Merge branch 'better-settings' into 'master'

Better settings

Closes #185 and #156

See merge request openflexure/openflexure-microscope-server!95

openflexure_microscope/api/static/src/assets/less/theme.less

@@ -170,6 +170,12 @@
 /* UIkit modifiers
  ========================================================================== */
 
+h4, .uk-h4 {
+    line-height: normal;
+    font-size: 20px;
+    margin: 0;
+}
+
 /*
  * Navbar
  */

openflexure_microscope/api/static/src/components/appContent.vue

@@ -17,7 +17,7 @@
         class="uk-flex uk-flex-column uk-padding-remove uk-width-auto uk-height-1-1 uk-text-center"
       >
         <!-- For each top tab -->
-        <template v-for="(item, index) in enabledTopTabs">
+        <template v-for="(item, index) in topTabs">
           <!-- Render the tab icon -->
           <tabIcon
             :id="item.id + '-tab-icon'"
@@ -34,8 +34,6 @@
           <hr v-if="item.divide" :key="'tab-divider-' + index" />
         </template>
 
-        <hr id="extension-tab-divider" />
-
         <!-- For each plugin tab -->
         <tabIcon
           v-for="plugin in pluginsGuiList"
@@ -79,7 +77,7 @@
     >
       <!-- For each top tab -->
       <tabContent
-        v-for="item in enabledTopTabs"
+        v-for="item in topTabs"
         :id="item.id + '-tab-content'"
         :key="item.id + '-tab-content'"
         :tab-i-d="item.id"
@@ -212,18 +210,6 @@ export default {
   },
 
   computed: {
-    enabledTopTabs: function() {
-      var enabledTabs = this.topTabs;
-      if (this.$store.state.IHIEnabled) {
-        enabledTabs.push({
-          id: "slidescan",
-          icon: "settings_overscan",
-          component: slideScanContent
-        });
-      }
-      return enabledTabs;
-    },
-
     pluginsUri: function() {
       return `${this.$store.getters.baseUri}/api/v2/extensions`;
     },
@@ -241,7 +227,7 @@ export default {
 
     tabOrder: function() {
       var ind = [];
-      for (const tab of this.enabledTopTabs) {
+      for (const tab of this.topTabs) {
         ind.push(tab.id);
       }
       for (const plugin of this.pluginsGuiList) {
@@ -270,12 +256,24 @@ export default {
         this.$store.commit("changeAutoGpuPreview", true);
         this.$store.commit("changeTrackWindow", true);
       }
+      // Update top tabs
+      this.updateTopTabs(this.$store.state.IHIEnabled);
       // Update plugins
       this.updatePlugins().then(() => {
         // Start initialisation modals
         this.startModals();
       });
     }
+
+    // Watch for host 'ready', then update status
+    this.unwatchStoreFunction = this.$store.watch(
+      state => {
+        return state.IHIEnabled;
+      },
+      IHIEnabled => {
+        this.updateTopTabs(IHIEnabled);
+      }
+    );
   },
 
   mounted() {
@@ -302,6 +300,19 @@ export default {
   },
 
   methods: {
+    updateTopTabs: function(IHIEnabled) {
+      if (IHIEnabled) {
+        this.topTabs.push({
+          id: "slidescan",
+          icon: "settings_overscan",
+          component: slideScanContent,
+          divide: true
+        });
+      } else {
+        // If the connection is now disconnected, empty capture list
+        this.topTabs = this.topTabs.filter(tab => tab.id != "slidescan");
+      }
+    },
     updatePlugins: function() {
       return axios
         .get(this.pluginsUri)

openflexure_microscope/api/static/src/components/tabContentComponents/settingsComponents/CSMSettingsComponents/CSMCalibrationSettings.vue

@@ -1,32 +1,30 @@
 <template>
   <div id="CSMCalibrationSettings">
-    <form @submit.prevent="applyConfigRequest">
+    <!--Show auto calibrate if default plugin is enabled-->
-      <!--Show auto calibrate if default plugin is enabled-->
+    <div v-if="'calibrate_xy' in recalibrationLinks" class="uk-margin-small">
-      <div v-if="'calibrate_xy' in recalibrationLinks" class="uk-margin-small">
+      <taskSubmitter
-        <taskSubmitter
+        :button-primary="true"
-          :button-primary="true"
+        :can-terminate="false"
-          :can-terminate="false"
+        :requires-confirmation="true"
-          :requires-confirmation="true"
+        :confirmation-message="
-          :confirmation-message="
+          'Start recalibration of the stage to the camera? This may take a while, and the microscope will be locked during this time.'
-            'Start recalibration of the stage to the camera? This may take a while, and the microscope will be locked during this time.'
+        "
-          "
+        :submit-url="recalibrationLinks.calibrate_xy.href"
-          :submit-url="recalibrationLinks.calibrate_xy.href"
+        :submit-label="'Auto-Calibrate using camera'"
-          :submit-label="'Auto-Calibrate using camera'"
+        @response="onRecalibrateResponse"
-          @response="onRecalibrateResponse"
+        @error="onRecalibrateError"
-          @error="onRecalibrateError"
-        >
-        </taskSubmitter>
-      </div>
-      <button
-        v-if="'get_calibration' in recalibrationLinks"
-        v-show="dataAvailable && showExtraSettings"
-        type="button"
-        class="uk-button uk-button-default uk-width-1-1"
-        @click="getCalibrationData()"
       >
-        Download calibration data
+      </taskSubmitter>
-      </button>
+    </div>
-    </form>
+    <button
+      v-if="'get_calibration' in recalibrationLinks"
+      v-show="dataAvailable && showExtraSettings"
+      type="button"
+      class="uk-button uk-button-default uk-width-1-1"
+      @click="getCalibrationData()"
+    >
+      Download calibration data
+    </button>
   </div>
 </template>
 

openflexure_microscope/api/static/src/components/tabContentComponents/settingsComponents/cameraSettings.vue

@@ -1,31 +1,32 @@
 <template>
-  <div v-if="settings" id="cameraSettings">
+  <div id="cameraSettings">
     <div class="uk-grid uk-grid-divider uk-child-width-expand" uk-grid>
       <div class="uk-width-large">
         <h3>Manual camera settings</h3>
-        <form @submit.prevent="applyConfigRequest">
+        <form @submit.prevent="applySettingsRequest">
-          <div v-if="settings.picamera">
+          <div class="uk-margin-small-bottom">
+            <h4>Raspberry Pi Camera</h4>
             <!--PiCamera settings block-->
-            <div v-if="settings.picamera.shutter_speed !== undefined">
+            <div v-if="picamera.shutter_speed !== undefined">
               <label class="uk-form-label" for="form-stacked-text"
                 >Exposure time</label
               >
               <div class="uk-form-controls">
                 <input
-                  v-model="settings.picamera.shutter_speed"
+                  v-model="picamera.shutter_speed"
                   class="uk-input uk-form-small"
                   type="number"
                 />
               </div>
             </div>
 
-            <div v-if="settings.picamera.analog_gain !== undefined">
+            <div v-if="picamera.analog_gain !== undefined">
               <label class="uk-form-label" for="form-stacked-text"
                 >Analogue gain</label
               >
               <div class="uk-form-controls">
                 <input
-                  v-model="settings.picamera.analog_gain"
+                  v-model="picamera.analog_gain"
                   class="uk-input uk-form-small"
                   type="number"
                   step="0.000001"
@@ -33,13 +34,13 @@
               </div>
             </div>
 
-            <div v-if="settings.picamera.digital_gain !== undefined">
+            <div v-if="picamera.digital_gain !== undefined">
               <label class="uk-form-label" for="form-stacked-text"
                 >Digital gain</label
               >
               <div class="uk-form-controls">
                 <input
-                  v-model="settings.picamera.digital_gain"
+                  v-model="picamera.digital_gain"
                   class="uk-input uk-form-small"
                   type="number"
                   step="0.000001"
@@ -48,6 +49,40 @@
             </div>
           </div>
 
+          <div class="uk-margin-small-bottom">
+            <h4>Image quality</h4>
+
+            <div class="uk-child-width-1-2" uk-grid>
+              <div v-if="mjpeg_quality !== undefined">
+                <label class="uk-form-label" for="form-stacked-text"
+                  >Web stream quality (%)</label
+                >
+                <div class="uk-form-controls">
+                  <input
+                    v-model="mjpeg_quality"
+                    class="uk-input uk-form-small"
+                    type="number"
+                    step="1"
+                  />
+                </div>
+              </div>
+
+              <div v-if="jpeg_quality !== undefined">
+                <label class="uk-form-label" for="form-stacked-text"
+                  >JPEG capture quality (%)</label
+                >
+                <div class="uk-form-controls">
+                  <input
+                    v-model="jpeg_quality"
+                    class="uk-input uk-form-small"
+                    type="number"
+                    step="1"
+                  />
+                </div>
+              </div>
+            </div>
+          </div>
+
           <button
             type="submit"
             class="uk-button uk-button-primary uk-margin-small uk-width-1-1"
@@ -83,7 +118,13 @@ export default {
 
   data: function() {
     return {
-      settings: {}
+      picamera: {
+        shutter_speed: undefined,
+        analog_gain: undefined,
+        digital_gain: undefined
+      },
+      mjpeg_quality: undefined,
+      jpeg_quality: undefined
     };
   },
 
@@ -102,24 +143,37 @@ export default {
       axios
         .get(this.settingsUri)
         .then(response => {
-          this.settings = response.data.camera;
+          const cameraSettings = response.data.camera;
+          // Get base camera settings
+          this.mjpeg_quality = cameraSettings.mjpeg_quality;
+          this.jpeg_quality = cameraSettings.jpeg_quality;
+          // Get Pi Camera settings if they exist
+          if (cameraSettings.picamera) {
+            this.picamera.analog_gain = cameraSettings.picamera.analog_gain;
+            this.picamera.digital_gain = cameraSettings.picamera.digital_gain;
+            this.picamera.shutter_speed = cameraSettings.picamera.shutter_speed;
+          }
         })
         .catch(error => {
           this.modalError(error); // Let mixin handle error
         });
     },
 
-    applyConfigRequest: function() {
+    applySettingsRequest: function() {
+      // We have to use parseInt/parseFloat because JS sometimes seems to
+      // make the numbers be strings... TypeScript would solve this...
       var payload = {
         camera: {
+          mjpeg_quality: parseInt(this.mjpeg_quality),
+          jpeg_quality: parseInt(this.jpeg_quality),
           picamera: {
-            shutter_speed: this.settings.picamera.shutter_speed,
+            shutter_speed: parseFloat(this.picamera.shutter_speed),
-            analog_gain: this.settings.picamera.analog_gain,
+            analog_gain: parseFloat(this.picamera.analog_gain),
-            digital_gain: this.settings.picamera.digital_gain
+            digital_gain: parseFloat(this.picamera.digital_gain)
           }
         }
       };
-
+      console.log(payload);
       // Send request
       axios
         .put(this.settingsUri, payload)

openflexure_microscope/api/static/src/components/tabContentComponents/settingsComponents/microscopeSettings.vue

@@ -1,46 +1,6 @@
 <template>
   <div v-if="settings" id="microscopeSettings" class="uk-width-large">
-    <form @submit.prevent="applyConfigRequest">
+    <form @submit.prevent="applySettingsRequest">
-      <label class="uk-form-label" for="form-stacked-text"
-        >Backlash compensation</label
-      >
-      <div class="uk-grid-small uk-child-width-1-3" uk-grid>
-        <div>
-          <label class="uk-form-label" for="form-stacked-text">x</label>
-          <div class="uk-form-controls">
-            <input
-              v-model="settings.stage.backlash.x"
-              class="uk-input uk-form-small"
-              type="number"
-            />
-          </div>
-        </div>
-
-        <div>
-          <label class="uk-form-label" for="form-stacked-text">y</label>
-          <div class="uk-form-controls">
-            <input
-              v-model="settings.stage.backlash.y"
-              class="uk-input uk-form-small"
-              type="number"
-            />
-          </div>
-        </div>
-
-        <div>
-          <label class="uk-form-label" for="form-stacked-text">z</label>
-          <div class="uk-form-controls">
-            <input
-              v-model="settings.stage.backlash.z"
-              class="uk-input uk-form-small"
-              type="number"
-            />
-          </div>
-        </div>
-      </div>
-
-      <br />
-
       <div>
         <label class="uk-form-label" for="form-stacked-text"
           >Microscope name</label
@@ -57,7 +17,7 @@
 
       <button
         type="submit"
-        class="uk-button uk-button-primary uk-form-small uk-float-right uk-margin-small uk-width-1-1"
+        class="uk-button uk-button-primary uk-margin-small uk-width-1-1"
       >
         Apply Settings
       </button>
@@ -100,12 +60,9 @@ export default {
         });
     },
 
-    applyConfigRequest: function() {
+    applySettingsRequest: function() {
       var payload = {
-        name: this.settings.name,
+        name: this.settings.name
-        stage: {
-          backlash: this.settings.stage.backlash
-        }
       };
 
       // Send request to update config

openflexure_microscope/api/static/src/components/tabContentComponents/settingsComponents/stageSettings.vue

@@ -1,31 +1,96 @@
 <template>
   <div id="stageSettings" class="uk-width-large">
-    <div>
+    <div v-if="stageType === 'MissingStage'" class="uk-text-danger">
+      <b>No stage connected</b>
+    </div>
+    <div v-else>
       <h3>Stage settings</h3>
-      <p>
+      <form @submit.prevent="setStageType">
-        <label class="uk-form-label">
+        <div class="uk-margin-small-bottom">
-          Stage geometry
+          <h4>Stage geometry</h4>
-          <div v-if="stageType != 'MissingStage'">
+          <select v-model="stageType" class="uk-select uk-margin-small-top">
-            <form @submit.prevent="setStageType">
+            <option value="SangaStage">SangaStage (Standard)</option>
-              <div class="uk-margin-small">
+            <option value="SangaDeltaStage"> SangaStage (Delta)</option>
-                <select v-model="stageType" class="uk-select">
+          </select>
-                  <option value="SangaStage">SangaStage (Standard)</option>
+
-                  <option value="SangaDeltaStage"> SangaStage (Delta)</option>
+          <button
-                </select>
+            type="submit"
+            class="uk-button uk-button-primary uk-margin-small uk-width-1-1"
+          >
+            Change stage geometry
+          </button>
+        </div>
+      </form>
+
+      <form @submit.prevent="applySettingsRequest">
+        <div class="uk-margin-small-bottom">
+          <h4>Backlash compensation</h4>
+          <p class="uk-margin-remove">
+            Backlash compentation causes movements to overshoot by that number
+            of motor steps, reducing the effect of mechanical backlash.
+          </p>
+          <div
+            class="uk-grid-small uk-child-width-1-3 uk-margin-small-bottom"
+            uk-grid
+          >
+            <div>
+              <label class="uk-form-label" for="form-stacked-text">x</label>
+              <div class="uk-form-controls">
+                <input
+                  v-model="backlash.x"
+                  class="uk-input uk-form-small"
+                  type="number"
+                />
               </div>
-              <div>
+            </div>
-                <button
+
-                  type="submit"
+            <div>
-                  class="uk-button uk-button-primary uk-width-1-1"
+              <label class="uk-form-label" for="form-stacked-text">y</label>
-                >
+              <div class="uk-form-controls">
-                  Change stage geometry
+                <input
-                </button>
+                  v-model="backlash.y"
+                  class="uk-input uk-form-small"
+                  type="number"
+                />
               </div>
-            </form>
+            </div>
+
+            <div>
+              <label class="uk-form-label" for="form-stacked-text">z</label>
+              <div class="uk-form-controls">
+                <input
+                  v-model="backlash.z"
+                  class="uk-input uk-form-small"
+                  type="number"
+                />
+              </div>
+            </div>
           </div>
-          <div v-else class="uk-text-danger"><b>No stage connected</b></div>
+
-        </label>
+          <h4>Settle time</h4>
-      </p>
+          <div v-if="settle_time !== undefined">
+            <p class="uk-margin-small-bottom">
+              When moving or scanning, captures will be delayed by the settle
+              time (in seconds) to reduce motion blur.
+            </p>
+            <div class="uk-form-controls">
+              <input
+                v-model="settle_time"
+                class="uk-input uk-form-small"
+                type="number"
+                step="0.1"
+              />
+            </div>
+          </div>
+
+          <button
+            type="submit"
+            class="uk-button uk-button-primary uk-margin-small uk-width-1-1"
+          >
+            Apply Settings
+          </button>
+        </div>
+      </form>
     </div>
   </div>
 </template>
@@ -40,11 +105,20 @@ export default {
 
   data: function() {
     return {
-      stageType: "MissingStage"
+      stageType: "MissingStage",
+      backlash: {
+        x: undefined,
+        y: undefined,
+        z: undefined
+      },
+      settle_time: undefined
     };
   },
 
   computed: {
+    settingsUri: function() {
+      return `${this.$store.getters.baseUri}/api/v2/instrument/settings`;
+    },
     stageTypeUri: function() {
       return `${this.$store.getters.baseUri}/api/v2/instrument/stage/type`;
     }
@@ -52,9 +126,42 @@ export default {
 
   mounted() {
     this.getStageType();
+    this.updateSettings();
   },
 
   methods: {
+    updateSettings: function() {
+      axios
+        .get(this.settingsUri)
+        .then(response => {
+          const stageSettings = response.data.stage;
+          this.backlash.x = stageSettings.backlash.x;
+          this.backlash.y = stageSettings.backlash.y;
+          this.backlash.z = stageSettings.backlash.z;
+          this.settle_time = stageSettings.settle_time;
+        })
+        .catch(error => {
+          this.modalError(error); // Let mixin handle error
+        });
+    },
+    applySettingsRequest: function() {
+      var payload = {
+        stage: {
+          backlash: this.backlash
+        }
+      };
+      // Send request to update settings
+      axios
+        .put(this.settingsUri, payload)
+        .then(() => {
+          // Update local settings
+          this.updateSettings();
+          this.modalNotify("Stage settings applied.");
+        })
+        .catch(error => {
+          this.modalError(error); // Let mixin handle error
+        });
+    },
     getStageType: function() {
       axios
         .get(this.stageTypeUri)