemptOpenAsDvidVolume(self, filePath):
"""
Two ways to specify a dvid volume.
1) via a file that contains the hostname, uuid, and dataset name (1 per line)
2) as a url, e.g. http://localhost:8000/api/node/uuid/dataname
"""
if os.path.splitext(filePath)[1] == '.dvidvol':
with open(filePath) as f:
filetext = f.read()
hostname, uuid, dataname = filetext.splitlines()
opDvidVolume = OpDvidVolume(hostname,
uuid,
dataname,
transpose_axes=True,
parent=self)
return [opDvidVolume], opDvidVolume.Output
if '://' not in filePath:
return ([], None) # not a url
url_format = "^protocol://hostname/api/node/uuid/dataname(\\?query_string)?"
for field in [
'protocol', 'hostname', 'uuid', 'dataname', 'query_string'
]:
url_format = url_format.replace(field, '(?P<' + field + '>[^?]+)')
match = re.match(url_format, filePath)
if not match:
# DVID is the only url-based format we support right now.
# So if it looks like the user gave a URL that isn't a valid DVID node, then error.
raise OpInputDataReader.DatasetReadError(
"Invalid URL format for DVID: {}".format(filePath))
fields = match.groupdict()
try:
query_string = fields['query_string']
query_args = {}
if query_string:
query_args = dict(
map(lambda s: s.split('='), query_string.split('&')))
try:
opDvidVolume = OpDvidVolume(fields['hostname'],
fields['uuid'],
fields['dataname'],
query_args,
transpose_axes=True,
parent=self)
return [opDvidVolume], opDvidVolume.Output
except:
# Maybe this is actually a roi
opDvidRoi = OpDvidRoi(fields['hostname'],
fields['uuid'],
fields['dataname'],
transpose_axes=True,
parent=self)
return [opDvidRoi], opDvidRoi.Output
except OpDvidVolume.DatasetReadError as e:
raise OpInputDataReader.DatasetReadError(*e.args)
def _attemptOpenAsDvidVolume(self, filePath):
"""
Two ways to specify a dvid volume.
1) via a file that contains the hostname, uuid, and dataset name (1 per line)
2) as a url, e.g. http://localhost:8000/api/node/uuid/dataname
"""
if os.path.splitext(filePath)[1] == ".dvidvol":
with open(filePath) as f:
filetext = f.read()
hostname, uuid, dataname = filetext.splitlines()
opDvidVolume = OpDvidVolume(hostname, uuid, dataname, parent=self)
return [opDvidVolume], opDvidVolume.Output
if "://" not in filePath:
return ([], None) # not a url
url_format = "^protocol://hostname/api/node/uuid/dataname(\\?query_string)?"
for field in [
"protocol", "hostname", "uuid", "dataname", "query_string"
]:
url_format = url_format.replace(field, "(?P<" + field + ">[^?]+)")
match = re.match(url_format, filePath)
if not match:
# DVID is the only url-based format we support right now.
# So if it looks like the user gave a URL that isn't a valid DVID node, then error.
raise OpInputDataReader.DatasetReadError(
"Invalid URL format for DVID: {}".format(filePath))
fields = match.groupdict()
try:
query_string = fields["query_string"]
query_args = {}
if query_string:
query_args = dict(
[s.split("=") for s in query_string.split("&")])
try:
opDvidVolume = OpDvidVolume(fields["hostname"],
fields["uuid"],
fields["dataname"],
query_args,
parent=self)
return [opDvidVolume], opDvidVolume.Output
except:
# Maybe this is actually a roi
opDvidRoi = OpDvidRoi(fields["hostname"],
fields["uuid"],
fields["dataname"],
parent=self)
return [opDvidRoi], opDvidRoi.Output
except OpDvidVolume.DatasetReadError as e:
raise OpInputDataReader.DatasetReadError(*e.args) from e