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>

openflexure_microscope/api/static/public/OpenFlexureScriptEditor.imjoy.html

@@ -0,0 +1,131 @@
+<config lang="json">
+{
+  "name": "Script Editor",
+  "type": "web-worker",
+  "tags": [],
+  "ui": "",
+  "version": "0.1.0",
+  "cover": "",
+  "description": "A Script Editor for Controlling OpenFlexure Microscope with ImJoy",
+  "icon": "extension",
+  "inputs": null,
+  "outputs": null,
+  "api_version": "0.1.8",
+  "env": "",
+  "permissions": [],
+  "requirements": [],
+  "dependencies": []
+}
+</config>
+
+<script lang="javascript">
+class ImJoyPlugin {
+  async setup() {
+    api.log('initialized')
+  }
+
+  async run(ctx) {
+    let pluginInEditor, stopped, editorWindow;
+    const config = {lang: 'javascript'}
+    config.templates = [
+        {
+          name: "New",
+          url: null,
+          lang: 'javascript',
+        },
+        {
+          name: "Snap Image Template",
+          url: "./OpenFlexureSnapImageTemplate.imjoy.html",
+          lang: "html",
+        }
+      ]
+    config.ui_elements = {
+      save: {
+          _rintf: true,
+          type: 'button',
+          label: "Save",
+          visible: false,
+          icon: "content-save",
+          callback(content) {
+              console.log(content)
+          }
+      },
+      run: {
+          _rintf: true,
+          type: 'button',
+          label: "Run",
+          icon: "play",
+          visible: true,
+          shortcut: 'Shift-Enter',
+          async callback(content) {
+              try {
+                  editorWindow.setLoader(true);
+                  editorWindow.updateUIElement('stop', {
+                      visible: true
+                  })
+                  api.showProgress(0);
+                  pluginInEditor = await api.getPlugin({src: content, hot_reloading: true})
+             
+                  if (stopped) {
+                      pluginInEditor = null;
+                      return;
+                  }
+                  if (pluginInEditor && pluginInEditor.run) {
+                      return await pluginInEditor.run({
+                          config: {},
+                          data: {}
+                      });
+                  }
+                  if (stopped) {
+                      pluginInEditor = null;
+                      return;
+                  }
+              } catch (e) {
+                  api.showMessage("Failed to load plugin, error: " + e.toString());
+              } finally {
+                  editorWindow.updateUIElement('stop', {
+                      visible: false
+                  })
+                  editorWindow.setLoader(false);
+                  api.showProgress(100);
+              }
+          }
+      },
+      stop: {
+          _rintf: true,
+          type: 'button',
+          label: "Stop",
+          style: "color: #ff0080cf;",
+          icon: "stop",
+          visible: false,
+          async callback() {
+              stopped = true;
+              await editorWindow.setLoader(false);
+              await editorWindow.updateUIElement('stop', {
+                  visible: false
+              })
+          }
+      },
+      export: {
+          _rintf: true,
+          type: 'button',
+          label: "Export",
+          icon: "file-download-outline",
+          visible: true,
+          async callback(content) {
+            const fileName = (pluginInEditor && pluginInEditor.config.name && pluginInEditor.config.name + '.imjoy.html') || config.name + '.imjoy.html' || "myPlugin.imjoy.html";
+            await api.exportFile(content, fileName);
+          }
+      }
+    }
+    editorWindow = await api.createWindow({
+        src: 'https://if.imjoy.io',
+        name: (ctx && ctx.data && ctx.data.name) ||'OpenFlexure Script Editor',
+        config,
+        data: {code: ctx && ctx.data && ctx.data.code}
+    })
+  }
+}
+
+api.export(new ImJoyPlugin())
+</script>

openflexure_microscope/api/static/public/OpenFlexureSnapImageTemplate.imjoy.html

@@ -0,0 +1,43 @@
+<docs>
+[TODO: write documentation for this plugin.]
+</docs>
+
+<config lang="json">
+{
+  "name": "OpenFlexureSnapImageTemplate",
+  "type": "web-worker",
+  "tags": [],
+  "ui": "",
+  "version": "0.1.0",
+  "cover": "",
+  "description": "[TODO: describe this plugin with one sentence.]",
+  "icon": "extension",
+  "inputs": null,
+  "outputs": null,
+  "api_version": "0.1.8",
+  "env": "",
+  "permissions": [],
+  "requirements": [],
+  "dependencies": []
+}
+</config>
+
+<script lang="javascript">
+class ImJoyPlugin {
+  async setup() {
+    api.log('initialized')
+  }
+
+  async run(ctx) {
+    // get a list of service
+    const services = await api.getServices({name: "OpenFlexure"});
+    // get the first service
+    const ofm = services[0];
+    // snap an image
+    await ofm.snapImage();
+    console.log("snapped an image");
+  }
+}
+
+api.export(new ImJoyPlugin())
+</script>

openflexure_microscope/api/static/public/OpenFlexureTestMoveStage.imjoy.html

@@ -0,0 +1,48 @@
+<docs>
+[TODO: write documentation for this plugin.]
+</docs>
+
+<config lang="json">
+{
+    "name": "Test OFM Stage",
+    "type": "web-worker",
+    "tags": [],
+    "ui": "",
+    "version": "0.1.0",
+    "cover": "",
+    "description": "Move the OFM stage to test the API works",
+    "icon": "extension",
+    "inputs": null,
+    "outputs": null,
+    "api_version": "0.1.8",
+    "env": "",
+    "permissions": [],
+    "requirements": [],
+    "dependencies": []
+}
+</config>
+
+<script lang="javascript">
+class ImJoyPlugin {
+    async setup() {
+    api.log('initialized')
+    }
+
+    async run(ctx) {
+    // get a list of service
+    const services = await api.getServices({name: "OpenFlexure"});
+    // get the first service
+    const ofm = services[0];
+    // snap an image
+    const start = await ofm.getXYZPosition();
+    console.log(`Starting position: ${start}`);
+    // move the Z axis up and down
+    await ofm.setPosition(start[2] + 100);
+    console.log(`Moved Z to ${await ofm.getPosition()}`);
+    await ofm.setPosition(start[2]);
+    console.log(`Moved Z to ${await ofm.getPosition()}`);
+    }
+}
+
+api.export(new ImJoyPlugin())
+</script>

openflexure_microscope/api/static/src/components/tabContentComponents/imjoyContent.vue

@@ -98,6 +98,21 @@ import * as imjoyCore from "imjoy-core";
 import axios from "axios";
 import UIkit from "uikit";
 
+// TODO: move this to a module or something...
+async function pollAction(response) {
+  // Poll an action until its status is completed
+  // TODO: raise an error if it fails or is cancelled
+  // For ease, this accepts and returns a response object from
+  // axios.get
+  // FIXME: this could be an infinite loop if the task is cancelled/errored
+  let r = response;
+  while ((r.data.status == "running") | (r.data.status == "pending")) {
+    await new Promise(resolve => setTimeout(resolve, 100));
+    r = await axios.get(r.data.href);
+  }
+  return r;
+}
+
 export default {
   name: "ImJoyContent",
 
@@ -123,6 +138,9 @@ export default {
     },
     moveActionUri: function() {
       return `${this.$store.getters.baseUri}/api/v2/actions/stage/move`;
+    },
+    baseUri: function() {
+      return this.$store.getters.baseUri;
     }
   },
   mounted() {
@@ -168,7 +186,7 @@ export default {
       }
     });
 
-    imjoy.start({ workspace: "default" }).then(() => {
+    imjoy.start({ workspace: "default" }).then(async () => {
       console.log("ImJoy started");
       imjoy.event_bus.on("add_window", w => {
         this.addWindow(w);
@@ -176,8 +194,16 @@ export default {
       this.setupMicroscopeAPI();
       this.setupViewers();
       // load the script editor for openflexure
-      this.loadPlugin(
+      await this.loadPlugin(
-        "https://gist.githubusercontent.com/oeway/7a9dcb49c51b1f99b2c3619f470fe35c/raw/OpenFlexureScriptEditor.imjoy.html"
+        `${window.location.origin}/OpenFlexureScriptEditor.imjoy.html`
+      );
+      // Load the snap image template
+      await this.loadPlugin(
+        `${window.location.origin}/OpenFlexureSnapImageTemplate.imjoy.html`
+      );
+      // Load the snap image template
+      await this.loadPlugin(
+        `${window.location.origin}/OpenFlexureTestMoveStage.imjoy.html`
       );
       this.setupPluginEngine();
     });
@@ -232,22 +258,10 @@ export default {
       // See here: https://valelab4.ucsf.edu/~MM/doc/MMCore/html/class_c_m_m_core.html
       const snapshotUri = this.snapshotStreamUri;
       const captureActionUri = this.captureActionUri;
-      const getPositionUri = this.getPositionUri;
-      const moveActionUri = this.moveActionUri;
       const modalError = this.modalError;
-      async function pollUntilComplete(response) {
+      const getPositionAsObject = this.getStagePosition;
-        // Poll an action until its status is completed
+      const setPositionAsObject = this.setStagePosition;
-        // TODO: raise an error if it fails or is cancelled
+
-        // For ease, this accepts and returns a response object from
-        // axios.get
-        // FIXME: this could be an infinite loop if the task is cancelled/errored
-        let r = response;
-        while (r.data.status == "running" | r.data.status == "pending") {
-          await new Promise(resolve => setTimeout(resolve, 100));
-          r = await axios.get(r.data.href);
-        }
-        return r;
-      }
       const service = {
         type: "_microscope-control",
         name: "OpenFlexure",
@@ -276,9 +290,7 @@ export default {
         async getImage() {
           // FIXME: handle nicely getImage() being called before snapImage()
           // Wait until the capture has completed and we can retrieve it
-          service.lastSnapResponse = await pollUntilComplete(
+          service.lastSnapResponse = await pollAction(service.lastSnapResponse);
-            service.lastSnapResponse
-          );
           let capture = service.lastSnapResponse.data.output;
           // TODO: check links.download.href exists and is JPEG
           let jpeg = await axios
@@ -299,35 +311,37 @@ export default {
         setPosition(z) {
           // The C api suggests this defaults to just Z, and can accept a "label" to
           // select the stage.
-          return service.setXYZPosition({
+          return setPositionAsObject({
-            "z": z,
+            z: z,
-            "absolute": true,
+            absolute: true
           });
         },
         async getPosition() {
-          const pos = await service.getXYZPosition();
+          const {z} = await getPositionAsObject();
-          return pos.z;
+          return z;
         },
         async setXYPosition(x, y) {
-          return service.setXYZPosition({
+          return setPositionAsObject({
-            "x": x,
+            x: x,
-            "y": y,
+            y: y,
-            "absolute": true,
+            absolute: true
           });
         },
         async getXYPosition() {
-          const pos = await service.getXYZPosition();
+          const {x, y} = await getPositionAsObject();
-          return [pos.x, pos.y];
+          return [x, y];
         },
         async getXYZPosition() {
-          return axios
+          const {x, y, z} = await getPositionAsObject();
-            .get(getPositionUri)
+          return [x, y, z];
-            .then(r => r.data)
         },
-        async setXYZPosition(payload) {
+        async setXYZPosition(x, y, z) {
-          return axios
+          return setPositionAsObject({
-            .post(moveActionUri, payload)
+            x: x,
-            .then(pollUntilComplete)
+            y: y,
+            z: z,
+            absolute: true
+          });
         }
       };
       this.imjoy.pm.registerService({ name: "openflexure" }, service);
@@ -463,6 +477,29 @@ export default {
       if (uri) {
         this.loadPlugin(uri);
       }
+    } /*
+    async getPosition() {
+          const pos = await service.getXYZPosition();
+          return pos.z;
+        },
+        async setXYPosition(x, y) {
+          return service.setXYZPosition({
+            "x": x,
+            "y": y,
+            "absolute": true,
+          });
+        },
+        async getXYPosition() {
+          const pos = await service.getXYZPosition();
+          return [pos.x, pos.y];
+        },*/,
+    async getStagePosition() {
+      return axios.get(this.getPositionUri).then(r => r.data);
+    },
+    async setStagePosition(payload) {
+      return axios
+        .post(this.moveActionUri, payload)
+        .then(pollAction)
     }
   }
 };