Complex coordination port (#266)

* Complex coordination port * Lint * Lint * Rename functions * Add docstrings for new functions * Lint * Implement link_views_by_dict
vitessce · Sep 12, 2023 · 8a2b710 · 8a2b710
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diff --git a/docs/notebooks/widget_imaging_beta.ipynb b/docs/notebooks/widget_imaging_beta.ipynb
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+{
+ "cells": [
+  {
+   "cell_type": "markdown",
+   "metadata": {
+    "nbsphinx": "hidden"
+   },
+   "source": [
+    "# Vitessce Widget Tutorial"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "# Visualization of Multi-Modal Imaging Data\n",
+    "We visualize IMS, PAS, and AF imaging data overlaid from the Spraggins Lab of the Biomolecular Multimodal Imaging Center (BIOMC) at Vanderbilt University, uploaded to the HuBMAP data portal."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 1,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "from vitessce import (\n",
+    "    VitessceConfig,\n",
+    "    Component as cm,\n",
+    "    CoordinationType as ct,\n",
+    "    OmeTiffWrapper,\n",
+    "    MultiImageWrapper,\n",
+    "    CoordinationLevel as CL,\n",
+    ")\n",
+    "from os.path import join"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "## 1. Configure Vitessce\n",
+    "Set up the images from the three different assays, with the `use_physical_size_scaling` set to `True` so that the IMS image scales to the other images based on their physical sizes."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 2,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "vc = VitessceConfig(schema_version=\"1.0.16\", name='Spraggins Multi-Modal', description='PAS + IMS + AF From https://portal.hubmapconsortium.org/browse/collection/6a6efd0c1a2681dc7d2faab8e4ab0bca')\n",
+    "dataset = vc.add_dataset(name='Spraggins').add_file(\n",
+    "    url='https://assets.hubmapconsortium.org/f4188a148e4c759092d19369d310883b/ometiff-pyramids/processedMicroscopy/VAN0006-LK-2-85-PAS_images/VAN0006-LK-2-85-PAS_registered.ome.tif?token=',\n",
+    "    file_type=\"image.ome-tiff\",\n",
+    "    coordination_values={\n",
+    "        \"fileUid\": \"PAS\",\n",
+    "    },\n",
+    ")\n",
+    "\n",
+    "imageScopes = vc.add_coordination_by_dict({\n",
+    "    \"imageLayer\": CL([\n",
+    "      {\n",
+    "        \"fileUid\": 'PAS',\n",
+    "        \"spatialLayerOpacity\": 1,\n",
+    "        \"spatialLayerVisible\": True,\n",
+    "        \"photometricInterpretation\": 'RGB',\n",
+    "        \"imageChannel\": CL([\n",
+    "          {\n",
+    "            \"spatialTargetC\": 0,\n",
+    "            \"spatialChannelColor\": [255, 0, 0],\n",
+    "            \"spatialChannelVisible\": True,\n",
+    "            \"spatialChannelOpacity\": 1.0,\n",
+    "            \"spatialChannelWindow\": [0, 255],\n",
+    "          },\n",
+    "          {\n",
+    "            \"spatialTargetC\": 1,\n",
+    "            \"spatialChannelColor\": [0, 255, 0],\n",
+    "            \"spatialChannelVisible\": True,\n",
+    "            \"spatialChannelOpacity\": 1.0,\n",
+    "            \"spatialChannelWindow\": [0, 255],\n",
+    "          },\n",
+    "          {\n",
+    "            \"spatialTargetC\": 2,\n",
+    "            \"spatialChannelColor\": [0, 0, 255],\n",
+    "            \"spatialChannelVisible\": True,\n",
+    "            \"spatialChannelOpacity\": 1.0,\n",
+    "            \"spatialChannelWindow\": [0, 255],\n",
+    "          },\n",
+    "        ]),\n",
+    "      }\n",
+    "    ])\n",
+    "})\n",
+    "\n",
+    "metaCoordinationScope = vc.add_meta_coordination()\n",
+    "metaCoordinationScope.use_coordination_by_dict(imageScopes)\n",
+    "\n",
+    "spatial = vc.add_view(\"spatialBeta\", dataset=dataset)\n",
+    "lc = vc.add_view(\"layerControllerBeta\", dataset=dataset)\n",
+    "\n",
+    "spatial.use_meta_coordination(metaCoordinationScope)\n",
+    "lc.use_meta_coordination(metaCoordinationScope)\n",
+    "\n",
+    "vc.layout(spatial | lc);"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "## 2. Create the Vitessce widget"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 3,
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "application/vnd.jupyter.widget-view+json": {
+       "model_id": "a5efa92286df4ad58cf94cfb3d12b703",
+       "version_major": 2,
+       "version_minor": 0
+      },
+      "text/plain": [
+       "VitessceWidget(config={'version': '1.0.16', 'name': 'Spraggins Multi-Modal', 'description': 'PAS + IMS + AF Fr…"
+      ]
+     },
+     "execution_count": 3,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "vw = vc.widget(custom_js_url='http://localhost:8000/packages/main/prod/dist/index.min.js')\n",
+    "vw"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": []
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Python 3 (ipykernel)",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.9.0"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 4
+}