def label_update(request,
project_id=None,
location_id=None,
ntype=None,
logged_in_user=None):
labeled_as_relation = Relation.objects.get(project=project_id,
relation_name='labeled_as')
p = get_object_or_404(Project, pk=project_id)
if ntype == 'treenode':
TreenodeClassInstance.objects.filter(
treenode__id=location_id,
relation=labeled_as_relation,
class_instance__class_column__class_name='label').delete()
elif ntype == 'connector' or ntype == 'location':
ConnectorClassInstance.objects.filter(
connector__id=location_id,
relation=labeled_as_relation,
class_instance__class_column__class_name='label').delete()
else:
raise Http404('Unknown node type: "%s"' % (ntype, ))
label_class = Class.objects.get(project=project_id, class_name='label')
for tag_name in json.loads(request.POST['tags']):
existing_tags = list(
ClassInstance.objects.filter(project=p,
name=tag_name,
class_column=label_class))
if len(existing_tags) < 1:
tag = ClassInstance(project=p,
name=tag_name,
user=logged_in_user,
class_column=label_class)
tag.save()
else:
tag = existing_tags[0]
if ntype == 'treenode':
tci = TreenodeClassInstance(user=logged_in_user,
project=p,
relation=labeled_as_relation,
treenode=Treenode(id=location_id),
class_instance=tag)
else:
tci = ConnectorClassInstance(user=logged_in_user,
project=p,
relation=labeled_as_relation,
connector=Connector(id=location_id),
class_instance=tag)
tci.save()
return HttpResponse(json.dumps({'message': 'success'}),
mimetype='text/json')
def label_update(request, project_id=None, location_id=None, ntype=None, logged_in_user=None):
labeled_as_relation = Relation.objects.get(project=project_id, relation_name='labeled_as')
p = get_object_or_404(Project, pk=project_id)
if ntype == 'treenode':
TreenodeClassInstance.objects.filter(
treenode__id=location_id,
relation=labeled_as_relation,
class_instance__class_column__class_name='label').delete()
elif ntype == 'connector' or ntype == 'location':
ConnectorClassInstance.objects.filter(
connector__id=location_id,
relation=labeled_as_relation,
class_instance__class_column__class_name='label').delete()
else:
raise Http404('Unknown node type: "%s"' % (ntype,))
label_class = Class.objects.get(project=project_id, class_name='label')
for tag_name in json.loads(request.POST['tags']):
existing_tags = list(ClassInstance.objects.filter(
project=p,
name=tag_name,
class_column=label_class))
if len(existing_tags) < 1:
tag = ClassInstance(
project=p,
name=tag_name,
user=logged_in_user,
class_column=label_class)
tag.save()
else:
tag = existing_tags[0]
if ntype == 'treenode':
tci = TreenodeClassInstance(
user=logged_in_user,
project=p,
relation=labeled_as_relation,
treenode=Treenode(id=location_id),
class_instance=tag)
else:
tci = ConnectorClassInstance(
user=logged_in_user,
project=p,
relation=labeled_as_relation,
connector=Connector(id=location_id),
class_instance=tag)
tci.save()
return HttpResponse(json.dumps({'message': 'success'}), mimetype='text/json')
def lines_add(request, project_id=None, logged_in_user=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, logged_in_user=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 split_skeleton(request, project_id=None, logged_in_user=None):
treenode_id = request.POST['tnid']
p = get_object_or_404(Project, pk=project_id)
# retrieve skeleton
ci = ClassInstance.objects.get(
project=project_id,
class_column__class_name='skeleton',
treenodeclassinstance__relation__relation_name='element_of',
treenodeclassinstance__treenode__id=treenode_id)
skeleton_id = ci.id
# retrieve neuron id of this skeleton
sk = get_object_or_404(ClassInstance, pk=skeleton_id, project=project_id)
neuron = ClassInstance.objects.filter(
project=p,
cici_via_b__relation__relation_name='model_of',
cici_via_b__class_instance_a=sk)
# retrieve all nodes of the skeleton
treenode_qs = Treenode.objects.filter(
treenodeclassinstance__class_instance__id=skeleton_id,
treenodeclassinstance__relation__relation_name='element_of',
treenodeclassinstance__class_instance__class_column__class_name='skeleton',
project=project_id).order_by('id')
# build the networkx graph from it
graph = nx.DiGraph()
for e in treenode_qs:
graph.add_node( e.id )
if e.parent_id:
graph.add_edge( e.parent_id, e.id )
# find downstream nodes starting from target treenode_id
# generate id list from it
change_list = nx.bfs_tree(graph, int(treenode_id)).nodes()
# create a new skeleton
new_skeleton = ClassInstance()
new_skeleton.name = 'Skeleton'
new_skeleton.project = p
new_skeleton.user = logged_in_user
new_skeleton.class_column = Class.objects.get(class_name='skeleton', project=p)
new_skeleton.save()
new_skeleton.name = 'Skeleton {0}'.format( new_skeleton.id )
new_skeleton.save()
r = Relation.objects.get(relation_name='model_of', project=p)
cici = ClassInstanceClassInstance()
cici.class_instance_a = new_skeleton
cici.class_instance_b = neuron[0]
cici.relation = r
cici.user = logged_in_user
cici.project = p
cici.save()
# update skeleton_id of list in treenode table
tns = Treenode.objects.filter(
id__in=change_list,
project=project_id).update(skeleton=new_skeleton)
# update treenodeclassinstance element_of relation
tci = TreenodeClassInstance.objects.filter(
relation__relation_name='element_of',
treenode__id__in=change_list,
project=project_id).update(class_instance=new_skeleton)
# setting parent of target treenode to null
tc = TreenodeConnector.objects.filter(
project=project_id,
relation__relation_name__endswith = 'synaptic_to',
treenode__in=change_list,
).update(skeleton=new_skeleton)
Treenode.objects.filter(
id=treenode_id,
project=project_id).update(parent=None)
locations = Location.objects.filter(
project=project_id,
id=treenode_id
)
if len(locations) > 0:
location = locations[0].location
insert_into_log( project_id, logged_in_user.id, "split_skeleton", location, "Split skeleton with ID {0} (neuron: {1})".format( skeleton_id, neuron[0].name ) )
return HttpResponse(json.dumps({}), mimetype='text/json')
