From 63b633ba444838389e928433746917954e13a42e Mon Sep 17 00:00:00 2001
From: Joel Collins <2579603-jtc42@users.noreply.gitlab.com>
Date: Fri, 4 Dec 2020 13:35:11 +0000
Subject: [PATCH] 2.9 dev numpy types

---
 README.md                                     |  6 ++
 .../api/default_extensions/autofocus.py       | 98 +++++++++++--------
 .../recalibrate_utils.py                      |  8 +-
 .../api/dev_extensions/__init__.py            |  4 +-
 .../api/dev_extensions/tools.py               | 21 ++--
 openflexure_microscope/camera/base.py         | 19 ++--
 openflexure_microscope/stage/sanga.py         |  2 +-
 openflexure_microscope/utilities.py           | 43 +++++---
 poetry.lock                                   | 38 +++++--
 pyproject.toml                                |  7 +-
 10 files changed, 156 insertions(+), 90 deletions(-)

diff --git a/README.md b/README.md
index fce94990..c18cdd85 100644
--- a/README.md
+++ b/README.md
@@ -10,9 +10,15 @@ This includes installing the server in a mode better suited for active developme
 
 # Developer guidelines
 
+The Raspberry Pi image we use currently ships with Python 3.7.3. For local development, please use PyEnv or similar to make sure you're running on this version. For example, Windows users can use [Scoop](https://scoop.sh/) to install specific Python versions.
 ## Installation
 
 * `git clone https://gitlab.com/openflexure/openflexure-microscope-server.git`
+* `cd openflexure-microscope-server`
+* (Optional) Set local Python version
+  * `pyenv init`
+  * `pyenv install 3.7.3`
+  * `pyenv local 3.7.3`
 * `poetry install`
   * Building the static interface will require a valid Node.js installation
   * To build on a Raspberry Pi:
diff --git a/openflexure_microscope/api/default_extensions/autofocus.py b/openflexure_microscope/api/default_extensions/autofocus.py
index d2c616a5..91fe08fb 100644
--- a/openflexure_microscope/api/default_extensions/autofocus.py
+++ b/openflexure_microscope/api/default_extensions/autofocus.py
@@ -1,7 +1,7 @@
 import logging
 import time
 from contextlib import contextmanager
-from typing import Callable, List, Optional, Tuple
+from typing import Callable, Dict, List, Optional, Tuple
 
 import numpy as np
 from labthings import current_action, fields, find_component
@@ -39,7 +39,7 @@ class JPEGSharpnessMonitor:
         self.camera.stream.stop_tracking()
         self.camera.stream.reset_tracking()
 
-    def focus_rel(self, dz: int, backlash: bool = False, **kwargs):
+    def focus_rel(self, dz: int, backlash: bool = False, **kwargs) -> Tuple[int, int]:
         # Store the start time and position
         self.camera.stream.start_tracking()
         self.stage_times.append(time.time())
@@ -62,22 +62,28 @@ class JPEGSharpnessMonitor:
         self.camera.stream.reset_tracking()
 
         # Index of the data for this movement
-        data_index = len(self.stage_positions) - 2
+        data_index: int = len(self.stage_positions) - 2
         # Final z position after move
-        final_z_position = self.stage_positions[-1][2]
+        final_z_position: int = self.stage_positions[-1][2]
         return data_index, final_z_position
 
-    def move_data(self, istart: int, istop: Optional[int] = None):
+    def move_data(
+        self, istart: int, istop: Optional[int] = None
+    ) -> Tuple[np.ndarray, np.ndarray, np.ndarray]:
         """Extract sharpness as a function of (interpolated) z"""
         if istop is None:
             istop = istart + 2
-        jpeg_times = np.array(self.jpeg_times)
-        jpeg_sizes = np.array(self.jpeg_sizes)
-        stage_times = np.array(self.stage_times)[istart:istop]
-        stage_zs = np.array(self.stage_positions)[istart:istop, 2]
+        jpeg_times: np.ndarray = np.array(self.jpeg_times)  # np.ndarray[float]
+        jpeg_sizes: np.ndarray = np.array(self.jpeg_sizes)  # np.ndarray[int]
+        stage_times: np.ndarray = np.array(self.stage_times)[
+            istart:istop
+        ]  # np.ndarray[float]
+        stage_zs: np.ndarray = np.array(self.stage_positions)[
+            istart:istop, 2
+        ]  # np.ndarray[int]
         try:
-            start = np.argmax(jpeg_times > stage_times[0])
-            stop = np.argmax(jpeg_times > stage_times[1])
+            start: int = int(np.argmax(jpeg_times > stage_times[0]))
+            stop: int = int(np.argmax(jpeg_times > stage_times[1]))
         except ValueError as e:
             if np.sum(jpeg_times > stage_times[0]) == 0:
                 raise ValueError(
@@ -89,10 +95,12 @@ class JPEGSharpnessMonitor:
             stop = len(jpeg_times)
             logging.debug("changing stop to %s", (stop))
         jpeg_times = jpeg_times[start:stop]
-        jpeg_zs = np.interp(jpeg_times, stage_times, stage_zs)
+        jpeg_zs: np.ndarray = np.interp(
+            jpeg_times, stage_times, stage_zs
+        )  # np.ndarray[float]
         return jpeg_times, jpeg_zs, jpeg_sizes[start:stop]
 
-    def sharpest_z_on_move(self, index: int):
+    def sharpest_z_on_move(self, index: int) -> int:
         """Return the z position of the sharpest image on a given move"""
         _, jz, js = self.move_data(index)
         if len(js) == 0:
@@ -101,7 +109,7 @@ class JPEGSharpnessMonitor:
             )
         return jz[np.argmax(js)]
 
-    def data_dict(self):
+    def data_dict(self) -> Dict[str, np.ndarray]:
         """Return the gathered data as a single convenient dictionary"""
         data = {}
         for k in ["jpeg_times", "jpeg_sizes", "stage_times", "stage_positions"]:
@@ -111,7 +119,7 @@ class JPEGSharpnessMonitor:
 
 @contextmanager
 def monitor_sharpness(microscope: Microscope):
-    m = JPEGSharpnessMonitor(microscope)
+    m: JPEGSharpnessMonitor = JPEGSharpnessMonitor(microscope)
     m.start()
     try:
         yield m
@@ -119,18 +127,18 @@ def monitor_sharpness(microscope: Microscope):
         m.stop()
 
 
-def sharpness_sum_lap2(rgb_image: np.ndarray):
+def sharpness_sum_lap2(rgb_image: np.ndarray) -> np.float:
     """Return an image sharpness metric: sum(laplacian(image)**")"""
-    image_bw = np.mean(rgb_image, 2)
-    image_lap = ndimage.filters.laplace(image_bw)
+    image_bw: np.float = np.mean(rgb_image, 2)
+    image_lap: np.float = ndimage.filters.laplace(image_bw)
     return np.mean(image_lap.astype(np.float) ** 4)
 
 
-def sharpness_edge(image: np.ndarray):
+def sharpness_edge(image: np.ndarray) -> np.float:
     """Return a sharpness metric optimised for vertical lines"""
-    gray = np.mean(image.astype(float), 2)
-    n = 20
-    edge = np.array([[-1] * n + [1] * n])
+    gray: np.float = np.mean(image.astype(float), 2)
+    n: int = 20
+    edge: np.ndarray = np.array([[-1] * n + [1] * n])
     return np.sum(
         [np.sum(ndimage.filters.convolve(gray, W) ** 2) for W in [edge, edge.T]]
     )
@@ -161,7 +169,7 @@ class AutofocusExtension(BaseExtension):
 
     def measure_sharpness(
         self, microscope: Microscope, metric_fn: Callable = sharpness_sum_lap2
-    ):
+    ) -> np.float:
         """Measure the sharpness of the camera's current view."""
 
         if hasattr(microscope.camera, "array") and callable(
@@ -177,7 +185,7 @@ class AutofocusExtension(BaseExtension):
         dz: List[int],
         settle: float = 0.5,
         metric_fn: Callable = sharpness_sum_lap2,
-    ):
+    ) -> Tuple[List[int], List[np.float]]:
         """Perform a simple autofocus routine.
         The stage is moved to z positions (relative to current position) in dz,
         and at each position an image is captured and the sharpness function 
@@ -185,12 +193,12 @@ class AutofocusExtension(BaseExtension):
         highest.  No interpolation is performed.
         dz is assumed to be in ascending order (starting at -ve values)
         """
-        camera = microscope.camera
-        stage = microscope.stage
+        camera: BaseCamera = microscope.camera
+        stage: BaseStage = microscope.stage
 
         with set_properties(stage, backlash=256), stage.lock, camera.lock:
-            sharpnesses = []
-            positions = []
+            sharpnesses: List[np.float] = []
+            positions: List[int] = []
 
             # Some cameras may not have annotate_text. Reset if it does
             if getattr(camera, "annotate_text"):
@@ -198,29 +206,33 @@ class AutofocusExtension(BaseExtension):
 
             for _ in stage.scan_z(dz, return_to_start=False):
                 if current_action() and current_action().stopped:
-                    return
+                    return [], []
                 positions.append(stage.position[2])
                 time.sleep(settle)
                 sharpnesses.append(self.measure_sharpness(microscope, metric_fn))
 
-            newposition = positions[np.argmax(sharpnesses)]
+            newposition: int = positions[int(np.argmax(sharpnesses))]
             stage.move_rel((0, 0, newposition - stage.position[2]))
 
         return positions, sharpnesses
 
-    def move_and_find_focus(self, microscope: Microscope, dz: int):
+    def move_and_find_focus(self, microscope: Microscope, dz: int) -> int:
         """Make a relative Z move and return the peak sharpness position"""
         with monitor_sharpness(microscope) as m:
             m.focus_rel(dz)
             return m.sharpest_z_on_move(0)
 
-    def move_and_measure(self, microscope: Microscope, dz: int):
+    def move_and_measure(
+        self, microscope: Microscope, dz: int
+    ) -> Dict[str, np.ndarray]:
         """Make a relative Z move and return the sharpness data"""
         with monitor_sharpness(microscope) as m:
             m.focus_rel(dz)
             return m.data_dict()
 
-    def fast_autofocus(self, microscope: Microscope, dz: int = 2000):
+    def fast_autofocus(
+        self, microscope: Microscope, dz: int = 2000
+    ) -> Dict[str, np.ndarray]:
         """Perform a down-up-down-up autofocus"""
         with microscope.camera.lock, microscope.stage.lock:
             with monitor_sharpness(microscope) as m:
@@ -231,7 +243,7 @@ class AutofocusExtension(BaseExtension):
                 # z: Final z position after move
                 i, z = m.focus_rel(dz)
                 # Get the z position with highest sharpness from the previous move (index i)
-                fz = m.sharpest_z_on_move(i)
+                fz: int = m.sharpest_z_on_move(i)
                 # Move all the way to the start so it's consistent
                 # Store final absolute z position from this return move
                 i, z = m.focus_rel(-dz)
@@ -248,7 +260,7 @@ class AutofocusExtension(BaseExtension):
         target_z: int = 0,
         initial_move_up: bool = True,
         mini_backlash: int = 25,
-    ):
+    ) -> Dict[str, np.ndarray]:
         """Autofocus by measuring on the way down, and moving back up with feedback.
 
         This autofocus method is very efficient, as it only passes the peak once.
@@ -294,11 +306,15 @@ class AutofocusExtension(BaseExtension):
                     m.focus_rel(dz / 2)
                 # move down
                 logging.debug("Move down")
+                i: int
+                z: int
                 i, z = m.focus_rel(-dz)
                 # now inspect where the sharpest point is, and estimate the sharpness
                 # (JPEG size) that we should find at the start of the Z stack
+                jz: np.ndarray  # np.ndarray[float]
+                js: np.ndarray  # np.ndarray[float]
                 _, jz, js = m.move_data(i)
-                best_z = jz[np.argmax(js)]
+                best_z: int = jz[np.argmax(js)]
 
                 # now move to the start of the z stack
                 logging.debug("Move to the start of the z stack")
@@ -309,17 +325,19 @@ class AutofocusExtension(BaseExtension):
                 # We've deliberately undershot - figure out how much further we should move based on the curve
                 logging.debug("Calculate remining movement")
                 current_js = m.camera.stream.last.size
-                imax = np.argmax(js)  # we want to crop out just the bit below the peak
+                imax: int = int(
+                    np.argmax(js)
+                )  # we want to crop out just the bit below the peak
                 js = js[imax:]  # NB z is in DECREASING order
                 jz = jz[imax:]
-                inow = np.argmax(
-                    js < current_js
+                inow: int = int(
+                    np.argmax(js < current_js)
                 )  # use the curve we recorded to estimate our position
 
                 # So, the Z position corresponding to our current sharpness value is zs[inow]
                 # That means we should move forwards, by best_z - zs[inow]
                 logging.debug("Correction move")
-                correction_move = best_z + target_z - jz[inow]
+                correction_move: int = best_z + target_z - jz[inow]
                 logging.debug(
                     "Fast autofocus scan: correcting backlash by moving %s steps",
                     (correction_move),
diff --git a/openflexure_microscope/api/default_extensions/picamera_autocalibrate/recalibrate_utils.py b/openflexure_microscope/api/default_extensions/picamera_autocalibrate/recalibrate_utils.py
index 94d22a90..9f79b1de 100644
--- a/openflexure_microscope/api/default_extensions/picamera_autocalibrate/recalibrate_utils.py
+++ b/openflexure_microscope/api/default_extensions/picamera_autocalibrate/recalibrate_utils.py
@@ -78,10 +78,12 @@ def auto_expose_and_freeze_settings(camera: PiCamera):
 def channels_from_bayer_array(bayer_array: np.ndarray) -> np.ndarray:
     """Given the 'array' from a PiBayerArray, return the 4 channels."""
     bayer_pattern: List[Tuple[int, int]] = [(0, 0), (0, 1), (1, 0), (1, 1)]
-    channels: np.ndarray = np.zeros(
-        (4, bayer_array.shape[0] // 2, bayer_array.shape[1] // 2),
-        dtype=bayer_array.dtype,
+    channels_shape: Tuple[int, ...] = (
+        4,
+        bayer_array.shape[0] // 2,
+        bayer_array.shape[1] // 2,
     )
+    channels: np.ndarray = np.zeros(channels_shape, dtype=bayer_array.dtype)
     for i, offset in enumerate(bayer_pattern):
         # We simplify life by dealing with only one channel at a time.
         channels[i, :, :] = np.sum(
diff --git a/openflexure_microscope/api/dev_extensions/__init__.py b/openflexure_microscope/api/dev_extensions/__init__.py
index c5a0a811..0f098ecf 100644
--- a/openflexure_microscope/api/dev_extensions/__init__.py
+++ b/openflexure_microscope/api/dev_extensions/__init__.py
@@ -1,3 +1,3 @@
-from .tools import devtools_extension_v2
+from .tools import DevToolsExtension
 
-LABTHINGS_EXTENSIONS = [devtools_extension_v2]
+LABTHINGS_EXTENSIONS = [DevToolsExtension]
diff --git a/openflexure_microscope/api/dev_extensions/tools.py b/openflexure_microscope/api/dev_extensions/tools.py
index 81231bef..f8da0a03 100644
--- a/openflexure_microscope/api/dev_extensions/tools.py
+++ b/openflexure_microscope/api/dev_extensions/tools.py
@@ -6,6 +6,17 @@ from labthings.extensions import BaseExtension
 from labthings.views import ActionView
 
 
+class DevToolsExtension(BaseExtension):
+    def __init__(self) -> None:
+        super().__init__(
+            "org.openflexure.dev.tools",
+            version="0.1.0",
+            description="Actions to cause various traumatic events in the microscope, used for testing.",
+        )
+        self.add_view(RaiseException, "/raise")
+        self.add_view(SleepFor, "/sleep")
+
+
 class RaiseException(ActionView):
     def post(self):
         raise Exception("The developer raised an exception")
@@ -23,13 +34,3 @@ class SleepFor(ActionView):
         end = time.time()
         logging.info("Waking up!")
         return {"TimeAsleep": (end - start)}
-
-
-devtools_extension_v2 = BaseExtension(
-    "org.openflexure.dev.tools",
-    version="0.1.0",
-    description="Actions to cause various traumatic events in the microscope, used for testing.",
-)
-
-devtools_extension_v2.add_view(RaiseException, "/raise")
-devtools_extension_v2.add_view(SleepFor, "/sleep")
diff --git a/openflexure_microscope/camera/base.py b/openflexure_microscope/camera/base.py
index 126d3070..7f515d56 100644
--- a/openflexure_microscope/camera/base.py
+++ b/openflexure_microscope/camera/base.py
@@ -3,14 +3,16 @@ import io
 import logging
 import time
 from abc import ABCMeta, abstractmethod
-from collections import namedtuple
 from types import TracebackType
-from typing import BinaryIO, List, Optional, Tuple, Type, Union
+from typing import BinaryIO, List, NamedTuple, Optional, Tuple, Type, Union
 
 from labthings import ClientEvent, StrictLock
 
+
 # Class to store a frames metadata
-TrackerFrame = namedtuple("TrackerFrame", ["size", "time"])
+class TrackerFrame(NamedTuple):
+    size: int
+    time: float
 
 
 class FrameStream(io.BytesIO):
@@ -172,16 +174,17 @@ class BaseCamera(metaclass=ABCMeta):
 
     def start_worker(self, **_) -> bool:
         """Start the background camera thread if it isn't running yet."""
-        logging.debug(
+        logging.warning(
             "`start_worker` method has been deprecated and is no longer required. Please avoid calling this method."
         )
         return True
 
     def get_frame(self):
-        """Return the current camera frame."""
-        logging.debug(
-            "`camera.get_frame` method has been deprecated. Please use `camera.stream.getframe()."
-        )
+        """
+        Return the current camera frame.
+
+        Just an alias of self.stream.getframe()
+        """
         return self.stream.getframe()
 
     def __enter__(self):
diff --git a/openflexure_microscope/stage/sanga.py b/openflexure_microscope/stage/sanga.py
index 7d941987..22be38f3 100644
--- a/openflexure_microscope/stage/sanga.py
+++ b/openflexure_microscope/stage/sanga.py
@@ -101,7 +101,7 @@ class SangaStage(BaseStage):
         if "backlash" in config:
             # Construct backlash array
             backlash = axes_to_array(config["backlash"], ["x", "y", "z"], [0, 0, 0])
-            self.backlash = backlash
+            self.backlash = np.array(backlash)
         if "settle_time" in config:
             self.settle_time = config.get("settle_time")
 
diff --git a/openflexure_microscope/utilities.py b/openflexure_microscope/utilities.py
index 58d816ca..b0b22e28 100644
--- a/openflexure_microscope/utilities.py
+++ b/openflexure_microscope/utilities.py
@@ -1,18 +1,25 @@
 import base64
 import copy
 import logging
+import sys
 import time
 from contextlib import contextmanager
-from typing import Dict, List, Optional
+from typing import Dict, List, Optional, Tuple, Type, Union
 
 import numpy as np
 
+# TypedDict was added to typing in 3.8. Use typing_extensions for <3.8
+if sys.version_info >= (3, 8):
+    from typing import TypedDict  # pylint: disable=no-name-in-module
+else:
+    from typing_extensions import TypedDict
+
 
 class Timer(object):
-    def __init__(self, name):
-        self.name = name
-        self.start = None
-        self.end = None
+    def __init__(self, name: str):
+        self.name: str = name
+        self.start: Optional[float] = None
+        self.end: Optional[float] = None
 
     def __enter__(self):
         self.start = time.time()
@@ -22,19 +29,27 @@ class Timer(object):
         logging.debug("%s time: %s", self.name, self.end - self.start)
 
 
-def deserialise_array_b64(b64_string: str, dtype: str, shape: List[int]):
-    flat_arr = np.frombuffer(base64.b64decode(b64_string), dtype)
+JSONArrayType = TypedDict(
+    "JSONArrayType",
+    {"@type": str, "base64": str, "dtype": str, "shape": Tuple[int, ...]},
+)
+
+
+def deserialise_array_b64(
+    b64_string: str, dtype: Union[Type[np.dtype], str], shape: Tuple[int, ...]
+):
+    flat_arr: np.ndarray = np.frombuffer(base64.b64decode(b64_string), dtype)
     return flat_arr.reshape(shape)
 
 
-def serialise_array_b64(npy_arr: np.ndarray):
-    b64_string = base64.b64encode(npy_arr).decode("ascii")
-    dtype = str(npy_arr.dtype)
-    shape = npy_arr.shape
+def serialise_array_b64(npy_arr: np.ndarray) -> Tuple[str, str, Tuple[int, ...]]:
+    b64_string: str = base64.b64encode(npy_arr.tobytes()).decode("ascii")
+    dtype: str = str(npy_arr.dtype)
+    shape: Tuple[int, ...] = npy_arr.shape
     return b64_string, dtype, shape
 
 
-def ndarray_to_json(arr: np.ndarray):
+def ndarray_to_json(arr: np.ndarray) -> JSONArrayType:
     if isinstance(arr, memoryview):
         # We can transparently convert memoryview objects to arrays
         # This comes in very handy for the lens shading table.
@@ -43,7 +58,7 @@ def ndarray_to_json(arr: np.ndarray):
     return {"@type": "ndarray", "dtype": dtype, "shape": shape, "base64": b64_string}
 
 
-def json_to_ndarray(json_dict: dict):
+def json_to_ndarray(json_dict: JSONArrayType):
     if not json_dict.get("@type") != "ndarray":
         logging.warning("No valid @type attribute found. Conversion may fail.")
     for required_param in ("dtype", "shape", "base64"):
@@ -52,7 +67,7 @@ def json_to_ndarray(json_dict: dict):
 
     b64_string: Optional[str] = json_dict.get("base64")
     dtype: Optional[str] = json_dict.get("dtype")
-    shape: Optional[List[int]] = json_dict.get("shape")
+    shape: Optional[Tuple[int, ...]] = json_dict.get("shape")
 
     if b64_string and dtype and shape:
         return deserialise_array_b64(b64_string, dtype, shape)
diff --git a/poetry.lock b/poetry.lock
index b4c41f6a..ff67e3a7 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -278,7 +278,7 @@ python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
 
 [[package]]
 name = "importlib-metadata"
-version = "3.1.0"
+version = "3.1.1"
 description = "Read metadata from Python packages"
 category = "main"
 optional = false
@@ -288,8 +288,8 @@ python-versions = ">=3.6"
 zipp = ">=0.5"
 
 [package.extras]
-docs = ["sphinx", "rst.linker"]
-testing = ["packaging", "pep517", "unittest2", "importlib-resources (>=1.3)"]
+docs = ["sphinx", "jaraco.packaging (>=3.2)", "rst.linker (>=1.9)"]
+testing = ["pytest (>=3.5,!=3.7.3)", "pytest-checkdocs (>=1.2.3)", "pytest-flake8", "pytest-cov", "jaraco.test (>=3.2.0)", "packaging", "pep517", "pyfakefs", "flufl.flake8", "pytest-black (>=0.3.7)", "pytest-mypy", "importlib-resources (>=1.3)"]
 
 [[package]]
 name = "iniconfig"
@@ -336,7 +336,7 @@ i18n = ["Babel (>=0.8)"]
 
 [[package]]
 name = "labthings"
-version = "1.2.1"
+version = "1.2.2"
 description = "Python implementation of LabThings, based on the Flask microframework"
 category = "main"
 optional = false
@@ -421,6 +421,25 @@ category = "main"
 optional = false
 python-versions = ">=3.6"
 
+[[package]]
+name = "numpy-stubs"
+version = "0.0.1"
+description = ""
+category = "main"
+optional = false
+python-versions = "*"
+develop = false
+
+[package.dependencies]
+numpy = ">=1.16.0"
+typing_extensions = {version = ">=3.7.4", markers = "python_version < \"3.8\""}
+
+[package.source]
+type = "git"
+url = "https://github.com/numpy/numpy-stubs.git"
+reference = "master"
+resolved_reference = "c49d2d6875971a669a166ea93ef998911af283a1"
+
 [[package]]
 name = "opencv-python-headless"
 version = "4.4.0.44"
@@ -948,7 +967,7 @@ rpi = ["RPi.GPIO"]
 [metadata]
 lock-version = "1.1"
 python-versions = "^3.7.3"
-content-hash = "ec95ce987cd855cbcbdc4d7689dcbee7ca1f0154a60f5dddc3cecc02c92ddc75"
+content-hash = "2c0faa244099ec3433edfc2cb9321f5de8bd5c0c32e135cae23f91e717cb07d7"
 
 [metadata.files]
 alabaster = [
@@ -1082,8 +1101,8 @@ imagesize = [
     {file = "imagesize-1.2.0.tar.gz", hash = "sha256:b1f6b5a4eab1f73479a50fb79fcf729514a900c341d8503d62a62dbc4127a2b1"},
 ]
 importlib-metadata = [
-    {file = "importlib_metadata-3.1.0-py2.py3-none-any.whl", hash = "sha256:590690d61efdd716ff82c39ca9a9d4209252adfe288a4b5721181050acbd4175"},
-    {file = "importlib_metadata-3.1.0.tar.gz", hash = "sha256:d9b8a46a0885337627a6430db287176970fff18ad421becec1d64cfc763c2099"},
+    {file = "importlib_metadata-3.1.1-py3-none-any.whl", hash = "sha256:6112e21359ef8f344e7178aa5b72dc6e62b38b0d008e6d3cb212c5b84df72013"},
+    {file = "importlib_metadata-3.1.1.tar.gz", hash = "sha256:b0c2d3b226157ae4517d9625decf63591461c66b3a808c2666d538946519d170"},
 ]
 iniconfig = [
     {file = "iniconfig-1.1.1-py2.py3-none-any.whl", hash = "sha256:011e24c64b7f47f6ebd835bb12a743f2fbe9a26d4cecaa7f53bc4f35ee9da8b3"},
@@ -1102,8 +1121,8 @@ jinja2 = [
     {file = "Jinja2-2.11.2.tar.gz", hash = "sha256:89aab215427ef59c34ad58735269eb58b1a5808103067f7bb9d5836c651b3bb0"},
 ]
 labthings = [
-    {file = "labthings-1.2.1-py3-none-any.whl", hash = "sha256:0b4bf4b7348cab8638bc9ec6028a48197f201410e352c866d131618a9877acbc"},
-    {file = "labthings-1.2.1.tar.gz", hash = "sha256:f5f0fe319ef7aa2697e06f5969eb47dc834e7981c3726eab29472ee4f34c01ea"},
+    {file = "labthings-1.2.2-py3-none-any.whl", hash = "sha256:0f4fb76feed5ce9213d471f97700c4b52d9563f940954e1efb644889d3381d2d"},
+    {file = "labthings-1.2.2.tar.gz", hash = "sha256:62a8c5bceea25883a7f329a8e19bd95d211d4fe8ac7eb39ee2a2bd51befa4bd5"},
 ]
 lazy-object-proxy = [
     {file = "lazy-object-proxy-1.4.3.tar.gz", hash = "sha256:f3900e8a5de27447acbf900b4750b0ddfd7ec1ea7fbaf11dfa911141bc522af0"},
@@ -1219,6 +1238,7 @@ numpy = [
     {file = "numpy-1.19.2-pp36-pypy36_pp73-manylinux2010_x86_64.whl", hash = "sha256:0bfd85053d1e9f60234f28f63d4a5147ada7f432943c113a11afcf3e65d9d4c8"},
     {file = "numpy-1.19.2.zip", hash = "sha256:0d310730e1e793527065ad7dde736197b705d0e4c9999775f212b03c44a8484c"},
 ]
+numpy-stubs = []
 opencv-python-headless = [
     {file = "opencv-python-headless-4.4.0.44.tar.gz", hash = "sha256:6eefcacfb9b2da305277e1a93c7bf074dcd10b7aa154a0c963ded08fc0ffc02e"},
     {file = "opencv_python_headless-4.4.0.44-cp36-cp36m-macosx_10_13_x86_64.whl", hash = "sha256:0896413b35b4b64acae42b84f740a458e0520d51f806946adf185e710a2ab300"},
diff --git a/pyproject.toml b/pyproject.toml
index 8b1b33d3..59019852 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -43,10 +43,11 @@ expiringdict = "^1.2.1"
 camera-stage-mapping = "0.1.4"
 picamerax = ">=20.9.1"
 pyyaml = "^5.3.1"
-typing-extensions = "^3.7.4"  # Needed for some type-hints in Python < 3.8 (e.g. Literal)
 pytest-cov = "^2.10.1"
 piexif = "^1.1.3"
-labthings = "1.2.1"
+labthings = "1.2.2"
+typing-extensions = "^3.7.4"  # Needed for some type-hints in Python < 3.8 (e.g. Literal)
+numpy-stubs = {git = "https://github.com/numpy/numpy-stubs.git"}  # Needed for Numpy < 1.20
 
 [tool.poetry.extras]
 rpi = ["RPi.GPIO"]
@@ -66,7 +67,7 @@ poethepoet = "^0.9.0"
 freezegun = "^1.0.0"
 
 [tool.black]
-exclude = '(\.eggs|\.git|\.venv|node_modules/)'
+exclude = '(\.eggs|\.git|\.venv|\venv|node_modules/)'
 
 [tool.isort]
 multi_line_output = 3