From 132efa8033bf909d9302cca7d775a352df49b5f0 Mon Sep 17 00:00:00 2001
From: jaknapper <jaknapper@hotmail.com>
Date: Thu, 1 May 2025 14:47:12 +0100
Subject: [PATCH] Options for capture method, default downsampling of
 correlations

---
 .../things/autofocus.py                       | 46 ++++++++++---------
 .../things/smart_scan.py                      | 34 ++++++++++++--
 2 files changed, 54 insertions(+), 26 deletions(-)

diff --git a/src/openflexure_microscope_server/things/autofocus.py b/src/openflexure_microscope_server/things/autofocus.py
index 21223f6f..33b42f98 100644
--- a/src/openflexure_microscope_server/things/autofocus.py
+++ b/src/openflexure_microscope_server/things/autofocus.py
@@ -294,6 +294,7 @@ class AutofocusThing(Thing):
         capture: CaptureDep,
         images_dir: str,
         stack_dir: str,
+        capture_method: str = 'array'
     ) -> None:
         """Run a z stack, saving all images to stack_dir and copying the
         central image to stack_dir"""
@@ -307,30 +308,31 @@ class AutofocusThing(Thing):
             time.sleep(SETTLING_TIME)
 
             jpeg_path = os.path.join(
-                stack_dir,
-                f"{capture_count}.jpeg",
-            )
-            # The pre-existing capture_jpeg
-            # capture.capture_jpeg(filename=jpeg_path, cam=cam)
-            
-            # A new way to get the full array
-            img = capture.capture_jpeg_array()
-            
+                    stack_dir,
+                    f"{capture_count}.jpeg",
+                )
             metadata = metadata_getter()
-            _save_capture(
-                jpeg_path,
-                img,
-                metadata,
-                logger
-            )
-            
+            if capture_method == "blob":                
+                capture.capture_jpeg(filename=jpeg_path, cam=cam)
+            elif capture_method == "hires_array":
+            # A new way to get the full array
+                img = capture.capture_jpeg_array()
+                _save_capture(
+                    jpeg_path,
+                    img,
+                    metadata,
+                    logger
+                )
+            elif capture_method == "array":
             # The old capture and save a "main" res image
-            # capture._capture_and_save(
-            #     jpeg_path=jpeg_path,
-            #     cam=cam,
-            #     logger=logger,
-            #     metadata_getter=metadata_getter,
-            # )
+                capture._capture_and_save(
+                    jpeg_path=jpeg_path,
+                    cam=cam,
+                    logger=logger,
+                    metadata_getter=metadata_getter,
+                )
+            else:
+                raise ValueError('Capture method must be one of "array", "blob" or "hires_array"')
 
             # If the stack isn't complete yet, move
             if capture_count + 1 < images_to_capture:
diff --git a/src/openflexure_microscope_server/things/smart_scan.py b/src/openflexure_microscope_server/things/smart_scan.py
index f0d45d1d..8094f632 100644
--- a/src/openflexure_microscope_server/things/smart_scan.py
+++ b/src/openflexure_microscope_server/things/smart_scan.py
@@ -143,6 +143,7 @@ class SmartScanThing(Thing):
         self._scan_images_taken: Optional[int] = None
         # TODO Scan data is a dict during refactoring, should become a dataclass
         self._scan_data: Optional[dict] = None
+        self._stitch_resize: Optional[float] = None
 
     @thing_action
     def sample_scan(
@@ -179,6 +180,7 @@ class SmartScanThing(Thing):
         self._background_detect = background_detect
         self._capture_thread = None
         self._scan_images_taken = 0
+        self._stitch_resize = 1
 
         # Don't set self._scan_data dictionary. This is done at the start of _run_scan
 
@@ -214,6 +216,7 @@ class SmartScanThing(Thing):
             self._scan_images_taken = None
             self._scan_data = None
             self._scan_lock.release()
+            self._stitch_resize = None
 
     def promote_stitch_files(
         self,
@@ -375,8 +378,24 @@ class SmartScanThing(Thing):
 
         return (next_point[0], next_point[1], z_estimate)
 
+    # @_scan_running
+    # def _calc_resize_from_test_image(self):
+    #     """
+    #     Take a test image to set the amount to downsample images for stitching
+
+    #     Return the decimal value to scale x and y by when stitching
+    #     """
+
+    #     #TODO: This needs to match how the capture in the z stack is done
+    #     test_jpg = self._cam.capture_jpeg(resolution="full")
+    #     test_jpg = test_jpg.content
+
+    #     test_image = Image.open(io.BytesIO(test_jpg))
+    #     test_image_res = list(test_image.size)
+    #     return STITCH_IMAGE_WIDTH / test_image_res[0]
+
     @_scan_running
-    def _take_test_image_to_calc_displacement(self, overlap):
+    def _calc_displacement_from_test_image(self, overlap):
         """
         Take a test image and use camera stage mapping to calculate x and y displacement
 
@@ -421,7 +440,14 @@ class SmartScanThing(Thing):
         dataclass.
         """
         overlap = self.overlap
-        dx, dy = self._take_test_image_to_calc_displacement(overlap)
+        dx, dy = self._calc_displacement_from_test_image(overlap)
+        # self._stitch_resize = self._calc_resize_from_test_image()
+        self._stitch_resize = 0.25
+
+        self._scan_logger.info(
+            f'Resizing images by {self._stitch_resize}'
+        )
+
         self._scan_logger.info(
             f"Based on an overlap of {overlap}, we will make steps of {dx}, {dy}"
         )
@@ -989,7 +1015,7 @@ class SmartScanThing(Thing):
                     "--minimum_overlap",
                     f"{min_overlap}",
                     "--resize",
-                    "0.25",
+                    f"{self._stitch_resize}",
                     self._ongoing_scan_images_dir,
                 ]
             )
@@ -1107,7 +1133,7 @@ class SmartScanThing(Thing):
                 "--minimum_overlap",
                 f"{round(overlap * 0.9, 2)}",
                 "--resize",
-                "0.25",
+                f"{self._stitch_resize}",
                 images_folder,
             ],
         )