diff --git a/neuvue_project/neuvue/settings.py b/neuvue_project/neuvue/settings.py index 9460acea..d17acc06 100644 --- a/neuvue_project/neuvue/settings.py +++ b/neuvue_project/neuvue/settings.py @@ -208,6 +208,8 @@ NEUVUE_CLIENT_SETTINGS = { # "local" : True } +NUCLEUS_NUERON_SVM = 'nucleus_neuron_svm' +CELL_CLASS_MODEL = 'allen_soma_coarse_cell_class_model_v2' # Task Timeout in Seconds TIMEOUT = 900 diff --git a/neuvue_project/neuvue/urls.py b/neuvue_project/neuvue/urls.py index 2075cf4f..0270ff17 100644 --- a/neuvue_project/neuvue/urls.py +++ b/neuvue_project/neuvue/urls.py @@ -26,6 +26,7 @@ LineageView, TokenView, SynapseView, + NucleiView, GettingStartedView, SaveStateView, SaveOperationsView @@ -56,6 +57,8 @@ path('synapse/', SynapseView.as_view(), name="synapse"), path('synapse/', SynapseView.as_view(), name="synapse"), path('synapse/////', SynapseView.as_view(), name="synapse"), + path('nuclei/', NucleiView.as_view(), name="nuclei"), + path('nuclei/', NucleiView.as_view(), name="nuclei"), path('report/', ReportView.as_view(), name="report"), path('userNamespace/', UserNamespaceView.as_view(), name="user-namespace"), path('save_state', SaveStateView.as_view(), name="save-state"), diff --git a/neuvue_project/templates/base.html b/neuvue_project/templates/base.html index 2e356c78..403eb933 100644 --- a/neuvue_project/templates/base.html +++ b/neuvue_project/templates/base.html @@ -55,8 +55,15 @@
  • Inspect Task
    • -
  • - Synapse Viewer +
  • + +
  • diff --git a/neuvue_project/templates/nuclei.html b/neuvue_project/templates/nuclei.html new file mode 100644 index 00000000..ddc0b40a --- /dev/null +++ b/neuvue_project/templates/nuclei.html @@ -0,0 +1,127 @@ +{% extends "base.html" %} +{% load static %} +{% load socialaccount %} + +{% block content %} + +{% if not nuclei_ids or error %} + +
    +
    +
    + {% csrf_token %} +
    + + +
    +
    +
    + +
    + {% if error%} + {{error}} + {% endif %} +
    +
    +
    +
    + +{% else %} + +
    + +
    + + +
    +
    + Nuclei Information +
    +
    + + {{cell_types|safe}} +
    +
    +
    +
    +
    +
    +
    +
    +
    + +
    +
    + +
    +
    +
    +
    + +
    +
    +
    + + +{% endif%} + + + + + + + + + +{% endblock %} diff --git a/neuvue_project/workspace/neuroglancer.py b/neuvue_project/workspace/neuroglancer.py index 382f1d34..38eac333 100644 --- a/neuvue_project/workspace/neuroglancer.py +++ b/neuvue_project/workspace/neuroglancer.py @@ -154,7 +154,7 @@ def create_path_state(): def create_point_state(name='annotations', group=None, description=None, color=None): """Create the annotation state for points. - Dontt tuse linemapper, just creates a neuroglancer link that is just Points + Dont use linemapper, just creates a neuroglancer link that is just Points nglui statebuilder Returns: StateBuilder: Annotation State @@ -323,11 +323,11 @@ def _get_soma_center(root_ids: List, cave_client): array: array for the position of the soma """ try: - soma_df = cave_client.materialize.query_table('nucleus_neuron_svm', filter_in_dict={ + soma_df = cave_client.materialize.query_table(settings.NUCLEUS_NUERON_SVM, filter_in_dict={ 'pt_root_id': root_ids[:3] }) if not len(soma_df): - soma_df = cave_client.materialize.query_table('nucleus_neuron_svm', filter_in_dict={ + soma_df = cave_client.materialize.query_table(settings.NUCLEUS_NUERON_SVM, filter_in_dict={ 'pt_root_id': root_ids }) if len(soma_df) > 3: @@ -672,6 +672,79 @@ def construct_synapse_state(root_ids: List, flags: dict = None): }) return json.dumps(state_dict), synapse_stats +def construct_nuclei_state(nuclei_ids: List): + """Construct state for the synapse viewer. + + Args: + root_ids (list): segment root id + flags (dict): query parameters + - pre_synapses + - post_synapses + - cleft_layer + - timestamp + + Returns: + string: json-formatted state + dict: synapse stats + """ + cave_client = CAVEclient('minnie65_phase3_v1', auth_token=os.environ['CAVECLIENT_TOKEN']) + soma_df = cave_client.materialize.query_table(settings.NUCLEUS_NUERON_SVM, filter_in_dict={ + 'id': nuclei_ids + }) + + root_ids = soma_df['pt_root_id'].values + nuclei_points = np.array(soma_df['pt_position'].values) + position = nuclei_points[0] if len(nuclei_points) else [] # check what happens when bad values are returned -- add an error case + + data_list = [None] + base_state = create_base_state(root_ids, position) + + # Random color generation + r = lambda: random.randint(0, 255) + states = [base_state] + + def generate_cell_type_table(soma_df): + """Generates Cell type table + returns filtered list of valid ids (i.e. listed in NUCLEUS_NEURON_SVM table) and their cell types if available, else NaN + """ + def get_cell_type(nuclei_id, cell_class_df): + filtered_row = cell_class_df[cell_class_df.id == nuclei_id] + cell_type = filtered_row.cell_type.values[0] if len(filtered_row) else "NaN" + return cell_type + + cell_class_info_df = cave_client.materialize.query_table(settings.CELL_CLASS_MODEL, filter_in_dict={ + 'id': soma_df.id.values + }) + + updated_soma_df = pd.merge(soma_df, cell_class_info_df, on='id', how='outer') + updated_soma_df.cell_type_y = updated_soma_df.cell_type_y.fillna('unknown') + + type_table = 'Nuclei IDType' + for nucleus_id in updated_soma_df.id.values: + cell_type = get_cell_type(nucleus_id, cell_class_info_df) + type_table += ''+str(nucleus_id)+''+cell_type+'' + type_table += '' + + return type_table, updated_soma_df + + + cell_type_table, soma_df = generate_cell_type_table(soma_df) + + for cell_type, type_df in soma_df.groupby('cell_type_y'): + data_list.append(generate_point_df(np.array(type_df['pt_position_x'].values))) + states.append( + create_point_state(name=f'{cell_type}_nuclei_points', color='#{:02x}{:02x}{:02x}'.format(r(), r(), r()))) + + chained_state = ChainedStateBuilder(states) + + state_dict = chained_state.render_state(return_as='dict', data_list=data_list) + state_dict['layout'] = '3d' + state_dict["selectedLayer"] = {"layer": "seg", "visible": True} + state_dict['jsonStateServer'] = settings.JSON_STATE_SERVER + + return json.dumps(state_dict), cell_type_table + + def refresh_ids(ng_state:str, namespace:str): namespace = Namespace.objects.get(namespace=namespace) if not namespace.refresh_selected_root_ids: diff --git a/neuvue_project/workspace/views.py b/neuvue_project/workspace/views.py index 8181eb5a..48cfe363 100644 --- a/neuvue_project/workspace/views.py +++ b/neuvue_project/workspace/views.py @@ -17,6 +17,7 @@ construct_proofreading_state, construct_lineage_state_and_graph, construct_synapse_state, + construct_nuclei_state, get_from_state_server, post_to_state_server, get_from_json, @@ -820,6 +821,42 @@ def post(self, request, *args, **kwargs): "timestamp": timestamp })) +class NucleiView(View): + def get(self, request, nuclei_ids=None, *args, **kwargs): + if not is_authorized(request.user): + logging.warning(f'Unauthorized requests from {request.user}.') + return redirect(reverse('index')) + + if nuclei_ids in settings.STATIC_NG_FILES: + return redirect(f'/static/workspace/{nuclei_ids}', content_type='application/javascript') + + context = { + "nuclei_ids": None, + "error": None + } + + if nuclei_ids is None: + return render(request, "nuclei.html", context) + + nuclei_ids = [x.strip() for x in nuclei_ids.split(',')] + + try: + context['nuclei_ids'] = nuclei_ids + context['ng_state'], context['cell_types'] = construct_nuclei_state(nuclei_ids=nuclei_ids) + except Exception as e: + context['error'] = e + + return render(request, "nuclei.html", context) + + + def post(self, request, *args, **kwargs): + nuclei_ids = request.POST.get("nuclei_ids") + + return redirect(reverse('nuclei', kwargs={ + "nuclei_ids": nuclei_ids, + })) + + #TODO: Move simple views to other file class IndexView(View):