def test_isdvidversion(self):
"""Tests is_dvidversion function.
"""
service = DVIDServerService(dvidserver)
uuid = service.create_new_repo("foo", "bar")
self.assertTrue(is_dvidversion(dvidserver, uuid))
self.assertFalse(is_dvidversion(dvidserver, uuid + "JUNK"))
def test_create_label_instance(self):
"""Test creation of labelarray and block size fetch
"""
service = DVIDServerService(dvidserver)
uuid = service.create_new_repo("foo", "bar")
create_label_instance(dvidserver, uuid, "labels", typename='labelmap')
blocksize = get_blocksize(dvidserver, uuid, "labels")
self.assertEqual(blocksize, (64, 64, 64))
def createrepo():
"""Creates a repo which results in a new gbucket.
"""
try:
ds = DVIDServerService(DVIDLOCATION)
uuid = ds.create_new_repo("test", "test description")
except Exception as e:
return False, str(e)
return True, uuid
def createrepo():
"""Creates a repo which results in a new gbucket.
"""
try:
ds = DVIDServerService(DVIDLOCATION)
uuid = ds.create_new_repo("test", "test description")
except Exception as e:
return False, str(e)
return True, uuid
def test_create_rawarray8(self):
"""Test creation of rawarray and block size fetch.
"""
service = DVIDServerService(dvidserver)
uuid = service.create_new_repo("foo", "bar")
create_rawarray8(dvidserver, uuid, "gray", (32, 16, 14),
Compression.JPEG)
blocksize = get_blocksize(dvidserver, uuid, "gray")
self.assertEqual(blocksize, (32, 16, 14))
def test_isdatainstance(self):
"""Tests is_datainstance function.
"""
service = DVIDServerService(dvidserver)
uuid = service.create_new_repo("foo", "bar")
ns = DVIDNodeService(dvidserver, uuid)
ns.create_labelblk("labels")
self.assertTrue(is_datainstance(dvidserver, uuid, "labels"))
self.assertFalse(is_datainstance(dvidserver, uuid, "labels2"))
def setUpClass(cls):
server_service = DVIDServerService(TEST_DVID_SERVER)
cls.uuid = server_service.create_new_repo("foo", "bar")
cls.instance = 'labels_test_mask_utils'
cls.labels = np.zeros((256, 256, 256), np.uint64)
cls.labels[50, 50, 40:140] = 1
cls.labels[50, 60:200, 30] = 2
ns = DVIDNodeService(TEST_DVID_SERVER, cls.uuid)
ns.create_label_instance(cls.instance, 64)
ns.put_labels3D(cls.instance, cls.labels, (0, 0, 0))
def get_testrepo_root_uuid():
connection = DVIDConnection(TEST_DVID_SERVER)
status, body, error_message = connection.make_request( "/repos/info", ConnectionMethod.GET)
assert status == http.client.OK, "Request for /repos/info returned status {}".format( status )
assert error_message == ""
repos_info = json.loads(body)
test_repos = [uuid_repo_info for uuid_repo_info in list(repos_info.items()) if uuid_repo_info[1] and uuid_repo_info[1]['Alias'] == 'testrepo']
if test_repos:
uuid = test_repos[0][0]
return str(uuid)
else:
from libdvid import DVIDServerService
server = DVIDServerService(TEST_DVID_SERVER)
uuid = server.create_new_repo("testrepo", "This repo is for unit tests to use and abuse.");
return str(uuid)
def get_testrepo_root_uuid():
connection = DVIDConnection(TEST_DVID_SERVER)
status, body, error_message = connection.make_request( "/repos/info", ConnectionMethod.GET)
assert status == httplib.OK, "Request for /repos/info returned status {}".format( status )
assert error_message == ""
repos_info = json.loads(body)
test_repos = filter( lambda (uuid, repo_info): repo_info and repo_info['Alias'] == 'testrepo',
repos_info.items() )
if test_repos:
uuid = test_repos[0][0]
return str(uuid)
else:
from libdvid import DVIDServerService
server = DVIDServerService(TEST_DVID_SERVER)
uuid = server.create_new_repo("testrepo", "This repo is for unit tests to use and abuse.");
return str(uuid)
def get_testrepo_root_uuid():
connection = DVIDConnection(TEST_DVID_SERVER, "*****@*****.**", "myapp")
status, body, _error_message = connection.make_request(
"/repos/info", ConnectionMethod.GET)
repos_info = json.loads(body)
test_repos = [
uuid_repo_info for uuid_repo_info in list(repos_info.items())
if uuid_repo_info[1] and uuid_repo_info[1]['Alias'] == 'testrepo'
]
if test_repos:
uuid = test_repos[0][0]
return str(uuid)
else:
from libdvid import DVIDServerService
server = DVIDServerService(TEST_DVID_SERVER)
uuid = server.create_new_repo(
"testrepo", "This repo is for unit tests to use and abuse.")
return str(uuid)
def get_testrepo_root_uuid():
connection = DVIDConnection(TEST_DVID_SERVER)
status, body, error_message = connection.make_request("/repos/info", ConnectionMethod.GET)
assert status == http.client.OK, "Request for /repos/info returned status {}".format(status)
assert error_message == ""
repos_info = json.loads(body)
test_repos = [
uuid_repo_info
for uuid_repo_info in list(repos_info.items())
if uuid_repo_info[1] and uuid_repo_info[1]["Alias"] == "testrepo"
]
if test_repos:
uuid = test_repos[0][0]
return str(uuid)
else:
from libdvid import DVIDServerService
server = DVIDServerService(TEST_DVID_SERVER)
uuid = server.create_new_repo("testrepo", "This repo is for unit tests to use and abuse.")
return str(uuid)
def test_dvidpadlabels(self):
"""Check padding data with DVID labels.
"""
service = DVIDServerService(dvidserver)
uuid = service.create_new_repo("foo", "bar")
ns = DVIDNodeService(dvidserver, uuid)
ns.create_labelblk("labels")
arr = np.random.randint(12442, size=(58, 58, 58)).astype(np.uint64)
arr2 = np.zeros((64, 64, 64), np.uint64)
arr2[0:58, 0:58, 0:58] = arr
# load gray data
ns.put_labels3D("labels", arr2, (0, 0, 0))
# load shifted data for comparison
arr2[6:64, 6:64, 6:64] = arr
# read and pad data
schema = partitionSchema(PartitionDims(32, 64, 64),
enablemask=True,
padding=8,
blank_delimiter=99999)
volpart = volumePartition(0, VolumeOffset(6, 6, 6))
partitions = schema.partition_data([(volpart, arr)])
# fetch with mask
dvidreader = dvidSrc(dvidserver, uuid, "labels", partitions)
newparts = dvidreader.extract_volume()
self.assertEqual(len(newparts), 2)
for (part, vol) in newparts:
if part.get_offset().z == 0:
match = np.array_equal(arr2[0:32, :, :], vol)
self.assertTrue(match)
else:
match = np.array_equal(arr2[32:64, :, :], vol)
self.assertTrue(match)
def test_sycns(self):
"""Test sync check and setting a sync.
"""
service = DVIDServerService(dvidserver)
uuid = service.create_new_repo("foo", "bar")
create_label_instance(dvidserver, uuid, "labels")
# check if labels is listening to labels2
self.assertFalse(has_sync(dvidserver, uuid, "labels", "bodies"))
# create labelvol and sync to it
conn = DVIDConnection(dvidserver)
endpoint = "/repo/" + uuid + "/instance"
data = {"typename": "labelvol", "dataname": "bodies"}
conn.make_request(endpoint, ConnectionMethod.POST,
json.dumps(data).encode())
set_sync(dvidserver, uuid, "labels", "bodies")
self.assertTrue(has_sync(dvidserver, uuid, "labels", "bodies"))
def create_repo(self, name, description=""):
"""Create repo.
Note:
DVID does not require unique names but unique names
will be enforced through this interface. This will
simplify access for most common use cases. In general,
users should use the web console and specific version
ids to ensure access to the desired data.
Args:
name (str): name of DVID respository (must be unique)
description (str): description of repository
"""
try:
curr_repos = self.list_repos()
for (reponame, uuid) in curr_repos:
if reponame == name:
raise DicedException("Repo name already exists")
service = DVIDServerService(self._server)
uuid = service.create_new_repo(name, description)
except DVIDException as err:
raise DicedException("Failed to create repo")
def test_dvidfetchgray(self):
"""Check reading grayscale from DVID from partitions.
This also checks basic iteration and overwrite of
previous data.
"""
service = DVIDServerService(dvidserver)
uuid = service.create_new_repo("foo", "bar")
ns = DVIDNodeService(dvidserver, uuid)
ns.create_grayscale8("gray")
arr = np.random.randint(255, size=(64, 64, 64)).astype(np.uint8)
# load gray data
ns.put_gray3D("gray", arr, (0, 0, 0))
# read data
schema = partitionSchema(PartitionDims(32, 64, 64))
volpart = volumePartition(0, VolumeOffset(0, 0, 0))
overwrite = np.random.randint(255, size=(64, 64, 64)).astype(np.uint8)
partitions = schema.partition_data([(volpart, overwrite)])
dvidreader = dvidSrc(dvidserver,
uuid,
"gray",
partitions,
maskonly=False)
newparts = dvidreader.extract_volume()
self.assertEqual(len(newparts), 2)
for (part, vol) in newparts:
if part.get_offset().z == 0:
match = np.array_equal(arr[0:32, :, :], vol)
self.assertTrue(match)
else:
match = np.array_equal(arr[32:64, :, :], vol)
self.assertTrue(match)
# test iteration
dvidreader2 = dvidSrc(dvidserver,
uuid,
"gray",
partitions,
maskonly=False)
newparts2 = []
for newpart in dvidreader2:
self.assertEqual(len(newpart), 1)
newparts2.extend(newpart)
self.assertEqual(len(newparts2), 2)
for (part, vol) in newparts2:
if part.get_offset().z == 0:
match = np.array_equal(arr[0:32, :, :], vol)
self.assertTrue(match)
else:
match = np.array_equal(arr[32:64, :, :], vol)
self.assertTrue(match)
help='verbose logs')
args = parser.parse_args()
if args.verbose:
logging.basicConfig(level=logging.DEBUG)
else:
logging.basicConfig(level=logging.INFO)
# initialize plugin manager
plugin_manager = TrackingPluginManager(verbose=False)
image_provider = plugin_manager.getImageProvider()
# create dataset on server and get uuid
server_address = args.dvidAddress
server_service = DVIDServerService(server_address)
uuid = server_service.create_new_repo(args.datasetName, "description")
logging.info('UUID:\n{}'.format(uuid))
# get node service
node_service = DVIDNodeService(server_address, uuid)
# get dataset size and store in dvid
shape = image_provider.getImageShape(args.ilpFilename, args.labelImagePath)
time_range = image_provider.getTimeRange(args.ilpFilename, args.labelImagePath)
if args.timeRange is not None:
time_range = (max(time_range[0], args.timeRange[0]), min(time_range[1], args.timeRange[1]))
logging.info('Uploading time range {} to {}'.format(time_range, server_address))
keyvalue_store = "config"
node_service.create_keyvalue(keyvalue_store)
settings = { "shape": shape, "time_range": time_range }
node_service.put(keyvalue_store, "imageInfo", json.dumps(settings))
parser = argparse.ArgumentParser(description="Batch mode nrrd file to dvid migration script")
existingNode = parser.add_argument_group('existing node', 'for working with a node that already exists on the dvid server')
parser.add_argument('address', metavar='address', help='address to a valid dvid server in the form x.x.x.x:yyyy')
parser.add_argument('file', metavar='nrrdfile', help='filepath for uploading to dvid')
existingNode.add_argument('--uuid', '-u', metavar='uuid', help='minimal uid of the node to access on the dvid server')
newNode = parser.add_argument_group('new node', 'for creating a new node before migrating the nrrd files')
newNode.add_argument('--alias', '-a', metavar='alias', help='alias for a new node to create')
newNode.add_argument('--description', '-d', metavar='description', help='description for new node')
newNode.add_argument('--segmentation', '-s', action='store_true', help='flags data as a segmentation block in the case that there was no indication in the header')
args = parser.parse_args()
addr = args.address
if args.alias:
service = DVIDServerService(addr)
uid = service.create_new_repo(args.alias, args.description)
else:
uid = args.uuid
def push_to_dvid(method, handle, data, preoffset=(0, 0, 0), throttle=False, compress=True, chunkDepth=512):
"""Function for pushing to DVID."""
zsize = data.shape[0]
numsplits = zsize / 512
offset = 0
pdb.set_trace()
for i in xrange(numsplits):
seg = data[i * chunkDepth:(i + 1) * chunkDepth, :, :]
offsetTuple = (preoffset[0] + i * chunkDepth, preoffset[1], preoffset[2])
method(handle, seg, offsetTuple, throttle, compress)
def main():
# Read cmd-line args
parser = argparse.ArgumentParser()
parser.add_argument("--hostname", default="localhost:8000")
parser.add_argument(
"--uuid",
required=False,
help=
"The node to upload to. If not provided, a new repo will be created (see --new-repo-alias)."
)
parser.add_argument(
"--data-name",
required=False,
help=
"The name of the data instance to modify. If it doesn't exist, it will be created first."
)
parser.add_argument(
"--new-repo-alias",
required=False,
help="If no uuid is provided, a new repo is created, with this name.")
parser.add_argument("input_file",
help="For example: /tmp/myfile.h5/dataset")
args = parser.parse_args()
if '.h5' not in args.input_file:
sys.stderr.write("File name does not indicate hdf5.\n")
sys.exit(1)
filepath, dset_name = args.input_file.split('.h5')
filepath += '.h5'
if not dset_name:
sys.stderr.write(
"You must provide a dataset name, e.g. myfile.h5/mydataset\n")
sys.exit(1)
if not os.path.exists(filepath):
sys.stderr.write("File doesn't exist: {}\n".format(filepath))
sys.exit(1)
# If no uuid given, create a new repo on the server
uuid = args.uuid
if uuid is None:
alias = args.new_repo_alias or "testrepo"
server = DVIDServerService(args.hostname)
uuid = server.create_new_repo(
alias, "This is a test repo loaded with data from ".format(
args.input_file))
uuid = str(uuid)
# Read the input data from the file
print("Reading {}{}".format(filepath, dset_name))
with h5py.File(filepath) as f_in:
data = f_in[dset_name][:]
# We assume data is 3D or 4D, in C-order
# We adjust it to 4D, fortran-order
if data.ndim == 3:
data = data[..., None]
data = data.transpose()
assert data.flags['F_CONTIGUOUS'], "Data is not contiguous!"
assert data.ndim == 4, "Data must be 3D with axes zyx or 4D with axes zyxc (C-order)"
assert data.shape[
0] == 1, "Data must have exactly 1 channel, not {}".format(
data.shape[0])
# Choose a default data instance name if necessary
if data.dtype == numpy.uint8:
data_name = args.data_name or "grayscale"
elif data.dtype == numpy.uint64:
data_name = args.data_name or "segmentation"
else:
sys.stderr.write("Unsupported dtype: {}\n".format(data.dtype))
sys.exit(1)
# Create the new data instance if it doesn't exist already
try:
metadata = VoxelsAccessor.get_metadata(args.hostname, uuid, data_name)
print("Data instance '{}' already exists. Will update.".format(
data_name))
except DVIDException:
print("Creating new data instance: {}".format(data_name))
metadata = VoxelsMetadata.create_default_metadata(
data.shape, data.dtype, 'cxyz', 1.0, 'nanometers')
VoxelsAccessor.create_new(args.hostname, uuid, data_name, metadata)
# Finally, push the data to the server
print("Pushing data to {}".format('{}/api/node/{}/{}'.format(
args.hostname, uuid, data_name)))
accessor = VoxelsAccessor(args.hostname, uuid, data_name)
accessor.post_ndarray((0, 0, 0, 0), data.shape, data)
print("DONE.")
def get_testrepo_root_uuid():
from libdvid import DVIDServerService
server = DVIDServerService(TEST_DVID_SERVER)
uuid = server.create_new_repo(
"testrepo", "This repo is for unit tests to use and abuse.")
return str(uuid)
def get_testrepo_root_uuid():
from libdvid import DVIDServerService
server = DVIDServerService(TEST_DVID_SERVER)
uuid = server.create_new_repo("testrepo", "This repo is for unit tests to use and abuse.");
return str(uuid)
def main():
# Read cmd-line args
parser = argparse.ArgumentParser()
parser.add_argument("--hostname", default="localhost:8000")
parser.add_argument("--uuid", required=False, help="The node to upload to. If not provided, a new repo will be created (see --new-repo-alias).")
parser.add_argument("--data-name", required=False, help="The name of the data instance to modify. If it doesn't exist, it will be created first.")
parser.add_argument("--new-repo-alias", required=False, help="If no uuid is provided, a new repo is created, with this name.")
parser.add_argument("input_file", help="For example: /tmp/myfile.h5/dataset")
args = parser.parse_args()
if '.h5' not in args.input_file:
sys.stderr.write("File name does not indicate hdf5.\n")
sys.exit(1)
filepath, dset_name = args.input_file.split('.h5')
filepath += '.h5'
if not dset_name:
sys.stderr.write("You must provide a dataset name, e.g. myfile.h5/mydataset\n")
sys.exit(1)
if not os.path.exists(filepath):
sys.stderr.write("File doesn't exist: {}\n".format(filepath))
sys.exit(1)
# If no uuid given, create a new repo on the server
uuid = args.uuid
if uuid is None:
alias = args.new_repo_alias or "testrepo"
server = DVIDServerService(args.hostname)
uuid = server.create_new_repo(alias, "This is a test repo loaded with data from ".format(args.input_file))
uuid = str(uuid)
# Read the input data from the file
print("Reading {}{}".format( filepath, dset_name ))
with h5py.File(filepath) as f_in:
data = f_in[dset_name][:]
# We assume data is 3D or 4D, in C-order
# We adjust it to 4D, fortran-order
if data.ndim == 3:
data = data[...,None]
data = data.transpose()
assert data.flags['F_CONTIGUOUS'], "Data is not contiguous!"
assert data.ndim == 4, "Data must be 3D with axes zyx or 4D with axes zyxc (C-order)"
assert data.shape[0] == 1, "Data must have exactly 1 channel, not {}".format( data.shape[0] )
# Choose a default data instance name if necessary
if data.dtype == numpy.uint8:
data_name = args.data_name or "grayscale"
elif data.dtype == numpy.uint64:
data_name = args.data_name or "segmentation"
else:
sys.stderr.write("Unsupported dtype: {}\n".format(data.dtype))
sys.exit(1)
# Create the new data instance if it doesn't exist already
try:
metadata = VoxelsAccessor.get_metadata(args.hostname, uuid, data_name)
print("Data instance '{}' already exists. Will update.".format( data_name ))
except DVIDException:
print("Creating new data instance: {}".format( data_name ))
metadata = VoxelsMetadata.create_default_metadata(data.shape, data.dtype, 'cxyz', 1.0, 'nanometers')
VoxelsAccessor.create_new(args.hostname, uuid, data_name, metadata)
# Finally, push the data to the server
print("Pushing data to {}".format( '{}/api/node/{}/{}'.format( args.hostname, uuid, data_name ) ))
accessor = VoxelsAccessor(args.hostname, uuid, data_name)
accessor.post_ndarray((0,0,0,0), data.shape, data)
print("DONE.")