def to_volumecutout(img,
image_type,
resolution=None,
offset=None,
hostname='localhost'):
from cloudvolume.volumecutout import VolumeCutout
if type(img) == VolumeCutout:
try:
img.dataset_name # check if it's an intact VolumeCutout
return img
except AttributeError:
pass
resolution = getresolution(img, resolution)
offset = getoffset(img, offset)
return VolumeCutout(
buf=img,
path=ExtractedPath('mem', hostname, '/', '', '', '', ''),
cloudpath='IN MEMORY',
resolution=resolution,
mip=-1,
layer_type=image_type,
bounds=Bbox(offset, offset + Vec(*(img.shape[:3]))),
handle=None,
)
def view(img,
segmentation=False,
resolution=None,
offset=None,
hostname="localhost",
port=DEFAULT_PORT):
from cloudvolume.volumecutout import VolumeCutout
img = to3d(img)
resolution = getresolution(img, resolution)
offset = getoffset(img, offset)
# Makes sense for viewing not segmentation
# which requires uints currently. (Jan. 2019)
if np.dtype(img.dtype).itemsize == 8 and not np.issubdtype(
img.dtype, np.float64):
print(
yellow("""
Converting {} to float64 for display.
Javascript does not support native 64-bit integer arrays.
""".format(img.dtype)))
img = img.astype(np.float64)
cutout = VolumeCutout(
buf=img,
path=ExtractedPath('mem', hostname, '/', '', '', '', ''),
cloudpath='IN MEMORY',
resolution=resolution,
mip=-1,
layer_type=('segmentation' if segmentation else 'image'),
bounds=Bbox(offset, offset + Vec(*(img.shape[:3]))),
handle=None,
)
return run([cutout], hostname=hostname, port=port)
def view(
img, segmentation=False, resolution=None, offset=None,
hostname="localhost", port=DEFAULT_PORT
):
from cloudvolume.volumecutout import VolumeCutout
img = to3d(img)
resolution = getresolution(img, resolution)
offset = getoffset(img, offset)
cutout = VolumeCutout(
buf=img,
path=ExtractedPath('mem', hostname, '/', '', '', '', ''),
cloudpath='IN MEMORY',
resolution=resolution,
mip=-1,
layer_type=('segmentation' if segmentation else 'image'),
bounds=Bbox( offset, offset + Vec(*(img.shape[:3])) ),
handle=None,
)
return run([ cutout ], hostname=hostname, port=port)
def test_path_extraction():
extract = paths.extract(r'file://C:\wow\this\is\a\cool\path', windows=True, disable_toabs=True)
print(extract)
assert extract.protocol == 'file'
assert extract.bucket == 'C:\\wow\\'
# on linux the toabs prepends the current path because it
# doesn't understand C:\... so we can't test that here.
# assert extract.path == 'this\\is\\a\\cool\\path'
try:
extract = paths.strict_extract(r'file://C:\wow\this\is\a\cool\path', windows=False, disable_toabs=True)
assert False
except UnsupportedProtocolError:
pass
def shoulderror(url):
try:
paths.strict_extract(url)
assert False, url
except:
pass
def okgoogle(url):
path = paths.strict_extract(url)
assert path.protocol == 'gs', url
assert path.bucket == 'bucket', url
assert path.intermediate_path == '', url
assert path.dataset == 'dataset', url
assert path.layer == 'layer', url
okgoogle('gs://bucket/dataset/layer')
shoulderror('s4://dataset/layer')
shoulderror('dataset/layer')
shoulderror('s3://dataset')
firstdir = lambda x: '/' + x.split('/')[1]
homepath = lib.toabs('~')
homerintermediate = homepath.replace(firstdir(homepath), '')[1:]
curpath = lib.toabs('.')
curintermediate = curpath.replace(firstdir(curpath), '')[1:]
print(curintermediate)
assert (paths.extract('s3://seunglab-test/intermediate/path/dataset/layer')
== ExtractedPath(
'precomputed', 's3', 'seunglab-test',
'intermediate/path/dataset/layer', 'intermediate/path/',
'dataset', 'layer'
))
assert (paths.extract('file:///tmp/dataset/layer')
== ExtractedPath('precomputed', 'file', "/tmp", 'dataset/layer', '', 'dataset', 'layer'))
assert (paths.extract('file://seunglab-test/intermediate/path/dataset/layer')
== ExtractedPath(
'precomputed', 'file', firstdir(curpath),
os.path.join(curintermediate, 'seunglab-test/intermediate/path/dataset/layer'),
os.path.join(curintermediate, 'seunglab-test', 'intermediate/path/'),
'dataset', 'layer'))
assert (paths.extract('gs://seunglab-test/intermediate/path/dataset/layer')
== ExtractedPath(
'precomputed', 'gs',
'seunglab-test', 'intermediate/path/dataset/layer',
'intermediate/path/', 'dataset', 'layer'
))
assert (paths.extract('file://~/seunglab-test/intermediate/path/dataset/layer')
== ExtractedPath(
'precomputed', 'file',
firstdir(homepath),
os.path.join(homerintermediate, 'seunglab-test', 'intermediate/path/dataset/layer'),
os.path.join(homerintermediate, 'seunglab-test', 'intermediate/path/'),
'dataset',
'layer'
)
)
assert (paths.extract('file:///User/me/.cloudvolume/cache/gs/bucket/dataset/layer')
== ExtractedPath(
'precomputed', 'file',
'/User', 'me/.cloudvolume/cache/gs/bucket/dataset/layer',
'me/.cloudvolume/cache/gs/bucket/', 'dataset', 'layer'
))
shoulderror('s3://dataset/layer/')
shoulderror('ou3bouqjsa fkj aojsf oaojf ojsaf')
okgoogle('gs://bucket/dataset/layer/')
shoulderror('gs://bucket/dataset/layer/info')
path = paths.extract('s3://bucketxxxxxx/datasetzzzzz91h8__3/layer1br9bobasjf/')
assert path.format == 'precomputed'
assert path.protocol == 's3'
assert path.bucket == 'bucketxxxxxx'
assert path.dataset == 'datasetzzzzz91h8__3'
assert path.layer == 'layer1br9bobasjf'
path = paths.extract('file:///bucket/dataset/layer/')
assert path.format == 'precomputed'
assert path.protocol == 'file'
assert path.bucket == '/bucket'
assert path.dataset == 'dataset'
assert path.layer == 'layer'
shoulderror('lucifer://bucket/dataset/layer/')
shoulderror('gs://///')
shoulderror('gs://seunglab-test//segmentation')
path = paths.extract('file:///tmp/removeme/layer/')
assert path.format == 'precomputed'
assert path.protocol == 'file'
assert path.bucket == '/tmp'
assert path.dataset == 'removeme'
assert path.layer == 'layer'
def test_path_extraction():
def shoulderror(url):
try:
paths.strict_extract(url)
assert False, url
except:
pass
def okgoogle(url):
path = paths.extract(url)
assert path.protocol == 'gs', url
assert path.bucket == 'bucket', url
assert path.basepath == 'bucket/dataset', url
assert path.no_bucket_basepath == 'dataset', url
assert path.dataset == 'dataset', url
assert path.layer == 'layer', url
okgoogle('gs://bucket/dataset/layer')
shoulderror('s4://dataset/layer')
shoulderror('dataset/layer')
shoulderror('s3://dataset')
# don't error
assert (strict_extract(
'graphene://http://localhost:8080/segmentation/1.0/testvol') ==
ExtractedPath('graphene', 'http', 'localhost:8080',
'localhost:8080/segmentation/1.0',
'segmentation/1.0', '1.0', 'testvol'))
assert (strict_extract('precomputed://gs://fafb-ffn1-1234567/segmentation')
== ExtractedPath('precomputed', 'gs', 'fafb-ffn1-1234567',
'fafb-ffn1-1234567', '', 'fafb-ffn1-1234567',
'segmentation'))
firstdir = lambda x: '/' + x.split('/')[1]
homepath = lib.toabs('~')
homerintermediate = homepath.replace(firstdir(homepath), '')[1:]
curpath = lib.toabs('.')
curintermediate = curpath.replace(firstdir(curpath), '')[1:]
match = re.match(r'((?:(?:\w:\\\\)|/).+?)\b', lib.toabs('.'))
bucket, = match.groups()
print(bucket, curintermediate)
assert (paths.extract('s3://seunglab-test/intermediate/path/dataset/layer')
== ExtractedPath('precomputed', 's3', 'seunglab-test',
'seunglab-test/intermediate/path/dataset',
'intermediate/path/dataset', 'dataset', 'layer'))
assert (paths.extract('file:///tmp/dataset/layer') == ExtractedPath(
'precomputed', 'file', "/tmp", '/tmp/dataset', 'dataset', 'dataset',
'layer'))
assert (
paths.extract('file://seunglab-test/intermediate/path/dataset/layer')
== ExtractedPath(
'precomputed', 'file', firstdir(curpath),
os.path.join(bucket, curintermediate,
'seunglab-test/intermediate/path/dataset'),
os.path.join(curintermediate, 'seunglab-test',
'intermediate/path/dataset'), 'dataset', 'layer'))
assert (paths.extract('gs://seunglab-test/intermediate/path/dataset/layer')
== ExtractedPath('precomputed', 'gs', 'seunglab-test',
'seunglab-test/intermediate/path/dataset',
'intermediate/path/dataset', 'dataset', 'layer'))
assert (
paths.extract('file://~/seunglab-test/intermediate/path/dataset/layer')
== ExtractedPath(
'precomputed', 'file', firstdir(homepath),
os.path.join(bucket, homerintermediate, 'seunglab-test',
'intermediate/path/dataset'),
os.path.join(homerintermediate, 'seunglab-test',
'intermediate/path/dataset'), 'dataset', 'layer'))
assert (paths.extract(
'file:///User/me/.cloudvolume/cache/gs/bucket/dataset/layer') ==
ExtractedPath('precomputed', 'file', '/User',
'/User/me/.cloudvolume/cache/gs/bucket/dataset',
'me/.cloudvolume/cache/gs/bucket/dataset', 'dataset',
'layer'))
shoulderror('ou3bouqjsa fkj aojsf oaojf ojsaf')
okgoogle('gs://bucket/dataset/layer/')
shoulderror('gs://bucket/dataset/layer/info')
path = paths.extract(
's3://bucketxxxxxx/datasetzzzzz91h8__3/layer1br9bobasjf/')
assert path.format == 'precomputed'
assert path.protocol == 's3'
assert path.bucket == 'bucketxxxxxx'
assert path.dataset == 'datasetzzzzz91h8__3'
assert path.layer == 'layer1br9bobasjf'
path = paths.extract('file:///bucket/dataset/layer/')
assert path.format == 'precomputed'
assert path.protocol == 'file'
assert path.bucket == '/bucket'
assert path.dataset == 'dataset'
assert path.layer == 'layer'
shoulderror('lucifer://bucket/dataset/layer/')
shoulderror('gs://///')
shoulderror('gs://seunglab-test//segmentation')
path = paths.extract('file:///tmp/removeme/layer/')
assert path.format == 'precomputed'
assert path.protocol == 'file'
assert path.bucket == '/tmp'
assert path.dataset == 'removeme'
assert path.layer == 'layer'