@abi-software/flatmap-viewer 2.2.10-devel.2 → 2.2.11-devel.1

package/src/newcontrols.js

@@ -0,0 +1,617 @@
+/******************************************************************************
+
+Flatmap viewer and annotation tool
+
+Copyright (c) 2019  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.
+
+******************************************************************************/
+
+'use strict';
+
+//==============================================================================
+
+// Needed for Webpack
+import zoomInButton from '../static/images/zoom-in-button.png'
+
+//==============================================================================
+
+// Make sure colour string is in `#rrggbb` form.
+// Based on https://stackoverflow.com/a/47355187
+
+function standardise_color(str){
+    const canvas = document.createElement("canvas");
+    const ctx = canvas.getContext("2d");
+    ctx.fillStyle = str;
+    const colour = ctx.fillStyle;
+    canvas.remove()
+    return colour;
+}
+
+//==============================================================================
+
+export class NavigationControl
+{
+    constructor(flatmap)
+    {
+        this._flatmap = flatmap;
+        this._map = undefined;
+    }
+
+    getDefaultPosition()
+    //==================
+    {
+        return 'top-right';
+    }
+
+    onAdd(map)
+    //========
+    {
+        this._map = map;
+        this._container = document.createElement('div');
+        this._container.className = 'maplibregl-ctrl navigation-group';
+        this._container.innerHTML = `<button id="flatmap-zoom-in" class="navigation-zoom-in" type="button" title="Zoom in" aria-label="Zoom in"></button>
+<button id="flatmap-zoom-out" class="navigation-zoom-out" type="button" title="Zoom out" aria-label="Zoom out"></button>
+<button id="flatmap-reset" class="navigation-reset" type="button" title="Reset" aria-label="Reset"></button>`;
+        this._container.onclick = this.onClick_.bind(this);
+        return this._container;
+    }
+
+    onRemove()
+    //========
+    {
+        this._container.parentNode.removeChild(this._container);
+        this._map = undefined;
+    }
+
+    onClick_(e)
+    //=========
+    {
+        if        (e.target.id === 'flatmap-zoom-in') {
+            this._flatmap.zoomIn();
+        } else if (e.target.id === 'flatmap-zoom-out') {
+            this._flatmap.zoomOut();
+        } else if (e.target.id === 'flatmap-reset') {
+            this._flatmap.resetMap();
+        }
+    }
+}
+
+//==============================================================================
+
+export class PathControl
+{
+    constructor(flatmap, pathTypes)
+    {
+        this._flatmap = flatmap;
+        this._map = undefined;
+        this.__pathTypes = pathTypes;
+    }
+
+    getDefaultPosition()
+    //==================
+    {
+        return 'top-right';
+    }
+
+    onAdd(map)
+    //========
+    {
+        this._map = map;
+        this._container = document.createElement('div');
+        this._container.className = 'maplibregl-ctrl';
+        this._container.id = 'flatmap-nerve-key';
+
+        this._legend = document.createElement('div');
+        this._legend.id = 'nerve-key-text';
+        this._legend.className = 'flatmap-nerve-grid';
+
+        const innerHTML = [];
+        innerHTML.push(`<label for="path-all-paths">ALL PATHS:</label><div class="nerve-line"></div><input id="path-all-paths" type="checkbox" checked/>`);
+        for (const path of this.__pathTypes) {
+            // need to set style background instead of class...
+            // background: #2A62F6;
+            // background: repeating-linear-gradient(to right,#EA3423 0,#EA3423 6px,transparent 6px,transparent 9px)
+            innerHTML.push(`<label for="path-${path.type}">${path.label}</label><div class="nerve-line nerve-${path.type}"></div><input id="path-${path.type}" type="checkbox" checked/>`);
+        }
+        this._legend.innerHTML = innerHTML.join('\n');
+        this.__checkedCount = this.__pathTypes.length;
+        this.__halfCount = Math.trunc(this.__checkedCount/2);
+
+        this._button = document.createElement('button');
+        this._button.id = 'nerve-key-button';
+        this._button.className = 'control-button text-button';
+        this._button.setAttribute('type', 'button');
+        this._button.setAttribute('aria-label', 'Nerve paths legend');
+        this._button.setAttribute('control-visible', 'false');
+        this._button.textContent = 'PATHS';
+        this._button.title = 'Show/hide neuron paths';
+        this._container.appendChild(this._button);
+
+        this._container.addEventListener('click', this.onClick_.bind(this));
+        return this._container;
+    }
+
+    onRemove()
+    //========
+    {
+        this._container.parentNode.removeChild(this._container);
+        this._map = undefined;
+    }
+
+    onClick_(event)
+    //=============
+    {
+        if (event.target.id === 'nerve-key-button') {
+            if (this._button.getAttribute('control-visible') === 'false') {
+                this._container.appendChild(this._legend);
+                this._button.setAttribute('control-visible', 'true');
+                this._legend.focus();
+            } else {
+                this._legend = this._container.removeChild(this._legend);
+                this._button.setAttribute('control-visible', 'false');
+            }
+        } else if (event.target.tagName === 'INPUT') {
+            if (event.target.id === 'path-all-paths') {
+                if (event.target.indeterminate) {
+                    event.target.checked = (this.__checkedCount >= this.__halfCount);
+                    event.target.indeterminate = false;
+                }
+                if (event.target.checked) {
+                    this.__checkedCount = this.__pathTypes.length;
+                } else {
+                    this.__checkedCount = 0;
+                }
+                for (const path of this.__pathTypes) {
+                    const pathCheckbox = document.getElementById(`path-${path.type}`);
+                    if (pathCheckbox) {
+                        pathCheckbox.checked = event.target.checked;
+                        this._flatmap.enablePath(path.type, event.target.checked);
+                    }
+                }
+            } else if (event.target.id.startsWith('path-')) {
+                const pathType = event.target.id.substring(5);
+                this._flatmap.enablePath(pathType, event.target.checked);
+                if (event.target.checked) {
+                    this.__checkedCount += 1;
+                } else {
+                    this.__checkedCount -= 1;
+                }
+                const allPathsCheckbox = document.getElementById('path-all-paths');
+                if (this.__checkedCount === 0) {
+                    allPathsCheckbox.checked = false;
+                    allPathsCheckbox.indeterminate = false;
+                } else if (this.__checkedCount === this.__pathTypes.length) {
+                    allPathsCheckbox.checked = true;
+                    allPathsCheckbox.indeterminate = false;
+                } else {
+                    allPathsCheckbox.indeterminate = true;
+                }
+            }
+        }
+        event.stopPropagation();
+    }
+}
+
+//==============================================================================
+
+export class LayerControl
+{
+    constructor(flatmap, layerManager)
+    {
+        this.__flatmap = flatmap;
+        this.__manager = layerManager;
+        this.__map = undefined;
+    }
+
+    getDefaultPosition()
+    //==================
+    {
+        return 'top-right';
+    }
+
+    onAdd(map)
+    //========
+    {
+        this.__map = map;
+        this.__container = document.createElement('div');
+        this.__container.className = 'maplibregl-ctrl';
+        this.__container.id = 'flatmap-layer-control';
+
+        this.__layers = document.createElement('div');
+        this.__layers.id = 'layer-control-text';
+        this.__layers.className = 'flatmap-layer-grid';
+
+        const innerHTML = [];
+        innerHTML.push(`<label for="layer-all-layers">ALL LAYERS:</label><input id="layer-all-layers" type="checkbox" checked/>`);
+        for (const layer of this.__manager.layers) {
+            innerHTML.push(`<label for="layer-${layer.id}">${layer.description}</label><input id="layer-${layer.id}" type="checkbox" checked/>`);
+        }
+        this.__layers.innerHTML = innerHTML.join('\n');
+
+        this.__layersCount = this.__manager.layers.length;
+        this.__checkedCount = this.__layersCount;
+        this.__halfCount = Math.trunc(this.__checkedCount/2);
+
+        this.__button = document.createElement('button');
+        this.__button.id = 'map-layers-button';
+        this.__button.className = 'control-button text-button';
+        this.__button.setAttribute('type', 'button');
+        this.__button.setAttribute('aria-label', 'Show/hide map layers');
+        this.__button.setAttribute('control-visible', 'false');
+        this.__button.textContent = 'LAYERS';
+        this.__button.title = 'Show/hide map layers';
+        this.__container.appendChild(this.__button);
+
+        this.__container.addEventListener('click', this.onClick_.bind(this));
+        return this.__container;
+    }
+
+    onRemove()
+    //========
+    {
+        this.__container.parentNode.removeChild(this.__container);
+        this.__map = undefined;
+    }
+
+    onClick_(event)
+    //=============
+    {
+        if (event.target.id === 'map-layers-button') {
+            if (this.__button.getAttribute('control-visible') === 'false') {
+                this.__container.appendChild(this.__layers);
+                this.__button.setAttribute('control-visible', 'true');
+                this.__layers.focus();
+            } else {
+                this.__layers = this.__container.removeChild(this.__layers);
+                this.__button.setAttribute('control-visible', 'false');
+            }
+        } else if (event.target.tagName === 'INPUT') {
+            if (event.target.id === 'layer-all-layers') {
+                if (event.target.indeterminate) {
+                    event.target.checked = (this.__checkedCount >= this.__halfCount);
+                    event.target.indeterminate = false;
+                }
+                if (event.target.checked) {
+                    this.__checkedCount = this.__layersCount;
+                } else {
+                    this.__checkedCount = 0;
+                }
+                for (const layer of this.__manager.layers) {
+                    const layerCheckbox = document.getElementById(`layer-${layer.id}`);
+                    if (layerCheckbox) {
+                        layerCheckbox.checked = event.target.checked;
+                        this.__manager.activate(layer.id, event.target.checked);
+                    }
+                }
+            } else if (event.target.id.startsWith('layer-')) {
+                const layerId = event.target.id.substring(6);
+                this.__manager.activate(layerId, event.target.checked);
+                if (event.target.checked) {
+                    this.__checkedCount += 1;
+                } else {
+                    this.__checkedCount -= 1;
+                }
+                const allLayersCheckbox = document.getElementById('layer-all-layers');
+                if (this.__checkedCount === 0) {
+                    allLayersCheckbox.checked = false;
+                    allLayersCheckbox.indeterminate = false;
+                } else if (this.__checkedCount === this.__layersCount) {
+                    allLayersCheckbox.checked = true;
+                    allLayersCheckbox.indeterminate = false;
+                } else {
+                    allLayersCheckbox.indeterminate = true;
+                }
+            }
+        }
+        event.stopPropagation();
+    }
+}
+
+//==============================================================================
+
+
+const SCKAN_STATES = [
+    {
+        'id': 'VALID',
+        'description': 'Path consistent with SCKAN'
+    },
+    {
+        'id': 'INVALID',
+        'description': 'Path inconsistent with SCKAN'
+    }
+];
+
+
+export class SCKANControl
+{
+    constructor(flatmap)
+    {
+        this.__flatmap = flatmap;
+        this.__map = undefined;
+    }
+
+    getDefaultPosition()
+    //==================
+    {
+        return 'top-right';
+    }
+
+    onAdd(map)
+    //========
+    {
+        this.__map = map;
+        this.__container = document.createElement('div');
+        this.__container.className = 'maplibregl-ctrl';
+        this.__container.id = 'flatmap-layer-control';
+
+        this.__sckan = document.createElement('div');
+        this.__sckan.id = 'sckan-control-text';
+        this.__sckan.className = 'flatmap-layer-grid';
+
+        const innerHTML = [];
+        innerHTML.push(`<label for="sckan-all-paths">ALL PATHS:</label><input id="sckan-all-paths" type="checkbox" checked/>`);
+        for (const state of SCKAN_STATES) {
+            innerHTML.push(`<label for="sckan-${state.id}">${state.description}</label><input id="sckan-${state.id}" type="checkbox" checked/>`);
+        }
+        this.__sckan.innerHTML = innerHTML.join('\n');
+
+        this.__sckanCount = SCKAN_STATES.length;
+        this.__checkedCount = this.__sckanCount;
+        this.__halfCount = Math.trunc(this.__checkedCount/2);
+
+        this.__button = document.createElement('button');
+        this.__button.id = 'map-sckan-button';
+        this.__button.className = 'control-button text-button';
+        this.__button.setAttribute('type', 'button');
+        this.__button.setAttribute('aria-label', 'Show/hide valid SCKAN paths');
+        this.__button.setAttribute('control-visible', 'false');
+        this.__button.textContent = 'SCKAN';
+        this.__button.title = 'Show/hide valid SCKAN paths';
+        this.__container.appendChild(this.__button);
+
+        this.__container.addEventListener('click', this.onClick_.bind(this));
+        return this.__container;
+    }
+
+    onRemove()
+    //========
+    {
+        this.__container.parentNode.removeChild(this.__container);
+        this.__map = undefined;
+    }
+
+    onClick_(event)
+    //=============
+    {
+        if (event.target.id === 'map-sckan-button') {
+            if (this.__button.getAttribute('control-visible') === 'false') {
+                this.__container.appendChild(this.__sckan);
+                this.__button.setAttribute('control-visible', 'true');
+                this.__sckan.focus();
+            } else {
+                this.__sckan = this.__container.removeChild(this.__sckan);
+                this.__button.setAttribute('control-visible', 'false');
+            }
+        } else if (event.target.tagName === 'INPUT') {
+            if (event.target.id === 'sckan-all-paths') {
+                if (event.target.indeterminate) {
+                    event.target.checked = (this.__checkedCount >= this.__halfCount);
+                    event.target.indeterminate = false;
+                }
+                if (event.target.checked) {
+                    this.__checkedCount = this.__sckanCount;
+                } else {
+                    this.__checkedCount = 0;
+                }
+                for (const state of SCKAN_STATES) {
+                    const sckanCheckbox = document.getElementById(`sckan-${state.id}`);
+                    if (sckanCheckbox) {
+                        sckanCheckbox.checked = event.target.checked;
+                        this.__flatmap.showSckanPaths(state.id, event.target.checked);
+                    }
+                }
+            } else if (event.target.id.startsWith('sckan-')) {
+                const sckanId = event.target.id.substring(6);
+                this.__flatmap.showSckanPaths(sckanId, event.target.checked);
+                if (event.target.checked) {
+                    this.__checkedCount += 1;
+                } else {
+                    this.__checkedCount -= 1;
+                }
+                const allLayersCheckbox = document.getElementById('sckan-all-paths');
+                if (this.__checkedCount === 0) {
+                    allLayersCheckbox.checked = false;
+                    allLayersCheckbox.indeterminate = false;
+                } else if (this.__checkedCount === this.__sckanCount) {
+                    allLayersCheckbox.checked = true;
+                    allLayersCheckbox.indeterminate = false;
+                } else {
+                    allLayersCheckbox.indeterminate = true;
+                }
+            }
+        }
+        event.stopPropagation();
+    }
+}
+
+
+
+
+class StateControl
+{
+    constructor(id, flatmap, states, controlFunction)
+    {
+        this.__id = id;
+        this.__flatmap = flatmap;
+        this.__states = states;
+        this.__controlFunction = controlFunction;
+        this.__map = undefined;
+    }
+
+    getDefaultPosition()
+    //==================
+    {
+        return 'top-right';
+    }
+
+    onAdd(map)
+    //========
+    {
+        this.__map = map;
+        this.__container = document.createElement('div');
+        this.__container.className = 'maplibregl-ctrl';
+        this.__container.id = 'flatmap-state-control';
+
+        this.__control = document.createElement('div');
+        this.__control.id = `${this.__id}-control-text`;
+        this.__control.className = 'flatmap-state-grid';
+
+        const innerHTML = [];
+        innerHTML.push(`<label for="sckan-all-paths">ALL PATHS:</label><input id="sckan-all-paths" type="checkbox" checked/>`);
+        for (const state of SCKAN_STATES) {
+            innerHTML.push(`<label for="sckan-${state.id}">${state.description}</label><input id="sckan-${state.id}" type="checkbox" checked/>`);
+        }
+        this.__sckan.innerHTML = innerHTML.join('\n');
+
+        this.__sckanCount = SCKAN_STATES.length;
+        this.__checkedCount = this.__sckanCount;
+        this.__halfCount = Math.trunc(this.__checkedCount/2);
+
+        this.__button = document.createElement('button');
+        this.__button.id = 'map-sckan-button';
+        this.__button.className = 'control-button text-button';
+        this.__button.setAttribute('type', 'button');
+        this.__button.setAttribute('aria-label', 'Show/hide valid SCKAN paths');
+        this.__button.setAttribute('control-visible', 'false');
+        this.__button.textContent = 'SCKAN';
+        this.__button.title = 'Show/hide valid SCKAN paths';
+        this.__container.appendChild(this.__button);
+
+        this.__container.addEventListener('click', this.onClick_.bind(this));
+        return this.__container;
+    }
+
+    onRemove()
+    //========
+    {
+        this.__container.parentNode.removeChild(this.__container);
+        this.__map = undefined;
+    }
+
+    onClick_(event)
+    //=============
+    {
+        if (event.target.id === 'map-sckan-button') {
+            if (this.__button.getAttribute('control-visible') === 'false') {
+                this.__container.appendChild(this.__sckan);
+                this.__button.setAttribute('control-visible', 'true');
+                this.__sckan.focus();
+            } else {
+                this.__sckan = this.__container.removeChild(this.__sckan);
+                this.__button.setAttribute('control-visible', 'false');
+            }
+        } else if (event.target.tagName === 'INPUT') {
+            if (event.target.id === 'sckan-all-paths') {
+                if (event.target.indeterminate) {
+                    event.target.checked = (this.__checkedCount >= this.__halfCount);
+                    event.target.indeterminate = false;
+                }
+                if (event.target.checked) {
+                    this.__checkedCount = this.__sckanCount;
+                } else {
+                    this.__checkedCount = 0;
+                }
+                for (const state of SCKAN_STATES) {
+                    const sckanCheckbox = document.getElementById(`sckan-${state.id}`);
+                    if (sckanCheckbox) {
+                        sckanCheckbox.checked = event.target.checked;
+                        this.__flatmap.showSckanPaths(state.id, event.target.checked);
+                    }
+                }
+            } else if (event.target.id.startsWith('sckan-')) {
+                const sckanId = event.target.id.substring(6);
+                this.__flatmap.showSckanPaths(sckanId, event.target.checked);
+                if (event.target.checked) {
+                    this.__checkedCount += 1;
+                } else {
+                    this.__checkedCount -= 1;
+                }
+                const allLayersCheckbox = document.getElementById('sckan-all-paths');
+                if (this.__checkedCount === 0) {
+                    allLayersCheckbox.checked = false;
+                    allLayersCheckbox.indeterminate = false;
+                } else if (this.__checkedCount === this.__sckanCount) {
+                    allLayersCheckbox.checked = true;
+                    allLayersCheckbox.indeterminate = false;
+                } else {
+                    allLayersCheckbox.indeterminate = true;
+                }
+            }
+        }
+        event.stopPropagation();
+    }
+}
+
+//==============================================================================
+
+export class BackgroundControl
+{
+    constructor(flatmap)
+    {
+        this.__flatmap = flatmap;
+        this.__map = undefined;
+    }
+
+    getDefaultPosition()
+    //==================
+    {
+        return 'bottom-right';
+    }
+
+    onAdd(map)
+    //========
+    {
+        this.__map = map;
+        this.__container = document.createElement('div');
+        this.__container.className = 'maplibregl-ctrl';
+        this.__colourDiv = document.createElement('div');
+        this.__colourDiv.setAttribute('aria-label', 'Change background colour');
+        this.__colourDiv.title = 'Change background colour';
+        const background = standardise_color(this.__flatmap.getBackgroundColour());
+        this.__colourDiv.innerHTML = `<input type="color" id="colourPicker" value="${background}">`;
+        this.__container.appendChild(this.__colourDiv);
+        this.__colourDiv.addEventListener('input', this.__updateColour.bind(this), false);
+        this.__colourDiv.addEventListener('change', this.__updateColour.bind(this), false);
+        return this.__container;
+    }
+
+    onRemove()
+    //========
+    {
+        this.__container.parentNode.removeChild(this.__container);
+        this.__map = undefined;
+    }
+
+    __updateColour(event)
+    //===================
+    {
+        const colour = event.target.value;
+        this.__flatmap.setBackgroundColour(colour);
+        this.__flatmap.controlEvent('change', 'background', colour)
+        event.stopPropagation();
+    }
+}
+
+//==============================================================================

package/src/pathways.js

@@ -28,6 +28,7 @@ export const PATHWAYS_LAYER = 'pathways';
 
 export const PATH_TYPES = [
     { type: "cns", label: "CNS", colour: "#9B1FC1"},
+    { type: "intracardiac", label: "Local circuit neuron", colour: "#F19E38"},
     { type: "lcn", label: "Local circuit neuron", colour: "#F19E38"},
     { type: "para-pre", label: "Parasympathetic pre-ganglionic", colour: "#3F8F4A"},
     { type: "para-post", label: "Parasympathetic post-ganglionic", colour: "#3F8F4A"},
@@ -35,9 +36,14 @@ export const PATH_TYPES = [
     { type: "somatic", label: "Somatic lower motor", colour: "#98561D"},
     { type: "symp-pre", label: "Sympathetic pre-ganglionic", colour: "#EA3423"},
     { type: "symp-post", label: "Sympathetic post-ganglionic", colour: "#EA3423"},
-    { type: "other", label: "Other neuron type", colour: "#888"}
+    { type: "other", label: "Other neuron type", colour: "#888"},
+    { type: "arterial", label: "Arterial blood vessel", colour: "#F00"},
+    { type: "venous", label: "Venous blood vessel", colour: "#2F6EBA"}
 ];
 
+export const PATH_STYLE_RULES =
+    PATH_TYPES.flatMap(pathType => [['==', ['get', 'kind'], pathType.type], pathType.colour]);
+
 //==============================================================================
 
 function reverseMap(mapping)
@@ -138,6 +144,19 @@ export class Pathways
         }
     }
 
+    get pathTypes()
+    //=============
+    {
+        const pathTypes = [];
+        for (const pathType of PATH_TYPES) {
+            if (pathType.type in this.__typePaths
+            && this.__typePaths[pathType.type].length > 0) {
+                pathTypes.push(pathType);
+            }
+        }
+        return pathTypes;
+    }
+
     addPathsToFeatureSet_(paths, featureSet)
     //======================================
     {

package/src/search.js

@@ -29,6 +29,7 @@ import MiniSearch from 'minisearch';
 // The properties of a feature we index and show
 
 export const indexedProperties = [
+    'id',
     'label',
     'models',
     'source'