From 9646058c373995bf3744451613ce752188152b70 Mon Sep 17 00:00:00 2001
From: Joel Collins <jtc9242@gmail.com>
Date: Tue, 28 Apr 2020 13:20:38 +0100
Subject: [PATCH 1/7] Code format

---
 openflexure_microscope/api/app.py             |   1 +
 .../api/default_extensions/__init__.py        |   2 +
 .../api/default_extensions/autofocus.py       |  33 +++--
 .../camera_stage_mapping/array_with_attrs.py  |  35 +++--
 .../camera_stage_calibration_1d.py            | 126 +++++++++-------
 .../camera_stage_tracker.py                   | 135 ++++++++++++------
 .../camera_stage_mapping/extension.py         |  85 +++++++----
 .../image_with_location.py                    |  99 ++++++++-----
 .../picamera_autocalibrate/extension.py       |  42 ++++--
 .../api/default_extensions/scan.py            |   2 +-
 .../api/v2/views/actions/__init__.py          |   2 +-
 openflexure_microscope/config.py              |   1 -
 openflexure_microscope/microscope.py          |   7 +-
 openflexure_microscope/utilities.py           |  12 +-
 14 files changed, 381 insertions(+), 201 deletions(-)

diff --git a/openflexure_microscope/api/app.py b/openflexure_microscope/api/app.py
index 3e8a8209..e3cce530 100644
--- a/openflexure_microscope/api/app.py
+++ b/openflexure_microscope/api/app.py
@@ -1,5 +1,6 @@
 #!/usr/bin/env python
 from gevent import monkey
+
 monkey.patch_all()
 
 import time
diff --git a/openflexure_microscope/api/default_extensions/__init__.py b/openflexure_microscope/api/default_extensions/__init__.py
index e90646d7..87ad694d 100644
--- a/openflexure_microscope/api/default_extensions/__init__.py
+++ b/openflexure_microscope/api/default_extensions/__init__.py
@@ -2,6 +2,7 @@ import logging
 import traceback
 from contextlib import contextmanager
 
+
 @contextmanager
 def handle_extension_error(extension_name):
     """'gracefully' log an error if an extension fails to load."""
@@ -12,6 +13,7 @@ def handle_extension_error(extension_name):
             f"Exception loading builtin extension picamera_autocalibrate: \n{traceback.format_exc()}"
         )
 
+
 with handle_extension_error("autofocus"):
     from .autofocus import autofocus_extension_v2
 with handle_extension_error("scan"):
diff --git a/openflexure_microscope/api/default_extensions/autofocus.py b/openflexure_microscope/api/default_extensions/autofocus.py
index fc9f4a0a..97ea2e45 100644
--- a/openflexure_microscope/api/default_extensions/autofocus.py
+++ b/openflexure_microscope/api/default_extensions/autofocus.py
@@ -51,7 +51,9 @@ class JPEGSharpnessMonitor:
     def start(self):
         "Start monitoring sharpness by looking at JPEG size"
         if not self.camera.stream_active:
-            logging.warn("Autofocus sharpness monitor was started but the camera isn't streaming.  Attempting to start the stream...")
+            logging.warn(
+                "Autofocus sharpness monitor was started but the camera isn't streaming.  Attempting to start the stream..."
+            )
             self.camera.start_stream_recording()
         self.background_thread = Thread(target=self._measure_jpegs)
         self.background_thread.start()
@@ -106,7 +108,9 @@ class JPEGSharpnessMonitor:
             stop = np.argmax(jpeg_times > stage_times[1])
         except ValueError as e:
             if np.sum(jpeg_times > stage_times[0]) == 0:
-                raise ValueError("No images were captured during the move of the stage.  Perhaps the camera is not streaming images?")
+                raise ValueError(
+                    "No images were captured during the move of the stage.  Perhaps the camera is not streaming images?"
+                )
             else:
                 raise e
         if stop < 1:
@@ -120,7 +124,9 @@ class JPEGSharpnessMonitor:
         """Return the z position of the sharpest image on a given move"""
         jt, jz, js = self.move_data(index)
         if len(js) == 0:
-            raise ValueError("No images were captured during the move of the stage.  Perhaps the camera is not streaming images?")
+            raise ValueError(
+                "No images were captured during the move of the stage.  Perhaps the camera is not streaming images?"
+            )
         return jz[np.argmax(js)]
 
     def data_dict(self):
@@ -212,7 +218,9 @@ def move_and_find_focus(microscope, dz):
 
 def fast_autofocus(microscope, dz=2000, backlash=None):
     """Perform a down-up-down-up autofocus"""
-    with monitor_sharpness(microscope) as m, microscope.camera.lock, microscope.stage.lock:
+    with monitor_sharpness(
+        microscope
+    ) as m, microscope.camera.lock, microscope.stage.lock:
         i, z = m.focus_rel(-dz / 2)
         i, z = m.focus_rel(dz)
         fz = m.sharpest_z_on_move(i)
@@ -262,7 +270,9 @@ def fast_up_down_up_autofocus(
             might slightly hurt accuracy, but is unlikely to be a big issue.  Too big
             may cause you to overshoot, which is a problem.
     """
-    with monitor_sharpness(microscope) as m, microscope.camera.lock, microscope.stage.lock:
+    with monitor_sharpness(
+        microscope
+    ) as m, microscope.camera.lock, microscope.stage.lock:
         # Ensure the MJPEG stream has started
         microscope.camera.start_stream_recording()
 
@@ -372,7 +382,9 @@ class FastAutofocusAPI(View):
 
         if microscope.has_real_stage():
             logging.debug("Running autofocus...")
-            task = taskify(fast_up_down_up_autofocus)(microscope, dz=dz, mini_backlash=backlash)
+            task = taskify(fast_up_down_up_autofocus)(
+                microscope, dz=dz, mini_backlash=backlash
+            )
 
             # return a handle on the autofocus task
             return task
@@ -382,12 +394,15 @@ class FastAutofocusAPI(View):
 
 
 autofocus_extension_v2 = BaseExtension(
-    "org.openflexure.autofocus", version="2.0.0",
-    description="Actions to move the microscope in Z and pick the point with the sharpest image."
+    "org.openflexure.autofocus",
+    version="2.0.0",
+    description="Actions to move the microscope in Z and pick the point with the sharpest image.",
 )
 
 autofocus_extension_v2.add_method(fast_autofocus, "fast_autofocus")
-autofocus_extension_v2.add_method(fast_up_down_up_autofocus, "fast_up_down_up_autofocus")
+autofocus_extension_v2.add_method(
+    fast_up_down_up_autofocus, "fast_up_down_up_autofocus"
+)
 autofocus_extension_v2.add_method(autofocus, "autofocus")
 
 autofocus_extension_v2.add_view(MeasureSharpnessAPI, "/measure_sharpness")
diff --git a/openflexure_microscope/api/default_extensions/camera_stage_mapping/array_with_attrs.py b/openflexure_microscope/api/default_extensions/camera_stage_mapping/array_with_attrs.py
index 61fe164a..db99d630 100644
--- a/openflexure_microscope/api/default_extensions/camera_stage_mapping/array_with_attrs.py
+++ b/openflexure_microscope/api/default_extensions/camera_stage_mapping/array_with_attrs.py
@@ -7,13 +7,14 @@ Created on Tue May 26 08:08:14 2015
 
 import numpy as np
 
+
 class AttributeDict(dict):
     """This class extends a dictionary to have a "create" method for
     compatibility with h5py attrs objects."""
-    
+
     def create(self, name, data):
         self[name] = data
-        
+
     def modify(self, name, data):
         self[name] = data
 
@@ -22,7 +23,8 @@ class AttributeDict(dict):
         for k in list(self.keys()):
             if isinstance(self[k], np.ndarray):
                 self[k] = np.copy(self[k])
-        
+
+
 def ensure_attribute_dict(obj, copy=False):
     """Given a mapping that may or not be an AttributeDict, return an
     AttributeDict object that either is, or copies the data of, the input."""
@@ -33,15 +35,17 @@ def ensure_attribute_dict(obj, copy=False):
         if copy:
             out.copy_arrays()
         return out
-        
+
+
 def ensure_attrs(obj):
     """Return an ArrayWithAttrs version of an array-like object, may be the
     original object if it already has attrs."""
-    if hasattr(obj, 'attrs'):
-        return obj #if it has attrs, do nothing
+    if hasattr(obj, "attrs"):
+        return obj  # if it has attrs, do nothing
     else:
-        return ArrayWithAttrs(obj) #otherwise, wrap it
-        
+        return ArrayWithAttrs(obj)  # otherwise, wrap it
+
+
 class ArrayWithAttrs(np.ndarray):
     """A numpy ndarray, with an AttributeDict accessible as array.attrs.
     
@@ -50,7 +54,7 @@ class ArrayWithAttrs(np.ndarray):
     a lot to the ``InfoArray`` example in `numpy` documentation on subclassing
     `numpy.ndarray`.
     """
-    
+
     def __new__(cls, input_array, attrs={}):
         """Make a new ndarray, based on an existing one, with an attrs dict.
         
@@ -64,26 +68,29 @@ class ArrayWithAttrs(np.ndarray):
         obj.attrs = ensure_attribute_dict(attrs)
         # return the new object
         return obj
-        
+
     def __array_finalize__(self, obj):
         # this is called by numpy when the object is created (__new__ may or
         # may not get called)
-        if obj is None: return # if obj is None, __new__ was called - do nothing
+        if obj is None:
+            return  # if obj is None, __new__ was called - do nothing
         # if we didn't create the object with __new__,  we must add the attrs
         # dictionary.  We copy this from the source object if possible (while
         # ensuring it's the right type) or create a new, empty one if not.
         # NB we don't use ensure_attribute_dict because we want to make sure the
         # dict object is *copied* not merely referenced.
-        self.attrs = ensure_attribute_dict(getattr(obj, 'attrs', {}), copy=True)
+        self.attrs = ensure_attribute_dict(getattr(obj, "attrs", {}), copy=True)
+
 
 def attribute_bundler(attrs):
     """Return a function that bundles the supplied attributes with an array."""
+
     def bundle_attrs(array):
         return ArrayWithAttrs(array, attrs=attrs)
 
 
 class DummyHDF5Group(dict):
-    def __init__(self,dictionary, attrs ={}, name="DummyHDF5Group"):
+    def __init__(self, dictionary, attrs={}, name="DummyHDF5Group"):
         super(DummyHDF5Group, self).__init__()
         self.attrs = attrs
         for key in dictionary:
@@ -92,4 +99,4 @@ class DummyHDF5Group(dict):
         self.basename = name
 
     file = None
-    parent = None
\ No newline at end of file
+    parent = None
diff --git a/openflexure_microscope/api/default_extensions/camera_stage_mapping/camera_stage_calibration_1d.py b/openflexure_microscope/api/default_extensions/camera_stage_mapping/camera_stage_calibration_1d.py
index 12554440..84636afc 100644
--- a/openflexure_microscope/api/default_extensions/camera_stage_mapping/camera_stage_calibration_1d.py
+++ b/openflexure_microscope/api/default_extensions/camera_stage_mapping/camera_stage_calibration_1d.py
@@ -12,9 +12,11 @@ from numpy.linalg import norm
 from .camera_stage_tracker import Tracker, move_until_motion_detected
 import logging
 
+
 def displacements(positions):
     """Calculate the absolute distance of each point from the first point."""
-    return norm(positions - positions[0,:][np.newaxis,:], axis=1)
+    return norm(positions - positions[0, :][np.newaxis, :], axis=1)
+
 
 def direction_from_points(points):
     """Given an Nx2 array of points, figure out the principal component.
@@ -25,7 +27,8 @@ def direction_from_points(points):
     points = points.astype(np.float)
     points -= np.mean(points, axis=0)[np.newaxis, :]
     eigenvalues, eigenvectors = np.linalg.eig(np.cov(points.T))
-    return eigenvectors[:,np.argmax(eigenvalues)]
+    return eigenvectors[:, np.argmax(eigenvalues)]
+
 
 def apply_backlash(x, backlash=0, start_unwound=True):
     """Apply a basic model of backlash to a set of coordinates.
@@ -42,14 +45,15 @@ def apply_backlash(x, backlash=0, start_unwound=True):
         y[0] = x[0] + initial_direction * backlash
     else:
         y[0] = x[0]
-    for i in range(1,len(x)):
-        d = x[i] - y[i-1]
+    for i in range(1, len(x)):
+        d = x[i] - y[i - 1]
         if np.abs(d) >= backlash:
             y[i] = x[i] - np.sign(d) * backlash
         else:
-            y[i] = y[i-1]
+            y[i] = y[i - 1]
     return y
 
+
 def fit_backlash(moves):
     """Given a set of linear moves forwards and back, estimate backlash.
 
@@ -99,7 +103,7 @@ def fit_backlash(moves):
         residuals = yfit - (xfit_blsh * m + c)
         return m, c, np.std(residuals, ddof=3)
 
-    max_backlash = (np.max(xfit) - np.min(xfit))/3
+    max_backlash = (np.max(xfit) - np.min(xfit)) / 3
     backlash_values = []
     residual_values = []
     backlash = 0
@@ -107,18 +111,18 @@ def fit_backlash(moves):
         m, c, residual = fit_motion(xfit, yfit, backlash)
         residual_values.append(residual)
         backlash_values.append(backlash)
-        backlash += max(1, backlash/3)
+        backlash += max(1, backlash / 3)
 
     backlash = backlash_values[np.argmin(residual_values)]
     m, c, residual = fit_motion(xfit, yfit, backlash)
 
-    fractional_error = residual/norm(np.diff(yfit))
+    fractional_error = residual / norm(np.diff(yfit))
     if fractional_error > 0.1:
         raise ValueError("The fit didn't look successful")
 
     return {
-        "backlash": backlash, 
-        "pixels_per_step": m, 
+        "backlash": backlash,
+        "pixels_per_step": m,
         "fractional_error": fractional_error,
         "stage_direction": stage_direction,
         "image_direction": image_direction,
@@ -126,36 +130,42 @@ def fit_backlash(moves):
     }
 
 
-def calibrate_backlash_1d(tracker, move, direction=np.array([1,0,0])):
+def calibrate_backlash_1d(tracker, move, direction=np.array([1, 0, 0])):
     """Figure out reasonable step sizes for calibration, and estimate the backlash."""
-    try: # Ensure that the tracker has a template set
+    try:  # Ensure that the tracker has a template set
         _ = tracker.template
     except:
         tracker.acquire_template()
     assert tracker.stage_positions.shape[0] == 1
-    original_stage_pos = tracker.stage_positions[-1,:]
+    original_stage_pos = tracker.stage_positions[-1, :]
 
-    direction = direction / np.sum(direction**2)**0.5 # ensure "direction" is normalised
+    direction = (
+        direction / np.sum(direction ** 2) ** 0.5
+    )  # ensure "direction" is normalised
 
     logging.info("Moving the stage until we see motion...")
     # Move the stage until we can see a significant amount of motion
     i, m = move_until_motion_detected(
-        tracker, move, direction, threshold=tracker.max_safe_displacement * 0.2)
-    
+        tracker, move, direction, threshold=tracker.max_safe_displacement * 0.2
+    )
+
     logging.info("Moving the stage to the edge of the field of view...")
     i, m = move_until_motion_detected(
-        tracker, move, direction, 
+        tracker,
+        move,
+        direction,
         threshold=tracker.max_safe_displacement * 0.7,
-        multipliers=m/2.0 * np.arange(20),
-        detect_cumulative_motion=True)
+        multipliers=m / 2.0 * np.arange(20),
+        detect_cumulative_motion=True,
+    )
     exponential_moves = tracker.history
 
     # Include this final step, and make a rough estimate of the scaling from stage to image
     stage_pos, image_pos = tracker.history
     stage_step = stage_pos[-1, :] - stage_pos[-1 - i, :]
     image_step = image_pos[-1, :] - image_pos[-1 - i, :]
-    steps_per_pixel = norm(stage_step)/norm(image_step)
-    
+    steps_per_pixel = norm(stage_step) / norm(image_step)
+
     # Calculate a step that moves roughly 0.2 times the max. displacement (i.e. 0.1 times the FoV)
     sensible_step = direction * tracker.max_safe_displacement * 0.2 * steps_per_pixel
     tracker.reset_history()
@@ -167,27 +177,35 @@ def calibrate_backlash_1d(tracker, move, direction=np.array([1,0,0])):
     starting_stage_pos, starting_camera_pos = tracker.append_point()
     for i in range(15):
         move(starting_stage_pos - sensible_step * (i + 1))
-        #print(".", end="")
+        # print(".", end="")
         stage_pos, image_pos = tracker.append_point()
-        if (i > 3 and tracker.moving_away_from_centre 
-            and norm(image_pos) > 0.65 * tracker.max_safe_displacement):
-            break # Stop once we have moved far enough
+        if (
+            i > 3
+            and tracker.moving_away_from_centre
+            and norm(image_pos) > 0.65 * tracker.max_safe_displacement
+        ):
+            break  # Stop once we have moved far enough
 
     logging.info("Moving the stage forwards to measure backlash (2/2)")
     # Move forwards again, in 10 steps
     starting_stage_pos, starting_camera_pos = tracker.append_point()
     for i in range(15):
         move(starting_stage_pos + sensible_step * (i + 1))
-        #print(".", end="")
+        # print(".", end="")
         stage_pos, image_pos = tracker.append_point()
-        if (i > 3 and tracker.moving_away_from_centre 
-            and norm(image_pos) > 0.65 * tracker.max_safe_displacement):
-            break # Stop once we have moved far enough
+        if (
+            i > 3
+            and tracker.moving_away_from_centre
+            and norm(image_pos) > 0.65 * tracker.max_safe_displacement
+        ):
+            break  # Stop once we have moved far enough
     linear_moves = tracker.history
 
     try:
         res = fit_backlash(linear_moves)
-        backlash_correction = sensible_step / norm(sensible_step) * res["backlash"] * 1.5
+        backlash_correction = (
+            sensible_step / norm(sensible_step) * res["backlash"] * 1.5
+        )
 
         # Finally, move back to the starting position, doing backlash-corrected moves.
         logging.info("Moving back to the start, correcting for backlash...")
@@ -200,32 +218,39 @@ def calibrate_backlash_1d(tracker, move, direction=np.array([1,0,0])):
         backlash_corrected_moves = tracker.history
         move(original_stage_pos - backlash_correction)
     except ValueError:
-        return {"exponential_moves": exponential_moves, "linear_moves": linear_moves,}
+        return {"exponential_moves": exponential_moves, "linear_moves": linear_moves}
     finally:
         # Reset position
         move(original_stage_pos)
 
     logging.info(f"Estimated backlash {res['backlash']:.0f} steps")
-    logging.info(f"Stage-to-image ratio {np.abs(res['pixels_per_step']):.3f} pixels/step")
-    logging.info(f"Residuals were about {res['fractional_error']:.2f} times the step size")
+    logging.info(
+        f"Stage-to-image ratio {np.abs(res['pixels_per_step']):.3f} pixels/step"
+    )
+    logging.info(
+        f"Residuals were about {res['fractional_error']:.2f} times the step size"
+    )
 
-    res.update({
-        "exponential_moves": exponential_moves,
-        "linear_moves": linear_moves,
-        "backlash_corrected_moves": backlash_corrected_moves
-    })
+    res.update(
+        {
+            "exponential_moves": exponential_moves,
+            "linear_moves": linear_moves,
+            "backlash_corrected_moves": backlash_corrected_moves,
+        }
+    )
     return res
 
 
 def plot_1d_backlash_calibration(results):
     """Plot the results of a calibration run"""
     from matplotlib import pyplot as plt
-    f, ax = plt.subplots(1,2)
-    
+
+    f, ax = plt.subplots(1, 2)
+
     for k in ["exponential", "linear", "backlash_corrected"]:
-        moves = results[k+"_moves"]
+        moves = results[k + "_moves"]
         if moves is not None:
-            ax[0].plot(moves[1][:,0], moves[1][:,1], 'o-')
+            ax[0].plot(moves[1][:, 0], moves[1][:, 1], "o-")
     ax[0].set_aspect(1, adjustable="datalim")
 
     image_direction = results["image_direction"]
@@ -237,19 +262,20 @@ def plot_1d_backlash_calibration(results):
         image_1d = np.sum(image_pos * image_direction[np.newaxis, :], axis=1)
         return stage_1d, image_1d
 
-    ax[1].plot(*convert_moves(results["exponential_moves"]), 'o-')
-    
+    ax[1].plot(*convert_moves(results["exponential_moves"]), "o-")
+
     stage_pos, image_pos = convert_moves(results["linear_moves"])
     model = apply_backlash(stage_pos, results["backlash"])
     model *= results["pixels_per_step"]
     model += np.mean(image_pos) - np.mean(model)
-    ax[1].plot(stage_pos, model, '-')
-    ax[1].plot(stage_pos, image_pos, 'o')
+    ax[1].plot(stage_pos, model, "-")
+    ax[1].plot(stage_pos, image_pos, "o")
     if results["backlash_corrected_moves"] is not None:
-        ax[1].plot(*convert_moves(results["backlash_corrected_moves"]), '+')
+        ax[1].plot(*convert_moves(results["backlash_corrected_moves"]), "+")
 
     return f, ax
 
+
 def image_to_stage_displacement_from_1d(calibrations):
     """Combine X and Y calibrations
 
@@ -271,9 +297,11 @@ def image_to_stage_displacement_from_1d(calibrations):
         c_blash = np.abs(cal["backlash"] * cal["stage_direction"])
         backlash[backlash < c_blash] = c_blash[backlash < c_blash]
 
-    A, res, rank, s = np.linalg.lstsq(image_vectors, stage_vectors) # we solve image*A = stage
+    A, res, rank, s = np.linalg.lstsq(
+        image_vectors, stage_vectors
+    )  # we solve image*A = stage
     return {
         "image_to_stage_displacement": A,
         "backlash_vector": backlash,
         "backlash": np.max(backlash),
-    }
\ No newline at end of file
+    }
diff --git a/openflexure_microscope/api/default_extensions/camera_stage_mapping/camera_stage_tracker.py b/openflexure_microscope/api/default_extensions/camera_stage_mapping/camera_stage_tracker.py
index 9c7a7235..a065216b 100644
--- a/openflexure_microscope/api/default_extensions/camera_stage_mapping/camera_stage_tracker.py
+++ b/openflexure_microscope/api/default_extensions/camera_stage_mapping/camera_stage_tracker.py
@@ -12,10 +12,11 @@ from numpy.linalg import norm
 import cv2
 from scipy import ndimage
 
+
 def central_half(image):
     """Return the central 50% (in X and Y) of an image"""
     w, h = image.shape[:2]
-    return image[int(w/4):int(3*w/4),int(h/4):int(3*h/4), ...]
+    return image[int(w / 4) : int(3 * w / 4), int(h / 4) : int(3 * h / 4), ...]
 
 
 def datum_pixel(image):
@@ -23,7 +24,8 @@ def datum_pixel(image):
     try:
         return np.array(image.datum_pixel)
     except:
-        return (np.array(image.shape[:2]) - 1) / 2.
+        return (np.array(image.shape[:2]) - 1) / 2.0
+
 
 def locate_feature_in_image(image, feature, margin=0, restrict=False):
     """Find the given feature (small image) and return the position of its datum (or centre) in the image's pixels.
@@ -47,31 +49,51 @@ def locate_feature_in_image(image, feature, margin=0, restrict=False):
     image to yield the position in the sample of the feature you're looking for.
     """
     # The line below is superfluous if we keep the datum-aware code below it.
-    assert image.shape[0] > feature.shape[0] and image.shape[1] > feature.shape[1], "Image must be larger than feature!"
+    assert (
+        image.shape[0] > feature.shape[0] and image.shape[1] > feature.shape[1]
+    ), "Image must be larger than feature!"
     # Check that there's enough space around the feature image
     lower_margin = datum_pixel(image) - datum_pixel(feature)
-    upper_margin = (image.shape[:2] - datum_pixel(image)) - (feature.shape[:2] - datum_pixel(feature))
-    assert np.all(np.array([lower_margin, upper_margin]) >= margin), "The feature image is too large."
-    #TODO: sensible auto-crop of the template if it's too large?
-    image_shift = np.array((0,0))
+    upper_margin = (image.shape[:2] - datum_pixel(image)) - (
+        feature.shape[:2] - datum_pixel(feature)
+    )
+    assert np.all(
+        np.array([lower_margin, upper_margin]) >= margin
+    ), "The feature image is too large."
+    # TODO: sensible auto-crop of the template if it's too large?
+    image_shift = np.array((0, 0))
     if restrict:
         # if requested, crop the larger image so that our search area is (2*margin + 1) square.
-        image_shift = np.array(lower_margin - margin,dtype = int)
-        image = image[image_shift[0]:image_shift[0] + feature.shape[0] + 2 * margin + 1,
-                      image_shift[1]:image_shift[1] + feature.shape[1] + 2 * margin + 1, ...]
+        image_shift = np.array(lower_margin - margin, dtype=int)
+        image = image[
+            image_shift[0] : image_shift[0] + feature.shape[0] + 2 * margin + 1,
+            image_shift[1] : image_shift[1] + feature.shape[1] + 2 * margin + 1,
+            ...,
+        ]
 
-    corr = cv2.matchTemplate(image, feature,
-                             cv2.TM_SQDIFF_NORMED)  # correlate them: NB the match position is the MINIMUM
-    corr = -corr # invert the image so we can find a peak
-    corr += (corr.max() - corr.min()) * 0.1 - corr.max()  # background-subtract 90% of maximum
+    corr = cv2.matchTemplate(
+        image, feature, cv2.TM_SQDIFF_NORMED
+    )  # correlate them: NB the match position is the MINIMUM
+    corr = -corr  # invert the image so we can find a peak
+    corr += (
+        corr.max() - corr.min()
+    ) * 0.1 - corr.max()  # background-subtract 90% of maximum
     corr = cv2.threshold(corr, 0, 0, cv2.THRESH_TOZERO)[
-        1]  # zero out any negative pixels - but there should always be > 0 nonzero pixels
-    assert np.sum(corr) > 0, "Error: the correlation image doesn't have any nonzero pixels."
-    peak = ndimage.measurements.center_of_mass(corr)  # take the centroid (NB this is of grayscale values, not binary)
-    pos = np.array(peak) + image_shift + datum_pixel(feature) # return the position of the feature's datum point.
+        1
+    ]  # zero out any negative pixels - but there should always be > 0 nonzero pixels
+    assert (
+        np.sum(corr) > 0
+    ), "Error: the correlation image doesn't have any nonzero pixels."
+    peak = ndimage.measurements.center_of_mass(
+        corr
+    )  # take the centroid (NB this is of grayscale values, not binary)
+    pos = (
+        np.array(peak) + image_shift + datum_pixel(feature)
+    )  # return the position of the feature's datum point.
     return pos
 
-class Tracker():
+
+class Tracker:
     def __init__(self, grab_image, get_position, settle=None):
         """A class to manage moving the stage and following motion in the image
         
@@ -98,11 +120,11 @@ class Tracker():
         self.margin = np.array([0, 0])
         self._template_position = np.array([0.0, 0.0])
         self.image_shape = None
-    
+
     def get_position(self):
         """Get the position of the stage"""
         return np.array(self._get_position())
-    
+
     def settle(self):
         """Wait a short time and discard an image so the stage is no longer wobbling."""
         if self._settle is not None:
@@ -110,7 +132,7 @@ class Tracker():
         else:
             time.sleep(0.3)
             self._grab_image()
-            
+
     @property
     def template(self):
         """The template image (should be a numpy array)"""
@@ -118,12 +140,14 @@ class Tracker():
             raise ValueError("Attempt to use the tracker before setting the template")
         else:
             return self._template
-        
+
     @template.setter
     def template(self, new_value):
         self._template = new_value
-        
-    def acquire_template(self, settle=True, reset_history=True, relative_positions=True):
+
+    def acquire_template(
+        self, settle=True, reset_history=True, relative_positions=True
+    ):
         """Take a new image, and use it as the template.  NB this records the initial point.
         
         We will wait for the stage to settle, then acquire a new image to use as the template.
@@ -151,26 +175,32 @@ class Tracker():
         self.margin = np.array(image.shape)[:2] - np.array(self.template.shape)[:2]
         if reset_history:
             self.reset_history()
-        self._template_position = np.array([0., 0.])
+        self._template_position = np.array([0.0, 0.0])
         if relative_positions:
-            self._template_position = self.track_image(image) # Position should be zero initially
+            self._template_position = self.track_image(
+                image
+            )  # Position should be zero initially
         self.append_point(settle=False)
-        
+
     @property
     def max_displacement(self):
         """The highest position values that can be tracked"""
-        return self.margin // 2 # TODO: be cleverer about non-trivial values of template_position
-    
+        return (
+            self.margin // 2
+        )  # TODO: be cleverer about non-trivial values of template_position
+
     @property
     def min_displacement(self):
         """The lowest position values that can be tracked"""
-        return -self.max_displacement # TODO: be cleverer about non-trivial template_position values
-    
+        return (
+            -self.max_displacement
+        )  # TODO: be cleverer about non-trivial template_position values
+
     @property
     def max_safe_displacement(self):
         """The biggest displacement we can safely attempt to track without knowing direction."""
         return np.min(np.concatenate([self.max_displacement, -self.min_displacement]))
-            
+
     def track_image(self, image):
         """Find the position of the image relative to the template
         
@@ -182,8 +212,8 @@ class Tracker():
         a minus sign in front of `locate_feature_in_image` in the source
         code.
         """
-        return - locate_feature_in_image(image, self.template) - self._template_position
-    
+        return -locate_feature_in_image(image, self.template) - self._template_position
+
     def append_point(self, settle=True, image=None):
         """Find the current position using both stage and image, and append it"""
         if settle:
@@ -195,22 +225,22 @@ class Tracker():
         self._image_positions.append(image_pos)
         self._stage_positions.append(stage_pos)
         return stage_pos, image_pos
-        
+
     @property
     def stage_positions(self):
         """An array of positions we have moved the stage to"""
         return np.array(self._stage_positions)
-    
+
     @property
     def image_positions(self):
         """An array of positions we have moved the stage to"""
         return np.array(self._image_positions)
-    
+
     @property
     def history(self):
         """Return arrays of stage, image positions"""
         return self.stage_positions, self.image_positions
-    
+
     def reset_history(self, leave_first_point=False):
         """Reset the positions and displacements recorded"""
         if leave_first_point:
@@ -232,10 +262,17 @@ class Tracker():
         if len(self.image_positions) < 2:
             return None
         else:
-            return norm(self.image_positions[-1,:]) > norm(self.image_positions[-2])
-    
-   
-def move_until_motion_detected(tracker, move, displacement, threshold=10, multipliers=2**np.arange(16), detect_cumulative_motion=False):
+            return norm(self.image_positions[-1, :]) > norm(self.image_positions[-2])
+
+
+def move_until_motion_detected(
+    tracker,
+    move,
+    displacement,
+    threshold=10,
+    multipliers=2 ** np.arange(16),
+    detect_cumulative_motion=False,
+):
     """Move the stage until we can detect motion in the camera.
     
     We move the stage in the direction given by ``displacement`` until the 
@@ -259,14 +296,21 @@ def move_until_motion_detected(tracker, move, displacement, threshold=10, multip
     `displacement * m`.
     """
     displacement = np.array(displacement)
-    starting_image_position = tracker.image_positions[0 if detect_cumulative_motion else -1, :]
+    starting_image_position = tracker.image_positions[
+        0 if detect_cumulative_motion else -1, :
+    ]
     starting_stage_position = tracker.stage_positions[-1, :]
     for i, m in enumerate(multipliers):
         move(starting_stage_position + displacement * m)
         tracker.append_point()
         if norm(tracker.image_positions[-1, :] - starting_image_position) >= threshold:
             return i + 1, m
-    raise Exception("Moved the stage by {} but saw no motion.".format(multipliers[-1] * displacement))
+    raise Exception(
+        "Moved the stage by {} but saw no motion.".format(
+            multipliers[-1] * displacement
+        )
+    )
+
 
 def concatenate_tracker_histories(histories):
     """Combine a number of separate tracker history entries into one
@@ -286,4 +330,3 @@ def concatenate_tracker_histories(histories):
     """
     components = zip(*histories)
     return tuple(np.concatenate(c, axis=1) for c in components)
-    
\ No newline at end of file
diff --git a/openflexure_microscope/api/default_extensions/camera_stage_mapping/extension.py b/openflexure_microscope/api/default_extensions/camera_stage_mapping/extension.py
index 50648237..cbb02235 100644
--- a/openflexure_microscope/api/default_extensions/camera_stage_mapping/extension.py
+++ b/openflexure_microscope/api/default_extensions/camera_stage_mapping/extension.py
@@ -6,7 +6,12 @@ This file contains the HTTP API for camera/stage calibration.
 from labthings.server.view import View
 from labthings.server.find import find_component
 from labthings.server.extensions import BaseExtension
-from labthings.server.decorators import marshal_task, ThingAction, use_args, ThingProperty
+from labthings.server.decorators import (
+    marshal_task,
+    ThingAction,
+    use_args,
+    ThingProperty,
+)
 from labthings.server import fields
 
 from labthings.core.tasks import taskify
@@ -23,7 +28,10 @@ import io
 import os
 import json
 
-from .camera_stage_calibration_1d import calibrate_backlash_1d, image_to_stage_displacement_from_1d
+from .camera_stage_calibration_1d import (
+    calibrate_backlash_1d,
+    image_to_stage_displacement_from_1d,
+)
 from .camera_stage_tracker import Tracker
 
 from openflexure_microscope.utilities import axes_to_array
@@ -33,15 +41,15 @@ from openflexure_microscope.config import JSONEncoder
 CSM_DATAFILE_NAME = "csm_calibration.json"
 CSM_DATAFILE_PATH = data_file_path(CSM_DATAFILE_NAME)
 
+
 class CSMExtension(BaseExtension):
     """
     Use the camera as an encoder, so we can relate camera and stage coordinates
     """
+
     def __init__(self):
         BaseExtension.__init__(
-            self,
-            "org.openflexure.camera_stage_mapping",
-            version="0.0.1",
+            self, "org.openflexure.camera_stage_mapping", version="0.0.1"
         )
 
     _microscope = None
@@ -52,10 +60,10 @@ class CSMExtension(BaseExtension):
         if self._microscope is None:
             self._microscope = find_component("org.openflexure.microscope")
         return self._microscope
-    
+
     def update_settings(self, settings):
         """Update the stored extension settings dictionary"""
-        keys = ["extensions",self.name]
+        keys = ["extensions", self.name]
         dictionary = create_from_path(keys)
         set_by_path(dictionary, keys, settings)
         logging.info(f"Updating settings with {dictionary}")
@@ -64,20 +72,20 @@ class CSMExtension(BaseExtension):
 
     def get_settings(self):
         """Retrieve the settings for this extension"""
-        keys = ["extensions",self.name]
+        keys = ["extensions", self.name]
         return get_by_path(self.microscope.read_settings(), keys)
 
     def camera_stage_functions(self):
         """Return functions that allow us to interface with the microscope"""
-        self.microscope.camera.start_worker() # ensure the worker thread is running, so there is an MJPEG stream
-        
+        self.microscope.camera.start_worker()  # ensure the worker thread is running, so there is an MJPEG stream
+
         def grab_image():
             jpeg = self.microscope.camera.get_frame()
             return np.array(PIL.Image.open(io.BytesIO(jpeg)))
-        
+
         def get_position():
             return self.microscope.stage.position
-        
+
         move = self.microscope.stage.move_abs
 
         return grab_image, get_position, move
@@ -96,10 +104,10 @@ class CSMExtension(BaseExtension):
     def calibrate_xy(self):
         """Move the microscope's stage in X and Y, to calibrate its relationship to the camera"""
         logging.info("Calibrating X axis:")
-        cal_x = self.calibrate_1d(np.array([1,0,0]))
+        cal_x = self.calibrate_1d(np.array([1, 0, 0]))
         logging.info("Calibrating Y axis:")
-        cal_y = self.calibrate_1d(np.array([0,1,0]))
-        
+        cal_y = self.calibrate_1d(np.array([0, 1, 0]))
+
         # Combine X and Y calibrations to make a 2D calibration
         cal_xy = image_to_stage_displacement_from_1d([cal_x, cal_y])
         self.update_settings(cal_xy)
@@ -110,7 +118,7 @@ class CSMExtension(BaseExtension):
             "linear_calibration_y": cal_y,
         }
 
-        with open(CSM_DATAFILE_PATH, 'w') as f:
+        with open(CSM_DATAFILE_PATH, "w") as f:
             json.dump(data, f, cls=JSONEncoder)
 
         return data
@@ -130,27 +138,28 @@ class CSMExtension(BaseExtension):
         self.microscope.stage.move_rel([relative_move[0], relative_move[1], 0])
 
 
-
-
 csm_extension = CSMExtension()
 
+
 @ThingAction
 class Calibrate1DView(View):
-    @use_args({
-        "direction": fields.List(fields.Float(), required=True, example=[1,0,0])
-    })
+    @use_args(
+        {"direction": fields.List(fields.Float(), required=True, example=[1, 0, 0])}
+    )
     @marshal_task
     def post(self, args):
         """Calibrate one axis of the microscope stage against the camera."""
-        
+
         direction = np.array(args.get("direction"))
 
         task = taskify(csm_extension.calibrate_1d)(direction)
 
         return task
 
+
 csm_extension.add_view(Calibrate1DView, "/calibrate_1d")
 
+
 @ThingAction
 class CalibrateXYView(View):
     @marshal_task
@@ -160,24 +169,39 @@ class CalibrateXYView(View):
 
         return task
 
+
 csm_extension.add_view(CalibrateXYView, "/calibrate_xy")
 
 
 @ThingAction
 class MoveInImageCoordinatesView(View):
-    @use_args({
-        "x": fields.Float(description="The number of pixels to move in X", required=True, example=100),
-        "y": fields.Float(description="The number of pixels to move in Y", required=True, example=100),
-    })
+    @use_args(
+        {
+            "x": fields.Float(
+                description="The number of pixels to move in X",
+                required=True,
+                example=100,
+            ),
+            "y": fields.Float(
+                description="The number of pixels to move in Y",
+                required=True,
+                example=100,
+            ),
+        }
+    )
     def post(self, args):
         logging.debug("moving in pixels")
         """Move the microscope stage, such that we move by a given number of pixels on the camera"""
-        csm_extension.move_in_image_coordinates(np.array([args.get("x"), args.get("y")]))
-        
+        csm_extension.move_in_image_coordinates(
+            np.array([args.get("x"), args.get("y")])
+        )
+
         return csm_extension.microscope.state["stage"]["position"]
 
+
 csm_extension.add_view(MoveInImageCoordinatesView, "/move_in_image_coordinates")
 
+
 @ThingProperty
 class GetCalibrationFile(View):
     def get(self):
@@ -186,9 +210,10 @@ class GetCalibrationFile(View):
         datafile_path = CSM_DATAFILE_PATH
 
         if os.path.isfile(datafile_path):
-            with open(datafile_path, 'rb') as f:
+            with open(datafile_path, "rb") as f:
                 return json.load(f)
         else:
             return {}
 
-csm_extension.add_view(GetCalibrationFile, "/get_calibration")
\ No newline at end of file
+
+csm_extension.add_view(GetCalibrationFile, "/get_calibration")
diff --git a/openflexure_microscope/api/default_extensions/camera_stage_mapping/image_with_location.py b/openflexure_microscope/api/default_extensions/camera_stage_mapping/image_with_location.py
index baef69d6..a0063169 100644
--- a/openflexure_microscope/api/default_extensions/camera_stage_mapping/image_with_location.py
+++ b/openflexure_microscope/api/default_extensions/camera_stage_mapping/image_with_location.py
@@ -38,9 +38,11 @@ from past.utils import old_div
 import numpy as np
 from array_with_attrs import ArrayWithAttrs, ensure_attrs
 import cv2
-#import cv2.cv
+
+# import cv2.cv
 from scipy import ndimage
 
+
 class ImageWithLocation(ArrayWithAttrs):
     """An image, as a numpy array, with attributes to provide location information
     
@@ -49,9 +51,10 @@ class ImageWithLocation(ArrayWithAttrs):
     that we use to store the crucial mapping from pixels in the image to position in the
     sample.  
     """
-#    def __array_finalize__(self, obj):
-#        """Ensure that the object is a properly set-up ImageWithLocation"""
-#        ArrayWithAttrs.__array_finalize__(self, obj) # Ensure we have self.attrs
+
+    #    def __array_finalize__(self, obj):
+    #        """Ensure that the object is a properly set-up ImageWithLocation"""
+    #        ArrayWithAttrs.__array_finalize__(self, obj) # Ensure we have self.attrs
     def __getitem__(self, item):
         """Update the metadata when we extract a slice"""
         try:
@@ -61,18 +64,24 @@ class ImageWithLocation(ArrayWithAttrs):
             assert isinstance(item[0], slice), "First index was not a slice"
             assert isinstance(item[1], slice), "Second index was not a slice"
             start = np.array([item[i].start for i in range(2)])
-            start = np.where(start == np.array(None), 0, start) # missing start points are equivalent to zero
+            start = np.where(
+                start == np.array(None), 0, start
+            )  # missing start points are equivalent to zero
             step = np.array([item[i].step for i in range(2)])
-            step = np.where(step == np.array(None), 1, step) # missing step is equivalent to step==1
+            step = np.where(
+                step == np.array(None), 1, step
+            )  # missing step is equivalent to step==1
         except:
             # If the above doesn't work, assume we're not dealing with a 2D slice and give up.
-            return super(ImageWithLocation, self).__getitem__(item) # pass it on up
+            return super(ImageWithLocation, self).__getitem__(item)  # pass it on up
 
-        out = super(ImageWithLocation, self).__getitem__(item) # retrieve the slice
-        out.datum_pixel -= start # adjust the datum pixel so it refers to the same part of the image
+        out = super(ImageWithLocation, self).__getitem__(item)  # retrieve the slice
+        out.datum_pixel -= (
+            start
+        )  # adjust the datum pixel so it refers to the same part of the image
         # Next, we adjust the constant part of the pixel-sample matrix so pixels stay in the same place
-        location_shift = np.dot(ensure_3d(start), self.pixel_to_sample_matrix[:3,:3])
-        out.pixel_to_sample_matrix[3,:3] += location_shift
+        location_shift = np.dot(ensure_3d(start), self.pixel_to_sample_matrix[:3, :3])
+        out.pixel_to_sample_matrix[3, :3] += location_shift
         if not np.all(step == 1):
             # if we're downsampling, remember to scale datum_pixel accordingly
             out.datum_pixel = old_div(out.datum_pixel, step)
@@ -105,18 +114,22 @@ class ImageWithLocation(ArrayWithAttrs):
         A 2- or 3- element position, to match the size of location passed in.
         """
         l = ensure_2d(location)
-        l = l[:2]-self.pixel_to_sample_matrix[3,:2]
-        p = np.dot(l, np.linalg.inv(self.pixel_to_sample_matrix[:2,:2]))
+        l = l[:2] - self.pixel_to_sample_matrix[3, :2]
+        p = np.dot(l, np.linalg.inv(self.pixel_to_sample_matrix[:2, :2]))
         if check_bounds:
             assert np.all(0 <= p[0:2]), "The location was not within the image"
-            assert np.all(p[0:2] <= self.shape[0:2]), "The location was not within the image"
-            assert np.abs(p[2]) < z_tolerance, "The location was too far away from the plane of the image"
+            assert np.all(
+                p[0:2] <= self.shape[0:2]
+            ), "The location was not within the image"
+            assert (
+                np.abs(p[2]) < z_tolerance
+            ), "The location was too far away from the plane of the image"
         if len(location) == 2:
             return p[:2]
         else:
             return p[:3]
 
-    def feature_at(self, centre_position, size=(100,100), set_datum_to_centre=True):
+    def feature_at(self, centre_position, size=(100, 100), set_datum_to_centre=True):
         """Return a thumbnail cropped out of this image, centred on a particular pixel position.
 
         This is simply a convenience method that saves typing over the usual slice syntax.  Below are two equivalent
@@ -139,14 +152,25 @@ class ImageWithLocation(ArrayWithAttrs):
             float(size[0])
             float(size[1])
         except:
-            raise IndexError("Error: arguments of feature_at were invalid: {}, {}".format(centre_position, size))
+            raise IndexError(
+                "Error: arguments of feature_at were invalid: {}, {}".format(
+                    centre_position, size
+                )
+            )
         pos = centre_position
 
         # For now, rely on numpy to complain if the feature is outside the image.  May do bound-checking at some point.
         # If so, we might need to think carefully about the datum pixel of the resulting image.
-        thumb = self[pos[0] - old_div(size[0],2):pos[0] + old_div(size[0],2), pos[1] - old_div(size[1],2):pos[1] + old_div(size[1],2), ...]
+        thumb = self[
+            pos[0] - old_div(size[0], 2) : pos[0] + old_div(size[0], 2),
+            pos[1] - old_div(size[1], 2) : pos[1] + old_div(size[1], 2),
+            ...,
+        ]
         if set_datum_to_centre:
-            thumb.datum_pixel = (old_div(size[0],2), old_div(size[1],2)) # Make the datum point of the new image its centre.
+            thumb.datum_pixel = (
+                old_div(size[0], 2),
+                old_div(size[1], 2),
+            )  # Make the datum point of the new image its centre.
         return thumb
 
     def downsample(self, n):
@@ -156,7 +180,9 @@ class ImageWithLocation(ArrayWithAttrs):
         to noise.  Currently it just decimates (i.e. throws away rows and columns).
         """
         assert n > 0, "The downsampling factor must be an integer greater than 0"
-        return self[::int(n), ::int(n), ...] # The slicing code handles updating metadata
+        return self[
+            :: int(n), :: int(n), ...
+        ]  # The slicing code handles updating metadata
 
     @property
     def datum_pixel(self):
@@ -165,14 +191,16 @@ class ImageWithLocation(ArrayWithAttrs):
         Usually the datum pixel is the central pixel, and if the metadata required is not present,
         we will silently assume that this is the case.
         """
-        datum = self.attrs.get('datum_pixel', old_div((np.array(self.shape[:2]) - 1),2))
+        datum = self.attrs.get(
+            "datum_pixel", old_div((np.array(self.shape[:2]) - 1), 2)
+        )
         assert len(datum) == 2, "The datum pixel didn't have length 2!"
         return datum
 
     @datum_pixel.setter
     def datum_pixel(self, datum):
         assert len(datum) == 2, "The datum pixel didn't have length 2!"
-        self.attrs['datum_pixel'] = datum
+        self.attrs["datum_pixel"] = datum
 
     @property
     def datum_location(self):
@@ -186,34 +214,36 @@ class ImageWithLocation(ArrayWithAttrs):
         np.dot(p, M) yields a location for the given pixel, where p is [x,y,0,1] and M is this matrix.  The location
         given will be 4 elements long, and will have 1 as the final element.
         """
-        M = self.attrs['pixel_to_sample_matrix']
+        M = self.attrs["pixel_to_sample_matrix"]
         assert M.shape == (4, 4), "The pixel-to-sample matrix is the wrong shape!"
         assert M.dtype.kind == "f", "The pixel-to-sample matrix is not floating point!"
         return M
 
     @pixel_to_sample_matrix.setter
     def pixel_to_sample_matrix(self, M):
-        M = np.asanyarray(M) #ensure it's an ndarray subclass
+        M = np.asanyarray(M)  # ensure it's an ndarray subclass
         assert M.shape == (4, 4), "The pixel-to-sample matrix must be 4x4!"
         assert M.dtype.kind == "f", "The pixel-to-sample matrix must be floating point!"
-        self.attrs['pixel_to_sample_matrix'] = M
+        self.attrs["pixel_to_sample_matrix"] = M
+
+    # TODO: split the data type out of this module and put it somewhere sensible
 
-    #TODO: split the data type out of this module and put it somewhere sensible
 
 def add_location_metadata(image, pixel_to_sample_matrix, datum_pixel=None):
     """Wrap an image if needed, and set its pixel to sample matrix."""
-    awa = ensure_attrs(image) # if needed, convert the image to an ArrayWithAttrs
-    awa.attrs['pixel_to_sample_matrix'] = pixel_to_sample_matrix
+    awa = ensure_attrs(image)  # if needed, convert the image to an ArrayWithAttrs
+    awa.attrs["pixel_to_sample_matrix"] = pixel_to_sample_matrix
     if datum_pixel is not None:
-        awa.attrs['datum_pixel'] = datum_pixel
+        awa.attrs["datum_pixel"] = datum_pixel
     return awa
 
+
 def datum_pixel(image):
     """Get the datum pixel of an image - if no property is present, assume the central pixel."""
     try:
         return np.array(image.datum_pixel)
     except:
-        return (np.array(image.shape[:2]) - 1) / 2.
+        return (np.array(image.shape[:2]) - 1) / 2.0
 
 
 def ensure_3d(vector):
@@ -223,7 +253,9 @@ def ensure_3d(vector):
     elif len(vector) == 2:
         return np.array([vector[0], vector[1], 0])
     else:
-        raise ValueError("Tried to ensure a vector was 3D, but it had neither 2 nor 3 elements!")
+        raise ValueError(
+            "Tried to ensure a vector was 3D, but it had neither 2 nor 3 elements!"
+        )
 
 
 def ensure_2d(vector):
@@ -233,5 +265,6 @@ def ensure_2d(vector):
     elif len(vector) == 3:
         return np.array(vector[:2])
     else:
-        raise ValueError("Tried to ensure a vector was 2D, but it had neither 2 nor 3 elements!")
-
+        raise ValueError(
+            "Tried to ensure a vector was 2D, but it had neither 2 nor 3 elements!"
+        )
diff --git a/openflexure_microscope/api/default_extensions/picamera_autocalibrate/extension.py b/openflexure_microscope/api/default_extensions/picamera_autocalibrate/extension.py
index 8a22e7f8..ff48ed0b 100644
--- a/openflexure_microscope/api/default_extensions/picamera_autocalibrate/extension.py
+++ b/openflexure_microscope/api/default_extensions/picamera_autocalibrate/extension.py
@@ -13,7 +13,12 @@ import logging
 # Type hinting
 from typing import Tuple
 
-from .recalibrate_utils import recalibrate_camera, auto_expose_and_freeze_settings, flat_lens_shading_table
+from .recalibrate_utils import (
+    recalibrate_camera,
+    auto_expose_and_freeze_settings,
+    flat_lens_shading_table,
+)
+
 
 @contextmanager
 def pause_stream(scamera, resolution: Tuple[int, int] = None):
@@ -23,7 +28,9 @@ def pause_stream(scamera, resolution: Tuple[int, int] = None):
     block has finished.
     """
     with scamera.lock:
-        assert not scamera.record_active, "We can't pause the camera's video stream while a recording is in progress."
+        assert (
+            not scamera.record_active
+        ), "We can't pause the camera's video stream while a recording is in progress."
         streaming = scamera.stream_active
         old_resolution = scamera.camera.resolution
         if streaming:
@@ -37,6 +44,7 @@ def pause_stream(scamera, resolution: Tuple[int, int] = None):
                 logging.info("Restarting stream in pause_stream context manager")
                 scamera.start_stream_recording()
 
+
 def recalibrate(microscope):
     """Reset the camera's settings.
 
@@ -45,7 +53,9 @@ def recalibrate(microscope):
     with a gray level of 230.  It takes a little while to run.
     """
     with pause_stream(microscope.camera) as scamera:
-        auto_expose_and_freeze_settings(scamera.camera) # scamera.camera is the PiCamera object
+        auto_expose_and_freeze_settings(
+            scamera.camera
+        )  # scamera.camera is the PiCamera object
         recalibrate_camera(scamera.camera)
     microscope.save_settings()
 
@@ -63,13 +73,17 @@ class RecalibrateView(View):
 
         return taskify(recalibrate)(microscope)
 
+
 @ThingAction
 class FlattenLSTView(View):
     def post(self):
         microscope = find_component("org.openflexure.microscope")
 
         if not microscope:
-            abort(503, "No microscope connected. Unable to flatten the lens shading table.")
+            abort(
+                503,
+                "No microscope connected. Unable to flatten the lens shading table.",
+            )
 
         try:
             with pause_stream(microscope.camera) as scamera:
@@ -78,7 +92,11 @@ class FlattenLSTView(View):
             microscope.save_settings()
         except:
             logging.exception("Error flattening the lens shading table.")
-            abort(503, "Couldn't flatten the lens shading table - do you have the forked PiCamera library installed?")
+            abort(
+                503,
+                "Couldn't flatten the lens shading table - do you have the forked PiCamera library installed?",
+            )
+
 
 @ThingAction
 class DeleteLSTView(View):
@@ -86,7 +104,10 @@ class DeleteLSTView(View):
         microscope = find_component("org.openflexure.microscope")
 
         if not microscope:
-            abort(503, "No microscope connected. Unable to flatten the lens shading table.")
+            abort(
+                503,
+                "No microscope connected. Unable to flatten the lens shading table.",
+            )
 
         try:
             with pause_stream(microscope.camera) as scamera:
@@ -94,11 +115,16 @@ class DeleteLSTView(View):
             microscope.save_settings()
         except:
             logging.exception("Error deleting the lens shading table.")
-            abort(503, "Couldn't flatten the lens shading table - do you have the forked PiCamera library installed?")
+            abort(
+                503,
+                "Couldn't flatten the lens shading table - do you have the forked PiCamera library installed?",
+            )
 
 
 lst_extension_v2 = BaseExtension(
-    "org.openflexure.calibration.picamera", version="2.0.0-beta.1", description="Routines to perform flat-field correction on the camera."
+    "org.openflexure.calibration.picamera",
+    version="2.0.0-beta.1",
+    description="Routines to perform flat-field correction on the camera.",
 )
 
 lst_extension_v2.add_method(
diff --git a/openflexure_microscope/api/default_extensions/scan.py b/openflexure_microscope/api/default_extensions/scan.py
index ef788a05..30a0baa1 100644
--- a/openflexure_microscope/api/default_extensions/scan.py
+++ b/openflexure_microscope/api/default_extensions/scan.py
@@ -199,7 +199,7 @@ def tile(
                     # Run slow autofocus. Client should provide dz ~ 50
                     autofocus_extension.autofocus(
                         microscope,
-                        range(-3 * autofocus_dz, 4 * autofocus_dz, autofocus_dz)
+                        range(-3 * autofocus_dz, 4 * autofocus_dz, autofocus_dz),
                     )
                     logging.debug("Finished autofocus")
                     time.sleep(1)
diff --git a/openflexure_microscope/api/v2/views/actions/__init__.py b/openflexure_microscope/api/v2/views/actions/__init__.py
index 19bf25eb..e06454c5 100644
--- a/openflexure_microscope/api/v2/views/actions/__init__.py
+++ b/openflexure_microscope/api/v2/views/actions/__init__.py
@@ -58,7 +58,7 @@ def enabled_root_actions():
     return {k: v for k, v in _actions.items() if v["conditions"]}
 
 
-#@Tag("actions")
+# @Tag("actions")
 class ActionsView(View):
     def get(self):
         """
diff --git a/openflexure_microscope/config.py b/openflexure_microscope/config.py
index 6657de24..74ffb3f0 100644
--- a/openflexure_microscope/config.py
+++ b/openflexure_microscope/config.py
@@ -203,4 +203,3 @@ with open(DEFAULT_CONFIGURATION_FILE_PATH, "r") as default_configuration:
 user_configuration = OpenflexureSettingsFile(
     path=CONFIGURATION_FILE_PATH, defaults=DEFAULT_CONFIGURATION
 )
-
diff --git a/openflexure_microscope/microscope.py b/openflexure_microscope/microscope.py
index c36d4690..d8db1def 100644
--- a/openflexure_microscope/microscope.py
+++ b/openflexure_microscope/microscope.py
@@ -175,7 +175,12 @@ class Microscope:
         don't get removed from the settings file.
         """
 
-        settings_current = {"id": self.id, "name": self.name, "fov": self.fov, "extensions": self.extension_settings}
+        settings_current = {
+            "id": self.id,
+            "name": self.name,
+            "fov": self.fov,
+            "extensions": self.extension_settings,
+        }
 
         # If attached to a camera
         if self.camera:
diff --git a/openflexure_microscope/utilities.py b/openflexure_microscope/utilities.py
index 63db1651..185478f6 100644
--- a/openflexure_microscope/utilities.py
+++ b/openflexure_microscope/utilities.py
@@ -28,12 +28,7 @@ def ndarray_to_json(arr: np.ndarray):
         # This comes in very handy for the lens shading table.
         arr = np.array(arr)
     b64_string, dtype, shape = serialise_array_b64(arr)
-    return {
-        "@type": "ndarray",
-        "dtype": dtype,
-        "shape": shape,
-        "base64": b64_string
-    }
+    return {"@type": "ndarray", "dtype": dtype, "shape": shape, "base64": b64_string}
 
 
 def json_to_ndarray(json_dict: dict):
@@ -42,9 +37,10 @@ def json_to_ndarray(json_dict: dict):
     for required_param in ("dtype", "shape", "base64"):
         if not json_dict.get(required_param):
             raise KeyError(f"Missing required key {required_param}")
-    
-    return deserialise_array_b64(json_dict.get("base64"), json_dict.get("dtype"), json_dict.get("shape"))
 
+    return deserialise_array_b64(
+        json_dict.get("base64"), json_dict.get("dtype"), json_dict.get("shape")
+    )
 
 
 @contextmanager

From d4dbafcb52add280178e9c2a7b354ef74e42aa7a Mon Sep 17 00:00:00 2001
From: Joel Collins <jtc9242@gmail.com>
Date: Tue, 28 Apr 2020 13:20:48 +0100
Subject: [PATCH 2/7] Explicit __all__ in devel submodule

---
 openflexure_microscope/devel/__init__.py | 12 ++++++++++++
 1 file changed, 12 insertions(+)

diff --git a/openflexure_microscope/devel/__init__.py b/openflexure_microscope/devel/__init__.py
index d777ea1a..519e2ce1 100644
--- a/openflexure_microscope/devel/__init__.py
+++ b/openflexure_microscope/devel/__init__.py
@@ -18,3 +18,15 @@ from labthings.core.tasks import (
 
 # Flask things
 from flask import abort, escape, Response, request
+
+
+__all__ = [
+    "current_task",
+    "update_task_progress",
+    "update_task_data",
+    "taskify",
+    "abort",
+    "escape",
+    "Response",
+    "request",
+]

From 9ff24e8e374a9089ab65ddee9423b67f529c5f42 Mon Sep 17 00:00:00 2001
From: Joel Collins <jtc9242@gmail.com>
Date: Tue, 28 Apr 2020 13:36:53 +0100
Subject: [PATCH 3/7] Added updated opencv-python-headless for Py38
 installations

---
 poetry.lock    | 88 ++++++++++++++++++++++++++++++++++++--------------
 pyproject.toml |  7 ++--
 2 files changed, 68 insertions(+), 27 deletions(-)

diff --git a/poetry.lock b/poetry.lock
index f6ca48d9..5be0bcfc 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -123,7 +123,7 @@ description = "Composable command line interface toolkit"
 name = "click"
 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*"
-version = "7.1.1"
+version = "7.1.2"
 
 [[package]]
 category = "dev"
@@ -340,6 +340,7 @@ version = "1.18.2"
 [[package]]
 category = "main"
 description = "Wrapper package for OpenCV python bindings."
+marker = "python_version >= \"3.7\" and python_version < \"3.8\""
 name = "opencv-python-headless"
 optional = false
 python-versions = "*"
@@ -348,6 +349,18 @@ version = "4.1.0.25"
 [package.dependencies]
 numpy = ">=1.11.1"
 
+[[package]]
+category = "main"
+description = "Wrapper package for OpenCV python bindings."
+marker = "python_version >= \"3.8\" and python_version < \"4.0\""
+name = "opencv-python-headless"
+optional = false
+python-versions = "*"
+version = "4.2.0.34"
+
+[package.dependencies]
+numpy = ">=1.11.1"
+
 [[package]]
 category = "dev"
 description = "Core utilities for Python packages"
@@ -374,7 +387,7 @@ doc = ["sphinx"]
 test = ["pillow", "coverage", "mock", "numpy", "pytest"]
 
 [package.source]
-reference = "79177fa7f28d6d5c6eab5ba814b420b1785b6b24"
+reference = "e50a34826fc8691e9f8554c529a1700662724ade"
 type = "git"
 url = "https://github.com/rwb27/picamera.git"
 [[package]]
@@ -461,7 +474,7 @@ description = "World timezone definitions, modern and historical"
 name = "pytz"
 optional = false
 python-versions = "*"
-version = "2019.3"
+version = "2020.1"
 
 [[package]]
 category = "dev"
@@ -503,7 +516,7 @@ description = "SciPy: Scientific Library for Python"
 name = "scipy"
 optional = false
 python-versions = ">=3.5"
-version = "1.3.0"
+version = "1.4.1"
 
 [package.dependencies]
 numpy = ">=1.13.3"
@@ -722,7 +735,7 @@ ifaddr = "*"
 rpi = ["picamera", "RPi.GPIO"]
 
 [metadata]
-content-hash = "0d199a2b60763d46e7864814f8cb78037f358fdbf64d32c9f233ea6384449510"
+content-hash = "f880f4ec9bc5aacc0b508e234779c32fe418f96db56eb4bc805ab22cba695d7e"
 python-versions = "^3.6"
 
 [metadata.files]
@@ -793,8 +806,8 @@ chardet = [
     {file = "chardet-3.0.4.tar.gz", hash = "sha256:84ab92ed1c4d4f16916e05906b6b75a6c0fb5db821cc65e70cbd64a3e2a5eaae"},
 ]
 click = [
-    {file = "click-7.1.1-py2.py3-none-any.whl", hash = "sha256:e345d143d80bf5ee7534056164e5e112ea5e22716bbb1ce727941f4c8b471b9a"},
-    {file = "click-7.1.1.tar.gz", hash = "sha256:8a18b4ea89d8820c5d0c7da8a64b2c324b4dabb695804dbfea19b9be9d88c0cc"},
+    {file = "click-7.1.2-py2.py3-none-any.whl", hash = "sha256:dacca89f4bfadd5de3d7489b7c8a566eee0d3676333fbb50030263894c38c0dc"},
+    {file = "click-7.1.2.tar.gz", hash = "sha256:d2b5255c7c6349bc1bd1e59e08cd12acbbd63ce649f2588755783aa94dfb6b1a"},
 ]
 colorama = [
     {file = "colorama-0.4.3-py2.py3-none-any.whl", hash = "sha256:7d73d2a99753107a36ac6b455ee49046802e59d9d076ef8e47b61499fa29afff"},
@@ -1010,6 +1023,26 @@ opencv-python-headless = [
     {file = "opencv_python_headless-4.1.0.25-cp37-cp37m-manylinux1_x86_64.whl", hash = "sha256:7709abc1c1341b831bf30d2b2afaa4877bdcab7dd775c94864608c08067e65b9"},
     {file = "opencv_python_headless-4.1.0.25-cp37-cp37m-win32.whl", hash = "sha256:3020c6a996cea3a8d36ef5c49c8641a8f32a2bb77944128749af756de2946d6e"},
     {file = "opencv_python_headless-4.1.0.25-cp37-cp37m-win_amd64.whl", hash = "sha256:5f1f5b0325cfd50cd58fc64bf66feed56238305e41450f04ab450092e18ee95b"},
+    {file = "opencv_python_headless-4.2.0.34-cp35-cp35m-macosx_10_9_x86_64.whl", hash = "sha256:45f90a872bc2e3d3257e06508ea18b3e2d429cf1b20de1a8f5c57251cc39fae4"},
+    {file = "opencv_python_headless-4.2.0.34-cp35-cp35m-manylinux1_i686.whl", hash = "sha256:1641d82b94ce496e6f3df8f2a337eae94cd608e0e61dbb4b697577438d88c258"},
+    {file = "opencv_python_headless-4.2.0.34-cp35-cp35m-manylinux1_x86_64.whl", hash = "sha256:3aadcd93f1ad9a92dbfbfdeacb7ffca115f137aa2b07d36495fd141f2a553479"},
+    {file = "opencv_python_headless-4.2.0.34-cp35-cp35m-win32.whl", hash = "sha256:cef7e844f5fd73cb602b8ba3f048a68dc2c59b7abb55ca99cceee9f688e909a4"},
+    {file = "opencv_python_headless-4.2.0.34-cp35-cp35m-win_amd64.whl", hash = "sha256:70117cd51b158f7628cf2dab24805df40173c3794ca3dfeec22defb326ec0173"},
+    {file = "opencv_python_headless-4.2.0.34-cp36-cp36m-macosx_10_9_x86_64.whl", hash = "sha256:4c3004573ecfbdf46785682a294923661903eb18e4c188106998ef5be255df1f"},
+    {file = "opencv_python_headless-4.2.0.34-cp36-cp36m-manylinux1_i686.whl", hash = "sha256:64292b593367e5b37556900b132861d94c05f616d8569c5625b02be6d51e13f7"},
+    {file = "opencv_python_headless-4.2.0.34-cp36-cp36m-manylinux1_x86_64.whl", hash = "sha256:ffe74fc421fc77b649f4b762e115fd2b9cea9ba86b4590f7939bd15f92f11f80"},
+    {file = "opencv_python_headless-4.2.0.34-cp36-cp36m-win32.whl", hash = "sha256:ed5c7d2fd8dc08ebcb9f8ed09883e3a083a5e0bc35f863ac280f61cec9560b09"},
+    {file = "opencv_python_headless-4.2.0.34-cp36-cp36m-win_amd64.whl", hash = "sha256:28b28e3462500dccf75ac5efb2b885494d050fb6444fee37b53f9f950bccca57"},
+    {file = "opencv_python_headless-4.2.0.34-cp37-cp37m-macosx_10_9_x86_64.whl", hash = "sha256:4e9de88b1376f904158698c3335f184cbcdc68eda018eb8f751e27e7407dddd1"},
+    {file = "opencv_python_headless-4.2.0.34-cp37-cp37m-manylinux1_i686.whl", hash = "sha256:edfaeea04982166a02c87b85ed5451b77485c86db7a4b216a42e6b686e1b5f1a"},
+    {file = "opencv_python_headless-4.2.0.34-cp37-cp37m-manylinux1_x86_64.whl", hash = "sha256:aca7419cae1390a8f2d6776571d1d19db66dadbff2ded79e4ff4bad5d9df6633"},
+    {file = "opencv_python_headless-4.2.0.34-cp37-cp37m-win32.whl", hash = "sha256:1df0adfc1b893615ab8487cd207aae356936b0ba1823520e2292c928853c2930"},
+    {file = "opencv_python_headless-4.2.0.34-cp37-cp37m-win_amd64.whl", hash = "sha256:67c6ff682e413db759f49a206bafa5ebb8b01dfdefa5199df32741b58772c3d7"},
+    {file = "opencv_python_headless-4.2.0.34-cp38-cp38-macosx_10_9_x86_64.whl", hash = "sha256:904f0b4a358b3260d7572956026bf6a0fa0cda31d5a6afeed3e55341a3f36c8d"},
+    {file = "opencv_python_headless-4.2.0.34-cp38-cp38-manylinux1_i686.whl", hash = "sha256:f93bec89d943ca1877c38920e934ed1d6193cdc6ff09cb910c19c15643ee07df"},
+    {file = "opencv_python_headless-4.2.0.34-cp38-cp38-manylinux1_x86_64.whl", hash = "sha256:ca9a5f4b04f2b423892ef5934fdd685edd0bc458c77fc7e164156a50e6be0377"},
+    {file = "opencv_python_headless-4.2.0.34-cp38-cp38-win32.whl", hash = "sha256:06a96ec4866aa40c68c255042ea0ab8a96c07f2eb54f5b0dc6b8ac08b00c1b7e"},
+    {file = "opencv_python_headless-4.2.0.34-cp38-cp38-win_amd64.whl", hash = "sha256:20c450943acebd9aa04566fdef4a658b94eec80a0c39a8f480c9aa1696034fcb"},
 ]
 packaging = [
     {file = "packaging-20.3-py2.py3-none-any.whl", hash = "sha256:82f77b9bee21c1bafbf35a84905d604d5d1223801d639cf3ed140bd651c08752"},
@@ -1107,8 +1140,8 @@ python-dateutil = [
     {file = "python_dateutil-2.8.1-py2.py3-none-any.whl", hash = "sha256:75bb3f31ea686f1197762692a9ee6a7550b59fc6ca3a1f4b5d7e32fb98e2da2a"},
 ]
 pytz = [
-    {file = "pytz-2019.3-py2.py3-none-any.whl", hash = "sha256:1c557d7d0e871de1f5ccd5833f60fb2550652da6be2693c1e02300743d21500d"},
-    {file = "pytz-2019.3.tar.gz", hash = "sha256:b02c06db6cf09c12dd25137e563b31700d3b80fcc4ad23abb7a315f2789819be"},
+    {file = "pytz-2020.1-py2.py3-none-any.whl", hash = "sha256:a494d53b6d39c3c6e44c3bec237336e14305e4f29bbf800b599253057fbb79ed"},
+    {file = "pytz-2020.1.tar.gz", hash = "sha256:c35965d010ce31b23eeb663ed3cc8c906275d6be1a34393a1d73a41febf4a048"},
 ]
 requests = [
     {file = "requests-2.23.0-py2.py3-none-any.whl", hash = "sha256:43999036bfa82904b6af1d99e4882b560e5e2c68e5c4b0aa03b655f3d7d73fee"},
@@ -1123,22 +1156,27 @@ rope = [
     {file = "RPi.GPIO-0.6.5.tar.gz", hash = "sha256:a4210ad63bfe844e43995286de0d3950dfacfa0f3799bb9392770ac54a7d2e47"},
 ]
 scipy = [
-    {file = "scipy-1.3.0-cp35-cp35m-macosx_10_6_intel.macosx_10_9_intel.macosx_10_9_x86_64.macosx_10_10_intel.macosx_10_10_x86_64.whl", hash = "sha256:4907040f62b91c2e170359c3d36c000af783f0fa1516a83d6c1517cde0af5340"},
-    {file = "scipy-1.3.0-cp35-cp35m-manylinux1_i686.whl", hash = "sha256:1db9f964ed9c52dc5bd6127f0dd90ac89791daa690a5665cc01eae185912e1ba"},
-    {file = "scipy-1.3.0-cp35-cp35m-manylinux1_x86_64.whl", hash = "sha256:adadeeae5500de0da2b9e8dd478520d0a9945b577b2198f2462555e68f58e7ef"},
-    {file = "scipy-1.3.0-cp35-cp35m-win32.whl", hash = "sha256:03b1e0775edbe6a4c64effb05fff2ce1429b76d29d754aa5ee2d848b60033351"},
-    {file = "scipy-1.3.0-cp35-cp35m-win_amd64.whl", hash = "sha256:a7695a378c2ce402405ea37b12c7a338a8755e081869bd6b95858893ceb617ae"},
-    {file = "scipy-1.3.0-cp36-cp36m-macosx_10_6_intel.macosx_10_9_intel.macosx_10_9_x86_64.macosx_10_10_intel.macosx_10_10_x86_64.whl", hash = "sha256:826b9f5fbb7f908a13aa1efd4b7321e36992f5868d5d8311c7b40cf9b11ca0e7"},
-    {file = "scipy-1.3.0-cp36-cp36m-manylinux1_i686.whl", hash = "sha256:b283a76a83fe463c9587a2c88003f800e08c3929dfbeba833b78260f9c209785"},
-    {file = "scipy-1.3.0-cp36-cp36m-manylinux1_x86_64.whl", hash = "sha256:db61a640ca20f237317d27bc658c1fc54c7581ff7f6502d112922dc285bdabee"},
-    {file = "scipy-1.3.0-cp36-cp36m-win32.whl", hash = "sha256:409846be9d6bdcbd78b9e5afe2f64b2da5a923dd7c1cd0615ce589489533fdbb"},
-    {file = "scipy-1.3.0-cp36-cp36m-win_amd64.whl", hash = "sha256:c19a7389ab3cd712058a8c3c9ffd8d27a57f3d84b9c91a931f542682bb3d269d"},
-    {file = "scipy-1.3.0-cp37-cp37m-macosx_10_6_intel.macosx_10_9_intel.macosx_10_9_x86_64.macosx_10_10_intel.macosx_10_10_x86_64.whl", hash = "sha256:09d008237baabf52a5d4f5a6fcf9b3c03408f3f61a69c404472a16861a73917e"},
-    {file = "scipy-1.3.0-cp37-cp37m-manylinux1_i686.whl", hash = "sha256:a84c31e8409b420c3ca57fd30c7589378d6fdc8d155d866a7f8e6e80dec6fd06"},
-    {file = "scipy-1.3.0-cp37-cp37m-manylinux1_x86_64.whl", hash = "sha256:c5ea60ece0c0c1c849025bfc541b60a6751b491b6f11dd9ef37ab5b8c9041921"},
-    {file = "scipy-1.3.0-cp37-cp37m-win32.whl", hash = "sha256:6c0543f2fdd38dee631fb023c0f31c284a532d205590b393d72009c14847f5b1"},
-    {file = "scipy-1.3.0-cp37-cp37m-win_amd64.whl", hash = "sha256:10325f0ffac2400b1ec09537b7e403419dcd25d9fee602a44e8a32119af9079e"},
-    {file = "scipy-1.3.0.tar.gz", hash = "sha256:c3bb4bd2aca82fb498247deeac12265921fe231502a6bc6edea3ee7fe6c40a7a"},
+    {file = "scipy-1.4.1-cp35-cp35m-macosx_10_6_intel.whl", hash = "sha256:c5cac0c0387272ee0e789e94a570ac51deb01c796b37fb2aad1fb13f85e2f97d"},
+    {file = "scipy-1.4.1-cp35-cp35m-manylinux1_i686.whl", hash = "sha256:a144811318853a23d32a07bc7fd5561ff0cac5da643d96ed94a4ffe967d89672"},
+    {file = "scipy-1.4.1-cp35-cp35m-manylinux1_x86_64.whl", hash = "sha256:71eb180f22c49066f25d6df16f8709f215723317cc951d99e54dc88020ea57be"},
+    {file = "scipy-1.4.1-cp35-cp35m-win32.whl", hash = "sha256:770254a280d741dd3436919d47e35712fb081a6ff8bafc0f319382b954b77802"},
+    {file = "scipy-1.4.1-cp35-cp35m-win_amd64.whl", hash = "sha256:a1aae70d52d0b074d8121333bc807a485f9f1e6a69742010b33780df2e60cfe0"},
+    {file = "scipy-1.4.1-cp36-cp36m-macosx_10_6_intel.whl", hash = "sha256:bb517872058a1f087c4528e7429b4a44533a902644987e7b2fe35ecc223bc408"},
+    {file = "scipy-1.4.1-cp36-cp36m-manylinux1_i686.whl", hash = "sha256:dba8306f6da99e37ea08c08fef6e274b5bf8567bb094d1dbe86a20e532aca088"},
+    {file = "scipy-1.4.1-cp36-cp36m-manylinux1_x86_64.whl", hash = "sha256:386086e2972ed2db17cebf88610aab7d7f6e2c0ca30042dc9a89cf18dcc363fa"},
+    {file = "scipy-1.4.1-cp36-cp36m-win32.whl", hash = "sha256:8d3bc3993b8e4be7eade6dcc6fd59a412d96d3a33fa42b0fa45dc9e24495ede9"},
+    {file = "scipy-1.4.1-cp36-cp36m-win_amd64.whl", hash = "sha256:dc60bb302f48acf6da8ca4444cfa17d52c63c5415302a9ee77b3b21618090521"},
+    {file = "scipy-1.4.1-cp37-cp37m-macosx_10_6_intel.whl", hash = "sha256:787cc50cab3020a865640aba3485e9fbd161d4d3b0d03a967df1a2881320512d"},
+    {file = "scipy-1.4.1-cp37-cp37m-manylinux1_i686.whl", hash = "sha256:0902a620a381f101e184a958459b36d3ee50f5effd186db76e131cbefcbb96f7"},
+    {file = "scipy-1.4.1-cp37-cp37m-manylinux1_x86_64.whl", hash = "sha256:00af72998a46c25bdb5824d2b729e7dabec0c765f9deb0b504f928591f5ff9d4"},
+    {file = "scipy-1.4.1-cp37-cp37m-win32.whl", hash = "sha256:9508a7c628a165c2c835f2497837bf6ac80eb25291055f56c129df3c943cbaf8"},
+    {file = "scipy-1.4.1-cp37-cp37m-win_amd64.whl", hash = "sha256:a2d6df9eb074af7f08866598e4ef068a2b310d98f87dc23bd1b90ec7bdcec802"},
+    {file = "scipy-1.4.1-cp38-cp38-macosx_10_9_x86_64.whl", hash = "sha256:3092857f36b690a321a662fe5496cb816a7f4eecd875e1d36793d92d3f884073"},
+    {file = "scipy-1.4.1-cp38-cp38-manylinux1_i686.whl", hash = "sha256:8a07760d5c7f3a92e440ad3aedcc98891e915ce857664282ae3c0220f3301eb6"},
+    {file = "scipy-1.4.1-cp38-cp38-manylinux1_x86_64.whl", hash = "sha256:1e3190466d669d658233e8a583b854f6386dd62d655539b77b3fa25bfb2abb70"},
+    {file = "scipy-1.4.1-cp38-cp38-win32.whl", hash = "sha256:cc971a82ea1170e677443108703a2ec9ff0f70752258d0e9f5433d00dda01f59"},
+    {file = "scipy-1.4.1-cp38-cp38-win_amd64.whl", hash = "sha256:2cce3f9847a1a51019e8c5b47620da93950e58ebc611f13e0d11f4980ca5fecb"},
+    {file = "scipy-1.4.1.tar.gz", hash = "sha256:dee1bbf3a6c8f73b6b218cb28eed8dd13347ea2f87d572ce19b289d6fd3fbc59"},
 ]
 six = [
     {file = "six-1.14.0-py2.py3-none-any.whl", hash = "sha256:8f3cd2e254d8f793e7f3d6d9df77b92252b52637291d0f0da013c76ea2724b6c"},
diff --git a/pyproject.toml b/pyproject.toml
index b5444a8a..52e45351 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -27,7 +27,7 @@ python = "^3.6"
 Flask = "^1.0"
 numpy = "1.18.2"
 Pillow = "^5.4"
-scipy = "1.3.0" # Exact version until we can guarantee a wheel
+scipy = "1.4.1" # Exact version so we can guarantee a wheel
 
 picamera = { git = "https://github.com/rwb27/picamera.git", branch = "master", optional = true }  # Lens shading requires >1.14 or RWB fork, lens-shading branch.
 "RPi.GPIO" = { version = "^0.6.5", optional = true }
@@ -35,7 +35,10 @@ pyserial = "^3.4" # Used for sangaboard (basic_serial_instrument) until we move
 
 python-dateutil = "^2.8"
 psutil = "^5.6.7" # Autostorage extension
-opencv-python-headless = "4.1.0.25"
+opencv-python-headless = [
+    {version = "4.1.0.25", python = "~3.7"},  # PiWheels build for RPi running Py37
+    {version = "4.2.0.34", python = "^3.8"}  # Latest for Py38 systems
+]
 labthings = "0.5.2"
 
 [tool.poetry.extras]

From 1a6088a816c21d6d05453a91ef14b7c178a38dd4 Mon Sep 17 00:00:00 2001
From: Joel Collins <jtc9242@gmail.com>
Date: Tue, 28 Apr 2020 13:42:26 +0100
Subject: [PATCH 4/7] Code formatting

---
 .../camera_stage_calibration_2d.py            | 53 +++++++++++--------
 1 file changed, 31 insertions(+), 22 deletions(-)

diff --git a/openflexure_microscope/api/default_extensions/camera_stage_mapping/camera_stage_calibration_2d.py b/openflexure_microscope/api/default_extensions/camera_stage_mapping/camera_stage_calibration_2d.py
index 6e189b0f..9f090994 100644
--- a/openflexure_microscope/api/default_extensions/camera_stage_mapping/camera_stage_calibration_2d.py
+++ b/openflexure_microscope/api/default_extensions/camera_stage_mapping/camera_stage_calibration_2d.py
@@ -14,19 +14,22 @@ from camera_stage_tracker import Tracker, move_until_motion_detected
 
 from functools import partial
 
+
 def backlash_corrected_move(get_position, move, backlash_amount, pos):
     """Make two moves, arriving at `pos` from a consistent direction"""
     displacement = pos - get_position()
-    backlash_vector = (displacement < 0).astype(np.int)*backlash_amount
+    backlash_vector = (displacement < 0).astype(np.int) * backlash_amount
     if np.any(backlash_vector > 0):
         move(pos - backlash_vector)
     move(pos)
 
+
 def bake_backlash_corrected_move(get_position, move, backlash_amount):
     """Return a function that performs backlash-corrected moves"""
     return partial(backlash_corrected_move, get_position, move, backlash_amount)
-    
-def calibrate_xy_grid(tracker, move, step = 100, n_steps=4, backlash_compensation=0):
+
+
+def calibrate_xy_grid(tracker, move, step=100, n_steps=4, backlash_compensation=0):
     """Make a series of moves in X and Y to determine the XY components of the pixel-to-sample matrix.
 
     Arguments:
@@ -38,44 +41,50 @@ def calibrate_xy_grid(tracker, move, step = 100, n_steps=4, backlash_compensatio
     step : float, optional (default 100)
         The amount to move the stage by.  This should move the sample by approximately 1/10th of the field of view.
     """
-    try: # Ensure that the tracker has a template set
+    try:  # Ensure that the tracker has a template set
         _ = tracker.template
     except:
         tracker.acquire_template()
-    tracker.reset_history() # make sure we get rid of the initial (0,0) point
+    tracker.reset_history()  # make sure we get rid of the initial (0,0) point
     starting_position = tracker.get_position()
     # Move the stage in a square, recording the displacement from both the stage and the camera
     try:
-        for x in (np.arange(n_steps) - n_steps/2.0)*step:
-            for y in (np.arange(n_steps) - n_steps/2.0)*step:
+        for x in (np.arange(n_steps) - n_steps / 2.0) * step:
+            for y in (np.arange(n_steps) - n_steps / 2.0) * step:
                 move(starting_position + np.array([x, y, 0]))
                 tracker.append_point()
     finally:
         move(starting_position)
-    # We then use least-squares to fit the XY part of the matrix relating 
+    # We then use least-squares to fit the XY part of the matrix relating
     # pixels to distance
     # stage_positions should be the stage positions, with a zero mean.
     # image_positions should be the same, but calculated from the images
     stage_positions, image_positions = tracker.history
     stage_positions = stage_positions.astype(np.float)
     stage_positions -= np.mean(stage_positions, axis=0)
-    stage_positions = stage_positions[:,:2] # ensure it's 2d
+    stage_positions = stage_positions[:, :2]  # ensure it's 2d
     image_positions -= np.mean(image_positions, axis=0)
-    #image_positions *= -1 # To get the matrix right, we want the position of each
-                        # image relative to the template, rather than the other way around
-    A, res, rank, s = np.linalg.lstsq(image_positions, stage_positions) # we solve pixel_shifts*A = location_shifts
+    # image_positions *= -1 # To get the matrix right, we want the position of each
+    # image relative to the template, rather than the other way around
+    A, res, rank, s = np.linalg.lstsq(
+        image_positions, stage_positions
+    )  # we solve pixel_shifts*A = location_shifts
 
     transformed_image_positions = np.dot(image_positions, A)
     residuals = transformed_image_positions - stage_positions
-    fractional_error = norm(residuals) / stage_positions.shape[0] step
+    fractional_error = norm(residuals) / stage_positions.shape[0]
     print(f"Ratio of residuals to displacement is {fractional_error})")
-    if fractional_error > 0.05: # Check it was a reasonably good fit
-        print("Warning: the error fitting measured displacements was %.1f%%" % (fractional_error*100))
-    print(f"Calibrated the pixel-location matrix.\nResiduals were {fractional_error*100:.1f}% of the shift.")
-    
-    return {
-        "image_to_stage_displacement": A, 
-        "moves": (stage_positions, image_positions), 
-        "fractional_error": fractional_error
-    }
+    if fractional_error > 0.05:  # Check it was a reasonably good fit
+        print(
+            "Warning: the error fitting measured displacements was %.1f%%"
+            % (fractional_error * 100)
+        )
+    print(
+        f"Calibrated the pixel-location matrix.\nResiduals were {fractional_error*100:.1f}% of the shift."
+    )
 
+    return {
+        "image_to_stage_displacement": A,
+        "moves": (stage_positions, image_positions),
+        "fractional_error": fractional_error,
+    }

From caf553db7a5de1327f5cc44979e314b93cdd4839 Mon Sep 17 00:00:00 2001
From: Joel Collins <jtc9242@gmail.com>
Date: Tue, 28 Apr 2020 14:32:56 +0100
Subject: [PATCH 5/7] Moved capture management into separate object

---
 openflexure_microscope/api/app.py             |   2 +
 .../api/default_extensions/autostorage.py     |  30 +--
 .../api/default_extensions/scan.py            |  28 +--
 .../custom_element/__init__.py                |   2 -
 openflexure_microscope/api/microscope.py      |   2 +-
 .../api/v2/views/actions/camera.py            |  20 +-
 openflexure_microscope/camera/base.py         | 170 +--------------
 openflexure_microscope/camera/mock.py         |   3 +-
 openflexure_microscope/camera/pi.py           |   3 +-
 openflexure_microscope/captures/__init__.py   |   3 +
 .../{camera => captures}/capture.py           |   0
 .../captures/capture_manager.py               | 193 ++++++++++++++++++
 openflexure_microscope/microscope.py          |  67 +++++-
 .../rescue/check_capture_reload.py            |   6 +-
 14 files changed, 302 insertions(+), 227 deletions(-)
 create mode 100644 openflexure_microscope/captures/__init__.py
 rename openflexure_microscope/{camera => captures}/capture.py (100%)
 create mode 100644 openflexure_microscope/captures/capture_manager.py

diff --git a/openflexure_microscope/api/app.py b/openflexure_microscope/api/app.py
index e3cce530..795357cc 100644
--- a/openflexure_microscope/api/app.py
+++ b/openflexure_microscope/api/app.py
@@ -57,6 +57,7 @@ logger.setLevel(logging.INFO)
 # Log server paths being used
 logging.info(f"Running with data path {OPENFLEXURE_VAR_PATH}")
 
+print("Creating app")
 # Create flask app
 app, labthing = create_app(
     __name__,
@@ -175,5 +176,6 @@ atexit.register(cleanup)
 if __name__ == "__main__":
     from labthings.server.wsgi import Server
 
+    print("Starting OpenFlexure Microscope Server...")
     server = Server(app)
     server.run(host="::", port=5000, debug=False, zeroconf=True)
diff --git a/openflexure_microscope/api/default_extensions/autostorage.py b/openflexure_microscope/api/default_extensions/autostorage.py
index 345ca73d..a237b41c 100644
--- a/openflexure_microscope/api/default_extensions/autostorage.py
+++ b/openflexure_microscope/api/default_extensions/autostorage.py
@@ -6,8 +6,8 @@ from labthings.server.find import find_component
 
 from openflexure_microscope.paths import settings_file_path, check_rw
 from openflexure_microscope.config import OpenflexureSettingsFile
-from openflexure_microscope.camera.base import BASE_CAPTURE_PATH
-from openflexure_microscope.camera.capture import build_captures_from_exif
+from openflexure_microscope.captures.capture_manager import BASE_CAPTURE_PATH
+from openflexure_microscope.captures.capture import build_captures_from_exif
 
 from openflexure_microscope.api.utilities.gui import build_gui
 
@@ -37,17 +37,17 @@ def get_permissive_locations():
     ]
 
 
-def get_current_location(camera):
-    return camera.paths.get("default")
+def get_current_location(capture_manager):
+    return capture_manager.paths.get("default")
 
 
-def set_current_location(camera, location: str):
+def set_current_location(capture_manager, location: str):
     if not os.path.isdir(location):
         os.makedirs(location)
     logging.debug("Updating location...")
-    camera.paths.update({"default": location})
+    capture_manager.paths.update({"default": location})
     logging.debug("Rebuilding captures...")
-    camera.rebuild_captures()
+    capture_manager.rebuild_captures()
     logging.debug("Capture location changed successfully.")
 
 
@@ -93,7 +93,7 @@ class AutostorageExtension(BaseExtension):
         )
 
         # We'll store a reference to a camera object, who's capture paths will be modified
-        self.camera = None
+        self.capture_manager = None
 
         self.initial_location = get_default_location()
 
@@ -107,9 +107,9 @@ class AutostorageExtension(BaseExtension):
             logging.debug(f"Autostorage extension bound to camera {self.camera}")
 
             # Store a reference to the camera
-            self.camera = microscope_obj.camera
+            self.capture_manager = microscope_obj.captures
             # Store the initial storage location
-            self.initial_location = get_current_location(self.camera)
+            self.initial_location = get_current_location(self.capture_manager)
 
             # If preferred path does not exist, or cannot be written to
             self.check_location(self.initial_location)
@@ -118,20 +118,20 @@ class AutostorageExtension(BaseExtension):
 
     def check_location(self, location=None):
         if not location:
-            location = get_current_location(self.camera)
+            location = get_current_location(self.capture_manager)
         # If preferred path does not exist, or cannot be written to
         if not (os.path.isdir(location) and check_rw(location)):
             logging.error(
                 f"Preferred capture path {location} is missing or cannot be written to. Restoring defaults."
             )
             # Reset the storage location to default
-            set_current_location(self.camera, get_default_location())
+            set_current_location(self.capture_manager, get_default_location())
 
     def get_locations(self):
         if self.camera:
             locations = get_all_locations()
 
-            current_location = get_current_location(self.camera)
+            current_location = get_current_location(self.capture_manager)
             if current_location not in locations.values():
                 locations.update({"Custom": current_location})
             # Add location from the cameras settings file
@@ -140,7 +140,7 @@ class AutostorageExtension(BaseExtension):
             return {}
 
     def get_preferred_key(self):
-        current = get_current_location(self.camera)
+        current = get_current_location(self.capture_manager)
         locations = self.get_locations()
 
         matches = [k for k, v in locations.items() if v == current]
@@ -157,7 +157,7 @@ class AutostorageExtension(BaseExtension):
             raise KeyError(f"No location named {new_path_key}")
 
         location = self.get_locations().get(new_path_key)
-        set_current_location(self.camera, location)
+        set_current_location(self.capture_manager, location)
 
     def key_to_title(self, path_key: str):
         if not path_key in self.get_locations().keys():
diff --git a/openflexure_microscope/api/default_extensions/scan.py b/openflexure_microscope/api/default_extensions/scan.py
index 30a0baa1..5ba0edcf 100644
--- a/openflexure_microscope/api/default_extensions/scan.py
+++ b/openflexure_microscope/api/default_extensions/scan.py
@@ -85,27 +85,17 @@ def capture(
     filename = "{}_{}_{}_{}".format(basename, *microscope.stage.position)
     folder = "SCAN_{}".format(basename)
 
-    # Create output object
-    output = microscope.camera.new_image(
-        temporary=temporary, filename=filename, folder=folder
+    # Do capture
+    return microscope.capture(
+        filename=filename,
+        folder=folder,
+        temporary=temporary,
+        use_video_port=use_video_port, resize=resize, bayer=bayer,
+        annotations=annotations,
+        tags=tags,
+        metadata=metadata
     )
 
-    # Capture
-    microscope.camera.capture(
-        output.file, use_video_port=use_video_port, resize=resize, bayer=bayer
-    )
-
-    # Inject system metadata
-    output.put_metadata({"instrument": microscope.metadata})
-
-    # Insert custom metadata
-    output.put_metadata(metadata)
-
-    # Insert custom metadata
-    output.put_annotations(annotations)
-    # Insert custom tags
-    output.put_tags(tags)
-
 
 ### Scanning
 
diff --git a/openflexure_microscope/api/example_extensions/custom_element/__init__.py b/openflexure_microscope/api/example_extensions/custom_element/__init__.py
index d8fa14cb..5669464c 100644
--- a/openflexure_microscope/api/example_extensions/custom_element/__init__.py
+++ b/openflexure_microscope/api/example_extensions/custom_element/__init__.py
@@ -7,8 +7,6 @@ from labthings.core.utilities import path_relative_to
 
 from openflexure_microscope.paths import settings_file_path, check_rw
 from openflexure_microscope.config import OpenflexureSettingsFile
-from openflexure_microscope.camera.base import BASE_CAPTURE_PATH
-from openflexure_microscope.camera.capture import build_captures_from_exif
 
 from openflexure_microscope.api.utilities.gui import build_gui
 
diff --git a/openflexure_microscope/api/microscope.py b/openflexure_microscope/api/microscope.py
index d9496684..87773bd4 100644
--- a/openflexure_microscope/api/microscope.py
+++ b/openflexure_microscope/api/microscope.py
@@ -7,6 +7,6 @@ default_microscope = Microscope()
 
 # Restore loaded capture array to camera object
 logging.debug("Restoring captures...")
-default_microscope.camera.rebuild_captures()
+default_microscope.captures.rebuild_captures()
 
 logging.debug("Microscope successfully attached!")
diff --git a/openflexure_microscope/api/v2/views/actions/camera.py b/openflexure_microscope/api/v2/views/actions/camera.py
index c9d42e49..9e8c6d8a 100644
--- a/openflexure_microscope/api/v2/views/actions/camera.py
+++ b/openflexure_microscope/api/v2/views/actions/camera.py
@@ -63,26 +63,16 @@ class CaptureAPI(View):
 
         # Explicitally acquire lock (prevents empty files being created if lock is unavailable)
         with microscope.camera.lock:
-            output = microscope.camera.new_image(
-                temporary=args.get("temporary"), filename=args.get("filename")
-            )
-
-            microscope.camera.capture(
-                output.file,
+            return microscope.capture(
+                filename=args.get("filename"),
+                temporary=args.get("temporary"),
                 use_video_port=args.get("use_video_port"),
                 resize=resize,
                 bayer=args.get("bayer"),
+                annotations=args.get("annotations"),
+                tags=args.get("tags")
             )
 
-            # Inject system metadata
-            output.put_metadata({"instrument": microscope.metadata})
-
-            # Insert custom metadata
-            output.put_annotations(args.get("annotations"))
-            # Insert custom tags
-            output.put_tags(args.get("tags"))
-
-        return output
 
 
 @ThingAction
diff --git a/openflexure_microscope/camera/base.py b/openflexure_microscope/camera/base.py
index 821b133d..8ba6ea2b 100644
--- a/openflexure_microscope/camera/base.py
+++ b/openflexure_microscope/camera/base.py
@@ -10,43 +10,11 @@ import threading
 import gevent
 
 from abc import ABCMeta, abstractmethod
-from collections import OrderedDict
 
-from .capture import CaptureObject, build_captures_from_exif
-from openflexure_microscope.utilities import entry_by_uuid
+
 from labthings.core.lock import StrictLock
 from labthings.core.event import ClientEvent
 
-from openflexure_microscope.paths import data_file_path
-
-BASE_CAPTURE_PATH = data_file_path("micrographs")
-TEMP_CAPTURE_PATH = os.path.join(BASE_CAPTURE_PATH, "tmp")
-
-
-def last_entry(object_list: list):
-    """Return the last entry of a list, if the list contains items."""
-    if object_list:  # If any images have been captured
-        return object_list[-1]  # Return the latest captured image
-    else:
-        return None
-
-
-def generate_basename():
-    """Return a default filename based on the capture datetime"""
-    return datetime.datetime.now().strftime("%Y-%m-%d_%H-%M-%S")
-
-
-def generate_numbered_basename(obj_list: list) -> str:
-    initial_basename = generate_basename()
-    basename = initial_basename
-    # Handle clashing
-    iterator = 1
-    while basename in [obj.basename for obj in obj_list]:
-        basename = initial_basename + "_{}".format(iterator)
-        iterator += 1
-
-    return basename
-
 
 class BaseCamera(metaclass=ABCMeta):
     """
@@ -70,12 +38,6 @@ class BaseCamera(metaclass=ABCMeta):
         self.stream_active = False
         self.record_active = False
 
-        self.paths = {"default": BASE_CAPTURE_PATH, "temp": TEMP_CAPTURE_PATH}
-
-        # Capture data
-        self.images = OrderedDict()
-        self.videos = OrderedDict()
-
     @property
     @abstractmethod
     def configuration(self):
@@ -104,7 +66,7 @@ class BaseCamera(metaclass=ABCMeta):
     @abstractmethod
     def read_settings(self) -> dict:
         """Return the current settings as a dictionary"""
-        return {"paths": self.paths}
+        return {}
 
     def __enter__(self):
         """Create camera on context enter."""
@@ -127,134 +89,6 @@ class BaseCamera(metaclass=ABCMeta):
         self.stop_worker()
         logging.info("Closed {}".format(self))
 
-    def clear_tmp(self):
-        """
-        Removes all files in the temporary capture directories
-        """
-
-        if os.path.isdir(self.paths["temp"]):
-            logging.info("Clearing {}...".format(self.paths["temp"]))
-            shutil.rmtree(self.paths["temp"])
-            logging.debug("Cleared {}.".format(self.paths["temp"]))
-
-    def rebuild_captures(self):
-        self.images = build_captures_from_exif(self.paths["default"])
-
-    # RETURNING CAPTURES
-
-    @property
-    def image(self):
-        """Return the latest captured image."""
-        return last_entry(self.images.values())
-
-    @property
-    def video(self):
-        """Return the latest recorded video."""
-        return last_entry(self.videos.values())
-
-    def image_from_id(self, image_id):
-        """Return an image StreamObject with a matching ID."""
-        logging.warning("image_from_id is deprecated. Access captures as a dictionary.")
-        return entry_by_uuid(image_id, self.images.values())
-
-    def video_from_id(self, video_id):
-        """Return a video StreamObject with a matching ID."""
-        logging.warning("video_from_id is deprecated. Access captures as a dictionary.")
-        return entry_by_uuid(video_id, self.videos.values())
-
-    # CREATING NEW CAPTURES
-
-    def new_image(
-        self,
-        temporary: bool = True,
-        filename: str = None,
-        folder: str = "",
-        fmt: str = "jpeg",
-    ):
-
-        """
-        Create a new image capture object.
-
-        Args:
-            temporary (bool): Should the data be deleted after session ends. 
-                Creating the capture with a content manager sets this to true.
-            filename (str): Name of the stored file. Defaults to timestamp.
-            folder (str): Name of the folder in which to store the capture.
-            fmt (str): Format of the capture.
-        """
-
-        # Generate file name
-        if not filename:
-            filename = generate_numbered_basename(self.images.values())
-            logging.debug(filename)
-        filename = "{}.{}".format(filename, fmt)
-
-        # Generate folder
-        base_folder = self.paths["temp"] if temporary else self.paths["default"]
-        folder = os.path.join(base_folder, folder)
-
-        # Generate file path
-        filepath = os.path.join(folder, filename)
-
-        # Create capture object
-        output = CaptureObject(filepath=filepath)
-        # Insert a temporary tag if temporary
-        if temporary:
-            output.put_tags(["temporary"])
-
-        # Update capture list
-        capture_key = str(output.id)
-        logging.debug(f"Adding image {output} with key {capture_key}")
-        self.images[capture_key] = output
-
-        return output
-
-    def new_video(
-        self,
-        temporary: bool = False,
-        filename: str = None,
-        folder: str = "",
-        fmt: str = "h264",
-    ):
-
-        """
-        Create a new video capture object.
-
-        Args:
-            temporary (bool): Should the data be deleted after session ends. 
-                Creating the capture with a content manager sets this to true.
-            filename (str): Name of the stored file. Defaults to timestamp.
-            folder (str): Name of the folder in which to store the capture.
-            fmt (str): Format of the capture.
-        """
-        # TODO: Remove the redundancy here
-
-        # Generate file name
-        if not filename:
-            filename = generate_numbered_basename(self.videos.values())
-            logging.debug(filename)
-        filename = "{}.{}".format(filename, fmt)
-
-        # Generate folder
-        base_folder = self.paths["temp"] if temporary else self.paths["default"]
-        folder = os.path.join(base_folder, folder)
-
-        # Generate file path
-        filepath = os.path.join(folder, filename)
-
-        # Create capture object
-        output = CaptureObject(filepath=filepath)
-        # Insert a temporary tag if temporary
-        if temporary:
-            output.put_tags(["temporary"])
-
-        # Update capture list
-        capture_key = str(output.id)
-        logging.debug(f"Adding video {output} with key {capture_key}")
-        self.videos[capture_key] = output
-
-        return output
-
     # START AND STOP WORKER THREAD
 
     def start_worker(self, timeout: int = 5) -> bool:
diff --git a/openflexure_microscope/camera/mock.py b/openflexure_microscope/camera/mock.py
index 65e65a32..9dc727c4 100644
--- a/openflexure_microscope/camera/mock.py
+++ b/openflexure_microscope/camera/mock.py
@@ -17,7 +17,8 @@ import logging
 # Type hinting
 from typing import Tuple
 
-from openflexure_microscope.camera.base import BaseCamera, CaptureObject
+from openflexure_microscope.camera.base import BaseCamera
+from openflexure_microscope.captures import CaptureObject
 
 
 """
diff --git a/openflexure_microscope/camera/pi.py b/openflexure_microscope/camera/pi.py
index 29ab938b..a73ea5d1 100644
--- a/openflexure_microscope/camera/pi.py
+++ b/openflexure_microscope/camera/pi.py
@@ -41,7 +41,8 @@ import picamera.array
 # Type hinting
 from typing import Tuple
 
-from .base import BaseCamera, CaptureObject
+from openflexure_microscope.camera.base import BaseCamera
+from openflexure_microscope.captures import CaptureObject
 
 # Richard's fix gain
 from .set_picamera_gain import set_analog_gain, set_digital_gain
diff --git a/openflexure_microscope/captures/__init__.py b/openflexure_microscope/captures/__init__.py
new file mode 100644
index 00000000..16cab515
--- /dev/null
+++ b/openflexure_microscope/captures/__init__.py
@@ -0,0 +1,3 @@
+from .capture_manager import CaptureManager
+from .capture import CaptureObject
+from . import capture_manager, capture
\ No newline at end of file
diff --git a/openflexure_microscope/camera/capture.py b/openflexure_microscope/captures/capture.py
similarity index 100%
rename from openflexure_microscope/camera/capture.py
rename to openflexure_microscope/captures/capture.py
diff --git a/openflexure_microscope/captures/capture_manager.py b/openflexure_microscope/captures/capture_manager.py
new file mode 100644
index 00000000..0ccefc89
--- /dev/null
+++ b/openflexure_microscope/captures/capture_manager.py
@@ -0,0 +1,193 @@
+import os
+import datetime
+import shutil
+import logging
+from collections import OrderedDict
+
+from labthings.core.lock import StrictLock
+
+from openflexure_microscope.utilities import entry_by_uuid
+from openflexure_microscope.paths import data_file_path
+
+from .capture import CaptureObject, build_captures_from_exif
+
+BASE_CAPTURE_PATH = data_file_path("micrographs")
+TEMP_CAPTURE_PATH = os.path.join(BASE_CAPTURE_PATH, "tmp")
+
+
+def last_entry(object_list: list):
+    """Return the last entry of a list, if the list contains items."""
+    if object_list:  # If any images have been captured
+        return object_list[-1]  # Return the latest captured image
+    else:
+        return None
+
+
+def generate_basename():
+    """Return a default filename based on the capture datetime"""
+    return datetime.datetime.now().strftime("%Y-%m-%d_%H-%M-%S")
+
+
+def generate_numbered_basename(obj_list: list) -> str:
+    initial_basename = generate_basename()
+    basename = initial_basename
+    # Handle clashing
+    iterator = 1
+    while basename in [obj.basename for obj in obj_list]:
+        basename = initial_basename + "_{}".format(iterator)
+        iterator += 1
+
+    return basename
+
+
+class CaptureManager:
+    def __init__(self):
+        self.paths = {"default": BASE_CAPTURE_PATH, "temp": TEMP_CAPTURE_PATH}
+
+        self.lock = StrictLock(timeout=1, name="Captures")
+
+        # Capture data
+        self.images = OrderedDict()
+        self.videos = OrderedDict()
+
+    # FILE MANAGEMENT
+
+    def clear_tmp(self):
+        """
+        Removes all files in the temporary capture directories
+        """
+
+        if os.path.isdir(self.paths["temp"]):
+            logging.info("Clearing {}...".format(self.paths["temp"]))
+            shutil.rmtree(self.paths["temp"])
+            logging.debug("Cleared {}.".format(self.paths["temp"]))
+
+    def rebuild_captures(self):
+        self.images = build_captures_from_exif(self.paths["default"])
+
+    def update_settings(self, config: dict):
+        """Update settings from a config dictionary"""
+        with self.lock:
+            # Apply valid config params to camera object
+            for key, value in config.items():  # For each provided setting
+                if hasattr(self, key):  # If the instance has a matching property
+                    setattr(self, key, value)  # Set to the target value
+
+    def read_settings(self) -> dict:
+        """Return the current settings as a dictionary"""
+        return {"paths": self.paths}
+
+    # RETURNING CAPTURES
+
+    @property
+    def image(self):
+        """Return the latest captured image."""
+        return last_entry(self.images.values())
+
+    @property
+    def video(self):
+        """Return the latest recorded video."""
+        return last_entry(self.videos.values())
+
+    def image_from_id(self, image_id):
+        """Return an image StreamObject with a matching ID."""
+        logging.warning("image_from_id is deprecated. Access captures as a dictionary.")
+        return entry_by_uuid(image_id, self.images.values())
+
+    def video_from_id(self, video_id):
+        """Return a video StreamObject with a matching ID."""
+        logging.warning("video_from_id is deprecated. Access captures as a dictionary.")
+        return entry_by_uuid(video_id, self.videos.values())
+
+    # CREATING NEW CAPTURES
+
+    def new_image(
+        self,
+        temporary: bool = True,
+        filename: str = None,
+        folder: str = "",
+        fmt: str = "jpeg",
+    ):
+
+        """
+        Create a new image capture object.
+
+        Args:
+            temporary (bool): Should the data be deleted after session ends. 
+                Creating the capture with a content manager sets this to true.
+            filename (str): Name of the stored file. Defaults to timestamp.
+            folder (str): Name of the folder in which to store the capture.
+            fmt (str): Format of the capture.
+        """
+
+        # Generate file name
+        if not filename:
+            filename = generate_numbered_basename(self.images.values())
+            logging.debug(filename)
+        filename = "{}.{}".format(filename, fmt)
+
+        # Generate folder
+        base_folder = self.paths["temp"] if temporary else self.paths["default"]
+        folder = os.path.join(base_folder, folder)
+
+        # Generate file path
+        filepath = os.path.join(folder, filename)
+
+        # Create capture object
+        output = CaptureObject(filepath=filepath)
+        # Insert a temporary tag if temporary
+        if temporary:
+            output.put_tags(["temporary"])
+
+        # Update capture list
+        capture_key = str(output.id)
+        logging.debug(f"Adding image {output} with key {capture_key}")
+        self.images[capture_key] = output
+
+        return output
+
+    def new_video(
+        self,
+        temporary: bool = False,
+        filename: str = None,
+        folder: str = "",
+        fmt: str = "h264",
+    ):
+
+        """
+        Create a new video capture object.
+
+        Args:
+            temporary (bool): Should the data be deleted after session ends. 
+                Creating the capture with a content manager sets this to true.
+            filename (str): Name of the stored file. Defaults to timestamp.
+            folder (str): Name of the folder in which to store the capture.
+            fmt (str): Format of the capture.
+        """
+        # TODO: Remove the redundancy here
+
+        # Generate file name
+        if not filename:
+            filename = generate_numbered_basename(self.videos.values())
+            logging.debug(filename)
+        filename = "{}.{}".format(filename, fmt)
+
+        # Generate folder
+        base_folder = self.paths["temp"] if temporary else self.paths["default"]
+        folder = os.path.join(base_folder, folder)
+
+        # Generate file path
+        filepath = os.path.join(folder, filename)
+
+        # Create capture object
+        output = CaptureObject(filepath=filepath)
+        # Insert a temporary tag if temporary
+        if temporary:
+            output.put_tags(["temporary"])
+
+        # Update capture list
+        capture_key = str(output.id)
+        logging.debug(f"Adding video {output} with key {capture_key}")
+        self.videos[capture_key] = output
+
+        return output
diff --git a/openflexure_microscope/microscope.py b/openflexure_microscope/microscope.py
index d8db1def..f7e06d14 100644
--- a/openflexure_microscope/microscope.py
+++ b/openflexure_microscope/microscope.py
@@ -5,6 +5,9 @@ Defines a microscope object, binding a camera and stage with basic functionality
 import logging
 import pkg_resources
 import uuid
+from typing import Tuple
+
+from openflexure_microscope.captures import CaptureManager
 
 from openflexure_microscope.stage.mock import MissingStage
 from openflexure_microscope.camera.mock import MissingCamera
@@ -33,6 +36,8 @@ class Microscope:
         self.id = uuid.uuid4()
         self.name = self.id
 
+        self.captures = CaptureManager()
+
         self.fov = [0, 0]  #: Microscope field-of-view in stage motor steps
 
         # Store settings and configuration files
@@ -47,6 +52,7 @@ class Microscope:
 
         self.camera = None  #: Currently connected camera object
         self.stage = None  #: Currently connected stage object
+
         self.setup(self.configuration_file.load())  # Attach components
 
         # Apply settings loaded from file
@@ -75,6 +81,7 @@ class Microscope:
         """
 
         ### Detector
+        print("Creating camera")
         if configuration.get("camera"):
             camera_type = configuration["camera"].get("type")
             if camera_type in ("PiCamera", "PiCameraStreamer"):
@@ -85,6 +92,7 @@ class Microscope:
                     logging.warning("No compatible camera hardware found.")
 
         ### Stage
+        print("Creating stage")
         if configuration.get("stage"):
             stage_type = configuration["stage"].get("type")
             stage_port = configuration["stage"].get("port")
@@ -95,6 +103,7 @@ class Microscope:
                     logging.error(e)
                     logging.warning("No compatible Sangaboard hardware found.")
 
+        print("Handling fallbacks")
         ### Fallbacks
         if not self.camera:
             self.camera = MissingCamera()
@@ -102,6 +111,7 @@ class Microscope:
             self.stage = MissingStage()
 
         ### Locks
+        print("Creating locks")
         if hasattr(self.camera, "lock"):
             self.lock.locks.append(self.camera.lock)
         if hasattr(self.stage, "lock"):
@@ -144,11 +154,14 @@ class Microscope:
 
         # If attached to a camera
         if ("camera" in settings) and self.camera:
-            self.camera.update_settings(settings["camera"])
+            self.camera.update_settings(settings.get("camera", {}))
 
         # If attached to a stage
         if ("stage" in settings) and self.stage:
-            self.stage.update_settings(settings["stage"])
+            self.stage.update_settings(settings.get("stage", {}))
+
+        # Capture manager
+        self.captures.update_settings(settings.get("captures", {}))
 
         # Microscope settings
         if "id" in settings:
@@ -207,6 +220,10 @@ class Microscope:
             settings_current_stage = self.stage.read_settings()
             settings_current["stage"] = settings_current_stage
 
+        # Capture manager
+        settings_current_captures = self.captures.read_settings()
+        settings_current["captures"] = settings_current_captures
+
         settings_full = self.settings_file.merge(settings_current)
 
         if full:
@@ -260,3 +277,49 @@ class Microscope:
         }
 
         return system_metadata
+
+    def capture(
+        self,
+        filename: str = None,
+        folder: str = "",
+        temporary: bool = False,
+        use_video_port: bool = False,
+        resize: Tuple[int, int] = None,
+        bayer: bool = True,
+        fmt: str = "jpeg",
+        annotations: dict = None,
+        tags: list = None,
+        metadata: dict = None
+    ):
+        if not annotations:
+            annotations = {}
+        if not metadata:
+            metadata = {}
+        if not tags:
+            tags = []
+        
+        with self.camera.lock:
+            # Create output object
+            output = self.captures.new_image(
+                temporary=temporary, filename=filename, folder=folder, fmt=fmt
+            )
+
+            # Capture to output object
+            self.camera.capture(
+                output.file,
+                use_video_port=use_video_port,
+                resize=resize,
+                bayer=bayer,
+                fmt=fmt
+            )
+
+            # Inject system metadata
+            output.put_metadata({"instrument": self.metadata})
+            # Insert custom metadata
+            output.put_metadata(metadata)
+            # Insert custom metadata
+            output.put_annotations(annotations)
+            # Insert custom tags
+            output.put_tags(tags)
+
+        return output
\ No newline at end of file
diff --git a/openflexure_microscope/rescue/check_capture_reload.py b/openflexure_microscope/rescue/check_capture_reload.py
index 3a61c692..c79d76d6 100644
--- a/openflexure_microscope/rescue/check_capture_reload.py
+++ b/openflexure_microscope/rescue/check_capture_reload.py
@@ -1,6 +1,6 @@
 from openflexure_microscope.rescue.monitor_timeout import launch_timeout_test_process
-from openflexure_microscope.camera.capture import build_captures_from_exif
-from openflexure_microscope.camera.base import BASE_CAPTURE_PATH
+from openflexure_microscope.captures.capture_manager import BASE_CAPTURE_PATH
+from openflexure_microscope.captures.capture import build_captures_from_exif
 from openflexure_microscope.config import user_settings
 
 import logging
@@ -10,7 +10,7 @@ def check_capture_rebuild(timeout=10):
     logging.info("Loading user settings...")
     settings = user_settings.load()
 
-    cap_path = str(settings.get("camera", {}).get("paths", {}).get("default"))
+    cap_path = str(settings.get("captures", {}).get("paths", {}).get("default"))
     logging.info(f"Capture path found: {cap_path}")
     if not cap_path:
         logging.error(

From 45ee112e6f6894666c92f12438a002792596f031 Mon Sep 17 00:00:00 2001
From: Joel Collins <joel@jtcollins.net>
Date: Tue, 28 Apr 2020 14:40:09 +0100
Subject: [PATCH 6/7] Fixed broken references

---
 .../api/default_extensions/autostorage.py          | 14 ++++++++------
 .../api/default_extensions/scan.py                 |  8 +++++---
 2 files changed, 13 insertions(+), 9 deletions(-)

diff --git a/openflexure_microscope/api/default_extensions/autostorage.py b/openflexure_microscope/api/default_extensions/autostorage.py
index a237b41c..a00109bd 100644
--- a/openflexure_microscope/api/default_extensions/autostorage.py
+++ b/openflexure_microscope/api/default_extensions/autostorage.py
@@ -92,7 +92,7 @@ class AutostorageExtension(BaseExtension):
             description="Handle switching capture storage devices",
         )
 
-        # We'll store a reference to a camera object, who's capture paths will be modified
+        # We'll store a reference to a CaptureManager object, who's capture paths will be modified
         self.capture_manager = None
 
         self.initial_location = get_default_location()
@@ -103,10 +103,12 @@ class AutostorageExtension(BaseExtension):
     def on_microscope(self, microscope_obj):
         """Function to automatically call when the parent LabThing has a microscope attached."""
         logging.debug(f"Autostorage extension found microscope {microscope_obj}")
-        if hasattr(microscope_obj, "camera"):
-            logging.debug(f"Autostorage extension bound to camera {self.camera}")
+        if hasattr(microscope_obj, "captures"):
+            logging.debug(
+                f"Autostorage extension bound to CaptureManager {self.capture_manager}"
+            )
 
-            # Store a reference to the camera
+            # Store a reference to the CaptureManager
             self.capture_manager = microscope_obj.captures
             # Store the initial storage location
             self.initial_location = get_current_location(self.capture_manager)
@@ -128,13 +130,13 @@ class AutostorageExtension(BaseExtension):
             set_current_location(self.capture_manager, get_default_location())
 
     def get_locations(self):
-        if self.camera:
+        if self.capture_manager:
             locations = get_all_locations()
 
             current_location = get_current_location(self.capture_manager)
             if current_location not in locations.values():
                 locations.update({"Custom": current_location})
-            # Add location from the cameras settings file
+            # Add location from the CaptureManager settings file
             return locations
         else:
             return {}
diff --git a/openflexure_microscope/api/default_extensions/scan.py b/openflexure_microscope/api/default_extensions/scan.py
index 5ba0edcf..88fcf771 100644
--- a/openflexure_microscope/api/default_extensions/scan.py
+++ b/openflexure_microscope/api/default_extensions/scan.py
@@ -5,7 +5,7 @@ import datetime
 from typing import Tuple
 from functools import reduce
 
-from openflexure_microscope.camera.base import generate_basename
+from openflexure_microscope.captures.capture_manager import generate_basename
 from labthings.server.find import find_component, find_extension
 from labthings.server.extensions import BaseExtension
 from labthings.server.decorators import marshal_task, use_args, ThingAction
@@ -90,10 +90,12 @@ def capture(
         filename=filename,
         folder=folder,
         temporary=temporary,
-        use_video_port=use_video_port, resize=resize, bayer=bayer,
+        use_video_port=use_video_port,
+        resize=resize,
+        bayer=bayer,
         annotations=annotations,
         tags=tags,
-        metadata=metadata
+        metadata=metadata,
     )
 
 

From a34214b9fb86ab9115339a29f567622a7d9c19b9 Mon Sep 17 00:00:00 2001
From: Joel Collins <jtc9242@gmail.com>
Date: Tue, 28 Apr 2020 14:47:22 +0100
Subject: [PATCH 7/7] Fixed broken references to capture list

---
 .../api/default_extensions/zip_builder.py     |  2 +-
 .../api/v2/views/captures.py                  | 20 +++++++++----------
 openflexure_microscope/camera/base.py         |  6 ------
 .../captures/capture_manager.py               | 17 ++++++++++++++++
 openflexure_microscope/microscope.py          |  1 +
 5 files changed, 29 insertions(+), 17 deletions(-)

diff --git a/openflexure_microscope/api/default_extensions/zip_builder.py b/openflexure_microscope/api/default_extensions/zip_builder.py
index 1b1b53d1..0ac6de82 100644
--- a/openflexure_microscope/api/default_extensions/zip_builder.py
+++ b/openflexure_microscope/api/default_extensions/zip_builder.py
@@ -80,7 +80,7 @@ class ZipManager:
 
         # Get array of captures from IDs
         capture_list = [
-            microscope.camera.images.get(capture_id) for capture_id in capture_id_list
+            microscope.captures.images.get(capture_id) for capture_id in capture_id_list
         ]
         # Remove Nones from list (missing/invalid captures)
         capture_list = [capture for capture in capture_list if capture]
diff --git a/openflexure_microscope/api/v2/views/captures.py b/openflexure_microscope/api/v2/views/captures.py
index abe7e895..70bb03d2 100644
--- a/openflexure_microscope/api/v2/views/captures.py
+++ b/openflexure_microscope/api/v2/views/captures.py
@@ -100,7 +100,7 @@ class CaptureList(View):
         List all image captures
         """
         microscope = find_component("org.openflexure.microscope")
-        image_list = microscope.camera.images.values()
+        image_list = microscope.captures.images.values()
         return image_list
 
 
@@ -112,7 +112,7 @@ class CaptureView(View):
         Description of a single image capture
         """
         microscope = find_component("org.openflexure.microscope")
-        capture_obj = microscope.camera.images.get(id)
+        capture_obj = microscope.captures.images.get(id)
 
         if not capture_obj:
             return abort(404)  # 404 Not Found
@@ -124,7 +124,7 @@ class CaptureView(View):
         Delete a single image capture
         """
         microscope = find_component("org.openflexure.microscope")
-        capture_obj = microscope.camera.images.get(id)
+        capture_obj = microscope.captures.images.get(id)
 
         if not capture_obj:
             return abort(404)  # 404 Not Found
@@ -132,7 +132,7 @@ class CaptureView(View):
         # Delete the capture file
         capture_obj.delete()
         # Delete from capture list
-        del microscope.camera.images[id]
+        del microscope.captures.images[id]
 
         return "", 204
 
@@ -145,7 +145,7 @@ class CaptureDownload(View):
         Image data for a single image capture
         """
         microscope = find_component("org.openflexure.microscope")
-        capture_obj = microscope.camera.images.get(id)
+        capture_obj = microscope.captures.images.get(id)
 
         if not capture_obj:
             return abort(404)  # 404 Not Found
@@ -180,7 +180,7 @@ class CaptureTags(View):
         Get tags associated with a single image capture
         """
         microscope = find_component("org.openflexure.microscope")
-        capture_obj = microscope.camera.images.get(id)
+        capture_obj = microscope.captures.images.get(id)
 
         if not capture_obj:
             return abort(404)  # 404 Not Found
@@ -192,7 +192,7 @@ class CaptureTags(View):
         Add tags to a single image capture
         """
         microscope = find_component("org.openflexure.microscope")
-        capture_obj = microscope.camera.images.get(id)
+        capture_obj = microscope.captures.images.get(id)
 
         if not capture_obj:
             return abort(404)  # 404 Not Found
@@ -212,7 +212,7 @@ class CaptureTags(View):
         Delete tags from a single image capture
         """
         microscope = find_component("org.openflexure.microscope")
-        capture_obj = microscope.camera.images.get(id)
+        capture_obj = microscope.captures.images.get(id)
 
         if not capture_obj:
             return abort(404)  # 404 Not Found
@@ -235,7 +235,7 @@ class CaptureAnnotations(View):
         Get annotations associated with a single image capture
         """
         microscope = find_component("org.openflexure.microscope")
-        capture_obj = microscope.camera.images.get(id)
+        capture_obj = microscope.captures.images.get(id)
 
         if not capture_obj:
             return abort(404)  # 404 Not Found
@@ -247,7 +247,7 @@ class CaptureAnnotations(View):
         Update metadata for a single image capture
         """
         microscope = find_component("org.openflexure.microscope")
-        capture_obj = microscope.camera.images.get(id)
+        capture_obj = microscope.captures.images.get(id)
 
         if not capture_obj:
             return abort(404)  # 404 Not Found
diff --git a/openflexure_microscope/camera/base.py b/openflexure_microscope/camera/base.py
index 8ba6ea2b..d8531a1f 100644
--- a/openflexure_microscope/camera/base.py
+++ b/openflexure_microscope/camera/base.py
@@ -79,12 +79,6 @@ class BaseCamera(metaclass=ABCMeta):
     def close(self):
         """Close the BaseCamera and all attached StreamObjects."""
         logging.info("Closing {}".format(self))
-        # Close all StreamObjects
-        for capture_list in [self.images.values(), self.videos.values()]:
-            for stream_object in capture_list:
-                stream_object.close()
-        # Empty temp directory
-        self.clear_tmp()
         # Stop worker thread
         self.stop_worker()
         logging.info("Closed {}".format(self))
diff --git a/openflexure_microscope/captures/capture_manager.py b/openflexure_microscope/captures/capture_manager.py
index 0ccefc89..96599460 100644
--- a/openflexure_microscope/captures/capture_manager.py
+++ b/openflexure_microscope/captures/capture_manager.py
@@ -52,6 +52,23 @@ class CaptureManager:
 
     # FILE MANAGEMENT
 
+    def __enter__(self):
+        """Create camera on context enter."""
+        return self
+
+    def __exit__(self, exc_type, exc_value, traceback):
+        """Close camera stream on context exit."""
+        self.close()
+
+    def close(self):
+        logging.info("Closing {}".format(self))
+        # Close all StreamObjects
+        for capture_list in [self.images.values(), self.videos.values()]:
+            for stream_object in capture_list:
+                stream_object.close()
+        # Empty temp directory
+        self.clear_tmp()
+
     def clear_tmp(self):
         """
         Removes all files in the temporary capture directories
diff --git a/openflexure_microscope/microscope.py b/openflexure_microscope/microscope.py
index f7e06d14..8a401b86 100644
--- a/openflexure_microscope/microscope.py
+++ b/openflexure_microscope/microscope.py
@@ -73,6 +73,7 @@ class Microscope:
             self.camera.close()
         if self.stage:
             self.stage.close()
+        self.captures.close()
         logging.info("Closed {}".format(self))
 
     def setup(self, configuration):