diff --git a/.github/workflows/pytest.yml b/.github/workflows/pytest.yml new file mode 100644 index 00000000..c051f7df --- /dev/null +++ b/.github/workflows/pytest.yml @@ -0,0 +1,24 @@ +name: Python Tests + +on: [push, pull_request] + +jobs: + pytest: + runs-on: ubuntu-latest + defaults: + run: + working-directory: ./applications/visualizer/backend + steps: + - uses: actions/checkout@v4 + - name: Set up Python + uses: actions/setup-python@v5 + with: + python-version: '3.12' + - name: Install dependencies and dev dependencies + run: | + python -m pip install --upgrade pip + pip install -r requirements.txt + pip install -r requirements-dev.txt + - name: Test with pytest + run: | + python -m pytest \ No newline at end of file diff --git a/applications/visualizer/api/openapi.json b/applications/visualizer/api/openapi.json index 90d68f86..2e6b80c7 100644 --- a/applications/visualizer/api/openapi.json +++ b/applications/visualizer/api/openapi.json @@ -530,9 +530,12 @@ "title": "Datasetids", "type": "array" }, - "model3DUrl": { - "title": "Model3Durl", - "type": "string" + "model3DUrls": { + "items": { + "type": "string" + }, + "title": "Model3Durls", + "type": "array" }, "nclass": { "maxLength": 30, @@ -568,7 +571,7 @@ "required": [ "name", "datasetIds", - "model3DUrl", + "model3DUrls", "nclass", "neurotransmitter", "type" diff --git a/applications/visualizer/api/openapi.yaml b/applications/visualizer/api/openapi.yaml index 9171cbf8..617f653f 100644 --- a/applications/visualizer/api/openapi.yaml +++ b/applications/visualizer/api/openapi.yaml @@ -142,9 +142,11 @@ components: default: false title: Intail type: boolean - model3DUrl: - title: Model3Durl - type: string + model3DUrls: + items: + type: string + title: Model3Durls + type: array name: title: Name type: string @@ -163,7 +165,7 @@ components: required: - name - datasetIds - - model3DUrl + - model3DUrls - nclass - neurotransmitter - type diff --git a/applications/visualizer/backend/api/api.py b/applications/visualizer/backend/api/api.py index bcb601d9..c738a6d1 100644 --- a/applications/visualizer/backend/api/api.py +++ b/applications/visualizer/backend/api/api.py @@ -14,7 +14,7 @@ Neuron as NeuronModel, Connection as ConnectionModel, ) -from .services.connectivity import query_connections +from .services.connectivity import query_nematode_connections class ErrorMessage(Schema): @@ -132,7 +132,7 @@ def annotate_neurons(neurons: BaseManager[NeuronModel]) -> None: for neuron in neurons: name = neuron.name neuron.dataset_ids = neurons_dataset_ids[name] # type: ignore - neuron.model3D_url = settings.NEURON_REPRESENTATION_3D_URL_FORMAT.format(name=name) # type: ignore + neuron.model3D_urls = [settings.NEURON_REPRESENTATION_3D_URL_FORMAT.format(name=name)] # type: ignore def neurons_from_datasets( @@ -218,7 +218,7 @@ def get_connections( include_annotations: bool = False, ): """Gets the connections of a dedicated Dataset""" - return query_connections( + return query_nematode_connections( [c.strip() for c in cells.split(",")], [d.strip() for d in dataset_ids.split(",")], [d.strip() for d in dataset_type.split(",")], diff --git a/applications/visualizer/backend/api/schemas.py b/applications/visualizer/backend/api/schemas.py index 65e77b39..36705c32 100644 --- a/applications/visualizer/backend/api/schemas.py +++ b/applications/visualizer/backend/api/schemas.py @@ -56,7 +56,7 @@ class Meta: class Neuron(ModelSchema, BilingualSchema): name: str dataset_ids: list[str] - model3D_url: str + model3D_urls: list[str] class Meta: model = NeuronModel diff --git a/applications/visualizer/backend/api/services/connectivity.py b/applications/visualizer/backend/api/services/connectivity.py index b45b3f8f..1f710a12 100644 --- a/applications/visualizer/backend/api/services/connectivity.py +++ b/applications/visualizer/backend/api/services/connectivity.py @@ -1,11 +1,12 @@ from collections import defaultdict +from api.models import Annotation, Connection -from django.db.models import Q -from api.models import Annotation, Connection +## This module was converted from the original nemanode code found here: +## https://github.com/zhenlab-ltri/NemaNode/blob/master/src/server/db/nematode-connections.js -def query_connections( +def query_nematode_connections( cells: list[str], dataset_ids: list[str], dataset_type: list[str], @@ -14,7 +15,21 @@ def query_connections( include_neighboring_cells: bool, include_annotations: bool, ): - connections = _query_raw_connections( + if not cells: + return [] + + annotations_map = defaultdict(list) + if include_annotations: + annotations = query_annotations(cells, include_neighboring_cells, dataset_type) + for annotation in annotations: + pre = annotation["pre"] + post = annotation["post"] + connection_type = annotation["type"] + annotation_type = annotation["annotation"] + key = get_connection_primary_key(pre, post, connection_type) + annotations_map[key].append(annotation_type) + + raw_connections = query_connections( cells, dataset_ids, include_neighboring_cells, @@ -22,100 +37,158 @@ def query_connections( threshold_electrical, ) - annotations_map = _query_annotations( - cells, dataset_type, include_annotations, include_neighboring_cells - ) - + connections = [] + # Group raw_connections by the connection key grouped_connections = defaultdict(list) - for connection in connections: - key = _get_connection_key(connection.pre, connection.post, connection.type) - grouped_connections[key].append(connection) + for raw_conn in raw_connections: + key = get_connection_primary_key( + raw_conn["pre"], raw_conn["post"], raw_conn["type"] + ) + grouped_connections[key].append(raw_conn) - response_data = [] - for key, group in grouped_connections.items(): - synapses = {conn.dataset_id: conn.synapses for conn in group} + for key, grouped in grouped_connections.items(): + pre = grouped[0]["pre"] + post = grouped[0]["post"] + type_ = grouped[0]["type"] + annotations = annotations_map[key] if include_annotations else [] - # It's safe to access the first item directly as group won't be empty by design of the grouping process - connection = group[0] - response_data.append( + # Accumulate all synapses for the grouped connections + synapses = {g["dataset_id"]: g["synapses"] for g in grouped} + + connections.append( { - "pre": connection.pre, - "post": connection.post, - "type": connection.type, - "annotations": ( - annotations_map.get(key, []) if include_annotations else [] - ), + "pre": pre, + "post": post, + "type": type_, + "annotations": annotations, "synapses": synapses, } ) + gap_junctions = [c for c in connections if c["type"] == "electrical"] + chemical_synapses = [c for c in connections if c["type"] == "chemical"] - return response_data + merged_gap_junctions = merge_gap_junctions(gap_junctions) + return merged_gap_junctions + chemical_synapses -# SELECT pre, post, type, annotation -# FROM annotations -# WHERE (pre in (${cells}) -# ${includeNeighboringCells ? 'OR' : 'AND'} post in (${cells})) -# AND collection in (${datasetType}) +def get_connection_primary_key(pre, post, type_): + return hash(f"{pre}-{post}-{type_}") -def _query_annotations( - cells, dataset_type, include_annotations, include_neighboring_cells -): - if not include_annotations: - return {} - annotations_map = defaultdict(list) - annotations = Annotation.objects.filter( - ( - Q(pre__in=cells) | Q(post__in=cells) - if include_neighboring_cells - else Q(pre__in=cells, post__in=cells) - ), - collection__in=dataset_type, - ) - for annotation in annotations: - key = _get_connection_key(annotation.pre, annotation.post, annotation.type) - annotations_map[key].append(annotation.annotation) - return annotations_map - - -# SELECT c.pre, c.post, c.type, c.dataset_id, c.synapses from ( -# SELECT pre, post, type -# FROM connections -# WHERE (pre IN (${cells}) -# ${includeNeighboringCells ? 'OR' : 'AND'} post IN (${cells})) -# AND dataset_id IN (${datasetIds}) -# AND ( -# (type = 'chemical' && synapses >= ${thresholdChemical}) -# OR (type = 'electrical' && synapses >= ${thresholdElectrical}) -# ) -# GROUP BY pre, post, type -# ) f -# LEFT JOIN connections c ON f.pre = c.pre AND f.post = c.post AND f.type = c.type -# WHERE c.dataset_id IN (${datasetIds}) - - -def _query_raw_connections( +def merge_gap_junctions(gap_junctions): + gap_junctions_key_map = {} + + for gj in gap_junctions: + pre, post = gj["pre"], gj["post"] + synapses = gj["synapses"] + key = "$".join(sorted([pre, post])) + + if key not in gap_junctions_key_map: + gap_junctions_key_map[key] = gj + else: + for dataset, synapse_count in synapses.items(): + if dataset in gap_junctions_key_map[key]["synapses"]: + gap_junctions_key_map[key]["synapses"][dataset] += synapse_count + else: + gap_junctions_key_map[key]["synapses"][dataset] = synapse_count + + merged = [] + for gj_key, gj in gap_junctions_key_map.items(): + pre, post = gj_key.split("$") + type_, synapses, annotations = gj["type"], gj["synapses"], gj["annotations"] + merged.append( + { + "pre": pre, + "post": post, + "type": type_, + "synapses": synapses, + "annotations": annotations, + } + ) + + return merged + + +def query_annotations(cells, include_neighboring_cells, dataset_type): + # Prepare the SQL query + sql_query = f""" + SELECT id, pre, post, type, annotation + FROM api_annotation + WHERE (pre IN ({', '.join(['%s'] * len(cells))}) + {'OR' if include_neighboring_cells else 'AND'} post IN ({', '.join(['%s'] * len(cells))})) + AND collection IN ({', '.join(['%s'] * len(dataset_type))}) + """ + + # Combine all parameters into a single list for passing to the query + params = cells + cells + dataset_type + + # Execute the raw query using Django's raw() method + annotations = Annotation.objects.raw(sql_query, params) + + # Convert the result to a list of dictionaries + results = [ + { + "pre": annotation.pre, + "post": annotation.post, + "type": annotation.type, + "annotation": annotation.annotation, + } + for annotation in annotations + ] + + return results + + +def query_connections( cells, dataset_ids, include_neighboring_cells, threshold_chemical, threshold_electrical, ): - connection_query = ( - Q(pre__in=cells) | Q(post__in=cells) - if include_neighboring_cells - else Q(pre__in=cells, post__in=cells) - ) - connection_query &= Q(dataset_id__in=dataset_ids) - connection_query &= Q(type="chemical", synapses__gte=threshold_chemical) | Q( - type="electrical", synapses__gte=threshold_electrical + # Prepare the SQL query + sql_query = f""" + SELECT c.id, c.pre, c.post, c.type, c.dataset_id, c.synapses + FROM ( + SELECT pre, post, type + FROM api_connection + WHERE (pre IN ({', '.join(['%s'] * len(cells))}) + {'OR' if include_neighboring_cells else 'AND'} post IN ({', '.join(['%s'] * len(cells))})) + AND dataset_id IN ({', '.join(['%s'] * len(dataset_ids))}) + AND ( + (type = 'chemical' AND synapses >= %s) + OR (type = 'electrical' AND synapses >= %s) + ) + GROUP BY pre, post, type + ) f + LEFT JOIN api_connection c ON f.pre = c.pre AND f.post = c.post AND f.type = c.type + WHERE c.dataset_id IN ({', '.join(['%s'] * len(dataset_ids))}) + """ + + # Combine all parameters into a single list for passing to the query + params = ( + cells + + cells + + dataset_ids + + [threshold_chemical, threshold_electrical] + + dataset_ids ) - return ( - Connection.objects.filter(connection_query).select_related("dataset").distinct() - ) - -def _get_connection_key(pre, post, connection_type): - return pre, post, connection_type + # Execute the raw query using Django's raw() method + connections = Connection.objects.raw(sql_query, params) + + # Convert the result to a list of dictionaries (similar to what Django ORM's .values() would return) + results = [ + { + "id": connection.id, + "pre": connection.pre, + "post": connection.post, + "type": connection.type, + "dataset_id": connection.dataset_id, + "synapses": connection.synapses, + } + for connection in connections + ] + + return results diff --git a/applications/visualizer/backend/openapi/openapi.json b/applications/visualizer/backend/openapi/openapi.json index 90d68f86..2e6b80c7 100644 --- a/applications/visualizer/backend/openapi/openapi.json +++ b/applications/visualizer/backend/openapi/openapi.json @@ -530,9 +530,12 @@ "title": "Datasetids", "type": "array" }, - "model3DUrl": { - "title": "Model3Durl", - "type": "string" + "model3DUrls": { + "items": { + "type": "string" + }, + "title": "Model3Durls", + "type": "array" }, "nclass": { "maxLength": 30, @@ -568,7 +571,7 @@ "required": [ "name", "datasetIds", - "model3DUrl", + "model3DUrls", "nclass", "neurotransmitter", "type" diff --git a/applications/visualizer/backend/tests/test_neurons.py b/applications/visualizer/backend/tests/test_neurons.py index 860ff934..2b70b4a6 100644 --- a/applications/visualizer/backend/tests/test_neurons.py +++ b/applications/visualizer/backend/tests/test_neurons.py @@ -4,7 +4,6 @@ from pytest_unordered import unordered from api.models import ( - Dataset as DatasetModel, Neuron as NeuronModel, Connection as ConnectionModel, ) @@ -13,21 +12,6 @@ # Some test data -datasets = [ - { - "id": "ds1", - "name": "Dataset 1", - }, - { - "id": "ds2", - "name": "Gamma Goblin", - }, - { - "id": "ds3", - "name": "Dr. Seuss", - }, -] - neurons = [ { "name": "ADAL", @@ -67,24 +51,39 @@ }, ] -connections = lambda: [ +datasets = [ + { + "id": "ds1", + "name": "Dataset 1", + }, + { + "id": "ds2", + "name": "Gamma Goblin", + }, + { + "id": "ds3", + "name": "Dr. Seuss", + }, +] + +connections = [ { - "dataset": DatasetModel.objects.get(id="ds1"), + "dataset": datasets[0], "pre": "ADAL", "post": "ADAR", }, { - "dataset": DatasetModel.objects.get(id="ds2"), + "dataset": datasets[1], "pre": "ADEL", "post": "ADER", }, { - "dataset": DatasetModel.objects.get(id="ds2"), + "dataset": datasets[1], "pre": "ADAR", "post": "ADEL", }, { - "dataset": DatasetModel.objects.get(id="ds3"), + "dataset": datasets[2], "pre": "ADFR", "post": "ADAR", }, @@ -98,9 +97,8 @@ @pytest.fixture(scope="module") def django_db_setup(django_db_setup, django_db_blocker): with django_db_blocker.unblock(): - generate_instance(DatasetModel, datasets) generate_instance(NeuronModel, neurons) - generate_instance(ConnectionModel, connections()) + generate_instance(ConnectionModel, connections) # Fixture to access the test client in all test functions @@ -125,6 +123,8 @@ def test__get_all_cells(api_client): assert response.status_code == 200 neurons = response.json()["items"] + assert len(neurons) == len(expected_dataset_ids) + for neuron in neurons: name = neuron["name"] @@ -154,6 +154,9 @@ def test__get_all_cells_from_specific_datasets(api_client): assert response.status_code == 200 neurons = response.json()["items"] + + assert len(neurons) == len(expected_dataset_ids) + for neuron in neurons: name = neuron["name"] @@ -174,12 +177,11 @@ def test__search_cells(api_client): expected_neurons_names ), f"expected to query {len(expected_neurons_names)} and got {len(neurons)}" - for neuron in neurons: - assert neuron["name"] in expected_neurons_names + assert [n["name"] for n in neurons] == expected_neurons_names @pytest.mark.django_db # required to access the DB -def test__search_cells_in_datasets(api_client): +def test__search_cells_in_datasets_without_match(api_client): search_query = "ade" dataset_ids = ["ds1", "ds3"] @@ -193,22 +195,23 @@ def test__search_cells_in_datasets(api_client): neurons = response.json() assert len(neurons) == 0, f"expected datasets to not contain search matches" + +@pytest.mark.django_db # required to access the DB +def test__search_cells_in_datasets_with_match(api_client): + dataset_ids = ["ds1", "ds3", "ds2"] + search_query = "ade" + # Search dataset with matching neurons - dataset_ids.append("ds2") expected_neurons_names = ["ADEL", "ADER"] query_params = f"?name={search_query}&" + 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"^18.3.3", "@types/react-dom": "^18.3.0", - "@types/cytoscape": "^3.21.5", "@types/three": "^0.166.0", "@vitejs/plugin-react": "^4.2.1", "openapi-typescript-codegen": "^0.29.0", diff --git a/applications/visualizer/frontend/src/App.tsx b/applications/visualizer/frontend/src/App.tsx index e85ea373..44799a37 100644 --- a/applications/visualizer/frontend/src/App.tsx +++ b/applications/visualizer/frontend/src/App.tsx @@ -4,12 +4,14 @@ import { Provider } from "react-redux"; import theme from "./theme/index.tsx"; import "./App.css"; import React from "react"; +import { BrowserRouter, Route, Routes } from "react-router-dom"; import AppLauncher from "./components/AppLauncher.tsx"; import Layout from "./components/ViewerContainer/Layout.tsx"; import WorkspaceComponent from "./components/WorkspaceComponent.tsx"; import CompareWrapper from "./components/wrappers/Compare.tsx"; import DefaultWrapper from "./components/wrappers/Default.tsx"; import { useGlobalContext } from "./contexts/GlobalContext.tsx"; +import GlobalContextReloader from "./contexts/GlobalContextReloader.tsx"; import { ViewMode } from "./models"; function App() { @@ -44,19 +46,27 @@ function App() { }; return ( - <> + - {hasLaunched ? ( - - - {renderWorkspaces()} - - ) : ( - - )} + + + + {renderWorkspaces()} + + ) : ( + + ) + } + /> + } /> + - + ); } diff --git a/applications/visualizer/frontend/src/components/CreateNewWorkspaceDialog.tsx b/applications/visualizer/frontend/src/components/CreateNewWorkspaceDialog.tsx index 89c8155d..0810ee40 100644 --- a/applications/visualizer/frontend/src/components/CreateNewWorkspaceDialog.tsx +++ b/applications/visualizer/frontend/src/components/CreateNewWorkspaceDialog.tsx @@ -4,38 +4,47 @@ import { useCallback, useState } from "react"; import { v4 as uuidv4 } from "uuid"; import { useGlobalContext } from "../contexts/GlobalContext.tsx"; import { CaretIcon, CheckIcon, CloseIcon } from "../icons"; -import { type Dataset, type Neuron, NeuronsService } from "../rest"; +import { GlobalError } from "../models/Error.ts"; +import { type Dataset, NeuronsService } from "../rest"; import { vars as colors } from "../theme/variables.ts"; import CustomAutocomplete from "./CustomAutocomplete.tsx"; import CustomDialog from "./CustomDialog.tsx"; const CreateNewWorkspaceDialog = ({ onCloseCreateWorkspace, showCreateWorkspaceDialog, isCompareMode, title, subTitle, submitButtonText }) => { - const [neurons, setNeurons] = useState([]); - const { workspaces, datasets, createWorkspace, setSelectedWorkspacesIds } = useGlobalContext(); + const [neuronNames, setNeuronsNames] = useState([]); + const { workspaces, datasets, createWorkspace, setSelectedWorkspacesIds, handleErrors } = useGlobalContext(); const [searchedNeuron, setSearchedNeuron] = useState(""); const [formValues, setFormValues] = useState<{ workspaceName: string; selectedDatasets: Dataset[]; - selectedNeurons: Neuron[]; + selectedNeurons: string[]; }>({ workspaceName: "", selectedDatasets: [], selectedNeurons: [], }); - const [errorMessage, setErrorMessage] = useState(""); const workspaceFieldName = "workspaceName"; + const fetchNeurons = async (name, datasetsIds) => { try { const Ids = datasetsIds.map((dataset) => dataset.id); - const response = await NeuronsService.searchCells({ + const neuronArrays = await NeuronsService.searchCells({ name: name, datasetIds: Ids, }); - setNeurons(response); + + // We add the neurons classes + const uniqueNeurons = new Set(); + for (const neuron of neuronArrays.flat()) { + uniqueNeurons.add(neuron.name); + uniqueNeurons.add(neuron.nclass); + } + + setNeuronsNames([...uniqueNeurons]); } catch (error) { - console.error("Failed to fetch datasets", error); + handleErrors(new GlobalError(error.message)); } }; @@ -78,7 +87,7 @@ const CreateNewWorkspaceDialog = ({ onCloseCreateWorkspace, showCreateWorkspaceD const randomNumber = uuidv4().replace(/\D/g, "").substring(0, 13); const newWorkspaceId = `workspace-${randomNumber}`; - const activeNeurons = new Set(formValues.selectedNeurons.map((neuron) => neuron.name)); + const activeNeurons = new Set(formValues.selectedNeurons); const activeDatasets = new Set(formValues.selectedDatasets.map((dataset) => dataset.id)); createWorkspace(newWorkspaceId, formValues.workspaceName, activeDatasets, activeNeurons); @@ -138,12 +147,11 @@ const CreateNewWorkspaceDialog = ({ onCloseCreateWorkspace, showCreateWorkspaceD Neurons option.name} + options={neuronNames} renderOption={(props, option) => (
  • - {option.name} + {option}
    • )} onInputChange={onSearchNeurons} diff --git a/applications/visualizer/frontend/src/components/CustomAutocomplete.tsx b/applications/visualizer/frontend/src/components/CustomAutocomplete.tsx index bfda7929..2b52570c 100644 --- a/applications/visualizer/frontend/src/components/CustomAutocomplete.tsx +++ b/applications/visualizer/frontend/src/components/CustomAutocomplete.tsx @@ -3,9 +3,10 @@ import type { ChipProps } from "@mui/material/Chip"; import TextField from "@mui/material/TextField"; import type { SxProps } from "@mui/system"; import type React from "react"; + interface CustomAutocompleteProps { options: T[]; - getOptionLabel: (option: T) => string; + getOptionLabel?: (option: T) => string; renderOption: (props: React.HTMLAttributes, option: T) => React.ReactNode; renderInput?: (params: AutocompleteRenderInputParams) => React.ReactNode; groupBy?: (option: T) => string; @@ -19,10 +20,10 @@ interface CustomAutocompleteProps { ChipProps?: ChipProps; sx?: SxProps; componentsProps?: AutocompleteProps["componentsProps"]; - value?: any; - onChange: (v) => void; + value?: T[]; + onChange: (v: T | T[]) => void; disabled?: boolean; - onInputChange?: (v) => void; + onInputChange?: (v: string) => void; } const CommonAutocomplete = ({ @@ -65,7 +66,7 @@ const CommonAutocomplete = ({ groupBy={groupBy} renderGroup={renderGroup} renderOption={renderOption} - renderInput={(params) => onInputChange(e.target.value)} />} + renderInput={(params) => onInputChange?.(e.target.value)} />} sx={sx} componentsProps={componentsProps} /> diff --git a/applications/visualizer/frontend/src/components/ErrorAlert.tsx b/applications/visualizer/frontend/src/components/ErrorAlert.tsx new file mode 100644 index 00000000..a31253e4 --- /dev/null +++ b/applications/visualizer/frontend/src/components/ErrorAlert.tsx @@ -0,0 +1,70 @@ +import { Alert, AlertTitle, Box, Collapse } from "@mui/material"; +import { useEffect } from "react"; + +const ErrorAlert = ({ open, setOpen, errorMessage, autoCloseDuration = 5000 }) => { + useEffect(() => { + if (open) { + const timer = setTimeout(() => { + setOpen(false); + }, autoCloseDuration); + + return () => clearTimeout(timer); + } + }, [open, setOpen, autoCloseDuration]); + + return ( + + + setOpen(false)} + sx={{ + height: "auto !important", + padding: ".5rem 1rem !important", + "& .MuiSvgIcon-root": { + color: "#d32f2f", + "&:hover": { + backgroundColor: "transparent", + }, + }, + "& .MuiAlert-action": { + "& .MuiButtonBase-root": { + "& .MuiSvgIcon-root": { + color: "#d32f2f", + }, + "&:hover": { + backgroundColor: "transparent", + }, + }, + }, + }} + > + + An error has occurred + + {errorMessage} + + + + ); +}; + +export default ErrorAlert; diff --git a/applications/visualizer/frontend/src/components/ErrorBoundary.tsx b/applications/visualizer/frontend/src/components/ErrorBoundary.tsx new file mode 100644 index 00000000..a9996a0b --- /dev/null +++ b/applications/visualizer/frontend/src/components/ErrorBoundary.tsx @@ -0,0 +1,45 @@ +import { Component, type ReactNode } from "react"; + +interface ErrorBoundaryProps { + onError: (error: Error) => void; + children: ReactNode; +} + +interface ErrorBoundaryState { + hasError: boolean; + errorMessage: string; +} + +class ErrorBoundary extends Component { + constructor(props: ErrorBoundaryProps) { + super(props); + this.state = { + hasError: false, + errorMessage: "", + }; + } + + static getDerivedStateFromError(error: Error) { + return { hasError: true, errorMessage: error.message }; + } + + componentDidCatch(error: Error) { + const { onError } = this.props; + this.setState({ hasError: true, errorMessage: error.message }); + onError(error); + } + + render() { + const { hasError } = this.state; + const { children } = this.props; + + return ( + <> + {children} + {hasError && null} + + ); + } +} + +export default ErrorBoundary; diff --git a/applications/visualizer/frontend/src/components/ViewerContainer/CustomEntitiesDropdown.tsx b/applications/visualizer/frontend/src/components/ViewerContainer/CustomEntitiesDropdown.tsx index 051327e8..d9a38e4d 100644 --- a/applications/visualizer/frontend/src/components/ViewerContainer/CustomEntitiesDropdown.tsx +++ b/applications/visualizer/frontend/src/components/ViewerContainer/CustomEntitiesDropdown.tsx @@ -5,7 +5,7 @@ import type React from "react"; import { useEffect, useRef, useState } from "react"; import { CheckIcon } from "../../icons"; import { vars } from "../../theme/variables.ts"; -import type { EnhancedNeuron } from "../../models/models.ts"; +import type { Neuron } from "../../rest/index.ts"; const { gray50, brand600 } = vars; @@ -25,8 +25,8 @@ interface CustomEntitiesDropdownProps { activeNeurons: Set; onNeuronClick?: (neuron: Option) => void; onSearchNeurons?: (value: string) => void; - setNeurons?: (neurons: Record) => void; - availableNeurons: Record; + setNeurons?: (neurons: Record) => void; + availableNeurons: Record; } const CustomEntitiesDropdown = ({ options, activeNeurons, onNeuronClick, onSearchNeurons, setNeurons, availableNeurons }: CustomEntitiesDropdownProps) => { @@ -86,7 +86,7 @@ const CustomEntitiesDropdown = ({ options, activeNeurons, onNeuronClick, onSearc InputProps={{ startAdornment: ( - + ), endAdornment: open && ( @@ -178,7 +178,7 @@ const CustomEntitiesDropdown = ({ options, activeNeurons, onNeuronClick, onSearc >     - {option?.label?.length > 100 ? option?.label.slice(0, 100) + "..." : option?.label} + {option?.label?.length > 100 ? `${option?.label.slice(0, 100)}...` : option?.label} ))} diff --git a/applications/visualizer/frontend/src/components/ViewerContainer/CustomListItem.tsx b/applications/visualizer/frontend/src/components/ViewerContainer/CustomListItem.tsx index 9da39502..aa751522 100644 --- a/applications/visualizer/frontend/src/components/ViewerContainer/CustomListItem.tsx +++ b/applications/visualizer/frontend/src/components/ViewerContainer/CustomListItem.tsx @@ -77,7 +77,7 @@ const CustomListItem = ({ <> + } @@ -116,7 +116,7 @@ const CustomListItem = ({ /> )} - {data?.label?.length > 32 ? data?.label.slice(0, 32) + "..." : data?.label} + {data?.label?.length > 32 ? `${data?.label.slice(0, 32)}...` : data?.label} {showTooltip && ( diff --git a/applications/visualizer/frontend/src/components/ViewerContainer/CustomSwitch.tsx b/applications/visualizer/frontend/src/components/ViewerContainer/CustomSwitch.tsx index 8fc8fda7..4c2b9048 100644 --- a/applications/visualizer/frontend/src/components/ViewerContainer/CustomSwitch.tsx +++ b/applications/visualizer/frontend/src/components/ViewerContainer/CustomSwitch.tsx @@ -1,6 +1,7 @@ import Switch from "@mui/material/Switch"; import Tooltip from "@mui/material/Tooltip"; import type React from "react"; +import { forwardRef } from "react"; import { vars } from "../../theme/variables.ts"; const { white, brand600, gray100 } = vars; @@ -16,57 +17,60 @@ interface CustomSwitchProps { disabled?: boolean; } -const CustomSwitch: React.FC = ({ width, height, thumbDimension, checkedPosition, checked, onChange, showTooltip, disabled }) => { - return ( - - ({ - marginRight: ".5rem", - width: width ?? 23, - height: height ?? 13, - padding: 0, - "& .MuiSwitch-switchBase": { +const CustomSwitch = forwardRef( + ({ width, height, thumbDimension, checkedPosition, checked, onChange, showTooltip, disabled }, ref) => { + return ( + + ({ + marginRight: ".5rem", + width: width ?? 23, + height: height ?? 13, padding: 0, - margin: "0.0938rem", - transitionDuration: "300ms", - "&.Mui-checked": { - transform: checkedPosition ?? "translateX(0.5775rem)", - color: white, - "& + .MuiSwitch-track": { - backgroundColor: brand600, - opacity: 1, - border: 0, + "& .MuiSwitch-switchBase": { + padding: 0, + margin: "0.0938rem", + transitionDuration: "300ms", + "&.Mui-checked": { + transform: checkedPosition ?? "translateX(0.5775rem)", + color: white, + "& + .MuiSwitch-track": { + backgroundColor: brand600, + opacity: 1, + border: 0, + }, + "&.Mui-disabled + .MuiSwitch-track": { + opacity: 0.5, + }, }, - "&.Mui-disabled + .MuiSwitch-track": { - opacity: 0.5, + "&.Mui-disabled .MuiSwitch-thumb": { + color: gray100, }, }, - "&.Mui-disabled .MuiSwitch-thumb": { - color: gray100, + "& .MuiSwitch-thumb": { + boxSizing: "border-box", + width: thumbDimension ?? 10.24, + height: thumbDimension ?? 10.24, + boxShadow: "none", }, - }, - "& .MuiSwitch-thumb": { - boxSizing: "border-box", - width: thumbDimension ?? 10.24, - height: thumbDimension ?? 10.24, - boxShadow: "none", - }, - "& .MuiSwitch-track": { - borderRadius: 26 / 2, - backgroundColor: gray100, - opacity: 1, - transition: theme.transitions.create(["background-color"], { - duration: 500, - }), - }, - })} - /> - - ); -}; + "& .MuiSwitch-track": { + borderRadius: 26 / 2, + backgroundColor: gray100, + opacity: 1, + transition: theme.transitions.create(["background-color"], { + duration: 500, + }), + }, + })} + /> + + ); + }, +); export default CustomSwitch; diff --git a/applications/visualizer/frontend/src/components/ViewerContainer/DataSets.tsx b/applications/visualizer/frontend/src/components/ViewerContainer/DataSets.tsx index 0bd2a3dc..dde2cc1d 100644 --- a/applications/visualizer/frontend/src/components/ViewerContainer/DataSets.tsx +++ b/applications/visualizer/frontend/src/components/ViewerContainer/DataSets.tsx @@ -18,20 +18,23 @@ const categorizeDatasets = (datasets: Dataset[]) => { L1: [], L2: [], L3: [], + L4: [], Adult: [], }; - datasets.forEach((dataset) => { - if (dataset.visualTime >= 0 && dataset.visualTime < 10) { - categories["L1"].push(dataset); - } else if (dataset.visualTime >= 10 && dataset.visualTime < 20) { - categories["L2"].push(dataset); - } else if (dataset.visualTime >= 20 && dataset.visualTime < 30) { - categories["L3"].push(dataset); - } else if (dataset.visualTime >= 30) { - categories["Adult"].push(dataset); + for (const dataset of datasets) { + if (dataset.visualTime >= 0 && dataset.visualTime < 16) { + categories.L1.push(dataset); + } else if (dataset.visualTime >= 16 && dataset.visualTime < 25) { + categories.L2.push(dataset); + } else if (dataset.visualTime >= 25 && dataset.visualTime < 34) { + categories.L3.push(dataset); + } else if (dataset.visualTime >= 34 && dataset.visualTime < 45) { + categories.L4.push(dataset); + } else if (dataset.visualTime >= 45) { + categories.Adult.push(dataset); } - }); + } return categories; }; @@ -97,6 +100,7 @@ const DataSets = ({ children }) => { L1: [], L2: [], L3: [], + L4: [], Adult: [], }; @@ -106,10 +110,18 @@ const DataSets = ({ children }) => { const filteredActiveList = inputValue ? activeDatasetsList.filter((dataset) => dataset.name.toLowerCase().includes(inputValue)) : activeDatasetsList; - setFilteredDatasets(filteredCategories); - setFilterActiveDatasets(filteredActiveList); + if (filterGroupsValue === "All") { + setFilteredDatasets(filteredCategories); + setFilterActiveDatasets(filteredActiveList); + } else { + const activeGroup = filteredCategories[filterGroupsValue]; + const updatedFilteredDatasets = { ...filteredActiveList, [filterGroupsValue]: activeGroup }; + // @ts-ignore + setFilteredDatasets(updatedFilteredDatasets); + const updatedFilteredActiveDatasets = filteredActiveList.filter((dataset) => activeGroup.some((catDataset) => catDataset.id === dataset.id)); + setFilterActiveDatasets(updatedFilteredActiveDatasets); + } }; - const onSelectGroupChange = (e) => { const selectedGroup = e.target.value; setFilterGroupsValue(selectedGroup); @@ -133,11 +145,11 @@ const DataSets = ({ children }) => { const getDatasetsTypes = (datasets: { [key: string]: Dataset }) => { const types = new Set(); - Object.values(datasets).forEach((dataset) => { + for (const dataset of Object.values(datasets)) { if (dataset.type) { types.add(dataset.type); } - }); + } return Array.from(types); }; @@ -149,6 +161,7 @@ const DataSets = ({ children }) => { L1: [], L2: [], L3: [], + L4: [], Adult: [], }; @@ -213,7 +226,7 @@ const DataSets = ({ children }) => { InputProps={{ startAdornment: ( - + ), }} @@ -306,8 +319,8 @@ const DataSets = ({ children }) => { }, }} > - {datasetsTypes.map((type, i) => ( - handleTypeSelect(type)}> + {datasetsTypes.map((type) => ( + handleTypeSelect(type)}> (null); - const { workspaces, setSelectedWorkspacesIds, setViewMode, selectedWorkspacesIds, viewMode, setCurrentWorkspace } = useGlobalContext(); + const { workspaces, setSelectedWorkspacesIds, setViewMode, selectedWorkspacesIds, viewMode, setCurrentWorkspace, serializeGlobalContext } = + useGlobalContext(); const open = Boolean(anchorEl); const handleClick = (event: React.MouseEvent) => { @@ -133,7 +134,7 @@ const Header = ({ } else { setViewMode(ViewMode.Compare); } - }, [selectedWorkspacesIds]); + }, [selectedWorkspacesIds, setViewMode]); return ( <> {VIEW_OPTIONS.map((item, index) => { return ( - + @@ -186,7 +187,17 @@ const Header = ({ {viewMode === ViewMode.Default && ( - )} diff --git a/applications/visualizer/frontend/src/components/ViewerContainer/Neurons.tsx b/applications/visualizer/frontend/src/components/ViewerContainer/Neurons.tsx index ba766c77..ecbb345a 100644 --- a/applications/visualizer/frontend/src/components/ViewerContainer/Neurons.tsx +++ b/applications/visualizer/frontend/src/components/ViewerContainer/Neurons.tsx @@ -1,21 +1,19 @@ import AddIcon from "@mui/icons-material/Add"; import { Box, IconButton, Stack, Typography } from "@mui/material"; import Tooltip from "@mui/material/Tooltip"; -import { debounce } from "lodash"; -import { useCallback, useState } from "react"; +import { useState } from "react"; import { useGlobalContext } from "../../contexts/GlobalContext.tsx"; import type { Neuron } from "../../rest"; -import { NeuronsService } from "../../rest"; import { vars } from "../../theme/variables.ts"; import CustomEntitiesDropdown from "./CustomEntitiesDropdown.tsx"; import CustomListItem from "./CustomListItem.tsx"; -import type { EnhancedNeuron } from "../../models/models.ts"; +import { Visibility, type ViewerData } from "../../models/models.ts"; const { gray900, gray500 } = vars; -const mapNeuronsToListItem = (neuron: string, isActive: boolean) => ({ +const mapNeuronsToListItem = (neuron: string, visibility: ViewerData) => ({ id: neuron, label: neuron, - checked: isActive, + checked: Object.values(visibility).every((e) => e === undefined || e.visibility === Visibility.Visible), }); const mapNeuronsAvailableNeuronsToOptions = (neuron: Neuron) => ({ id: neuron.name, @@ -24,62 +22,46 @@ const mapNeuronsAvailableNeuronsToOptions = (neuron: Neuron) => ({ }); const Neurons = ({ children }) => { - const { workspaces, datasets, currentWorkspaceId } = useGlobalContext(); - const currentWorkspace = workspaces[currentWorkspaceId]; + const { getCurrentWorkspace } = useGlobalContext(); + const currentWorkspace = getCurrentWorkspace(); + const activeNeurons = currentWorkspace.activeNeurons; - const recentNeurons = Object.values(currentWorkspace.availableNeurons).filter((neuron) => neuron.isInteractant); const availableNeurons = currentWorkspace.availableNeurons; + const groups = currentWorkspace.neuronGroups; const [neurons, setNeurons] = useState(availableNeurons); - const handleSwitchChange = async (neuronId: string, checked: boolean) => { - const neuron = availableNeurons[neuronId]; - - if (!neuron) return; - if (checked) { - await currentWorkspace.activateNeuron(neuron); + const handleSwitchChange = async (neuronId: string, isChecked: boolean) => { + if (isChecked) { + await currentWorkspace.showNeuron(neuronId); } else { - await currentWorkspace.deactivateNeuron(neuronId); + await currentWorkspace.hideNeuron(neuronId); } }; const onNeuronClick = (option) => { const neuron = availableNeurons[option.id]; + if (neuron && !activeNeurons.has(option.id)) { - currentWorkspace.activateNeuron(neuron); + currentWorkspace.activateNeuron(neuron).showNeuron(neuron.name); } else { - currentWorkspace.deleteNeuron(option.id); + currentWorkspace.deactivateNeuron(option.id); } }; const handleDeleteNeuron = (neuronId: string) => { - currentWorkspace.deleteNeuron(neuronId); - }; - - const fetchNeurons = async (name: string, datasetsIds: { id: string }[]) => { - try { - const ids = datasetsIds.map((dataset) => dataset.id); - const response = await NeuronsService.searchCells({ name: name, datasetIds: ids }); - - // Convert the object to a Record - const neuronsRecord = Object.entries(response).reduce((acc: Record, [_, neuron]: [string, EnhancedNeuron]) => { - acc[neuron.name] = neuron; - return acc; - }, {}); - - setNeurons(neuronsRecord); - } catch (error) { - console.error("Failed to fetch datasets", error); - } + currentWorkspace.deactivateNeuron(neuronId); }; - const debouncedFetchNeurons = useCallback(debounce(fetchNeurons, 300), []); - - const onSearchNeurons = (value) => { - const datasetsIds = Object.keys(datasets); - debouncedFetchNeurons(value, datasetsIds); + const onSearchNeurons = (nameFragment) => { + const filteredNeurons = Object.fromEntries( + Object.entries(availableNeurons).filter(([_, neuron]) => neuron.name.toLowerCase().startsWith(nameFragment.toLowerCase())), + ); + setNeurons(filteredNeurons); }; - const autoCompleteOptions = Object.values(neurons).map((neuron: Neuron) => mapNeuronsAvailableNeuronsToOptions(neuron)); + const autoCompleteOptions = Object.values(neurons) + .map((neuron: Neuron) => mapNeuronsAvailableNeuronsToOptions(neuron)) + .sort((a, b) => a.label.localeCompare(b.label)); return ( { - {Array.from(recentNeurons).map((neuron) => ( + {Array.from(activeNeurons).map((neuronId) => ( { deleteTooltipTitle="Remove neuron from the workspace" /> ))} + + + All Groups + + + + + + + + {Array.from(Object.keys(groups)).map((groupId) => ( + console.log("switch")} + onDelete={() => console.log("delete")} + deleteTooltipTitle="Remove group from the workspace" + /> + ))} diff --git a/applications/visualizer/frontend/src/components/ViewerContainer/WorkspaceSelector.tsx b/applications/visualizer/frontend/src/components/ViewerContainer/WorkspaceSelector.tsx index 8407d309..ec782710 100644 --- a/applications/visualizer/frontend/src/components/ViewerContainer/WorkspaceSelector.tsx +++ b/applications/visualizer/frontend/src/components/ViewerContainer/WorkspaceSelector.tsx @@ -2,6 +2,7 @@ import { Box, Button, Menu, MenuItem, Typography } from "@mui/material"; import type React from "react"; import { useGlobalContext } from "../../contexts/GlobalContext.tsx"; import { CheckIcon, DownIcon } from "../../icons"; +import type { Workspace } from "../../models/workspace.ts"; import { vars } from "../../theme/variables.ts"; const { gray500, gray50, brand600 } = vars; @@ -11,7 +12,7 @@ interface WorkspaceSelectorProps { openWorkspace: boolean; handleClickWorkspace: (event: React.MouseEvent) => void; handleCloseWorkspace: () => void; - onClickWorkspace: (workspace: any) => void; + onClickWorkspace: (workspace: Workspace) => void; } const WorkspaceSelector: React.FC = ({ diff --git a/applications/visualizer/frontend/src/components/ViewerSettings.tsx b/applications/visualizer/frontend/src/components/ViewerSettings.tsx index 40890b18..1f7f25e8 100644 --- a/applications/visualizer/frontend/src/components/ViewerSettings.tsx +++ b/applications/visualizer/frontend/src/components/ViewerSettings.tsx @@ -5,7 +5,7 @@ import { useDispatch } from "react-redux"; import { useGlobalContext } from "../contexts/GlobalContext.tsx"; import { CloseIcon, LinkIcon } from "../icons"; import { emDataViewerWidget, threeDViewerWidget, twoDViewerWidget } from "../layout-manager/widgets.ts"; -import { ViewerType } from "../models/models.ts"; +import { ViewerSynchronizationPair, ViewerType } from "../models/models.ts"; import { vars } from "../theme/variables.ts"; import CustomSwitch from "./ViewerContainer/CustomSwitch.tsx"; @@ -27,14 +27,17 @@ const SyncViewersData = [ { primaryText: "Connectivity graph", secondaryText: "Instance details", + syncPair: ViewerSynchronizationPair.Graph_InstanceDetails, }, { primaryText: "3D viewer", secondaryText: "EM viewer", + syncPair: ViewerSynchronizationPair.ThreeD_EM, }, { primaryText: "Connectivity graph", secondaryText: "3D viewer", + syncPair: ViewerSynchronizationPair.Graph_ThreeD, }, ]; @@ -65,8 +68,8 @@ const ViewerSettings = ({ open, toggleDrawer }) => { return; } }; - const handleChangeSynchronizations = (_, index, status) => { - currentWorkspace.updateViewerSynchronizationStatus(index, !status); + const handleChangeSynchronizations = (_, syncPair) => { + currentWorkspace.switchViewerSynchronizationStatus(syncPair); }; return ( @@ -164,13 +167,13 @@ const ViewerSettings = ({ open, toggleDrawer }) => { Sync viewers - {SyncViewersData?.map((data, index) => ( - + {SyncViewersData?.map((data) => ( + {data.primaryText} handleChangeSynchronizations(e, index, currentWorkspace?.synchronizations[index])} + onClick={(e) => handleChangeSynchronizations(e, data.syncPair)} > diff --git a/applications/visualizer/frontend/src/components/WorkspaceComponent.tsx b/applications/visualizer/frontend/src/components/WorkspaceComponent.tsx index 12105cf1..141adf49 100644 --- a/applications/visualizer/frontend/src/components/WorkspaceComponent.tsx +++ b/applications/visualizer/frontend/src/components/WorkspaceComponent.tsx @@ -119,7 +119,7 @@ function WorkspaceComponent({ sidebarOpen }) { const workspaceKeys = Object.keys(workspaces); const workspaceIndex = workspaceKeys.indexOf(workspaceId); - let workspaceIdToView; + let workspaceIdToView: string; if (workspaceKeys.length === 2) { workspaceIdToView = workspaceKeys.find((id) => id !== workspaceId); diff --git a/applications/visualizer/frontend/src/components/viewers/EM/EMStackTilesViewer.tsx b/applications/visualizer/frontend/src/components/viewers/EM/EMStackTilesViewer.tsx index cf5700b2..23ba2c21 100644 --- a/applications/visualizer/frontend/src/components/viewers/EM/EMStackTilesViewer.tsx +++ b/applications/visualizer/frontend/src/components/viewers/EM/EMStackTilesViewer.tsx @@ -1,6 +1,6 @@ import { Box } from "@mui/material"; import "ol/ol.css"; -import { type Feature, Map, View } from "ol"; +import { type Feature, Map as OLMap, View } from "ol"; import type { FeatureLike } from "ol/Feature"; import ScaleLine from "ol/control/ScaleLine"; import { shiftKeyOnly } from "ol/events/condition"; @@ -98,6 +98,7 @@ const newEMLayer = (dataset: Dataset, slice: number): TileLayer => { // url: `emdata/${slice}/{x}_{y}_{z}.jpg`, url: getEMDataURL(dataset, slice), projection: projection, + crossOrigin: "anonymous", }), zIndex: 0, }); @@ -126,10 +127,13 @@ const EMStackViewer = () => { const startSlice = 537; const ringSize = 11; - const mapRef = useRef(null); + const mapRef = useRef(null); const currSegLayer = useRef | null>(null); const clickedFeature = useRef(null); + let ringEM: SlidingRing>; + let ringSeg: SlidingRing>; + // const debugLayer = new TileLayer({ // source: new TileDebug({ // projection: projection, @@ -154,7 +158,7 @@ const EMStackViewer = () => { return; } - const map = new Map({ + const map = new OLMap({ target: "emviewer", layers: [], view: new View({ @@ -171,7 +175,7 @@ const EMStackViewer = () => { const minZoomAvailable = tilegrid.getMinZoom(); map.getView().setZoom(minZoomAvailable); - const ringEM = new SlidingRing({ + ringEM = new SlidingRing({ cacheSize: ringSize, startAt: startSlice, extent: [minSlice, maxSlice], @@ -192,7 +196,7 @@ const EMStackViewer = () => { }, }); - const ringSeg = new SlidingRing({ + ringSeg = new SlidingRing({ cacheSize: ringSize, startAt: startSlice, extent: [minSlice, maxSlice], @@ -269,6 +273,10 @@ const EMStackViewer = () => { }; const onResetView = () => { + // reset sliding window + ringEM.goto(startSlice); + ringSeg.goto(startSlice); + if (!mapRef.current) return; const view = mapRef.current.getView(); @@ -297,7 +305,7 @@ const EMStackViewer = () => { export default EMStackViewer; -function printEMView(map: Map) { +function printEMView(map: OLMap) { const mapCanvas = document.createElement("canvas"); const size = map.getSize(); @@ -310,7 +318,7 @@ function printEMView(map: Map) { if (canvas.width > 0) { const opacity = canvas.parentNode.style.opacity || canvas.style.opacity; mapContext.globalAlpha = opacity === "" ? 1 : Number(opacity); - let matrix; + let matrix: Array; const transform = canvas.style.transform; if (transform) { // Get the transform parameters from the style's transform matrix diff --git a/applications/visualizer/frontend/src/components/viewers/ThreeD/STLMesh.tsx b/applications/visualizer/frontend/src/components/viewers/ThreeD/STLMesh.tsx index 773d407b..bd5a36c8 100644 --- a/applications/visualizer/frontend/src/components/viewers/ThreeD/STLMesh.tsx +++ b/applications/visualizer/frontend/src/components/viewers/ThreeD/STLMesh.tsx @@ -1,12 +1,13 @@ -import type { FC } from "react"; import { Outlines } from "@react-three/drei"; -import { useGlobalContext } from "../../../contexts/GlobalContext"; +import type { ThreeEvent } from "@react-three/fiber"; +import type { FC } from "react"; import { useSelector } from "react-redux"; -import type { Workspace } from "../../../models/workspace"; -import type { RootState } from "../../../layout-manager/layoutManagerFactory"; import { type BufferGeometry, DoubleSide, NormalBlending } from "three"; -import type { ThreeEvent } from "@react-three/fiber"; +import { useGlobalContext } from "../../../contexts/GlobalContext"; import { getFurthestIntersectedObject } from "../../../helpers/threeDHelpers"; +import type { RootState } from "../../../layout-manager/layoutManagerFactory"; +import type { Workspace } from "../../../models"; +import { ViewerType } from "../../../models"; import { OUTLINE_COLOR, OUTLINE_THICKNESS } from "../../../settings/threeDSettings"; interface Props { @@ -22,14 +23,21 @@ const STLMesh: FC = ({ id, color, opacity, renderOrder, isWireframe, stl const { workspaces } = useGlobalContext(); const workspaceId = useSelector((state: RootState) => state.workspaceId); const workspace: Workspace = workspaces[workspaceId]; + const selectedNeurons = workspace.getViewerSelecedNeurons(ViewerType.Graph); + const isSelected = selectedNeurons.includes(id); + const onClick = (event: ThreeEvent) => { const clicked = getFurthestIntersectedObject(event); + const { id } = clicked.userData; if (clicked) { - workspace.toggleSelectedNeuron(clicked.userData.id); + if (isSelected) { + console.log(`Neurons selected: ${id}`); + } else { + console.log(`Neurons un selected: ${id}`); + } } }; - const isSelected = id in workspace.selectedNeurons; return ( diff --git a/applications/visualizer/frontend/src/components/viewers/ThreeD/ThreeDViewer.tsx b/applications/visualizer/frontend/src/components/viewers/ThreeD/ThreeDViewer.tsx index 90004df9..2ef4dd95 100644 --- a/applications/visualizer/frontend/src/components/viewers/ThreeD/ThreeDViewer.tsx +++ b/applications/visualizer/frontend/src/components/viewers/ThreeD/ThreeDViewer.tsx @@ -18,13 +18,13 @@ import { useSelector } from "react-redux"; import { useGlobalContext } from "../../../contexts/GlobalContext.tsx"; import { CheckIcon, CloseIcon } from "../../../icons"; import type { RootState } from "../../../layout-manager/layoutManagerFactory.ts"; +import type { Dataset } from "../../../rest"; import { vars } from "../../../theme/variables.ts"; import CustomAutocomplete from "../../CustomAutocomplete.tsx"; import Gizmo from "./Gizmo.tsx"; import Loader from "./Loader.tsx"; import STLViewer from "./STLViewer.tsx"; import SceneControls from "./SceneControls.tsx"; -import type { Dataset } from "../../../rest"; const { gray100, gray600 } = vars; export interface Instance { @@ -55,7 +55,7 @@ function ThreeDViewer() { id: "nerve_ring", url: "resources/nervering-SEM_adult.stl", color: "white", - opacity: 0.5, + opacity: 0.3, }, { id: "adal_sem", diff --git a/applications/visualizer/frontend/src/components/viewers/TwoD/ContextMenu.tsx b/applications/visualizer/frontend/src/components/viewers/TwoD/ContextMenu.tsx index 5d1177d8..cfca9464 100644 --- a/applications/visualizer/frontend/src/components/viewers/TwoD/ContextMenu.tsx +++ b/applications/visualizer/frontend/src/components/viewers/TwoD/ContextMenu.tsx @@ -1,270 +1,418 @@ +import { + ArrowRightOutlined, + CallSplitOutlined, + CloseFullscreen, + FormatAlignJustifyOutlined, + GroupOutlined, + HubOutlined, + MergeOutlined, + OpenInFull, + VisibilityOutlined, + WorkspacesOutlined, +} from "@mui/icons-material"; +import { Box, Divider, Menu, MenuItem, Popover } from "@mui/material"; +import type { Core } from "cytoscape"; import type React from "react"; -import { useMemo } from "react"; -import { Menu, MenuItem } from "@mui/material"; -import { type NeuronGroup, ViewerType } from "../../../models"; -import { calculateMeanPosition, calculateSplitPositions, isNeuronClass } from "../../../helpers/twoD/twoDHelpers.ts"; +import { useEffect, useMemo, useState } from "react"; +import { alignNeurons, distributeNeurons } from "../../../helpers/twoD/alignHelper.ts"; +import { groupNeurons, removeNodeFromGroup } from "../../../helpers/twoD/groupHelper.ts"; +import { processNeuronJoin, processNeuronSplit } from "../../../helpers/twoD/splitJoinHelper.ts"; import { useSelectedWorkspace } from "../../../hooks/useSelectedWorkspace.ts"; -import type { Position } from "cytoscape"; -import type { GraphViewerData } from "../../../models/models.ts"; +import { AlignBottomIcon, AlignLeftIcon, AlignRightIcon, AlignTopIcon, DistributeHorizontallyIcon, DistributeVerticallyIcon } from "../../../icons"; +import { Alignment, ViewerType, Visibility } from "../../../models"; +import { emptyViewerData } from "../../../models/models.ts"; +import { vars } from "../../../theme/variables.ts"; + +const { gray700 } = vars; interface ContextMenuProps { open: boolean; onClose: () => void; position: { mouseX: number; mouseY: number } | null; setSplitJoinState: React.Dispatch; join: Set }>>; - setHiddenNodes: React.Dispatch>>; + openGroups: Set; + setOpenGroups: React.Dispatch>>; + cy: Core; } -const ContextMenu: React.FC = ({ open, onClose, position, setSplitJoinState, setHiddenNodes }) => { +const ContextMenu: React.FC = ({ open, onClose, position, setSplitJoinState, openGroups, setOpenGroups, cy }) => { const workspace = useSelectedWorkspace(); + const [submenuAnchorEl, setSubmenuAnchorEl] = useState(null); + const selectedNeurons = workspace.getViewerSelecedNeurons(ViewerType.Graph); + + const submenuOpen = Boolean(submenuAnchorEl); + + const handlePopoverOpen = (event: React.MouseEvent) => { + setSubmenuAnchorEl(event.currentTarget); + }; + const handlePopoverClose = () => { + setSubmenuAnchorEl(null); + }; + + const handleContextMenuClose = () => { + onClose(); + handlePopoverClose(); // Ensure the submenu is also closed when the context menu closes. + }; + + const handleAlignOption = (option: Alignment) => { + alignNeurons(option, selectedNeurons, cy); + setSubmenuAnchorEl(null); + onClose(); + setSubmenuAnchorEl(null); + }; + + const handleDistributeOption = (option: Alignment) => { + distributeNeurons(option, selectedNeurons, cy); + setSubmenuAnchorEl(null); + onClose(); + }; const handleHide = () => { - setHiddenNodes((prevHiddenNodes) => { - const newHiddenNodes = new Set([...prevHiddenNodes]); - workspace.selectedNeurons.forEach((neuronId) => { - newHiddenNodes.add(neuronId); - }); - return newHiddenNodes; + workspace.customUpdate((draft) => { + for (const neuronId of selectedNeurons) { + if (!(neuronId in draft.visibilities)) { + draft.visibilities[neuronId] = emptyViewerData(Visibility.Hidden); + } else { + draft.visibilities[neuronId][ViewerType.Graph].visibility = Visibility.Hidden; + } + } + draft.clearSelection(ViewerType.Graph); }); - workspace.clearSelectedNeurons(); onClose(); }; const handleGroup = () => { - const newGroupId = `group_${Date.now()}`; - const newGroupNeurons = new Set(); - const groupsToDelete = new Set(); - - for (const neuronId of workspace.selectedNeurons) { - const group = workspace.neuronGroups[neuronId]; - if (group) { - for (const groupedNeuronId of group.neurons) { - newGroupNeurons.add(groupedNeuronId); + const selectedNeuronsSet = new Set(selectedNeurons); + const { newGroupId, newGroup, groupsToDelete } = groupNeurons(selectedNeuronsSet, workspace); + + workspace.customUpdate((draft) => { + // Add the new group + draft.neuronGroups[newGroupId] = newGroup; + draft.visibilities[newGroupId] = emptyViewerData(Visibility.Visible); + + // Remove the old groups that were merged into the new group + for (const groupId of groupsToDelete) { + delete draft.neuronGroups[groupId]; + delete draft.visibilities[groupId]; + } + + // Clear the current selection and select the new group + draft.setSelection([newGroupId], ViewerType.Graph); + }); + + setOpenGroups((prevOpenGroups: Set) => { + const updatedOpenGroups = new Set(prevOpenGroups); + let wasGroupOpen = false; + + for (const groupId of groupsToDelete) { + if (updatedOpenGroups.has(groupId)) { + updatedOpenGroups.delete(groupId); + wasGroupOpen = true; } - groupsToDelete.add(neuronId); - } else { - newGroupNeurons.add(neuronId); } - } - const newGroup: NeuronGroup = { - id: newGroupId, - name: newGroupId, - color: "#9FEE9A", - neurons: newGroupNeurons, - }; + // Only add the new group if any of the deleted groups were open + if (wasGroupOpen) { + updatedOpenGroups.add(newGroupId); + } - workspace.customUpdate((draft) => { - draft.neuronGroups[newGroupId] = newGroup; - groupsToDelete.forEach((groupId) => delete draft.neuronGroups[groupId]); - draft.selectedNeurons.clear(); - draft.selectedNeurons.add(newGroupId); + return updatedOpenGroups; }); + onClose(); }; - const handleUngroup = () => { + const groupsToRemoveFromOpen = new Set(); + workspace.customUpdate((draft) => { const nextSelected = new Set(); - for (const elementId of draft.selectedNeurons) { + + for (const elementId of selectedNeurons) { if (draft.neuronGroups[elementId]) { + // Handle the case where the selected element is a group const group = draft.neuronGroups[elementId]; for (const groupedNeuronId of group.neurons) { nextSelected.add(groupedNeuronId); + removeNodeFromGroup(cy, groupedNeuronId, true); + } + delete draft.neuronGroups[elementId]; // Delete the entire group + if (openGroups.has(elementId)) { + groupsToRemoveFromOpen.add(elementId); + } + } else { + // Handle the case where the selected element is a neuron within a group + for (const [groupId, group] of Object.entries(draft.neuronGroups)) { + if (group.neurons.has(elementId)) { + group.neurons.delete(elementId); // Remove the neuron from the group + nextSelected.add(elementId); + removeNodeFromGroup(cy, elementId, true); + + if (group.neurons.size === 0) { + // If the group is now empty, delete it + delete draft.neuronGroups[groupId]; + if (openGroups.has(groupId)) { + groupsToRemoveFromOpen.add(groupId); + } + } + } } - delete draft.neuronGroups[elementId]; } } - draft.selectedNeurons = nextSelected; + + draft.setSelection(Array.from(nextSelected), ViewerType.Graph); + }); + + // Remove groups from the openGroups set + setOpenGroups((prevOpenGroups: Set) => { + const updatedOpenGroups = new Set(prevOpenGroups); + for (const groupId of groupsToRemoveFromOpen) { + updatedOpenGroups.delete(groupId); + } + return updatedOpenGroups; }); + onClose(); }; const handleSplit = () => { setSplitJoinState((prevState) => { - const newSplit = new Set(prevState.split); - const newJoin = new Set(prevState.join); - - const newSelectedNeurons = new Set(workspace.selectedNeurons); - const graphViewDataUpdates: Record = {}; - - workspace.selectedNeurons.forEach((neuronId) => { - if (isNeuronClass(neuronId, workspace)) { - newSplit.add(neuronId); - newSelectedNeurons.delete(neuronId); - - const individualNeurons = Object.values(workspace.availableNeurons) - .filter((neuron) => { - return neuron.nclass === neuronId && neuron.nclass !== neuron.name; - }) - .map((neuron) => neuron.name); - - // Calculate the positions for the individual neurons - const basePosition = workspace.availableNeurons[neuronId].viewerData[ViewerType.Graph]?.defaultPosition || { - x: 0, - y: 0, - }; - const positions = calculateSplitPositions(individualNeurons, basePosition); - - // Update the selected neurons with individual neurons - individualNeurons.forEach((neuronName) => { - newSelectedNeurons.add(neuronName); - // Only set the position if it doesn't exist yet - if (!workspace.availableNeurons[neuronName].viewerData[ViewerType.Graph]?.defaultPosition) { - graphViewDataUpdates[neuronName] = { position: positions[neuronName], visibility: true }; - } else { - graphViewDataUpdates[neuronName] = { visibility: true }; - } - }); - - // Remove the corresponding class from the toJoin set - newJoin.forEach((joinNeuronId) => { - if (workspace.availableNeurons[joinNeuronId].nclass === neuronId) { - newJoin.delete(joinNeuronId); - } - }); - - graphViewDataUpdates[neuronId] = { visibility: false }; - } - }); - - // Update the selected neurons in the workspace - updateWorkspace(newSelectedNeurons, graphViewDataUpdates); - - return { split: newSplit, join: newJoin }; + return processNeuronSplit(workspace, prevState); }); onClose(); }; const handleJoin = () => { setSplitJoinState((prevState) => { - const newJoin = new Set(prevState.join); - const newSplit = new Set(prevState.split); - - const newSelectedNeurons = new Set(workspace.selectedNeurons); - const graphViewDataUpdates: Record = {}; - - workspace.selectedNeurons.forEach((neuronId) => { - const neuronClass = workspace.availableNeurons[neuronId].nclass; - - const individualNeurons = Object.values(workspace.availableNeurons).filter((neuron) => neuron.nclass === neuronClass && neuron.name !== neuronClass); - const individualNeuronIds = individualNeurons.map((neuron) => neuron.name); - - // Calculate and set the class position if not set already - const classPosition = calculateMeanPosition(individualNeuronIds, workspace); - - if (!workspace.availableNeurons[neuronClass].viewerData[ViewerType.Graph]?.defaultPosition) { - graphViewDataUpdates[neuronClass] = { position: classPosition, visibility: true }; - } else { - graphViewDataUpdates[neuronClass] = { ...graphViewDataUpdates[neuronClass], visibility: true }; - } - // Remove the individual neurons from the selected neurons and add the class neuron - individualNeuronIds.forEach((neuronName) => { - newSelectedNeurons.delete(neuronName); - newJoin.add(neuronName); - - // Set individual neurons' visibility to false - graphViewDataUpdates[neuronName] = { visibility: false }; - }); - newSelectedNeurons.add(neuronClass); - - // Remove the corresponding cells from the toSplit set - newSplit.forEach((splitNeuronId) => { - if (workspace.availableNeurons[splitNeuronId].nclass === neuronClass) { - newSplit.delete(splitNeuronId); - } - }); - }); - - // Update the selected neurons in the workspace - updateWorkspace(newSelectedNeurons, graphViewDataUpdates); - - return { split: newSplit, join: newJoin }; + return processNeuronJoin(workspace, prevState); }); onClose(); }; - const updateWorkspace = (newSelectedNeurons: Set, graphViewDataUpdates: Record>) => { - workspace.customUpdate((draft) => { - // Update the selected neurons - draft.selectedNeurons = newSelectedNeurons; - - // Update the positions and visibility for the individual neurons and class neuron - Object.entries(graphViewDataUpdates).forEach(([neuronName, update]) => { - if (draft.availableNeurons[neuronName]) { - if (update.defaultPosition !== undefined) { - draft.availableNeurons[neuronName].viewerData[ViewerType.Graph].defaultPosition = update.defaultPosition; - } - draft.availableNeurons[neuronName].viewerData[ViewerType.Graph].visibility = update.visibility; - } - }); - }); - }; - const handleAddToWorkspace = () => { workspace.customUpdate((draft) => { - workspace.selectedNeurons.forEach((neuronId) => { + for (const neuronId of selectedNeurons) { const group = workspace.neuronGroups[neuronId]; if (group) { - group.neurons.forEach((groupedNeuronId) => { + for (const groupedNeuronId of group.neurons) { draft.activeNeurons.add(groupedNeuronId); - }); + draft.visibilities[groupedNeuronId] = emptyViewerData(Visibility.Visible); + } } else { draft.activeNeurons.add(neuronId); + draft.visibilities[neuronId] = emptyViewerData(Visibility.Visible); } - }); + } }); onClose(); }; + const handleOpenGroup = () => { + for (const neuronId of selectedNeurons) { + if (workspace.neuronGroups[neuronId] && !openGroups.has(neuronId)) { + // Mark the group as open + setOpenGroups((prevOpenGroups: Set) => { + const updatedOpenGroups = new Set(prevOpenGroups); + updatedOpenGroups.add(neuronId); + return updatedOpenGroups; + }); + } + } + onClose(); + }; + const handleCloseGroup = () => { + for (const neuronId of selectedNeurons) { + if (workspace.neuronGroups[neuronId] && openGroups.has(neuronId)) { + // Mark the group as closed + setOpenGroups((prevOpenGroups: Set) => { + const updatedOpenGroups = new Set(prevOpenGroups); + updatedOpenGroups.delete(neuronId); + return updatedOpenGroups; + }); + } + } + onClose(); + }; + const groupEnabled = useMemo(() => { - return Array.from(workspace.selectedNeurons).some((neuronId) => !workspace.neuronGroups[neuronId]); - }, [workspace.selectedNeurons, workspace.neuronGroups]); + const groupOrPartOfGroupSet = new Set(); + let nonGroupOrPartCount = 0; + for (const neuronId of selectedNeurons) { + const isGroup = Boolean(workspace.neuronGroups[neuronId]); + const isPartOfGroup = Object.entries(workspace.neuronGroups).find(([, group]) => group.neurons.has(neuronId)); + + if (isGroup) { + groupOrPartOfGroupSet.add(neuronId); + } else if (isPartOfGroup) { + groupOrPartOfGroupSet.add(isPartOfGroup[0]); + } else { + nonGroupOrPartCount++; + } + } + + // Enable grouping if there are neurons not in any group and at most one group or part of a group is selected. + return nonGroupOrPartCount > 0 && groupOrPartOfGroupSet.size <= 1; + }, [selectedNeurons, workspace.neuronGroups]); const ungroupEnabled = useMemo(() => { - return Array.from(workspace.selectedNeurons).some((neuronId) => workspace.neuronGroups[neuronId]); - }, [workspace.selectedNeurons, workspace.neuronGroups]); + return selectedNeurons.some((neuronId) => { + // Check if the neuronId is a group itself + const isGroup = Boolean(workspace.neuronGroups[neuronId]); + + // Check if the neuronId is part of any group + const isPartOfGroup = Object.values(workspace.neuronGroups).some((group) => group.neurons.has(neuronId)); + + // Enable ungroup if the neuron is a group or is part of a group + return isGroup || isPartOfGroup; + }); + }, [selectedNeurons, workspace.neuronGroups]); const splitEnabled = useMemo(() => { - return Array.from(workspace.selectedNeurons).some((neuronId) => { + return selectedNeurons.some((neuronId) => { const neuron = workspace.availableNeurons[neuronId]; return neuron && neuron.name === neuron.nclass; }); - }, [workspace.selectedNeurons, workspace.availableNeurons]); + }, [selectedNeurons, workspace.availableNeurons]); const joinEnabled = useMemo(() => { - return Array.from(workspace.selectedNeurons).some((neuronId) => { + return selectedNeurons.some((neuronId) => { const neuron = workspace.availableNeurons[neuronId]; return neuron && neuron.name !== neuron.nclass; }); - }, [workspace.selectedNeurons, workspace.availableNeurons]); + }, [selectedNeurons, workspace.availableNeurons]); + + const openGroupEnabled = useMemo(() => { + return selectedNeurons.some((neuronId) => workspace.neuronGroups[neuronId] && !openGroups.has(neuronId)); + }, [selectedNeurons, workspace.neuronGroups, openGroups]); + const closeGroupEnabled = useMemo(() => { + return selectedNeurons.some((neuronId) => workspace.neuronGroups[neuronId] && openGroups.has(neuronId)); + }, [selectedNeurons, workspace.neuronGroups, openGroups]); const handleContextMenu = (event: React.MouseEvent) => { event.preventDefault(); // Prevent default context menu }; + useEffect(() => { + if (open) { + setSubmenuAnchorEl(null); + } + }, [open]); + return ( - Hide - - Group - - - Ungroup + + + Hide - - Join Left-Right + + + Add to Workspace - - Split Left-Right + {joinEnabled && ( + + + Join Left-Right + + )} + {splitEnabled && ( + + + Split Left-Right + + )} + + + {groupEnabled && ( + + + Group + + )} + {ungroupEnabled && ( + + + Ungroup + + )} + {openGroupEnabled && ( + + + Open Group + + )} + {closeGroupEnabled && ( + + + Close Group + + )} + + + + Align + + - Add to Workspace + + handleAlignOption(Alignment.Left)}> + + Align left + + handleAlignOption(Alignment.Right)}> + + Align right + + handleAlignOption(Alignment.Top)}> + + Align top + + handleAlignOption(Alignment.Bottom)}> + + Align bottom + + + handleDistributeOption(Alignment.Horizontal)}> + + Distribute horizontally + + handleDistributeOption(Alignment.Vertical)}> + + Distribute vertically + + ); }; diff --git a/applications/visualizer/frontend/src/components/viewers/TwoD/TwoDLegend.tsx b/applications/visualizer/frontend/src/components/viewers/TwoD/TwoDLegend.tsx index 0b4d1626..862a3539 100644 --- a/applications/visualizer/frontend/src/components/viewers/TwoD/TwoDLegend.tsx +++ b/applications/visualizer/frontend/src/components/viewers/TwoD/TwoDLegend.tsx @@ -1,7 +1,7 @@ import { Box, Divider, IconButton, Typography } from "@mui/material"; import type React from "react"; import { type ColoringOptions, getColorMap, legendNodeNameMapping } from "../../../helpers/twoD/coloringHelper"; -import { LegendType, connectionsLegend, annotationLegend } from "../../../settings/twoDSettings"; +import { LegendType, annotationLegend, connectionsLegend } from "../../../settings/twoDSettings"; import { vars } from "../../../theme/variables"; const { gray100 } = vars; @@ -11,6 +11,7 @@ interface LegendNodeProps { color: string; onClick: () => void; highlighted: boolean; + shape: string; } interface LegendConnectionProps { @@ -20,7 +21,7 @@ interface LegendConnectionProps { highlighted: boolean; } -const LegendNode: React.FC = ({ name, color, onClick, highlighted }) => ( +const LegendNode: React.FC = ({ name, color, onClick, highlighted, shape }) => ( = ({ name, color, onClick, highlight }} onClick={onClick} > - + {name} ); @@ -50,6 +59,7 @@ const LegendConnection: React.FC = ({ name, icon, onClick = ({ coloringOption, setLegendHighlights sx={{ padding: "1rem", borderRadius: "0.5rem", - backgroundColor: "rgba(245, 245, 244, 0.80)", - backdropFilter: "blur(20px)", + backgroundColor: "transparent", }} > {Object.entries(colorMap).map(([name, color]) => ( @@ -103,6 +112,7 @@ const TwoDLegend: React.FC = ({ coloringOption, setLegendHighlights color={color} onClick={() => handleLegendClick(LegendType.Node, name)} highlighted={!nodeHighlight || legendHighlights.get(LegendType.Node) === name} + shape={name === "muscle" || name === "others" ? "rectangle" : "circle"} /> ))} diff --git a/applications/visualizer/frontend/src/components/viewers/TwoD/TwoDMenu.tsx b/applications/visualizer/frontend/src/components/viewers/TwoD/TwoDMenu.tsx index f9ebe402..bca8d9c1 100644 --- a/applications/visualizer/frontend/src/components/viewers/TwoD/TwoDMenu.tsx +++ b/applications/visualizer/frontend/src/components/viewers/TwoD/TwoDMenu.tsx @@ -1,15 +1,17 @@ import { GetAppOutlined, HomeOutlined, TuneOutlined, VisibilityOutlined } from "@mui/icons-material"; import ZoomInIcon from "@mui/icons-material/ZoomIn"; import ZoomOutIcon from "@mui/icons-material/ZoomOut"; -import { Box, Divider, FormControlLabel, FormGroup, IconButton, Popover, ToggleButton, ToggleButtonGroup, Tooltip, Typography } from "@mui/material"; +import { Box, Divider, FormControlLabel, FormGroup, IconButton, Popover, Switch, ToggleButton, ToggleButtonGroup, Tooltip, Typography } from "@mui/material"; import { useState } from "react"; import { ColoringOptions } from "../../../helpers/twoD/coloringHelper.ts"; +import { downloadConnectivityViewer } from "../../../helpers/twoD/downloadHelper.ts"; +import { applyLayout } from "../../../helpers/twoD/twoDHelpers.ts"; +import { useSelectedWorkspace } from "../../../hooks/useSelectedWorkspace.ts"; +import { ViewerType, Visibility } from "../../../models"; import { GRAPH_LAYOUTS, ZOOM_DELTA } from "../../../settings/twoDSettings.tsx"; import { vars } from "../../../theme/variables.ts"; import CustomSwitch from "../../ViewerContainer/CustomSwitch.tsx"; import QuantityInput from "./NumberInput.tsx"; -import { useSelectedWorkspace } from "../../../hooks/useSelectedWorkspace.ts"; -import { applyLayout } from "../../../helpers/twoD/twoDHelpers.ts"; const { gray500 } = vars; @@ -35,7 +37,8 @@ const TwoDMenu = ({ setIncludePostEmbryonic, }) => { const workspace = useSelectedWorkspace(); - const [anchorEl, setAnchorEl] = useState(null); + const [settingsAnchorEl, setSettingsAnchorEl] = useState(null); + const [visibilityAnchorEl, setVisibilityAnchorEl] = useState(null); const onZoomIn = () => { if (!cy) { @@ -66,40 +69,53 @@ const TwoDMenu = ({ if (!cy) { return; } - applyLayout(cy, layout); + applyLayout(cy, layout as GRAPH_LAYOUTS); }; const handleOpenSettings = (event) => { - setAnchorEl(event.currentTarget); + setSettingsAnchorEl(event.currentTarget); }; const handleCloseSettings = () => { - setAnchorEl(null); + setSettingsAnchorEl(null); }; - const handleDownloadClick = () => { - if (!cy) return; + const handleDownloadClick = async () => { + await downloadConnectivityViewer(cy, workspace.name); + }; - const pngDataUrl = cy.png({ - output: "base64uri", - bg: "white", - full: true, - scale: 2, - }); + const handleOpenVisibility = (event) => { + setVisibilityAnchorEl(event.currentTarget); + }; - // Create a link element - const link = document.createElement("a"); - link.href = pngDataUrl; - link.download = `${workspace.name}.png`; + const handleCloseVisibility = () => { + setVisibilityAnchorEl(null); + }; - // Programmatically trigger a click event to download the image - document.body.appendChild(link); - link.click(); - document.body.removeChild(link); + const handleToggleVisibility = (neuronId) => { + workspace.customUpdate((draft) => { + const neuron = draft.visibilities[neuronId]; + if (neuron) { + const currentVisibility = neuron[ViewerType.Graph]?.visibility; + neuron[ViewerType.Graph].visibility = currentVisibility === Visibility.Visible ? Visibility.Hidden : Visibility.Visible; + draft.removeSelection(neuronId, ViewerType.Graph); + } + }); }; - const open = Boolean(anchorEl); - const id = open ? "settings-popover" : undefined; + const openSettings = Boolean(settingsAnchorEl); + const settingsId = openSettings ? "settings-popover" : undefined; + + const openVisibility = Boolean(visibilityAnchorEl); + const visibilityId = openVisibility ? "visibility-popover" : undefined; + + const visibleNeurons = Object.entries(workspace.visibilities) + .filter(([_, data]) => data[ViewerType.Graph].visibility === Visibility.Visible) + .map(([key, _]) => key); + + const hiddenNeurons = Object.entries(workspace.visibilities) + .filter(([_, data]) => data[ViewerType.Graph].visibility === Visibility.Hidden) + .map(([key, _]) => key); return ( { if (newColoringOption !== null) { - // Prevent deselecting all options onColoringOptionChange(newColoringOption); } }} @@ -193,14 +208,7 @@ const TwoDMenu = ({ Neuroconnectors have at least: - + Chemical Synapses @@ -240,7 +248,6 @@ const TwoDMenu = ({ exclusive onChange={(_, newLayout) => { if (newLayout !== null) { - // Prevent deselecting all options onLayoutChange(newLayout); } }} @@ -298,11 +305,70 @@ const TwoDMenu = ({ - - + + + + + Visible Neurons + + + {visibleNeurons.map((neuronId) => ( + handleToggleVisibility(neuronId)} + /> + } + label={neuronId} + /> + ))} + + + + Hidden Neurons + + + {hiddenNeurons.map((neuronId) => ( + handleToggleVisibility(neuronId)} + /> + } + label={neuronId} + /> + ))} + + diff --git a/applications/visualizer/frontend/src/components/viewers/TwoD/TwoDViewer.tsx b/applications/visualizer/frontend/src/components/viewers/TwoD/TwoDViewer.tsx index 11affa32..b1068cc5 100644 --- a/applications/visualizer/frontend/src/components/viewers/TwoD/TwoDViewer.tsx +++ b/applications/visualizer/frontend/src/components/viewers/TwoD/TwoDViewer.tsx @@ -1,34 +1,50 @@ -import { useState, useEffect, useRef } from "react"; +import { Box, Snackbar } from "@mui/material"; import cytoscape, { type Core, type EventHandler } from "cytoscape"; -import fcose from "cytoscape-fcose"; import dagre from "cytoscape-dagre"; +import fcose from "cytoscape-fcose"; +import { debounce } from "lodash"; +import { useEffect, useMemo, useRef, useState } from "react"; +import { useGlobalContext } from "../../../contexts/GlobalContext.tsx"; +import { ColoringOptions, getColor } from "../../../helpers/twoD/coloringHelper"; +import { computeGraphDifferences, updateHighlighted, updateParallelEdges, updateParentNodes } from "../../../helpers/twoD/graphRendering.ts"; +import { + applyLayout, + getHiddenNeuronsIn2D, + getVisibleActiveNeuronsIn2D, + isNeuronPartOfClosedGroup, + refreshLayout, + updateWorkspaceNeurons2DViewerData, +} from "../../../helpers/twoD/twoDHelpers"; +import { areSetsEqual } from "../../../helpers/utils.ts"; import { useSelectedWorkspace } from "../../../hooks/useSelectedWorkspace"; +import { ViewerType } from "../../../models"; +import { GlobalError } from "../../../models/Error.ts"; import { type Connection, ConnectivityService } from "../../../rest"; -import { GRAPH_STYLES } from "../../../theme/twoDStyles"; -import { applyLayout, refreshLayout, updateWorkspaceNeurons2DViewerData } from "../../../helpers/twoD/twoDHelpers"; import { CHEMICAL_THRESHOLD, ELECTRICAL_THRESHOLD, + FOCUS_CLASS, GRAPH_LAYOUTS, - type LegendType, + HOVER_CLASS, INCLUDE_ANNOTATIONS, - INCLUDE_NEIGHBORING_CELLS, INCLUDE_LABELS, + INCLUDE_NEIGHBORING_CELLS, INCLUDE_POST_EMBRYONIC, + type LegendType, + SELECTED_CLASS, + SHOW_EDGE_LABEL_CLASS, } from "../../../settings/twoDSettings"; -import TwoDMenu from "./TwoDMenu"; -import TwoDLegend from "./TwoDLegend"; -import { Box } from "@mui/material"; -import { ColoringOptions, getColor } from "../../../helpers/twoD/coloringHelper"; +import { GRAPH_STYLES } from "../../../theme/twoDStyles"; import ContextMenu from "./ContextMenu"; -import { computeGraphDifferences, updateHighlighted } from "../../../helpers/twoD/graphRendering.ts"; -import { areSetsEqual } from "../../../helpers/utils.ts"; +import TwoDLegend from "./TwoDLegend"; +import TwoDMenu from "./TwoDMenu"; cytoscape.use(fcose); cytoscape.use(dagre); const TwoDViewer = () => { const workspace = useSelectedWorkspace(); + const { handleErrors } = useGlobalContext(); const cyContainer = useRef(null); const cyRef = useRef(null); const [connections, setConnections] = useState([]); @@ -47,12 +63,41 @@ const TwoDViewer = () => { const [includePostEmbryonic, setIncludePostEmbryonic] = useState(INCLUDE_POST_EMBRYONIC); const [mousePosition, setMousePosition] = useState<{ mouseX: number; mouseY: number } | null>(null); const [legendHighlights, setLegendHighlights] = useState>(new Map()); - const [hiddenNodes, setHiddenNodes] = useState>(new Set()); + const [openGroups, setOpenGroups] = useState>(new Set()); + + const [missingNeuronsState, setMissingNeuronsState] = useState({ + reportedNeurons: new Set(), + unreportedNeurons: new Set(), + }); + + const selectedNeurons = workspace.getViewerSelecedNeurons(ViewerType.Graph); + + const visibleActiveNeurons = useMemo(() => { + return getVisibleActiveNeuronsIn2D(workspace); + }, [ + Array.from(workspace.activeNeurons) + .map((neuronId) => workspace.visibilities[neuronId]?.[ViewerType.Graph]?.visibility || "") + .join(","), + ]); + + const hiddenNeurons = useMemo(() => { + return getHiddenNeuronsIn2D(workspace); + }, [ + Object.keys(workspace.availableNeurons) + .map((neuronId) => workspace.visibilities[neuronId]?.[ViewerType.Graph]?.visibility || "") + .join(","), + ]); const handleContextMenuClose = () => { setMousePosition(null); }; + const handleCloseSnackbar = () => { + setMissingNeuronsState((prevState) => ({ + reportedNeurons: new Set([...prevState.reportedNeurons, ...prevState.unreportedNeurons]), + unreportedNeurons: new Set(), + })); + }; // Initialize and update Cytoscape useEffect(() => { if (!cyContainer.current) return; @@ -63,6 +108,9 @@ const TwoDViewer = () => { layout: { name: layout, }, + boxSelectionEnabled: true, + motionBlur: true, + selectionType: "additive", }); cyRef.current = cy; @@ -89,8 +137,8 @@ const TwoDViewer = () => { useEffect(() => { if (!workspace) return; - // Convert activeNeurons and activeDatasets to comma-separated strings - const cells = Array.from(workspace.activeNeurons || []).join(","); + // Convert visibleActiveNeurons and activeDatasets to comma-separated strings + const cells = Array.from(visibleActiveNeurons || []).join(","); const datasetIds = Object.values(workspace.activeDatasets) .map((dataset) => dataset.id) .join(","); @@ -110,12 +158,12 @@ const TwoDViewer = () => { .then((connections) => { setConnections(connections); }) - .catch((error) => { - console.error("Failed to fetch connections:", error); + .catch(() => { + handleErrors(new GlobalError("Failed to fetch connections")); }); }, [ workspace.activeDatasets, - workspace.activeNeurons, + visibleActiveNeurons, includeNeighboringCells, includeNeighboringCellsAsIndividualCells, includeAnnotations, @@ -128,7 +176,7 @@ const TwoDViewer = () => { if (cyRef.current) { updateGraphElements(cyRef.current, connections); } - }, [connections, hiddenNodes, workspace.neuronGroups, includePostEmbryonic, splitJoinState]); + }, [connections, hiddenNeurons, workspace.neuronGroups, includePostEmbryonic, splitJoinState, openGroups]); useEffect(() => { if (cyRef.current) { @@ -138,15 +186,61 @@ const TwoDViewer = () => { useEffect(() => { if (cyRef.current) { - updateHighlighted(cyRef.current, Array.from(workspace.activeNeurons), Array.from(workspace.selectedNeurons), legendHighlights, workspace.neuronGroups); + updateHighlighted(cyRef.current, Array.from(visibleActiveNeurons), selectedNeurons, legendHighlights); } - }, [legendHighlights, workspace.selectedNeurons, workspace.neuronGroups]); + }, [legendHighlights, selectedNeurons, workspace.neuronGroups]); // Update layout when layout setting changes useEffect(() => { updateLayout(); }, [layout, connections]); + const correctGjSegments = (edgeSel = '[type="electrical"]') => { + const cy = cyRef.current; + if (!cy) return; + + const edges = cy.edges(edgeSel); + const disFactors = [-2.0, -1.5, -0.5, 0.5, 1.5, 2.0]; + + cy.startBatch(); + + for (const e of edges) { + const sourcePos = e.source().position(); + const targetPos = e.target().position(); + + const length = Math.sqrt((targetPos.x - sourcePos.x) ** 2 + (targetPos.y - sourcePos.y) ** 2); + + const divider = (length > 60 ? 7 : length > 40 ? 5 : 3) / length; + + const segweights = disFactors.map((d) => 0.5 + d * divider).join(" "); + + if (e.style("segment-weights") !== segweights) { + e.style({ "segment-weights": segweights }); + } + } + + cy.endBatch(); + }; + + useEffect(() => { + if (!cyRef.current) return; + + const cy = cyRef.current; + + const debouncedCorrectGjSegments = debounce(() => { + correctGjSegments(); + }, 100); + + cy.on("position", "node", debouncedCorrectGjSegments); + cy.on("layoutstop", debouncedCorrectGjSegments); + + return () => { + cy.off("position", "node", debouncedCorrectGjSegments); + cy.off("layoutstop", debouncedCorrectGjSegments); + debouncedCorrectGjSegments.cancel(); + }; + }, []); + // Add event listener for node clicks to toggle neuron selection and right-click context menu useEffect(() => { if (!cyRef.current) return; @@ -155,20 +249,22 @@ const TwoDViewer = () => { const handleNodeClick = (event) => { const neuronId = event.target.id(); - const isSelected = workspace.selectedNeurons.has(neuronId); - workspace.toggleSelectedNeuron(neuronId); + const selectedNeurons = workspace.getSelection(ViewerType.Graph); + const isSelected = selectedNeurons.includes(neuronId); if (isSelected) { - event.target.removeClass("selected"); + workspace.removeSelection(neuronId, ViewerType.Graph); + event.target.removeClass(SELECTED_CLASS); } else { - event.target.addClass("selected"); + workspace.addSelection(neuronId, ViewerType.Graph); + event.target.addClass(SELECTED_CLASS); } }; const handleBackgroundClick = (event) => { if (event.target === cy) { - workspace.clearSelectedNeurons(); - cy.nodes(".selected").removeClass("selected"); + workspace.clearSelection(ViewerType.Graph); + cy.nodes(`.${SELECTED_CLASS}`).removeClass(SELECTED_CLASS); setLegendHighlights(new Map()); // Reset legend highlights } @@ -179,8 +275,8 @@ const TwoDViewer = () => { const cyEvent = event as any; // Cast to any to access originalEvent const originalEvent = cyEvent.originalEvent as MouseEvent; - - if (workspace.selectedNeurons.size > 0) { + const selectedNeurons = workspace.getViewerSelecedNeurons(ViewerType.Graph); + if (selectedNeurons.length > 0) { setMousePosition({ mouseX: originalEvent.clientX, mouseY: originalEvent.clientY, @@ -191,16 +287,18 @@ const TwoDViewer = () => { }; const handleEdgeMouseOver = (event) => { - event.target.addClass("hover"); + event.target.addClass(HOVER_CLASS); }; const handleEdgeMouseOut = (event) => { - event.target.removeClass("hover"); - event.target.removeClass("focus"); + event.target.removeClass(HOVER_CLASS); + event.target.removeClass(FOCUS_CLASS); + event.target.removeClass(SHOW_EDGE_LABEL_CLASS); }; const handleEdgeFocus = (event) => { - event.target.addClass("focus"); + event.target.toggleClass(SHOW_EDGE_LABEL_CLASS); + event.target.toggleClass(FOCUS_CLASS); }; cy.on("tap", "node", handleNodeClick); @@ -222,34 +320,34 @@ const TwoDViewer = () => { // Update active neurons when split or join state changes useEffect(() => { - const activeNeurons = new Set(workspace.activeNeurons); + const nextActiveNeurons = new Set(workspace.activeNeurons); - splitJoinState.split.forEach((neuronId) => { + for (const neuronId of splitJoinState.split) { if (workspace.activeNeurons.has(neuronId)) { - activeNeurons.delete(neuronId); - Object.values(workspace.availableNeurons).forEach((neuron) => { + nextActiveNeurons.delete(neuronId); + for (const neuron of Object.values(workspace.availableNeurons)) { if (neuron.nclass === neuronId && neuron.name !== neuron.nclass) { - activeNeurons.add(neuron.name); + nextActiveNeurons.add(neuron.name); } - }); + } } - }); + } - splitJoinState.join.forEach((neuronId) => { + for (const neuronId of splitJoinState.join) { const neuronClass = workspace.availableNeurons[neuronId].nclass; if (workspace.activeNeurons.has(neuronId)) { - activeNeurons.delete(neuronId); - Object.values(workspace.availableNeurons).forEach((neuron) => { + nextActiveNeurons.delete(neuronId); + for (const neuron of Object.values(workspace.availableNeurons)) { if (neuron.nclass === neuronClass) { - activeNeurons.delete(neuron.name); + nextActiveNeurons.delete(neuron.name); } - }); - activeNeurons.add(neuronClass); + } + nextActiveNeurons.add(neuronClass); } - }); + } - if (!areSetsEqual(activeNeurons, workspace.activeNeurons)) { - workspace.setActiveNeurons(activeNeurons); + if (!areSetsEqual(nextActiveNeurons, workspace.activeNeurons)) { + workspace.setActiveNeurons(nextActiveNeurons); } }, [splitJoinState, workspace.id]); @@ -258,13 +356,13 @@ const TwoDViewer = () => { if (!cyRef.current) return; cyRef.current.batch(() => { - cyRef.current.edges().forEach((edge) => { + for (const edge of cyRef.current.edges()) { if (includeLabels) { edge.addClass("showEdgeLabel"); } else { edge.removeClass("showEdgeLabel"); } - }); + } }); }, [includeLabels]); @@ -274,27 +372,65 @@ const TwoDViewer = () => { connections, workspace, splitJoinState, - hiddenNodes, + hiddenNeurons, + openGroups, includeNeighboringCellsAsIndividualCells, includeAnnotations, includePostEmbryonic, ); cy.batch(() => { - cy.remove(nodesToRemove); - cy.remove(edgesToRemove); cy.add(nodesToAdd); cy.add(edgesToAdd); + updateParentNodes(cy, workspace, openGroups); + cy.remove(nodesToRemove); + cy.remove(edgesToRemove); + updateParallelEdges(cy); }); updateNodeColors(); - updateHighlighted(cy, Array.from(workspace.activeNeurons), Array.from(workspace.selectedNeurons), legendHighlights, workspace.neuronGroups); + updateHighlighted(cy, Array.from(visibleActiveNeurons), selectedNeurons, legendHighlights); + checkSplitNeuronsInGraph(); + }; + + const checkSplitNeuronsInGraph = () => { + const newMissingNeurons = new Set(); + for (const neuronId of splitJoinState.split) { + const cells = workspace.getNeuronCellsByClass(neuronId); + for (const cellId of cells) { + // Check if the cell is part of a closed group, if not, check if it's missing + if (!isNeuronPartOfClosedGroup(cellId, workspace, openGroups) && !cyRef.current.getElementById(cellId).length) { + newMissingNeurons.add(cellId); + } + } + } + + const { reportedNeurons } = missingNeuronsState; + + // Find the newly missing neurons that haven't been reported yet + const unreportedNeurons = new Set([...newMissingNeurons].filter((neuron) => !reportedNeurons.has(neuron))); + + // Remove neurons from reportedNeurons that are no longer part of the splitJoinState.split + const updatedReportedNeurons = new Set( + [...reportedNeurons].filter((neuron) => { + const nclass = workspace.getNeuronClass(neuron); + return splitJoinState.split.has(nclass); + }), + ); + + // Check if there are any changes + if (!areSetsEqual(missingNeuronsState.unreportedNeurons, unreportedNeurons) || !areSetsEqual(missingNeuronsState.reportedNeurons, updatedReportedNeurons)) { + setMissingNeuronsState({ + unreportedNeurons: unreportedNeurons, + reportedNeurons: updatedReportedNeurons, + }); + } }; const updateLayout = () => { if (cyRef.current) { const cy = cyRef.current; - applyLayout(cy, layout); + applyLayout(cy, layout as GRAPH_LAYOUTS); updateWorkspaceNeurons2DViewerData(workspace, cy); } }; @@ -303,23 +439,26 @@ const TwoDViewer = () => { if (!cyRef.current) { return; } - cyRef.current.nodes().forEach((node) => { + for (const node of cyRef.current.nodes()) { + if (node.hasClass("groupNode")) { + return; + } const nodeId = node.id(); const group = workspace.neuronGroups[nodeId]; + let colors = []; if (group) { // If the node is a group, collect colors from all neurons in the group - group.neurons.forEach((neuronId) => { + for (const neuronId of group.neurons) { const neuron = workspace.availableNeurons[neuronId]; if (neuron) { colors = colors.concat(getColor(neuron, coloringOption)); } - }); + } // Ensure unique colors are used - const uniqueColors = [...new Set(colors)]; - colors = uniqueColors; + colors = [...new Set(colors)]; } else { const neuron = workspace.availableNeurons[nodeId]; if (neuron == null) { @@ -328,13 +467,16 @@ const TwoDViewer = () => { } colors = getColor(neuron, coloringOption); } - - colors.forEach((color, index) => { - node.style(`pie-${index + 1}-background-color`, color); - node.style(`pie-${index + 1}-background-size`, 100 / colors.length); // Equal size for each slice - }); - node.style("pie-background-opacity", 1); - }); + if (colors.length > 1 && node.style("shape") === "ellipse") { + colors.forEach((color, index) => { + node.style(`pie-${index + 1}-background-color`, color); + node.style(`pie-${index + 1}-background-size`, 100 / colors.length); + }); + node.style("pie-background-opacity", 1); + } else { + node.style("background-color", colors[0]); + } + } }; return ( @@ -360,7 +502,7 @@ const TwoDViewer = () => { includePostEmbryonic={includePostEmbryonic} setIncludePostEmbryonic={setIncludePostEmbryonic} /> - + { onClose={handleContextMenuClose} position={mousePosition} setSplitJoinState={setSplitJoinState} - setHiddenNodes={setHiddenNodes} + openGroups={openGroups} + setOpenGroups={setOpenGroups} + cy={cyRef.current} + /> + 0} + onClose={handleCloseSnackbar} + message={`Warning: The following neurons are missing from the graph due to the threshold filters: + ${Array.from(missingNeuronsState.unreportedNeurons).join(", ")}`} + autoHideDuration={6000} /> ); diff --git a/applications/visualizer/frontend/src/components/wrappers/Compare.tsx b/applications/visualizer/frontend/src/components/wrappers/Compare.tsx index 68118a57..b57c07ab 100644 --- a/applications/visualizer/frontend/src/components/wrappers/Compare.tsx +++ b/applications/visualizer/frontend/src/components/wrappers/Compare.tsx @@ -3,6 +3,7 @@ import { type Theme, ThemeProvider } from "@mui/material/styles"; import { Suspense } from "react"; import "@metacell/geppetto-meta-ui/flex-layout/style/light.scss"; import { Box } from "@mui/system"; +import { useGlobalContext } from "../../contexts/GlobalContext.tsx"; import { DownloadIcon, LinkIcon } from "../../icons"; import theme from "../../theme"; import { vars } from "../../theme/variables.ts"; @@ -11,6 +12,8 @@ const { gray100 } = vars; const drawerWidth = "22.31299rem"; const drawerHeight = "3.5rem"; function CompareWrapper({ children, sidebarOpen }) { + const { serializeGlobalContext } = useGlobalContext(); + return ( <> @@ -73,7 +76,17 @@ function CompareWrapper({ children, sidebarOpen }) { - diff --git a/applications/visualizer/frontend/src/contexts/GlobalContext.tsx b/applications/visualizer/frontend/src/contexts/GlobalContext.tsx index d034feb6..e7fce491 100644 --- a/applications/visualizer/frontend/src/contexts/GlobalContext.tsx +++ b/applications/visualizer/frontend/src/contexts/GlobalContext.tsx @@ -1,8 +1,27 @@ +import { produce } from "immer"; +import pako from "pako"; import type React from "react"; import { type ReactNode, createContext, useContext, useEffect, useState } from "react"; +import ErrorAlert from "../components/ErrorAlert.tsx"; +import ErrorBoundary from "../components/ErrorBoundary.tsx"; import { ViewMode } from "../models"; import { Workspace } from "../models"; +import { GlobalError } from "../models/Error.ts"; import { type Dataset, DatasetsService } from "../rest"; +import type { SerializedGlobalContext } from "./SerializedContext.tsx"; + +function b64Tob64Url(buffer: string): string { + return buffer.replace(/\+/g, "-").replace(/\//g, "_").replace(/=+$/, ""); +} + +function b64UrlTo64(value: string): string { + const m = value.length % 4; + return value + .replace(/-/g, "+") + .replace(/_/g, "/") + .padEnd(value.length + (m === 0 ? 0 : 4 - m), "="); +} + export interface GlobalContextType { workspaces: Record; currentWorkspaceId: string | undefined; @@ -16,8 +35,11 @@ export interface GlobalContextType { getCurrentWorkspace: () => Workspace; setSelectedWorkspacesIds: (workspaceId: Set) => void; datasets: Record; - fetchDatasets: () => void; setAllWorkspaces: (workspaces: Record) => void; + handleErrors: (error: Error) => void; + serializeGlobalContext: () => string; + restoreGlobalContext: (context: SerializedGlobalContext) => void; + restoreGlobalContextFromBase64: (base64Context: string) => void; } interface GlobalContextProviderProps { @@ -32,16 +54,17 @@ export const GlobalContextProvider: React.FC = ({ ch const [viewMode, setViewMode] = useState(ViewMode.Default); const [selectedWorkspacesIds, setSelectedWorkspacesIds] = useState>(new Set()); const [datasets, setDatasets] = useState>({}); - + const [openErrorAlert, setOpenErrorAlert] = useState(false); + const [errorMessage, setErrorMessage] = useState(""); const createWorkspace = (id: string, name: string, activeDatasetKeys: Set, activeNeurons: Set) => { // Convert the activeDatasetKeys into a Record const activeDatasets: Record = {}; - activeDatasetKeys.forEach((key) => { + for (const key of activeDatasetKeys) { if (datasets[key]) { activeDatasets[key] = datasets[key]; } - }); + } // Create a new workspace using the activeDatasets record const newWorkspace = new Workspace(id, name, activeDatasets, activeNeurons, updateWorkspace); @@ -70,8 +93,88 @@ export const GlobalContextProvider: React.FC = ({ ch }; const getCurrentWorkspace = () => { - return workspaces[currentWorkspaceId]; + return workspaces?.[currentWorkspaceId]; }; + + const handleErrors = (error: Error) => { + if (error instanceof GlobalError) { + setErrorMessage(error.message); + setOpenErrorAlert(true); + } + }; + + const serializeGlobalContext = () => { + // Create a special context with only the information we need + const subContext = { + workspaces: {}, + currentWorkspaceId, + viewMode, + selectedWorkspacesIds: [...selectedWorkspacesIds], + }; + + // Modify this context to remove the elements we don't want by workspace and to simplify it + // - layoutManager (not serializable) + // - store (related to the layour manager) + // - availableNeurons (they are computed when a workspace is created) + // - activeDatasets, we replace only with the keys of the datasets + // - synchronizerOrchestrator, we move some of its properties to the simplified workspace (gain space) + // - contexts comes from the synchronizer orchestrator + // - active viewers comes from the synchronizer orchestrator + const updatedSubContext = produce(subContext, (draft) => { + const simpleWorkspace = {}; + for (const [key, workspace] of Object.entries(workspaces)) { + const copy = { + ...workspace, + layoutManager: undefined, + store: undefined, + availableNeurons: undefined, + syncOrchestrator: undefined, + activeDatasets: Object.keys(workspace.activeDatasets), + contexts: workspace.syncOrchestrator.contexts, + activeSyncs: Object.fromEntries(workspace.syncOrchestrator.synchronizers.map((sync) => [sync.pair, sync.active])), + }; + simpleWorkspace[key] = copy; + } + draft.workspaces = simpleWorkspace; + }); + + const jsonContext = JSON.stringify(updatedSubContext, (_key, value) => (value instanceof Set ? [...value] : value)); + const gzipContext = pako.gzip(jsonContext); + const base64UrlFragment = btoa(String.fromCharCode.apply(null, gzipContext)); + return b64Tob64Url(base64UrlFragment); + }; + + const restoreGlobalContext = (context: SerializedGlobalContext) => { + setCurrentWorkspaceId(context.currentWorkspaceId); + setSelectedWorkspacesIds(new Set(context.selectedWorkspacesIds)); + setViewMode(context.viewMode); + + const reconstructedWorkspaces = {}; + for (const [wsId, ws] of Object.entries(context.workspaces)) { + const activeDatasets: Record = {}; + for (const key of ws.activeDatasets) { + if (datasets[key]) { + activeDatasets[key] = datasets[key]; + } + } + const workspace = new Workspace(ws.id, ws.name, activeDatasets, new Set(ws.activeNeurons), updateWorkspace, ws.activeSyncs, ws.contexts, ws.visibilities); + workspace.viewers = ws.viewers; + + reconstructedWorkspaces[wsId] = workspace; + } + setWorkspaces(reconstructedWorkspaces); + }; + + const restoreGlobalContextFromBase64 = (base64UrlContext: string) => { + const base64Context = b64UrlTo64(base64UrlContext); + const gzipedContext = Uint8Array.from(atob(base64Context), (c) => c.charCodeAt(0)); + const serializedContext = pako.ungzip(gzipedContext); + const jsonContext = new TextDecoder().decode(serializedContext); + + const ctx = JSON.parse(jsonContext) as SerializedGlobalContext; + restoreGlobalContext(ctx); + }; + const getGlobalContext = () => ({ workspaces, currentWorkspaceId, @@ -84,32 +187,43 @@ export const GlobalContextProvider: React.FC = ({ ch setViewMode, selectedWorkspacesIds, setSelectedWorkspacesIds, - fetchDatasets, datasets, setAllWorkspaces, + handleErrors, + serializeGlobalContext, + restoreGlobalContext, + restoreGlobalContextFromBase64, }); - const fetchDatasets = async () => { - try { - const response = await DatasetsService.getDatasets({}); - const datasetsRecord = response.reduce( - (acc, dataset) => { - acc[dataset.id] = dataset; - return acc; - }, - {} as Record, - ); - - setDatasets(datasetsRecord); - } catch (error) { - console.error("Failed to fetch datasets", error); - } - }; useEffect(() => { + const fetchDatasets = async () => { + try { + const response = await DatasetsService.getDatasets({}); + const datasetsRecord = response.reduce( + (acc, dataset) => { + acc[dataset.id] = dataset; + return acc; + }, + {} as Record, + ); + + setDatasets(datasetsRecord); + } catch (error) { + setOpenErrorAlert(true); + setErrorMessage("Failed to fetch datasets"); + } + }; fetchDatasets(); }, []); - return {children}; + return ( + + + {children} + + + + ); }; export const useGlobalContext = () => { const context = useContext(GlobalContext); diff --git a/applications/visualizer/frontend/src/contexts/GlobalContextReloader.tsx b/applications/visualizer/frontend/src/contexts/GlobalContextReloader.tsx new file mode 100644 index 00000000..b2a980c0 --- /dev/null +++ b/applications/visualizer/frontend/src/contexts/GlobalContextReloader.tsx @@ -0,0 +1,21 @@ +import { useEffect } from "react"; +import { useNavigate, useParams } from "react-router-dom"; +import { useGlobalContext } from "./GlobalContext"; + +const GlobalContextReloader = () => { + const { code } = useParams(); + const navigate = useNavigate(); + const { restoreGlobalContextFromBase64, datasets } = useGlobalContext(); + + // biome-ignore lint/correctness/useExhaustiveDependencies: navigate and restoreGlobalContextFromBase64 are function from global context + useEffect(() => { + if (code && datasets && Object.keys(datasets).length > 0) { + restoreGlobalContextFromBase64(code); + navigate("/"); + } + }, [datasets, code]); + + return
    Loading datasets
    ; +}; + +export default GlobalContextReloader; diff --git a/applications/visualizer/frontend/src/contexts/SerializedContext.tsx b/applications/visualizer/frontend/src/contexts/SerializedContext.tsx new file mode 100644 index 00000000..3fcff481 --- /dev/null +++ b/applications/visualizer/frontend/src/contexts/SerializedContext.tsx @@ -0,0 +1,23 @@ +import type { NeuronGroup, ViewMode, ViewerType } from "../models"; +import type { ViewerData, ViewerSynchronizationPair } from "../models/models"; +import type { SynchronizerContext } from "../models/synchronizer"; + +type SerializedWorkspace = { + id: string; + name: string; + activeNeurons: Array; + selectedNeurons: Array; + activeDatasets: Array; + viewers: Record; + neuronGroups: Record; + contexts: Record; + activeSyncs: Record; + visibilities: Record; +}; + +export type SerializedGlobalContext = { + workspaces: Record; + currentWorkspaceId: string; + viewMode: ViewMode; + selectedWorkspacesIds: Array; +}; diff --git a/applications/visualizer/frontend/src/helpers/slidingRing.ts b/applications/visualizer/frontend/src/helpers/slidingRing.ts index 6c5352c5..05b22ab4 100644 --- a/applications/visualizer/frontend/src/helpers/slidingRing.ts +++ b/applications/visualizer/frontend/src/helpers/slidingRing.ts @@ -76,13 +76,18 @@ export class SlidingRing { onEvict: options.onEvict, }; + this.initRing(options.startAt); + } + + private initRing(at: number) { // initialize ring const halfSize = Math.floor(this.ring.length / 2); - let tailN = options.startAt - halfSize; - let headN = options.startAt + halfSize; + let tailN = at - halfSize; + let headN = at + halfSize; // the ring may start near the extent // this account for that adjustment + const [min, max] = this.extent; if (tailN < min) tailN = min; if (headN > max) { headN = max; @@ -97,11 +102,11 @@ export class SlidingRing { this.ring[i] = { n, o }; } - this.pos = options.startAt - tailN; + this.pos = at - tailN; this.tail = 0; this.head = this.ring.length - 1; - this.cb.onSelected(options.startAt, this.ring[this.pos].o); + this.cb.onSelected(at, this.ring[this.pos].o); } next() { @@ -166,6 +171,14 @@ export class SlidingRing { this.pos = prevPos; } + goto(n: number) { + this.cb.onUnselected(this.ring[this.pos].n, this.ring[this.pos].o); + for (const item of this.ring) { + this.cb.onEvict(item.n, item.o); + } + this.initRing(n); + } + debug() { let text = "["; diff --git a/applications/visualizer/frontend/src/helpers/twoD/alignHelper.ts b/applications/visualizer/frontend/src/helpers/twoD/alignHelper.ts new file mode 100644 index 00000000..0934d05b --- /dev/null +++ b/applications/visualizer/frontend/src/helpers/twoD/alignHelper.ts @@ -0,0 +1,86 @@ +import type { Core } from "cytoscape"; +import { Alignment } from "../../models"; + +export const alignNeurons = (alignment: Alignment, selectedNeurons: string[], cy: Core) => { + // Get Cytoscape elements for selected neurons + const cyNodes = selectedNeurons.map((neuronId) => cy.getElementById(neuronId)); + + if (cyNodes.some((node) => !node || !node.position())) { + console.error("Some selected neurons do not have positions set in Cytoscape."); + return; + } + + const xPositions = cyNodes.map((node) => node.position("x")); + const yPositions = cyNodes.map((node) => node.position("y")); + + let targetX: number | undefined; + let targetY: number | undefined; + + switch (alignment) { + case Alignment.Left: + targetX = Math.min(...xPositions); + break; + case Alignment.Right: + targetX = Math.max(...xPositions); + break; + case Alignment.Top: + targetY = Math.min(...yPositions); + break; + case Alignment.Bottom: + targetY = Math.max(...yPositions); + break; + } + + // Align nodes in Cytoscape + cy.batch(() => { + cyNodes.forEach((node) => { + const currentPos = node.position(); + if (alignment === Alignment.Left || alignment === Alignment.Right) { + node.position({ x: targetX!, y: currentPos.y }); + } else { + node.position({ x: currentPos.x, y: targetY! }); + } + }); + }); +}; + +export const distributeNeurons = (alignment: Alignment, selectedNeurons: string[], cy: Core) => { + if (selectedNeurons.length <= 1) { + return; + } + // Get Cytoscape elements for selected neurons + const cyNodes = selectedNeurons.map((neuronId) => cy.getElementById(neuronId)); + + if (cyNodes.some((node) => !node || !node.position())) { + console.error("Some selected neurons do not have positions set in Cytoscape."); + return; + } + + // Sort nodes by their current position along the axis to distribute + cyNodes.sort((a, b) => { + if (alignment === Alignment.Horizontal) { + return a.position("x") - b.position("x"); + } else { + return a.position("y") - b.position("y"); + } + }); + + // Get the range of positions along the distribution axis + const minPos = alignment === Alignment.Horizontal ? cyNodes[0].position("x") : cyNodes[0].position("y"); + const maxPos = alignment === Alignment.Horizontal ? cyNodes[cyNodes.length - 1].position("x") : cyNodes[cyNodes.length - 1].position("y"); + + // Calculate the spacing + const spacing = (maxPos - minPos) / (cyNodes.length - 1); + + // Distribute nodes + cy.batch(() => { + cyNodes.forEach((node, index) => { + const currentPos = node.position(); + if (alignment === Alignment.Horizontal) { + node.position({ x: minPos + index * spacing, y: currentPos.y }); + } else { + node.position({ x: currentPos.x, y: minPos + index * spacing }); + } + }); + }); +}; diff --git a/applications/visualizer/frontend/src/helpers/twoD/coloringHelper.ts b/applications/visualizer/frontend/src/helpers/twoD/coloringHelper.ts index ab1db5ec..20691190 100644 --- a/applications/visualizer/frontend/src/helpers/twoD/coloringHelper.ts +++ b/applications/visualizer/frontend/src/helpers/twoD/coloringHelper.ts @@ -20,12 +20,12 @@ interface CellDesign { } export const cellConfig: { [key: string]: CellDesign } = { - b: { type: CellType.Muscle, color: "#A8F5A2" }, - u: { type: CellType.Others, color: "#D9D9D9" }, s: { type: CellType.Sensory, color: "#F9CEF9" }, i: { type: CellType.Inter, color: "#FF887A" }, m: { type: CellType.Motor, color: "#B7DAF5" }, n: { type: CellType.Neurosecretory, color: "#F9D77B" }, + b: { type: CellType.Muscle, color: "#A8F5A2" }, + u: { type: CellType.Others, color: "#D9D9D9" }, }; enum NeurotransmitterType { diff --git a/applications/visualizer/frontend/src/helpers/twoD/concentricLayoutHelper.ts b/applications/visualizer/frontend/src/helpers/twoD/concentricLayoutHelper.ts new file mode 100644 index 00000000..f1ae76a2 --- /dev/null +++ b/applications/visualizer/frontend/src/helpers/twoD/concentricLayoutHelper.ts @@ -0,0 +1,71 @@ +import type { Core } from "cytoscape"; + +export function getConcentricLayoutPositions(cy: Core) { + const center = { + x: cy.width() / 2, + y: cy.height() / 2, + }; + + const innerNodes = cy.nodes(".searchedfor"); + const innerNodeIds = innerNodes.map((n) => n.id()).sort(); + + const outerNodes = cy.nodes().not(".searchedfor"); + const edgeTypes: Record = {}; + + outerNodes.forEach((node) => { + const edges = node.edgesWith(innerNodes); + const edgesElectrical = edges.filter('[type="electrical"]'); + const edgesChemical = edges.filter('[type="chemical"]'); + const hasElectrical = edgesElectrical.length > 0; + const isTarget = edgesChemical.sources().contains(innerNodes); + const isSource = edgesChemical.targets().contains(innerNodes); + let idx = 0; + + if (hasElectrical) { + idx = 3 - (isTarget ? 1 : 0) + (isSource ? 1 : 0); + } else { + idx = (isTarget ? 1 : 0) + (isSource ? 5 : 0); + } + + edgeTypes[node.id()] = idx; + }); + + const outerNodeIds = outerNodes + .map((n) => n.id()) + .sort((a, b) => { + if (edgeTypes[a] === edgeTypes[b]) { + return a.localeCompare(b); + } + return edgeTypes[a] - edgeTypes[b]; + }); + + const innerPositions = createCircle(innerNodeIds, center, outerNodes.length > 0); + const outerPositions = createCircle(outerNodeIds, center); + + return Object.assign({}, innerPositions, outerPositions); +} + +function createCircle(nodes: string[], center: { x: number; y: number }, smallCircle = false) { + const positions: Record = {}; + const count = nodes.length; + const dTheta = (2 * Math.PI - (2 * Math.PI) / count) / Math.max(1, count - 1); + let r = Math.ceil(Math.min(center.x * 2, center.y * 2) / 2.5); + + if (smallCircle) { + r /= count < 4 ? 3 : 2; + } + + if (smallCircle && count === 1) { + positions[nodes[0]] = { x: center.x, y: center.y }; + } else { + for (let i = 0; i < count; i++) { + const theta = -i * dTheta; + positions[nodes[i]] = { + x: center.x - r * Math.sin(theta), + y: center.y - r * Math.cos(theta), + }; + } + } + + return positions; +} diff --git a/applications/visualizer/frontend/src/helpers/twoD/downloadHelper.ts b/applications/visualizer/frontend/src/helpers/twoD/downloadHelper.ts new file mode 100644 index 00000000..71438394 --- /dev/null +++ b/applications/visualizer/frontend/src/helpers/twoD/downloadHelper.ts @@ -0,0 +1,57 @@ +import html2canvas from "html2canvas"; + +export const downloadConnectivityViewer = async (cy, name) => { + if (!cy) return; + + // Capture Cytoscape graph as an image + const pngDataUrl = cy.png({ + output: "base64uri", + bg: "white", + full: true, + scale: 2, + }); + + // Create an image element to load the Cytoscape image + const graphImage = new Image(); + graphImage.src = pngDataUrl; + + await new Promise((resolve) => { + graphImage.onload = resolve; + }); + + // Get the actual size of the captured image + const graphWidth = graphImage.width; + const graphHeight = graphImage.height; + + // Capture the legend as an image + const legendElement = document.querySelector("#legend-container"); + const legendCanvas = await html2canvas(legendElement); + + // Create a new canvas to combine the graph and the legend + const canvas = document.createElement("canvas"); + const context = canvas.getContext("2d"); + + // Set the canvas size to fit both the graph and the legend side by side + canvas.width = graphWidth + legendCanvas.width; + canvas.height = Math.max(graphHeight, legendCanvas.height); + + // Fill the canvas with a white background + context.fillStyle = "white"; + context.fillRect(0, 0, canvas.width, canvas.height); + + // Draw the Cytoscape image onto the canvas + context.drawImage(graphImage, 0, 0, graphWidth, graphHeight); + + // Draw the legend to the right of the graph + context.drawImage(legendCanvas, graphWidth, 0); + + // Download the combined image + const combinedDataUrl = canvas.toDataURL("image/png"); + const link = document.createElement("a"); + link.href = combinedDataUrl; + link.download = `${name}.png`; + + document.body.appendChild(link); + link.click(); + document.body.removeChild(link); +}; diff --git a/applications/visualizer/frontend/src/helpers/twoD/graphRendering.ts b/applications/visualizer/frontend/src/helpers/twoD/graphRendering.ts index 343675db..49c364b6 100644 --- a/applications/visualizer/frontend/src/helpers/twoD/graphRendering.ts +++ b/applications/visualizer/frontend/src/helpers/twoD/graphRendering.ts @@ -1,9 +1,19 @@ -import type { Core, ElementDefinition, CollectionReturnValue } from "cytoscape"; -import { calculateMeanPosition, createEdge, createNode, extractNeuronAttributes, getEdgeId, getNclassSet, isNeuronCell, isNeuronClass } from "./twoDHelpers"; +import type { CollectionReturnValue, Core, ElementDefinition } from "cytoscape"; import type { NeuronGroup, Workspace } from "../../models"; import { ViewerType } from "../../models"; import type { Connection } from "../../rest"; -import { LegendType } from "../../settings/twoDSettings.tsx"; +import { FADED_CLASS, LegendType } from "../../settings/twoDSettings.tsx"; +import { + calculateMeanPosition, + createEdge, + createNode, + extractNeuronAttributes, + getEdgeId, + getNclassSet, + getVisibleActiveNeuronsIn2D, + isNeuronCell, + isNeuronClass, +} from "./twoDHelpers"; export const computeGraphDifferences = ( cy: Core, @@ -11,10 +21,14 @@ export const computeGraphDifferences = ( workspace: Workspace, splitJoinState: { split: Set; join: Set }, hiddenNodes: Set, + openGroups: Set, includeNeighboringCellsAsIndividualCells: boolean, includeAnnotations: boolean, includePostEmbryonic: boolean, ) => { + const visibleActiveNeurons = getVisibleActiveNeuronsIn2D(workspace); + const selectedNeurons = workspace.getViewerSelecedNeurons(ViewerType.Graph); + // Current nodes and edges in the Cytoscape instance const currentNodes = new Set(cy.nodes().map((node) => node.id())); const currentEdges = new Set(cy.edges().map((edge) => edge.id())); @@ -30,13 +44,13 @@ export const computeGraphDifferences = ( // Create a map of connections by edgeId const connectionMap = new Map(); - connections.forEach((conn) => { + for (const conn of connections) { const edgeId = getEdgeId(conn, includeAnnotations); connectionMap.set(edgeId, conn); - }); + } - // Compute expected nodes based on workspace.activeNeurons and connections - const filteredActiveNeurons = Array.from(workspace.activeNeurons).filter((neuronId: string) => { + // Compute expected nodes based on visibleActiveNeurons and connections + const filteredActiveNeurons = Array.from(visibleActiveNeurons).filter((neuronId: string) => { const neuron = workspace.availableNeurons[neuronId]; if (!neuron || hiddenNodes.has(neuronId)) { return false; @@ -48,7 +62,7 @@ export const computeGraphDifferences = ( if (neuronId === nclass) { return true; } - return !(workspace.activeNeurons.has(neuronId) && workspace.activeNeurons.has(nclass)); + return !(visibleActiveNeurons.has(neuronId) && visibleActiveNeurons.has(nclass)); }); // Add active neurons to expected nodes @@ -71,12 +85,19 @@ export const computeGraphDifferences = ( } // Apply split and join rules to expected nodes and edges - expectedNodes = applySplitJoinRulesToNodes(expectedNodes, splitJoinState.split, splitJoinState.join, includeNeighboringCellsAsIndividualCells, workspace); + expectedNodes = applySplitJoinRulesToNodes( + expectedNodes, + splitJoinState.split, + splitJoinState.join, + includeNeighboringCellsAsIndividualCells, + workspace, + visibleActiveNeurons, + ); expectedEdges = applySplitJoinRulesToEdges(expectedEdges, expectedNodes, connectionMap); // Replace individual neurons and edges with groups if necessary - expectedNodes = replaceNodesWithGroups(expectedNodes, workspace.neuronGroups, hiddenNodes); - replaceEdgesWithGroups(expectedEdges, workspace.neuronGroups, connectionMap, includeAnnotations); + expectedNodes = applyGroupingRulesToNodes(expectedNodes, workspace.neuronGroups, hiddenNodes, openGroups); + expectedEdges = applyGroupingRulesToEdges(expectedEdges, workspace.neuronGroups, connectionMap, includeAnnotations, openGroups); // Determine nodes to add and remove for (const nodeId of expectedNodes) { @@ -87,17 +108,34 @@ export const computeGraphDifferences = ( const attributes = new Set(); const groupNeurons = Array.from(group.neurons); - groupNeurons.forEach((neuronId) => { + for (const neuronId of groupNeurons) { const neuron = workspace.availableNeurons[neuronId]; - extractNeuronAttributes(neuron).forEach((attr) => attributes.add(attr)); - }); + for (const attr of extractNeuronAttributes(neuron)) { + attributes.add(attr); + } + } const groupPosition = calculateMeanPosition(groupNeurons, workspace); - nodesToAdd.push(createNode(nodeId, workspace.selectedNeurons.has(nodeId), Array.from(attributes), groupPosition)); + nodesToAdd.push( + createNode(nodeId, selectedNeurons.includes(nodeId), Array.from(attributes), groupPosition, true, undefined, workspace.activeNeurons.has(nodeId)), + ); } else { + let parent = undefined; + + // Check if the neuron belongs to an open group + for (const groupId of openGroups) { + if (workspace.neuronGroups[groupId]?.neurons.has(nodeId)) { + parent = groupId; + break; + } + } const neuron = workspace.availableNeurons[nodeId]; const attributes = extractNeuronAttributes(neuron); - const position = neuron.viewerData[ViewerType.Graph]?.defaultPosition ?? null; - nodesToAdd.push(createNode(nodeId, workspace.selectedNeurons.has(nodeId), attributes, position)); + const neuronVisibility = workspace.visibilities[nodeId]; + const position = neuronVisibility?.[ViewerType.Graph]?.defaultPosition ?? null; + nodesToAdd.push(createNode(nodeId, selectedNeurons.includes(nodeId), attributes, position, false, parent, workspace.activeNeurons.has(nodeId))); + if (!(nodeId in workspace.visibilities)) { + workspace.showNeuron(nodeId); + } } } } @@ -112,8 +150,16 @@ export const computeGraphDifferences = ( for (const edgeId of expectedEdges) { if (!currentEdges.has(edgeId)) { const conn = connectionMap.get(edgeId); + const syns = Object.values(conn.synapses).reduce((acc, num) => acc + num, 0); + const meanSyn = syns / Object.values(conn.synapses).length; + let width; + if (conn.type === "chemical") { + width = Math.max(1, 2 * Math.pow(meanSyn, 1 / 4) - 2); + } else { + width = Math.min(4, meanSyn * 0.8); + } if (conn) { - edgesToAdd.push(createEdge(edgeId, conn, workspace, includeAnnotations)); + edgesToAdd.push(createEdge(edgeId, conn, workspace, includeAnnotations, width)); } } } @@ -129,52 +175,82 @@ export const computeGraphDifferences = ( }; // Replace individual neurons with group nodes -const replaceNodesWithGroups = (expectedNodes: Set, neuronGroups: Record, hiddenNodes: Set) => { +const applyGroupingRulesToNodes = ( + expectedNodes: Set, + neuronGroups: Record, + hiddenNodes: Set, + openGroups: Set, +) => { const nodesToAdd = new Set(); const nodesToRemove = new Set(); - expectedNodes.forEach((nodeId) => { + for (const nodeId of expectedNodes) { for (const groupId in neuronGroups) { const group = neuronGroups[groupId]; + if (group.neurons.has(nodeId)) { if (!hiddenNodes.has(groupId)) { nodesToAdd.add(groupId); } - nodesToRemove.add(nodeId); + if (!openGroups.has(groupId)) { + nodesToRemove.add(nodeId); + } } } - }); + } + + // Remove individual nodes if they are replaced by a closed group node + for (const nodeId of nodesToRemove) { + expectedNodes.delete(nodeId); + } + // Add group nodes + for (const nodeId of nodesToAdd) { + expectedNodes.add(nodeId); + } - nodesToRemove.forEach((nodeId) => expectedNodes.delete(nodeId)); - nodesToAdd.forEach((nodeId) => expectedNodes.add(nodeId)); return expectedNodes; }; // Replace edges involving individual neurons with edges involving group nodes -const replaceEdgesWithGroups = ( +const applyGroupingRulesToEdges = ( expectedEdges: Set, neuronGroups: Record, connectionMap: Map, includeAnnotations: boolean, + openGroups: Set, ) => { const edgesToAdd = new Set(); const edgesToRemove = new Set(); const groupedConnections: Map = new Map(); - expectedEdges.forEach((edgeId) => { + for (const edgeId of expectedEdges) { const conn = connectionMap.get(edgeId); if (!conn) return; let newPre = conn.pre; let newPost = conn.post; - for (const groupId in neuronGroups) { - const group = neuronGroups[groupId]; - if (group.neurons.has(conn.pre)) { - newPre = groupId; + // Skip grouping if either pre or post neuron is in an open group + const preInOpenGroup = Array.from(openGroups).some((groupId) => neuronGroups[groupId]?.neurons.has(conn.pre)); + const postInOpenGroup = Array.from(openGroups).some((groupId) => neuronGroups[groupId]?.neurons.has(conn.post)); + + if (!preInOpenGroup) { + for (const groupId in neuronGroups) { + const group = neuronGroups[groupId]; + if (group.neurons.has(conn.pre)) { + newPre = groupId; + break; + } } - if (group.neurons.has(conn.post)) { - newPost = groupId; + } + + if (!postInOpenGroup) { + for (const groupId in neuronGroups) { + const group = neuronGroups[groupId]; + if (group.neurons.has(conn.post)) { + newPost = groupId; + break; + } } } @@ -198,16 +274,22 @@ const replaceEdgesWithGroups = ( if (fullNewEdgeId !== edgeId) { edgesToRemove.add(edgeId); } - }); + } - groupedConnections.forEach((conn) => { + for (const conn of groupedConnections.values()) { const fullNewEdgeId = getEdgeId(conn, includeAnnotations); edgesToAdd.add(fullNewEdgeId); connectionMap.set(fullNewEdgeId, conn); - }); + } - edgesToRemove.forEach((edgeId) => expectedEdges.delete(edgeId)); - edgesToAdd.forEach((edgeId) => expectedEdges.add(edgeId)); + for (const edgeId of edgesToRemove) { + expectedEdges.delete(edgeId); + } + for (const edgeId of edgesToAdd) { + expectedEdges.add(edgeId); + } + + return expectedEdges; }; const getSimpleEdgeId = (pre: string, post: string, type: string): string => { @@ -221,16 +303,22 @@ const applySplitJoinRulesToNodes = ( toJoin: Set, includeNeighboringCellsAsIndividualCells: boolean, workspace: Workspace, + visibleActiveNeurons: Set, ) => { const nodesToRemove = new Set(); - expectedNodes.forEach((nodeId) => { - if (!workspace.activeNeurons.has(nodeId) && shouldRemoveNode(nodeId, toSplit, toJoin, includeNeighboringCellsAsIndividualCells, workspace)) { + for (const nodeId of expectedNodes) { + if ( + !visibleActiveNeurons.has(nodeId) && + shouldRemoveNode(nodeId, toSplit, toJoin, includeNeighboringCellsAsIndividualCells, workspace, visibleActiveNeurons) + ) { nodesToRemove.add(nodeId); } - }); + } - nodesToRemove.forEach((nodeId) => expectedNodes.delete(nodeId)); + for (const nodeId of nodesToRemove) { + expectedNodes.delete(nodeId); + } return expectedNodes; }; @@ -239,7 +327,7 @@ const applySplitJoinRulesToNodes = ( const applySplitJoinRulesToEdges = (expectedEdges: Set, expectedNodes: Set, connectionMap: Map) => { const edgesToRemove = new Set(); - expectedEdges.forEach((edgeId) => { + for (const edgeId of expectedEdges) { const conn = connectionMap.get(edgeId); if (conn) { @@ -250,9 +338,11 @@ const applySplitJoinRulesToEdges = (expectedEdges: Set, expectedNodes: S edgesToRemove.add(edgeId); } } - }); + } - edgesToRemove.forEach((edgeId) => expectedEdges.delete(edgeId)); + for (const edgeId of edgesToRemove) { + expectedEdges.delete(edgeId); + } return expectedEdges; }; @@ -263,8 +353,9 @@ const shouldRemoveNode = ( toJoin: Set, includeNeighboringCellsAsIndividualCells: boolean, workspace: Workspace, + visibleActiveNeurons: Set, ): boolean => { - const isActive = workspace.activeNeurons.has(nodeId); + const isActive = visibleActiveNeurons.has(nodeId); const isClass = isNeuronClass(nodeId, workspace); const isCell = isNeuronCell(nodeId, workspace); const neuron = workspace.availableNeurons[nodeId]; @@ -281,8 +372,19 @@ const shouldRemoveNode = ( return true; } - // 3. Remove individual cells if showing class nodes and the node is not active and it's not a split exception - if (!includeNeighboringCellsAsIndividualCells && isCell && !isActive && !toSplit.has(neuron.nclass)) { + // 3. Remove individual cells if showing class nodes and the node is not active, it's not a split exception, and there's no active neuron in the same class + const isAnyNeuronInClassActive = + !includeNeighboringCellsAsIndividualCells && isCell && workspace.getNeuronCellsByClass(neuron.nclass).some((cellId) => visibleActiveNeurons.has(cellId)); + + if (!includeNeighboringCellsAsIndividualCells && isCell && !isActive && !toSplit.has(neuron.nclass) && !isAnyNeuronInClassActive) { + return true; + } + + // 4. Remove class nodes if showing individual cells and there's an active cell in the same class + const hasActiveCellInClass = + !includeNeighboringCellsAsIndividualCells && isClass && workspace.getNeuronCellsByClass(nodeId).some((cellId) => visibleActiveNeurons.has(cellId)); + + if (!includeNeighboringCellsAsIndividualCells && isClass && hasActiveCellInClass) { return true; } @@ -295,7 +397,7 @@ const shouldRemoveEdge = (pre: string, post: string, expectedNodes: Set) return !expectedNodes.has(pre) || !expectedNodes.has(post); }; -export const updateHighlighted = (cy, inputIds, selectedIds, legendHighlights, neuronGroups) => { +export const updateHighlighted = (cy, inputIds, selectedIds, legendHighlights) => { // Remove all highlights and return if nothing is selected and no legend item activated. cy.elements().removeClass("faded"); if (selectedIds.length === 0 && legendHighlights.size === 0) { @@ -306,30 +408,23 @@ export const updateHighlighted = (cy, inputIds, selectedIds, legendHighlights, n const sourceIds = selectedIds.length ? selectedIds : inputIds; let sourceNodes = cy.collection(); - sourceIds.forEach((id) => { - let node = cy.getElementById(id); + for (const id of sourceIds) { + const node = cy.getElementById(id); - if (node.empty()) { - // If node is not found, search in neuron groups - for (const groupId in neuronGroups) { - const group = neuronGroups[groupId]; - if (group.neurons.has(id)) { - node = cy.getElementById(groupId); - break; - } - } + if (node.isParent()) { + sourceNodes = sourceNodes.union(node.children()); + } else { + sourceNodes = sourceNodes.union(node); } - - sourceNodes = sourceNodes.union(node); - }); + } // Filter network by edges, as set by legend. let edgeSel = "edge"; legendHighlights.forEach((highlight, type) => { if (type === LegendType.Connection) { edgeSel += `[type="${highlight}"]`; - } else if (type == LegendType.Annotation) { - edgeSel += "." + highlight; + } else if (type === LegendType.Annotation) { + edgeSel += `.${highlight}`; } }); @@ -338,7 +433,7 @@ export const updateHighlighted = (cy, inputIds, selectedIds, legendHighlights, n // Filter network by nodes, as set by legend. legendHighlights.forEach((highlight, type) => { if (type === LegendType.Node) { - connectedNodes = connectedNodes.filter("[?" + highlight + "]"); + connectedNodes = connectedNodes.filter(`[?${highlight}]`); } }); @@ -366,5 +461,33 @@ export const updateHighlighted = (cy, inputIds, selectedIds, legendHighlights, n let highlightedEdges = highlightedNodes.edgesWith(highlightedNodes); highlightedEdges = highlightedEdges.filter(edgeSel); - cy.elements().not(highlightedNodes).not(highlightedEdges).addClass("faded"); + cy.elements().not(highlightedNodes).not(highlightedEdges).addClass(FADED_CLASS); +}; + +export const updateParentNodes = (cy: Core, workspace: Workspace, openGroups: Set) => { + // Iterate through each neuron group in the workspace + for (const [groupId, group] of Object.entries(workspace.neuronGroups)) { + const groupIsOpen = openGroups.has(groupId); + + for (const neuronId of group.neurons) { + const cyNode = cy.getElementById(neuronId); + + if (groupIsOpen) { + // If the group is open, the neuron should have the group as its parent + const parentId = cyNode.parent().first().id(); + + if (parentId !== groupId) { + cyNode.move({ parent: groupId }); + } + } + } + } +}; + +export const updateParallelEdges = (cy: Core) => { + // Remove 'parallel' class from all edges + cy.edges().removeClass("parallel"); + + // Add 'parallel' class to parallel edges + cy.edges('[type = "electrical"]').parallelEdges().filter('[type = "chemical"]').addClass("parallel"); }; diff --git a/applications/visualizer/frontend/src/helpers/twoD/groupHelper.ts b/applications/visualizer/frontend/src/helpers/twoD/groupHelper.ts new file mode 100644 index 00000000..c4b9f641 --- /dev/null +++ b/applications/visualizer/frontend/src/helpers/twoD/groupHelper.ts @@ -0,0 +1,64 @@ +import type { Core } from "cytoscape"; +import type { NeuronGroup, Workspace } from "../../models"; +import { SELECTED_CLASS } from "../../settings/twoDSettings.tsx"; + +export const groupNeurons = (selectedNeurons: Set, workspace: Workspace) => { + const newGroupId = `group_${Date.now()}`; + const newGroupNeurons = new Set(); + const groupsToDelete = new Set(); + let originalGroupName = ""; + let originalGroupColor = "#9FEE9A"; // Default color if no group to delete + + // Gather all neurons that should be part of the new group + for (const neuronId of selectedNeurons) { + let isPartOfAnotherGroup = false; + const group = workspace.neuronGroups[neuronId]; + + // Check if the neuronId is a group itself or part of another group + if (group) { + group.neurons.forEach((groupedNeuronId) => { + newGroupNeurons.add(groupedNeuronId); + }); + groupsToDelete.add(neuronId); + originalGroupName = group.name; + originalGroupColor = group.color; + } else { + Object.entries(workspace.neuronGroups).forEach(([groupId, existingGroup]) => { + if (existingGroup.neurons.has(neuronId)) { + existingGroup.neurons.forEach((groupedNeuronId) => { + newGroupNeurons.add(groupedNeuronId); + }); + groupsToDelete.add(groupId); + originalGroupName = existingGroup.name; + originalGroupColor = existingGroup.color; + isPartOfAnotherGroup = true; + } + }); + + // If neuronId is not part of any group, add it directly + if (!isPartOfAnotherGroup) { + newGroupNeurons.add(neuronId); + } + } + } + + // Create the new group with the gathered neurons + const newGroup: NeuronGroup = { + id: newGroupId, + name: originalGroupName || newGroupId, + color: originalGroupColor, + neurons: newGroupNeurons, + }; + + return { newGroupId, newGroup, groupsToDelete }; +}; + +export function removeNodeFromGroup(cy: Core, nodeId: string, setSelected: boolean) { + const cyNode = cy.getElementById(nodeId); + if (cyNode && cyNode.isNode()) { + cyNode.move({ parent: null }); + if (setSelected) { + cyNode.addClass(SELECTED_CLASS); + } + } +} diff --git a/applications/visualizer/frontend/src/helpers/twoD/splitJoinHelper.ts b/applications/visualizer/frontend/src/helpers/twoD/splitJoinHelper.ts new file mode 100644 index 00000000..f07663e8 --- /dev/null +++ b/applications/visualizer/frontend/src/helpers/twoD/splitJoinHelper.ts @@ -0,0 +1,240 @@ +import { ViewerType, type Workspace } from "../../models"; +import { emptyViewerData, type GraphViewerData, Visibility } from "../../models/models.ts"; +import { calculateMeanPosition, calculateSplitPositions, isNeuronCell, isNeuronClass } from "./twoDHelpers.ts"; + +interface SplitJoinState { + split: Set; + join: Set; +} + +export const processNeuronSplit = (workspace: Workspace, splitJoinState: SplitJoinState): SplitJoinState => { + const newSplit = new Set(splitJoinState.split); + const newJoin = new Set(splitJoinState.join); + const selectedNeurons = workspace.getViewerSelecedNeurons(ViewerType.Graph); + + const newSelectedNeurons = new Set(selectedNeurons); + const graphViewDataUpdates: Record> = {}; + + const groupModifications: Record> = {}; + const groupsToDelete = new Set(); + + for (const neuronId of selectedNeurons) { + if (!isNeuronClass(neuronId, workspace)) { + return; + } + + newSplit.add(neuronId); + newSelectedNeurons.delete(neuronId); + + const individualNeurons = workspace.getNeuronCellsByClass(neuronId); + + const basePosition = workspace.visibilities[neuronId][ViewerType.Graph]?.defaultPosition || { + x: 0, + y: 0, + }; + const positions = calculateSplitPositions(individualNeurons, basePosition); + + updateGroupWithSplitNeurons(workspace, neuronId, individualNeurons, groupModifications, groupsToDelete); + + for (const neuronName of individualNeurons) { + newSelectedNeurons.add(neuronName); + graphViewDataUpdates[neuronName] = { + defaultPosition: positions[neuronName], + visibility: Visibility.Visible, + }; + } + + for (const joinNeuronId of newJoin) { + if (workspace.availableNeurons[joinNeuronId].nclass === neuronId) { + newJoin.delete(joinNeuronId); + } + } + + graphViewDataUpdates[neuronId] = { visibility: Visibility.Unset }; + } + + workspace.customUpdate((draft) => { + draft.setSelection(Array.from(newSelectedNeurons), ViewerType.Graph); + + for (const [groupId, neurons] of Object.entries(groupModifications)) { + if (neurons.size === 0) { + delete draft.neuronGroups[groupId]; + } else { + draft.neuronGroups[groupId].neurons = neurons; + } + } + for (const groupId of groupsToDelete) { + delete draft.neuronGroups[groupId]; + } + + for (const [neuronName, update] of Object.entries(graphViewDataUpdates)) { + if (!(neuronName in draft.visibilities)) { + draft.visibilities[neuronName] = emptyViewerData(update.visibility); + } + if (update.defaultPosition !== undefined) { + draft.visibilities[neuronName][ViewerType.Graph].defaultPosition = update.defaultPosition; + } + } + }); + + return { split: newSplit, join: newJoin }; +}; + +export const processNeuronJoin = (workspace: Workspace, splitJoinState: SplitJoinState): SplitJoinState => { + const newJoin = new Set(splitJoinState.join); + const newSplit = new Set(splitJoinState.split); + const selectedNeurons = workspace.getViewerSelecedNeurons(ViewerType.Graph); + + const newSelectedNeurons = new Set(selectedNeurons); + const graphViewDataUpdates: Record> = {}; + + const groupModifications: Record> = {}; + const groupsToDelete = new Set(); + + for (const neuronId of selectedNeurons) { + if (!isNeuronCell(neuronId, workspace)) { + return; + } + const neuronClass = workspace.availableNeurons[neuronId].nclass; + + const individualNeurons = Object.values(workspace.availableNeurons) + .filter((neuron) => neuron.nclass === neuronClass && neuron.name !== neuronClass) + .map((neuron) => neuron.name); + + const classPosition = calculateMeanPosition(individualNeurons, workspace); + + if (!workspace.visibilities[neuronClass][ViewerType.Graph]?.defaultPosition) { + graphViewDataUpdates[neuronClass] = { + defaultPosition: classPosition, + visibility: Visibility.Visible, + }; + } else { + graphViewDataUpdates[neuronClass] = { + ...graphViewDataUpdates[neuronClass], + visibility: Visibility.Visible, + }; + } + + updateGroupWithJoinedNeurons(workspace, neuronId, neuronClass, individualNeurons, groupModifications, groupsToDelete); + + for (const neuronName of individualNeurons) { + newSelectedNeurons.delete(neuronName); + newJoin.add(neuronName); + graphViewDataUpdates[neuronName] = { visibility: Visibility.Unset }; + } + newSelectedNeurons.add(neuronClass); + + for (const splitNeuronId of newSplit) { + if (workspace.availableNeurons[splitNeuronId].nclass === neuronClass) { + newSplit.delete(splitNeuronId); + } + } + } + + workspace.customUpdate((draft) => { + draft.setSelection(Array.from(newSelectedNeurons), ViewerType.Graph); + + for (const [groupId, neurons] of Object.entries(groupModifications)) { + if (neurons.size === 0) { + delete draft.neuronGroups[groupId]; + } else { + draft.neuronGroups[groupId].neurons = neurons; + } + } + for (const groupId of groupsToDelete) { + delete draft.neuronGroups[groupId]; + } + + for (const [neuronName, update] of Object.entries(graphViewDataUpdates)) { + if (!(neuronName in draft.visibilities)) { + draft.visibilities[neuronName] = emptyViewerData(update.visibility); + } + if (update.defaultPosition !== undefined) { + draft.visibilities[neuronName][ViewerType.Graph].defaultPosition = update.defaultPosition; + } + } + }); + + return { split: newSplit, join: newJoin }; +}; + +export const updateGroupWithSplitNeurons = ( + workspace: Workspace, + neuronId: string, + individualNeurons: string[], + groupModifications: Record>, + groupsToDelete: Set, +) => { + for (const groupId of Object.keys(workspace.neuronGroups)) { + const group = workspace.neuronGroups[groupId]; + + if (group.neurons.has(neuronId)) { + // Replace the class neuron with individual neurons in the group + groupModifications[groupId] = new Set(group.neurons); + groupModifications[groupId].delete(neuronId); + for (const indNeuronId of individualNeurons) { + groupModifications[groupId].add(indNeuronId); + } + + // Remove individual neurons from any other groups + for (const otherGroupId of Object.keys(workspace.neuronGroups)) { + if (otherGroupId !== groupId) { + const otherGroup = workspace.neuronGroups[otherGroupId]; + for (const indNeuronId of individualNeurons) { + if (otherGroup.neurons.has(indNeuronId)) { + if (!groupModifications[otherGroupId]) { + groupModifications[otherGroupId] = new Set(otherGroup.neurons); + } + groupModifications[otherGroupId].delete(indNeuronId); + if (groupModifications[otherGroupId].size === 0) { + groupsToDelete.add(otherGroupId); + } + } + } + } + } + } + } +}; + +export const updateGroupWithJoinedNeurons = ( + workspace: Workspace, + neuronId: string, + neuronClass: string, + individualNeurons: string[], + groupModifications: Record>, + groupsToDelete: Set, +) => { + // If the neuronId (cell) is part of a group, update the group + for (const groupId of Object.keys(workspace.neuronGroups)) { + const group = workspace.neuronGroups[groupId]; + + if (group.neurons.has(neuronId)) { + // Add the class neuron to the group of the selected cell + if (!groupModifications[groupId]) { + groupModifications[groupId] = new Set(group.neurons); + } + groupModifications[groupId].add(neuronClass); + + // Remove individual neurons from any groups they belong to + for (const neuronName of individualNeurons) { + for (const otherGroupId of Object.keys(workspace.neuronGroups)) { + if (workspace.neuronGroups[otherGroupId].neurons.has(neuronName)) { + if (!groupModifications[otherGroupId]) { + groupModifications[otherGroupId] = new Set(workspace.neuronGroups[otherGroupId].neurons); + } + groupModifications[otherGroupId].delete(neuronName); + if (groupModifications[otherGroupId].size === 0) { + groupsToDelete.add(otherGroupId); + } + } + } + } + + // Remove the individual neurons from the group + for (const neuronName of individualNeurons) { + groupModifications[groupId].delete(neuronName); + } + } + } +}; diff --git a/applications/visualizer/frontend/src/helpers/twoD/twoDHelpers.ts b/applications/visualizer/frontend/src/helpers/twoD/twoDHelpers.ts index e48a9458..887178b6 100644 --- a/applications/visualizer/frontend/src/helpers/twoD/twoDHelpers.ts +++ b/applications/visualizer/frontend/src/helpers/twoD/twoDHelpers.ts @@ -1,31 +1,27 @@ import type { Core, ElementDefinition, Position } from "cytoscape"; +import { ViewerType, Visibility, type Workspace } from "../../models"; import type { Connection } from "../../rest"; -import type { Workspace } from "../../models"; -import { ViewerType } from "../../models"; - -import { annotationLegend } from "../../settings/twoDSettings.tsx"; +import { GRAPH_LAYOUTS, LAYOUT_OPTIONS, annotationLegend } from "../../settings/twoDSettings.tsx"; import { cellConfig, neurotransmitterConfig } from "./coloringHelper.ts"; +import { emptyViewerData } from "../../models/models.ts"; +import { getConcentricLayoutPositions } from "./concentricLayoutHelper.ts"; -export const createEdge = (id: string, conn: Connection, workspace: Workspace, includeAnnotations: boolean): ElementDefinition => { +export const createEdge = (id: string, conn: Connection, workspace: Workspace, includeAnnotations: boolean, width: number): ElementDefinition => { const synapses = conn.synapses || {}; const annotations = conn.annotations || []; const label = createEdgeLabel(workspace, synapses); const longLabel = createEdgeLongLabel(workspace, synapses); - let annotationClasses: string[] = []; + const annotationClasses: string[] = annotations.map((annotation) => annotationLegend[annotation]?.id).filter(Boolean); - if (includeAnnotations) { - annotationClasses = annotations.map((annotation) => annotationLegend[annotation]?.id).filter(Boolean); - if (annotationClasses.length === 0) { - annotationClasses.push(annotationLegend.notClassified.id); - } - } else { - annotationClasses.push(conn.type); + if (includeAnnotations && annotationClasses.length === 0) { + annotationClasses.push(annotationLegend.notClassified.id); } - const classes = annotationClasses.join(" "); + annotationClasses.push(conn.type); + const classes = annotationClasses.join(" "); return { group: "edges", data: { @@ -35,6 +31,7 @@ export const createEdge = (id: string, conn: Connection, workspace: Workspace, i label: label, longLabel: longLabel, type: conn.type, + width, }, classes: classes, }; @@ -56,11 +53,29 @@ const createEdgeLongLabel = (workspace: Workspace, synapses: Record { +export const createNode = ( + nodeId: string, + selected: boolean, + attributes: string[], + position?: Position, + isGroupNode?: boolean, + parent?: string, // Optional parent node ID for compound nodes + activeNeuron?: boolean, +): ElementDefinition => { + let classes = ""; + if (isGroupNode) classes += "groupNode "; + if (selected) classes += "selected "; + if (activeNeuron) classes += "searchedfor "; + const node: ElementDefinition = { group: "nodes", - data: { id: nodeId, label: nodeId, ...attributes.reduce((acc, attr) => ({ ...acc, [attr]: true }), {}) }, - classes: selected ? "selected" : "", + data: { + id: nodeId, + label: nodeId, + ...attributes.reduce((acc, attr) => ({ ...acc, [attr]: true }), {}), + parent: parent || undefined, // Set the parent if provided + }, + classes: classes, }; if (position) { node.position = { x: position.x, y: position.y }; @@ -68,14 +83,26 @@ export const createNode = (nodeId: string, selected: boolean, attributes: string return node; }; -export function applyLayout(cy: Core, layout: string) { - cy.layout({ - name: layout, - }).run(); +export function applyLayout(cy: Core, layout: GRAPH_LAYOUTS) { + const options = getLayoutOptions(cy, layout); + cy.makeLayout(options).run(); refreshLayout(cy); } +function getLayoutOptions(cy: Core, layout: GRAPH_LAYOUTS) { + const baseOptions = LAYOUT_OPTIONS[layout]; + + if (layout === GRAPH_LAYOUTS.Concentric) { + return { + ...baseOptions, + positions: getConcentricLayoutPositions(cy), + }; + } + + return baseOptions; +} + export function refreshLayout(cy: Core) { cy.resize(); // Adjust the viewport size cy.center(); // Center the graph in the container @@ -114,12 +141,12 @@ export const extractNeuronAttributes = (neuron) => { export const getNclassSet = (neuronIds: Set, workspace: Workspace): Set => { const nclassSet = new Set(); - neuronIds.forEach((neuronId) => { + for (const neuronId of neuronIds) { const neuron = workspace.availableNeurons[neuronId]; - if (neuron && neuron.nclass) { + if (neuron?.nclass) { nclassSet.add(neuron.nclass); } - }); + } return nclassSet; }; @@ -128,15 +155,15 @@ export const calculateMeanPosition = (nodeIds: string[], workspace: Workspace): let totalY = 0; let count = 0; - nodeIds.forEach((nodeId) => { - const neuron = workspace.availableNeurons[nodeId]; - const position = neuron?.viewerData[ViewerType.Graph]?.defaultPosition; + for (const nodeId of nodeIds) { + const neuron = workspace.visibilities[nodeId]; + const position = neuron?.[ViewerType.Graph]?.defaultPosition; if (position) { totalX += position.x; totalY += position.y; count++; } - }); + } return { x: totalX / count, @@ -150,27 +177,28 @@ export const calculateSplitPositions = (nodes, basePosition) => { const positions = {}; const n = nodes.length; - if (n == 1) { + if (n === 1) { positions[nodes[0]] = { x: offsetX, y: offsetY }; return positions; - } else if (n == 2) { + } + if (n === 2) { positions[nodes[0]] = { x: offsetX - 35, y: offsetY }; positions[nodes[1]] = { x: offsetX + 35, y: offsetY }; - } else if (n == 3) { + } else if (n === 3) { positions[nodes[0]] = { x: offsetX, y: offsetY - 35 }; positions[nodes[1]] = { x: offsetX - 35, y: offsetY + 35 }; positions[nodes[2]] = { x: offsetX + 35, y: offsetY + 35 }; - } else if (n == 4 && nodes[0] == "RMED") { + } else if (n === 4 && nodes[0] === "RMED") { positions[nodes[0]] = { x: offsetX, y: offsetY - 50 }; positions[nodes[1]] = { x: offsetX - 50, y: offsetY }; positions[nodes[2]] = { x: offsetX + 50, y: offsetY }; positions[nodes[3]] = { x: offsetX, y: offsetY + 50 }; - } else if (n == 4) { + } else if (n === 4) { positions[nodes[0]] = { x: offsetX - 35, y: offsetY - 35 }; positions[nodes[1]] = { x: offsetX + 35, y: offsetY - 35 }; positions[nodes[2]] = { x: offsetX - 35, y: offsetY + 35 }; positions[nodes[3]] = { x: offsetX + 35, y: offsetY + 35 }; - } else if (n == 6) { + } else if (n === 6) { positions[nodes[0]] = { x: offsetX - 35, y: offsetY - 60 }; positions[nodes[1]] = { x: offsetX + 35, y: offsetY - 60 }; positions[nodes[2]] = { x: offsetX - 70, y: offsetY }; @@ -194,12 +222,51 @@ export const updateWorkspaceNeurons2DViewerData = (workspace: Workspace, cy: Cor // Update the workspace availableNeurons with the positions and visibility workspace.customUpdate((draft) => { // Set visibility and position for nodes in the cytoscape graph - cy.nodes().forEach((node) => { + for (const node of cy.nodes()) { const neuronId = node.id(); - if (draft.availableNeurons[neuronId]) { - draft.availableNeurons[neuronId].viewerData[ViewerType.Graph].defaultPosition = { ...node.position() }; - draft.availableNeurons[neuronId].viewerData[ViewerType.Graph].visibility = true; + if (!(neuronId in draft.visibilities)) { + draft.visibilities[neuronId] = emptyViewerData(Visibility.Visible); } - }); + draft.visibilities[neuronId][ViewerType.Graph].defaultPosition = { ...node.position() }; + draft.visibilities[neuronId][ViewerType.Graph].visibility = Visibility.Visible; + } }); }; + +export function getVisibleActiveNeuronsIn2D(workspace: Workspace): Set { + const activeVisibleNeurons = Array.from(workspace.activeNeurons).filter((neuronId) => { + return workspace.visibilities[neuronId]?.[ViewerType.Graph]?.visibility === Visibility.Visible; + }); + + // Create a set to store the class neurons that are active and visible + const activeVisibleClasses = new Set( + activeVisibleNeurons.filter((neuronId) => { + const neuron = workspace.availableNeurons[neuronId]; + return neuron && isNeuronClass(neuronId, workspace); + }), + ); + + // Filter out individual cells if their class neuron is active and visible + return new Set( + activeVisibleNeurons.filter((neuronId) => { + const neuron = workspace.availableNeurons[neuronId]; + const isCellFilteredOut = neuron && neuron.name !== neuron.nclass && activeVisibleClasses.has(neuron.nclass); + + return !isCellFilteredOut; // Return only those that should not be filtered out + }), + ); +} + +export function getHiddenNeuronsIn2D(workspace: Workspace): Set { + return new Set( + Object.entries(workspace.visibilities) + .filter(([_, data]) => data[ViewerType.Graph].visibility === Visibility.Hidden) + .map(([name, _]) => name), + ); +} + +export function isNeuronPartOfClosedGroup(neuronId: string, workspace: Workspace, openGroups: Set): boolean { + return Object.entries(workspace.neuronGroups).some(([groupId, group]) => { + return group.neurons.has(neuronId) && !openGroups.has(groupId); + }); +} diff --git a/applications/visualizer/frontend/src/helpers/workspaceHelper.ts b/applications/visualizer/frontend/src/helpers/workspaceHelper.ts deleted file mode 100644 index d10687d3..00000000 --- a/applications/visualizer/frontend/src/helpers/workspaceHelper.ts +++ /dev/null @@ -1,12 +0,0 @@ -import type { Dataset } from "../rest"; - -export const getWorkspaceActiveDatasets = (datasets: Record, datasetIds: Set): Record => { - const datasetsArray = Object.values(datasets).filter((dataset) => datasetIds.has(dataset.id)); - return datasetsArray.reduce( - (acc, dataset) => { - acc[dataset.id] = dataset; - return acc; - }, - {} as Record, - ); -}; diff --git a/applications/visualizer/frontend/src/icons/index.tsx b/applications/visualizer/frontend/src/icons/index.tsx index b1162bf7..7fcd56a8 100644 --- a/applications/visualizer/frontend/src/icons/index.tsx +++ b/applications/visualizer/frontend/src/icons/index.tsx @@ -165,3 +165,51 @@ export const GapJunctionIcon = () => ( ); + +export const AlignLeftIcon = () => ( + + + +); + +export const AlignRightIcon = () => ( + + + +); + +export const AlignTopIcon = () => ( + + + +); + +export const AlignBottomIcon = () => ( + + + +); + +export const DistributeHorizontallyIcon = () => ( + + + +); + +export const DistributeVerticallyIcon = () => ( + + + +); diff --git a/applications/visualizer/frontend/src/models/Error.ts b/applications/visualizer/frontend/src/models/Error.ts new file mode 100644 index 00000000..5603609a --- /dev/null +++ b/applications/visualizer/frontend/src/models/Error.ts @@ -0,0 +1,6 @@ +export class GlobalError extends Error { + constructor(message: string) { + super(message); + this.name = "GlobalError"; + } +} diff --git a/applications/visualizer/frontend/src/models/index.ts b/applications/visualizer/frontend/src/models/index.ts index 04e06279..28cc7ff7 100644 --- a/applications/visualizer/frontend/src/models/index.ts +++ b/applications/visualizer/frontend/src/models/index.ts @@ -2,3 +2,5 @@ export { Workspace } from "./workspace.ts"; export type { NeuronGroup } from "./models.ts"; export { ViewMode } from "./models.ts"; export { ViewerType } from "./models.ts"; +export { Alignment } from "./models.ts"; +export { Visibility } from "./models.ts"; diff --git a/applications/visualizer/frontend/src/models/models.ts b/applications/visualizer/frontend/src/models/models.ts index 680d707b..aaa74055 100644 --- a/applications/visualizer/frontend/src/models/models.ts +++ b/applications/visualizer/frontend/src/models/models.ts @@ -26,14 +26,18 @@ export interface NeuronGroup { neurons: Set; } -export interface EnhancedNeuron extends Neuron { - viewerData: ViewerData; - isInteractant: boolean; -} - export interface GraphViewerData { defaultPosition: Position | null; - visibility: boolean; + visibility: Visibility; +} + +export function emptyViewerData(visibility?: Visibility): ViewerData { + return { + [ViewerType.Graph]: { + defaultPosition: null, + visibility: visibility ?? Visibility.Hidden, + }, + }; } export interface ViewerData { @@ -47,18 +51,33 @@ const buildUrlFromFormat = (s: string, param: string) => { return s.replace(s.match("{[^}]+}")?.[0], param); }; -export function getNeuronUrlForDataset(neuron: Neuron, datasetId: string) { - return buildUrlFromFormat(neuron.model3DUrl, datasetId); +export function getNeuronUrlForDataset(neuron: Neuron, datasetId: string): string[] { + return neuron.model3DUrls.map((url) => buildUrlFromFormat(url, datasetId)); } -export function getNeuronURL(dataset: Dataset, neuronName: string) { +export function getNeuronURL(dataset: Dataset, neuronName: string): string { return buildUrlFromFormat(dataset.neuron3DUrl, neuronName); } -export function getSegmentationURL(dataset: Dataset, sliceIndex: number) { +export function getSegmentationURL(dataset: Dataset, sliceIndex: number): string { return buildUrlFromFormat(dataset.emData.segmentation_url, sliceIndex?.toString()); } -export function getEMDataURL(dataset: Dataset, sliceIndex: number) { +export function getEMDataURL(dataset: Dataset, sliceIndex: number): string { return buildUrlFromFormat(dataset.emData.resource_url, sliceIndex?.toString()); } + +export enum Alignment { + Left = "left", + Right = "right", + Top = "top", + Bottom = "bottom", + Horizontal = "Horizontal", + Vertical = "Vertical", +} + +export enum Visibility { + Visible = "Visible", + Hidden = "Hidden", + Unset = "Unset", +} diff --git a/applications/visualizer/frontend/src/models/synchronizer.ts b/applications/visualizer/frontend/src/models/synchronizer.ts new file mode 100644 index 00000000..499dfd66 --- /dev/null +++ b/applications/visualizer/frontend/src/models/synchronizer.ts @@ -0,0 +1,165 @@ +import type { Neuron } from "../rest"; +import { ViewerSynchronizationPair, ViewerType } from "./models"; + +export type SynchronizerContext = Array; +export type Selection = Array; + +const syncViewerDefs: Record = { + [ViewerSynchronizationPair.Graph_InstanceDetails]: [ViewerType.Graph, ViewerType.InstanceDetails], + [ViewerSynchronizationPair.Graph_ThreeD]: [ViewerType.Graph, ViewerType.ThreeD], + [ViewerSynchronizationPair.ThreeD_EM]: [ViewerType.ThreeD, ViewerType.EM], +}; + +class Synchronizer { + active: boolean; + viewers: [ViewerType, ViewerType]; + readonly pair: ViewerSynchronizationPair; + + private constructor(active: boolean, pair: ViewerSynchronizationPair) { + this.active = active; + this.viewers = syncViewerDefs[pair]; + this.pair = pair; + } + + public static create(active: boolean, pair: ViewerSynchronizationPair) { + return new Synchronizer(active, pair); + } + + private canHandle(viewer: ViewerType) { + return this.viewers.includes(viewer); + } + + sync(selection: Array, initiator: ViewerType, contexts: Record) { + if (!this.canHandle(initiator)) { + return; + } + + if (!this.active) { + contexts[initiator] = selection.map((n) => n); + return; + } + + for (const viewer of this.viewers) { + contexts[viewer] = selection.map((n) => n); + } + } + + select(selection: string, initiator: ViewerType, contexts: Record) { + if (!this.canHandle(initiator)) { + return; + } + + if (!this.active) { + contexts[initiator] = [...new Set([...contexts[initiator], selection])]; + return; + } + + for (const viewer of this.viewers) { + contexts[viewer] = [...new Set([...contexts[viewer], selection])]; + } + } + unSelect(selection: string, initiator: ViewerType, contexts: Record) { + if (!this.canHandle(initiator)) { + return; + } + + if (!this.active) { + const storedNodes = [...contexts[initiator]]; + contexts[initiator] = storedNodes.filter((n) => n !== selection); + return; + } + + for (const viewer of this.viewers) { + const storedNodes = [...contexts[viewer]]; + contexts[viewer] = storedNodes.filter((n) => n !== selection); + } + } + + clear(initiator: ViewerType, contexts: Record) { + if (!this.canHandle(initiator)) { + return; + } + + if (!this.active) { + contexts[initiator] = []; + return; + } + + for (const viewer of this.viewers) { + contexts[viewer] = []; + } + } + + setActive(isActive: boolean) { + this.active = isActive; + } +} + +export class SynchronizerOrchestrator { + contexts: Record; + synchronizers: Array; + + private constructor(synchronizers: Array, contexts?: Record) { + this.synchronizers = synchronizers; + if (contexts) { + this.contexts = { ...contexts }; + } else { + this.contexts = { + [ViewerType.EM]: [], + [ViewerType.Graph]: [], + [ViewerType.InstanceDetails]: [], + [ViewerType.ThreeD]: [], + }; + } + } + + public static create(activesSync?: Record, contexts?: Record) { + const synchronizers = [ + Synchronizer.create(activesSync?.[ViewerSynchronizationPair.Graph_InstanceDetails] || true, ViewerSynchronizationPair.Graph_InstanceDetails), + Synchronizer.create(activesSync?.[ViewerSynchronizationPair.Graph_ThreeD] || true, ViewerSynchronizationPair.Graph_ThreeD), + Synchronizer.create(activesSync?.[ViewerSynchronizationPair.ThreeD_EM] || true, ViewerSynchronizationPair.ThreeD_EM), + ]; + + return new SynchronizerOrchestrator(synchronizers, contexts); + } + + public select(selection: Array, initiator: ViewerType) { + for (const synchronizer of this.synchronizers) { + synchronizer.sync(selection, initiator, this.contexts); + } + } + + public selectNeuron(selection: string, initiator: ViewerType) { + for (const synchronizer of this.synchronizers) { + synchronizer.select(selection, initiator, this.contexts); + } + } + + public unSelectNeuron(selection: string, initiator: ViewerType) { + for (const synchronizer of this.synchronizers) { + synchronizer.unSelect(selection, initiator, this.contexts); + } + } + + public clearSelection(initiator: ViewerType) { + for (const synchronizer of this.synchronizers) { + synchronizer.clear(initiator, this.contexts); + } + } + + public getSelection(viewerType: ViewerType): SynchronizerContext { + return this.contexts[viewerType]; + } + public setActive(synchronizer: ViewerSynchronizationPair, isActive: boolean) { + this.synchronizers[synchronizer].setActive(isActive); + } + + public isActive(synchronizer: ViewerSynchronizationPair) { + return this.synchronizers[synchronizer].active; + } + + public switchSynchronizer(syncPair: ViewerSynchronizationPair) { + const synchronizer = this.synchronizers[syncPair]; + synchronizer.setActive(!synchronizer.active); + } +} diff --git a/applications/visualizer/frontend/src/models/workspace.ts b/applications/visualizer/frontend/src/models/workspace.ts index 9123a6eb..fe961ac6 100644 --- a/applications/visualizer/frontend/src/models/workspace.ts +++ b/applications/visualizer/frontend/src/models/workspace.ts @@ -3,7 +3,9 @@ import type { configureStore } from "@reduxjs/toolkit"; import { immerable, produce } from "immer"; import getLayoutManagerAndStore from "../layout-manager/layoutManagerFactory"; import { type Dataset, type Neuron, NeuronsService } from "../rest"; -import { type EnhancedNeuron, type NeuronGroup, ViewerSynchronizationPair, ViewerType } from "./models"; +import { GlobalError } from "./Error.ts"; +import { type NeuronGroup, type ViewerData, type ViewerSynchronizationPair, ViewerType, Visibility, emptyViewerData } from "./models"; +import { type SynchronizerContext, SynchronizerOrchestrator } from "./synchronizer"; export class Workspace { [immerable] = true; @@ -13,78 +15,94 @@ export class Workspace { // datasetID -> Dataset activeDatasets: Record; // neuronID -> Neurons - availableNeurons: Record; + availableNeurons: Record; // neuronId activeNeurons: Set; - selectedNeurons: Set; + visibilities: Record; viewers: Record; - synchronizations: Record; neuronGroups: Record; store: ReturnType; layoutManager: LayoutManager; + + syncOrchestrator: SynchronizerOrchestrator; updateContext: (workspace: Workspace) => void; - constructor(id: string, name: string, activeDatasets: Record, activeNeurons: Set, updateContext: (workspace: Workspace) => void) { + constructor( + id: string, + name: string, + activeDatasets: Record, + activeNeurons: Set, + updateContext: (workspace: Workspace) => void, + activeSynchronizers?: Record, + contexts?: Record, + visibilities?: Record, + ) { this.id = id; this.name = name; this.activeDatasets = activeDatasets; this.availableNeurons = {}; this.activeNeurons = activeNeurons || new Set(); - this.selectedNeurons = new Set(); this.viewers = { - [ViewerType.Graph]: false, - [ViewerType.ThreeD]: true, + [ViewerType.Graph]: true, + [ViewerType.ThreeD]: false, [ViewerType.EM]: false, [ViewerType.InstanceDetails]: false, }; - this.synchronizations = { - [ViewerSynchronizationPair.Graph_InstanceDetails]: true, - [ViewerSynchronizationPair.Graph_ThreeD]: true, - [ViewerSynchronizationPair.ThreeD_EM]: true, - }; this.neuronGroups = {}; const { layoutManager, store } = getLayoutManagerAndStore(id); this.layoutManager = layoutManager; + this.syncOrchestrator = SynchronizerOrchestrator.create(activeSynchronizers, contexts); + + this.visibilities = visibilities || Object.fromEntries([...activeNeurons].map((n) => [n, emptyViewerData(Visibility.Visible)])); + this.store = store; this.updateContext = updateContext; this._initializeAvailableNeurons(); } - activateNeuron(neuron: Neuron): void { + activateNeuron(neuron: Neuron): Workspace { const updated = produce(this, (draft: Workspace) => { draft.activeNeurons.add(neuron.name); - // Set isInteractant to true if the neuron exists in availableNeurons - if (draft.availableNeurons[neuron.name]) { - draft.availableNeurons[neuron.name].isInteractant = true; - } + draft.visibilities[neuron.name] = emptyViewerData(); }); - this.updateContext(updated); + return updated; } deactivateNeuron(neuronId: string): void { const updated = produce(this, (draft: Workspace) => { draft.activeNeurons.delete(neuronId); + delete draft.visibilities[neuronId]; }); this.updateContext(updated); } - deleteNeuron(neuronId: string): void { + hideNeuron(neuronId: string): void { const updated = produce(this, (draft: Workspace) => { - // Remove the neuron from activeNeurons - draft.activeNeurons.delete(neuronId); - - // Set isInteractant to false if the neuron exists in availableNeurons - if (draft.availableNeurons[neuronId]) { - draft.availableNeurons[neuronId].isInteractant = false; + if (!(neuronId in draft.visibilities)) { + draft.visibilities[neuronId] = emptyViewerData(Visibility.Hidden); + draft.removeSelection(neuronId, ViewerType.Graph); } + // todo: add actions for other viewers + draft.visibilities[neuronId][ViewerType.Graph].visibility = Visibility.Hidden; }); this.updateContext(updated); } + showNeuron(neuronId: string): void { + const updated = produce(this, (draft: Workspace) => { + if (!(neuronId in draft.visibilities)) { + draft.visibilities[neuronId] = emptyViewerData(Visibility.Visible); + } + // todo: add actions for other viewers + draft.visibilities[neuronId][ViewerType.Graph].visibility = Visibility.Visible; + }); + + this.updateContext(updated); + } async activateDataset(dataset: Dataset): Promise { const updated: Workspace = produce(this, (draft: Workspace) => { draft.activeDatasets[dataset.id] = dataset; @@ -101,35 +119,22 @@ export class Workspace { const updatedWithNeurons = await this._getAvailableNeurons(updated); this.updateContext(updatedWithNeurons); } - - toggleSelectedNeuron(neuronId: string): void { - const updated = produce(this, (draft: Workspace) => { - if (draft.selectedNeurons.has(neuronId)) { - draft.selectedNeurons.delete(neuronId); - } else { - draft.selectedNeurons.add(neuronId); - } - }); - this.updateContext(updated); - } - setActiveNeurons(newActiveNeurons: Set): void { const updated = produce(this, (draft: Workspace) => { draft.activeNeurons = newActiveNeurons; }); this.updateContext(updated); } - - clearSelectedNeurons(): void { + updateViewerSynchronizationStatus(pair: ViewerSynchronizationPair, isActive: boolean): void { const updated = produce(this, (draft: Workspace) => { - draft.selectedNeurons.clear(); + draft.syncOrchestrator.setActive(pair, isActive); }); this.updateContext(updated); } - updateViewerSynchronizationStatus(pair: ViewerSynchronizationPair, isActive: boolean): void { + switchViewerSynchronizationStatus(pair: ViewerSynchronizationPair): void { const updated = produce(this, (draft: Workspace) => { - draft.synchronizations[pair] = isActive; + draft.syncOrchestrator.switchSynchronizer(pair); }); this.updateContext(updated); } @@ -175,40 +180,27 @@ export class Workspace { const datasetIds = Object.keys(updatedWorkspace.activeDatasets); const neuronArrays = await NeuronsService.searchCells({ datasetIds }); + // Flatten and add neurons classes const uniqueNeurons = new Set(); - - // Flatten and deduplicate neurons - for (const neuronArray of neuronArrays.flat()) { - uniqueNeurons.add(neuronArray); - const classNeuron = { ...neuronArray, name: neuronArray.nclass }; - uniqueNeurons.add(classNeuron); + const neuronsClass: Record = {}; + for (const neuron of neuronArrays.flat()) { + uniqueNeurons.add(neuron); + + const className = neuron.nclass; + if (!(className in neuronsClass)) { + const neuronClass = { ...neuron, name: className }; + neuronsClass[className] = neuronClass; + uniqueNeurons.add(neuronClass); + } else { + neuronsClass[className].model3DUrls.push(...neuron.model3DUrls); + } } return produce(updatedWorkspace, (draft: Workspace) => { - draft.availableNeurons = {}; - for (const neuron of uniqueNeurons) { - const previousNeuron = draft.availableNeurons[neuron.name]; - - const enhancedNeuron: EnhancedNeuron = { - ...neuron, - viewerData: { - [ViewerType.Graph]: { - defaultPosition: previousNeuron?.viewerData[ViewerType.Graph]?.defaultPosition || null, - visibility: previousNeuron?.viewerData[ViewerType.Graph]?.visibility || false, - }, - [ViewerType.ThreeD]: previousNeuron?.viewerData[ViewerType.ThreeD] || {}, - [ViewerType.EM]: previousNeuron?.viewerData[ViewerType.EM] || {}, - [ViewerType.InstanceDetails]: previousNeuron?.viewerData[ViewerType.InstanceDetails] || {}, - }, - isInteractant: previousNeuron?.isInteractant ?? draft.activeNeurons.has(neuron.name), - }; - - draft.availableNeurons[neuron.name] = enhancedNeuron; - } + draft.availableNeurons = Object.fromEntries([...uniqueNeurons].map((n) => [n.name, n])); }); } catch (error) { - console.error("Failed to fetch neurons:", error); - return updatedWorkspace; + throw new GlobalError("Failed to fetch neurons:"); } } @@ -216,4 +208,48 @@ export class Workspace { const updated = produce(this, updateFunction); this.updateContext(updated); } + + setSelection(selection: Array, initiator: ViewerType) { + this.customUpdate((draft) => { + draft.syncOrchestrator.select(selection, initiator); + }); + } + clearSelection(initiator: ViewerType): Workspace { + const updated = produce(this, (draft: Workspace) => { + draft.syncOrchestrator.clearSelection(initiator); + }); + this.updateContext(updated); + return updated; + } + + addSelection(selection: string, initiator: ViewerType) { + this.customUpdate((draft) => { + draft.syncOrchestrator.selectNeuron(selection, initiator); + }); + } + + removeSelection(selection: string, initiator: ViewerType) { + this.customUpdate((draft) => { + draft.syncOrchestrator.unSelectNeuron(selection, initiator); + }); + } + + getSelection(viewerType: ViewerType): string[] { + return this.syncOrchestrator.getSelection(viewerType); + } + + getViewerSelecedNeurons(viewerType: ViewerType): string[] { + return this.syncOrchestrator.getSelection(viewerType); + } + + getNeuronCellsByClass(neuronClassId: string): string[] { + return Object.values(this.availableNeurons) + .filter((neuron) => neuron.nclass === neuronClassId && neuron.nclass !== neuron.name) + .map((neuron) => neuron.name); + } + + getNeuronClass(neuronId: string): string { + const neuron = this.availableNeurons[neuronId]; + return neuron.nclass; + } } diff --git a/applications/visualizer/frontend/src/rest/models/Neuron.ts b/applications/visualizer/frontend/src/rest/models/Neuron.ts index 7fcaa049..5e371bb3 100644 --- a/applications/visualizer/frontend/src/rest/models/Neuron.ts +++ b/applications/visualizer/frontend/src/rest/models/Neuron.ts @@ -3,10 +3,9 @@ /* tslint:disable */ /* eslint-disable */ export type Neuron = { - id: string; name: string; datasetIds: Array; - model3DUrl: string; + model3DUrls: Array; nclass: string; neurotransmitter: string; type: string; diff --git a/applications/visualizer/frontend/src/settings/templateWorkspaceSettings.ts b/applications/visualizer/frontend/src/settings/templateWorkspaceSettings.ts index 2afe725a..962a4cb6 100644 --- a/applications/visualizer/frontend/src/settings/templateWorkspaceSettings.ts +++ b/applications/visualizer/frontend/src/settings/templateWorkspaceSettings.ts @@ -1,2 +1,2 @@ export const TEMPLATE_ACTIVE_DATASETS = ["witvliet_2020_7", "witvliet_2020_8"]; -export const TEMPLATE_ACTIVE_NEURONS = ["ASEL", "AIYR"]; +export const TEMPLATE_ACTIVE_NEURONS = ["AIY", "ASEL"]; diff --git a/applications/visualizer/frontend/src/settings/twoDSettings.tsx b/applications/visualizer/frontend/src/settings/twoDSettings.tsx index 631e970a..d5c5e1b1 100644 --- a/applications/visualizer/frontend/src/settings/twoDSettings.tsx +++ b/applications/visualizer/frontend/src/settings/twoDSettings.tsx @@ -1,5 +1,6 @@ -import { ChemicalSynapseIcon, GapJunctionIcon } from "../icons"; import ArrowForwardIcon from "@mui/icons-material/ArrowForward"; +import type { LayoutOptions, NodeCollection, NodeSingular } from "cytoscape"; +import { ChemicalSynapseIcon, GapJunctionIcon } from "../icons"; export const CHEMICAL_THRESHOLD = 3; export const ELECTRICAL_THRESHOLD = 2; @@ -16,6 +17,52 @@ export enum GRAPH_LAYOUTS { Hierarchical = "dagre", Concentric = "concentric", } +type FcoseLayoutOptions = LayoutOptions & { + nodeRepulsion: number; + idealEdgeLength: number; + numIter: number; + nestingFactor: number; + gravity: number; +}; + +type DagreLayoutOptions = LayoutOptions & { + rankDir: string; + nodeSep: number; + rankSep: number; +}; + +type ConcentricLayoutOptions = LayoutOptions & { + concentric: (node: NodeSingular) => number; + levelWidth: (nodes: NodeCollection) => number; + spacingFactor: number; +}; + +type ExtendedLayoutOptions = FcoseLayoutOptions | DagreLayoutOptions | ConcentricLayoutOptions; + +export const LAYOUT_OPTIONS: Record = { + [GRAPH_LAYOUTS.Force]: { + name: "fcose", + nodeRepulsion: 1500, + idealEdgeLength: 150, + numIter: 2500, + nestingFactor: 0.1, + gravity: 0.2, + }, + [GRAPH_LAYOUTS.Hierarchical]: { + name: "dagre", + rankDir: "TB", + nodeSep: 10, + rankSep: 100, + }, + [GRAPH_LAYOUTS.Concentric]: { + name: "preset", + concentric: (node: NodeSingular) => node.degree(true), + levelWidth: (nodes: NodeCollection) => nodes.maxDegree(true) / 4, + animate: false, + padding: 30, + spacingFactor: 1, + }, +}; export enum LegendType { Node = 0, @@ -78,3 +125,9 @@ export const annotationLegend = { icon: , }, }; + +export const SELECTED_CLASS = "selected"; +export const FADED_CLASS = "faded"; +export const HOVER_CLASS = "hover"; +export const FOCUS_CLASS = "focus"; +export const SHOW_EDGE_LABEL_CLASS = "showEdgeLabel"; diff --git a/applications/visualizer/frontend/src/theme/index.tsx b/applications/visualizer/frontend/src/theme/index.tsx index ad7567c8..81a9ecce 100644 --- a/applications/visualizer/frontend/src/theme/index.tsx +++ b/applications/visualizer/frontend/src/theme/index.tsx @@ -1,4 +1,4 @@ -import { createTheme } from "@mui/material/styles"; +import createTheme from "@mui/material/styles/createTheme"; import { vars } from "./variables.ts"; const { primaryFont, diff --git a/applications/visualizer/frontend/src/theme/twoDStyles.ts b/applications/visualizer/frontend/src/theme/twoDStyles.ts index 545e4e21..337bc2d2 100644 --- a/applications/visualizer/frontend/src/theme/twoDStyles.ts +++ b/applications/visualizer/frontend/src/theme/twoDStyles.ts @@ -1,16 +1,11 @@ import type { Stylesheet } from "cytoscape"; import { annotationLegend } from "../settings/twoDSettings.tsx"; -const NODE_STYLE = { - "background-color": "#666", - label: "data(label)", - color: "#fff", - "text-valign": "center", - "text-halign": "center", - "font-size": 8, - width: 24, - height: 24, -}; +const searchedforNeuronBackground = + "data:image/svg+xml;base64,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"; // original: image/node_background_neuron.svg + +const searchedforMuscleBackground = + "data:image/svg+xml;base64,PHN2ZyB4bWxucz0iaHR0cDovL3d3dy53My5vcmcvMjAwMC9zdmciIHdpZHRoPSIyOSIgaGVpZ2h0PSIyOSIgdmlld0JveD0iMCAwIDI5IDI5Ij48ZyB0cmFuc2Zvcm09InJvdGF0ZSg0NSAxMjM1LjMwOCAtNTExLjY4KSI+PHBhdGggZD0iTTcyOC4yNCA3MTkuMDE4YS45NzcgMjAuNDgyIDAgMCAwLS43MjQgOC41bDEuNjM3IDEuNjM2YS45NzcgMjAuNDgyIDAgMCAwLS44NDQtMTAuMTg2Ljk3NyAyMC40ODIgMCAwIDAtLjA3LjA1ek03NDguNTgyIDcwNy41N2EuOTc3IDIwLjQ4MiAwIDAgMC0uMTQ3IDEwLjc3Ni45NzcgMjAuNDgyIDAgMCAwIC45NzcgMjAuNDgyLjk3NyAyMC40ODIgMCAwIDAgLjk3Ny0yMC40OC45NzcgMjAuNDgyIDAgMCAwLS4xMDMtOS4wNzJsLTEuNzA1LTEuNzA2ek03NTkuMTIgNzE4LjExYS45NzcgMjAuNDgyIDAgMCAwIC44NDMgMTAuMTY3Ljk3NyAyMC40ODIgMCAwIDAgLjc5My04LjUzMmwtMS42MzYtMS42MzZ6TTc1My43MTIgNzEyLjdhLjk3NyAyMC40ODIgMCAwIDAgMCAuMzcuOTc3IDIwLjQ4MiAwIDAgMCAuOTc1IDIwLjQ4My45NzcgMjAuNDgyIDAgMCAwIC45NzQtMTguOTAzbC0xLjk0OC0xLjk1ek03MzMuNTE1IDcxMy43NDJhLjk3NyAyMC40ODIgMCAwIDAtLjkwNCAxOC44N2wxLjk1IDEuOTVhLjk3NyAyMC40ODIgMCAwIDAgLjAwMi0uMzg4Ljk3NyAyMC40ODIgMCAwIDAtLjk3Ny0yMC40OC45NzcgMjAuNDgyIDAgMCAwLS4wNy4wNDh6TTczOC43OSA3MDguNDY3YS45NzcgMjAuNDgyIDAgMCAwLS45MDggMjAuNDMuOTc3IDIwLjQ4MiAwIDAgMCAuMTAzIDkuMDlsMS43MDQgMS43MDNhLjk3NyAyMC40ODIgMCAwIDAgLjE0OC0xMC43OTIuOTc3IDIwLjQ4MiAwIDAgMC0uOTc2LTIwLjQ4Mi45NzcgMjAuNDgyIDAgMCAwLS4wNy4wNXoiLz48ZWxsaXBzZSByeT0iMjAuNDgyIiByeD0iLjk3NyIgY3k9IjcyMy42MjIiIGN4PSI3NDQuMTM2Ii8+PC9nPjwvc3ZnPg=="; // original: image/node_background_muscle.svg const SELECTED_NODE_STYLE = { "border-width": 2, @@ -18,16 +13,143 @@ const SELECTED_NODE_STYLE = { "border-opacity": 1, }; -const EDGE_STYLE = { - "line-color": "#63625F", - "target-arrow-color": "#63625F", - "target-arrow-shape": "triangle", - "curve-style": "bezier", - "arrow-scale": 0.3, +const SEARCHED_FOR_NODE_STYLE = { + "background-image": searchedforNeuronBackground, + "background-image-opacity": ".2", + "z-index": 0, + "background-repeat": "no-repeat", + "background-height": 22, + "background-width": 22, +}; + +const GROUP_NODE_STYLE = { + label: "Group", + shape: "roundrectangle", + "background-color": "#ECECE9", + "font-size": "10px", + width: 20, + height: 20, + "background-opacity": 0.7, + padding: "7px", + "text-wrap": "wrap", + "text-valign": "center", + "text-halign": "center", + color: "black", + "border-width": 1, + "border-color": "black", + "font-weight": "normal", + "background-image": "none", + "pie-size": "75%", + "border-opacity": 1, +}; + +const UNSELECTED_GROUP_NODE_STYLE = { + ...GROUP_NODE_STYLE, + "background-color": "#D3D3CF", + "border-width": 0, }; -const CHEMICAL_STYLE = { "line-color": "#63625F", width: 0.5 }; -const ELECTRICAL_STYLE = { "line-color": "yellow", width: 0.5 }; +const EDGE_STYLE = [ + { + selector: "edge", + style: { + "line-color": "#63625F", + "target-arrow-color": "#63625F", + "target-arrow-shape": "triangle", + "curve-style": "bezier", + "arrow-scale": 0.6, + "source-distance-from-node": 1, + "target-distance-from-node": 1, + width: (node: any) => node.data("width"), + }, + }, + { + selector: "edge:loop", + css: { + "source-distance-from-node": 0, + "target-distance-from-node": 0, + "arrow-scale": 0.6, + }, + }, +]; + +const CHEMICAL_STYLE = [ + { + selector: ".chemical", + style: { "line-color": "#63625F", width: (node: any) => node.data("width") }, + }, + { + selector: "edge.chemical.parallel", + style: { + "curve-style": "unbundled-bezier", + "control-point-distances": 40, + "control-point-weights": 0.5, + }, + }, +]; + +const ELECTRICAL_STYLE = [ + { + selector: ".electrical", + style: { + "line-color": "#63625F", + width: (node: any) => node.data("width"), + "curve-style": "segments", + "target-arrow-color": "#666666", + "source-arrow-color": "#666666", + "segment-distances": "0 -4 4 -4 4 0", + "segment-weights": (ele) => { + const sourcePos = ele.source().position(); + const targetPos = ele.target().position(); + const length = Math.sqrt(Math.pow(targetPos.x - sourcePos.x, 2) + Math.pow(targetPos.y - sourcePos.y, 2)); + const divider = (length > 60 ? 7 : length > 40 ? 5 : 3) / length; + return [-2.0, -1.5, -0.5, 0.5, 1.5, 2.0].map((d) => 0.5 + d * divider).join(" "); + }, + "target-arrow-shape": "none", + }, + }, + { + selector: ".electrical:loop", + css: { + "target-arrow-shape": "tee", + "source-arrow-shape": "tee", + }, + }, + { + selector: ".electrical.not_classified:loop", + css: { + "target-arrow-shape": "tee", + "source-arrow-shape": "tee", + "source-arrow-color": "#228B22", + "target-arrow-color": "#228B22", + }, + }, +]; + +const OPEN_GROUP_STYLE = { + "background-image": "none", + "pie-size": "0%", + "text-valign": "top", + "text-halign": "center", + "text-background-opacity": 1, + "text-background-shape": "roundrectangle", + "text-border-width": 2, + "text-background-padding": "2px", + "text-margin-y": "-3px", + "text-border-opacity": 1, + "background-color": "#eaeaea", + "border-color": "#d0d0d0", + "text-background-color": "#d0d0d0", + "text-border-color": "#d0d0d0", + "border-opacity": 1, + shape: "roundrectangle", + "font-size": "10px", + "background-opacity": 0.7, + "text-wrap": "wrap", + color: "black", + "border-width": 3, + "font-weight": "bold", +}; const FADED_STYLE = [ { @@ -50,7 +172,15 @@ const EDGE_LABEL_STYLES = [ selector: "edge.hover, edge.showEdgeLabel", style: { label: "data(label)", - "font-size": "8px", + "font-size": "12px", + "font-weight": "bold", + "text-background-opacity": 0, + "text-background-padding": "3px", + "z-index": 10, + "z-compound-depth": "top", + shape: "roundrectangle", + "text-outline-width": 0.8, + "text-outline-color": "rgb(244,244,244)", }, }, { @@ -59,39 +189,90 @@ const EDGE_LABEL_STYLES = [ label: "data(longLabel)", "font-size": "8px", "text-wrap": "wrap", + "text-background-opacity": 0, + "text-background-padding": "3px", + "z-index": 10, }, }, ]; -const ANNOTATION_STYLES = Object.entries(annotationLegend).map(([, { id, color }]) => ({ - selector: `.${id}`, - style: { - "line-color": color, - "target-arrow-color": color, - }, -})); - -export const GRAPH_STYLES = [ +const NODE_STYLE = [ { selector: "node", - style: NODE_STYLE, + style: { + "background-color": "#666", + label: "data(label)", + color: "black", + "text-valign": "center", + "text-halign": "center", + "font-size": 8, + width: 24, + height: 24, + }, + }, + { + selector: "node.groupNode.selected", + style: GROUP_NODE_STYLE, + }, + { + selector: "node.groupNode", + style: UNSELECTED_GROUP_NODE_STYLE, }, { selector: "node.selected", style: SELECTED_NODE_STYLE, }, { - selector: "edge", - style: EDGE_STYLE, + selector: "node.searchedfor", + style: SEARCHED_FOR_NODE_STYLE, }, { - selector: ".chemical", - style: CHEMICAL_STYLE, + selector: ":parent", + style: OPEN_GROUP_STYLE, }, { - selector: ".electrical", - style: ELECTRICAL_STYLE, + selector: ":parent.selected", + style: { + ...OPEN_GROUP_STYLE, + "font-weight": "bold", + padding: "9px", + "text-margin-y": "-4px", + }, + }, + { + selector: "node[?none], node[?muscle], node[?others]", + css: { + "font-size": 8, + shape: "roundrectangle", + height: "10px", + padding: "8px", + "z-index": 10, + }, + }, + { + selector: "node.searchedfor[?none], node.searchedfor[?muscle], node.searchedfor[?others]", + css: { + "background-image": searchedforMuscleBackground, + "background-repeat": "repeat-x", + "background-image-opacity": "0.1", + }, }, +]; + +const ANNOTATION_STYLES = Object.entries(annotationLegend).map(([, { id, color }]) => ({ + selector: `.${id}`, + style: { + "line-color": color, + "target-arrow-color": color, + "source-arrow-color": color, + }, +})); + +export const GRAPH_STYLES = [ + ...NODE_STYLE, + ...EDGE_STYLE, + ...ELECTRICAL_STYLE, + ...CHEMICAL_STYLE, ...EDGE_LABEL_STYLES, ...FADED_STYLE, ...ANNOTATION_STYLES, diff --git a/applications/visualizer/frontend/yarn.lock b/applications/visualizer/frontend/yarn.lock index ea6c8545..ef40a121 100644 --- a/applications/visualizer/frontend/yarn.lock +++ b/applications/visualizer/frontend/yarn.lock @@ -881,6 +881,11 @@ redux-thunk "^3.1.0" reselect "^5.1.0" +"@remix-run/router@1.19.2": + version "1.19.2" + resolved "https://registry.yarnpkg.com/@remix-run/router/-/router-1.19.2.tgz#0c896535473291cb41f152c180bedd5680a3b273" + integrity sha512-baiMx18+IMuD1yyvOGaHM9QrVUPGGG0jC+z+IPHnRJWUAUvaKuWKyE8gjDj2rzv3sz9zOGoRSPgeBVHRhZnBlA== + "@rollup/rollup-android-arm-eabi@4.19.0": version "4.19.0" resolved "https://registry.yarnpkg.com/@rollup/rollup-android-arm-eabi/-/rollup-android-arm-eabi-4.19.0.tgz#3d9fd50164b94964f5de68c3c4ce61933b3a338d" @@ -1177,6 +1182,11 @@ babel-plugin-macros@^3.1.0: cosmiconfig "^7.0.0" resolve "^1.19.0" +base64-arraybuffer@^1.0.2: + version "1.0.2" + resolved "https://registry.yarnpkg.com/base64-arraybuffer/-/base64-arraybuffer-1.0.2.tgz#1c37589a7c4b0746e34bd1feb951da2df01c1bdc" + integrity sha512-I3yl4r9QB5ZRY3XuJVEPfc2XhZO6YweFPI+UovAzn+8/hb3oJ6lnysaFcjVpkCPfVWFUDvoZ8kmVDP7WyRtYtQ== + base64-js@^1.3.1, base64-js@^1.5.1: version "1.5.1" resolved "https://registry.yarnpkg.com/base64-js/-/base64-js-1.5.1.tgz#1b1b440160a5bf7ad40b650f095963481903930a" @@ -1364,6 +1374,13 @@ cross-spawn@^7.0.1: shebang-command "^2.0.0" which "^2.0.1" +css-line-break@^2.1.0: + version "2.1.0" + resolved "https://registry.yarnpkg.com/css-line-break/-/css-line-break-2.1.0.tgz#bfef660dfa6f5397ea54116bb3cb4873edbc4fa0" + integrity sha512-FHcKFCZcAha3LwfVBhCQbW2nCNbkZXn7KVUJcsT5/P8YmfsVja0FMPJr0B903j/E69HUphKiV9iQArX8SDYA4w== + dependencies: + utrie "^1.0.2" + css-vendor@^2.0.8: version "2.0.8" resolved "https://registry.yarnpkg.com/css-vendor/-/css-vendor-2.0.8.tgz#e47f91d3bd3117d49180a3c935e62e3d9f7f449d" @@ -1632,6 +1649,14 @@ hoist-non-react-statics@^3.3.0, hoist-non-react-statics@^3.3.1, hoist-non-react- dependencies: react-is "^16.7.0" +html2canvas@^1.4.1: + version "1.4.1" + resolved "https://registry.yarnpkg.com/html2canvas/-/html2canvas-1.4.1.tgz#7cef1888311b5011d507794a066041b14669a543" + integrity sha512-fPU6BHNpsyIhr8yyMpTLLxAbkaK8ArIBcmZIRiBLiDhjeqvXolaEmDGmELFuX9I4xDcaKKcJl+TKZLqruBbmWA== + dependencies: + css-line-break "^2.1.0" + text-segmentation "^1.0.3" + hyphenate-style-name@^1.0.3: version "1.1.0" resolved "https://registry.yarnpkg.com/hyphenate-style-name/-/hyphenate-style-name-1.1.0.tgz#1797bf50369588b47b72ca6d5e65374607cf4436" @@ -1958,7 +1983,7 @@ pako@^1.0.3: resolved "https://registry.yarnpkg.com/pako/-/pako-1.0.11.tgz#6c9599d340d54dfd3946380252a35705a6b992bf" integrity sha512-4hLB8Py4zZce5s4yd9XzopqwVv/yGNhV1Bl8NTmCq1763HeK2+EwVTv+leGeL13Dnh2wfbqowVPXCIO0z4taYw== -pako@^2.0.4: +pako@^2.0.4, pako@^2.1.0: version "2.1.0" resolved "https://registry.yarnpkg.com/pako/-/pako-2.1.0.tgz#266cc37f98c7d883545d11335c00fbd4062c9a86" integrity sha512-w+eufiZ1WuJYgPXbV/PO3NCMEc3xqylkKHzp8bxp1uW4qaSNQUkwmLLEc3kKsfz8lpV1F8Ht3U1Cm+9Srog2ug== @@ -2173,6 +2198,21 @@ react-rnd@^7.3.0: re-resizable "4.5.1" react-draggable "^3.0.5" +react-router-dom@^6.26.2: + version "6.26.2" + resolved "https://registry.yarnpkg.com/react-router-dom/-/react-router-dom-6.26.2.tgz#a6e3b0cbd6bfd508e42b9342099d015a0ac59680" + integrity sha512-z7YkaEW0Dy35T3/QKPYB1LjMK2R1fxnHO8kWpUMTBdfVzZrWOiY9a7CtN8HqdWtDUWd5FY6Dl8HFsqVwH4uOtQ== + dependencies: + "@remix-run/router" "1.19.2" + react-router "6.26.2" + +react-router@6.26.2: + version "6.26.2" + resolved "https://registry.yarnpkg.com/react-router/-/react-router-6.26.2.tgz#2f0a68999168954431cdc29dd36cec3b6fa44a7e" + integrity sha512-tvN1iuT03kHgOFnLPfLJ8V95eijteveqdOSk+srqfePtQvqCExB8eHOYnlilbOcyJyKnYkr1vJvf7YqotAJu1A== + dependencies: + "@remix-run/router" "1.19.2" + react-transition-group@^4.4.0, react-transition-group@^4.4.5: version "4.4.5" resolved "https://registry.yarnpkg.com/react-transition-group/-/react-transition-group-4.4.5.tgz#e53d4e3f3344da8521489fbef8f2581d42becdd1" @@ -2386,6 +2426,13 @@ suspend-react@^0.1.3: resolved "https://registry.yarnpkg.com/suspend-react/-/suspend-react-0.1.3.tgz#a52f49d21cfae9a2fb70bd0c68413d3f9d90768e" integrity sha512-aqldKgX9aZqpoDp3e8/BZ8Dm7x1pJl+qI3ZKxDN0i/IQTWUwBx/ManmlVJ3wowqbno6c2bmiIfs+Um6LbsjJyQ== +text-segmentation@^1.0.3: + version "1.0.3" + resolved "https://registry.yarnpkg.com/text-segmentation/-/text-segmentation-1.0.3.tgz#52a388159efffe746b24a63ba311b6ac9f2d7943" + integrity 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