Merge branch 'change-stage-geometry' into 'master'

Change stage geometry

See merge request openflexure/openflexure-microscope-server!73

openflexure_microscope/api/app.py

@@ -129,6 +129,9 @@ labthing.add_view(
 )
 labthing.add_root_link(views.ConfigurationProperty, "instrumentConfiguration")
 
+# Attach stage resources
+labthing.add_view(views.StageTypeProperty, "/instrument/stage/type")
+
 
 # Attach streams resources
 labthing.add_view(views.MjpegStream, f"/streams/mjpeg")

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

@@ -0,0 +1,88 @@
+<template>
+    <div id="stageSettings">
+        <div>
+            <h3>Stage settings</h3>
+            <p>
+                <label>
+                    Stage Type
+                    <div v-if="this.stageType != 'MissingStage'">
+                        <form @submit.prevent="setStageType">
+                            <div>
+                                <select v-model="stageType" class="uk-select">
+                                    <option value="SangaStage">SangaStage (Standard)</option>
+                                    <option value= "SangaDeltaStage"> SangaStage (Delta)</option>
+                                </select>
+                            </div>
+                            <div>
+                            <button type="submit" class="uk-button uk-button-primary uk-form-small uk-float-right uk-margin-small uk-width-1-1">
+                                Change stage type
+                            </button>
+                            </div>
+                        </form>   
+                    </div>
+                    <div v-else class="uk-text-danger"><b>No stage connected</b></div>
+                </label>
+            </p>
+        </div>
+    </div>
+</template>
+
+<script>
+
+import axios from "axios";
+import taskSubmitter from "../../genericComponents/taskSubmitter";
+
+export default {
+    name: "StageSettings",
+
+    components:{
+        taskSubmitter
+    },
+
+    data: function(){
+        return {
+            stageType: "MissingStage",
+        }
+    },
+    
+    computed: {
+        stageTypeUri: function() {
+        return `${this.$store.getters.baseUri}/api/v2/properties/stage/type`;
+        },
+    },
+
+    mounted(){
+        this.getStageType();
+    },
+
+    methods: {
+        getStageType: function(){
+            console.log("Getting stage type")
+            axios
+                .get(this.stageTypeUri)
+                .then(response => {
+                    console.log("Stage type is  "+ response.data);
+                    this.stageType = response.data;
+                })
+                .catch(error => {
+                    this.modalError(error);
+                });
+        },
+        setStageType: function(){
+            console.log("Setting stage type")
+            axios
+                .put(this.stageTypeUri,this.stageType)
+                .then(response => {
+                    this.stageType = response.data;
+                    console.log("Stage type set to " + this.stageType);
+                    this.modalNotify("Stage type changed.");
+                })
+                .catch(error => {
+                    this.modalError(error);
+                });
+        }
+    }
+}
+</script>
+
+<style lang="less"></style>

openflexure_microscope/api/static/src/components/viewComponents/settingsDisplay.vue

@@ -44,6 +44,19 @@
             Camera
           </tabIcon>
         </li>
+        <li>
+          <tabIcon
+            id="settings-stage-icon"
+            tab-i-d="stage"
+            :show-title="false"
+            :show-tooltip="false"
+            :require-connection="true"
+            :current-tab="currentTab"
+            @set-tab="setTab"
+          >
+            Stage
+          </tabIcon>
+        </li>
         <li>
           <tabIcon
             id="settings-mapping-icon"
@@ -104,6 +117,16 @@
         </div>
       </tabContent>
 
+      <tabContent
+        tab-i-d="stage"
+        :require-connection="true"
+        :current-tab="currentTab"
+      >
+        <div class="settings-pane uk-padding-small">
+          <stageSettings />
+        </div>
+      </tabContent>
+
       <tabContent
         tab-i-d="mapping"
         :require-connection="true"
@@ -141,7 +164,7 @@ import cameraSettings from "./settingsComponents/cameraSettings.vue";
 import appSettings from "./settingsComponents/appSettings.vue";
 import featuresSettings from "./settingsComponents/featuresSettings.vue";
 import cameraStageMappingSettings from "./settingsComponents/cameraStageMappingSettings.vue";
-
+import stageSettings from "./settingsComponents/stageSettings.vue";
 // Import generic components
 import tabIcon from "../genericComponents/tabIcon";
 import tabContent from "../genericComponents/tabContent";
@@ -153,6 +176,7 @@ export default {
   components: {
     streamSettings,
     cameraSettings,
+    stageSettings,
     microscopeSettings,
     cameraStageMappingSettings,
     appSettings,

openflexure_microscope/api/v2/views/__init__.py

@@ -2,3 +2,4 @@ from .actions import enabled_root_actions
 from .captures import *
 from .instrument import *
 from .streams import *
+from .stage import *

openflexure_microscope/api/v2/views/actions/stage.py

@@ -65,3 +65,5 @@ class ZeroStageAPI(ActionView):
 
         # TODO: Make schema for microscope state
         return microscope.state["stage"]
+
+

openflexure_microscope/api/v2/views/stage.py

@@ -0,0 +1,30 @@
+from labthings import find_component, fields, schema
+from labthings.views import PropertyView
+
+import logging
+
+
+class StageTypeProperty(PropertyView):
+    """The type of the stage"""
+
+    schema = fields.String(
+        missing=None,
+        example="SangaStage",
+        OneOf=["SangaStage", "SangaDeltaStage"],
+        description="The translation stage geometry",
+    )
+
+    def get(self):
+        """
+        Get the stage geometry.
+        """
+        microscope = find_component("org.openflexure.microscope")
+        return microscope.configuration["stage"]["type"]
+
+    def put(self, stage_type):
+        """
+        Set the stage geometry.
+        """
+        microscope = find_component("org.openflexure.microscope")
+        microscope.set_stage(stage_type=stage_type)
+        return microscope.configuration["stage"]["type"]

openflexure_microscope/microscope.py

@@ -105,24 +105,8 @@ class Microscope:
                     logging.warning("No compatible camera hardware found.")
 
         ### Stage
-        logging.info("Creating stage")
+        self.set_stage(configuration=configuration)
-        if configuration.get("stage"):
+                 
-            stage_type = configuration["stage"].get("type")
-            stage_port = configuration["stage"].get("port")
-            if stage_type in ("SangaBoard", "SangaStage"):
-                try:
-                    logging.info("Trying SangaStage")
-                    self.stage = SangaStage(port=stage_port)
-                except Exception as e:
-                    logging.error(e)
-                    logging.warning("No compatible Sangaboard hardware found.")
-            elif stage_type in ("SangaDeltaStage"):
-                try:
-                    logging.info("Trying SangaDeltaStage")
-                    self.stage = SangaDeltaStage(port=stage_port)
-                except Exception as e:
-                    logging.error(e)
-                    logging.warning("No compatible Sangaboard hardware found.")                    
 
         logging.info("Handling fallbacks")
         ### Fallbacks
@@ -138,6 +122,51 @@ class Microscope:
         if hasattr(self.stage, "lock"):
             self.lock.locks.append(self.stage.lock)
 
+    def set_stage(self, configuration=None, stage_type=None):
+        """
+        Set or change the stage geometry
+        """
+        if not configuration:
+            configuration = self.configuration
+
+        if stage_type:
+            if stage_type == configuration["stage"].get("type"):
+                    logging.info("Stage already set to that stage type")
+                    return
+        else:
+            stage_type = configuration["stage"].get("type")
+        
+        ### Close any existing stages
+        if self.stage:
+                stage_port = self.stage.port
+                self.stage.close()
+
+
+        logging.info("Setting stage")
+        stage_port = configuration["stage"].get("port")             
+                    
+        if stage_type in ("SangaBoard", "SangaStage"):
+            try:
+                logging.info("Trying SangaStage")
+                self.stage = SangaStage(port=stage_port)
+            except Exception as e:
+                logging.error(e)
+                logging.warning("No compatible Sangaboard hardware found.")
+        elif stage_type in ("SangaDeltaStage"):
+            try:
+                logging.info("Trying SangaDeltaStage")
+                self.stage = SangaDeltaStage(port=stage_port)
+                
+            except Exception as e:
+                logging.error(e)
+                logging.warning("No compatible Sangaboard hardware found.")
+        else:
+            logging.warning("The stage type is incorrectly defined.")   
+
+        logging.info("Saving new stage type configuration")
+        configuration["stage"]["type"] = stage_type
+        self.configuration_file.save(configuration)
+        
     def has_real_stage(self) -> bool:
         """
         Check if a real (non-mock) stage is currently attached.
@@ -363,6 +392,7 @@ class Microscope:
 
             # Capture to output object
             logging.info(f"Starting microscope capture {output.file}")
+            print(output)
             self.camera.capture(
                 output,
                 use_video_port=use_video_port,