From dbb65d55b5edb9587b8874f3175d7f8a9cd0c93b Mon Sep 17 00:00:00 2001
From: jaknapper <jaknapper@hotmail.com>
Date: Tue, 17 Jun 2025 12:05:46 +0100
Subject: [PATCH] Use scan autofocus dz

---
 src/openflexure_microscope_server/things/autofocus.py  | 3 ++-
 src/openflexure_microscope_server/things/smart_scan.py | 1 +
 2 files changed, 3 insertions(+), 1 deletion(-)

diff --git a/src/openflexure_microscope_server/things/autofocus.py b/src/openflexure_microscope_server/things/autofocus.py
index eadc26dc..117e40b0 100644
--- a/src/openflexure_microscope_server/things/autofocus.py
+++ b/src/openflexure_microscope_server/things/autofocus.py
@@ -297,6 +297,7 @@ class AutofocusThing(Thing):
         capture: CaptureDep,
         sharpness_monitor: SharpnessMonitorDep,
         images_dir: str,
+        autofocus_dz: int,
     ) -> None:
         """Run a z stack, saving all images to stack_dir and copying the
         central image to stack_dir"""
@@ -360,7 +361,7 @@ class AutofocusThing(Thing):
                     self.looping_autofocus(
                         stage=stage,
                         sharpness_monitor=sharpness_monitor,
-                        dz=2000,
+                        dz=autofocus_dz,
                     )
                     stage.move_relative(
                         z=-(overshoot + BACKLASH_CORRECTION + stack_z_range / 2)
diff --git a/src/openflexure_microscope_server/things/smart_scan.py b/src/openflexure_microscope_server/things/smart_scan.py
index 92f5f5aa..2eb5d285 100644
--- a/src/openflexure_microscope_server/things/smart_scan.py
+++ b/src/openflexure_microscope_server/things/smart_scan.py
@@ -646,6 +646,7 @@ class SmartScanThing(Thing):
 
             focused_height = self._autofocus.run_z_stack(
                 images_dir=self._ongoing_scan_images_dir,
+                autofocus_dz = self._scan_data['autofocus_dz']
             )
 
             current_pos_xyz = (