def setup(self):
f = h5py.File(self.filename, 'r')
self.spec = ProviderSpec()
self.ndims = None
for (volume_type, ds) in self.datasets.items():
if ds not in f:
raise RuntimeError("%s not in %s" % (ds, self.filename))
dims = f[ds].shape
self.spec.volumes[volume_type] = Roi((0, ) * len(dims), dims)
if self.ndims is None:
self.ndims = len(dims)
else:
assert self.ndims == len(dims)
if self.specified_resolution is None:
if 'resolution' in f[ds].attrs:
self.resolutions[volume_type] = tuple(
f[ds].attrs['resolution'])
else:
default_resolution = (1, ) * self.ndims
logger.warning(
"WARNING: your source does not contain resolution information"
" (no attribute 'resolution' in {} dataset). I will assume {}. "
"This might not be what you want.".format(
ds, default_resolution))
self.resolutions[volume_type] = default_resolution
else:
self.resolutions[volume_type] = self.specified_resolution
f.close()
def provides(self, key, spec):
'''Introduce a new output provided by this :class:`BatchProvider`.
Implementations should call this in their :func:`setup` method, which
will be called when the pipeline is build.
Args:
key (:class:`ArrayKey` or :class:`PointsKey`):
The array or point set key provided.
spec (:class:`ArraySpec` or :class:`PointsSpec`):
The spec of the array or point set provided.
'''
logger.debug("Current spec of %s:\n%s", self.name(), self.spec)
if self.spec is None:
self._spec = ProviderSpec()
assert key not in self.spec, (
"Node %s is trying to add spec for %s, but is already "
"provided." % (type(self).__name__, key))
self.spec[key] = copy.deepcopy(spec)
self.provided_items.append(key)
logger.debug("%s provides %s with spec %s", self.name(), key, spec)
def __init__(self,
hostname,
port,
uuid,
raw_array_name,
gt_array_name=None,
gt_mask_roi_name=None,
resolution=None):
"""
:param hostname: hostname for DVID server
:type hostname: str
:param port: port for DVID server
:type port: int
:param uuid: UUID of node on DVID server
:type uuid: str
:param raw_array_name: DVID data instance for image data
:type raw_array_name: str
:param gt_array_name: DVID data instance for segmentation label data
:type gt_array_name: str
:param gt_mask_roi_name: DVID region of interest for masking the segmentation
:type gt_mask_roi_name: str
:param resolution: resolution of source voxels in nanometers
:type resolution: tuple
"""
self.hostname = hostname
self.port = port
self.url = "http://{}:{}".format(self.hostname, self.port)
self.uuid = uuid
self.raw_array_name = raw_array_name
self.gt_array_name = gt_array_name
self.gt_mask_roi_name = gt_mask_roi_name
self.specified_resolution = resolution
self.node_service = None
self.dims = 0
self.spec = ProviderSpec()