Stage move API now works
The test plugin seems to have problems calling setPosition more than once. We don't understand this... Co-authored-by: Kaspar Emanuel <kaspar@monostable.co.uk>
This commit is contained in:
Richard
parent
757ee216cf
commit
297908fbc8
4 changed files with 298 additions and 39 deletions
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@ -0,0 +1,131 @@
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<config lang="json">
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{
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"name": "Script Editor",
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"type": "web-worker",
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"tags": [],
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"ui": "",
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"version": "0.1.0",
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"cover": "",
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"description": "A Script Editor for Controlling OpenFlexure Microscope with ImJoy",
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"icon": "extension",
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"inputs": null,
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"outputs": null,
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"api_version": "0.1.8",
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"env": "",
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"permissions": [],
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"requirements": [],
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"dependencies": []
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}
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</config>
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<script lang="javascript">
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class ImJoyPlugin {
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async setup() {
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api.log('initialized')
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}
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async run(ctx) {
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let pluginInEditor, stopped, editorWindow;
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const config = {lang: 'javascript'}
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config.templates = [
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{
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name: "New",
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url: null,
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lang: 'javascript',
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},
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{
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name: "Snap Image Template",
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url: "./OpenFlexureSnapImageTemplate.imjoy.html",
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lang: "html",
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}
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]
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config.ui_elements = {
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save: {
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_rintf: true,
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type: 'button',
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label: "Save",
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visible: false,
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icon: "content-save",
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callback(content) {
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console.log(content)
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}
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},
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run: {
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_rintf: true,
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type: 'button',
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label: "Run",
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icon: "play",
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visible: true,
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shortcut: 'Shift-Enter',
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async callback(content) {
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try {
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editorWindow.setLoader(true);
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editorWindow.updateUIElement('stop', {
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visible: true
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})
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api.showProgress(0);
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pluginInEditor = await api.getPlugin({src: content, hot_reloading: true})
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if (stopped) {
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pluginInEditor = null;
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return;
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}
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if (pluginInEditor && pluginInEditor.run) {
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return await pluginInEditor.run({
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config: {},
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data: {}
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});
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}
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if (stopped) {
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pluginInEditor = null;
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return;
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}
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} catch (e) {
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api.showMessage("Failed to load plugin, error: " + e.toString());
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} finally {
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editorWindow.updateUIElement('stop', {
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visible: false
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})
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editorWindow.setLoader(false);
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api.showProgress(100);
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}
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}
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},
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stop: {
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_rintf: true,
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type: 'button',
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label: "Stop",
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style: "color: #ff0080cf;",
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icon: "stop",
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visible: false,
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async callback() {
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stopped = true;
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await editorWindow.setLoader(false);
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await editorWindow.updateUIElement('stop', {
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visible: false
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})
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}
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},
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export: {
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_rintf: true,
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type: 'button',
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label: "Export",
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icon: "file-download-outline",
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visible: true,
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async callback(content) {
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const fileName = (pluginInEditor && pluginInEditor.config.name && pluginInEditor.config.name + '.imjoy.html') || config.name + '.imjoy.html' || "myPlugin.imjoy.html";
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await api.exportFile(content, fileName);
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}
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}
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}
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editorWindow = await api.createWindow({
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src: 'https://if.imjoy.io',
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name: (ctx && ctx.data && ctx.data.name) ||'OpenFlexure Script Editor',
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config,
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data: {code: ctx && ctx.data && ctx.data.code}
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})
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}
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}
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api.export(new ImJoyPlugin())
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</script>
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@ -0,0 +1,43 @@
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<docs>
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[TODO: write documentation for this plugin.]
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</docs>
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<config lang="json">
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{
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"name": "OpenFlexureSnapImageTemplate",
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"type": "web-worker",
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"tags": [],
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"ui": "",
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"version": "0.1.0",
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"cover": "",
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"description": "[TODO: describe this plugin with one sentence.]",
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"icon": "extension",
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"inputs": null,
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"outputs": null,
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"api_version": "0.1.8",
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"env": "",
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"permissions": [],
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"requirements": [],
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"dependencies": []
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}
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</config>
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<script lang="javascript">
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class ImJoyPlugin {
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async setup() {
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api.log('initialized')
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}
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async run(ctx) {
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// get a list of service
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const services = await api.getServices({name: "OpenFlexure"});
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// get the first service
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const ofm = services[0];
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// snap an image
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await ofm.snapImage();
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console.log("snapped an image");
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}
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}
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api.export(new ImJoyPlugin())
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</script>
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@ -0,0 +1,48 @@
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<docs>
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[TODO: write documentation for this plugin.]
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</docs>
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<config lang="json">
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{
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"name": "Test OFM Stage",
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"type": "web-worker",
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"tags": [],
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"ui": "",
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"version": "0.1.0",
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"cover": "",
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"description": "Move the OFM stage to test the API works",
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"icon": "extension",
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"inputs": null,
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"outputs": null,
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"api_version": "0.1.8",
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"env": "",
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"permissions": [],
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"requirements": [],
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"dependencies": []
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}
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</config>
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<script lang="javascript">
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class ImJoyPlugin {
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async setup() {
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api.log('initialized')
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}
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async run(ctx) {
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// get a list of service
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const services = await api.getServices({name: "OpenFlexure"});
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// get the first service
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const ofm = services[0];
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// snap an image
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const start = await ofm.getXYZPosition();
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console.log(`Starting position: ${start}`);
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// move the Z axis up and down
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await ofm.setPosition(start[2] + 100);
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console.log(`Moved Z to ${await ofm.getPosition()}`);
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await ofm.setPosition(start[2]);
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console.log(`Moved Z to ${await ofm.getPosition()}`);
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}
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}
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api.export(new ImJoyPlugin())
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</script>
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@ -98,6 +98,21 @@ import * as imjoyCore from "imjoy-core";
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import axios from "axios";
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import UIkit from "uikit";
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// TODO: move this to a module or something...
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async function pollAction(response) {
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// Poll an action until its status is completed
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// TODO: raise an error if it fails or is cancelled
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// For ease, this accepts and returns a response object from
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// axios.get
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// FIXME: this could be an infinite loop if the task is cancelled/errored
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let r = response;
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while ((r.data.status == "running") | (r.data.status == "pending")) {
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await new Promise(resolve => setTimeout(resolve, 100));
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r = await axios.get(r.data.href);
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}
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return r;
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}
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export default {
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name: "ImJoyContent",
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@ -123,6 +138,9 @@ export default {
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},
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moveActionUri: function() {
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return `${this.$store.getters.baseUri}/api/v2/actions/stage/move`;
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},
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baseUri: function() {
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return this.$store.getters.baseUri;
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}
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},
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mounted() {
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@ -168,7 +186,7 @@ export default {
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}
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});
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imjoy.start({ workspace: "default" }).then(() => {
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imjoy.start({ workspace: "default" }).then(async () => {
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console.log("ImJoy started");
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imjoy.event_bus.on("add_window", w => {
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this.addWindow(w);
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@ -176,8 +194,16 @@ export default {
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this.setupMicroscopeAPI();
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this.setupViewers();
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// load the script editor for openflexure
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this.loadPlugin(
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"https://gist.githubusercontent.com/oeway/7a9dcb49c51b1f99b2c3619f470fe35c/raw/OpenFlexureScriptEditor.imjoy.html"
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await this.loadPlugin(
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`${window.location.origin}/OpenFlexureScriptEditor.imjoy.html`
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);
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// Load the snap image template
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await this.loadPlugin(
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`${window.location.origin}/OpenFlexureSnapImageTemplate.imjoy.html`
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);
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// Load the snap image template
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await this.loadPlugin(
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`${window.location.origin}/OpenFlexureTestMoveStage.imjoy.html`
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);
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this.setupPluginEngine();
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});
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@ -232,22 +258,10 @@ export default {
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// See here: https://valelab4.ucsf.edu/~MM/doc/MMCore/html/class_c_m_m_core.html
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const snapshotUri = this.snapshotStreamUri;
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const captureActionUri = this.captureActionUri;
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const getPositionUri = this.getPositionUri;
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const moveActionUri = this.moveActionUri;
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const modalError = this.modalError;
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async function pollUntilComplete(response) {
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// Poll an action until its status is completed
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// TODO: raise an error if it fails or is cancelled
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// For ease, this accepts and returns a response object from
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// axios.get
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// FIXME: this could be an infinite loop if the task is cancelled/errored
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let r = response;
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while (r.data.status == "running" | r.data.status == "pending") {
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await new Promise(resolve => setTimeout(resolve, 100));
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r = await axios.get(r.data.href);
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}
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return r;
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}
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const getPositionAsObject = this.getStagePosition;
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const setPositionAsObject = this.setStagePosition;
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const service = {
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type: "_microscope-control",
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name: "OpenFlexure",
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@ -276,9 +290,7 @@ export default {
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async getImage() {
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// FIXME: handle nicely getImage() being called before snapImage()
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// Wait until the capture has completed and we can retrieve it
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service.lastSnapResponse = await pollUntilComplete(
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service.lastSnapResponse
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);
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service.lastSnapResponse = await pollAction(service.lastSnapResponse);
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let capture = service.lastSnapResponse.data.output;
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// TODO: check links.download.href exists and is JPEG
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let jpeg = await axios
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@ -299,35 +311,37 @@ export default {
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setPosition(z) {
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// The C api suggests this defaults to just Z, and can accept a "label" to
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// select the stage.
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return service.setXYZPosition({
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"z": z,
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"absolute": true,
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return setPositionAsObject({
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z: z,
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absolute: true
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});
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},
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async getPosition() {
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const pos = await service.getXYZPosition();
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return pos.z;
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const {z} = await getPositionAsObject();
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return z;
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},
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async setXYPosition(x, y) {
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return service.setXYZPosition({
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"x": x,
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"y": y,
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"absolute": true,
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return setPositionAsObject({
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x: x,
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y: y,
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absolute: true
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});
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},
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async getXYPosition() {
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const pos = await service.getXYZPosition();
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return [pos.x, pos.y];
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const {x, y} = await getPositionAsObject();
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return [x, y];
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},
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async getXYZPosition() {
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return axios
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.get(getPositionUri)
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.then(r => r.data)
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const {x, y, z} = await getPositionAsObject();
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return [x, y, z];
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},
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async setXYZPosition(payload) {
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return axios
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.post(moveActionUri, payload)
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.then(pollUntilComplete)
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async setXYZPosition(x, y, z) {
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return setPositionAsObject({
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x: x,
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y: y,
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z: z,
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absolute: true
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});
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}
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};
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this.imjoy.pm.registerService({ name: "openflexure" }, service);
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@ -463,6 +477,29 @@ export default {
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if (uri) {
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this.loadPlugin(uri);
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}
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} /*
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async getPosition() {
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const pos = await service.getXYZPosition();
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return pos.z;
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},
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async setXYPosition(x, y) {
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return service.setXYZPosition({
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"x": x,
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"y": y,
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"absolute": true,
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});
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},
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async getXYPosition() {
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const pos = await service.getXYZPosition();
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return [pos.x, pos.y];
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},*/,
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async getStagePosition() {
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return axios.get(this.getPositionUri).then(r => r.data);
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},
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async setStagePosition(payload) {
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return axios
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.post(this.moveActionUri, payload)
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.then(pollAction)
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}
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}
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};
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