new autofocus api in cytation docs

Author: rickwierenga

docs/user_guide/02_analytical/plate-reading/cytation5.ipynb

@@ -345,7 +345,7 @@
     "res = await pr.capture(\n",
     "  well=(1, 2),\n",
     "  mode=ImagingMode.BRIGHTFIELD,\n",
-    "  objective=Objective.O_4x_PL_FL_PHASE,\n",
+    "  objective=Objective.O_4X_PL_FL_Phase,\n",
     "  focal_height=0.833,\n",
     "  exposure_time=5,\n",
     "  gain=16,\n",
@@ -363,15 +363,6 @@
     "Auto-focus can be configured with `pr.backend.set_auto_focus_search_range` where the parameters are the minimum and maximum focus heights in mm respectively."
    ]
   },
-  {
-   "cell_type": "code",
-   "execution_count": 33,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "pr.backend.set_auto_focus_search_range(0.6, 1)"
-   ]
-  },
   {
    "cell_type": "code",
    "execution_count": null,
@@ -399,11 +390,19 @@
     }
    ],
    "source": [
+    "from pylabrobot.plate_reading.standard import AutoFocus\n",
+    "from pylabrobot.plate_reading.imager import evaluate_focus_nvmg_sobel\n",
+    "\n",
     "res = await pr.capture(\n",
     "  well=(1, 2),\n",
     "  mode=ImagingMode.BRIGHTFIELD,\n",
-    "  objective=Objective.O_4x_PL_FL_PHASE,\n",
-    "  focal_height=\"auto\", # <----- auto focus\n",
+    "  objective=Objective.O_4X_PL_FL_Phase,\n",
+    "  focal_height=AutoFocus(\n",
+    "    low=1.8,\n",
+    "    high=2.0,\n",
+    "    evaluate_focus=evaluate_focus_nvmg_sobel,\n",
+    "    timeout=30,\n",
+    "  ),\n",
     "  exposure_time=5,\n",
     "  gain=16,\n",
     "  led_intensity=10\n",
@@ -513,7 +512,7 @@
     "res = await pr.capture(\n",
     "  well=(1, 2),\n",
     "  mode=ImagingMode.BRIGHTFIELD,\n",
-    "  objective=Objective.O_4x_PL_FL_PHASE,\n",
+    "  objective=Objective.O_4X_PL_FL_Phase,\n",
     "  focal_height=0.833,\n",
     "  exposure_time=5,\n",
     "  gain=16,\n",

pylabrobot/plate_reading/biotek_backend.py

@@ -6,7 +6,7 @@
 import re
 import time
 from dataclasses import dataclass
-from typing import Any, Callable, Coroutine, Dict, List, Literal, Optional, Tuple, Union, cast
+from typing import List, Literal, Optional, Tuple, Union, cast
 
 from pylabrobot.resources.plate import Plate