@abi-software/map-utilities 1.2.0-beta.7 → 1.2.0

package/src/components/ConnectivityGraph/graph.js

@@ -0,0 +1,355 @@
+/*==============================================================================
+
+A viewer for neuron connectivity graphs.
+
+Copyright (c) 2019 - 2024  David Brooks
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+    http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
+
+==============================================================================*/
+
+import cytoscape from 'cytoscape'
+
+//==============================================================================
+
+
+//==============================================================================
+
+export class ConnectivityGraph extends EventTarget
+{
+    cyg = null
+    nodes = []
+    edges = []
+    axons = []
+    dendrites = []
+    somas = []
+    labelCache = new Map()
+    graphCanvas = null
+
+    constructor(labelCache, graphCanvas)
+    {
+        super()
+        this.labelCache = labelCache;
+        this.graphCanvas = graphCanvas;
+    }
+
+    async addConnectivity(knowledge)
+    //=====================================================
+    {
+        this.axons = knowledge.axons.map(node => JSON.stringify(node))
+        this.dendrites = knowledge.dendrites.map(node => JSON.stringify(node))
+        if (knowledge.somas?.length) {
+            this.somas = knowledge.somas.map(node => JSON.stringify(node))
+        }
+        if (knowledge.connectivity.length) {
+            for (const edge of knowledge.connectivity) {
+                const e0 = await this.graphNode(edge[0])
+                const e1 = await this.graphNode(edge[1])
+                this.nodes.push(e0)
+                this.nodes.push(e1)
+                this.edges.push({
+                    id: `${e0.id}_${e1.id}`,
+                    source: e0.id,
+                    target: e1.id
+                })
+            }
+        } else {
+            this.nodes.push({
+                id: 'MISSING',
+                label: 'NO PATHS'
+            })
+        }
+    }
+
+    showConnectivity(graphCanvas)
+    //================
+    {
+        this.cyg = new CytoscapeGraph(this, graphCanvas)
+
+        this.cyg.on('tap-node', (event) => {
+            const tapEvent = new CustomEvent('tap-node', {
+                detail: event.detail
+            })
+            this.dispatchEvent(tapEvent);
+        });
+    }
+
+    clearConnectivity()
+    //=================
+    {
+        if (this.cyg?.cy) {
+            this.cyg.cy.remove()
+            this.cyg.cy = null
+        }
+    }
+
+    reset()
+    //=====
+    {
+        if (this.cyg?.cy) {
+            this.cyg.cy.reset()
+        }
+    }
+
+    zoom(val)
+    //=======
+    {
+        if (this.cyg?.cy) {
+            const currentZoom = this.cyg.cy.zoom()
+            const width = this.cyg.cy.width()
+            const height = this.cyg.cy.height()
+            const positionToRender = {
+                x: width/2,
+                y: height/2,
+            }
+            this.cyg.cy.zoom({
+                level: currentZoom + val,
+                renderedPosition: positionToRender,
+            })
+        }
+    }
+
+    enableZoom(option)
+    //================
+    {
+        if (this.cyg?.cy) {
+            this.cyg.cy.userZoomingEnabled(option)
+        }
+    }
+
+    get elements()
+    //============
+    {
+        return [
+            ...this.nodes.map(n => { return {data: n}}),
+            ...this.edges.map(e => { return {data: e}})
+        ]
+    }
+
+    get roots()
+    //===================
+    {
+        return [
+            ...this.dendrites,
+            ...this.somas
+        ]
+    }
+
+    async graphNode(node)
+    //=======================================================
+    {
+        const id = JSON.stringify(node)
+        const label = [node[0], ...node[1]]
+        const humanLabels = []
+        for (const term of label) {
+            const humanLabel = this.labelCache.has(term) ? this.labelCache.get(term) : ''
+            humanLabels.push(humanLabel)
+        }
+        label.push(...humanLabels)
+
+        const result = {
+            id,
+            label: label.join('\n')
+        }
+        if (this.axons.includes(id)) {
+            if (this.dendrites.includes(id) || this.somas.includes(id)) {
+                result['both-a-d'] = true
+            } else {
+                result['axon'] = true
+            }
+        } else if (this.dendrites.includes(id) || this.somas.includes(id)) {
+            result['dendrite'] = true
+
+        }
+        return result
+    }
+
+    on(eventName, callback)
+    //=====================
+    {
+        this.addEventListener(eventName, callback)
+    }
+}
+
+//==============================================================================
+
+const GRAPH_STYLE = [
+    {
+        'selector': 'node',
+        'style': {
+            'label': function(ele) { return trimLabel(ele.data('label')) },
+            // 'background-color': '#80F0F0',
+            'background-color': 'transparent',
+            'background-opacity': '0',
+            'text-valign': 'center',
+            'text-wrap': 'wrap',
+            'width': '80px',
+            'height': '80px',
+            'text-max-width': '80px',
+            'font-size': '6px',
+            'shape': 'round-rectangle',
+            'border-width': 1,
+            'border-style': 'solid',
+            'border-color': 'gray',
+        }
+    },
+    {
+        'selector': 'node[axon]',
+        'style': {
+            // 'background-color': 'green',
+            'shape': 'round-diamond',
+            'width': '100px',
+            'height': '100px',
+        }
+    },
+    {
+        'selector': 'node[dendrite]',
+        'style': {
+            // 'background-color': 'red',
+            'shape': 'ellipse',
+        }
+    },
+    {
+        'selector': 'node[both-a-d]',
+        'style': {
+            // 'background-color': 'gray',
+            'shape': 'round-rectangle',
+        }
+    },
+    {
+        'selector': 'edge',
+        'style': {
+            'width': 1,
+            'line-color': 'dimgray',
+            'target-arrow-color': 'dimgray',
+            'target-arrow-shape': 'triangle',
+            'curve-style': 'bezier'
+        }
+    }
+]
+
+function trimLabel(label) {
+    const labels = label.split('\n')
+    const half = labels.length/2
+    const trimLabels = labels.slice(half)
+    return trimLabels.join('\n')
+}
+
+function capitalizeLabels(input) {
+    return input.split('\n').map(label => {
+        if (label && label[0] >= 'a' && label[0] <= 'z') {
+            return label.charAt(0).toUpperCase() + label.slice(1)
+        }
+        return label
+    }).join('\n')
+}
+
+//==============================================================================
+
+class CytoscapeGraph extends EventTarget
+{
+    cy
+    tooltip
+
+    constructor(connectivityGraph, graphCanvas)
+    {
+        super()
+        this.cy = cytoscape({
+            container: graphCanvas,
+            elements: connectivityGraph.elements,
+            layout: {
+                name: 'breadthfirst',
+                circle: false,
+                roots: connectivityGraph.roots
+            },
+            directed: true,
+            style: GRAPH_STYLE,
+            minZoom: 0.5,
+            maxZoom: 10,
+            wheelSensitivity: 0.4,
+        }).on('mouseover', 'node', this.overNode.bind(this))
+          .on('mouseout', 'node', this.exitNode.bind(this))
+          .on('position', 'node', this.moveNode.bind(this))
+          .on('tap', this.tapNode.bind(this))
+
+        this.tooltip = document.createElement('div')
+        this.tooltip.className = 'cy-graph-tooltip'
+        this.tooltip.hidden = true
+        graphCanvas?.lastChild?.appendChild(this.tooltip)
+    }
+
+    remove()
+    //======
+    {
+        if (this.cy) {
+            this.cy.destroy()
+        }
+    }
+
+    checkRightBoundary(leftPos)
+    //==================================
+    {
+        if ((leftPos + this.tooltip.offsetWidth) >= this.tooltip.parentElement?.offsetWidth) {
+            this.tooltip.style.left = `${leftPos - this.tooltip.offsetWidth}px`
+        }
+    }
+
+    overNode(event)
+    //==============
+    {
+        const node = event.target
+        const label = capitalizeLabels(node.data().label)
+
+        this.tooltip.innerText = label
+        this.tooltip.style.left = `${event.renderedPosition.x}px`
+        this.tooltip.style.top = `${event.renderedPosition.y}px`
+        this.tooltip.style.maxWidth = '240px'
+        this.tooltip.hidden = false
+
+        this.checkRightBoundary(event.renderedPosition.x)
+    }
+
+    moveNode(event)
+    //==============
+    {
+        const node = event.target
+        this.tooltip.style.left = `${node.renderedPosition().x}px`
+        this.tooltip.style.top = `${node.renderedPosition().y}px`
+        this.checkRightBoundary(node.renderedPosition().x)
+    }
+
+    exitNode(event)
+    //==============
+    {
+        this.tooltip.hidden = true
+    }
+
+    tapNode(event)
+    //============
+    {
+        const node = event.target
+        const data = node.data()
+        const tapEvent = new CustomEvent('tap-node', {
+            detail: data
+        })
+        this.dispatchEvent(tapEvent);
+    }
+
+    on(eventName, callback)
+    //=====================
+    {
+        this.addEventListener(eventName, callback)
+    }
+}
+
+//==============================================================================

package/src/components/Tooltip/AnnotationPopup.vue

@@ -267,6 +267,8 @@ export default {
                 "https://pubmed.ncbi.nlm.nih.gov/"
               );
               evidenceURLs.push(new URL(link));
+            } else {
+              evidenceURLs.push(evidence);
             }
           });
           const userAnnotation = {

package/src/components/TreeControls/TreeControls.vue

@@ -202,7 +202,7 @@ export default {
   methods: {
     filterNode: function(value, data) {
       if (!value) return true;
-      return data.label ? data.label.toLowerCase().includes(value) : false;
+      return data.label ? data.label.toLowerCase().includes(value.toLowerCase()) : false;
     },
     setColour: function (nodeData, value) {
       this.$emit("setColour", nodeData, value);
@@ -368,7 +368,7 @@ export default {
 
 :deep(.el-checkbox__label) {
   padding-left: 5px;
-  color: $app-primary-color !important;
+  color: inherit !important;
   font-size: 12px;
   font-weight: 500;
   letter-spacing: 0px;
@@ -385,7 +385,7 @@ export default {
 
 .region-tree-node {
   flex: 1;
-  color: $app-primary-color !important;
+  color: inherit !important;
   display: flex;
   font-size: 12px;
   line-height: 14px;

package/src/components/index.js

@@ -1,9 +1,19 @@
 import AnnotationPopup from "./Tooltip/AnnotationPopup.vue";
 import CreateTooltipContent from "./Tooltip/CreateTooltipContent.vue";
+import ConnectivityGraph from "./ConnectivityGraph/ConnectivityGraph.vue";
 import CopyToClipboard from "./CopyToClipboard/CopyToClipboard.vue";
 import DrawToolbar from "./DrawToolbar/DrawToolbar.vue";
 import HelpModeDialog from "./HelpModeDialog/HelpModeDialog.vue";
 import Tooltip from "./Tooltip/Tooltip.vue";
 import TreeControls from "./TreeControls/TreeControls.vue";
 
-export { AnnotationPopup, CreateTooltipContent, CopyToClipboard, DrawToolbar, HelpModeDialog, Tooltip, TreeControls };
+export {
+  AnnotationPopup,
+  CreateTooltipContent,
+  ConnectivityGraph,
+  CopyToClipboard,
+  DrawToolbar,
+  HelpModeDialog,
+  Tooltip,
+  TreeControls,
+};

package/src/components.d.ts

@@ -9,6 +9,7 @@ declare module 'vue' {
   export interface GlobalComponents {
     AnnotationPopup: typeof import('./components/Tooltip/AnnotationPopup.vue')['default']
     ConnectionDialog: typeof import('./components/DrawToolbar/ConnectionDialog.vue')['default']
+    ConnectivityGraph: typeof import('./components/ConnectivityGraph/ConnectivityGraph.vue')['default']
     CopyToClipboard: typeof import('./components/CopyToClipboard/CopyToClipboard.vue')['default']
     CreateTooltipContent: typeof import('./components/Tooltip/CreateTooltipContent.vue')['default']
     DrawToolbar: typeof import('./components/DrawToolbar/DrawToolbar.vue')['default']
@@ -20,6 +21,7 @@ declare module 'vue' {
     ElContainer: typeof import('element-plus/es')['ElContainer']
     ElHeader: typeof import('element-plus/es')['ElHeader']
     ElIcon: typeof import('element-plus/es')['ElIcon']
+    ElIconAim: typeof import('@element-plus/icons-vue')['Aim']
     ElIconArrowDown: typeof import('@element-plus/icons-vue')['ArrowDown']
     ElIconArrowUp: typeof import('@element-plus/icons-vue')['ArrowUp']
     ElIconClose: typeof import('@element-plus/icons-vue')['Close']
@@ -27,7 +29,11 @@ declare module 'vue' {
     ElIconDelete: typeof import('@element-plus/icons-vue')['Delete']
     ElIconEdit: typeof import('@element-plus/icons-vue')['Edit']
     ElIconFinished: typeof import('@element-plus/icons-vue')['Finished']
+    ElIconLock: typeof import('@element-plus/icons-vue')['Lock']
+    ElIconUnlock: typeof import('@element-plus/icons-vue')['Unlock']
     ElIconWarning: typeof import('@element-plus/icons-vue')['Warning']
+    ElIconZoomIn: typeof import('@element-plus/icons-vue')['ZoomIn']
+    ElIconZoomOut: typeof import('@element-plus/icons-vue')['ZoomOut']
     ElInput: typeof import('element-plus/es')['ElInput']
     ElMain: typeof import('element-plus/es')['ElMain']
     ElOption: typeof import('element-plus/es')['ElOption']