def _do_modify_data(self, uuid, dataname, dims, shape, offset):
"""
Respond to a POST request to modify a subvolume of data.
All parameters are strings from the REST string.
"""
dataset = self._get_h5_dataset(uuid, dataname)
roi_start, roi_stop = self._determine_request_roi( dataset, dims, shape, offset )
# Prepend channel to make "full" roi
full_roi_start = (0,) + roi_start
full_roi_stop = (dataset.shape[0],) + roi_stop
full_roi_shape = numpy.subtract(full_roi_stop, full_roi_start)
slicing = tuple( slice(x,y) for x,y in zip(full_roi_start, full_roi_stop) )
# If the user is writing data beoyond the current extents of the dataset,
# resize the dataset first.
if (numpy.array(full_roi_stop) > dataset.shape).any():
dataset.resize( full_roi_stop )
voxels_metadata = VoxelsMetadata.create_from_h5_dataset(dataset)
codec = VoxelsNddataCodec( voxels_metadata )
data = codec.decode_to_ndarray(self.rfile, full_roi_shape)
dataset[slicing] = data
self.server.h5_file.flush()
#self.send_response(httplib.NO_CONTENT) # "No Content" (accepted)
self.send_response(httplib.OK)
self.send_header("Content-length", 0 )
self.end_headers()
def _do_modify_data(self, uuid, dataname, dims, shape, offset):
"""
Respond to a POST request to modify a subvolume of data.
All parameters are strings from the REST string.
"""
dataset = self._get_h5_dataset(uuid, dataname)
roi_start, roi_stop = self._determine_request_roi(
dataset, dims, shape, offset)
# Prepend channel to make "full" roi
full_roi_start = (0, ) + roi_start
full_roi_stop = (dataset.shape[0], ) + roi_stop
full_roi_shape = numpy.subtract(full_roi_stop, full_roi_start)
slicing = tuple(
slice(x, y) for x, y in zip(full_roi_start, full_roi_stop))
if 'dvid_metadata' in dataset.attrs:
voxels_metadata = VoxelsMetadata(dataset.attrs['dvid_metadata'])
del dataset.attrs['dvid_metadata']
else:
voxels_metadata = VoxelsMetadata.create_from_h5_dataset(dataset)
# If the user is writing data beyond the current extents of the dataset,
# resize the dataset first.
if (numpy.array(full_roi_stop) > dataset.shape).any():
dataset.resize(numpy.maximum(full_roi_stop, dataset.shape))
voxels_metadata.shape = tuple(
map(int, numpy.maximum(voxels_metadata.shape, full_roi_stop)))
# Overwrite minindex is needed
if (numpy.array(full_roi_start) < voxels_metadata.minindex).any():
voxels_metadata.minindex = tuple(
numpy.minimum(voxels_metadata.minindex, full_roi_start))
dataset.attrs['dvid_metadata'] = voxels_metadata.to_json()
# Must read the entire message body, even if it isn't used below.
codec = VoxelsNddataCodec(dataset.dtype)
data = codec.decode_to_ndarray(self.rfile, full_roi_shape)
if (numpy.array(roi_start) < 0).any():
# We don't support negative coordinates in this mock server.
# But as a compromise, we don't choke here.
# Instead, we simply do nothing.
pass
else:
dataset[slicing] = data
self.server.h5_file.flush()
#self.send_response(httplib.NO_CONTENT) # "No Content" (accepted)
self.send_response(httplib.OK)
self.send_header("Content-length", 0)
self.end_headers()
def _do_modify_data(self, uuid, dataname, dims, shape, offset):
"""
Respond to a POST request to modify a subvolume of data.
All parameters are strings from the REST string.
"""
dataset = self._get_h5_dataset(uuid, dataname)
roi_start, roi_stop = self._determine_request_roi( dataset, dims, shape, offset )
# Prepend channel to make "full" roi
full_roi_start = (0,) + roi_start
full_roi_stop = (dataset.shape[0],) + roi_stop
full_roi_shape = numpy.subtract(full_roi_stop, full_roi_start)
slicing = tuple( slice(x,y) for x,y in zip(full_roi_start, full_roi_stop) )
if 'dvid_metadata' in dataset.attrs:
voxels_metadata = VoxelsMetadata(dataset.attrs['dvid_metadata'])
del dataset.attrs['dvid_metadata']
else:
voxels_metadata = VoxelsMetadata.create_from_h5_dataset(dataset)
# If the user is writing data beyond the current extents of the dataset,
# resize the dataset first.
if (numpy.array(full_roi_stop) > dataset.shape).any():
dataset.resize( numpy.maximum(full_roi_stop, dataset.shape) )
voxels_metadata.shape = tuple( map(int, numpy.maximum( voxels_metadata.shape, full_roi_stop )) )
# Overwrite minindex is needed
if (numpy.array(full_roi_start) < voxels_metadata.minindex).any():
voxels_metadata.minindex = tuple( numpy.minimum( voxels_metadata.minindex, full_roi_start ) )
dataset.attrs['dvid_metadata'] = voxels_metadata.to_json()
# Must read the entire message body, even if it isn't used below.
codec = VoxelsNddataCodec( dataset.dtype )
data = codec.decode_to_ndarray(self.rfile, full_roi_shape)
if (numpy.array(roi_start) < 0).any():
# We don't support negative coordinates in this mock server.
# But as a compromise, we don't choke here.
# Instead, we simply do nothing.
pass
else:
dataset[slicing] = data
self.server.h5_file.flush()
#self.send_response(httplib.NO_CONTENT) # "No Content" (accepted)
self.send_response(httplib.OK)
self.send_header("Content-length", 0 )
self.end_headers()
def _do_get_data(self, uuid, dataname, dims, shape, offset):
"""
Respond to a query for volume data.
All parameters are strings from the REST string.
"""
if self.server.busy_count:
self.server.busy_count -= 1
raise self.RequestError(httplib.SERVICE_UNAVAILABLE,
"I'm busy. Try again later.")
dataset = self._get_h5_dataset(uuid, dataname)
roi_start, roi_stop = self._determine_request_roi(
dataset, dims, shape, offset)
if (numpy.array(roi_start) < 0).any():
# prepend channel
roi_start = (0, ) + tuple(roi_start)
roi_stop = (dataset.shape[0], ) + tuple(roi_stop)
# This mock server doesn't really support negative coordinates,
# but as a compromise, we don't choke here. Instead, we return an array of zeros.
data = numpy.zeros(
numpy.array(roi_stop) - roi_start, dataset.dtype)
else:
if (numpy.array(roi_stop) > dataset.shape[1:]).any():
raise Exception(
"roi {} is out-of-bounds for dataset with shape {}".format(
(roi_start, roi_stop), dataset.shape[1:]))
# Prepend channel slicing
slicing = (slice(None), ) + tuple(
slice(x, y) for x, y in zip(roi_start, roi_stop))
data = dataset[slicing]
codec = VoxelsNddataCodec(dataset.dtype)
buffer_len = codec.calculate_buffer_len(data.shape)
self.send_response(httplib.OK)
self.send_header("Content-type", VoxelsNddataCodec.VOLUME_MIMETYPE)
self.send_header("Content-length", str(buffer_len))
self.end_headers()
codec.encode_from_ndarray(self.wfile, data)
def _do_get_data(self, uuid, dataname, dims, shape, offset):
"""
Respond to a query for volume data.
All parameters are strings from the REST string.
"""
if self.server.busy_count:
self.server.busy_count -= 1
raise self.RequestError( httplib.SERVICE_UNAVAILABLE, "I'm busy. Try again later." )
dataset = self._get_h5_dataset(uuid, dataname)
roi_start, roi_stop = self._determine_request_roi( dataset, dims, shape, offset )
if (numpy.array(roi_start) < 0).any():
# prepend channel
roi_start = (0,) + tuple(roi_start)
roi_stop = (dataset.shape[0],) + tuple(roi_stop)
# This mock server doesn't really support negative coordinates,
# but as a compromise, we don't choke here. Instead, we return an array of zeros.
data = numpy.zeros( numpy.array(roi_stop) - roi_start, dataset.dtype )
else:
if (numpy.array(roi_stop) > dataset.shape[1:]).any():
raise Exception("roi {} is out-of-bounds for dataset with shape {}".format( (roi_start, roi_stop), dataset.shape[1:] ) )
# Prepend channel slicing
slicing = (slice(None),) + tuple( slice(x,y) for x,y in zip(roi_start, roi_stop) )
data = dataset[slicing]
codec = VoxelsNddataCodec( dataset.dtype )
buffer_len = codec.calculate_buffer_len( data.shape )
self.send_response(httplib.OK)
self.send_header("Content-type", VoxelsNddataCodec.VOLUME_MIMETYPE)
self.send_header("Content-length", str(buffer_len) )
self.end_headers()
codec.encode_from_ndarray( self.wfile, data )
def _do_get_data(self, uuid, dataname, dims, shape, offset):
"""
Respond to a query for volume data.
All parameters are strings from the REST string.
"""
dataset = self._get_h5_dataset(uuid, dataname)
roi_start, roi_stop = self._determine_request_roi( dataset, dims, shape, offset )
# Prepend channel slicing
slicing = (slice(None),) + tuple( slice(x,y) for x,y in zip(roi_start, roi_stop) )
data = dataset[slicing]
voxels_metadata = VoxelsMetadata.create_from_h5_dataset(dataset)
codec = VoxelsNddataCodec( voxels_metadata )
buffer_len = codec.calculate_buffer_len( data.shape )
self.send_response(httplib.OK)
self.send_header("Content-type", VoxelsNddataCodec.VOLUME_MIMETYPE)
self.send_header("Content-length", str(buffer_len) )
self.end_headers()
codec.encode_from_ndarray( self.wfile, data )
