Merge branch 'rwanda-feedback' into 'v3'

Hide background detect settings in an accordion

See merge request openflexure/openflexure-microscope-server!172

src/openflexure_microscope_server/things/auto_recentre_stage.py

@@ -61,7 +61,6 @@ class RecentringThing(Thing):
                 stage.position["z"] - height_min < dz / 5
                 or height_max - stage.position["z"] < dz / 5
             ):
-                print(heights)
                 attempts += 1
             else:
                 repeat = False
@@ -111,8 +110,6 @@ class RecentringThing(Thing):
             focused_pos[direction] = [list(stage.position.values())]
             moves = +1
 
-            print(centre)
-
             stage.move_absolute(x=centre[0], y=centre[1], z=centre[2])
             steps = 0
             all_heights = []

src/openflexure_microscope_server/things/settings_manager.py

@@ -102,6 +102,11 @@ class SettingsManager(Thing):
             self.thing_settings["microscope_id"] = str(uuid4())
         return UUID(self.thing_settings["microscope_id"])
 
+    @thing_property
+    def hostname(self) -> str:
+        """The hostname of the microscope, as reported by its operating system."""
+        return gethostname()
+
     @thing_action
     def get_things_state(self, metadata_getter: GetThingStates) -> Mapping:
         """Metadata summarising the current state of all Things in the server"""
@@ -119,7 +124,7 @@ class SettingsManager(Thing):
     @property
     def thing_state(self) -> Mapping:
         state = {
-            "hostname": gethostname(),
+            "hostname": self.hostname,
             "microscope-uuid": str(self.microscope_id),
         }
         metadata = self.external_metadata

src/openflexure_microscope_server/things/smart_scan.py

@@ -1,4 +1,5 @@
 import shutil
+import zipfile
 import threading
 from typing import Mapping, Optional
 import cv2
@@ -312,6 +313,9 @@ DOWNLOADABLE_SCAN_FILES = (
 class JPEGBlob(BlobOutput):
     media_type = "image/jpeg"
 
+class ZipBlob(BlobOutput):
+    media_type = "application/zip"
+
 class SmartScanThing(Thing):
     def __init__(self, path_to_openflexure_stitch: str):
         self._script = path_to_openflexure_stitch
@@ -425,6 +429,11 @@ class SmartScanThing(Thing):
 
             r = cam.grab_jpeg()
             arr = np.array(Image.open(r.open()))
+            if csm.image_resolution is None:
+                raise RuntimeError(
+                    "Camera-stage mapping is not calibrated. This is required before "
+                    "scans can be carried out."
+                )
             if list(arr.shape[:2]) != [int(i) for i in csm.image_resolution]:
                 logger.error(
                     f"Images are, by default, {arr.shape[:2]}, but the CSM was "
@@ -564,9 +573,9 @@ class SmartScanThing(Thing):
                     positions.append(loc[:2])
                     names.append(name)
 
+                    if not self.preview_stitch_running():
+                        self.preview_stitch_start(images_folder)
                     if self.stitch_automatically:
-                        if not self.preview_stitch_running():
-                            self.preview_stitch_start(images_folder)
                         if not self.correlate_running():
                             self.correlate_start(images_folder, overlap=overlap)
 
@@ -593,15 +602,17 @@ class SmartScanThing(Thing):
         except InvocationCancelledError:
             logger.error("Stopping scan because it was cancelled.")
         except NotEnoughFreeSpaceError as e:
-            logger.exception(
+            logger.error(
                 f"Stopping scan to avoid filling up the disk: {e}",
+                exc_info=e,
             )
             raise e
         except Exception as e:
-            logger.exception(
+            logger.error(
                 f"The scan stopped because of an error: {e}",
                 "We will attempt to stitch and archive the images acquired "
-                "so far."
+                "so far.",
+                exc_info=e,
             )
             raise e
         finally:
@@ -614,18 +625,13 @@ class SmartScanThing(Thing):
             logger.info("Waiting for background processes to finish...")
             self.preview_stitch_wait()
             self.correlate_wait()
-            logger.info("Stitching final image (may take some time)...")
             try:
                 if scan_folder and self.stitch_automatically:
+                    logger.info("Stitching final image (may take some time)...")
                     self.stitch_scan(logger, os.path.basename(scan_folder), overlap=overlap)
             except SubprocessError as e:
-                logger.exception(f"Stitching failed: {e}")
-            logger.info("Creating zip archive of images (may take some time)...")
-            if images_folder and os.path.isdir(images_folder):
-                shutil.make_archive(
-                    os.path.join(scan_folder, "images"), "zip", images_folder
-                )
-    
+                logger.error(f"Stitching failed: {e}", exc_info=e)
+
     @thing_property
     def max_range(self) -> int:
         """The maximum distance from the centre of the scan before we break"""
@@ -777,12 +783,17 @@ class SmartScanThing(Thing):
 
     @thing_property
     def latest_preview_stitch_time(self) -> Optional[datetime]:
-        """The modification time of the latest preview image"""
-        fpath = self.latest_preview_stitch_path
-        if not os.path.exists(fpath):
+        """The modification time of the latest preview image
+        
+        This will return `null` if there is no preview image to return.
+        """
+        try:
+            fpath = self.latest_preview_stitch_path
+            if os.path.exists(fpath):
+                return os.path.getmtime(fpath)
+        except IOError:
             return None
-        else:
-            return os.path.getmtime(fpath)
+        return None
         
     @fastapi_endpoint(
             "get",
@@ -868,4 +879,33 @@ class SmartScanThing(Thing):
         """Generate a stitched image based on stage position metadata"""
         images_folder = self.images_folder(scan_name=scan_name)
         self.run_subprocess(logger, [self._script, "--stitching_mode", "all", "--minimum_overlap", f"{overlap*0.9}", images_folder])
+    
+    @thing_action
+    def create_zip_of_scan(self, logger: InvocationLogger, scan_name: Optional[str]=None) -> ZipBlob:
+        """Generate a zip file that can be downloaded, with all the scan files in it."""
+        images_folder = self.images_folder(scan_name=scan_name)
+        scan_folder = self.scan_folder_path(scan_name=scan_name)
+        if scan_folder != os.path.dirname(images_folder) or os.path.basename(images_folder) != "images":
+            logger.error(
+                "There is a problem with filenames, the archive may be incorrect."
+                f"scan_folder: {scan_folder}, images_folder: {images_folder}."
+            )
+        if not os.path.isdir(images_folder):
+            raise FileNotFoundError(f"Tried to make a zip archive of {images_folder} but it does not exist.")
+        logger.info("Creating zip archive of images (may take some time)...")
+        shutil.make_archive(
+            os.path.join(scan_folder, "images"),
+            "zip",
+            scan_folder,
+            "images/",
+            logger=logger
+        )
+        zip_fname = os.path.join(scan_folder, "images.zip")
+        # Promote key files to the top level of the zip
+        with zipfile.ZipFile(zip_fname, mode="a") as zip:
+            for fname in ["stitched_from_stage.jpg", "stitched.jpg"]:
+                fpath = os.path.join(images_folder, fname)
+                if os.path.exists(fpath):
+                    zip.write(fpath, arcname=fname)
+        return ZipBlob.from_file(zip_fname)
 

webapp/src/App.vue

@@ -321,6 +321,13 @@ export default {
             );
           }
         }
+        try {
+          let hostname = await this.readThingProperty("settings", "hostname");
+          this.$store.commit("changeMicroscopeHostname", hostname);
+          document.title = `OpenFlexure Microscope: ${hostname}`;
+        } catch {
+          this.$store.commit("changeMicroscopeHostname", null);
+        }
         this.$store.commit("setConnected");
         this.$store.commit("setErrorMessage", null);
       } catch (error) {

webapp/src/components/tabContentComponents/aboutComponents/statusPane.vue

@@ -2,11 +2,23 @@
   <div class="host-input">
     <div v-if="$store.state.available">
       <div>
+        <div class="uk-margin-small-bottom">
+          <b>Microscope hostname:</b>
+          <br />
+          {{ $store.state.microscopeHostname }}
+        </div>
         <div class="uk-margin-small-bottom">
           <b>API origin:</b>
           <br />
           {{ $store.state.origin }}
         </div>
+        <task-submitter
+          v-if="flashLedUri"
+          :submit-url="flashLedUri"
+          submit-label="Flash Illumination"
+          :can-terminate="false"
+          :submit-data="{'dt': 0.25}"
+        />
       </div>
 
       <hr />
@@ -71,13 +83,18 @@
 
 <script>
 import axios from "axios";
+import taskSubmitter from '../../genericComponents/taskSubmitter.vue';
 
 export default {
+  components: { taskSubmitter },
   name: "StatusPane",
 
   computed: {
     things: function() {
       return this.$store.getters["wot/thingDescriptions"];
+    },
+    flashLedUri() {
+      return this.thingActionUrl("stage", "flash_led");
     }
   },
 

webapp/src/components/tabContentComponents/backgroundDetectComponents/paneBackgroundDetect.vue

@@ -4,6 +4,37 @@
       The background detect Thing seems to be missing or incompatible.
     </div>
     <div v-show="backendOK">
+      <ul uk-accordion="multiple: true">
+          <li>
+            <a class="uk-accordion-title" href="#">Settings</a>
+            <div class="uk-accordion-content">
+              <div class="uk-margin">
+                <propertyControl
+                  thing-name="background_detect"
+                  property-name="tolerance"
+                  label="Tolerance"
+                />
+              </div>
+              <div class="uk-margin">
+                <propertyControl
+                  thing-name="background_detect"
+                  property-name="fraction"
+                  label="Sample coverage required (%)"
+                />
+              </div>
+              <div class="uk-margin">
+                <taskSubmitter
+                  :submit-url="backgroundFractionUri"
+                  submit-label="Check coverage"
+                  :can-terminate="false"
+                  :poll-interval="0.1"
+                  @response="alertBackgroundFraction"
+                  @error="backgroundDetectError"
+                />
+              </div>
+            </div>
+          </li>
+        </ul>
       <div class="uk-margin">
         <taskSubmitter
           :submit-url="setBackgroundUri"
@@ -13,34 +44,10 @@
           @response="alertBackgroundSet"
         />
       </div>
-      <div class="uk-margin">
-        <propertyControl
-          thing-name="background_detect"
-          property-name="tolerance"
-          label="Tolerance"
-        />
-      </div>
-      <div class="uk-margin">
-        <propertyControl
-          thing-name="background_detect"
-          property-name="fraction"
-          label="Sample coverage required (%)"
-        />
-      </div>
-      <div class="uk-margin">
-        <taskSubmitter
-          :submit-url="backgroundFractionUri"
-          submit-label="Check current image"
-          :can-terminate="false"
-          :poll-interval="0.1"
-          @response="alertBackgroundFraction"
-          @error="backgroundDetectError"
-        />
-      </div>
       <div class="uk-margin">
         <taskSubmitter
           :submit-url="labelImageUri"
-          submit-label="Label current image"
+          submit-label="Check current image"
           :can-terminate="false"
           :poll-interval="0.1"
           @response="alertImageLabel"

webapp/src/components/tabContentComponents/scanListContent.vue

@@ -42,16 +42,27 @@
           <div class="uk-card">
             <div class="uk-card-body">
               <h3 class="uk-card-title">{{ item.name }}</h3>
-              <a
-                :href="`${scansUri}/${item.name}/images.zip`"
-                :download="`${item.name}_images.zip`"
-                class="uk-button uk-button-default"
-              >
-                Download images
-              </a>
+              <task-submitter
+                submit-label="Download ZIP"
+                :can-terminate="false"
+                :submit-data="{'scan_name': item.name}"
+                :button-primary="true"
+                :submit-url="createZipOfScanUri"
+                @response="downloadZipFile"
+                @error="modalError"
+              />
               <button class="uk-button" @click="deleteScan(item.name)">
                 Delete
               </button>
+              <task-submitter
+                submit-label="Stitch Images"
+                :can-terminate="false"
+                :submit-data="{'scan_name': item.name}"
+                :button-primary="false"
+                :submit-url="stitchUri"
+                :modal-progress="true"
+                @error="modalError"
+              />
               <ul>
                 <li>{{ item.number_of_images }} images</li>
                 <li>created {{ formatDate(item.created) }}</li>
@@ -73,9 +84,11 @@
 
 <script>
 import axios from "axios";
+import taskSubmitter from '../genericComponents/taskSubmitter.vue';
 
 // Export main app
 export default {
+  components: { taskSubmitter },
   name: "ScanListContent",
 
   data: function() {
@@ -92,6 +105,12 @@ export default {
         "readproperty",
         true
       );
+    },
+    createZipOfScanUri() {
+      return this.thingActionUrl("smart_scan",  "create_zip_of_scan");
+    },
+    stitchUri() {
+      return this.thingActionUrl("smart_scan",  "stitch_scan");
     }
   },
 
@@ -186,6 +205,17 @@ export default {
         // if the confirmation was cancelled, it's rejected with null error
         if (e) this.modalError(e);
       }
+    },
+    async downloadZipFile(response) {
+      const scan_name = response.input.scan_name;
+      const filename = `${scan_name}_images.zip`
+      const url = response.output.href;
+      const link = document.createElement("a");
+      link.href = url;
+      link.setAttribute("download", filename);
+      console.log(link);
+      document.body.appendChild(link);
+      link.click();
     }
   }
 };

webapp/src/main.js

@@ -71,12 +71,12 @@ Vue.mixin({
       }
       await axios.put(url, value);
     },
-    thingActionUrl(thing, action) {
+    thingActionUrl(thing, action, allow_missing=false) {
       let url = this.$store.getters["wot/thingActionUrl"](
         thing,
         action,
         "invokeaction",
-        false
+        allow_missing
       );
       return url;
     },

webapp/src/store.js

@@ -91,7 +91,8 @@ export default new Vuex.Store({
     imjoyEnabled: false,
     galleryEnabled: true,
     appTheme: "system",
-    activeStreams: {}
+    activeStreams: {},
+    microscopeHostname: ""
   },
 
   mutations: {
@@ -144,6 +145,9 @@ export default new Vuex.Store({
     },
     removeStream(state, id) {
       state.activeStreams[id] = false;
+    },
+    changeMicroscopeHostname(state, value) {
+      state.microscopeHostname = value;
     }
   },
 

webapp/src/wot-client.js

@@ -120,6 +120,7 @@ export const wotStoreModule = {
 
 export function findFormHref(affordance, op) {
   // Find the form in the affordance that matches the given operation type
+  if (affordance == undefined) return undefined;
   let forms = affordance.forms;
   let matchingForm = forms.find(f => f.op == op || f.op.includes(op));
   if (matchingForm == undefined) return undefined;