def test_parse(self):
metadata = VoxelsMetadata(self.metadata_json)
assert metadata.shape == (3, 100, 200, 400), "Wrong shape: {}".format(
metadata.shape)
assert metadata.dtype == numpy.uint8
assert metadata.axiskeys == 'cxyz'
assert metadata['Axes'][0]["Resolution"] == 3.1
assert metadata['Axes'][1]["Resolution"] == 3.1
assert metadata['Axes'][2]["Resolution"] == 40
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 test_create_axistags(self):
try:
import vigra
except ImportError:
raise nose.SkipTest
metadata = VoxelsMetadata(self.metadata_json)
tags = metadata.create_axistags()
assert tags['x'].resolution == 3.1
assert tags['y'].resolution == 3.1
assert tags['z'].resolution == 40
assert tags.channelLabels == [
"intensity-R", "intensity-G", "intensity-B"
]
def __init__(self, connection, uuid, data_name, *args, **kwargs):
"""
Create a new VoxelsAccessor with all the same properties as the current instance,
except that it accesses a roi mask volume.
"""
# Create default mask metadata.
mask_metadata = {}
mask_metadata["Properties"] = {
"Values": [{
"DataType": "uint8",
"Label": "roi-mask"
}]
}
# For now, we hardcode XYZ order
# The size/offset are left as None, because that doesn't apply to ROI data.
default_axis_info = {
"Label": "",
"Resolution": 1,
"Units": "",
"Size": 0,
"Offset": 0
}
mask_metadata["Axes"] = [
copy.copy(default_axis_info),
copy.copy(default_axis_info),
copy.copy(default_axis_info)
]
mask_metadata["Axes"][0]["Label"] = "X"
mask_metadata["Axes"][1]["Label"] = "Y"
mask_metadata["Axes"][2]["Label"] = "Z"
assert '_metadata' not in kwargs or kwargs['_metadata'] is None
kwargs['_metadata'] = VoxelsMetadata(mask_metadata)
assert '_access_type' not in kwargs or kwargs['_access_type'] is None
kwargs['_access_type'] = 'mask'
# Init base class with pre-formed metadata instead of querying for it.
super(RoiMaskAccessor, self).__init__(connection, uuid, data_name,
*args, **kwargs)
