def lines_add(request, project_id=None):
p = Project.objects.get(pk=project_id)
# FIXME: for the moment, just hardcode the user ID:
user = User.objects.get(pk=3)
neuron = get_object_or_404(ClassInstance,
pk=request.POST['neuron_id'],
project=p)
# There's a race condition here, if two people try to add a line
# with the same name at the same time. The normal way to deal
# with this would be to make the `name` column unique in the
# table, but since the class_instance table isn't just for driver
# lines, we can't do that. (FIXME)
try:
line = ClassInstance.objects.get(name=request.POST['line_name'])
except ClassInstance.DoesNotExist:
line = ClassInstance()
line.name = request.POST['line_name']
line.project = p
line.user = user
line.class_column = Class.objects.get(class_name='driver_line',
project=p)
line.save()
r = Relation.objects.get(relation_name='expresses_in', project=p)
cici = ClassInstanceClassInstance()
cici.class_instance_a = line
cici.class_instance_b = neuron
cici.relation = r
cici.user = user
cici.project = p
cici.save()
return HttpResponseRedirect(
reverse('vncbrowser.views.view',
kwargs={
'neuron_id': neuron.id,
'project_id': p.id
}))
def lines_add(request, project_id=None):
p = Project.objects.get(pk=project_id)
# FIXME: for the moment, just hardcode the user ID:
user = User.objects.get(pk=3)
neuron = get_object_or_404(ClassInstance,
pk=request.POST['neuron_id'],
project=p)
# There's a race condition here, if two people try to add a line
# with the same name at the same time. The normal way to deal
# with this would be to make the `name` column unique in the
# table, but since the class_instance table isn't just for driver
# lines, we can't do that. (FIXME)
try:
line = ClassInstance.objects.get(name=request.POST['line_name'])
except ClassInstance.DoesNotExist:
line = ClassInstance()
line.name=request.POST['line_name']
line.project = p
line.user = user
line.class_column = Class.objects.get(class_name='driver_line', project=p)
line.save()
r = Relation.objects.get(relation_name='expresses_in', project=p)
cici = ClassInstanceClassInstance()
cici.class_instance_a = line
cici.class_instance_b = neuron
cici.relation = r
cici.user = user
cici.project = p
cici.save()
return HttpResponseRedirect(reverse('vncbrowser.views.view',
kwargs={'neuron_id':neuron.id,
'project_id':p.id}))
def _create_treenode(project_id,
creator,
editor,
x,
y,
z,
radius,
confidence,
neuron_id,
parent_id,
creation_time=None,
neuron_name=None):
relation_map = get_relation_to_id_map(project_id)
class_map = get_class_to_id_map(project_id)
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 relate_neuron_to_skeleton(neuron, skeleton):
return _create_relation(creator, project_id, relation_map['model_of'],
skeleton, neuron)
response_on_error = ''
try:
if -1 != int(parent_id): # A root node and parent node exist
# Select the parent treenode for update to prevent race condition
# updates to its skeleton ID while this node is being created.
cursor = connection.cursor()
cursor.execute(
'''
SELECT t.skeleton_id, t.edition_time FROM treenode t
WHERE t.id = %s FOR NO KEY UPDATE OF t
''', (parent_id, ))
if cursor.rowcount != 1:
raise ValueError('Parent treenode %s does not exist' %
parent_id)
parent_node = cursor.fetchone()
parent_skeleton_id = parent_node[0]
parent_edition_time = parent_node[1]
# Raise an Exception if the user doesn't have permission to edit
# the neuron the skeleton of the treenode is modeling.
can_edit_skeleton_or_fail(editor, project_id, parent_skeleton_id,
relation_map['model_of'])
response_on_error = 'Could not insert new treenode!'
new_treenode = insert_new_treenode(parent_id, parent_skeleton_id)
return NewTreenode(new_treenode.id, new_treenode.edition_time,
parent_skeleton_id, parent_edition_time)
else:
# No parent node: We must create a new root node, which needs a
# skeleton and a neuron to belong to.
response_on_error = 'Could not insert new treenode instance!'
new_skeleton = ClassInstance()
new_skeleton.user = creator
new_skeleton.project_id = project_id
new_skeleton.class_column_id = class_map['skeleton']
new_skeleton.name = 'skeleton'
new_skeleton.save()
new_skeleton.name = 'skeleton %d' % new_skeleton.id
new_skeleton.save()
if -1 != neuron_id:
# Check that the neuron to use exists
if 0 == ClassInstance.objects.filter(pk=neuron_id).count():
neuron_id = -1
if -1 != neuron_id:
# Raise an Exception if the user doesn't have permission to
# edit the existing neuron.
can_edit_class_instance_or_fail(editor, neuron_id, 'neuron')
# A neuron already exists, so we use it
response_on_error = 'Could not relate the neuron model to ' \
'the new skeleton!'
relate_neuron_to_skeleton(neuron_id, new_skeleton.id)
response_on_error = 'Could not insert new treenode!'
new_treenode = insert_new_treenode(None, new_skeleton.id)
return NewTreenode(new_treenode.id, new_treenode.edition_time,
new_skeleton.id, None)
else:
# A neuron does not exist, therefore we put the new skeleton
# into a new neuron.
response_on_error = 'Failed to insert new instance of a neuron.'
new_neuron = ClassInstance()
new_neuron.user = creator
new_neuron.project_id = project_id
new_neuron.class_column_id = class_map['neuron']
if neuron_name:
# Create a regular expression to find allowed patterns. The
# first group is the whole {nX} part, while the second group
# is X only.
counting_pattern = re.compile(r"(\{n(\d+)\})")
# Look for patterns, replace all {n} with {n1} to normalize.
neuron_name = neuron_name.replace("{n}", "{n1}")
if counting_pattern.search(neuron_name):
# Find starting values for each substitution.
counts = [
int(m.groups()[1])
for m in counting_pattern.finditer(neuron_name)
]
# Find existing matching neurons in database.
name_match = counting_pattern.sub(
r"(\d+)", neuron_name)
name_pattern = re.compile(name_match)
matching_neurons = ClassInstance.objects.filter(
project_id=project_id,
class_column_id=class_map['neuron'],
name__regex=name_match).order_by('name')
# Increment substitution values based on existing neurons.
for n in matching_neurons:
for i, (count, g) in enumerate(
zip(counts,
name_pattern.search(n.name).groups())):
if count == int(g):
counts[i] = count + 1
# Substitute values.
count_ind = 0
m = counting_pattern.search(neuron_name)
while m:
neuron_name = m.string[:m.start()] + str(
counts[count_ind]) + m.string[m.end():]
count_ind = count_ind + 1
m = counting_pattern.search(neuron_name)
new_neuron.name = neuron_name
else:
new_neuron.name = 'neuron'
new_neuron.save()
new_neuron.name = 'neuron %d' % new_neuron.id
new_neuron.save()
response_on_error = 'Could not relate the neuron model to ' \
'the new skeleton!'
relate_neuron_to_skeleton(new_neuron.id, new_skeleton.id)
response_on_error = 'Failed to insert instance of treenode.'
new_treenode = insert_new_treenode(None, new_skeleton.id)
response_on_error = 'Failed to write to logs.'
new_location = (new_treenode.location_x,
new_treenode.location_y,
new_treenode.location_z)
insert_into_log(
project_id, creator.id, 'create_neuron', new_location,
'Create neuron %d and skeleton '
'%d' % (new_neuron.id, new_skeleton.id))
return NewTreenode(new_treenode.id, new_treenode.edition_time,
new_skeleton.id, None)
except Exception as e:
import traceback
raise Exception(
"%s: %s %s" %
(response_on_error, str(e), str(traceback.format_exc())))
def create_treenode(request, project_id=None):
"""
Add a new treenode to the database
----------------------------------
1. Add new treenode for a given skeleton id. Parent should not be empty.
return: new treenode id
If the parent's skeleton has a single node and belongs to the
'Isolated synaptic terminals' group, then reassign ownership
of the skeleton and the neuron to the user. The treenode remains
property of the original user who created it.
2. Add new treenode (root) and create a new skeleton (maybe for a given
neuron) return: new treenode id and skeleton id.
If a neuron id is given, use that one to create the skeleton as a model of
it.
"""
params = {}
float_values = {
'x': 0,
'y': 0,
'z': 0,
'radius': 0}
int_values = {
'confidence': 0,
'useneuron': -1,
'parent_id': -1}
string_values = {}
for p in float_values.keys():
params[p] = float(request.POST.get(p, float_values[p]))
for p in int_values.keys():
params[p] = int(request.POST.get(p, int_values[p]))
for p in string_values.keys():
params[p] = request.POST.get(p, string_values[p])
relation_map = get_relation_to_id_map(project_id)
class_map = get_class_to_id_map(project_id)
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 relate_neuron_to_skeleton(neuron, skeleton):
return _create_relation(request.user, project_id,
relation_map['model_of'], skeleton, neuron)
response_on_error = ''
try:
if -1 != int(params['parent_id']): # A root node and parent node exist
# 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 = Treenode.objects.get(pk=params['parent_id'])
response_on_error = 'Could not insert new treenode!'
skeleton = ClassInstance.objects.get(pk=parent_treenode.skeleton_id)
new_treenode = insert_new_treenode(params['parent_id'], skeleton)
return HttpResponse(json.dumps({
'treenode_id': new_treenode.id,
'skeleton_id': skeleton.id
}))
else:
# No parent node: We must create a new root node, which needs a
# skeleton and a neuron to belong to.
response_on_error = 'Could not insert new treenode instance!'
new_skeleton = ClassInstance()
new_skeleton.user = request.user
new_skeleton.project_id = project_id
new_skeleton.class_column_id = class_map['skeleton']
new_skeleton.name = 'skeleton'
new_skeleton.save()
new_skeleton.name = 'skeleton %d' % new_skeleton.id
new_skeleton.save()
if -1 == params['useneuron']:
# Check that the neuron to use exists
if 0 == ClassInstance.objects.filter(pk=params['useneuron']).count():
params['useneuron'] = -1
if -1 != params['useneuron']:
# Raise an Exception if the user doesn't have permission to
# edit the existing neuron.
can_edit_class_instance_or_fail(request.user,
params['useneuron'], 'neuron')
# A neuron already exists, so we use it
response_on_error = 'Could not relate the neuron model to ' \
'the new skeleton!'
relate_neuron_to_skeleton(params['useneuron'], new_skeleton.id)
response_on_error = 'Could not insert new treenode!'
new_treenode = insert_new_treenode(None, new_skeleton)
return HttpResponse(json.dumps({
'treenode_id': new_treenode.id,
'skeleton_id': new_skeleton.id,
'neuron_id': params['useneuron']}))
else:
# A neuron does not exist, therefore we put the new skeleton
# into a new neuron.
response_on_error = 'Failed to insert new instance of a neuron.'
new_neuron = ClassInstance()
new_neuron.user = request.user
new_neuron.project_id = project_id
new_neuron.class_column_id = class_map['neuron']
new_neuron.name = 'neuron'
new_neuron.save()
new_neuron.name = 'neuron %d' % new_neuron.id
new_neuron.save()
response_on_error = 'Could not relate the neuron model to ' \
'the new skeleton!'
relate_neuron_to_skeleton(new_neuron.id, new_skeleton.id)
response_on_error = 'Failed to insert instance of treenode.'
new_treenode = insert_new_treenode(None, new_skeleton)
response_on_error = 'Failed to write to logs.'
new_location = (new_treenode.location_x, new_treenode.location_y,
new_treenode.location_z)
insert_into_log(project_id, request.user.id, 'create_neuron',
new_location, 'Create neuron %d and skeleton '
'%d' % (new_neuron.id, new_skeleton.id))
return HttpResponse(json.dumps({
'treenode_id': new_treenode.id,
'skeleton_id': new_skeleton.id,
}))
except Exception as e:
import traceback
raise Exception("%s: %s %s" % (response_on_error, str(e),
str(traceback.format_exc())))
def _create_treenode(project_id, creator, editor, x, y, z, radius, confidence,
neuron_id, parent_id, creation_time=None, neuron_name=None):
relation_map = get_relation_to_id_map(project_id)
class_map = get_class_to_id_map(project_id)
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 relate_neuron_to_skeleton(neuron, skeleton):
return _create_relation(creator, project_id,
relation_map['model_of'], skeleton, neuron)
response_on_error = ''
try:
if -1 != int(parent_id): # A root node and parent node exist
# Select the parent treenode for update to prevent race condition
# updates to its skeleton ID while this node is being created.
cursor = connection.cursor()
cursor.execute('''
SELECT t.skeleton_id, t.edition_time FROM treenode t
WHERE t.id = %s FOR NO KEY UPDATE OF t
''', (parent_id,))
if cursor.rowcount != 1:
raise ValueError('Parent treenode %s does not exist' % parent_id)
parent_node = cursor.fetchone()
parent_skeleton_id = parent_node[0]
parent_edition_time = parent_node[1]
# Raise an Exception if the user doesn't have permission to edit
# the neuron the skeleton of the treenode is modeling.
can_edit_skeleton_or_fail(editor, project_id, parent_skeleton_id,
relation_map['model_of'])
response_on_error = 'Could not insert new treenode!'
new_treenode = insert_new_treenode(parent_id, parent_skeleton_id)
return NewTreenode(new_treenode.id, new_treenode.edition_time,
parent_skeleton_id, parent_edition_time)
else:
# No parent node: We must create a new root node, which needs a
# skeleton and a neuron to belong to.
response_on_error = 'Could not insert new treenode instance!'
new_skeleton = ClassInstance()
new_skeleton.user = creator
new_skeleton.project_id = project_id
new_skeleton.class_column_id = class_map['skeleton']
new_skeleton.name = 'skeleton'
new_skeleton.save()
new_skeleton.name = 'skeleton %d' % new_skeleton.id
new_skeleton.save()
if -1 != neuron_id:
# Check that the neuron to use exists
if 0 == ClassInstance.objects.filter(pk=neuron_id).count():
neuron_id = -1
if -1 != neuron_id:
# Raise an Exception if the user doesn't have permission to
# edit the existing neuron.
can_edit_class_instance_or_fail(editor, neuron_id, 'neuron')
# A neuron already exists, so we use it
response_on_error = 'Could not relate the neuron model to ' \
'the new skeleton!'
relate_neuron_to_skeleton(neuron_id, new_skeleton.id)
response_on_error = 'Could not insert new treenode!'
new_treenode = insert_new_treenode(None, new_skeleton.id)
return NewTreenode(new_treenode.id, new_treenode.edition_time,
new_skeleton.id, None)
else:
# A neuron does not exist, therefore we put the new skeleton
# into a new neuron.
response_on_error = 'Failed to insert new instance of a neuron.'
new_neuron = ClassInstance()
new_neuron.user = creator
new_neuron.project_id = project_id
new_neuron.class_column_id = class_map['neuron']
if neuron_name:
# Create a regular expression to find allowed patterns. The
# first group is the whole {nX} part, while the second group
# is X only.
counting_pattern = re.compile(r"(\{n(\d+)\})")
# Look for patterns, replace all {n} with {n1} to normalize.
neuron_name = neuron_name.replace("{n}", "{n1}")
if counting_pattern.search(neuron_name):
# Find starting values for each substitution.
counts = [int(m.groups()[1]) for m in counting_pattern.finditer(neuron_name)]
# Find existing matching neurons in database.
name_match = counting_pattern.sub(r"(\d+)", neuron_name)
name_pattern = re.compile(name_match)
matching_neurons = ClassInstance.objects.filter(
project_id=project_id,
class_column_id=class_map['neuron'],
name__regex=name_match).order_by('name')
# Increment substitution values based on existing neurons.
for n in matching_neurons:
for i, (count, g) in enumerate(zip(counts, name_pattern.search(n.name).groups())):
if count == int(g):
counts[i] = count + 1
# Substitute values.
count_ind = 0
m = counting_pattern.search(neuron_name)
while m:
neuron_name = m.string[:m.start()] + str(counts[count_ind]) + m.string[m.end():]
count_ind = count_ind + 1
m = counting_pattern.search(neuron_name)
new_neuron.name = neuron_name
else:
new_neuron.name = 'neuron'
new_neuron.save()
new_neuron.name = 'neuron %d' % new_neuron.id
new_neuron.save()
response_on_error = 'Could not relate the neuron model to ' \
'the new skeleton!'
relate_neuron_to_skeleton(new_neuron.id, new_skeleton.id)
response_on_error = 'Failed to insert instance of treenode.'
new_treenode = insert_new_treenode(None, new_skeleton.id)
response_on_error = 'Failed to write to logs.'
new_location = (new_treenode.location_x, new_treenode.location_y,
new_treenode.location_z)
insert_into_log(project_id, creator.id, 'create_neuron',
new_location, 'Create neuron %d and skeleton '
'%d' % (new_neuron.id, new_skeleton.id))
return NewTreenode(new_treenode.id, new_treenode.edition_time,
new_skeleton.id, None)
except Exception as e:
import traceback
raise Exception("%s: %s %s" % (response_on_error, str(e),
str(traceback.format_exc())))
def split_skeleton(request, project_id=None):
""" The split is only possible if the neuron is not locked or if it is
locked by the current user or if the current user belongs to the group
of the user who locked it. Of course, the split is also possible if
the current user is a super-user. Also, all reviews of the treenodes in the
new neuron are updated to refer to the new skeleton.
"""
treenode_id = int(request.POST['treenode_id'])
treenode = Treenode.objects.get(pk=treenode_id)
skeleton_id = treenode.skeleton_id
upstream_annotation_map = json.loads(request.POST.get('upstream_annotation_map'))
downstream_annotation_map = json.loads(request.POST.get('downstream_annotation_map'))
cursor = connection.cursor()
# Check if the treenode is root!
if not treenode.parent:
return HttpResponse(json.dumps({'error': 'Can\'t split at the root node: it doesn\'t have a parent.'}))
# Check if annotations are valid
if not check_annotations_on_split(project_id, skeleton_id,
frozenset(upstream_annotation_map.keys()),
frozenset(downstream_annotation_map.keys())):
raise Exception("Annotation distribution is not valid for splitting. " \
"One part has to keep the whole set of annotations!")
skeleton = ClassInstance.objects.select_related('user').get(pk=skeleton_id)
project_id=int(project_id)
# retrieve neuron of this skeleton
neuron = ClassInstance.objects.get(
cici_via_b__relation__relation_name='model_of',
cici_via_b__class_instance_a_id=skeleton_id)
# Make sure the user has permissions to edit
can_edit_class_instance_or_fail(request.user, neuron.id, 'neuron')
# retrieve the id, parent_id of all nodes in the skeleton
# with minimal ceremony
cursor.execute('''
SELECT id, parent_id FROM treenode WHERE skeleton_id=%s
''' % skeleton_id) # no need to sanitize
# build the networkx graph from it
graph = nx.DiGraph()
for row in cursor.fetchall():
graph.add_node( row[0] )
if row[1]:
# edge from parent_id to id
graph.add_edge( row[1], row[0] )
# find downstream nodes starting from target treenode_id
# and generate the list of IDs to change, starting at treenode_id (inclusive)
change_list = nx.bfs_tree(graph, treenode_id).nodes()
if not change_list:
# When splitting an end node, the bfs_tree doesn't return any nodes,
# which is surprising, because when the splitted tree has 2 or more nodes
# the node at which the split is made is included in the list.
change_list.append(treenode_id)
# create a new skeleton
new_skeleton = ClassInstance()
new_skeleton.name = 'Skeleton'
new_skeleton.project_id = project_id
new_skeleton.user = skeleton.user # The same user that owned the skeleton to split
new_skeleton.class_column = Class.objects.get(class_name='skeleton', project_id=project_id)
new_skeleton.save()
new_skeleton.name = 'Skeleton {0}'.format( new_skeleton.id ) # This could be done with a trigger in the database
new_skeleton.save()
# Create new neuron
new_neuron = ClassInstance()
new_neuron.name = 'Neuron'
new_neuron.project_id = project_id
new_neuron.user = skeleton.user
new_neuron.class_column = Class.objects.get(class_name='neuron',
project_id=project_id)
new_neuron.save()
new_neuron.name = 'Neuron %s' % str(new_neuron.id)
new_neuron.save()
# Assign the skeleton to new neuron
cici = ClassInstanceClassInstance()
cici.class_instance_a = new_skeleton
cici.class_instance_b = new_neuron
cici.relation = Relation.objects.get(relation_name='model_of', project_id=project_id)
cici.user = skeleton.user # The same user that owned the skeleton to split
cici.project_id = project_id
cici.save()
# update skeleton_id of list in treenode table
# This creates a lazy QuerySet that, upon calling update, returns a new QuerySet
# that is then executed. It does NOT create an update SQL query for every treenode.
tns = Treenode.objects.filter(id__in=change_list).update(skeleton=new_skeleton)
# update the skeleton_id value of the treenode_connector table
tc = TreenodeConnector.objects.filter(
relation__relation_name__endswith = 'synaptic_to',
treenode__in=change_list,
).update(skeleton=new_skeleton)
# setting new root treenode's parent to null
Treenode.objects.filter(id=treenode_id).update(parent=None, editor=request.user)
# Update annotations of existing neuron to have only over set
_update_neuron_annotations(project_id, request.user, neuron.id,
upstream_annotation_map)
# Update all reviews of the treenodes that are moved to a new neuron to
# refer to the new skeleton.
Review.objects.filter(treenode_id__in=change_list).update(skeleton=new_skeleton)
# Update annotations of under skeleton
_annotate_entities(project_id, [new_neuron.id], downstream_annotation_map)
# Log the location of the node at which the split was done
location = (treenode.location_x, treenode.location_y, treenode.location_z)
insert_into_log(project_id, request.user.id, "split_skeleton", location,
"Split skeleton with ID {0} (neuron: {1})".format( skeleton_id, neuron.name ) )
return HttpResponse(json.dumps({}), content_type='text/json')
def create_treenode(request, project_id=None):
"""
Add a new treenode to the database
----------------------------------
1. Add new treenode for a given skeleton id. Parent should not be empty.
return: new treenode id
If the parent's skeleton has a single node and belongs to the
'Isolated synaptic terminals' group, then reassign ownership
of the skeleton and the neuron to the user. The treenode remains
property of the original user who created it.
2. Add new treenode (root) and create a new skeleton (maybe for a given
neuron) return: new treenode id and skeleton id.
If a neuron id is given, use that one to create the skeleton as a model of
it.
"""
params = {}
float_values = {'x': 0, 'y': 0, 'z': 0, 'radius': 0}
int_values = {'confidence': 0, 'useneuron': -1, 'parent_id': -1}
string_values = {}
for p in float_values.keys():
params[p] = float(request.POST.get(p, float_values[p]))
for p in int_values.keys():
params[p] = int(request.POST.get(p, int_values[p]))
for p in string_values.keys():
params[p] = request.POST.get(p, string_values[p])
relation_map = get_relation_to_id_map(project_id)
class_map = get_class_to_id_map(project_id)
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 relate_neuron_to_skeleton(neuron, skeleton):
return _create_relation(request.user, project_id,
relation_map['model_of'], skeleton, neuron)
response_on_error = ''
try:
if -1 != int(params['parent_id']): # A root node and parent node exist
# 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 = Treenode.objects.get(pk=params['parent_id'])
response_on_error = 'Could not insert new treenode!'
skeleton = ClassInstance.objects.get(
pk=parent_treenode.skeleton_id)
new_treenode = insert_new_treenode(params['parent_id'], skeleton)
return HttpResponse(
json.dumps({
'treenode_id': new_treenode.id,
'skeleton_id': skeleton.id
}))
else:
# No parent node: We must create a new root node, which needs a
# skeleton and a neuron to belong to.
response_on_error = 'Could not insert new treenode instance!'
new_skeleton = ClassInstance()
new_skeleton.user = request.user
new_skeleton.project_id = project_id
new_skeleton.class_column_id = class_map['skeleton']
new_skeleton.name = 'skeleton'
new_skeleton.save()
new_skeleton.name = 'skeleton %d' % new_skeleton.id
new_skeleton.save()
if -1 == params['useneuron']:
# Check that the neuron to use exists
if 0 == ClassInstance.objects.filter(
pk=params['useneuron']).count():
params['useneuron'] = -1
if -1 != params['useneuron']:
# Raise an Exception if the user doesn't have permission to
# edit the existing neuron.
can_edit_class_instance_or_fail(request.user,
params['useneuron'], 'neuron')
# A neuron already exists, so we use it
response_on_error = 'Could not relate the neuron model to ' \
'the new skeleton!'
relate_neuron_to_skeleton(params['useneuron'], new_skeleton.id)
response_on_error = 'Could not insert new treenode!'
new_treenode = insert_new_treenode(None, new_skeleton)
return HttpResponse(
json.dumps({
'treenode_id': new_treenode.id,
'skeleton_id': new_skeleton.id,
'neuron_id': params['useneuron']
}))
else:
# A neuron does not exist, therefore we put the new skeleton
# into a new neuron.
response_on_error = 'Failed to insert new instance of a neuron.'
new_neuron = ClassInstance()
new_neuron.user = request.user
new_neuron.project_id = project_id
new_neuron.class_column_id = class_map['neuron']
new_neuron.name = 'neuron'
new_neuron.save()
new_neuron.name = 'neuron %d' % new_neuron.id
new_neuron.save()
response_on_error = 'Could not relate the neuron model to ' \
'the new skeleton!'
relate_neuron_to_skeleton(new_neuron.id, new_skeleton.id)
response_on_error = 'Failed to insert instance of treenode.'
new_treenode = insert_new_treenode(None, new_skeleton)
response_on_error = 'Failed to write to logs.'
new_location = (new_treenode.location_x,
new_treenode.location_y,
new_treenode.location_z)
insert_into_log(
project_id, request.user.id, 'create_neuron', new_location,
'Create neuron %d and skeleton '
'%d' % (new_neuron.id, new_skeleton.id))
return HttpResponse(
json.dumps({
'treenode_id': new_treenode.id,
'skeleton_id': new_skeleton.id,
}))
except Exception as e:
import traceback
raise Exception(
"%s: %s %s" %
(response_on_error, str(e), str(traceback.format_exc())))
