Merge branch 'lst-image' into 'master'

Added interface to get LST as a PNG image

See merge request openflexure/openflexure-microscope-server!87

openflexure_microscope/api/app.py

@@ -29,10 +29,10 @@ from labthings import create_app
 from labthings.extensions import find_extensions
 from labthings.views import View
 
-from openflexure_microscope.microscope import Microscope
 from openflexure_microscope.api.utilities import init_default_extensions, list_routes
 from openflexure_microscope.api.v2 import views
 from openflexure_microscope.json import JSONEncoder
+from openflexure_microscope.microscope import Microscope
 from openflexure_microscope.paths import (
     OPENFLEXURE_EXTENSIONS_PATH,
     OPENFLEXURE_VAR_PATH,
@@ -135,6 +135,9 @@ labthing.add_root_link(views.ConfigurationProperty, "instrumentConfiguration")
 # Attach stage resources
 labthing.add_view(views.StageTypeProperty, "/instrument/stage/type")
 
+# Attach camera resources
+labthing.add_view(views.LSTImageProperty, "/instrument/camera/lst")
+
 # Attach streams resources
 labthing.add_view(views.MjpegStream, "/streams/mjpeg")
 labthing.add_view(views.SnapshotStream, "/streams/snapshot")

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

@@ -1,6 +1,18 @@
 <template>
-  <div id="CSMSettings">
+  <div
-    <CSMCalibrationSettings />
+    id="CSMSettings"
+    class="uk-grid uk-grid-divider uk-child-width-expand"
+    uk-grid
+  >
+    <div class="uk-width-large">
+      <h3>Camera/stage mapping</h3>
+      <p>
+        Camera/stage mapping allows the stage to move relative to the camera
+        view. This enables functions like click-to-move, and more precise tile
+        scans.
+      </p>
+      <CSMCalibrationSettings />
+    </div>
     <div id="mini-stream">
       <miniStreamDisplay />
     </div>
@@ -147,7 +159,8 @@ export default {
   margin-right: auto;
 }
 #mini-stream {
-  width: 500px;
+  min-width: 300px;
+  max-width: 600px;
   text-align: center;
   margin-left: auto;
   margin-right: auto;

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

@@ -167,11 +167,4 @@ export default {
   margin-left: auto;
   margin-right: auto;
 }
-#mini-stream {
-  width: 500px;
-  text-align: center;
-  margin-left: auto;
-  margin-right: auto;
-  margin-top: 50px;
-}
 </style>

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

@@ -1,5 +1,5 @@
 <template>
-  <div id="appSettings">
+  <div id="appSettings" class="uk-width-large">
     <h3>Appearance</h3>
     <p>
       <label>

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

@@ -1,67 +1,68 @@
 <template>
   <div v-if="settings" id="cameraSettings">
-    <div>
+    <div class="uk-grid uk-grid-divider uk-child-width-expand" uk-grid>
-      <h3>Manual camera settings</h3>
+      <div class="uk-width-large">
-      <form @submit.prevent="applyConfigRequest">
+        <h3>Manual camera settings</h3>
-        <div v-if="settings.picamera">
+        <form @submit.prevent="applyConfigRequest">
-          <!--PiCamera settings block-->
+          <div v-if="settings.picamera">
-          <div v-if="settings.picamera.shutter_speed !== undefined">
+            <!--PiCamera settings block-->
-            <label class="uk-form-label" for="form-stacked-text"
+            <div v-if="settings.picamera.shutter_speed !== undefined">
-              >Exposure time</label
+              <label class="uk-form-label" for="form-stacked-text"
-            >
+                >Exposure time</label
-            <div class="uk-form-controls">
+              >
-              <input
+              <div class="uk-form-controls">
-                v-model="settings.picamera.shutter_speed"
+                <input
-                class="uk-input uk-form-small"
+                  v-model="settings.picamera.shutter_speed"
-                type="number"
+                  class="uk-input uk-form-small"
-              />
+                  type="number"
+                />
+              </div>
+            </div>
+
+            <div v-if="settings.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"
+                  class="uk-input uk-form-small"
+                  type="number"
+                  step="0.000001"
+                />
+              </div>
+            </div>
+
+            <div v-if="settings.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"
+                  class="uk-input uk-form-small"
+                  type="number"
+                  step="0.000001"
+                />
+              </div>
             </div>
           </div>
 
-          <div v-if="settings.picamera.analog_gain !== undefined">
+          <button
-            <label class="uk-form-label" for="form-stacked-text"
+            type="submit"
-              >Analogue gain</label
+            class="uk-button uk-button-primary uk-margin-small uk-width-1-1"
-            >
+          >
-            <div class="uk-form-controls">
+            Apply Settings
-              <input
+          </button>
-                v-model="settings.picamera.analog_gain"
+        </form>
-                class="uk-input uk-form-small"
-                type="number"
-                step="0.000001"
-              />
-            </div>
-          </div>
 
-          <div v-if="settings.picamera.digital_gain !== undefined">
+        <h3>Automatic calibration</h3>
-            <label class="uk-form-label" for="form-stacked-text"
+        <cameraCalibrationSettings></cameraCalibrationSettings>
-              >Digital gain</label
+      </div>
-            >
-            <div class="uk-form-controls">
-              <input
-                v-model="settings.picamera.digital_gain"
-                class="uk-input uk-form-small"
-                type="number"
-                step="0.000001"
-              />
-            </div>
-          </div>
-        </div>
 
-        <button
+      <div id="mini-stream">
-          type="submit"
+        <miniStreamDisplay />
-          class="uk-button uk-button-primary uk-margin-small uk-width-1-1"
+      </div>
-        >
-          Apply Settings
-        </button>
-      </form>
-    </div>
-
-    <!--Show auto calibrate if default plugin is enabled-->
-    <h3>Automatic calibration</h3>
-    <cameraCalibrationSettings></cameraCalibrationSettings>
-
-    <div id="mini-stream">
-      <miniStreamDisplay />
     </div>
   </div>
 </template>
@@ -141,7 +142,8 @@ export default {
 
 <style lang="less">
 #mini-stream {
-  width: 500px;
+  min-width: 300px;
+  max-width: 600px;
   text-align: center;
   margin-left: auto;
   margin-right: auto;

openflexure_microscope/api/static/src/components/tabContentComponents/settingsComponents/cameraSettingsComponents/cameraCalibrationSettings.vue

@@ -16,24 +16,31 @@
       </taskSubmitter>
     </div>
 
-    <div v-show="showExtraSettings" class="uk-child-width-expand" uk-grid>
+    <div v-show="showExtraSettings" class="uk-child-width-expand">
-      <div v-if="'flatten_lens_shading_table' in recalibrationLinks">
+      <button
-        <button
+        v-if="'flatten_lens_shading_table' in recalibrationLinks"
-          class="uk-button uk-button-danger uk-width-1-1"
+        class="uk-button uk-button-danger uk-width-1-1"
-          @click="flattenLensShadingTableRequest"
+        @click="flattenLensShadingTableRequest"
-        >
+      >
-          Disable flat-field correction
+        Disable flat-field correction
-        </button>
+      </button>
-      </div>
 
-      <div v-if="'delete_lens_shading_table' in recalibrationLinks">
+      <button
-        <button
+        v-if="'delete_lens_shading_table' in recalibrationLinks"
-          class="uk-button uk-button-danger uk-width-1-1"
+        class="uk-button uk-button-danger uk-margin-small-top uk-width-1-1"
-          @click="deleteLensShadingTableRequest"
+        @click="deleteLensShadingTableRequest"
-        >
+      >
-          Adaptive flat-field correction
+        Adaptive flat-field correction
-        </button>
+      </button>
-      </div>
+    </div>
+
+    <div v-if="LstDownloadEnabled">
+      <a
+        class="uk-button uk-button-default uk-width-large uk-margin-small-top uk-align-center"
+        :href="LstDownloadUri"
+        download
+        >Download Lens-Shading Table</a
+      >
     </div>
   </div>
 </template>
@@ -61,18 +68,23 @@ export default {
   data: function() {
     return {
       recalibrationLinks: {},
-      isCalibrating: false
+      isCalibrating: false,
+      LstDownloadEnabled: false
     };
   },
 
   computed: {
     pluginsUri: function() {
       return `${this.$store.getters.baseUri}/api/v2/extensions`;
+    },
+    LstDownloadUri: function() {
+      return `${this.$store.getters.baseUri}/api/v2/instrument/camera/lst`;
     }
   },
 
   mounted() {
     this.updateRecalibrationLinks();
+    this.checkLstDownload();
   },
 
   methods: {
@@ -97,6 +109,21 @@ export default {
         });
     },
 
+    checkLstDownload: function() {
+      axios
+        .get(this.LstDownloadUri) // Get a list of plugins
+        .then(response => {
+          if (response.status === 200) {
+            this.LstDownloadEnabled = true;
+          } else {
+            this.LstDownloadEnabled = false;
+          }
+        })
+        .catch(error => {
+          this.modalError(error); // Let mixin handle error
+        });
+    },
+
     onRecalibrateResponse: function() {
       this.modalNotify("Finished recalibration.");
     },

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

@@ -1,5 +1,5 @@
 <template>
-  <div id="appSettings">
+  <div id="appSettings" class="uk-width-large">
     <h3>Additional features</h3>
     <p class="uk-margin-small">
       <label
@@ -7,7 +7,7 @@
         Enable IHI Slide Scan</label
       >
     </p>
-    <p class="uk-margin-small uk-width-xlarge">
+    <p class="uk-margin-small">
       Enabling IHI Slide Scan will add a new tab designed to simplify acquiring
       blood smear tile scans. <br />
       While this may be useful for other applications, it is primarily designed

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

@@ -1,5 +1,5 @@
 <template>
-  <div v-if="settings" id="microscopeSettings">
+  <div v-if="settings" id="microscopeSettings" class="uk-width-large">
     <form @submit.prevent="applyConfigRequest">
       <label class="uk-form-label" for="form-stacked-text"
         >Backlash compensation</label

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

@@ -1,5 +1,5 @@
 <template>
-  <div id="stageSettings">
+  <div id="stageSettings" class="uk-width-large">
     <div>
       <h3>Stage settings</h3>
       <p>

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

@@ -1,11 +1,14 @@
 <template>
-  <div id="streamSettings">
+  <div id="streamSettings" class="uk-width-large">
     <div>
       <h3>Stream settings</h3>
       <label
         ><input v-model="disableStream" class="uk-checkbox" type="checkbox" />
-        Disable live stream</label
+        Disable web stream</label
       >
+      <p class="uk-margin-small">
+        This will disable the embedded web stream of the camera.
+      </p>
     </div>
 
     <br />
@@ -30,6 +33,18 @@
           >
         </div>
       </div>
+      <p>
+        Enable GPU preview turns on a low-latency camera preview drawn directly
+        to the Raspberry Pi display output.
+      </p>
+      <p class="uk-margin-small">
+        <b
+          >Content, such as your mouse, won't be visible behind this preview.</b
+        >
+        Track Window will attempt to resize the GPU preview based on the current
+        window size, however this is often imperfect and cannot track window
+        movement.
+      </p>
     </div>
   </div>
 </template>

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

@@ -133,12 +133,6 @@
         :current-tab="currentTab"
       >
         <div class="settings-pane uk-padding-small">
-          <h3>Camera/stage mapping</h3>
-          <p>
-            Camera/stage mapping allows the stage to move relative to the camera
-            view. This enables functions like click-to-move, and more precise
-            tile scans.
-          </p>
           <CSMSettings />
         </div>
       </tabContent>

openflexure_microscope/api/v2/views/__init__.py

@@ -1,4 +1,5 @@
 from .actions import enabled_root_actions
+from .camera import *
 from .captures import *
 from .instrument import *
 from .stage import *

openflexure_microscope/api/v2/views/camera.py

@@ -0,0 +1,50 @@
+import logging
+from io import BytesIO
+import datetime
+import numpy as np
+from flask import send_file
+from labthings import find_component
+from labthings.views import PropertyView
+from PIL import Image
+
+
+class LSTImageProperty(PropertyView):
+    """Gets the lens-shading table as an image"""
+
+    responses = {
+        200: {
+            "content_type": "image/png",
+            "description": "Lens-shading table in RGB format",
+        }
+    }
+
+    def get(self):
+        """
+        Get the stage geometry.
+        """
+        microscope = find_component("org.openflexure.microscope")
+
+        # Return intentionally empty response if no LST is available
+        if microscope.get_configuration()["camera"]["type"] != "PiCameraStreamer":
+            logging.warning("Requested an LST from a non-PiCameraStreamer camera")
+            return ("", 204)
+        # Return intentionally empty response if we have a valid PiCamera but no LST
+        elif getattr(microscope.camera.camera, "lens_shading_table") is None:
+            logging.warning("PiCamera.lens_shading_table returned as None")
+            return ("", 204)
+        else:
+            lst = np.asarray(microscope.camera.camera.lens_shading_table)
+            # R next to G1
+            top = np.concatenate(lst[:2], axis=1)
+            # G2 next to B
+            bottom = np.concatenate(lst[2:], axis=1)
+            # Combined into a 2x2 grid of greyscale images
+            all_channels = np.concatenate((top, bottom), axis=0)
+            # Create a PNG
+            img_bytes = BytesIO()
+            Image.fromarray(np.uint8(all_channels), "L").save(img_bytes, "PNG")
+            img_bytes.seek(0)
+            # Return the image
+            #return Response(img_bytes.getvalue(), mimetype="image/png")
+            fname = f"lst-{datetime.date.today().isoformat()}.png"
+            return send_file(img_bytes, as_attachment=True, attachment_filename=fname)