From a0b98a1adce89c01f6281059823da2e85c291916 Mon Sep 17 00:00:00 2001
From: jaknapper <jaknapper@hotmail.com>
Date: Mon, 29 Jan 2024 19:56:24 +0000
Subject: [PATCH] Fixed autofocus to not combine logs

---
 .../things/auto_recentre_stage.py             | 26 +------------------
 .../things/autofocus.py                       |  6 ++---
 .../things/smart_scan.py                      |  2 ++
 3 files changed, 6 insertions(+), 28 deletions(-)

diff --git a/src/openflexure_microscope_server/things/auto_recentre_stage.py b/src/openflexure_microscope_server/things/auto_recentre_stage.py
index ba11a900..2eb77055 100644
--- a/src/openflexure_microscope_server/things/auto_recentre_stage.py
+++ b/src/openflexure_microscope_server/things/auto_recentre_stage.py
@@ -15,29 +15,6 @@ CamDep = direct_thing_client_dependency(StreamingPiCamera2, "/camera/")
 CSMDep = direct_thing_client_dependency(CameraStageMapper, "/camera_stage_mapping/")
 AutofocusDep = direct_thing_client_dependency(AutofocusThing, "/autofocus/")
 
-
-def turningpoints(lst):
-    dx = np.diff(lst)
-    return dx[1:] * dx[:-1] < 0
-
-
-def unpack_autofocus(scan_data):
-    """Extract z, sharpness data from a move_and_measure call"""
-    scan_data = dict(scan_data)
-    jpeg_times = scan_data["jpeg_times"]
-    jpeg_sizes = scan_data["jpeg_sizes"]
-    jpeg_sizes_MB = [x / 10**3 for x in jpeg_sizes]
-    stage_times = scan_data["stage_times"]
-    stage_positions = scan_data["stage_positions"]
-    stage_height = [pos["z"] for pos in stage_positions]
-
-    jpeg_heights = np.interp(jpeg_times, stage_times, stage_height)
-
-    turning = np.where(turningpoints(jpeg_heights))[0]
-
-    return jpeg_heights[turning[0] : turning[1]], jpeg_sizes_MB[turning[0] : turning[1]]
-
-
 class RecentringThing(Thing):
     @thing_action
     def looping_autofocus(self, autofocus: AutofocusDep, stage: StageDep, dz=2000, start='centre'):
@@ -51,8 +28,7 @@ class RecentringThing(Thing):
         repeat = True
         attempts = 0
         while repeat and attempts < 10:
-            data = autofocus.fast_autofocus(dz=dz, start=start)
-            heights, _ = unpack_autofocus(data)
+            heights, sizes = autofocus.fast_autofocus(dz=dz, start=start)
             height_min = np.min(heights)
             height_max = np.max(heights)
             # TODO: max heights seems badly wrong! Something about turning?
diff --git a/src/openflexure_microscope_server/things/autofocus.py b/src/openflexure_microscope_server/things/autofocus.py
index b70f8a44..01f41e58 100644
--- a/src/openflexure_microscope_server/things/autofocus.py
+++ b/src/openflexure_microscope_server/things/autofocus.py
@@ -119,7 +119,7 @@ class JPEGSharpnessMonitor:
             raise ValueError(
                 "No images were captured during the move of the stage.  Perhaps the camera is not streaming images?"
             )
-        return jz[np.argmax(js)]
+        return jz[np.argmax(js)], jz, js
 
     def data_dict(self) -> SharpnessDataArrays:
         """Return the gathered data as a single convenient dictionary"""
@@ -161,13 +161,13 @@ class AutofocusThing(Thing):
             # z: Final z position after move
             i, z = m.focus_rel(dz, block_cancellation=True)
             # Get the z position with highest sharpness from the previous move (index i)
-            fz: int = m.sharpest_z_on_move(i)
+            fz, heights, sizes = m.sharpest_z_on_move(i)
             # Move all the way to the start so it's consistent
             i, z = m.focus_rel(-dz)
             # Move to the target position fz (relative move of (fz - z))
             m.focus_rel(fz - z)
             # Return all focus data
-            return m.data_dict()
+            return heights, sizes
         
     @thing_action
     def move_and_measure(
diff --git a/src/openflexure_microscope_server/things/smart_scan.py b/src/openflexure_microscope_server/things/smart_scan.py
index 0230d16b..6f9791d7 100644
--- a/src/openflexure_microscope_server/things/smart_scan.py
+++ b/src/openflexure_microscope_server/things/smart_scan.py
@@ -484,6 +484,8 @@ class SmartScanThing(Thing):
                 if len(focused_path) > 1:
                     z_index = closest(loc, focused_path)
                     z=int(focused_path[z_index][2])
+                else:
+                    z = loc[2]
                     # print('Moving to {0}'.format([coords[0], coords[1], focused_path[z_index][2]]))
                     # print(focused_path)
                 stage.move_absolute(