Merge branch 'stage-dir-calibrate' into 'v3'

Stage direction calibrate

Closes #626 and #647

See merge request openflexure/openflexure-microscope-server!633

src/openflexure_microscope_server/things/stage/__init__.py

@@ -166,6 +166,15 @@ class BaseStage(lt.Thing):
     )
     """Used to convert coordinates between the program frame and the hardware frame."""
 
+    @lt.property
+    def calibration_required(self) -> bool:
+        """Whether the stage requires calibration.
+
+        Currently the only calibration method for the stage is the z-gear rotation
+        direction in the sangaboard stage.
+        """
+        return False
+
     def update_position(self) -> None:
         """Update the position property from the stage."""
         # Copy the position before the move.

src/openflexure_microscope_server/things/stage/sangaboard.py

@@ -80,6 +80,37 @@ class SangaboardThing(BaseStage):
     )
     """Used to convert coordinates between the program frame and the hardware frame."""
 
+    z_axis_calibrated: bool = lt.setting(default=False, readonly=True)
+
+    @lt.property
+    def calibration_required(self) -> bool:
+        """Whether the stage requires calibration.
+
+        Return False only if z-direction has been calibrated.
+        """
+        return not self.z_axis_calibrated
+
+    @lt.action
+    def calibrate_z_direction(
+        self, positive_motion: Literal["clockwise", "anti-clockwise"]
+    ) -> None:
+        """Calibrate the z motor direction based on the gear rotation direction.
+
+        Positive z motion should turn the exposed gear anti-clockwise. Calling this
+        action marks the z motor as calibrated.
+
+        :param positive_motion: The direction the gear moved during pisitive z motion.
+        """
+        if positive_motion == "clockwise":
+            # Wrong direction, mark as such.
+            self.invert_axis_direction(axis="z")
+        elif positive_motion != "anti-clockwise":
+            raise ValueError(
+                "Motion should be reported as either 'clockwise' or 'anti-clockwise'."
+            )
+        # Set z_axis_calibrated to true once this function is called.
+        self.z_axis_calibrated = True
+
     def _hardware_update_position(self) -> None:
         """Read position from the stage and set internal attribute _hardware_position.
 

tests/unit_tests/test_stage.py

@@ -603,10 +603,13 @@ def test_thing_description_equivalence(dummy_stage, mocker):
     dummy_properties = set(dummy_td.properties.keys())
 
     sanga_td = create_thing_without_server(SangaboardThing).thing_description()
-    # Remove known extra actions
-    sanga_actions = list(sanga_td.actions.keys())
-    sanga_actions = set(sanga_actions)
-    sanga_properties = set(sanga_td.properties.keys())
+
+    # Sangaboard has one extra action for calibrating z-motor direction. This is
+    # handled in the webapp calibration wizard, and an extra setting for persisting it
+    sanga_extra_actions = {"calibrate_z_direction"}
+    sanga_extra_properties = {"z_axis_calibrated"}
+    sanga_actions = set(sanga_td.actions.keys()) - sanga_extra_actions
+    sanga_properties = set(sanga_td.properties.keys()) - sanga_extra_properties
 
     assert sanga_actions == dummy_actions == base_actions
     assert sanga_properties == dummy_properties == base_properties

webapp/src/components/modalComponents/calibrationWizard.vue

@@ -28,6 +28,7 @@
 <script>
 import singleStepTask from "./calibrationWizardComponents/singleStepTask.vue";
 import welcomeStep from "./calibrationWizardComponents/welcomeStep.vue";
+import zMotorCalibrationTask from "./calibrationWizardComponents/zMotorCalibrationTask.vue";
 import cameraCalibrationTask from "./calibrationWizardComponents/cameraCalibrationTask.vue";
 import cameraStageMappingTask from "./calibrationWizardComponents/cameraStageMappingTask.vue";
 import finalStep from "./calibrationWizardComponents/finalStep.vue";
@@ -68,6 +69,7 @@ export default {
     this.$refs["calibrationModalEl"].addEventListener("hidden", this.onHide);
     // Check which Things are available on mount.
     const allCalibrationTasks = {
+      stage: markRaw(zMotorCalibrationTask),
       camera: markRaw(cameraCalibrationTask),
       camera_stage_mapping: markRaw(cameraStageMappingTask),
     };

webapp/src/components/modalComponents/calibrationWizardComponents/calibrationWizardTask.vue

@@ -29,6 +29,7 @@ gets very confusing.
       :key="stepIndex"
       @awaiting-user="handleAwaitingUser"
       @prevent-navigation="handlePreventNavigation"
+      @advance="nextStep"
     />
     <p class="uk-text-right">
       <button

webapp/src/components/modalComponents/calibrationWizardComponents/zMotorCalibrationTask.vue

@@ -0,0 +1,29 @@
+<template>
+  <singleStepTask
+    title="Stage Calibration"
+    :step-component="zMotorDirectionStep"
+    @next="$emit('next')"
+    @back="$emit('back')"
+  />
+</template>
+
+<script>
+import singleStepTask from "./singleStepTask.vue";
+import zMotorDirectionStep from "./zMotorDirectionStep.vue";
+
+export default {
+  name: "ZMotorCalibrationTask",
+
+  components: {
+    singleStepTask,
+  },
+
+  emits: ["next", "back"],
+
+  data() {
+    return {
+      zMotorDirectionStep,
+    };
+  },
+};
+</script>

webapp/src/components/modalComponents/calibrationWizardComponents/zMotorDirectionStep.vue

@@ -0,0 +1,148 @@
+<template>
+  <div>
+    <p>Look at the exposed z gear from above while holding the <b>Turn z motor</b> button.</p>
+    <div class="uk-margin uk-flex uk-flex-center">
+      <button
+        class="uk-button uk-button-primary jog-z-btn"
+        type="button"
+        @pointerdown="jogZ"
+        @pointerup="jogZStop"
+        @pointercancel="jogZStop"
+      >
+        <span>Turn z motor</span>
+      </button>
+    </div>
+    <p>Which way does the z gear turn?</p>
+    <!-- Direction selection -->
+    <div class="uk-margin uk-flex">
+      <!-- Anti-clockwise column -->
+      <div class="uk-width-1-2 dir-option">
+        <img
+          src="/direction_AC.png"
+          alt="Anti-clockwise"
+          class="dir-image clickable"
+          @click="reportDirection('anti-clockwise')"
+        />
+
+        <button
+          class="uk-button uk-button-default uk-width-1-1 uk-button-primary"
+          type="button"
+          @click="reportDirection('anti-clockwise')"
+        >
+          Anti-clockwise
+        </button>
+      </div>
+
+      <!-- Clockwise column -->
+      <div class="uk-width-1-2 dir-option">
+        <img
+          src="/direction_CW.png"
+          alt="Clockwise"
+          class="dir-image clickable"
+          @click="reportDirection('clockwise')"
+        />
+
+        <button
+          class="uk-button uk-button-default uk-width-1-1 uk-button-primary"
+          type="button"
+          @click="reportDirection('clockwise')"
+        >
+          Clockwise
+        </button>
+      </div>
+    </div>
+  </div>
+</template>
+
+<script>
+export default {
+  name: "ZMotorDirectionStep",
+
+  emits: ["advance", "awaiting-user"],
+
+  data: function () {
+    return {
+      jogIntervalId: null,
+      jogDistance: 100,
+      jogTime: 300,
+    };
+  },
+
+  async mounted() {
+    this.checkCalibrationState();
+  },
+
+  methods: {
+    jogZ(pointerEvent) {
+      if (pointerEvent.button !== 0) return;
+
+      if (this.jogIntervalId) {
+        clearInterval(this.jogIntervalId);
+      }
+
+      pointerEvent.target.setPointerCapture(pointerEvent.pointerId);
+
+      let invokeJog = () => this.invokeAction("stage", "jog", { z: this.jogDistance });
+      invokeJog();
+      this.jogIntervalId = setInterval(invokeJog, this.jogTime);
+    },
+    jogZStop() {
+      if (this.jogIntervalId) {
+        clearInterval(this.jogIntervalId);
+      }
+      this.invokeAction("stage", "jog", { stop: true });
+    },
+    /**
+     * Report the direction to the microscope then advance to next pane in wizard.
+     */
+    async reportDirection(direction) {
+      await this.invokeAction("stage", "calibrate_z_direction", { positive_motion: direction });
+      this.$emit("advance");
+    },
+    async checkCalibrationState() {
+      let needsCal = await this.readThingProperty("stage", "calibration_required");
+      if (needsCal) {
+        // If it needs calibration check the relevant calibration action exists.
+        const actions = this.thingDescription("stage").actions;
+        if (!("calibrate_z_direction" in actions)) {
+          console.error(
+            "Stage is requesting calibration but has no 'calibrate_z_direction' action",
+          );
+          needsCal = false;
+        }
+      }
+      this.$emit("awaiting-user", needsCal);
+    },
+  },
+};
+</script>
+
+<style lang="less">
+.jog-z-btn {
+  display: flex;
+  align-items: center;
+  padding: 0 30px;
+  gap: 4px;
+}
+
+.dir-option {
+  display: flex;
+  flex-direction: column;
+  align-items: center;
+  gap: 8px;
+  margin: 5px;
+}
+
+.dir-image {
+  width: 70%;
+  height: auto;
+}
+
+.clickable {
+  cursor: pointer;
+}
+
+.dir-option button {
+  text-align: center;
+}
+</style>

webapp/src/tests/unit/overrides.js

@@ -133,4 +133,17 @@ export const componentOverrides = {
   "cameraCalibrationSettings.vue": {
     props: { cameraUri: "" },
   },
+  "zMotorDirectionStep.vue": {
+    mocks: {
+      thingDescription: () => ({
+        properties: {
+          test_property_1: {},
+          test_property_2: {},
+        },
+        actions: {
+          calibrate_z_direction: {},
+        },
+      }),
+    },
+  },
 };