def _boss_cutout(self, requested_bbox, steps, channel_slice=slice(None)):
bounds = Bbox.clamp(requested_bbox, self.bounds)
if bounds.volume() < 1:
raise ValueError(
'Requested less than one pixel of volume. {}'.format(bounds))
x_rng = [bounds.minpt.x, bounds.maxpt.x]
y_rng = [bounds.minpt.y, bounds.maxpt.y]
z_rng = [bounds.minpt.z, bounds.maxpt.z]
layer_type = 'image' if self.layer_type == 'unknown' else self.layer_type
chan = ChannelResource(
collection_name=self.path.bucket,
experiment_name=self.path.dataset,
name=self.path.layer, # Channel
type=layer_type,
datatype=self.dtype,
)
rmt = BossRemote(boss_credentials)
cutout = rmt.get_cutout(chan,
self.mip,
x_rng,
y_rng,
z_rng,
no_cache=True)
cutout = cutout.T
cutout = cutout.astype(self.dtype)
cutout = cutout[::steps.x, ::steps.y, ::steps.z]
if len(cutout.shape) == 3:
cutout = cutout.reshape(tuple(list(cutout.shape) + [1]))
if self.bounded or self.autocrop or bounds == requested_bbox:
return VolumeCutout.from_volume(self, cutout, bounds)
# This section below covers the case where the requested volume is bigger
# than the dataset volume and the bounds guards have been switched
# off. This is useful for Marching Cubes where a 1px excess boundary
# is needed.
shape = list(requested_bbox.size3()) + [cutout.shape[3]]
renderbuffer = np.zeros(shape=shape, dtype=self.dtype, order='F')
txrx.shade(renderbuffer, requested_bbox, cutout, bounds)
return VolumeCutout.from_volume(self, renderbuffer, requested_bbox)
def __init__(self, host, token, collection, experiment, chanList):
self._collection = collection
self._experiment = experiment
self._bossRemote = BossRemote({'protocol':'https',
'host':host,
'token':token})
self._chanList = {}
for chanDict in chanList:
try:
self._chanList[chanDict['name']] = ChannelResource(chanDict['name'],
collection,
experiment,
'image',
datatype=chanDict['dtype'])
except:
#TODO error handle here
raise Exception("Failed to load")
sys.exit(1)
def setup_channel_boss(remote,
collection,
experiment,
channel,
channel_type='image',
datatype='uint16'):
(exp_setup, coord_actual) = setup_experiment_boss(remote, collection,
experiment)
chan_setup = ChannelResource(channel,
collection,
experiment,
channel_type,
datatype=datatype)
try:
chan_actual = remote.get_project(chan_setup)
return (exp_setup, coord_actual, chan_actual)
except Exception as e:
print(e.message)
def upload(self, image, offset, mip):
shape = Vec(*image.shape[:3])
offset = Vec(*offset)
bounds = Bbox(offset, shape + offset)
if bounds.subvoxel():
raise exceptions.EmptyRequestException(
'Requested less than one pixel of volume. {}'.format(bounds))
if self.autocrop:
image, bounds = autocropfn(self.meta, image, bounds, mip)
offset = bounds.minpt
check_grid_aligned(self.meta,
image,
bounds,
mip,
throw_error=(self.non_aligned_writes == False))
x_rng = [bounds.minpt.x, bounds.maxpt.x]
y_rng = [bounds.minpt.y, bounds.maxpt.y]
z_rng = [bounds.minpt.z, bounds.maxpt.z]
layer_type = 'image' if self.layer_type == 'unknown' else self.meta.layer_type
chan = ChannelResource(
collection_name=self.meta.path.bucket,
experiment_name=self.meta.path.dataset,
name=self.meta.path.layer, # Channel
type=layer_type,
datatype=self.meta.data_type,
)
if image.shape[3] == 1:
image = image.reshape(image.shape[:3])
rmt = BossRemote(boss_credentials)
image = image.T
image = np.asfortranarray(image.astype(self.meta.dtype))
rmt.create_cutout(chan, mip, x_rng, y_rng, z_rng, image)
def create_channel_resource(rmt,
chan_name,
coll_name,
exp_name,
type='image',
base_resolution=0,
sources=[],
datatype='uint16',
new_channel=True):
channel_resource = ChannelResource(chan_name,
coll_name,
exp_name,
type=type,
base_resolution=base_resolution,
sources=sources,
datatype=datatype)
if new_channel:
new_rsc = rmt.create_project(channel_resource)
return new_rsc
return channel_resource
def __init__(self,
resource: Union[BossResource, str],
remote: BossRemote = None):
self._remote = remote or BossRemote(_DEFAULT_BOSS_OPTIONS)
if isinstance(resource, str):
resource = resource.split("://")[-1]
path_items = resource.split("/")
if len(path_items) == 1:
self._resource = self._remote.get_project(
CollectionResource(path_items[0]))
elif len(path_items) == 2:
self._resource = self._remote.get_project(
ExperimentResource(path_items[1], path_items[0]))
elif len(path_items) == 3:
self._resource = self._remote.get_project(
ChannelResource(path_items[2], path_items[0],
path_items[1]))
else:
raise ValueError(f"Invalid resource path: {resource}")
else:
self._resource = resource
class BaseVersionTest(unittest.TestCase):
def setUp(self):
self.resource = CollectionResource('coll1')
self.chanResource = ChannelResource(
'chan1', 'coll1', 'exp1', 'image', 'null descr', 0, 'uint8', 0)
self.annoResource = ChannelResource(
'annChan', 'coll1', 'exp1', 'annotation', 'null descr',
0, 'uint64', 0, sources=['chan1'])
self.test_project = ProjectImpl()
self.test_meta = MetadataImpl()
self.test_volume = VolumeImpl()
self.url_prefix = 'https://api.theboss.io'
##
## Methods used for the project service.
##
def test_build_url_for_list(self):
"""A list operation's URL is different than any other operation. It
uses the plural form of the resource's type name rather than the
resource's name.
"""
actual = self.test_project.build_url(
self.resource, self.url_prefix, 'collection', req_type='list')
self.assertEqual(
self.url_prefix + '/' + self.test_project.version + '/' +
self.test_project.endpoint + '/' + self.resource.name + '/',
actual)
def test_build_url_for_cutout(self):
"""Cutout URLs are also different than standard operations."""
actual = self.test_project.build_url(
self.chanResource, self.url_prefix, 'cutout', req_type='cutout')
coll = self.chanResource.coll_name
exp = self.chanResource.exp_name
chan = self.chanResource.name
self.assertEqual(
self.url_prefix + '/' + self.test_project.version + '/' +
'cutout/' + coll + '/' + exp + '/' + chan,
actual)
def test_build_url_for_cutout_to_black(self):
"""
Test cutout to black URL
"""
actual = self.test_project.build_url(
self.chanResource, self.url_prefix, 'cutout/to_black', req_type='cutout')
coll = self.chanResource.coll_name
exp = self.chanResource.exp_name
chan = self.chanResource.name
expected = "/".join(
[
self.url_prefix,
self.test_project.version,
"cutout/to_black",
coll,
exp,
chan,
]
)
self.assertEqual(expected, actual)
def test_build_url_normal(self):
"""Test standard use of BaseVersion.build_url().
"""
actual = self.test_project.build_url(
self.resource, self.url_prefix, 'collection', req_type='normal')
self.assertEqual(
self.url_prefix + '/' + self.test_project.version + '/' +
self.test_project.endpoint + '/' + self.resource.name,
actual)
def test_get_headers_gives_dict_with_content_type(self):
actual = self.test_project.get_headers('application/json', 'my_token')
self.assertTrue('Content-Type' in actual)
self.assertEqual('application/json', actual['Content-Type'])
def test_get_headers_gives_dict_with_authorization(self):
actual = self.test_project.get_headers('application/json', 'my_token')
self.assertTrue('Authorization' in actual)
self.assertEqual('Token my_token', actual['Authorization'])
def test_get_request(self):
url_prefix = 'https://api.theboss.io'
token = 'foobar'
actual = self.test_project.get_request(
self.resource, 'GET', 'application/json', url_prefix, token,
proj_list_req=False)
self.assertEqual(
'{}/{}/{}/{}'.format(url_prefix, self.test_project.version, self.test_project.endpoint, self.resource.name),
actual.url)
self.assertEqual('Token {}'.format(token), actual.headers['Authorization'])
self.assertEqual('application/json', actual.headers['Content-Type'])
def test_get_group_request(self):
url_prefix = 'https://api.theboss.io'
token = 'foobar'
grp_name = 'fire'
expected = '{}/{}/groups/{}/'.format(
url_prefix, self.test_project.version, grp_name)
actual = self.test_project.get_group_request(
'GET', 'application/json', url_prefix, token, grp_name)
self.assertEqual(expected, actual.url)
def test_get_permission_request(self):
url_prefix = 'https://api.theboss.io'
token = 'foobar'
grp_name = 'fire'
post_data = {"group": grp_name,
"permissions": ['update', 'add', 'delete'],
}
post_data.update(self.chanResource.get_dict_route())
expected = '{}/{}/permissions/'.format(url_prefix, self.test_volume.version)
actual = self.test_project.get_permission_request(
'GET', 'application/json', url_prefix, token, post_data=post_data)
self.assertEqual(expected, actual.url)
def test_get_user_role_request(self):
url_prefix = 'https://api.theboss.io'
token = 'foobar'
user = '******'
role = 'admin'
expected = '{}/{}/sso/user-role/{}/{}'.format(
url_prefix, self.test_project.version, user, role)
actual = self.test_project.get_user_role_request(
'POST', 'application/json', url_prefix, token, user, role)
self.assertEqual(expected, actual.url)
def test_get_user_role_request_no_role(self):
url_prefix = 'https://api.theboss.io'
token = 'foobar'
user = '******'
expected = '{}/{}/sso/user-role/{}'.format(
url_prefix, self.test_project.version, user)
actual = self.test_project.get_user_role_request(
'POST', 'application/json', url_prefix, token, user)
self.assertEqual(expected, actual.url)
def test_get_user_request_just_username(self):
url_prefix = 'https://api.theboss.io'
token = 'foobar'
user = '******'
expected = '{}/{}/sso/user/{}'.format(
url_prefix, self.test_project.version, user)
actual = self.test_project.get_user_request(
'POST', 'application/json', url_prefix, token, user)
self.assertEqual(expected, actual.url)
def test_get_user_request_with_firstname(self):
url_prefix = 'https://api.theboss.io'
token = 'foobar'
user = '******'
first = 'Roger'
expected = '{}/{}/sso/user/{}'.format(
url_prefix, self.test_project.version, user)
expectedData = { 'first_name': first }
actual = self.test_project.get_user_request(
'POST', 'application/json', url_prefix, token, user, first)
self.assertEqual(expected, actual.url)
self.assertDictEqual(expectedData, actual.json)
def test_get_user_request_with_lastname(self):
url_prefix = 'https://api.theboss.io'
token = 'foobar'
user = '******'
last = 'Roger'
expected = '{}/{}/sso/user/{}'.format(
url_prefix, self.test_project.version, user)
expectedData = { 'last_name': last }
actual = self.test_project.get_user_request(
'POST', 'application/json', url_prefix, token, user, last_name=last)
self.assertEqual(expected, actual.url)
self.assertDictEqual(expectedData, actual.json)
def test_get_user_request_with_email(self):
url_prefix = 'https://api.theboss.io'
token = 'foobar'
user = '******'
email = '*****@*****.**'
expected = '{}/{}/sso/user/{}'.format(
url_prefix, self.test_project.version, user)
expectedData = { 'email': email }
actual = self.test_project.get_user_request(
'POST', 'application/json', url_prefix, token, user, email=email)
def test_get_user_request_with_password_and_user(self):
url_prefix = 'https://api.theboss.io'
token = 'foobar'
user = '******'
password = '******'
expected = '{}/{}/sso/user/{}'.format(
url_prefix, self.test_project.version, user)
expectedData = { 'password': password }
actual = self.test_project.get_user_request(
'POST', 'application/json', url_prefix, token, user, password=password)
self.assertEqual(expected, actual.url)
self.assertDictEqual(expectedData, actual.json)
def test_get_user_request_with_password_and_email(self):
url_prefix = 'https://api.theboss.io'
token = 'foobar'
user = '******'
first = 'Roger'
last = 'Dodger'
email = '*****@*****.**'
password = '******'
expected = '{}/{}/sso/user/{}'.format(
url_prefix, self.test_project.version, user)
expectedData = {
'first_name': first, 'last_name': last, 'email': email,
'password': password }
actual = self.test_project.get_user_request(
'POST', 'application/json', url_prefix, token, user, first, last,
email, password)
self.assertEqual(expected, actual.url)
self.assertDictEqual(expectedData, actual.json)
##
## Methods used for the metadata service.
##
def test_build_metadata_url_no_value(self):
key = 'foo'
actual = self.test_meta.build_metadata_url(
self.resource, self.url_prefix, key)
self.assertEqual(
self.url_prefix + '/' + self.test_meta.version + '/' +
self.test_meta.endpoint + '/' + self.resource.name + '/?key=' + key,
actual)
def test_build_metadata_url_key_and_value(self):
key = 'foo'
value = 'bar'
actual = self.test_meta.build_metadata_url(
self.resource, self.url_prefix, key, value)
self.assertEqual(
self.url_prefix + '/' + self.test_meta.version + '/' +
self.test_meta.endpoint + '/' + self.resource.name + '/?key=' +
key + '&value=' + value,
actual)
def test_get_metadata_request(self):
url_prefix = 'https://api.theboss.io'
token = 'foobar'
key = 'version'
actual = self.test_meta.get_metadata_request(
self.resource, 'GET', 'application/json', url_prefix, token, key)
self.assertEqual(
'{}/{}/{}/{}/?key={}'.format(url_prefix, self.test_meta.version,
self.test_meta.endpoint, self.resource.name, key),
actual.url)
self.assertEqual('Token {}'.format(token), actual.headers['Authorization'])
self.assertEqual('application/json', actual.headers['Content-Type'])
##
## Methods used for the volume service.
##
def test_convert_int_list_range_to_str(self):
exp = '2:7'
actual = self.test_volume.convert_int_list_range_to_str([2,7])
self.assertEqual(exp, actual)
def test_convert_int_list_range_to_str_bad_range(self):
with self.assertRaises(RuntimeError):
self.test_volume.convert_int_list_range_to_str([7,5])
def test_convert_int_list_range_to_str_wrong_number_of_elements(self):
with self.assertRaises(RuntimeError):
self.test_volume.convert_int_list_range_to_str([5, 7, 9])
def test_convert_int_list_range_to_str_no_list(self):
with self.assertRaises(RuntimeError):
self.test_volume.convert_int_list_range_to_str('5, 7')
def test_build_cutout_url_no_time_range(self):
res = 0
x_rng_lst = [20, 40]
x_range = '20:40'
y_rng_lst = [50, 70]
y_range = '50:70'
z_rng_lst = [30, 50]
z_range = '30:50'
t_rng_lst = None
actual = self.test_volume.build_cutout_url(
self.chanResource, self.url_prefix,
res, x_rng_lst, y_rng_lst, z_rng_lst, t_rng_lst)
self.assertEqual(
self.url_prefix + '/' + self.test_volume.version + '/' + self.test_volume.endpoint +
'/' + self.chanResource.coll_name + '/' + self.chanResource.exp_name +
'/' + self.chanResource.name + '/' + str(res) + '/' + x_range + '/' +
y_range + '/' + z_range + '/',
actual)
def test_build_cutout_to_black_url_no_time_range(self):
res = 0
x_rng_lst = [20, 40]
x_range = '20:40'
y_rng_lst = [50, 70]
y_range = '50:70'
z_rng_lst = [30, 50]
z_range = '30:50'
t_rng_lst = None
actual = self.test_volume.build_cutout_to_black_url(
self.chanResource, self.url_prefix,
res, x_rng_lst, y_rng_lst, z_rng_lst, t_rng_lst)
expected = '/'.join([
self.url_prefix,
self.test_volume.version,
"cutout/to_black",
self.chanResource.coll_name,
self.chanResource.exp_name,
self.chanResource.name,
str(res),
x_range,
y_range,
z_range,
]) + '/'
self.assertEqual(expected, actual)
def test_build_cutout_url_no_time_range_with_ids(self):
res = 0
x_rng_lst = [20, 40]
x_range = '20:40'
y_rng_lst = [50, 70]
y_range = '50:70'
z_rng_lst = [30, 50]
z_range = '30:50'
t_rng_lst = None
id_list = [2, 7]
id_list_str = '2,7'
actual = self.test_volume.build_cutout_url(
self.chanResource, self.url_prefix,
res, x_rng_lst, y_rng_lst, z_rng_lst, t_rng_lst, id_list)
self.assertEqual(
self.url_prefix + '/' + self.test_volume.version + '/' + self.test_volume.endpoint +
'/' + self.chanResource.coll_name + '/' + self.chanResource.exp_name +
'/' + self.chanResource.name + '/' + str(res) + '/' + x_range + '/' +
y_range + '/' + z_range + '/?filter=' + id_list_str,
actual)
def test_build_cutout_url_with_time_range(self):
res = 0
x_rng_lst = [20, 40]
x_range = '20:40'
y_rng_lst = [50, 70]
y_range = '50:70'
z_rng_lst = [30, 50]
z_range = '30:50'
t_rng_lst = [10, 25]
time_range = '10:25'
actual = self.test_volume.build_cutout_url(
self.chanResource, self.url_prefix,
res, x_rng_lst, y_rng_lst, z_rng_lst, t_rng_lst)
self.assertEqual(
self.url_prefix + '/' + self.test_volume.version + '/' + self.test_volume.endpoint +
'/' + self.chanResource.coll_name + '/' + self.chanResource.exp_name +
'/' + self.chanResource.name + '/' + str(res) + '/' + x_range + '/' +
y_range + '/' + z_range + '/' + time_range + '/',
actual)
def test_build_cutout_to_black_url_with_time_range(self):
res = 0
x_rng_lst = [20, 40]
x_range = '20:40'
y_rng_lst = [50, 70]
y_range = '50:70'
z_rng_lst = [30, 50]
z_range = '30:50'
t_rng_lst = [10, 25]
time_range = '10:25'
actual = self.test_volume.build_cutout_to_black_url(
self.chanResource, self.url_prefix,
res, x_rng_lst, y_rng_lst, z_rng_lst, t_rng_lst)
expected = '/'.join([
self.url_prefix,
self.test_volume.version,
"cutout/to_black",
self.chanResource.coll_name,
self.chanResource.exp_name,
self.chanResource.name,
str(res),
x_range,
y_range,
z_range,
time_range,
]) + '/'
self.assertEqual(expected, actual)
def test_build_cutout_url_with_time_range_and_ids(self):
res = 0
x_rng_lst = [20, 40]
x_range = '20:40'
y_rng_lst = [50, 70]
y_range = '50:70'
z_rng_lst = [30, 50]
z_range = '30:50'
t_rng_lst = [10, 25]
time_range = '10:25'
id_list = [2, 7]
id_list_str = '2,7'
actual = self.test_volume.build_cutout_url(
self.chanResource, self.url_prefix,
res, x_rng_lst, y_rng_lst, z_rng_lst, t_rng_lst, id_list)
self.assertEqual(
self.url_prefix + '/' + self.test_volume.version + '/' + self.test_volume.endpoint +
'/' + self.chanResource.coll_name + '/' + self.chanResource.exp_name +
'/' + self.chanResource.name + '/' + str(res) + '/' + x_range + '/' +
y_range + '/' + z_range + '/' + time_range + '/?filter=' + id_list_str,
actual)
def test_get_cutout_request(self):
url_prefix = 'https://api.theboss.io'
token = 'foobar'
resolution = 0
x_rng_lst = [20, 40]
x_range = '20:40'
y_rng_lst = [50, 70]
y_range = '50:70'
z_rng_lst = [30, 50]
z_range = '30:50'
t_rng_lst = [10, 25]
time_range = '10:25'
data = numpy.random.randint(0, 3000, (15, 20, 20, 20), numpy.uint16)
actual = self.test_volume.get_cutout_request(
self.chanResource, 'GET', 'application/blosc-python', url_prefix, token,
resolution, x_rng_lst, y_rng_lst, z_rng_lst, t_rng_lst, data)
self.assertEqual(
'{}/{}/{}/{}/{}/{}/{}/{}/{}/{}/{}/'.format(url_prefix, self.test_volume.version,
self.test_volume.endpoint, self.chanResource.coll_name,
self.chanResource.exp_name, self.chanResource.name, resolution,
x_range, y_range, z_range, time_range),
actual.url)
self.assertEqual('Token {}'.format(token), actual.headers['Authorization'])
self.assertEqual('application/blosc-python', actual.headers['Content-Type'])
def test_get_cutout_request_with_ids(self):
"""Test request generated for a filtered cutout."""
url_prefix = 'https://api.theboss.io'
token = 'foobar'
resolution = 0
x_rng_lst = [20, 40]
x_range = '20:40'
y_rng_lst = [50, 70]
y_range = '50:70'
z_rng_lst = [30, 50]
z_range = '30:50'
t_rng_lst = [10, 25]
time_range = '10:25'
id_list = [10, 5]
id_list_str = '10,5'
data = numpy.random.randint(0, 3000, (15, 20, 20, 20), numpy.uint16)
actual = self.test_volume.get_cutout_request(
self.chanResource, 'GET', 'application/blosc-python', url_prefix, token,
resolution, x_rng_lst, y_rng_lst, z_rng_lst, t_rng_lst, id_list=id_list)
self.assertEqual(
'{}/{}/{}/{}/{}/{}/{}/{}/{}/{}/{}/?filter={}'.format(url_prefix, self.test_volume.version,
self.test_volume.endpoint, self.chanResource.coll_name,
self.chanResource.exp_name, self.chanResource.name, resolution,
x_range, y_range, z_range, time_range, id_list_str),
actual.url)
self.assertEqual('Token {}'.format(token), actual.headers['Authorization'])
self.assertEqual('application/blosc-python', actual.headers['Content-Type'])
def test_get_cutout_request_with_ids_and_access_mode(self):
"""Test request generated for a filtered cutout."""
url_prefix = 'https://api.theboss.io'
token = 'foobar'
resolution = 0
x_rng_lst = [20, 40]
x_range = '20:40'
y_rng_lst = [50, 70]
y_range = '50:70'
z_rng_lst = [30, 50]
z_range = '30:50'
t_rng_lst = [10, 25]
time_range = '10:25'
id_list = [10, 5]
id_list_str = '10,5'
data = numpy.random.randint(0, 3000, (15, 20, 20, 20), numpy.uint16)
actual = self.test_volume.get_cutout_request(
self.chanResource, 'GET', 'application/blosc-python', url_prefix, token,
resolution, x_rng_lst, y_rng_lst, z_rng_lst, t_rng_lst, id_list=id_list, access_mode=CacheMode.no_cache)
self.assertEqual(
'{}/{}/{}/{}/{}/{}/{}/{}/{}/{}/{}/?filter={}&access-mode=no-cache'.format(url_prefix, self.test_volume.version,
self.test_volume.endpoint, self.chanResource.coll_name,
self.chanResource.exp_name, self.chanResource.name, resolution,
x_range, y_range, z_range, time_range, id_list_str),
actual.url)
self.assertEqual('Token {}'.format(token), actual.headers['Authorization'])
self.assertEqual('application/blosc-python', actual.headers['Content-Type'])
def test_get_reserve_request(self):
url_prefix = 'https://api.theboss.io'
token = 'foobar'
num_ids = 20
actual = self.test_volume.get_reserve_request(
self.annoResource, 'GET', 'application/json', url_prefix, token,
num_ids)
expected = '{}/{}/reserve/{}/{}/{}/{}'.format(
url_prefix, self.test_volume.version, self.annoResource.coll_name,
self.annoResource.exp_name, self.annoResource.name, num_ids)
self.assertEqual(expected, actual.url)
def test_get_bounding_box_request_loose(self):
url_prefix = 'https://api.theboss.io'
token = 'foobar'
resolution = 0
bb_type = 'loose'
id = 55555
actual = self.test_volume.get_bounding_box_request(
self.annoResource, 'GET', 'application/json', url_prefix, token,
resolution, id, bb_type)
expected = '{}/{}/boundingbox/{}/{}/{}/{}/{}/?type={}'.format(
url_prefix, self.test_volume.version, self.annoResource.coll_name,
self.annoResource.exp_name, self.annoResource.name, resolution,
id, bb_type)
self.assertEqual(expected, actual.url)
def test_build_ids_url(self):
url_prefix = 'https://api.theboss.io'
resolution = 0
x_range = [0, 100]
x_range_str = '0:100'
y_range = [10, 50]
y_range_str = '10:50'
z_range = [20, 42]
z_range_str = '20:42'
t_range = [0, 1]
t_range_str = '0:1'
actual = self.test_volume.build_ids_url(
self.annoResource, url_prefix, resolution,
x_range, y_range, z_range, t_range)
expected = '{}/{}/ids/{}/{}/{}/{}/{}/{}/{}/{}/'.format(
url_prefix, self.test_volume.version, self.annoResource.coll_name,
self.annoResource.exp_name, self.annoResource.name,
resolution, x_range_str, y_range_str, z_range_str, t_range_str)
self.assertEqual(expected, actual)
def test_get_ids_request(self):
url_prefix = 'https://api.theboss.io'
token = 'foobar'
resolution = 0
x_range = [0, 100]
x_range_str = '0:100'
y_range = [10, 50]
y_range_str = '10:50'
z_range = [20, 42]
z_range_str = '20:42'
t_range = [0, 1]
t_range_str = '0:1'
actual = self.test_volume.get_ids_request(
self.annoResource, 'GET', 'application/json', url_prefix, token,
resolution, x_range, y_range, z_range, t_range)
expected = '{}/{}/ids/{}/{}/{}/{}/{}/{}/{}/{}/'.format(
url_prefix, self.test_volume.version, self.annoResource.coll_name,
self.annoResource.exp_name, self.annoResource.name,
resolution, x_range_str, y_range_str, z_range_str, t_range_str)
self.assertEqual(expected, actual.url)
def test_convert_int_list_to_comma_sep_str_1_ele(self):
"""Test with a list with one element."""
expected = '2'
actual = self.test_volume.convert_int_list_to_comma_sep_str([2])
self.assertEqual(expected, actual)
def test_convert_int_list_to_comma_sep_str_multi_ele(self):
"""Test with a list with multiple elements."""
expected = '2,6,9'
actual = self.test_volume.convert_int_list_to_comma_sep_str([2, 6, 9])
self.assertEqual(expected, actual)
def test_setting_datatype_means_cutout_ready(self):
chan = ChannelResource('somechan', 'foo', 'bar')
chan.datatype = 'uint16'
self.assertTrue(chan.cutout_ready)
def test_setting_datatype_means_cutout_ready_at_construction(self):
chan = ChannelResource('somechan', 'foo', 'bar', datatype='uint8')
self.assertTrue(chan.cutout_ready)
def test_channel_defaults_to_uint8(self):
chan = ChannelResource('somechan', 'foo', 'bar')
self.assertEqual('uint8', chan.datatype)
def test_init_status_false(self):
chan = ChannelResource('somechan', 'foo', 'bar')
self.assertFalse(chan.cutout_ready)
def setUp(self):
self.chan = ChannelResource('mychan', 'foo', 'bar', 'image')
class TestChannelResource(unittest.TestCase):
def setUp(self):
self.chan = ChannelResource('mychan', 'foo', 'bar', 'image')
def test_init_status_false(self):
chan = ChannelResource('somechan', 'foo', 'bar')
self.assertFalse(chan.cutout_ready)
def test_channel_defaults_to_uint8(self):
chan = ChannelResource('somechan', 'foo', 'bar')
self.assertEqual('uint8', chan.datatype)
def test_setting_datatype_means_cutout_ready_at_construction(self):
chan = ChannelResource('somechan', 'foo', 'bar', datatype='uint8')
self.assertTrue(chan.cutout_ready)
def test_setting_datatype_means_cutout_ready(self):
chan = ChannelResource('somechan', 'foo', 'bar')
chan.datatype = 'uint16'
self.assertTrue(chan.cutout_ready)
def test_default_source_is_empty(self):
self.assertEqual([], self.chan.sources)
def test_default_related_is_empty(self):
self.assertEqual([], self.chan.related)
def test_source_string_stored_as_list(self):
self.chan.sources = 'foo'
self.assertEqual(['foo'], self.chan.sources)
def test_related_string_stored_as_list(self):
self.chan.related = 'foo'
self.assertEqual(['foo'], self.chan.related)
def test_source_list(self):
self.chan.source = ['foo', 'bar']
self.assertEqual(['foo', 'bar'], self.chan.source)
def test_related_list(self):
self.chan.related = ['foo', 'bar']
self.assertEqual(['foo', 'bar'], self.chan.related)
def test_valid_volume(self):
self.assertTrue(self.chan.valid_volume())
def test_get_route(self):
self.assertEqual(
'{}/experiment/{}/channel/{}'.format(self.chan.coll_name,
self.chan.exp_name,
self.chan.name),
self.chan.get_route())
def test_get_list_route(self):
self.assertEqual(
'{}/experiment/{}/channel/'.format(self.chan.coll_name,
self.chan.exp_name),
self.chan.get_list_route())
def test_validate_datatype_uint8(self):
exp = 'uint8'
self.assertEqual(exp, self.chan.validate_datatype(exp))
def test_validate_datatype_uint16(self):
exp = 'uint16'
self.assertEqual(exp, self.chan.validate_datatype(exp))
def test_validate_datatype_uint64(self):
exp = 'uint64'
self.assertEqual(exp, self.chan.validate_datatype(exp))
def test_validate_datatype_bad(self):
with self.assertRaises(ValueError):
self.chan.validate_datatype('bigint')
def __init__(
self,
channel: Union[ChannelResource, Tuple, str],
resolution: int = 0,
volume_provider: VolumeProvider = None,
axis_order: str = AxisOrder.ZYX,
create_new: bool = False,
description: Optional[str] = None,
dtype: Optional[str] = None,
extents: Optional[Tuple[int, int, int]] = None,
voxel_size: Optional[Tuple[int, int, int]] = None,
voxel_unit: Optional[str] = None,
downsample_levels: int = 6,
downsample_method: Optional[str] = "anisotropic",
coordinate_frame_name: Optional[str] = None,
coordinate_frame_desc: Optional[str] = None,
collection_desc: Optional[str] = None,
experiment_desc: Optional[str] = None,
source_channel: Optional[str] = None,
boss_config: Optional[dict] = None,
) -> None:
"""
Construct a new intern-backed array.
Arguments:
channel (intern.resource.boss.ChannelResource): The channel from
which data will be downloaded.
resolution (int: 0): The native resolution or MIP to use
volume_provider (VolumeProvider): The remote-like to use
axis_order (str = AxisOrder.ZYX): The axis-ordering to use for data
cutouts. Defaults to ZYX. DOES NOT affect the `voxel_size` or
`extents` arguments to this constructor.
create_new (bool: False): Whether to create new Resources if they
do not exist. Does not work with public token.
dtype (str): Only required if `create_new = True`. Specifies the
numpy-style datatype for this new dataset (e.g. "uint8").
description (str): Only required if `create_new = True`. Sets the
description for the newly-created collection, experiment,
channel, and coordframe resources.
extents: Optional[Tuple[int, int, int]]: Only required if
`create_new = True`. Specifies the total dataset extents of
this new dataset, in ZYX order.
voxel_size: Optional[Tuple[int, int, int]]: Only required if
`create_new = True`. Specifies the voxel dimensions of this new
dataset, in ZYX order.
voxel_unit: Optional[str]: Only required if `create_new = True`.
Specifies the voxel-dimension unit. For example, "nanometers".
downsample_levels (int: 6): The number of downsample levels.
downsample_method (Optional[str]): The type of downsample to use.
If unset, defaults to 'anisotropic'.
coordinate_frame_name (Optional[str]): If set, the name to use for
the newly created coordinate frame. If not set, the name of the
coordinate frame will be chosen automatically.
coordinate_frame_desc (Optional[str]): If set, the description text
to use for the newly created coordinate frame. If not set, the
description will be chosen automatically.
collection_desc (Optional[str]): The description text to use for a
newly created collection. If not set, the description will be
chosen automatically.
experiment_desc (Optional[str]): The description text to use for a
newly created experiment. If not set, the description will be
chosen automatically.
source_channel (Optional[str]): The channel to use as the source
for this new channel, if `create_new` is True and this is
going to be an annotation channel (dtype!=uint8).
boss_config (Optional[dict]): The BossRemote configuration dict to
use in order to authenticate with a BossDB remote. This option
is mutually exclusive with the VolumeProvider configuration. If
the `volume_provider` arg is set, this will be ignored.
"""
self.axis_order = axis_order
# Handle inferring the remote from the channel:
volume_provider = volume_provider or _infer_volume_provider(channel)
if volume_provider is None:
if boss_config:
volume_provider = _BossDBVolumeProvider(
BossRemote(boss_config))
else:
volume_provider = _BossDBVolumeProvider()
# Handle custom Remote:
self.volume_provider = volume_provider
if create_new:
if self.volume_provider.get_vp_type() != "bossdb":
raise ValueError(
"Creating new resources with a non-bossdb volume provider is not currently supported."
)
# We'll need at least `extents` and `voxel_size`.
description = description or "Created with intern"
dtype = dtype or "uint8"
if extents is None:
raise ValueError(
"If `create_new` is True, you must specify the extents of the new coordinate frame as a [x, y, z]."
)
if voxel_size is None:
raise ValueError(
"If `create_new` is True, you must specify the voxel_size of the new coordinate frame as a [x, y, z]."
)
uri = _parse_bossdb_uri(channel)
# create collection if it doesn't exist:
try:
# Try to get an existing collection:
collection = self.volume_provider.get_project(
CollectionResource(uri.collection))
except:
# Create the collection:
collection = CollectionResource(uri.collection,
description=collection_desc
or description)
self.volume_provider.create_project(collection)
# create coordframe if it doesn't exist:
try:
# Try to get an existing coordframe:
coordframe = self.volume_provider.get_project(
CoordinateFrameResource(
coordinate_frame_name
or f"CF_{uri.collection}_{uri.experiment}"))
except:
# Default to nanometers if a voxel unit isn't provided
voxel_unit = voxel_unit or "nanometers"
# Create the coordframe:
coordframe = CoordinateFrameResource(
coordinate_frame_name
or f"CF_{uri.collection}_{uri.experiment}",
description=coordinate_frame_desc or description,
x_start=0,
y_start=0,
z_start=0,
x_stop=extents[2],
y_stop=extents[1],
z_stop=extents[0],
x_voxel_size=voxel_size[2],
y_voxel_size=voxel_size[1],
z_voxel_size=voxel_size[0],
voxel_unit=voxel_unit,
)
self.volume_provider.create_project(coordframe)
# create experiment if it doesn't exist:
try:
# Try to get an existing experiment:
experiment = self.volume_provider.get_project(
ExperimentResource(uri.experiment, uri.collection))
except:
# Create the experiment:
experiment = ExperimentResource(
uri.experiment,
uri.collection,
description=experiment_desc or description,
coord_frame=coordframe.name,
num_hierarchy_levels=downsample_levels,
hierarchy_method=downsample_method,
)
self.volume_provider.create_project(experiment)
# create channel if it doesn't exist:
try:
# Try to get an existing channel:
channel = self.volume_provider.get_project(
ChannelResource(uri.channel, uri.collection,
uri.experiment))
except:
# Create the channel:
channel = ChannelResource(
uri.channel,
uri.collection,
uri.experiment,
description=description,
type="image"
if dtype in ["uint8", "uint16"] else "annotation",
datatype=dtype,
sources=[source_channel] if source_channel else [],
)
self.volume_provider.create_project(channel)
self.resolution = resolution
# If the channel is set as a Resource, then use that resource.
if isinstance(channel, ChannelResource):
self._channel = channel
# If it is set as a string, then parse the channel and generate an
# intern.Resource from a bossDB URI.
else: # if isinstance(channel, str):
uri = {
"BossDB": _parse_bossdb_uri,
"CloudVolumeOpenData": _parse_cloudvolume_uri,
}[self.volume_provider.get_vp_type()](channel)
self.resolution = (uri.resolution if not (uri.resolution is None)
else self.resolution)
self._channel = self.volume_provider.get_channel(
uri.channel, uri.collection, uri.experiment)
# Set col/exp/chan based upon the channel or URI provided.
self.collection_name = self._channel.coll_name
self.experiment_name = self._channel.exp_name
self.channel_name = self._channel.name
# Create a pointer to the metadata for the channel.
self._channel_metadata = Metadata(self._channel)