def insert_new_treenode(parent_id=None, skeleton_id=None):
""" If the parent_id is not None and the skeleton_id of the parent does
not match with the skeleton.id, then the database will throw an error
given that the skeleton_id, being defined as foreign key in the
treenode table, will not meet the being-foreign requirement.
"""
new_treenode = Treenode()
new_treenode.user = creator
new_treenode.editor = editor
new_treenode.project_id = project_id
if creation_time:
new_treenode.creation_time = creation_time
new_treenode.location_x = float(x)
new_treenode.location_y = float(y)
new_treenode.location_z = float(z)
new_treenode.radius = int(radius)
new_treenode.skeleton_id = skeleton_id
new_treenode.confidence = int(confidence)
if parent_id:
new_treenode.parent_id = parent_id
new_treenode.save()
return new_treenode
def insert_new_treenode(parent_id=None, skeleton=None):
""" If the parent_id is not None and the skeleton_id of the parent does
not match with the skeleton.id, then the database will throw an error
given that the skeleton_id, being defined as foreign key in the
treenode table, will not meet the being-foreign requirement.
"""
new_treenode = Treenode()
new_treenode.user = request.user
new_treenode.editor = request.user
new_treenode.project_id = project_id
new_treenode.location_x = float(params['x'])
new_treenode.location_y = float(params['y'])
new_treenode.location_z = float(params['z'])
new_treenode.radius = int(params['radius'])
new_treenode.skeleton = skeleton
new_treenode.confidence = int(params['confidence'])
if parent_id:
new_treenode.parent_id = parent_id
new_treenode.save()
return new_treenode
def _create_interpolated_treenode(request, params, project_id, skip_last):
""" Create interpolated treenodes between the 'parent_id' and the clicked
x,y,z coordinate. The skip_last is to prevent the creation of the last
node, used by the join_skeletons_interpolated. """
response_on_error = 'Could not create interpolated treenode'
try:
# Raise an Exception if the user doesn't have permission to edit
# the neuron the skeleton of the treenode is modeling.
can_edit_treenode_or_fail(request.user, project_id, params['parent_id'])
parent = Treenode.objects.get(pk=params['parent_id'])
parent_skeleton_id = parent.skeleton_id
parent_x = decimal.Decimal(parent.location_x)
parent_y = decimal.Decimal(parent.location_y)
parent_z = decimal.Decimal(parent.location_z)
steps = abs((params['z'] - parent_z) / params['resz']) \
.quantize(decimal.Decimal('1'), rounding=decimal.ROUND_FLOOR)
if steps == decimal.Decimal(0):
steps = decimal.Decimal(1)
dx = (params['x'] - parent_x) / steps
dy = (params['y'] - parent_y) / steps
dz = (params['z'] - parent_z) / steps
broken_slices = set(int(bs.index) for bs in \
BrokenSlice.objects.filter(stack=params['stack_id']))
sign = -1 if dz < 0 else 1
# Loop the creation of treenodes in z resolution steps until target
# section is reached
parent_id = params['parent_id']
atn_slice_index = ((parent_z - params['stack_translation_z']) / params['resz']) \
.quantize(decimal.Decimal('1'), rounding=decimal.ROUND_FLOOR)
for i in range(1, steps + (0 if skip_last else 1)):
if (atn_slice_index + i * sign) in broken_slices:
continue
response_on_error = 'Error while trying to insert treenode.'
new_treenode = Treenode()
new_treenode.user_id = request.user.id
new_treenode.editor_id = request.user.id
new_treenode.project_id = project_id
new_treenode.location_x = float(parent_x + dx * i)
new_treenode.location_y = float(parent_y + dy * i)
new_treenode.location_z = float(parent_z + dz * i)
new_treenode.radius = params['radius']
new_treenode.skeleton_id = parent_skeleton_id
new_treenode.confidence = params['confidence']
new_treenode.parent_id = parent_id # This is not a root node.
new_treenode.save()
parent_id = new_treenode.id
# parent_id contains the ID of the last added node
return parent_id, parent_skeleton_id
except Exception as e:
raise Exception(response_on_error + ':' + str(e))
def insert_new_treenode(parent_id=None, skeleton_id=None):
""" If the parent_id is not None and the skeleton_id of the parent does
not match with the skeleton.id, then the database will throw an error
given that the skeleton_id, being defined as foreign key in the
treenode table, will not meet the being-foreign requirement.
"""
new_treenode = Treenode()
new_treenode.user = creator
new_treenode.editor = editor
new_treenode.project_id = project_id
if creation_time:
new_treenode.creation_time = creation_time
new_treenode.location_x = float(x)
new_treenode.location_y = float(y)
new_treenode.location_z = float(z)
new_radius = int(radius if (radius and not math.isnan(radius)) else 0)
new_treenode.radius = new_radius
new_treenode.skeleton_id = skeleton_id
new_confidence = int(confidence if not math.isnan(confidence) and (confidence or confidence is 0) else 5)
new_treenode.confidence = new_confidence
if parent_id:
new_treenode.parent_id = parent_id
new_treenode.save()
return new_treenode
def insert_new_treenode(parent_id=None, skeleton=None):
""" If the parent_id is not None and the skeleton_id of the parent does
not match with the skeleton.id, then the database will throw an error
given that the skeleton_id, being defined as foreign key in the
treenode table, will not meet the being-foreign requirement.
"""
new_treenode = Treenode()
new_treenode.user = request.user
new_treenode.editor = request.user
new_treenode.project_id = project_id
new_treenode.location_x = float(params['x'])
new_treenode.location_y = float(params['y'])
new_treenode.location_z = float(params['z'])
new_treenode.radius = int(params['radius'])
new_treenode.skeleton = skeleton
new_treenode.confidence = int(params['confidence'])
if parent_id:
new_treenode.parent_id = parent_id
new_treenode.save()
return new_treenode
def _create_interpolated_treenode(request, params, project_id, skip_last):
""" Create interpolated treenodes between the 'parent_id' and the clicked
x,y,z coordinate. The skip_last is to prevent the creation of the last
node, used by the join_skeletons_interpolated. """
response_on_error = 'Could not create interpolated treenode'
try:
# Raise an Exception if the user doesn't have permission to edit
# the neuron the skeleton of the treenode is modeling.
can_edit_treenode_or_fail(request.user, project_id,
params['parent_id'])
parent = Treenode.objects.get(pk=params['parent_id'])
parent_skeleton_id = parent.skeleton_id
parent_x = decimal.Decimal(parent.location_x)
parent_y = decimal.Decimal(parent.location_y)
parent_z = decimal.Decimal(parent.location_z)
steps = abs((params['z'] - parent_z) / params['resz']) \
.quantize(decimal.Decimal('1'), rounding=decimal.ROUND_FLOOR)
if steps == decimal.Decimal(0):
steps = decimal.Decimal(1)
dx = (params['x'] - parent_x) / steps
dy = (params['y'] - parent_y) / steps
dz = (params['z'] - parent_z) / steps
broken_slices = set(int(bs.index) for bs in \
BrokenSlice.objects.filter(stack=params['stack_id']))
sign = -1 if dz < 0 else 1
# Loop the creation of treenodes in z resolution steps until target
# section is reached
parent_id = params['parent_id']
atn_slice_index = ((parent_z - params['stack_translation_z']) / params['resz']) \
.quantize(decimal.Decimal('1'), rounding=decimal.ROUND_FLOOR)
for i in range(1, steps + (0 if skip_last else 1)):
if (atn_slice_index + i * sign) in broken_slices:
continue
response_on_error = 'Error while trying to insert treenode.'
new_treenode = Treenode()
new_treenode.user_id = request.user.id
new_treenode.editor_id = request.user.id
new_treenode.project_id = project_id
new_treenode.location_x = float(parent_x + dx * i)
new_treenode.location_y = float(parent_y + dy * i)
new_treenode.location_z = float(parent_z + dz * i)
new_treenode.radius = params['radius']
new_treenode.skeleton_id = parent_skeleton_id
new_treenode.confidence = params['confidence']
new_treenode.parent_id = parent_id # This is not a root node.
new_treenode.save()
parent_id = new_treenode.id
# parent_id contains the ID of the last added node
return parent_id, parent_skeleton_id
except Exception as e:
raise Exception(response_on_error + ':' + str(e))
