Merge branch 'stitching-two' into 'v3'

Stitch 2 images

See merge request openflexure/openflexure-microscope-server!630

src/openflexure_microscope_server/things/smart_scan.py

@@ -406,9 +406,8 @@ class SmartScanThing(OFMThing):
         if self._preview_stitcher is None:
             # This scan can't stitch.
             return
-        # Assume 4 images means at least one offset in x and y, making the stitching
+        # Begin stitching once two images are captured
-        # well constrained.
+        if self.scan_data.image_count >= 2 and not self._preview_stitcher.running:
-        if self.scan_data.image_count > 3 and not self._preview_stitcher.running:
             self._preview_stitcher.start()
 
     @_scan_running
@@ -543,8 +542,8 @@ class SmartScanThing(OFMThing):
     @_scan_running
     def _perform_final_stitch(self) -> None:
         """Update the scan zip and perform final stitch of the data."""
-        if self.scan_data.image_count <= 3:
+        if self.scan_data.image_count <= 1:
-            self.logger.info("Not performing a stitch as 3 or fewer images taken")
+            self.logger.info("Not performing a stitch as not enough images captured")
             return
 
         self.ongoing_scan.zip_files()
@@ -758,6 +757,6 @@ class SmartScanThing(OFMThing):
         # Use the scan list (the data read by the gallery) to find any scans that
         # need stitching.
         for scan in self.get_data_for_gallery():
-            if scan.dzi is None:
+            if scan.dzi is None and scan.number_of_images >= 2:
                 self.logger.info(f"Stitching {scan.name}")
                 self.stitch_scan(scan_name=scan.name)

tests/unit_tests/test_stitching.py

@@ -333,10 +333,19 @@ def test_stitch_all_scans_continues_after_error(mocker, caplog, smart_scan_thing
         mocker.Mock(name="scan1", dzi=None),
         mocker.Mock(name="scan2", dzi=None),
         mocker.Mock(name="scan3", dzi=None),
+        mocker.Mock(name="scan4", dzi=None),
     ]
     scans[0].name = "scan1"
     scans[1].name = "scan2"
     scans[2].name = "scan3"
+    scans[3].name = "scan4"
+
+    # stitch_all skips any scans with less than 2 images, without logging
+
+    scans[0].number_of_images = 10
+    scans[1].number_of_images = 10
+    scans[2].number_of_images = 1
+    scans[3].number_of_images = 10
 
     mocker.patch.object(
         smart_scan_thing,
@@ -373,9 +382,10 @@ def test_stitch_all_scans_continues_after_error(mocker, caplog, smart_scan_thing
 
     messages = [r.message for r in caplog.records]
 
+    # scan3 is not logged as there is only 1 image so it is ignored by ``stitch_all_scans``
     assert messages == [
         "Stitching scan1",
         "Stitching scan2",
         "Stitching failed: test_message",
-        "Stitching scan3",
+        "Stitching scan4",
     ]

webapp/src/components/tabContentComponents/galleryComponents/galleryCard.vue

@@ -62,7 +62,7 @@
           <li>Duration: {{ formatDuration(itemData.duration) }}</li>
         </ul>
         <ul>
-          <li v-if="itemData.number_of_images < 3" class="warning-msg">
+          <li v-if="itemData.number_of_images < 2" class="warning-msg">
             Not enough images to stitch
           </li>
           <li v-else-if="!itemData.dzi && itemData.stitch_available" class="alert-msg">

webapp/src/components/tabContentComponents/galleryContent.vue

@@ -219,7 +219,7 @@ export default {
           return;
         }
         all_items.forEach((item) => {
-          item.can_stitch = !item.stitch_available && item.number_of_images > 3;
+          item.can_stitch = !item.stitch_available && item.number_of_images > 1;
         });
         all_items.sort((a, b) => {
           return b.created - a.created;