def __init__(self, hostname, 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__( hostname, uuid, data_name, *args, **kwargs )
def _update_subvol_widget(self, node_uuid, dataname, typename):
"""
Update the subvolume widget with the min/max extents of the given node and dataname.
Note: The node and dataname do not necessarily have to match the currently
selected node and dataname.
This enables the right-click behavior, which can be used to
limit your data volume to the size of a different data volume.
"""
error_msg = None
try:
if typename == "roi":
node_service = DVIDNodeService(self._hostname, str(node_uuid))
roi_blocks_zyx = numpy.array(
node_service.get_roi(str(dataname)))
maxindex = tuple(DVID_BLOCK_WIDTH *
(1 + numpy.max(roi_blocks_zyx, axis=0)))
minindex = (0, 0, 0) # Rois are always 3D
axiskeys = "zyx"
# If the current selection is a dataset, then include a channel dimension
if self.get_selection().typename != "roi":
axiskeys = "zyxc"
minindex = minindex + (0, )
maxindex = maxindex + (
1,
) # FIXME: This assumes that the selected data has only 1 channel...
else:
# Query the server
raw_metadata = VoxelsAccessor.get_metadata(
self._hostname, node_uuid, dataname)
voxels_metadata = VoxelsMetadata(raw_metadata)
maxindex = voxels_metadata.shape
minindex = voxels_metadata.minindex
axiskeys = voxels_metadata.axiskeys
# If the current selection is a roi, then remove the channel dimension
if self.get_selection().typename == "roi":
axiskeys = "zyx"
minindex = minindex[:-1]
maxindex = maxindex[:-1]
except (DVIDException, ErrMsg) as ex:
error_msg = str(ex)
log_exception(logger)
else:
self._buttonbox.button(QDialogButtonBox.Ok).setEnabled(True)
if error_msg:
self._buttonbox.button(QDialogButtonBox.Ok).setEnabled(False)
QMessageBox.critical(self, "DVID Error", error_msg)
self._subvol_widget.initWithExtents("", (), (), ())
return
self._subvol_widget.initWithExtents(axiskeys, maxindex, minindex,
maxindex)
def get_metadata( hostname, uuid, data_name ):
"""
Query the voxels metadata for the given node/data_name.
"""
connection = DVIDConnection(hostname)
rest_query = "/node/{uuid}/{data_name}/metadata".format( uuid=uuid, data_name=data_name )
status, response_body, _err_msg = connection.make_request( rest_query, ConnectionMethod.GET )
try:
json_data = json.loads(response_body)
except ValueError:
raise RuntimeError("Response body could not be parsed as valid json:\n"
"GET " + rest_query + "\n" + response_body)
return VoxelsMetadata( json_data )
def _update_display(self):
super(DvidDataSelectionBrowser, self)._update_display()
hostname, dset_uuid, dataname, node_uuid = self.get_selection()
enable_contents = self._repos_info is not None and dataname != "" and node_uuid != ""
self._roi_groupbox.setEnabled(enable_contents)
if not dataname or not node_uuid:
self._roi_widget.initWithExtents("", (), (), ())
return
error_msg = None
try:
# Query the server
raw_metadata = VoxelsAccessor.get_metadata(hostname, node_uuid,
dataname)
voxels_metadata = VoxelsMetadata(raw_metadata)
except DVIDException as ex:
error_msg = ex.message
except ErrMsg as ex:
error_msg = str(ErrMsg)
except VoxelsAccessor.BadRequestError as ex:
# DVID will return an error if the selected dataset
# isn't a 'voxels' dataset and thus has no voxels metadata
self._buttonbox.button(QDialogButtonBox.Ok).setEnabled(False)
return
else:
self._buttonbox.button(QDialogButtonBox.Ok).setEnabled(True)
if error_msg:
QMessageBox.critical(self, "DVID Error", error_msg)
self._roi_widget.initWithExtents("", (), (), ())
return
self._roi_widget.initWithExtents(voxels_metadata.axiskeys,
voxels_metadata.shape,
voxels_metadata.minindex,
voxels_metadata.shape)
